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Máquinas moleculares arti ciales

Sundus Erbas-Cakmak, David A. Leigh*, Charlie T. McTernany Alina L. Nussbaumer

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 Cite esto: Chem. Rev. 2015 , 115 , 18 , 10081–10206

Fecha de publicación : 8 de septiembre de 2015 
https://doi.org/10.1021/acs.chemrev.5b00146
Copyright © 2015 Sociedad Química Estadounidense
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ASIGNATURAS: Rotaxanos , Estructura molecular , 

BIOGRAFÍA
  

Sündüs Erbaş Çakmak obtuvo su B.Sc. Licenciado en Biología Molecular y Genética en 2007 de la
Universidad Boğaziçi en Estambul, Turquía. Realizó su Ph.D. Licenciada (2013) en Ciencia de
Materiales y Nanotecnología en el Instituto Nacional de Nanotecnología de la Universidad de Bilkent,
bajo la supervisión del Prof. Engin U. Akkaya, investigando la concatenación y el uso de puertas
lógicas moleculares para la modulación de la actividad de agentes de terapia fotodinámica. Trabajó
bajo la supervisión de Amar H. Flood en la Universidad de Indiana durante 6 meses durante su Ph.D.
trabajando en el desarrollo de sensores de aniones uorescentes. En 2013 se incorporó al grupo del
Prof. David A. Leigh como becaria posdoctoral intraeuropea Marie-Curie. Sus intereses de
investigación incluyen máquinas moleculares arti ciales, catálisis supramolecular y computación
molecular.

BIOGRAFÍA
   

David Leigh nació en Birmingham (Reino Unido) y obtuvo su B.Sc. y Ph.D. grados de la Universidad de
She eld. Después de una investigación postdoctoral en Ottawa (1987-1989), fue designado para una
cátedra en el Instituto de Ciencia y Tecnología de la Universidad de Manchester (Reino Unido).
Después de una temporada en las universidades de Warwick y Edimburgo, regresó a Manchester en
2012, donde actualmente ocupa la cátedra Sir Samuel Hall de Química. Los premios y galardones por
las contribuciones de investigación de su grupo incluyen el Premio Internacional Izatt-Christensen
2007 de Química Macrocíclica, el Premio Feynman 2007 de Nanotecnología, el Premio Descartes de
la UE 2007 para la Investigación, el Premio RSC Merck 2009, el Premio RSC Tilden 2010, la
Conferencia y Premio Panadero de la Royal Society 2013 y el premio RSC Pedler Prize 2014. En 2009
fue elegido miembro de la Beca de la Royal Society (Londres).

BIOGRAFÍA
   

Charlie Thomas McTernan nació en Londres y obtuvo su M.Chem. de la Universidad de Oxford. Su

proyecto de la Parte II se llevó a cabo bajo la supervisión del Prof. Tim Donohoe, investigando la
síntesis de motivos de isoquinolina usando α-arilación catalizada por paladio. Se unió al grupo de
David Leigh en 2013, nanciado por un premio Dean's Faculty Award de la Universidad de Manchester.
Sus intereses de investigación incluyen la síntesis de máquinas moleculares arti ciales, catalizadores
intercambiables y rotaxanos.

BIOGRAFÍA
   

Alina Laura Nussbaumer nació en Berna (Suiza) y obtuvo su B.Sc. y M.Sc. grados de la Universidad de
Berna. Completó su Ph.D. bajo la supervisión del Prof. Robert Häner en la misma Universidad,
investigando el ADN como andamio para el ensamblaje de cromóforos hacia el desarrollo de nuevos
materiales basados en ADN y la producción de polímeros supramoleculares basados en conjugados
de ADN que muestran una fuerte ampli cación de quiralidad. En 2012, se unió al grupo de David Leigh
como becaria postdoctoral de la Swiss National Science Foundation. Sus intereses de investigación
incluyen el movimiento molecular controlado y el desarrollo de nuevas tácticas sintéticas hacia
moléculas topológicamente complejas.

1. Introducción Salta a

El uso generalizado de máquinas moleculares en biología ha sugerido durante mucho

tiempo que se podrían obtener grandes recompensas al cerrar la brecha entre los sistemas
moleculares sintéticos y las máquinas del mundo macroscópico. En las últimas dos
décadas, se ha demostrado que es posible diseñar sistemas moleculares sintéticos con
arquitecturas en las que se producen cambios posicionales de gran amplitud de
componentes submoleculares. Quizás la mejor manera de apreciar el potencial tecnológico
del movimiento controlado a nivel molecular es reconocer que los nanomotores y las
máquinas a nivel molecular se encuentran en el corazón de todo proceso biológico
signi cativo. Durante miles de millones de años de evolución, la naturaleza no ha elegido
repetidamente esta solución para realizar tareas complejas sin una buena razón. Cuando la
humanidad aprenda a construir estructuras arti ciales que puedan controlar y explotar el
movimiento a nivel molecular e interconectar sus efectos directamente con otras  
subestructuras de nivel molecular y el mundo exterior, tendrá un impacto potencial en todos
los aspectos del diseño funcional de moléculas y materiales. Seguramente seguirá una
mejor comprensión de la física y la biología.

Los primeros pasos en el largo camino hacia la invención de las máquinas moleculares
arti ciales se dieron posiblemente en 1827 cuando el botánico escocés Robert Brown
observó el movimiento fortuito de pequeñas partículas bajo su microscopio.(1, 2) La
explicación del movimiento browniano, que es causado por el bombardeo de las partículas
por moléculas como consecuencia de la teoría cinética de la materia, fue proporcionada
más tarde por Einstein, seguida de la veri cación experimental por Perrin.(3, 4)El movimiento
térmico aleatorio de las moléculas y sus implicaciones para las leyes de la termodinámica
inspiraron a su vez Gedankenexperiments (“experimentos mentales”) que exploraron la
interacción (y aparentes paradojas) del movimiento browniano y la Segunda Ley de la
Termodinámica. La famosa conferencia de Richard Feynman de 1959 “ Hay mucho espacio
en la parte inferior ” describió algunas de las promesas que podrían cumplir las máquinas
moleculares arti ciales.(5, 6)Sin embargo, la charla de Feynman se produjo en un momento
antes de que los químicos tuvieran las herramientas sintéticas y analíticas necesarias para
fabricar máquinas moleculares. Si bien el interés entre los químicos sintéticos comenzó a
crecer en las décadas de 1970 y 1980, el progreso se aceleró en la década de 1990,
particularmente con la invención de métodos para hacer sistemas moleculares entrelazados
mecánicamente (catenanos y rotaxanos) y controlar y cambiar las posiciones relativas de
sus componentes.(7-24)

Aquí, revisamos los movimientos desencadenados de gran amplitud en las estructuras

moleculares y los cambios en las propiedades que pueden producir. Nos concentramos en
cambios conformacionales y con guracionales en moléculas totalmente unidas
covalentemente y en catenanos y rotaxanos en los que el cambio es provocado por varios
estímulos (luz, electroquímica, pH, calor, polaridad del solvente, unión catiónica o aniónica,
efectos alostéricos, temperatura, covalente reversible formación de enlaces, etc.).
Finalmente, discutimos las últimas generaciones de so sticados sistemas de máquinas
moleculares sintéticas en las que el movimiento controlado de subcomponentes se utiliza
para realizar tareas complejas, allanando el camino a las aplicaciones y la realización de una
nueva era de “nanotecnología molecular”.

1.1 El lenguaje utilizado para describir las máquinas

moleculares
La terminología debe de nirse de manera adecuada y apropiada y estos signi cados deben
usarse de manera consistente para transmitir conceptos cientí cos de manera efectiva. En
ninguna parte es más evidente la necesidad de un lenguaje cientí co preciso que en el
campo de las máquinas moleculares. Gran parte de la terminología utilizada para describir
las máquinas de nivel molecular tiene su origen en observaciones realizadas por biólogos y
físicos, y sus descubrimientos y descripciones a menudo han sido mal interpretados y mal 
comprendidos por los químicos. En 2007 formalizamos de niciones de algunos términos
comunes utilizados en el campo (por ejemplo, "máquina", "interruptor", "motor", "trinquete",
etc.) para que los químicos pudieran usarlos de una manera consistente con los signi cados
entendidos por biólogos y físicos que estudian máquinas de nivel molecular.(14)

La palabra "máquina" implica un movimiento mecánico que realiza una tarea útil. Esta
revisión se concentra en sistemas en los que un estímulo desencadena el movimiento
controlado, de amplitud relativamente grande (o direccional) de un componente molecular o
submolecular en relación con otro que potencialmente puede resultar en la realización de
una tarea neta. Las máquinas moleculares se pueden clasi car en varias clases, como
"motores" e "interruptores", cuyo comportamiento di ere signi cativamente.(14)Por ejemplo,
en un “conmutador” basado en rotaxano, el cambio de posición de un macrociclo en el hilo
del rotaxano in uye en el sistema solo en función del estado. Devolver los componentes de
un interruptor molecular a su posición original deshace cualquier trabajo realizado y, por lo
tanto, un interruptor no se puede usar de manera repetitiva y progresiva para realizar el
trabajo. Un "motor", en cambio, in uye en un sistema en función de la trayectoria, es decir,
cuando los componentes de un motor molecular vuelven a sus posiciones originales, por
ejemplo, después de una rotación direccional de 360 °, cualquier trabajo que se haya
realizado no se deshace a menos que el motor se gire posteriormente 360 ° en la dirección
inversa. Esta diferencia de comportamiento es signi cativa; No se puede utilizar ninguna
máquina molecular "basada en interruptores" para realizar el trabajo progresivamente de la
forma en que lo hacen los motores biológicos, como los de la kinesina,(14)

1.2 Los efectos de la escala

Las máquinas deben diseñarse de acuerdo con el entorno en el que deben funcionar. El
signi cado y las consecuencias del movimiento térmico aleatorio, la disipación de calor, la
solvatación, el momento, la inercia, la gravedad, etc., di eren signi cativamente a nivel
molecular y macroscópico, lo que signi ca que las máquinas a nanoescala no pueden
simplemente imitar los mecanismos de sus hermanos macroscópicos.

Las fuerzas con mayor in uencia en la dinámica del nano-mundo no son aquellas en las que
comúnmente con amos en el mundo macroscópico. Para los objetos grandes, los términos
inerciales, que dependen de la masa de la partícula, dominan el movimiento. A medida que el
tamaño de las partículas disminuye hasta o por debajo de la escala micrométrica, las
fuerzas viscosas y el movimiento browniano se vuelven dominantes, mientras que el
impulso y la gravedad se vuelven cada vez más irrelevantes. Este efecto se puede cuanti car
mediante el número de Reynolds ( R ) para una partícula de radio a , velocidad v en un medio
de densidad ρ y viscosidad μ:(25, 26)

(1)
Debido a que el número de Reynolds disminuye con el radio, las máquinas de tamaño
molecular normalmente operan en condiciones de bajo número de Reynolds. Además,
  la 
mayor relación super cie: volumen de las partículas pequeñas las hace cada vez más
adhesivas, disminuyendo la movilidad. Estos efectos deben considerarse cuidadosamente
en el diseño de máquinas moleculares.(14)

1.3 Máquinas de pensamiento que exploran el movimiento

browniano
Los motores moleculares se basan en la explotación de uctuaciones térmicas aleatorias
para el movimiento direccional mediante el empleo de mecanismos de trinquete.
Experimentos mentales como el demonio de Maxwell,(27, 28) La trampilla de Smoluchowski,
(29) y el trinquete y el trinquete de Feynman(30) han investigado posibles formas de
provocar el movimiento direccional de las partículas brownianas.(31)

La Segunda Ley de la Termodinámica establece que la entropía de un sistema aislado tiende

a aumentar, lo que lleva a una distribución de equilibrio con máxima entropía. Para lograr
cualquier distribución que no sea el equilibrio termodinámico, se debe trabajar en el sistema.
Se han propuesto varios experimentos mentales que intentan violar esta premisa y alejar a
un sistema del equilibrio sin gastar trabajo. En el experimento mental del demonio de
Maxwell, las partículas de un recipiente son clasi cadas por un "guardián inteligente", el
"demonio" ( Figura 1 ).(32)Las partículas de gas se distribuyen en un recipiente dividido en
dos secciones en un sistema aislado. La formación espontánea de un gradiente de calor o
presión conduciría a una disminución de la entropía y, por tanto, violaría la Segunda Ley. El
guardián puede detectar la velocidad de cada partícula y puede controlar la puerta en
consecuencia. El demonio permite que partículas con velocidades superiores a la media
(mostradas en rojo en la Figura 1 a) pasen de la sección derecha a la izquierda, pero no de la
izquierda a la derecha. Lo contrario es válido para partículas más lentas (que se muestran en
azul en la Figura 1un). El portero provoca así una distribución no uniforme de partículas
entre las dos secciones, creando un gradiente de temperatura. De manera similar, un
demonio capaz de detectar la dirección de la partícula y abrir la puerta en consecuencia,
puede concentrar partículas en una sección y generar así un gradiente de presión ( Figura 1
b). Si la puerta no tiene fricción, entonces en ambos casos se ha logrado una distribución de
desequilibrio aparentemente sin hacer trabajo, lo que violaría la Segunda Ley. La solución a
la aparente paradoja radica en considerar la información que requiere el demonio para saber
cuándo abrir la puerta. Como el demonio debe medir la velocidad o dirección de cada
partícula que se acerca a la puerta(33) y no puede tener memoria in nita,(34)en algún
momento el demonio debe "olvidar" esta información. La destrucción de información tiene
un costo entálpico mínimo asociado(35) como se ha veri cado experimentalmente,(36)que
siempre supera la disminución de entropía en el contenedor. Por lo tanto, una disminución
local en la entropía se paga mediante un aumento generalizado al eliminar la información.

Figura 1
   

Figura 1. Demonios de Maxwell. (a) Un "demonio de la temperatura" clasi ca las partículas

según la velocidad, generando un gradiente de temperatura. (b) Un “demonio de la presión”
clasi ca las partículas de acuerdo con su dirección de movimiento, generando un gradiente
de presión.(37)

Smoluchowski propuso un sistema que no dependía de un observador inteligente basado en

una puerta unidireccional cargada por resorte, abierta por uctuaciones térmicas ( Figura 2
a).(29, 38, 39)Sin embargo, se demostró que el transporte direccional es imposible en este
sistema, ya que la puerta no puede disipar la energía de las colisiones con las partículas de
gas. Esto conduce a períodos abiertos cada vez más largos para la compuerta y, por lo
tanto, al equilibrio de las partículas a través del contenedor.

Figura 2

Figura 2. (a) En la Trampilla de Smoluchowski, una puerta con resorte separa las dos
secciones de un contenedor. La falta de disipación de energía conduce a una mayor
duración de la apertura y, por lo tanto, a una distribución uniforme de partículas entre las
secciones.(29)(b) Dispositivo de trinquete y trinquete de Feynman. La asimetría de los
dientes del engranaje de trinquete estaba destinada a impulsar el movimiento direccional.
Sin embargo, cuando T 1 = T 2 , la rotación no es direccional.(30)
En el trinquete y el trinquete de Feynman, los dientes dentada asimétricos podrían haber
permitido la rotación direccional impulsada por el movimiento browniano ( Figura 2 b). 
(30, 40-44)Aunque de acuerdo con la segunda ley, no se pudo extraer trabajo cuando T 1 = T
2 (el trinquete está a la misma temperatura que el resto del dispositivo y, por lo tanto, uctúa
entre los estados abierto y cerrado y, por lo tanto, no actúa como un trinquete) , pero se
puede trabajar cuando T 1 > T 2 . Este es un punto importante para el diseño de máquinas a
nanoescala. A medida que el sistema pasa de un estado de no equilibrio al equilibrio ( T 1 = T
2), se puede realizar trabajo direccional. Por lo tanto, si se puede crear una situación de
desequilibrio, su relajación puede impulsar el movimiento direccional. En otras palabras, se
requiere una entrada de energía para realizar el trabajo y romper el equilibrio detallado (ver
sección 4.4 ).

1.4 Inspiración de la naturaleza

Quizás la lección más importante para aprender de los sistemas biológicos es que las
máquinas moleculares son viables y pueden realizar tareas extremadamente complejas. En
la naturaleza, las máquinas moleculares desempeñan un papel vital, ya que participan en
casi todos los procesos biológicos importantes y permiten realizar una amplia gama de
tareas químicas y mecánicas.(45-47) Las formas en que la naturaleza ha superado los
problemas de escala, movimiento browniano, viscosidad, distribución de desequilibrio y
medio ambiente proporcionan algunas direcciones generales para el diseño de máquinas
moleculares.

Los procesos celulares están compartimentados por barreras lipídicas, que permiten que se
acumulen y mantengan distribuciones en desequilibrio. Una gama de máquinas moleculares
controlan el transporte de diversas especies cargadas y polares a través de estas
membranas mediante canales de retransmisión o entidades portadoras móviles.(48-50)Esta
transferencia puede ser impulsada por difusión pasiva hacia abajo de un gradiente de
concentración o por la generación de un gradiente electroquímico (donde una especie se
mueve en contra de su gradiente de concentración pero hacia abajo por otro gradiente,
como el potencial eléctrico). Si el movimiento es impulsado por el transporte acoplado de
otro sistema, las dos especies pueden migrar en la misma (simportación) o en direcciones
opuestas (antipuerto) a través de la membrana. El transporte altamente selectivo a través de
las bicapas lipídicas es posible gracias al gran número de canales y portadores especí cos
en los sistemas biológicos impulsados por la relajación de los gradientes electroquímicos
transmembrana hacia el equilibrio termodinámico.

Estos gradientes electroquímicos son mantenidos por solo unas pocas bombas de iones,
más comúnmente ATPasas que hidrolizan ATP y generan transporte direccional utilizando la
liberación de energía resultante. Aunque el mecanismo del movimiento direccional en estas
proteínas motoras aún no se comprende completamente, los cambios conformacionales
que conducen a a nidades de unión alteradas parecen ser particularmente importantes.
(51-60) El acceso a los sitios de unión de estas bombas a menudo se "cierra" por cambios
conformacionales después de la unión de iones para aumentar la direccionalidad del
proceso.(58, 61)   
El bombeo de protones a través de las membranas es un proceso particularmente
importante, ya que crea la fuerza motriz del protón que impulsa la producción de ATP de las
ATP sintasas, que a su vez impulsa una gran variedad de procesos de transporte activo. Este
potencial transmembrana generado por protones es comúnmente creado por cadenas de
transporte de electrones donde se utilizan reacciones redox para separar cargas a través de
una membrana.(60)El bombeo de protones impulsado directamente por la luz, como en la
bacteriorrodopisina (donde la isomerización cis / trans conduce a la direccionalidad), es
menos común.(62-67) Las estructuras entrelazadas a menudo se explotan en biología para
ayudar a garantizar una alta secuencialidad, por ejemplo, en el ribosoma,(68-70) y diversas
ADN polimerasas.(71)

Las máquinas moleculares biológicas se utilizan para transportar carga alrededor de una
célula (p. Ej., Kinesina), para impulsar el movimiento de organismos (p. Ej., Motores
agelares bacterianos), para sintetizar proteínas (p. Ej., El ribosoma) y para separar hebras
de ADN (p. Ej., helicasas). Hay muchas diferencias cruciales entre estas máquinas y las que
conocemos en el mundo macroscópico, tanto en términos de las tareas que realizan como
de la forma en que lo hacen. A partir de estas máquinas naturales se pueden extrapolar
varios conceptos pertinentes a la síntesis de máquinas moleculares arti ciales.

(1) Las máquinas biológicas no pueden utilizar gradientes térmicos debido a la

rápida disipación de calor en la escala en la que operan.

(2) Los motores biológicos a menudo usan energía química de eventos favorables
de formación / ruptura de enlaces (por ejemplo, hidrólisis de ATP) o gradientes
de concentración para impulsar su funcionamiento.

(3) Las biomáquinas operan en solución y sobre super cies bajo condiciones de
alta viscosidad.

(4) Las máquinas biológicas explotan el movimiento browniano en lugar de luchar

contra él. Ellos "trincan" el movimiento térmico aleatorio de sus componentes y
sustratos. El movimiento browniano también asegura la mezcla rápida de
máquinas, combustible y sustratos.

(5) La fricción es irrelevante en un medio tan viscoso, donde el movimiento

browniano constante asegura la movilidad de las partes individuales.

(6) Las biomáquinas móviles, como la kinesina, a menudo operan a lo largo de las
 vías para reducir los grados de libertad disponibles de la máquina. La
asociación cinética de la máquina en la vía durante la duración de la operación
  
es vital para lograr un transporte dirigido.

(7) Las interacciones no covalentes son a menudo características importantes de

la estructura y el funcionamiento de los sistemas biológicos.

(8) Las biomáquinas se fabrican a menudo mediante procesos de autoensamblaje

a partir de una gama limitada de motivos básicos como aminoácidos, lípidos,
ácidos nucleicos y sacáridos.

(9) A menudo se requiere la compartimentación para permitir que los sistemas se

mantengan y operen fuera del equilibrio.

(10) Los pequeños eventos de unión a menudo pueden causar grandes cambios
conformacionales.

Aunque las máquinas moleculares biológicas tienen un nivel de complejidad inalcanzable

por la generación actual de máquinas moleculares, están constreñidas por los procesos
evolutivos que las dieron origen y el entorno en el que operan. La selección natural asegura
que la primera solución exitosa a un problema tiende a retenerse y mejorarse gradualmente
a lo largo de muchas iteraciones. Estas restricciones, en términos de química y soluciones,
no se aplican a los sistemas arti ciales. Las biomáquinas también operan en un entorno
muy desordenado y, por lo tanto, deben exhibir una tolerancia extremadamente alta a las
colisiones con especies no relacionadas o no reactivas. Además, el estudio de sistemas
arti ciales menos elaborados puede dar lugar a una mayor comprensión de los so sticados
sistemas biológicos que los inspiraron.

1.5 Transporte direccional y trabajo bajo movimiento

browniano
El principio del equilibrio detallado proporciona importantes restricciones sobre la relación
entre el equilibrio y las constantes de velocidad. La comprensión de este concepto es
importante en el campo de las máquinas moleculares sintéticas y para el diseño de posibles
mecanismos de movimiento direccional.(72-74)El Principio del Balance Detallado establece
que, en el equilibrio, cada transición tiene la misma probabilidad (y por lo tanto la tasa) de
ocurrir en una dirección hacia adelante o hacia atrás (por ejemplo, k 1 = k –1 ). Esto signi ca
que en el equilibrio no se genera ningún ujo neto a través de ninguna barrera y no se puede
realizar ninguna tarea. Esto descarta el mantenimiento de un equilibrio mediante un proceso
cíclico como A → B → C → A; más bien, cada sustrato debe estar en equilibrio con todos los
demás con los que intercambia, es decir, A⇆ B + B ⇆ C + C ⇆ A en su lugar. De ello se
deduce que la trampilla de Smoluchowski no podría funcionar, ya que rompería el principio
de reversibilidad microscópica. Romper el equilibrio detallado es un requisito paratrabajar
 
en las escalas de longitud en las que se produce el movimiento browniano.(75) El bombeo
estocástico rompe el equilibrio detallado utilizando un parámetro oscilante para generar un
ujo neto y mantener un estado estable de no equilibrio, y se ve en la naturaleza, por
ejemplo, en las ATPasas.(76, 77) Se han desarrollado varios marcos teóricos para explicar
varios modos de transporte impulsados por uctuaciones, como el bombeo estocástico, que
gobierna el transporte en motores y trinquetes brownianos.(78-126) A continuación se
comentan algunos ejemplos particularmente relevantes.

1.6 Mecanismos de trinquete

Los mecanismos de trinquete browniano se dividen en dos clases generales: trinquetes de
energía (los trinquetes pulsantes e inclinados son subcategorías de los trinquetes de
energía) y trinquetes de información.(127-129)

1.6.1 Trinquetes pulsantes

En trinquetes pulsantes, los mínimos y máximos de energía potencial se varían de manera

periódica o estocástica sin referencia a la posición de la partícula en la super cie de energía
potencial.(128)La forma más simple es un trinquete de encendido y apagado en el que el
potencial se enciende y apaga repetidamente más rápidamente que la difusión de las
partículas brownianas sobre su super cie de energía potencial. Esto da como resultado el
transporte direccional neto de partículas a través de la super cie ( Figura 3 ).

gura 3

Figura 3. Un trinquete de encendido-apagado: (a) las partículas están ubicadas en un mínimo

de energía, (b) el potencial se apaga para que la difusión pueda ocurrir por un corto tiempo, y
(c) el potencial se enciende nuevamente. Como el potencial es asimétrico, las partículas
tienen una mayor probabilidad de quedar atrapadas en un pozo adyacente a la derecha del
original que a la izquierda. (d) La relajación en los mínimos de energía local conduce a la
posición promedio de las partículas que se mueven hacia la derecha.(128)

Un trinquete intermitente es un subtipo del trinquete pulsante, que consta de una serie
repetida de máximos y mínimos. El descenso y aumento secuencial de partes de esta
super cie de energía potencial conduce al transporte direccional ( Figura 4 ).
Figura 4
  

Figura 4. Un trinquete intermitente. En (a) y (c), la partícula comienza en un pocillo verde o

naranja, respectivamente. El aumento de estos mínimos de energía mientras se reducen los
máximos y mínimos adyacentes desencadena el movimiento mediante el movimiento
browniano (b) a (c) o (d) a (e). Variando continuamente las alturas relativas de las barreras
de energía y los mínimos de los pozos de energía, la partícula se puede transportar
direccionalmente.(128)

Una super cie de energía potencial asimétrica no es estrictamente necesaria para generar
un trinquete pulsante.(128)Se puede utilizar una matriz periódica de mínimos locales que
viajan a una velocidad constante (es decir, una onda viajera) para formar un trinquete de
potencial viaje. En términos de sistemas realistas, el mecanismo de trinquete de potencial de
viaje tiene mayor relevancia para los procesos impulsados por el campo discutidos en la
sección 5 y los mecanismos de autopropulsión de la sección 6 .

1.6.2 Trinquetes basculantes

En un trinquete de inclinación, la super cie de energía potencial subyacente permanece sin

cambios y el equilibrio detallado se rompe mediante la aplicación de una fuerza impulsora
insesgada a las partículas, como el calor.(128)Cuando la fuerza aplicada es calor, los
trinquetes también se denominan trinquetes de temperatura o difusión ( Figura 5 ). En su
forma más simple, el mecanismo es muy similar al del trinquete de encendido y apagado.
Aquí, las partículas no pueden cruzar los máximos de energía a baja temperatura, pero un
breve aumento de temperatura permite la difusión de partículas a través de la super cie.
Una disminución de la temperatura atrapa este movimiento de una manera similar al
trinquete pulsante de encendido y apagado que conduce al transporte direccional. El período
de temperatura elevada debe ser breve para evitar la difusión general, que destruiría
cualquier direccionalidad ganada inicialmente.

Figura 5
   

Figure 5. A temperature or diffusion ratchet. (a) The particles are located in an energy
minima on the potential-energy surface, with energy barriers ≫kBT1. (b) The temperature is
increased so that the height of the barriers is ≪kBT2, and free diffusion is allowed to occur
for a short time. (c) As the temperature is lowered again, the asymmetric potential energy
surface means that the particles have a greater probability of being trapped to the right of
their initial position. (d) Relaxation to the local energy minima.(128)

El movimiento direccional también se puede lograr mediante la aplicación de una fuerza

direccional periódica a una super cie de energía potencial asimétrica en un trinquete
oscilante. Aunque la fuerza impulsora neta promedia cero, el movimiento direccional se
impulsa aprovechando la asimetría de la super cie de energía potencial ( Figura 6 ).

Figura 6

Figura 6. Un trinquete oscilante. (a) Las partículas están ubicadas en un mínimo de energía
en la super cie de energía potencial. (b) Se aplica una fuerza direccional hacia la izquierda.
(c) Se aplica una fuerza direccional igual y opuesta a la derecha. (d) La eliminación de la
fuerza y la relajación a un mínimo de energía conduce a la posición promedio de las
partículas que se mueven hacia la derecha.(128)

De manera similar, en un trinquete de fuerza uctuante, la fuerza impulsora aplicada se

genera aleatoriamente y varía estocásticamente. Finalmente, en un trinquete de inclinación
asimétrico, las partículas se encuentran en una super cie de energía potencial simétrica,
pero el potencial aplicado proporciona la asimetría requerida. Por ejemplo, en un trinquete
oscilante, la inclinación en una dirección sería más larga que en la otra.

1.6.3 Trinquetes de información

Los trinquetes de energía operan mediante la aplicación de una fuerza externa o la

modulación de una super cie de energía potencial independientemente de la posición de la
partícula.(128)Los trinquetes de información, por otro lado, se basan en subir o bajar una
barrera de energía según la posición de la partícula en la super cie de energía potencial (
Figura 7 ). Esto da como resultado que la distribución de partículas se aleje del equilibrio.
  
Este proceso requiere la transferencia de información de la partícula a la super cie de
energía potencial, de una manera que recuerda al demonio de Maxwell.

Figura 7

Figura 7. Un trinquete de información. En (a) y (d) las líneas punteadas representan la

transferencia de información sobre la posición de la partícula. (b) La posición de la partícula
baja la barrera de energía al movimiento hacia el pozo de la derecha pero no hacia la
izquierda. (c) La partícula se mueve por movimiento browniano.(128)

1.6.4 Lenguaje necesario para describir el funcionamiento de las máquinas

moleculares

Four terms are useful for describing the relationship of the components/substrates of
molecular machines in terms of dynamics: balance, linkage, ratcheting, and escapement.(75)
Having the components/substrates in a state of “balanced/unbalanced” or “linked/unlinked”
plays a crucial role in determining whether or not a machine can perform a task. “Balance” is
the thermodynamically preferred distribution of a particle (or submolecular component) in a
molecular system. The trigger for net transportation comes from the balance being broken
(i.e., the system being in a nonequilibrium state) (section 4.4). “Linkage” is the
communication necessary for the transport of a particle between parts of the machine.
However, the ability to exchange a particle between two parts of a machine does not
necessarily allow a task to be performed, as a driving force is also required. Linking and
unlinking operations are not limited to the addition or removal of steric bulk. They refer to any
action that has an in uence on the rate of a reaction. The movement of a particle up an
energy gradient is described as ratcheting. It involves capturing the transitory positional
displacement of a particle through the imposition of a kinetic energy barrier. Escapement is
the counterpart to ratcheting in which the lowering of a kinetic energy barrier allows a
ratcheted substrate to relax from a statistically unbalanced system toward a thermodynamic
sink.
2 Controlling Motion in Covalently Bonded Jump To

  
Molecular Systems

2.1 Controlling Conformational Changes

2.1.1 Correlated Motion through Nonbonded Interactions

At room temperature, organic compounds typically uctuate between rapidly equilibrating

stereoisomeric structures through the perturbation (rotation, lengthening, and shortening) of
covalent bonds. The relative stability and energy barrier to interconversion of con gurational
and conformational isomers depend on intramolecular and intermolecular interactions. The
rotational and vibrational freedom of a single substituent of a molecule is not only
determined by its connectivity, shape, and size, but also its interactions with neighboring
substituents.(130-133) For example, Mislow et al. demonstrated the steric in uence of
neighboring groups on rotation as part of their work on molecular propellers such as
compound 1 where two or more aryl rings are attached to a single atomic center (Z) (Figure
8). The rotation of one aryl ring about a C–Z axis is sensed by the other rings. Mislow
suggested that the motion of the rings is coupled in the sense that none of the rings move
independently of the others and described such correlated motion as “sympathic”.
(130, 134-138)

Figure 8
   

Figure 8. Chemical structure of a triaryl molecule as an example of a molecular propeller.

(130, 139)

Öki’s group conducted pioneering investigations into restricted rotation about sterically
hindered single bonds in molecules such as 9-aryl uorenes and triptycenes.(140-149) These
molecules showed very high rotational barriers, and, in some cases, it was possible to isolate
the rotational isomers (rotamers). Inspired by this work, Mislow and Iwamura simultaneously
introduced the concept of dynamic gearing of proximate substituents in crowded molecules
in molecular analogues of propellers and bevel gears.(150-167) The rst molecular bevel
gear consisted of two 9-triptycyl groups joined through their bridge head carbons to a central
atom (Figure 9). Experimental and theoretical studies con rmed that the triptycyl groups are
tightly intermeshed and undergo correlated disrotatory motion.(150, 156)

Figure 9
   

Figure 9. (a) Molecular bevel gear 2, consisting of two 9-triptycyl groups joined through a
bridge head carbon to a central atom.(150) (b) X-ray structure of the molecular bevel gear
(side view). (c) X-ray structure of the molecular bevel gear (top view). Adapted with
permission from ref 156. Copyright 1984 American Chemical Society.

Many other examples of dynamic gearing have since been published including a range of
triptycene derivatives,(168-174) metallocene-based gears,(175, 176) conformationally
restricted amides,(177-181) and a series of propeller molecules and other molecules with
selective rotation,(132, 133, 139, 182-194) such as 1,2-di-o-tolylnaphthalene moieties.
(195, 196)

The sandwich-shaped trinuclear silver(I) complex [Ag3(3)2] (Figure 10) developed by

Shionoya and co-workers(197-199) is an example of a different type of a rotational device.
The complex consists of two disk-shaped ligands, 3, consisting of three thiazolyl or 2-pyridyl
ligands and three p-tolyl groups attached to a central benzene ring. The three p-tolyl groups
force the neighboring ligands to adopt a nonplanar arrangement with respect to the central
aromatic ring, and make the coordination sites more accessible for silver(I) cations. The
exterior rings tilt at 30° in the same sense and thus form helical structures with P and M
geometries. A change from P to M helicity, and vice versa, was induced by 120° relative
rotation of the ligand in these complexes (Figure 10). These observations were further
studied using a heterotopic system [Ag3(3)(4)] consisting of a hexa-monodentate ligand 4
and a tris-monodentate thiazolyl ligand 3, which complex three silver(I) cations.(200) In the
case of the hexa-monodentate thiazolyl ligand 4, only every second ring is coordinated to a
silver cation. Correlated ipping motion of the coordinating rings (and ligand exchange)
results in the conversion from M to P and a 60° rotation of the two disks (Figure 10d).

Figure 10
   

Figure 10. (a) Chemical structure of tris-monodentate disk shaped ligand 3 and hexakis-
monodentate ligand 4. (b) Schematic representation of complex [Ag3(3)2] shown as its M-
helical enantiomer. (c) X-ray structure of complex [Ag3(3)2].(197) (d) Schematic
representation of the ipping motion of the rings attached to the disks and subsequent
ligand exchange from 1-A, 3-E, and 5-C in M to 1-B, 3-F, and 5-D in P. The direction of rotation
in the M to P transition is opposite to that of a subsequent P to M′ transition.(200) Reprinted
with permission from refs 197 and 200. Copyright 2003 and 2004 Wiley-VCH Verlag GmbH &
Co. KGaA, Weinheim.

Related heterotopic complexes were later used to transform the rotational motion of the
sandwich-shaped trinuclear silver(I) complex into translational motion using a molecular
crank mechanism. In molecular crank 5, a [2]rotaxane was attached as a translational
segment (Figure 11).(201)

Figure 11
   

Figure 11. (a) Schematic illustration of a crank mechanism that translates linear motion into
rotary motion in cylinder engines. (b) Schematic representation of a molecular crank
mechanism. (c) Chemical structure of a synthetic molecular crank 5.(201) Reprinted with
permission from ref 201. Copyright 2010 Royal Society of Chemistry.

Recently, Anderson et al. reported a zinc-porphyrin macrocycle coordinated by two templates

containing multiple pyridines (wheels) forming a caterpillar track complex.(202) NMR
exchange spectroscopy (EXSY) experiments showed that the ring underwent correlated
motion with correlated motion of the templating “wheels”.

The examples shown in this section clearly show the in uence that steric interactions can
have on submolecular motion. However, at equilibrium, these motions are nondirectional,
even during a partial rotation.

2.1.2 Stimuli-Induced Control of Conformation about a Single Bond

An early example of controlled random rotary motion about a single bond was provided by
Kelly et al.,(203-205) who utilized a cation binding event to halt the free rotation of a
triptycene moiety in “molecular brake” 6 (Scheme 1). The two pyridine groups must be
coplanar to maximize binding with Hg2+, thus raising the energy barrier to rotation by “putting
a stick in the spokes”. Sulfur oxidation has similarly been used to inhibit free rotation in 7
with mono- or dioxidation signi cantly slowing the rotation.(206) Rotation about a single
bond has also been promoted by substrate protonation by Shimizu and co-workers in 8.(207)
Protonation of the quinoline nitrogen led to an increase in the rate of rotation by 7 orders of
magnitude, through a proposed hydrogen-bonding stabilization of the rotation transition
  
state (Scheme 1). The same group observed that utilizing an acetate guest’s hydrogen-
bonding interactions to “turn on” rotation provided a more modest accelerating effect.(208)
Again, this was suggested to be via a lowering of the energy of the rotational transition state.
Other examples have also been reported.(209, 210)

Scheme 1

Scheme 1. Molecular Brakes Operated by (a) Hg2+ Binding and (b) Sulfur Oxidation; and (c)
Proposed Transition State Stabilization in Shimizu’s System(203, 206, 207)

Singlet oxygen has been used to promote rotation in combination with thermal relaxation in
a system based on rotation between the cis and trans isomers of 9 (Scheme 2). Reaction
with singlet oxygen forms the cis-substituted 9,10-endoperoxide selectively. Thermal
reversion generates the cis-anthracene, which upon extensive heating furnishes the more
thermodynamically stable trans-anthracene 9, completing the cycle.(211)

Scheme 2

Scheme 2. A Molecular Switch Flipped by Singlet Oxygen(211)

Kelly and co-workers reported an attempt to create a Feynman adiabatic ratchet-and-pawl.

(212-214) The design utilized a helicene pawl whose inherent helical chirality was intended to
bias the rotation of the triptycene cog. Although this design realizes an asymmetric potential
energy surface, 1H NMR showed no directional bias with equal rates of rotation in both
directions. This is in line with Feynman’s thought experiment(215) and illustrates that the rate
of rotation depends solely on transition state energy and temperature, and not on the shape
of the barrier to rotation. State functions, for example, free energy, do not depend on the
system’s history (Figure 12).
Figure 12
  

Figure 12. (a) Kelly’s ratchet-and-pawl 10. (b) Enthalpy change on rotation of helicene.
Reprinted with permission from ref 212. Copyright 1997 Wiley-VCH Verlag GmbH & Co.
KGaA, Weinheim.

The key factor required to break detailed balance and allow directional motion of the
triptycene cog is an energy input to drive the system away from equilibrium. Although a rapid
periodic variation in temperature could in theory cause the system to act as a temperature
ratchet, it would be very di cult to verify this experimentally. As such, Kelly et al. instead
proposed the modi ed structure 11,(216, 217) where a chemical reaction drives the system
from equilibrium (Scheme 3). The helicene pawl oscillates in the energy minima between
blades, and, ignoring the amine group, all three minima are identical. Formation of the
isocyanate from reaction with phosgene activates the system. In the course of random
uctuations, sometimes the helicene is close enough to the isocyanate to react. After
reaction, the helicene is trapped part way up the energy barrier; that is, the helicene is
“ratcheted” part way to rotation. Random thermal uctuations may then overcome the
smaller barrier to rotation, and the urethane can be cleaved to give overall 120° rotation. This
machine is a landmark achievement in the realization of chemically fueled directed rotation
in molecular machines and demonstrates most of the basic tenants of a directional motor.
However, attempts to modify the rotor to allow 360° rotation have thus far failed.(218)

Scheme 3
   

Scheme 3. Chemically Driven Directional 120° Rotation of Kelly’s Triptycene Rotor 11(216)

Mock and Ochwat have proposed a minimal molecular motor in which epimerization of a
stereogenic center, that is, a formal 180° rotation, is driven by the hydration of a ketenimine
fuel.(219) A biaryl lactone motif reported by Branchaud has been used to control motion
about a single bond in a nondirectional rotor based on the facially selective ring opening of a
chiral lactone.(220) They later improved on this system to report 180° directional rotation.
(221) Feringa et al. achieved full 360° directional motion about a single bond in a related
biaryl system (Scheme 4).(222, 223) Rotation was driven by four sequential chemical “power
strokes” with felicity of rotation for each step being between 90% and 100%. The cycle
involved four conformationally restricted intermediates, 12–15, with 12 and 14 locked by
covalent bonds, and 13 and 15 locked by their steric bulk. Although 13 and 15 are free to
dynamically equilibrate between helical forms, the chiral information in the reducing agent is
used to discriminate between them and thus drive directional motion. The rst step involved
asymmetric ring opening with the (S)-CBS reagent, and regioselective protection of the
resulting phenol with an allyl group. After oxidation and PMB deprotection with spontaneous
lactonization, 180° rotation was achieved. Another stereoselective ring opening and
regioselective phenol protection as the PMB ether followed, before oxidation and ring closure
furnished the product of 360° rotation in high delity. Additionally, rotation in the opposite
sense can be achieved by utilizing the (R)-CBS reagent and reversing the order of PMB/allyl
protection.

Scheme 4
   

Scheme 4. Directional 360° Rotation about a Single Bond via Four States A–Da

Scheme a Rotation is restricted in A and C by covalent bonds, although helical inversion is

allowed, and in B and D by nonbonded interactions, with directional control of rotation being
provided by stereospeci c covalent bond cleavage.(222)

2.1.3 Stimuli-Induced Conformational Control in Organometallic Systems

Control of the rotary motion of ligands in metal sandwich or double-decker complexes is

somewhat conceptually similar to controlling rotation around covalent single bonds. Aida
and co-workers demonstrated that porphyrin ligands in double decker complexes such as 16
can rotate with respect to each other depending on the central metal atom and their steric
bulk (Figure 13a).(224, 225) Studies on a variety of metal complexes found that the central
metal had an in uence on the speed of rotation.(226) Complexes synthesized from two D2h
symmetry porphyrin free-bases are chiral, and therefore their rotary motion corresponds to
enantiomerization and can thus be studied by CD spectroscopy. Racemization can be
induced by protonation or reduction of the metal center. The second reduces π–π
interactions between the two ligands as a consequence of the larger ionic radius of the metal
center.(227)

Figure 13
   

Figure 13. (a) X-ray crystal structure of porphyrin double decker complex 16 with cerium(IV).
Reprinted with permission from ref 228. Copyright 1989 Wiley-VCH Verlag GmbH & Co.
KGaA, Weinheim. (b) Representation of the cooperative binding of guest molecules to
porphyrin double decker complex 17.(229)

It was shown that the rotation of the cerium(IV) bis[tetrakis(4-pyridyl)porphyrinate] 17 could

be suppressed by successive cooperative guest binding of dicarboxylic acids (Figure 13b).
(229, 230) The double decker complex shows a large allosteric effect in this molecular
recognition event (once rotation has been suppressed by the rst guest molecule, guest
binding becomes increasingly favorable). Further guest molecules have been tested such as
β-dicarboxylate anions,(231) potassium ions,(232) mono- and oligosaccharides,(233-235)
and silver cations.(236) In the case of silver ions, it was shown that their cooperative binding
leads to a progressive and nonlinear increase in the rate of rotation.(237-244) The rotation of
a similar cerium double decker complex has been monitored on a single molecule level, by
the attachment of a bead visible under optical microscopy.(245)

Ever more complicated systems such as multidecker pophyrin complexes(246) and

mechanically interlocked porphyrin systems like 18 have been synthesized (Figure 14).
(247-249) The latter consist of cerium(IV) or lanthanum(III) bis(porphyrinate) double decker
complexes and one or two orthogonal porphyrin molecules. In these “molecular gears”, the
rotation of the top and side units could be partially coupled through mechanical interactions
between the different units. A folding ruler based on similar principles has been reported.
(250) A dodecanuclear four level complex that mimics a double ball bearing has also been
synthesized.(251)   

Figure 14

Figure 14. Cerium(IV) bis(porphyrinate) double decker (top unit) and a rhodium(III) porphyrin-
based side cog. The two units are connected through a coordination bond between
rhodium(III) and a pyridyl group.(249)

Ferrocene is a prototypical sandwich complex with an iron atom symmetrically aligned

between two C5H5 (cyclopentadienyl) rings.(252, 253) The barrier to rotation of the two rings
about the C5 axis is very small in the gas phase. Using electrospray ionization and theoretical
studies, it was shown that ferrocene derivative 192– can serve as a two-state rotary switch,
which works through proton transfer (Scheme 5). Differing electrostatic interactions lock
192– and [19·H]− in two different conformations. The trans conformation of 192– is more
stable because of Coulombic repulsion between the negative charges, while the cis
conformation of [19·H]− is stabilized through hydrogen bonding (Scheme 5).

Scheme 5
   

Scheme 5. Control of Rotation in Ferrocene Complex 19 through Protonation(253)

This nding was followed by studies of many more ferrocene derivatives, and the control of
their rotary motion through different stimuli such as electron transfer and photochemistry.
(254, 255) Ferrocene-based rotors have recently been used to form self-assembled
nanostructures.(256)

Metallocarboranes tend to have rather high barriers to rotation around the metal–ligand axis,
but some complexes, for example, nickel complex [Ni(20)2], can be used as
electrochemically controlled rotary switches (Figure 15).(257-261)

Figure 15

Figure 15. (a) Dicarbollide ligand 202–. (b) Metallocarborane [Ni(20)2], an electrochemically
controlled rotary switch.(261)

2.1.4 Stimuli-Induced Conformational Control over Several Covalent Bonds

In biological systems, host–guest binding is often used to induce conformational and

functional changes. These changes can vary from small, localized, bond deformations to
long-range rearrangements across multiple covalent bonds. These deformations are
frequently used to alter binding at distal sites, that is, allosteric regulation. There are several
synthetic examples where host–guest binding causes a su ciently large amplitude change
to merit discussion in this Review. Some of the earliest examples of allosteric receptors
came from Rebek and co-workers.(262) For example, the binding of tungsten by negative
  
allosteric receptor 21 reduces the receptor’s a nity for potassium ions, as in this more rigid
conformation binding to potassium would induce a degree of strain (Scheme 6).(263, 264)
The positive allosteric receptor 22 developed by the same group depends on the initial
mercury binding event preorganizing the linked receptor for a second, more favorable binding
event.(265) These early examples have sired an extraordinary and diverse array of synthetic
allosteric receptors.(262, 264, 266-279)

Scheme 6

Scheme 6. (a) Negative Allosteric Receptor 21, Where Binding of Tungsten Forces Ring
Contraction and Steric Clash of the 3- and 3′-Substituents of the Bipyridyl Unit; and (b)
Positive Allosteric Receptor 22(263, 264)

Organic guests can also cause large-scale changes to host molecules, as they maximize
favorable interactions such as in molecular tweezer 23 (Figure 16) where the distance
between sidewalls halves on binding certain guests.(280, 281) A large amplitude change was
observed in the exible system 24 with an extended conformation being exchanged for a
more rigid “sandwich” form to maximize guest binding.(282) Guest-induced change is also
observed in clip 25 where the sa form predominates in solution in the absence of a guest,
but the aa form dominates in the presence of a suitable guest (Figure 16).(283-285) This
system has been further modi ed in 26 where the binding of a potassium ion to each crown
ether preorganizes the system for organic guest binding with increased a nity.(286)

Figure 16
   

Figure 16. (a) Molecular tweezer 23, arrows indicate direction of contraction. (b) Clip 25,
where the aa form is favored in the presence of a guest. (c) Clip 26, where ion binding
enhances guest a nity. (d) Crystal structure of uncomplexed and complexed 24.
(282, 283, 286, 287) X-ray crystal structure reprinted with permission from ref 282. Copyright
2007 American Chemical Society.

Metal coordination has been used by Lehn et al. to switch from an arrangement where
parallel anthracene units can bind electron-poor 2,4,7-trinitro-9- uorenone (TNF) in a
tweezer-like manner, to an open form 27 (Scheme 7). Here, coordination of copper in a
bidentate manner by the aromatic nitrogens causes a rotation about the heterocyclic axis
and opens the guest binding cavity, preventing TNF coordination. In related 28, zinc
coordination is a prerequisite of TNF binding.(288)

Scheme 7
   

Scheme 7. (a) Prevention of Organic Guest Binding on Complexation of Copper to 27; and (b)
Organic Guest Is Only Bound in the Zinc-Complexed Form of 28(288)

A notable example of chelation control of conformation was provided by trisaccharide 29

(Scheme 8). Although the tetra-equatorial isomer is the dominant form in solution,(289) the
addition of Pt(II) led to coordination, and a preference for the tetra-axial form, the better to
bind the metal ion. This process could be reversed by removal of the Pt(II) with excess
NaCN.(290, 291) This process has been replicated with a variety of cyclic substrates using
both metal ion binding(292-294) and pH variation.(295-297) Sauvage reported the collapse
of a porphyrin containing [4] rotaxane on copper removal.(298) Haberhauer’s molecular
hinge, 30, based on a 2,2′-bipyridine motif, is another example of large amplitude motion
controlled by coordination of a metal ion. In this case, the open system was free to rotate
over 180° with its rotation being constrained by an in exible backbone. Upon coordination of
Cu(II), the hinge shut. Upon copper removal, the hinge was again able to open, but only in one
direction due to the constraints of the backbone.(299) A light-driven switch and a chirality
pendulum based on a similar system have been reported by the same group.(300, 301)

Scheme 8

Scheme 8. Chelation Control of Equatorial/Axial Conformers and Haberhauer’s Molecular

Hinge(290, 299),a

Scheme a Reprinted with permission from ref 299. Copyright 2008 Wiley-VCH Verlag GmbH
& Co. KGaA, Weinheim.
Cavitands derived from resorcin[4]arenes have been shown to undergo large conformational
changes between open “kite” and closed “vase” forms of 31 (Scheme 9).(302) Because   of 
solvation effects, the kite form is normally favored at lower temperatures and the vase at
higher.(302-304) However, this change has also been achieved using protonation of or metal
coordination to the quinoxaline nitrogens,(305-308) or by altering the design to incorporate
redox-active centers.(309, 310) Substitution of the cavitand with amide groups can lead to
stabilization of the vase form by dimerization or guest complexation.(311-320) As an
alternative to coordination of a guest causing a change in conformation, complexation can
be intramolecular as in macrocycle 32 reported by Stoddart et al. The system rests in the
self-complexed form until reduction of the cyclophane decreases subcomponent
interactions, followed by release of the system to an unrestrained, unencapsulated form.
(321-326) A similar system, 33, was realized by Feringa and Qu(327) with directional rotation
inhibited in the complexed state, but allowed when uncomplexed (Scheme 9).

Scheme 9

Scheme 9. Resorcin[4]arene 31, Vase and Kite Conformers, Stoddart’s Self-Complexing Lock
32, and Feringa’s Self-Complexing Rotor 33(98, 321, 322, 327),a

Scheme a Reprinted with permission from refs 321 and 327. Copyright 1997 and 2010 Wiley-
VCH Verlag GmbH & Co. KGaA, Weinheim.

Hamilton and co-workers introduced conformational switch 34 (Scheme 10) where in the
initial state the equilibrium is mildly biased toward the benzamide station (1.3:1). Upon
protonation of the dimethylamine with TFA, a dramatic reversal of this bias is observed
(1:99).(328) The oxidation of a copper center has been used to trigger coupled rotation and
copper exchange between two independent switches (based on the structure shown in
Scheme 45).(329)

Scheme 10
   

Scheme 10. Hamilton’s Acid Sensitive Switch(328)

Scheme 11

Scheme 11. pH-Driven Conformational Change in Oligomeric System 35(330)

Oligomeric systems have been used to great effect in generating large-scale conformational
changes, often exploiting the helical secondary structures that can be formed by many
species.(330-367) Polyamide 35 resides in a helical arrangement, but protonation of four
diaminopyridine units causes a dramatic extension to the linear form of 35 (Scheme 11).
Further protonation leads to another helical form, and the system can be returned to its initial
form by deprotonation.(330) An extension of this system was shown to expand from 12.5 to
57 Å upon protonation.(368) An alternating pyridine and pyrimidine oligomer formed helices
(due to the favored disposition of neighboring rings being transoid), but upon addition of
Pb(II) to 36, coordination led to a linear form with a concurrent increase in length from 7.5 to
38 Å (Scheme 12). This process could be made switchable by sequestering the Pb(II) until
needed in pH responsive cryptand 37.(369) A similar process has been achieved using Ag(I)
to modulate expansion.(370)   

Scheme 12

Scheme 12. Large-Scale Extension of a Ligand Strand upon Pb(II) Complexation(369, 370)

An interesting recent example was provided by Stadler and Lehn(371) where a linear and a
helical domain were synthesized in the same molecule. In this two-domain system,
coordination of Pb(II) led to the unfurling of the helical domain with concurrent curling of the
linear portion of the molecule. Upon removal of Pb(II), the system reverted to its original
state, thus representing a reversible device where an extension process is coupled to a
furling one, on both complexation and decomplexation of a metal ion.

2.2 Controlling Con gurational Changes

Changes in con guration, especially cis/trans isomerization, have been used in many
molecular systems to control motion.(372) Although the sometimes small amplitude motion
is not always useful for the design of molecular machines, it represents an interesting tool
for inducing directional motion in synthetic and supramolecular systems. The most
prominent examples of this type of system are the photoisomerization of stilbenes and
azobenzenes,(373-377) the reversible electrocyclization of diarylethenes,(378-382) the
photochromic reactions of fulgides,(383, 384) the interconversion of spiropyrans with
merocyanin,(385) as well as chiroptical switching of overcrowded alkenes.(386-388) In
recent years, this topic has become an extensive area of research, and a wide range of
applications exploiting switchable systems have been proposed and realized.(389-395) Most
of these applications rely on intrinsic electronic and spectroscopic changes on
interconversion between the two species, but some use small con gurational changes in a
more mechanical fashion, and the resulting devices can be seen as molecular machines.

Con gurational changes, especially the photoisomerization of azobenzenes, have been used
to induce changes in the structures of biologically relevant molecules such as antibiotics,
peptides, and DNA,(374, 396-406) but also as part of small-molecule systems such as
molecular scissors, tweezers, and other molecular machines.(407-412) Some of them will be
introduced in the following section.   

Scheme 13

Scheme 13. (a) Molecular Scissors 38;a and (b) Structure of Molecular Hinge 39(414)

Scheme a Irradiation at 350 nm initiates photoisomerization from the trans to cis isomer of
the azobenzene moiety (closed to open molecular scissor); irradiation at >400 nm induces
the reverse.(413)

Molecular scissors 38, described by Aida and co-workers, consist of an azobenzene unit and
a ferrocene unit (Scheme 13a).(413, 415) The open and closed forms were interconverted by
photoisomerization of the double bond of the azobenzene unit, which led to an angular
change of 49° around the cyclopentadienyl rings of the ferrocene. Another example was the
synthesis of the molecular hinge 39 where two xanthene rings were connected by −N═N–
linkers (Scheme 13b).(414) Photoisomerization at 366 nm from the trans/trans, which is
almost planar, to the cis/cis state resulted in a change of approximately 90° in the angle
between the two aromatic rings. Reisomerization could be achieved by irradiation at 436 nm.
Azobenzenes have been used for the construction of photoswitchable azo-macrocycles.
(389, 416) Azo-macrocycles have found applications in host–guest chemistry as they can
selectively and reversibly bind ions. Cyclic azobenzenes have been used to switch on or off
the rotation of subunits.(417, 418) A recent example showed that the rotation of a 2,5-
dimethylbenzene rotor in the cyclic azobenzene 40 could be switched off in the E-isomer of
the azobenzene, while rotation was allowed in the Z-isomer (Figure 17).

Figure 17
   

Figure 17. (a) Chemical structure of a molecular brake 40 with a 2,5-dimethylbenzene unit as
the rotor. (b) X-ray crystal structure. (c) Schematic representation of this photoinduced
molecular brake. X-ray crystal structure reprinted with permission from ref 418. Copyright
2011 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Azobenzenes have also been used to control motion in molecular shuttles (see also section
4.3) and to control the threading and dethreading rate of a macrocycle when attached to the
ends of a thread. In a recently published example, E → Z photoisomerization of azo-end
groups slowed the threading–dethreading of a ring and turned the pseudorotaxane into a
kinetically inert rotaxane.(419)

The substitution of an alkene can lead to steric overcrowding around a double bond. When
the substituents are large enough, the planarity of the double bond can be disrupted and a
variety of twisted and folded conformations can be adopted, including helices. The area
where the substituents come into close proximity is often referred to as the fjord region.
These types of compounds still undergo photoisomerization and can be used as chiroptical
molecular switches.(386, 420, 421) Feringa et al. have developed several molecular motors
exploiting overcrowded alkenes as chiroptical molecular switches.(422-428) The rst
generation of this molecular motor (Scheme 14, compound 41) featured two identical halves
connected by a central double bond.(429-436) Each of the halves had a stereocenter, which
was crucial to controlling the rotational process. Rotation of 360° around the double bond
was repetitive and directional. Two light induced cis–trans isomerizations led to a 180°
rotation and were each followed by thermally controlled helicity inversion, which effectively
blocked reverse rotation. The cis–trans photoisomerization was evident from 1H NMR, and
the simultaneous exchange of P to M was detected by circular dichroism (CD). A number of
different structures have been synthesized to optimize the rotation process and to
explore
 
the limits of the system.(437-444)

Scheme 14

Scheme 14. Minimization of Steric Interactions between Aromatic Groups and Substituent
Results in (P,P)-(trans)-41-Stable Ground-State Conformation, with Axial Substituentsa

Scheme a (i) Photochemical isomerization leaves substituents in the unstable equatorial

conformation (M,M)-(cis)-41-unstable. (ii) Steric strain is released by a thermally activated
helicity inversion leading to (P,P)-(cis)-41-stable. (iii) Photoisomerization from cis to trans.
(iv) Helical inversion completes a full rotation.(429)

In the second generation of Feringa’s molecular motor 42, two halves that are not identical
were connected by a central double bond.(445-447) One half was replaced by a tricyclic
aromatic group and there was only one stereogenic center present, but the rotation operated
according to the same principles as the rst generation motor 41 (Figure 18). Some dramatic
enhancements of rotary speed were achieved in the second generation of motors.
(428, 448-453)

Figure 18
   

Figure 18. Comparison of the general structures for the rst (41) and second (42)
generations of Feringa’s molecular motors.(425)

Feringa and co-workers have shown that transmission of molecular rotation from one part of
a molecule to another is possible. In motor 43, a xylyl unit was attached to the lower half of
an overcrowded alkene-based switch. By switching between the cis- and trans-forms, the
rotation of the xylyl group could be controlled (Figure 19).(454, 455) Imines have recently
been used as directional light-driven rotors by Lehn and Greb.(456)

Figure 19

Figure 19. Structure of molecular brake 43.(454)

It has long been known that irradiation of hydrazones can induce E → Z isomerization
around the imine bond (C═N). However, the Z-isomer is usually thermodynamically unstable
and thus short-lived.(457, 458) Intramolecular hydrogen bonding in various hydrazone
derivatives can kinetically stabilize the Z-isomer, which is formed by irradiation.(459-461) The
Aprahamian group has studied the E/Z isomerization of hydrazones using chemical
switching inputs such as protons and zinc ions.(462-467)

Scheme 15
   

Scheme 15. Hydrazone-Based Switchesa

Scheme a (a) Protonation of the pyridyl nitrogen of compound (E)-44 induces E → Z

isomerization.(468) (b) The quinoline unit in (E)-45 provides a binding site for a Zn2+ ion,
which is now the trigger for E → Z isomerization.(469)

In their original system, E→ Z isomerization was induced by protonation of a pyridyl ring that
initially acts as an intramolecular hydrogen-bond acceptor in the E-isomer (Scheme 15,
compound (E)-44).(468, 470) In the Z-isomer, the carbonyl oxygen stabilizes the Z-H+ form of
the molecule because the pyridyl unit is no longer available as a hydrogen-bond acceptor.
Upon deprotonation, the process is reversed. However, the Z-isomer is metastable, and as a
consequence the removal of the proton does not lead to an immediate change. The
thermodynamically more stable E-isomer reappears with time. The Aprahamian group has
also replaced the naphthalene unit with a quinoline unit (see (E)-45), thus introducing an
additional hydrogen-bond acceptor and an additional metal ion binding pocket next to the
hydrazone.(469) In this system, a Zn2+ ion now triggers E → Z isomerization. The most
recent system showed that on addition of Zn2+ to (E)-46 and (E)-47, a switching cascade
could be initiated.(471) Coordination of Zn2+ to (E)-46 lowers the pKa of the imidazole N–H
by 3 units and allows the protonation of (E)-47, which in turn allows switching of this moiety.
Without metal coordination, the imidazole is not acidic enough to catalyze switching in
(E)-47, making this sequence an elegant example of one switching event acting as the input
for another, in one pot. Because the stator and rotor are held in xed relative positions, the
switches developed by Aprahamian and co-workers represent very promising tools for the
control of directional motions in molecular machines (Scheme 16). A hydrazone switch has
been used to dope a liquid crystal with the color of the liquid changing upon switching.(472)
  

Scheme 16

Scheme 16. Switching Cascade of Hydrazone Rotary Switches(471)

3 Controlling Motion in Supramolecular Systems Jump To

The use of supramolecular systems in molecular machines is challenging as competing

processes such as the association and dissociation of subcomponents from and to the bulk
must be controlled.(473, 474) These processes can interfere with the integrity and/or
processivity of the machine unless the binding is part of the motion generation process itself
or the effect of unbound elements is restricted. If host–guest interactions are used to
assemble a machine, then exchange with free hosts or guests in solution should be avoided
to maintain the integrity and kinetic stability of the machine. Disassembly or exchange can,
in certain cases, be intentionally exploited for functional purposes and to provide
communication with external species. Controlled motion in supramolecular systems must
be built on cooperative interactions of individually weak but collectively strong noncovalent
interactions.

In biology, large-scale molecular motion generated upon guest binding is a common

process. Acetylcholine neurotransmitters are among such guests and bind to a
transmembrane channel receptor, inducing a large conformational change, resulting in the
controlled ux of ions through the membrane.(475) In this case, any guests in the bulk can
act as an inducer of molecular motion and at the same time as a messenger of the
microenvironment enabling dynamic communication with the surroundings. The stabilities
of most biological functional assemblies are well maintained by restriction of bulk exchange.
If this was not so, rapid exchange of the ribosome complex or individual subunits of the
ribosome during protein synthesis would detach the enzyme from the substrate mRNA and
release a partially synthesized peptide, unlikely to be of any use. However, mRNA and the
ribosome form a kinetically stable complex, subunit exchange with the bulk is restricted, and
the enzyme processively produces large proteins.(476)   

3.1 Guest Binding Generating, or Assisted by, Large-Scale

Intramolecular Motion
Considering the above discussion, molecular machines and devices based on noncovalent
assemblies require careful design. The relatively large molecular level motions generated
upon guest binding are of great importance in the design of practical molecular machines.
Guest-induced molecular motion has been widely studied in the literature with organic
compound,(477) anion,(478) cation,(479-481) metal,(464, 471, 482, 483) or proton guests.
(484, 485) Switches based on pseudorotaxanes have also been reported.(486-518) These
supramolecular complexes display interesting operational properties that are useful for
device development.(495, 519-564) These switches can be used to build relatively
sophisticated devices such as the molecular tweezers 23–26.(280, 281, 287, 288, 565-575)
This concept conventionally refers to receptors having a cavity with two binding motifs. The
binding pocket can either readily encapsulate the guest (lock and key type) or evolve to a
more suitable conformation upon guest binding (induced t type). Molecular machines can
be regulated by responsive tweezers, with motion induced and regulated through an external
stimulus such as the binding of guest molecules.

Scheme 17

Scheme 17. Light-Operated Molecular Tweezers(575)

One of the earliest examples of a molecular machine was a “molecular tweezer” based on
the photoisomerization-dependent binding of cations in a crown ether-bearing azobenzene,
developed by Shinkai et al. (Scheme 17).(575, 576) The open trans form can bind smaller
cations such as Na+ selectively, whereas the cis form prefers to bind larger Rb+ ions by
forming a sandwich complex with the cation. Moreover, the cis isomer can be stabilized by
the sandwich complex in the presence of Rb+, and the photostationary state biased toward
the cis isomer, causing the molecule to relax to the trans isomer much more slowly. Hence,
in addition to photoisomerization-dependent changes in the a nity of the receptor, guest
binding can alter the kinetics of the photoisomerization process.

Scheme 18
   

Scheme 18. Decreased Drug Binding A nity by a pH-Induced Conformational Change(573)

Intercalation of electron-poor aromatic guests by molecular tweezers having two π-systems

has also been explored by several groups.(577-581) The binding and release of the guest is
modulated by the motion of the receptor components. Intramolecular motion has been
induced allosterically by means of various stimuli including metals,(582-584) anions,
(585, 586) electrochemical reduction,(587) and pH change.(573) 2,6-Substituted pyridine 49
has been shown to change conformation upon protonation of the pyridine, such that the
methoxy groups form hydrogen bonds with the pyridinium proton (Scheme 18).(573) This
hydrogen bonding results in a rotation around the single bond moving the naphthyl moieties
away from each other. Intramolecular motion results in the release of the hydrophobic drug
mitoxanthron, which had been bound by π–π interactions between two naphthyl receptors.

Figure 20

Figure 20. Orthogonal exclusion of an azobenzene and a viologen encapsulated by CB[8].

(588)

Extracting work from machines depending solely on supramolecular interactions would be

di cult due to the rapid exchange of bound and unbound guests. However, some
supramolecular host–guest systems are moderately stable and might be suitable for use in
the assembly of molecular devices. A methylviologen (compound 50, MV2+) and a trans-
azobenzene derivative (compound 51, trans-AB) were encapsulated by a cucurbit[8]uril
(CB[8]) host (Figure 20). Each guest has distinct properties: MV2+ is redox active, and the
azobenzene can be isomerized to its cis-form (cis-AB) on irradiation.(588) One electron
reduction of methylviologen (MV+•) results in a binary encapsulation of the reduced species
in the host and trans-AB is kicked out. Photoisomerization of azobenzene to its cis -isomer
 
results in its ejection due to steric repulsion. Therefore, the initial heteroternary complex of
MV2+, trans-AB, and CB[8] can be orthogonally switched to give two distinct complexes. In
one complex, one-electron reduction of MV2+ forces out the azobenzene to form a
homoternary complex (MV+•)2CB[8], while in the other photoisomerization of the azobenzene
ejects cis-AB, while MV2+ stays encapsulated to form (MV2+)CB[8].

These three distinct, stimuli-dependent, modes of complexation allow greater control over
molecular behavior. To transfer this to the macroscopic world, thiol-functionalized trans-
azobenzenes were attached to a gold surface. Upon complexation by CB[8], together with the
uorescently labeled MV2+, the surface became uorescent, and due to the charged nature
of viologen, a substantial increase in wettability was observed. Upon irradiation, the
azobenzene was kicked out as its cis isomer, returning the surface to a non uorescent,
hydrophobic state, after the unbound uorescent viologen–CB[8] complex was washed away
from the surface. The orthogonal control of switching processes is a vital tool for the
creation of even more complex molecular devices, especially in memory device construction.
(588)

One of the interesting emerging properties of supramolecular host–guest systems is the

stimuli-dependent expansion and contraction of molecular constructs. This behavior will be
revisited in rotaxane systems in section 8. In double-stranded helicate 52 (bridged by
spiroborates at each end), sodium ion-induced reversible extension and contraction was
observed with an accompanying directional twisting (Figure 21).(589) In the presence of Na+,
the molecule was forced to twist its central tetraphenol moiety to better coordinate the
cation. The handedness of the helicate was preserved during this process. This process
could be reversed by the sequestration of Na+ by [2.2.1]cryptand.

Figure 21

Figure 21. Na+-induced twisting in helicate 52. Reprinted with permission from ref 589.
Copyright 2010 Nature Publishing Group.
The tetraphenolic central compartment could be replaced by two porphyrins to create a
hydrophobic cavity for aromatic guests to stack inside.(590) Upon intercalation ofelectron-
 
de cient aromatic guests between the porphyrin rings, the distance between the two
porphyrin units increased from 4.1 to 6.8 Å. This expansion in the central region induced a
rotation, which reduced the torsion angle, and, due to steric constraints, the capping
spiroborates unwound in a directional manner, demonstrating the rst guest-induced rotary
motion with accompanying corkscrewing motion. Guest control of screw motion, involving
simultaneous linear translation and rotation, has been reported.(591) In this case, the guest
acted as a template for the formation of helicates based on hydrogen bonding and biased
the formation of one of the two equilibrium structures.

Stimulus-driven molecular level conformational change and subsequent control over the
binding a nity of guest molecules have been used to regulate anion concentration in
solution.(592-594) Flood et al. developed a triazole-based foldamer bearing an azobenzene
moiety in the structure (Figure 22).(595) Hydrogen bonding between the triazole units and a
chloride anion together with π-stacking within the foldamer backbone kept the anion buried
in the interior.(592, 596-602) Photoisomerization of the azobenzene moieties disrupted the
stacking, inducing unfolding and releasing the anions. This photoinduced release and
capture of anions is completely reversible. Calculated K values in acetonitrile decrease
signi cantly from 3000 to 380 M–1 upon irradiation with UV-light. In addition, the conductivity
of the irradiated sample increased due to release of anions into solution. Helical inversion
caused by ion binding has also been observed.(603) Stimuli responsive switches have great
potential in drug release and ion-cargo transport applications. Nitschke et al. have reported a
complex system, where the addition of various signal molecules to a helical complex led to a
cascade of changes in the self-assembled system and various product distributions could be
formed.(604)

Figure 22
   

Figure 22. Control of anion concentration in solution by a photoresponsive foldamer.

Reprinted with permission from ref 595. Copyright 2010 American Chemical Society.

In the above examples, binding properties are regulated by an external stimulus or by

allosteric control. Large-scale molecular motions regulated by guest binding are of particular
interest in molecular machine design, because the presence of the regulator acts as a
chemical communication between the environment and the machine. This dynamic
interaction would allow the development of smart molecular machinery that performs
advanced operations dependent on the chemical environment, or perhaps allows
communication between machines.

3.2 Intramolecular Ion Translocation

The molecular basis for the conversion (in archea) of photon energy into more useful
potential energy relies on proton translocation between a photoisomerized retinal molecule
and the amino acid residues on the protein scaffold in which it is buried. This process occurs
with a well-de ned directionality, leading to light-mediated directional proton pumping across
a membrane.(384, 605) In supramolecular systems, for accurate translocation to take place,
the ion to be translocated should be more kinetically available for intramolecular motion than
the bulk ion. An electrochemical gradient cannot be achieved if each ion acceptor takes ions
from the bulk. Ion translocation can be controlled by changing the a nity of organic
receptors or metal centers for the ion of interest, through external stimuli such as light or
reduction/oxidation.(606) In the case of proton transfer, some molecules have distinct
photophysical properties such as a change in the pKa of the molecule in the excited state,
which enables rapid dissociation of the proton from one part of the molecule and
reassociation with another, intramolecular acceptor, in an “excited-state intramolecular
proton transfer” (ESIPT).(607) This process has been extensively studied using 2-(2-
hydroxyphenyl)-benzothiazole (HBT, Scheme 19).(608) Fast proton transfer from the hydroxyl
group to the nearby thiazole nitrogen takes place upon excitation of the molecule to generate
 
a cis-keto form with a distinct, solvent-dependent, spectroscopic character. In this molecule,
intramolecular hydrogen bonding mediates this fast proton transfer between different
regions of the molecule.

Scheme 19

Scheme 19. Excited-State Intramolecular Proton Transfer in HBT(607, 608)

Metals having more than one stable oxidation state can be translocated by oxidation or
reduction or incorporated into a scaffold along with other ions that can be translocated. For
either process, the molecule should bear more than one binding site, with different a nities,
to drive the motion of the ion. Flexible receptors are most often used for ion translocation,
but rigid aromatic systems can be suitable as well. These processes are usually
accompanied by a visible color change due to changes in absorption after a change in the
oxidation state of the metal, or due to ligand exchange. The reversible translocation of a
chloride anion from a Cu(II) center to a Ni(III) center was an early example of a exible
system (Scheme 20a).(609) The concentration-independent nature of the process indicated
that anions translocate from the Cu(II) center in an intramolecular fashion rather than via
exchange with the bulk.

Scheme 20

Scheme 20. Intramolecular Anion Translocation Mediated by (a) Redox(609) and (b) Ligand
Exchange(610)
Work by Mirkin et al. showed reversible intramolecular shuttling of a chloride anion from a
bisurea binding site to Rh(I) in the presence of carbon monoxide (Scheme 20b).(610) The 
hydrogen-bonding ability of the urea was further enhanced by attaching electron-
withdrawing 3,5-bis(tri uoromethyl)benzyl groups. Rh(I) adopts a distorted square-planar
geometry with these phosphine and thioether ligands, as shown by the crystal structure.
Initially, chloride was encapsulated between the urea tweezers. With the aid of polar solvents
(dimethyl sulfoxide or dimethylformamide) and in the presence of CO, chloride was
translocated to Rh(I) with accompanying CO coordination. The Rh–S bonds were cleaved
concurrently. Translocation was driven by both the weakening of hydrogen-bonding
interactions in the urea and the more favored and less distorted geometry adopted at the Rh
center with the new ligands. This is an important example of ion translocation in view of the
fact that it involves two different types of interaction (hydrogen bonding and metal–ligand
coordination) to enable shuttling and may open a path to the development of further
molecular devices by the orthogonal control of these two interactions.

The rst intramolecular cation translocation driven by auxiliary redox reactions was reported
by Shanzer et al.(611) A triple-stranded helical scaffold was used with ditopic hydroxamate
and bpy ligands, which bind preferentially to Fe(III) and Fe(II), respectively (Scheme 21).
Chemical reduction of Fe(III) with ascorbic acid relocated the cation to the bpy ligand with a
visually observable color change from pale brown to violet-red. Reversibility was obtained by
oxidation with (NH4)2S2O8. Even though the process takes place slowly (minutes to hours),
the overall movement of the cation is intramolecular.

Scheme 21

Scheme 21. Redox-Mediated Intramolecular Ion Translocation(611)

Several other examples of anion and cation translocation between ligands separated by
exible linkers have been investigated.(480, 612-614) Metals are also known to translocate
  
2
over rigid sp hybridized carbon surfaces.(615) Sandwich complexes of two dipalladium
units (four palladium nucleii arranged in two separate regions) clustered between π-
conjugated ligands showed redox-driven reversible translocation, resulting in a
tetrapalladium complex (Scheme 22).(616) In a complex with further extended conjugation,
redox reaction conditions resulted in reversible carbon–carbon formation between the
dipalladium clusters. This barrier (the new C–C bond) built by the mobility driving force used
in the rst complex (redox reaction) prevented translocation in the second complex and
hence con ned the metals to their original positions.

Scheme 22

Scheme 22. Redox-Mediated Pd Translocation in an Aromatic Sandwich Complex(616)

Supramolecular host–guest systems with distinct stimuli responsive switching behavior,

guest sorting character, and emergent photophysical properties have been developed with
implications for the design of molecular machines. To enable controlled mechanical motion,
these systems should be kinetically stable enough to avoid exchange of components with
the bulk on the time scale of the operation. Mechanically bonded molecular assemblies are
viable candidates for machine architectures, considering their stable interlocked structure,
and the relative ease of controlling their mobility.

4 Shuttling in Rotaxanes: Inherent Dynamics Jump To

Motion in rotaxanes is constrained by the nature of the mechanical bond. Very limited
motion is permitted orthogonal to the axle, while a “shuttling” motion “powered” by random
Brownian motion can be observed along the axle (as bounded by large stoppers). As the
templating methods typically used to form interlocked structures normally leave recognition
motifs,(23, 617-676) it is rare, although not unknown, to form a rotaxane without residual
interactions between thread and macrocycle.(504, 672, 677-689) These residual interactions
are typically viewed as “stations” on the rotaxane, and the shuttling of the macrocycle
between these stations grants a useful handle in these molecules. The rates of shuttling
between stations and their occupancy can be controlled by the strength of station–
macrocycle interactions.
4.1 Shuttling in Degenerate, Two-Station, Molecular Shuttles
  
The rst two-station degenerate [2]rotaxane 61 was reported by Stoddart et al. and exhibited
temperature-dependent shuttling between the two equivalent hydroquinol groups, as shown
by 1H NMR.(690) Many rotaxanes based on similar macrocycles and stations have since
been reported.(691, 692) Similar processes are observed in the amide rotaxanes 62–64
where two diglycine units are separated by various linkers. In 62–64, rapid shuttling of the
macrocycle between the degenerate stations was observed at 298 K. Only when the linker
was replaced with a bulky N-tosyl group was shuttling inhibited (removal of the tosyl group
restored rapid shuttling) (Scheme 23).(693)

Scheme 23

Scheme 23. (a) The First “Molecular Shuttle”, 61;(690) and (b) Degenerate Peptide-Based
Molecular Shuttles 62–64 of Varying Linker Length(693)

As movement between the binding sites must involve at least partial rupture of the
hydrogen-bonding network, the migration can be represented by the simpli ed energy
diagram in Figure 23. Hydrogen-bonding solvents have been shown to disrupt macrocycle–
thread interactions in single station rotaxanes,(694) and here addition of 5% [D4]methanol
increased the rate of shuttling 100-fold, consistent with lowering the energy barrier to
migration by disrupting station–macrocycle interactions and thus raising ground-state
energies.(693, 695-697) The effect of water on the rate of shuttling has been investigated
and was found to be greatly superior to that of other protic solvents.(698) This effect was
attributed to the ability of water to form three-dimensional hydrogen-bonding networks.
  

Figure 23

Figure 23. Idealized model of binding in degenerate molecular shuttles. Barrier height is
dependent on the energy required to break interactions between macrocycle and station and
a distance-dependent diffusional component.(14)

The use of a phenol/phenolate central group where the formation of a phenolate/cation pair
signi cantly slowed shuttling(699) has also been explored. Cleavage of a nitrogen protecting
group has been used to induce degenerate shuttling.(700) A large barrier to shuttling could
be introduced in 65 where the dimerization of the rotaxane, as templated by Cu(I) addition,
prevented shuttling (Scheme 24). This could be reversed by copper removal with an ion-
exchange resin.(701, 702) Berna and co-workers have recently reported a system in which
the binding of a guest hydrogen-bond acceptor–donor–acceptor molecule to the thread led
to the trapping of the macrocycle to the linker region between the two stations.(703) Upon
removal, by external complexation, of the guest, interstation shuttling was restored. Control
of shuttling rate has also been achieved by the oxidation/reduction of hydrogen-bonding
stations(704) and by photochemical ring contraction of a macrocycle.(705)

Scheme 24
   

Scheme 24. Complexation of Copper Leads to the Introduction of a Large Kinetic Barrier to
Shuttling(701)

4.2 Physical Models of Degenerate, Two-Station Rotaxanes

A decrease in the rate of shuttling was observed upon lengthening the alkyl chain of 63 as
compared to 62, the magnitude of which corresponds to an increase in activation barrier of
ca. 5 kJ mol–1. This effect was attributed to the increased distance the macrocycle must
travel between binding stations.(693) This process can be modeled by considering the
macrocycle as a particle con ned to a one-dimensional potential energy surface (the
mechanically interlocked nature of the rotaxane preventing signi cant motion of the
macrocycle orthogonal to the thread). Assuming that thread–macrocycle interactions
between stations are negligible leads to the energy pro le shown in Figure 24. The rate of
escape from the station energy well can then be modeled by an Arrhenius equation with a
contribution from a distance-dependent diffusion factor to the overall rate of shuttling. A
quantum mechanical treatment of this system has found that, as the lengthening of the
spacer has no effect on the activation for breaking the hydrogen bonds, the effect on the rate
of shuttling is due to the widening of the overall potential energy well. This leads to a greater
density of states per unit energy, thermal population of a greater number of energy levels,
and thus a larger partition function and activation energy.(706) An alternate explanation of
the dependence of shuttling rate on linker length was proposed by Brouwer and Günbaş who
proposed that shuttling in a similar system was facilitated by hydrogen bonding between the
macrocycle and the station to which it is not currently bound.(707) As the linker length
increases, this bridging conformation becomes increasingly entropically unfavorable.
 Some
 
support for this proposal comes from recent examples from Hirose et al. and Sissel and co-
workers,(708, 709) and Stoddart and co-workers,(710) who in different systems with rigid
spacing units found no correlation between spacer length and shuttling rate.

Figure 24

Figure 24. Idealized potential energy surface for macrocycle shuttling in a degenerate, two-
station molecular shuttle.

4.3 Stimuli Responsive Molecular Shuttles

Molecular motion in mechanically interlocked and thus kinetically stable rotaxanes can be
controlled using multiple binding sites with a nities for the macrocycle that vary under
different conditions. The conditions can be modi ed by electrochemical redox processes,
light, pH, and environmental changes. Once detailed balance is broken by the applied
stimulus, as with temperature difference in Feynmann’s ratchet-and-pawl, useful mechanical
work can be done, provided there is an additional operation to prevent it being undone. By
weakening the existing interaction or increasing the a nity of a competing binding site, the
macrocycle can be driven to shuttle to a new equilibrium position. For a reverse or further
translational motion to take place, a new stimulus is required to perturb the new equilibrium.

4.3.1 Stimuli Responsive Molecular Shuttles with Single Binding Site

Shuttling in a single binding site system can be obtained by reducing the a nity of either the
macrocycle for the station or the station to the macrocycle, by the application of an external
stimuli. Light controlled switching was observed in a rotaxane made from a “bluebox”
macrocycle, an electron-rich dioxyerene station, and redox-active ferrocenyl stoppers.(711)
Light-induced electron transfer from the station to the macrocycle was accompanied by
electron hole transfer to one of the ferrocenyl stoppers, thereby inducing unfolding of the
 
rotaxane and shuttling of the macrocycle away from the station. Photodriven shuttling in
single station rotaxanes was also observed with the increase of steric bulk generated upon
photoisomerization of an azobenzene or stilbene station.(712, 713) Among these examples,
directional shuttling of cyclodextrin (CD) on a symmetrical thread is of particular importance
due to the fact that it serves as a ratchet for a directional bias maintained purely by the
asymmetric nature of the CD rims.(713) Shuttling was biased to the direction that locates the
6-rim of the CD in a position facing the central stilbene unit (Scheme 25).

Scheme 25

Scheme 25. Light-Driven Directional CD Shuttling in a [2]Rotaxane(712)

Solvent-dependent shuttling is generally achieved by switching between hydrogen-bonding

and non-hydrogen-bonding solvents.(714) Hydrogen bonding between macrocycle and
thread is weakened in the presence of a competing solvent. In a peptide-based rotaxane with
a benzyl amide macrocycle, hydrogen-bonding interactions were weakened by addition of
MeOH (Scheme 26).(715) Because of a solvent-induced relocation of the macrocycle, the
chiral center located on the thread now had an in uence on the macrocycle. The original
system could be restored in CHCl3. More recently, a rotaxane based on a pillar[5]arene
macrocycle was shown to shuttle upon either solvent exchange or heating.(716) This system
was found to form supramolecular gels in pure DMSO, and in a similar system this shuttling
was exploited to form a solvent-driven molecular spring.(717)

Scheme 26
   

Scheme 26. Solvent-Dependent Shuttling and Induced CD Response in a [2]Rotaxane(715)

4.3.2 Stimuli Responsive Molecular Shuttles with Two or More Binding Sites

At a given temperature, the macrocycle of a rotaxane distributes itself among the existing
stations according to the binding a nity of each. Perturbation of the binding energies of any
of the stations results in the redistribution of the macrocycle toward a new equilibrium state,
as driven by thermal motion. Changing the position of the macrocycle in a well-determined
way is possible, by making the binding a nity of the less occupied station more favorable
(Figure 25, transformation of station B to B′),(14) or by destabilizing the interaction between
the most occupied station and the macrocycle (Figure 25, transformation of station A to A′).
Stimuli responsive modi cation of the macrocycle can also drive such shuttling processes.
Redox, pH, light, and microenvironment (temperature, solvent, etc.) switches are commonly
used to control translational movement in rotaxane architectures, and will be discussed in
the following sections.

Figure 25
   

Figure 25. Potential energy diagram of a rotaxane-based bistable molecular shuttle.(14)

4.3.2.1 pH-Driven Molecular Shuttles

Variation in pH is one of the most useful stimuli used to drive translational motion in
rotaxanes because hydrogen bonding, electrostatic, and ion–dipole interactions can be
effectively controlled by protonation or deprotonation. Indeed, the rst molecular shuttle
developed by Stoddart et al. depended on acid-driven relocation of the electron poor,
positively charged, cyclophane macrocycle from a protonated benzidine station to a biphenol
station (Scheme 27).(718) Initially, under neutral pH and at 229 K, the macrocycle
preferentially rested on the benzidine station (with 84:16 distribution), stabilized by donor–
acceptor interactions. Upon protonation of this station, a decrease in the strength of the
interaction and an increased electrostatic repulsion caused the macrocycle to relocate to the
other station with a new equilibrium distribution of more than 98:2 in favor of the biphenol
station. Complexation of the cyclophane macrocycle in similar systems has inspired a
variety of computational research.(719-728)

Scheme 27
   

Scheme 27. A pH-Driven Molecular Shuttle(718)

A relatively low temperature was required to obtain an acceptable distribution bias in favor of
the benzidine station under neutral conditions. This necessitated the development of a
system, which exclusively resided on one station under standard conditions. Positional
discrimination with a ratio of more than 98:2 was obtained in a rotaxane composed of a
dibenzocrown ether macrocycle and ammonium-bipyridinium and ammonium-triazole
stations. This interaction has been exploited in many systems.(729-743) In a structurally
similar rotaxane dimer, pH-induced contraction and expansion was made to function as a
“molecular muscle”.(744-746) The pH-dependent relocation of an amide-based macrocycle
from a succinamide to an hydroxyl-cinnamate station was observed, with enhanced
hydrogen bonding between the deprotonated cinnamate derivative and the macrocycle.(747)
Rotaxanes in which repositioning to another station was driven by macrocycle protonation
have been reported.(748, 749) Shuttling of a metal–macrocycle complex from one ligand to
another on a rotaxane as a result of protonation of one of the ligands has been investigated.
(750) The pH-driven shuttling of cucurbit[7]uril between bipyridinium and carboxylate
stations has recently been reported.(751) Attempts were made to couple this motion to an
oscillating pH background reaction, but the pH oscillation was rapidly damped in this case.
Autonomous translocation is an important concept in molecular machine design, but
requires further research.

4.3.2.2 Redox-Driven Molecular Shuttles

Rotaxanes with electron donor–acceptor units or transition metal complexes can be
controlled by redox chemistry, provided that redox potentials of the interacting units are
carefully chosen.(752-756) After the redox process, the products should be stable on the
shuttling time scale, and rapid charge recombination must be prevented. Redox control
  
processes can be chemical, electrochemical, or photochemical.

An early example of redox-mediated shuttling was reported by Leigh et al. and took
advantage of a redox-active naphthalimide, which was introduced at one end of the thread.
The amide-based macrocycle migrated from a succinimide station to the napthalamide
station upon one-electron reduction of the naphthalamide (Scheme 28).(757-759) Increased
electron density on the imide carbonyl of the naphthalamide station outcompeted the
succinimide station, and the macrocycle rested almost exclusively at the naphthalamide
station. The shuttling was reversible and could be performed through photochemical
excitation accompanied by reduction with an external electron donor.

Scheme 28

Scheme 28. A Redox-Driven Molecular Shuttle(757, 758)

Benzidine, tetrathiafulvalene, viologen, naphthalimide, and dioxynaphthalene derivatives have

been widely used as redox-active stations.(760-777) Redox-induced changes in the
coordination preference of transition metal complexes bound to the macrocycle have also
been used to drive biased Brownian motion toward different stations.(778) A tristable
rotaxane has been reported where the position of the macrocycle over each of the three
stations could be controlled solely using electrochemistry.(779)
4.3.2.3 Ion-Driven Molecular Shuttles
  
The presence of ions usually affects the conformation and stability of the macrocycle on a
station by either interfering with the existing hydrogen bonding, ion–dipole, and dipole–
dipole interactions or by sterically disfavoring the binding. This effect can be strong enough
to drive translocation of the macrocycle to another station on the thread. In crown ether-
based macrocycles, metal ions can be chelated by the macrocycle and thus alter the a nity
of the macrocycle for their binding sites, and in some cases induce shuttling. Lithium was
reported to mediate the shuttling of crown ether-based macrocycles from a naphthalimide
station to a pyromellitic diimide, presumably due to stronger ion–dipole interactions with this
station in the presence of a cation.(780) Shuttling could be reversed by the addition of an
excess of [18]crown-6, which sequestered the lithium cation, returning the macrocycle to its
original equilibrium distribution. Rather than interacting directly with the macrocycle or a
station, ions can bind to another position on the rotaxane and affect the a nity of the
macrocycle with either station. Shuttling under similar allosteric control was observed using
a bis(2-picolyl)amine stopper that chelates cadmium ions.(781, 782) Binding to the nearby
station was disrupted in the presence of cadmium, and the macrocycle repositioned itself to
the distal station. Cadmium could be removed by cyanide complexation to reverse the
process.

Chloride coordination to a palladium complex was reported to drive shuttling from a triazole
station to a pyridinium station (Scheme 29).(783) In the absence of chloride anions, the
palladium metal was chelated by the macrocycle with the fourth coordinate site being
occupied by the triazole unit on the thread. Addition of chloride to the solution as its
tetrabutylammonium salt resulted in displacement of the triazole ligand and the macrocycle
detached from the station. When this occurred, the crown-ether moiety of the macrocycle
was free to interact with the pyridinium station, which promoted translocation. The process
could be reversed by addition of AgPF6. Metal-free, anion-induced shuttling between
naphthalimide and triazolium stations was also reported in which shuttling could be
monitored by UV–vis spectroscopy.(784) Iodide addition has been used to induce shuttling in
a halogen/hydrogen-bonding rotaxane.(785)

Scheme 29
   

Scheme 29. Chloride-Induced Molecular Shuttling in a [2]Rotaxane(783)

In separate work, a shift in uorescence was obtained by chloride-induced displacement of a

macrocycle from a central squaraine station to either of two weakly binding degenerate
stations.(786) In a tristable rotaxane bearing urea, ammonium, and phosphine oxide (listed in
descending binding ability) stations on the thread, macrocycle shuttling could be induced by
the binding of an acetate anion to the urea and subsequently to the ammonium site, which
sequentially blocked these higher a nity stations and forced the macrocycle to bind to the
weakly coordinating phosphine oxide station.(669) Similarly, the binding of a macrocycle to a
guanidinium station was found to be inhibited by PO43– addition.(787) In the presence of
Zn2+, the macrocycle preferentially bound the central 2,2′-bipyridyl station. In the presence of
PO43–, but not Zn2+, the macrocycle moved to the weakly coordinating carbamate station.
Copper removal followed by guest complexation between porphyrins in the two macrocycles
has been used to drive shuttling of a [3]rotaxane.(788)

4.3.2.4 Shuttling Induced by Reversible Covalent

Modi cation
Dynamic covalent bond formation and reversible reactions are important tools in the
synthesis of supramolecular devices and machines. This is due to the ability to control their
stability and lability by varying external conditions. These chemical tools enable shuttles to
do work by “compartmentalizing” the macrocycle on a station and acting as a physical
barrier to prevent random Brownian motion reversing the desired translational motion during
re-equilibration steps. This phenomenon will be discussed in detail in the following sections.
Reaction-based shuttling can be achieved in several ways. A station can be blocked by
introducing a new chemical group, or destabilizing the binding of a macrocycle for steric
 or
electronic reasons. The macrocycle can be chemically trapped on one station. Shuttling
between hydrogen-bonding stations has been controlled by Diels–Alder and retro-Diels–
Alder reactions, which block and unblock the better-binding fumaramide station.(789) In
another example, photoinduced heterolytic cleavage of a C–O bond in a diaryl
cycloheptatriene generated a positively charged tropylium station, and thus repelled the
cationic cyclophane macrocycle, displacing it to a different station.(790, 791) Oxidation or
reduction of sulfoxide-based stations and subsequent changes in the hydrogen bonding to a
benzylic amide macrocycle have also been used to control shuttling.(627)

Scheme 30

Scheme 30. Hydrolytic or Entropically Driven Restriction of Shuttling in a [2]Rotaxane(792)

Kawai et al. reported intrarotaxane imine formation between a diamino macrocycle and two
formyl groups at one of the stations. This reaction locked the macrocycle at the station and
maintained a positional discrimination (Scheme 30).(792) Hydrolysis of the imine in wet
CDCl3 in the presence of acid released the macrocycle from the station and also protonated
the amino moieties, making the polyether station more favorable due to hydrogen bonding
and ion–dipole interactions. Shuttling of the macrocycle could also be promoted by heating
and cooling. This entropy-driven shuttling was possible because of the release of two water
molecules on formation of the imine bonds. The entropic favorability of the imine state could
be more easily overcome at lower temperatures by enthalpic contributions.

Scheme 31
   

Scheme 31. Chemically Driven Shuttling in a [2]Rotaxane(793)

As with fumaramides, trans-azodicarboxamide modules have chemical structures

preorganized for strong hydrogen bonding with benzylic amide-based macrocycles. The
interaction of the macrocycle with the trans-azodicarboxamide station is stronger than that
with the succinamide station. Induced shuttling of a macrocycle to the less favored
succinamide station could be achieved chemically by blocking the favored station by
reaction with triphenylphosphine (Scheme 31).(793) This bulky substituent drove the
macrocycle away from the station. Under subsequent Mitsunobu reaction conditions, in the
presence of a carboxylic acid and an alcohol, the triphenylphosphonium was cleaved from
the station as triphenylphosphine oxide. After oxidation, the macrocycle returned to its initial
position.

4.3.2.5 Photodriven Molecular Shuttles

Photoinduced shuttling is an attractive mode of control over translational motion due to the
ease of stimuli introduction and removal. Moreover, if the back reaction or operation is
spontaneous and does not require an additional input, then the overall process becomes
autonomous; shuttling will occur as long as energy is supplied in the form of light. However,
instead of a continuous light source, ashes of light must be used to prevent the system
reaching and staying at a steady-state distribution. Although photodriven shuttling can be an
e cient approach, the kinetics of translation and photochemical processes have to be
carefully considered. If the photoinduced process involves a redox reaction, then rapid
charge recombination can take place before positional displacement of the macrocycle. To
avoid this, either excited states with a long lifetime are required or external reagents must be
used to reduce or oxidize the species.

In a carefully designed shuttle reported by Stoddart et al., translational switching was

obtained by one-electron reduction of a viologen station by a ruthenium trisbipyridine stopper
(Figure 26).(794) Relatively slow back electron transfer permitted ca. 10% of the macrocycle
to reposition to the dimethyl viologen station on each electron transfer. Continuous
irradiation maintained a 95:5 distribution of the macrocycle in favor of the dimethyl viologen
station. The system equilibrated back to the original viologen position once irradiation
ceased with spontaneous back electron transfer allowing reversion.
Figure 26
  

Figure 26. Photoinitiated redox-driven shuttling in a [2]-rotaxane initiated by (i) irradiation and
(ii) subsequent reduction of viologen station. (iii) Competing back electron transfer from one-
electron reduced viologen to Ru3+. (iv, v) With continuous irradiation the macrocycle shuttles
to the dimethylviologen station. (vi) Ceasing illumination restores the macrocycle to its
original position.(794)

Alongside the photoinduced redox reactions discussed above, improved excited-state

hydrogen-bonding interactions(795) and the photoisomerization of stilbene,(796)
azobenzene,(797) and other ole nic moieties leading to altered hydrogen bonding or steric
bulk creation have also been used to drive shuttling processes.(798) Absorbance and
uorescence has been used to monitor the progress of shuttling along the rotaxane in some
of these systems.(16, 799-801) Likewise, other photochromic compounds such as
spiropyrans have been exploited to control molecular shuttles, by switching between
photoisomers that form hydrogen bonds of different strengths.(802)

4.3.2.6 Molecular Shuttles Driven by Changes in the

Microenvironment
The term “microenvironment” usually refers to the temperature and solvent system. The
easiest way to control shuttling via solvent choice is through the disruption of hydrogen-
bonding interactions between the macrocycle and the station. Several examples of
macrocycle relocation induced by a change in solvent polarity or rotaxane solvation have
been reported.(803) In some cases, solvent molecules facilitate a shuttling process already
driven by other stimuli.(698, 797, 804) For entropy-driven shuttles, the rearrangement of
solvent molecules in or around the macrocycle is an important parameter controlling the
shuttling process.   
Rotaxanes bearing more than two stations and even polymeric rotaxanes driven by these
stimuli have been reported.(797, 805, 806) In these shuttles, work is undone in each reverse
shuttling. Directional shuttling via a ratchet mechanism has been achieved and will be
discussed in the next section.

4.4 Compartmentalized Molecular Machines

Stimuli-responsive molecular shuttles are rotaxanes in which the net position of the
macrocycle on the thread is controlled by external triggers (light, heat, electrons, chemical,
pH, binding events, etc.). In general, these triggers change the properties of the binding sites
and subsequently have an in uence on macrocycle/thread interactions. In this section,
various stimuli-induced mechanisms to create and control nonequilibrium conformations will
be presented. Rotaxane succ1-74 has two identical stations, which are distinguishable due
to the differing stoppers. The thread is divided into two compartments by a bulky silyl ether
barrier, preventing the macrocycle from shuttling between the two stations.(75) By removing
the silyl ether group, dynamic exchange of the macrocycle was enabled and the system
moved toward equilibrium. This resulted in a 50:50 distribution of the macrocycle between
the two stations. The operation is irreversible, because the attachment of the bulky silyl
group again does not change the average position of the macrocycle, and will not restore the
initial distribution of the macrocycle; the position of the macrocycle is not determined by the
state of the machine. The machine starts in a statistically unbalanced state (the bulky silyl
group prevented the macrocycle restoring balance by moving toward an equilibrium
distribution). By “linking” the system, removing the bulky group, the machine could reach its
equilibrium state, because free movement of the macrocycle was no longer prevented by the
barrier. Therefore, the macrocycle had “escaped” to a lower energy distribution (Figure 27).

Figure 27
   

Figure 27. [2]Rotaxane 74 acts as an irreversible mechanical switch. The silyl ether is too
bulky to allow macrocycle shuttling between the two succinamide stations.(75)

Recently, Coutrot and co-workers synthesized a two-compartment molecular machine

consisting of a dibenzo-24-crown-8 macrocycle and a thread with anilinium and
monosubstituted pyridinium amide stations.(807) The rotaxane was synthesized via CuAAC
chemistry. Subsequent N-benzylation of the triazole moiety, which is located in the middle of
the thread, was found to serve as a barrier as well as a third station for the macrocycle.
Depending on which station the macrocycle was located, the N-benzylation of the triazole
allowed trapping of the macrocycle in either the left or the right compartment.

The Leigh group has extended their initial system using the same design described above,
but with two different stations 75 (a fumaramide station and succinamide station) (Figure
28).(75)

Figure 28
   

Figure 28. Operation of a compartmentalized molecular machine, which corresponds to a

two-state Brownian ip- op. Operation steps: (a) Desilylation (80% aqueous acetic acid); (b) E
→ Z photoisomerization (hν at 312 nm); (c) resilylation (TBDMSCl); and (d) Z → E thermal
isomerization (catalytic piperidine).(75)

In this system, the exchange of the macrocycle between stations could be controlled by the
introduction of a barrier in the middle of the thread (kinetic control) as well as by altering the
binding a nity of the macrocycle to the two different stations (thermodynamic control).
Initially, 85% of the macrocycle bound the fumaramide station and 15% the succinamide
station. The system was still unlinked because of the kinetic barrier and therefore not in
equilibrium. A balance-breaking stimulus (photoisomerization at 312 nm) generated a 49:51
E:Z photostationary state. Removal of the barrier, the linking stimulus, allowed the balance to
be restored by the macrocycle equilibration. Restoring the barrier unlinked the system. The
last step was Z → E ole n isomerization, which made the system statistically unbalanced,
unlinked, and not in equilibrium. After one operational cycle of the machine, 56% of the
macrocycles were located on the succinamide station. The thread had therefore changed the
net position of the macrocycle. Because the succinamide station binds the macrocycle less
strongly than the fumaramide station, this process has moved the macrocycle energetically
uphill; that is, it has performed a ratcheting operation, transporting a particle away from
equilibrium. This system and its function is an experimental realization of the transportation
task required in Smoluchowski’s trapdoor and Maxwell’s pressure demon, which are
discussed in the introduction (section 1) and are powered by chemical and light energy.
Figure 29 shows a schematic representation of the four sequential steps performed by
rotaxane 75 to transport the system energetically uphill: balance-breaking 1, linking,
  
unlinking, balance breaking 2 (resetting the machine but not the substrate).

Figure 29

Figure 29. Initially the system is balanced (in proportion to the sizes of the two
compartments), with an equal density of particles in the left and the right compartments. By
changing the volume of the left-hand compartment, the system becomes statistically
unbalanced. Opening the door allows the particle to redistribute according to the new size of
the compartments. Closing the door ratchets the new distribution of the particles. Restoring
the left compartment to its original size results in a concentration gradient of the Brownian
particles across the two compartments. Here, the size of the compartment represents the
energy level of the macrocycle-station system.(75)

There are many different types of compartmentalized molecular machines, some of which
have been described in this section. Three main machine types exist. First is the two-state
(or multistate) Brownian switch, which is a machine that can reversibly change the
distribution of a Brownian substrate between two distinguishable sites as a function of state
of the machine. It does this by biasing the Brownian motion of the substrate (section 4.3).
Second is a two-state (or multistate) Brownian ip- op, a machine that can reversibly change
the distribution of a Brownian substrate between two (or more) distinguishable sites and that
can be reset without restoring the original distribution of the substrate. The distribution of
the substrate cannot be determined from the state of the ip- op, but rather it is determined
by the history of the operation of the machine. Rotaxane 75 is an example of a two-state
Brownian ip- op. Third, a Brownian motor is a machine that can repetitively and
progressively change the distribution of a substrate while the machine can be reset without
restoring the original distribution of the substrate. The rotary motors designed by Feringa
and co-workers are examples of this category of device. Additional examples will follow in
section 4.5.
Brownian ratchet mechanisms fall into two general classes: energy ratchets and information
ratchets (section 1). The above rotaxane is an energy ratchet in which the energy minima
 
and maxima of the potential energy surface are varied without regard to the particle’s
location. In the next section, examples of the second class of Brownian ratchets, information
ratchets, will be explored where a barrier is raised or lowered according to the position of a
Brownian particle on a potential energy surface, resulting in the particle distribution being
directionally driven away from equilibrium.

4.4.1 Molecular Information Ratchets

An information ratchet, such as Maxwell’s pressure demon, requires knowledge of the

position of each particle and is able to open the door if the particle is approaching from a
certain direction. This positional sorting allows the accumulation of particles in one side of
the container and thus results in a pressure gradient. The rst example of a molecular
information ratchet was described by Leigh and co-workers (Scheme 32).(808) Molecular
machine 76 consisted of a dibenzo-24-crown-8-based macrocycle, which was mechanically
locked on a linear thread by bulky 3,5-di-t-butylphenyl stoppers. An α-methyl stilbene unit
divided the thread into two compartments, both with ammonium binding stations. The
rotaxane used photosensitized energy transfer from the macrocycle to the stilbene unit as
the key step in changing the macrocycle distribution. When the stilbene unit adopted the E
form, the macrocycle could move randomly along the full length of the thread by Brownian
motion, while when the Z form is adopted, the macrocycle was trapped in one or the other of
the two compartments. To keep the machine as the Z-isomer, it was operated in the
presence of the photosensitizer PhCOCOPh. The sensitized photostationary state of α-
methyl stilbene is 82:18 Z:E. Selective “gate opening” was achieved by photosensitized
energy transfer from the macrocycle (which has a benzophenone (PhCOPh) moeity
attached) to the stilbene unit. This led to a 55:45 Z:E ratio of the α-methyl stilbene. As energy
transfer was distance dependent, this photosensitized transfer was more likely to happen
when the macrocycle was in the blue compartment (Scheme 32). When the macrocycle was
on the green station, intramolecular energy transfer from the macrocycle was not e cient
and the gate stayed closed, biasing macrocyclic distribution. This is an example of using the
positional information on a Brownian particle to break detailed balance, driving macrocycle
distribution away from equilibrium.

Scheme 32
   

Scheme 32. Structure and Mechanism of the Information Ratcheta

Scheme a (a) Gate closed, but energy transfer from the macrocycle is e cient. (b and c)
Gate is open, allowing free shuttling of the macrocycle. (d) The macrocycle is on the green
station, intramolecular energy transfer (ET) from the macrocycle is ine cient; intermolecular
energy transfer from PhCOCOPh dominates (closing the gate).(808)

An alternate approach to a molecular information ratchet using chemical fuel to directionally

transport a macrocycle was later published by Leigh and co-workers (Scheme 33).(809) In
this example, a phenyl ester attached to a chiral carbon center separated two degenerate
fumaramide binding sites. The close proximity of the stations to the hydroxyl bearing carbon
enabled the chiral center to in uence the position of the macrocycle. At equilibrium, the
macrocycle rested equally at either degenerate station. When a barrier was introduced by
benzoylation with an achiral dimethylamino pyridine (DMAP) catalyst, an equal distribution of
products was obtained. However, when the chiral DMAP-based catalyst (S)-79 was used, a
33:67 distribution in favor of the pro-(S)-fumaramide (S)-80 station was obtained. Using
catalyst (R)-79 resulted in a reverse bias in the position of the macrocycle. Because the
stations were identical, macrocycle relocation resulted in a decrease in entropy, with identical
enthalpic interactions, and thus a ratcheting operation was achieved. Motion away from an
enthalpically favored location was achieved in a similar rotaxane, but with fumaramide and
succinamide stations of different binding strengths. Using the same chiral catalyst, 15% of
the molecules were relocated to the enthalpically unfavored succinamide station.
Scheme 33
  

Scheme 33. Chemically Driven Molecular Information Ratchet(809)

This concept was further developed in the three-compartment, chemically driven, molecular
information ratchet 82.(810) Here, the compartments contained fumaramide groups and
were separated by hydroxyl groups (Scheme 34). The macrocycle could be e ciently trapped
at either end of the track by sequential benzoylation of the hydroxyl groups in the presence of
the chiral catalyst 83 resulting in a 1:21:79 distribution of the macrocycle. The steric barriers
formed prevented the macrocycle from passing, and trapped the ring in a certain
compartment. It was shown that the macrocycle had an in uence on the rate of
benzoylation of the hydroxyl groups on the thread resulting in acylation taking place
preferentially far from the macrocycle. The distributional bias could be reversed with the
enantiomeric catalyst 83, and when both chiral catalysts were used the macrocycle
preferentially resided in the central station with a 10:77:13 distribution.

Scheme 34
   

Scheme 34. Directional Transport of a Macrocycle in a [2]Rotaxane Three-Compartment

Chemical Information Ratchet

Directional translational motion along the axis of pseudorotaxane has also been reported
(Figure 30).(553, 811, 812) Threading and dethreading of the macrocycle could be controlled
by photochemical, chemical, or electrochemical redox reactions. The pseudorotaxane axis
has three different chemical motifs responsible for directional translocation. The rst is a 2-
isopropylphenyl group, a neutral energy barrier at one side of the axle. An electron-rich 1,5-
dioxynaphthaline occupied the center, and at the other end was a positively charged 3,5-
dimethylpyridinium station. A tetracationic electron-poor cyclobis(paraquat-p-phenylene)
macrocycle formed a π-complex with the electron-rich 1,5-dioxynaphthaline group. To form
the complex, the macrocycle had to pass one of the energy barriers, and the neutral 2-
isopropylphenyl moiety presented a lower energy barrier. Hence, threading took place
selectively from this side of the axis. Upon one-electron reduction of the macrocycle,
interaction with the 1,5-dioxynaphthaline station was weakened. Additionally, as a result of
the reduced positive charge on the macrocycle, electrostatic repulsion from the pyridinium
site became less potent, allowing the macrocycle to pass over this barrier with greatly
reduced activation energy. Hence, once reduced, the macrocycle dethreaded over the
pyridinium group. The macrocycle threaded and dethreaded in a directional manner via a
ratcheting mechanism ( ashing ratchet) acting on the potential energy surface of the
pseudorotaxane axle. The same group later reported a ashing ratchet based on similar
principles, in a pseudorotaxane with one stopper, where threading was driven by reduction,
and dethreading slowly occurred after rapid shuttling away from a reoxidized bipyridinium
station.(813) Recently, Credi et al. also reported the photodriven directional   
threading/dethreading of a crown ether macrocycle on an axle using a ashing ratchet
mechanism.(814, 815)

Figure 30

Figure 30. Photodriven directional translational motion in pseudorotaxanes 86–87. Reprinted

with permission from ref 811. Copyright 2013 American Chemical Society.

4.5 Controlling Rotational Motion in Mechanically Bonded

Structures
An alternative way to extract work from mechanically interlocked structures would be to
control the relative rotation of their components. The rate of macrocycle pirouetting can
easily be controlled through temperature, electric eld strength, light, structural freedom, or
by altering its interaction using other chemical moieties or solvents.(564, 698, 816-819)
Nevertheless, controlling the directionality of this movement requires careful design.

4.5.1 Controlling Rotational Motion in Rotaxanes

The pirouetting frequency of a macrocycle around a thread depends strongly on the strength
of the interactions between the macrocycle and the thread (and environment), which must
be broken and reorganized during the movement of the macrocycle. The rate of macrocyclic
pirouetting in some hydrogen-bonding rotaxanes can be controlled by changing the strength
of an electric eld, which alters the strength of the hydrogen bonds.(820-824) In some cases,
direct manipulation of macrocycle/axle interactions can either restrict rotation or increase its
frequency by weakening intracomplex interactions. The formation of weaker hydrogen bonds
with maleamide units as compared to fumaramide units has been discussed in previous
sections. Fumaramide preorganizes two hydrogen-bonding motifs to bind the macrocycle,
leading to an increase in binding strength. On the other hand, the cis-form of this 
ole nic
 
structure can only form hydrogen bonds with one site of the macrocycle. As a consequence,
the station–macrocycle interactions are weaker, and thus rotation was observed to increase
in frequency by 6 orders of magnitude on photoisomerization.(825)

Figure 31

Figure 31. Effect of water on the rate of pirouetting of a macrocycle about an axle. Reprinted
with permission from ref 698. Copyright 2013 Nature Publishing Group.

Like photoisomerization-dependent disruption of hydrogen bonding,(825) solvent choice can

also play a role in controlling these noncovalent interactions and hence in uence the rate of
pirouetting in a rotaxane system.(826) Comparison of the rate of exchange between axial
(E1) and equatorial (E2) protons, which was determined by the pirouetting rate, showed that,
as compared to heating in dry pyridine, the exchange was greatly accelerated when the
pyridine contained 5% D2O (Figure 31).(698, 827) Addition of water sped up redox-driven
shuttling in a different rotaxane system by hydrogen-bonding dependent “lubrication” of the
mobile elements. Interestingly, other protic solvents (alcohols, nitromethane) had less effect
on the pirouetting rate. This was attributed to the ability of water to form 3-D hydrogen-
bonding networks. The effect on macrocycle–thread interactions of the sequential addition
of single methanol molecules has been probed by IR spectroscopy of rotaxane-solvent
clusters.(828, 829)

Besides hydrogen-bonding, cation-induced restraint of motion in a crown ether-based

macrocycle has been reported with a corresponding increase in pirouetting rate upon
demetalation.(817, 818, 830-834) Redox-dependent switching between coordinating ligands
on a macrocycle has been used to control rotational orientation of a macrocycle about a
rotaxane axle.(818) In a hybrid organic–inorganic rotaxane, hydrogen bonding between
uorines on the macrocycle and ammonium stations resulted in slow shuttling but fast
rotation.(835, 836) This rapid rotation was attributed to the array of hydrogen-bonding
interactions formed in which a new bond had already started to form before the original was
completely broken.
4.5.2 Controlling Rotational Motion in Catenanes
  
The points discussed above for rotaxanes also apply to rotational motion in catenanes. In a
catenane, the rate of rotation of one macrocycle with respect to the other depends on the
strength of interactions between the two. Therefore, any stimuli altering this interaction
should result in a change in rotational rate. The solvent dependence of the rate of
macrocycle rotation in catenanes containing benzylic amides has been measured by NMR
analysis and also by AFM-based single molecule measurement techniques.(837) In the
second method, catenanes with different intercomponent hydrogen-bonding ability were
attached to poly(ethylene oxide) polymers and analyzed in dimethylformamide (DMF) and
tetrachloroethane (C2H2Cl4). As a measure of equilibrium conformational entropy, the
persistence length of the polymer was analyzed for two different compounds in two different
solvents to estimate the restriction of motion of the macrocycle in the catenane. In
agreement with the NMR analysis, in a single molecule experiment using the AFM method,
the mobility of the macrocycle was shown to be accelerated by polar solvents or by
disrupting the hydrogen-bonding ability by chemical modi cation.

Ion exchange,(838-840) pH,(841-844) redox,(845-856) demetalation,(842, 857-869) light or

redox-mediated ligand exchange of metals,(853, 855, 870) photochemical switching,
(870-878) photoisomerization-dependent sequestering of macrocycle(879) and solvent,
(826, 880-882) photoisomerization-dependent change in hydrogen-bonding potency,(883)
and the self-assembly of liquid crystal phases(884) have also been reported to control the
rotation of the macrocycle in catenanes. However, directional rotation of one macrocycle
with respect to another in a catenane structure has rarely been investigated. Directional
rotation was achieved with a [3]catenane in which the presence of a third macrocyclic
component helps to restrict the rotational freedom of the molecule (Figure 32).(883) The
large macrocycle on which the two small macrocycles rotate bears four different interaction
sites: two fumaramide motifs with different binding a nities (light green and red, the
methylated station has a lower a nity for steric reasons), one succinic amide ester (orange),
and nally an amide group (dark green). A benzophenone unit is attached close to the rst
fumaramide station to enable selective photosensitized isomerization of this ole nic group
through energy transfer using a higher wavelength than required for nonsensitized
isomerization.

Figure 32
   

Figure 32. Directional circumrotation in a [3]catenane. (i) hν (350 nm), (ii) hν (254 nm), (iii)
heating; or heating with catalytic ethylenediamine; or catalytic Br2, hν (400–670 nm).
Adapted with permission from ref 883. Copyright 2003 Nature Publishing Group.

Initially, in the absence of any stimuli, one of the macrocycles (blue) rests on the most
favored fumaramide station, while the second macrocycle (purple) resides on the second
most favored, the methyl-fumaramide station (Figure 32). Upon photosensitized
isomerization of station A, hydrogen-bonding interactions between the blue macrocycle and
the station weaken, and because the second most favored site is already occupied by the
purple macrocycle, the blue macrocycle moves to the third most favored, succinimide amide
ester station C. Further photoisomerization of the methyl-fumaramide station triggers the
shuttling of the purple macrocycle to the nal binding site, station D. The fumaramide
stations are converted to the cis-isomers either by heating in the presence of a catalytic
amount of ethylenediamine or via irradiation at 400–670 nm in the presence of a catalytic
amount of Br2. This time, however, the relative orientations of the macrocycles force
repositioning to the newly formed fumaramide stations in the opposite, with respect to the
initial, distribution. A second round of stimuli is necessary to fully reset the system and to
bring the macrocycles back to their initial positions. The combination of control of station
binding a nity and macrocycle position allowed directional rotation in this catenane.

Scheme 35
   

Scheme 35. Directional Circumrotation in [2]Catenane 91(885)

A directional [2]catenane rotary motor has also been reported with a simpler
chemical/photoinduced mode of operation and well-de ned ratcheting mechanism.(885) In
this example, the balance breaking operation (to create a new equilibrium distribution) was
photoisomerization of the fumaramide station. However, the macrocycle’s rotation to the
new energy minima was blocked by two orthogonal protecting groups: an acid labile trityl
and base labile tert-butyl-dimethylsilyl. Selective deprotection of one of these protecting
groups allowed the movement of the macrocycle to the succinamide station in only one
direction. For clockwise rotation, trityl deprotection was required. Under equilibrium
conditions, the alcohol had to be protected once more to avoid the work being undone. Full
rotation was attained by deprotection and reprotection of the tert-butyldimethylsilyl moiety
with reisomerization of the fumaramide station. The sequence of deprotection–reprotection
reactions could be reversed to achieve counter clockwise circumrotation. The repositioning
of the macrocycle to its new equilibrium position was via only one of two degenerate
pathways, and thus the system acts as a directional molecular rotor (Scheme 35).

5 Molecular Level Motion Driven by External Jump To

Fields

In most synthetic molecular machines described to date, control over motion arises from the
selective restriction of Brownian uctuations through control of steric and noncovalent
bonding interactions (via manipulation of chemical structure). The application of external
elds can cause the bulk movement or orientation of a molecular species with electric eld-
directed alignment of liquid crystals being the most important technological application.
Several research groups aim to use electromagnetic elds to control submolecular motion,
with most examples concentrating on generating submolecular rotary motion. Molecular
  
rotation involves passage over the minima and maxima of a torsional potential energy
surface. An external eld can either induce an excited state, where the torsional potential
energy surface is altered, or interact with a permanent or induced molecular dipole and so
orient the molecule in a particular direction. The interaction between the eld and the rotor
provides the energy necessary to surmount kinetic barriers and overcome energy dissipation
and thermal randomization. To date, molecular dynamics simulations of molecular rotatory
systems have dominated the eld.(886-930) Only a few examples exist where theoretical
studies have led to the synthesis of rotors and their examination under the in uence of an
electric eld.

A recent example is the simulation of a single-molecule electric revolving door based on a

phenyl-acetylene macrocycle published by Hsu, Li, and Rabitz.(931, 932) The authors found,
based on simulations, that the opened and closed-door states of 92, whose exchange was
accompanied by signi cant conductance variation, could be operated by an external eld.
Furthermore, they proposed that due to the large on–off conductance ratio, the molecular
machine could also serve as an effective switching device (Figure 33).

Figure 33

Figure 33. Schematic representation of an electric revolving door. (a) Door closed-switch on
leading to high conductance. (b) Door open-switch off leading to low conductance.(932)

An earlier example of a computational investigation was published by Ratner and Troisi.

(933, 934) Compound 93 bound between two electrodes exhibited motion under the
in uence of an electric eld (Scheme 36). The authors suggested that the system could nd
applications in molecular electronics and could be used to create switchable molecular
junctions. Theoretical studies revealed that the conformers of 93 (which could be
interchanged by an external eld) also showed differences in conductance across the
junction and could thus be used as a conformational molecular recti er.(935-937)
Scheme 36
  

Scheme 36. A Molecular Recti era

Scheme a (a) High conductance predicted. (b) Low conductance predicted.(934)

Fujimura and co-workers undertook a series of theoretical studies into the mechanism of
rotation in gas-phase directional chiral motors driven by picosecond pulses of a linearly
polarized laser.(938-950) In one study, aldehyde 94 was examined as a chiral molecular
motor with the formyl group as the rotor (Figure 34). They considered both enantiomers in
their studies and came to the conclusion that directional motion originated from the
asymmetric potential-energy surface of the chiral molecules and time-correlated forces
created by laser-permanent dipole interactions.(940) The process is reminiscent of a rocking
Brownian ratchet (section 1.6.2), but here thermal energy is not required to surmount kinetic
barriers.(951)

Figure 34
   

Figure 34. One enantiomer of chiral molecule 94, in which directional rotational motion was
driven by linearly polarized laser pulses and studied by quantum and classical mechanical
simulations.(940)

Several examples of surface-mounted molecular rotors have been reported where motion
could be driven by alternating electric elds or the absorption of pulses of light.(952-962)
Michl and co-workers synthesized, on the basis of computational studies, a series of
surface-mounted rotors.(963-965)Figure 35 shows the structure of polar and nonpolar
versions of their altitudinal rotor. Polar rotor 96 consisted of a 9,10-dihydrophenanthrene
substituted by four uorine atoms on the central ring and had a calculated dipole moment of
3.7 D. The nonpolar rotor was a 4,5,9,10-tetrahydropyrene whose D2 symmetry precluded a
dipole moment. X-ray photoelectron spectroscopy (XPS), scanning tunneling microscopy
(STM), and IR spectroscopy showed that for a fraction of the molecules, the static electric
eld from an STM tip induced a change in the orientation of the polar rotor, but not in the
nonpolar analogue.(966) Several molecular dynamics simulations studying the in uence of
an electric eld or a uid ow on the rotation of a molecule xed on a surface have been
published by the same group.(967, 968) One recent example simulated carborane-based
molecular propellers and showed that they could be successfully driven at GHz rates by an
oscillating electric eld or by a ow of gas.(969)

Figure 35
   

Figure 35. Nonpolar 95 and dipolar 96 altitudinal rotors mounted on an Au(111) surface.
Note that rotor and anking aryl rings are arbitrarily shown perpendicular to the surface for
clarity.(966)

Molecular machines in the solid state and condensed phase will be discussed in more detail
in section 8.6.1. A number of research groups have been working in the eld of crystalline
molecular machines with the goal of creating new materials with interesting properties and
that are responsive to external stimuli such as external electric elds.(970-975)
Amphidynamic crystals are a form of condensed-phase matter with anisotropic molecular
order and controlled dynamics, and they offer a good platform for the design of these new
materials.(976) Molecular rotors are one of the most promising molecular structures for the
synthesis of amphidynamic crystals. Structural designs analogous to macroscopic
gyroscopes and compasses are one possibility in the design of such molecular rotors.
Several examples have been published consisting of a rotating unit linked to a shielding box
or stator by an axle.(977-980) The shielding box generates the local free volume required for
unhindered rotation in an otherwise densely packed environment. The study of the
orientation of and dipole–dipole interactions in dipolar rotor arrays are important in
understanding the dielectric properties of these materials and the dynamics of the dipolar
rotors. Furthermore, materials containing dipolar rotors can be controlled and reoriented by
external electromagnetic elds or optical stimuli.(981, 982) Examples of molecular
gyroscopes have been reported by Gladysz et al., who developed transition metal-based
systems in which trans phosphorus donor atoms are bridged by three methylene chains or
related linkers. For example, the system shown in Figure 36 contains either a Fe(CO)3 or a
Fe(CO)2(NO)+ rotor. The latter possesses a dipole moment, which could be a possible handle
for external control.(983) A series of studies have been carried out by the same group using
gyroscope-like platinum and palladium complexes with trans-spanning bis(pyridine) ligands.
(984)

Figure 36

Figure 36. (a) Molecular structure of transition-metal-based gyroscopes 97 and 98. (b) X-ray
structure of compound 97. X-ray crystal structure reprinted with permission from ref 983.
Copyright 2004 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.
  
Molecular gyroscopes with two bulky stators such as triarylmethyl or triptycyl groups,
creating space for a 1,4-phenylene, have been reported.(985-1002) Some of these wheel and
axle motifs (see also section 8.6.4) showed a dielectric response as a function of external
alternating electric elds.(981, 1003)

6 Self-Propelled Nanostructures Jump To

The mechanical self-propelled motion of microscopic objects such as bacteria and the
motion of camphor or soap “boats” driven by interfacial forces have long fascinated
scientists. More recently, focus has shifted to the control of nanoscale motion in synthetic
systems.(1004, 1005) These systems are driven not by thermal energy, but by other
mechanisms more relevant on the nanoscale. Motion may be generated either
autonomously when the energy required for movement is continuously supplied or
nonautonomously.

6.1 Propulsion by Manipulation of Surface Tension

If surface tension is not balanced between two sides of a droplet of liquid or a bubble of gas,
directional transport may occur. This is known as the Marangoni effect and is observed in
several natural systems exhibiting spontaneous ow.(1006, 1007) Temperature gradients
have typically been used in arti cial systems to generate Marangoni ows.(1008-1014) A
droplet containing a species that absorbs to the surface, irreversibly modifying the surface
energy thereof, has also been used to illustrate this effect in a “chemical Marangoni effect”.
(1015-1018)

The autonomous motion of millimeter scale objects on a liquid surface driven by the
catalytic decomposition of hydrogen peroxide was reported by Whitesides et al.(1019) A
small area of platinum near the edge of each disc catalyzes this decomposition and releases
oxygen bubbles, which drive the movement by a recoil force. Others, however, observed the
motion of platinum–gold rods toward the oxygen producing platinum end.(1020-1025) The
contributions of driven and Brownian motion could be distinguished at aqueous/organic
interfaces,(1022) and a rotor based on the same principles has also been synthesized.(1026)
A similar system was reported by Manners and co-workers.(1027) Ozin et al. reported
platinum–silica sphere dimers, which showed quasi-linear motion in bulk solution and
rotational motion at the solution–glass interface.(1028) Rotors of decreased size and
increased rotational rate have since been reported,(1029) both once more based on
hydrogen peroxide decomposition.(1030) The catalytic domain has been scaled down to a
molecular level by Feringa et al.,(1031) who utilized a surface bound dinuclear manganese
catalase analogue.

Recently, Fischer et al. reported a self-propelling nanoparticle of only 30 nm diameter, a size

comparable to certain enzymes, based on a Pt–Au system.(1032) Feringa and co-workers
reported the use of carbon nanotube bound enzymes in autonomous propulsion.(1033) As
an alternative to the ubiquitous use of hydrogen peroxide to propel nanoparticles,hydrogen
 
evolution by a magnesium domain has been exploited to drive autonomous motion.(1034)
Finally, Sen et al. reported the use of ring-opening metathesis polymerization using a
modi ed Grubbs’ catalyst to propel a nanoparticle. Motion was generated by the
consumption of monomer only on one side of the nanoparticle, that where the catalyst is
bound. This creates a concentration gradient across the nanoparticle and thus movement.
(1035)

6.2 Mechanical Self-Propulsion

In contrast to most synthetic, surface tension driven, self-propelled systems,
microorganisms almost exclusively utilize mechanical self-propulsion, akin to a swimming
motion or the corkscrew motion of a boat’s motor. The low Reynolds number at the
nanoscale limits the number of swimming mechanisms that are viable,(1036) as any useful
motion must involve a nonreciprocal motion to break the time reversal symmetry.
(26, 1037-1044) Various solutions have been proposed (Figure 37).(1041, 1045-1050) The
key point in each is that they must possess at least two hinge points; no system with a sole
hinge point can be nonreciprocal. The sequential use of each hinge point allows motion at
low Reynolds number.

Figure 37

Figure 37. (a,b) Proposed designs for swimmers viable at the nanoscale. (c,d) Potential
molecular solutions.(14)
No molecular solutions have yet been reported. However, a microscopic arti cial swimmer
has been reported.(1051) A major di culty in realizing any molecular design would be  
carrying out the driven motion rapidly and frequently enough to be observable against
random Brownian motion. The repetitive, directional, rotation of a chiral molecule is also a
nonreciprocal motion. The eld-driven directional motion of an uncon ned chiral molecular
rotor would result in its propulsion via a screw-propeller type mechanism, such as the
bacterial agella system. Such a system has been theoretically studied as a means to
spatially resolve a racemic mixture of propeller-like molecules.(1052, 1053)

7 Molecular-Level Motion Driven by Atomically Jump To

Sharp Tools

The development of single molecule imaging techniques such as atomic force microscopy
(AFM), scanning tunneling microscopy (STM), and optical and magnetic tweezers has
signi cantly enhanced our understanding of the mechanical properties and working
mechanisms of molecular motor proteins.(1054-1068)

Instead of average statistical information obtained from an ensemble of species, these

techniques allow direct measurement of molecular level forces, mechanical properties and
motions such as rotation, gliding, and translation, pivoting of an individual molecule,
supramolecular host–guest exchange, and coconformational changes within interlocked
molecular assemblies.(1061, 1069-1089) Beside their imaging abilities, the use of such tools
to drive molecular level motion has also been explored.

Molecular scale motion is driven by different forces than in the macroscopic world. Gravity is
essentially irrelevant at low Reynolds number, and frictional forces differ greatly.
(606, 1090-1101) The driving forces/interactions must be su cient to overcome signi cant
thermal uctuations. For the desired motion to be obtained (i.e., translational motion via
rotation of the wheels of a “nanocar” instead of gliding), surface–molecule interactions
should be neither too strong nor too weak to balance dissociation and immobility.

STM-driven positional displacement of xenon atoms at low temperature was reported by

Eigler et al.(1102) The rotation of oxygen and acetylene molecules adsorbed on Pt(111) and
Cu(111) surfaces, respectively, was shown to be induced by the tunneling of electrons from
an STM tip at low temperatures.(1103, 1104) STM- or AFM-driven motions of aromatic
molecules on surfaces have been investigated extensively.(1105-1116) The STM-driven
directional diffusion of 9,10-dithioanthracene over a Cu(111) surface has been reported.
(1117) STM-induced translational motion of porphyrins along the voids of a porphyrin
monolayer on a Cu(100) surface was attributed to the rotation of a t-butyl substituent.(1113)
Displacement to a region with less structural restriction led to more frequent rotation, and
thus the STM probe mediated a switch between a rotating and a nonrotating porphyrin.
Cyclic molecules and uorinated C60 derivatives were also shown to roll across surfaces.
(1118-1120)
Translational motion mediated through rolling structural units (wheels) has been reported in
a number of independent publications. Initial attempts to develop a “molecular wheelbarrow”
  
resulted in overly strong surface–-molecule interactions, and the STM tip caused
fragmentation.(1121-1124) STM-driven rolling of a single molecule deposited on a Cu(111)
surface was rst achieved by Grill et al.(1125) A chemically switchable metalloporphyrin
pinwheel was reported by Lambert et al.(1126) The reversible attachment of two CO2
molecules to a diffusing anthraquinone on a Cu(111) surface was an important example of
the potential of arti cial molecular cargo transporters.(1127) Chiaravalloti et al. designed the
rst molecular system acting as a rack and pinion device, using self-assembled hexa-tert-
butyl-pyrimido-pentaphenylbenzene on Cu(111).(1128) Interlocked arrays formed by self-
assembly allowed the rotation and translocation of a single molecule along the array by
manipulation with an STM tip.

Figure 38

Figure 38. (a) Chemical structure and (b–f) STM micrographs of translational motion of a
four-wheeled “nanocar” on an Au(111) surface at 200 °C. Wheels are shown by yellow spots,
and the path is highlighted with a white arrow. Reprinted with permission from ref 1129.
Copyright 2005 American Chemical Society.

In a four-wheeled “nanocar” with fullerene wheels, thermally induced translational motion on

a Au(111) surface was observed (Figure 38).(1129) Directional motion perpendicular to the
axles of the molecule suggested that the observed movement was generated by rolling of
the fullerene wheels rather than sliding of the entire molecule on the surface. In addition to
thermal activation, an STM tip could be used to drive the motion. Pivoting also took place,
clearly visible as small-angle perturbations to the path of translation in the STM images
(Figure 38e,f). In a structurally related three-wheeled molecule, pivoting was observed to be
the dominant motion on the surface, suggesting that the four-wheeled molecular structure
was important for a rolling translational motion. Similar examples of four- and three-wheeled
uorescent molecules with different wheel sizes (adamantane and p-carboranes as wheels)
have been reported, and their diffusion constants on glass surfaces were determined by
 uorescence measurement.(1130, 1131) The photoisomerization kinetics of a similar four-
wheeled molecule functionalized with a rotary motor have also been investigated.(1132)
  
When fullerene wheels were used no photoisomerization took place, whereas with carborane
wheels, e cient isomerization was observed in solution.

The rotation of dialkylthioethers adsorbed on Cu(111) surfaces has been extensively studied
and electrons from an STM tip found to drive a 5% bias in rotational direction.(1133)
Electrical excitation of C–H stretching modes in the molecule contributed to ratcheting in the
rotation. The direction and rate of rotation depended on the chiralities of both the molecule
and the STM tip. In a cerium-centered double-decker molecule self-assembled on a Au(111)
surface, an interesting phenomenon was detected (Figure 39).(1134) The rotational chirality
of individual molecules generated two different orientations on the gold surface, which could
clearly be distinguished by STM. Upon scanning the surface with the STM tip, an irreversible,
abrupt change in the chirality of some of the molecules was observed. The switch resulted
from the rotation of the upper porphyrins, and the irreversibility was attributed to damage
caused to the molecules by the high applied voltage.

Figure 39

Figure 39. (a) Structure of a cerium-centered double-decker molecule. (b) STM micrographs
of the molecules assembled on Au(111) surface. The two distinct isomers, due rotational
chirality, are shown in white and blue crosses. (c) Space- lling model of the two chiral
species. Reprinted with permission from ref 1134. Copyright 2011 American Chemical
Society.

Figure 40
   

Figure 40. (a) Chemical structure of a rotary motor with the groups responsible for double-
bond isomerization (red) and helix inversion (blue) highlighted. (b) Schematic representation
of a full 360° rotation with sequential double-bond isomerization and helix inversion (hexyl
substituents are omitted for clarity). (c) Schematic representation of electron tunneling
exciting the molecule and inducing translational motion on the surface. (d) Cartoon
representation of the motion. Reprinted with permission from ref 1135. Copyright 2011
Nature Publishing Group.

Directional rotary motors undergoing well-de ned structural and/or chemical changes on the
application of an external stimuli were discussed in section 5. Feringa et al. developed a
system utilizing paddle-wheel type directional motion over a Cu(111) surface upon
sequential electronic and vibrational excitation (Figure 40).(1135) Electron tunneling induced
by a STM tip stimulated double bond isomerization, which was followed by helicity inversion.
These sequential con gurational and conformational changes in the molecule propelled it
across the surface. For the molecule to move on the surface linearly, the four rotary wheels
had to rotate in the same direction upon application of the voltage. This is only possible
when the molecule was attached to the surface as the meso-(R,S–R,S) isomer. In other
isomers, a lack of coherent rotation prevented translational motion or induced spinning.

Hao et al. monitored the strength of metal–ligand complexation with an AFM tip.(1136) One
terpyridine ligand was attached to a gold surface while another was tethered to a gold-
coated AFM tip, and the bonding forces between osmium and the ligands were analyzed.
The use of atomic tools to induce relative motion in an interlocked molecular system is of
particular interest in the development of molecular machines, because each component can
be designed to function like the mechanical components of a macroscopic machine.   
(1137, 1138) In a polyrotaxane architecture adsorbed on MoS2, cyclodextrin ring was
translocated by a STM tip along a polyethylene glycol thread.(1139) Such shuttling was
thought to be responsible for the conductance switch observed upon the application of a
voltage via a STM tip in a bistable [2]rotaxane.(1140) The potential use of interlocked
molecular constructs in information storage was highlighted by Leigh et al., who showed
that regular patterns of deformations could be successfully generated on a rotaxane
monolayer with the aid of a STM tip.(1141) These arrays formed due to the relative ease of
intercomponent mobility in these molecular constructs. The effect of electrostatic and steric
forces on the shuttling of a bistable [2]rotaxane tethered to an AFM tip has been investigated
both experimentally and theoretically.(1142) A molecular shuttle made up of fumaramide
and succinamide stations has been attached to a gold surface by thiol linkers (Figure 41).
(1143) The macrocycle was tethered to an AFM probe using poly(ethylene oxide) (PEO).
Strong hydrogen-bonding interactions with the fumaramide station resulted in a 95:5
distribution of macrocycle in favor of this station. As the stretching of the PEO tether
continued, and the force exerted by the PEO linker exceeded the hydrogen-bonding forces
between the macrocycle and the fumaramide station, the ring moved away from the
fumaramide station. Tension in the tether decreased as a result of the shuttling. Further
movement of the cantilever resulted in the detachment of the PEO linker from the probe.

Figure 41

Figure 41. (a) Chemical structure of a rotaxane with fumaramide and succinamide stations
depicted in green and orange, respectively. (b) Schematic representation of macrocycle
movement on a thread attached to a gold surface as a result of the force exerted by an AFM
probe. Application of force by cantilever movement (I,II) was followed by repositioning of the
macrocycle (III) or detachment of the PEO tether (IV) depending on the strength of the force.
Reprinted with permission from ref 1143. Copyright 2011 Nature Publishing Group.  
In addition to molecular level motion generated by atomic tools, modulation of conductivity
by molecular switches attached to nanojunctions is of great interest.(1144-1152) A STM tip
could cause the rotation of selected moieties in the structure of a polyaromatic scaffold, in
the hope of developing switchable nanowires.(1110, 1153-1160) Although most examples
are still far from practical application, signi cant progress has been made in this area.
(1161-1182)

8 Toward Applications of Molecular Machines Jump To

8.1 Current Challenges: Constraining, Communicating,

Correlating
Extracting useful work at the molecular scale requires the restriction of the thermal
movement of submolecular components or the exploitation of thermal motion with
additional ratcheting. Shuttling, switching, and rotation processes in solution can be
modulated externally, and the directionality of each motion can be controlled in single
molecules. Considering an ensemble of such molecules in solution, however, the biased
motions average to give no net directionality. For various applications, the integrity of the
molecular system must be conveyed to the macroscopic world. Although there are possible
applications of molecular machines/devices in solution, such as their use in molecular logic
gate construction or molecular sensing, they are not compatible with typical solid-state
technology. For this reason, molecular machines on solid supports are needed. This
challenge is being addressed with molecular devices and machines being built on surfaces,
interfaces, and polymer matrixes with a variety of electronic, mechanical, or biological
applications.(1183-1209) Controlled drug release through nanovalves,(1210-1226) molecular
electronics,(1227-1234) arti cial molecular muscles,(18, 1224, 1235-1242) information
storage,(1141, 1243, 1244) and modulation of surface properties(1245) are topics of active
research in this area.

Figure 42
   

Figure 42. Communication between molecular devices. Acid generated upon conversion of
merocyanine (MEH+) to spiropyran (SP) protonates a pyridine, and leads to subsequent
complexation of the pyridinium ion (103+) by a calix[6]arene (104).(1246)

Communication between molecular machines is another pertinent challenge in this area. In

biological systems, the work done by one machine can be harvested by another and the
second can then operate. Raymo and Credi have developed a system that addresses this
challenge.(1246, 1247) They used a merocyanine-type photoacid to release protons as the
molecule transforms from its open form to the closed form. The acid protonated a
terpyridine osmium complex and decreased the e ciency of singlet oxygen generation.
(1247) These photogenerated protons were also used to reversibly complex and decomplex
a 1-alkyl-4,4′-bipyridin-1-ium (103+) in a calix[6]arene wheel (104) (Figure 42).(1246) Thus, the
control of one moiety caused a change in another via the transfer of a proton. Recently,
Aprahamian and co-workers successfully coupled a hydrazone switch (section 2.2) with a
merocyanine unit and used the photogeneration of acid to drive the switch reversibly with
high e ciency.(1248)

8.2 Reporting Controlled Motion in Solution

Submolecular movement can be designed to give a detectable output. The output can be
used as a measure of stimulant concentration (sensing) or it can be used for information
storage. In theory, any detectable nondestructive output that provides a reliable distinction
between states of the system is acceptable (NMR, CD response, etc.). However, for most
useful applications, more practical and easily readable optical, electronic, or mechanical
  
outputs are preferred. The response rate can be crucial in certain applications such as
memory devices and molecular sensors. In these systems, fast-responding reporters are
preferred. For a molecular system to be used repeatedly, stability and fatigue resistance are
important.

8.2.1 Conformational Switches in Solution

The restriction of molecular motion or switching between bistable conformations can be

achieved by external stimuli such as ion or organic molecule binding, pH change, or by
photoisomerization of the molecule. Conformational perturbations in polymers or carbon
chains with interesting properties have been reported.(1249-1261) Fluorescence readouts
have been widely used to detect such submolecular motions in part due to their high signal-
to-noise ratios.(16, 1262-1266) One way to obtain a uorescence response is by changing
the electron transfer e ciency between a uorescent component and other moieties in the
system by inducing an electronic change in the acceptor or donor units. Ligand binding or
protonation can effectively change the HOMO and/or LUMO levels of molecules, which in
turn affects electron transfer to or from the uorescent moiety. The change in relative energy
levels upon reduction or oxidization determines the ease of detection of the uorescence
response. A greater response can be obtained by decreasing rotational degrees of freedom
or by energy transfer. Because energy transfer processes are highly distance dependent,
variations in distance between the donor and acceptor units in different conformational
isomers can determine the e ciency of energy transfer. Emission from dimers of certain
chromophores is also widely used as a reporter of molecular processes. This emission
requires the close proximity of similar (excimer) or different (exciplex) chromophores.

Esquema 37
   

Esquema 37. Expansión y contracción controladas alostéricamente por coordinación de

ligandos a

Esquema a El centro de Zn (II) actúa como una unidad catalítica y se utiliza

dietilaminometilantraceno como indicador.(1267)

Mirkin y col. desarrollaron un catalizador supramolecular regulado alostéricamente basado

en la contracción o expansión dependiente del ligando para revelar u ocultar una unidad
catalítica ( Esquema 37 ). Pudieron medir el cambio conformacional indirectamente
utilizando el subproducto de la reacción, ácido acético.(1267)La especie tetrametálica
estaba formada por dos centros de Zn (II) alineados cofacialmente catalíticamente unidos
mediante dos centros Rh (I). La velocidad de catálisis de la reacción de transferencia de acilo
por los iones Zn (II) del núcleo se incrementó cuando la cavidad entre las dos unidades era
mayor. El intercambio de ligandos Rh (I) de tioéteres lábiles a cloruro y monóxido de carbono
condujo a una expansión y, por tanto, a una mejora de la actividad catalítica. A medida que el
subproducto de ácido acético protonaba la amina de dietilaminometilantraceno, se observó
un aumento de la uorescencia provocado por el bloqueo de la transferencia de electrones
fotoinducida del resto amina.

Lee y col. desarrollaron un interruptor conformacional basado en una red cíclica de enlaces
de hidrógeno en un derivado de tris ( N- salicilidenoanilina) ( Figura 43 ).(1268-1271)La
distorsión estructural inducida por los procesos de plegado y desplegado resultó en un
cambio signi cativo en las propiedades electrónicas del sistema. Los cromóforos BODIPY
estaban unidos a la molécula como aceptores de energía uorescente. En la forma plegada,
la molécula adoptó una matriz de enlaces de hidrógeno muy ordenada, y la transferencia
  de
energía tuvo lugar desde el núcleo de tris ( N -salicilidenanilina) a los BODIPY. Cuando se
añadió un aceptor de enlaces de hidrógeno como el uoruro, la molécula se desplegó y se
detectó una disminución sustancial en la uorescencia de los tintes BODIPY. Debido a que
cada elemento móvil cooperó en el proceso de plegado mediante enlaces de hidrógeno, el
cambio conformacional fue muy cooperativo. La intensidad de uorescencia inicial se pudo
recuperar cuando los aniones uoruro fueron capturados por cloruro de trimetilsililo.

Figura 43

Figure 43. (a) Chemical structure of the t-butylphenyl and BODIPY-substituted foldamers, and
(b) X-ray structure of the t-butylphenyl functionalized foldamer. Carbon atoms of the t-butyl
groups and all hydrogen atoms except OH and NH have been omitted for clarity. (c)
Schematic representation of conformational switching. D and A represent energy donor and
acceptor modules, respectively.(1268-1270) Parts (a) and (c) are adapted with permission
from ref 1268. Copyright 2007 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim. Part (b) is
reprinted with permission from ref 1269. Copyright 2006 American Chemical Society.

A number of different uorescent sensors reporting conformational changes have been

synthesized on the basis of energy transfer,(1272-1274) excimer formation,(1275-1282) or
charge transfer mechanisms.(1283-1286) Optical responses have been obtained by simple
stimuli-dependent conformational change,(796, 1262, 1273, 1275, 1287-1289) folding
processes,(1276-1278, 1290) shuttling,(799, 1272, 1283-1285, 1291-1294) switching,(1273)
and transitions between coiled and helical structures.(1295) Optical outputs have been used
to develop molecular logic gates.(1291, 1292, 1296) Recently, Tian et al. used both
phosphorescence and an induced circular dichroism output to develop an INHIBIT molecular
 
logic gate by taking advantage of the photoisomerization-dependent inclusion of an
azobenzene and a bromonaphthalene in the β-CD cavity.(1297)

Figure 44

Figure 44. (a) Ligand-induced variation of the chemical shifts (11B (160 MHz) and 1H NMR
(500 MHz)) of the helix in CD3OD at 298 K. (b) Schematic representation of fast exchange
between two degenerate helical conformers with a single NMR signal and (c) induced bias of
helicity upon ligand binding (yellow), and the anisochronous NMR signal generated. Adapted
with permission from ref 1298. Copyright 2013 Nature Publishing Group.

Techniques other than optical responses have been used to measure conformational
change. Flood et al. used a change in conductance to directly measure a folding process
because unfolding released a bound chloride anion and changed the conductance (Figure 22
in section 3.1).(595) A change in CD response can be a useful indicator of molecular motion
and helicity inversion.(1298-1308) Many shape changes can be easily analyzed by NMR
spectroscopy. Recently, Clayden et al. showed, by 11B, 1H, and 13C NMR, that the equal
distribution of left-handed (M) and right-handed (P) conformers of a helical foldamer could
be perturbed by the addition of a chiral ligand (Figure 44).(1298) Upon ligand complexation
to the boronic ester, chiral information was transferred along the helix, and the isochronous
NMR signals of the diastereotopic nuclei were transformed into anisochronous signals,
indicating a bias in the distribution of helical conformers. When the meso diastereoisomer of
the diol was used to complex the boronic ester, no splitting of the 1H NMR signals was
observed due to the symmetry of the ligand.   
8.2.2 Rotaxane Switches in Solution

Fluorescence spectroscopy has been widely used to detect shuttling processes in

interlocked systems, particularly in rotaxanes. The strong distance dependence of
uorescence quenching by electron transfer has frequently been exploited to measure the
relative position of molecular subcomponents. Photoisomerization-dependent shuttling of a
pyridinium bearing macrocycle along a two station thread was monitored by changes in the
uorescence of an anthracene group tethered near one station.(1285) When the distribution
of macrocycle was biased to this station, charge transfer from the anthracene to the
pyridinium moiety quenched the uorescence, thus providing a detectable uorescence
response due to macrocyclic position. The location of a macrocycle along an alkyl chain in a
rotaxane structure has also been probed using similar techniques.(1272)

Greater rotational and vibrational freedom leads to a greater probability of nonradiative

processes and hence a lower uorescence quantum yield. Any interaction affecting rotation
or vibration can in uence emission intensity. Tian et al. used this effect with a 4-
aminonaphthalimide uorophore in a stilbene bearing rotaxane where the steric hindrance
generated by photoisomerization of the stilbene unit resulted in the relocation of the α-
cyclodextrin macrocycle along the thread.(796) As a result of this movement, uorescence
increased by 46%, which was attributed to the restriction of molecular motion of the nearby
linker moieties. The same group utilized an azobenzene as an additional photoisomerizable
moiety to develop a molecular half adder logic gate (Scheme 38).(1291) This logic gate
performs binary addition using two inputs and two outputs to provide both XOR and AND
gates. When either the azobenzene or the stilbene moiety was isomerized, uorescence
emission of the naphthalimide close to photoisomerized species increased ((Z,E)-112 or
(E,Z)-112). However, if none or both of them were isomerized ((E,E)-112 or (Z,Z)-112),
uorescence intensity decreased due to rapid shuttling of the ring between the stations in
the nonisomerized form or because the ring was trapped in the center of the thread when
both functional moieties were isomerized. These uorescence outputs collectively result in a
XOR gate (output 1 in the truth table). The photoisomerization-dependent decrease in
absorbance at 350 nm and increase at 270 nm were used as an additional output for the
construction of the AND gate of the half adder. The change in absorbance at the isosbestic
point (301 nm) was followed and only breached a predetermined threshold when both units
were isomerized. As such, an interlocked molecular system was successfully used as an all-
photonic logic gate in solution where the inputs induce submolecular motion and outputs are
reporters of their motion. Acid–base and redox switchable bistable rotaxanes with crown
ether macrocycles have been used to create an INHIBIT logic gate.(1292) Room-temperature
phosphorescence and CD responses have been used in a pseudo[1]rotaxane to create a
primitive logic gate.(1297)

Scheme 38
   

Scheme 38. Photoisomerization-Dependent Shuttling of an α-Cyclodextrin on an Azobenzene

and Stilbene Bearing Thread with Two Naphthalimide Derivatives as Fluorescent Stoppersa

Scheme a The percentage of the major isomer in the photostationary state is shown over
the reaction arrows. The truth table for a half-adder logic gate is shown, with the inputs being
380 nm (I1) and 313 nm (I2) irradiation, and outputs being the change in absorbance (O2)
and uorescence (O1) values.(1291)

Indicator displacement assays involving supramolecular complexes and interlocked

molecules are widely used for molecular sensing applications.(1309) In these systems, a
uorescent molecule with complexation-dependent uorescence properties is usually used
as a guest. The optical change generated upon exchange of the uorescent guest with the
analyte is used as the reporting function. Smith et al. used a similar idea to develop a
chloride anion sensor based on a rotaxane (Figure 45).(1310, 1311) A [2]rotaxane (113) was
synthesized using a tetralactam macrocycle and a squaraine dye as building blocks.
Tetralactam macrocycles are known to bind to and quench the emission of red light from
squaraines.(1312) The exposure of this dye, upon chloride-induced displacement of the
macrocycle, restored uorescence. The process could be reversed by chloride precipitation
as the NaCl salt. When the same rotaxane was adsorbed on a C-18 coated reverse-phase
silica gel plate and dipped into different concentrations of aqueous solutions of chloride, the
change in uorescence was large enough to be visually observable. Later, a ratiometric
chloride sensor based on the same squaraine rotaxane was reported.(786) Interlocked
systems are useful in such dye-displacement assays, as the displaced dye typically diffuses
away preventing reversibility, whereas the stable rotaxane structure allows reversibility and
reusability. In a similar example, the sodium ion-dependent shuttling of a [2.2.2]cryptand
away from a squaraine station enhanced squaraine emission.(1312) Interlocked
architectures have been mounted on metal nanoparticles and shown to keep their switching
ability.(1313)   

Figure 45

Figure 45. (a) Chloride-dependent shuttling of tetralactam macrocycle, and (b) subsequent
uorescence enhancement in CHCl3 upon titration with tetrabutylammonium chloride. (c)
Rotaxane solution in the absence (left) or presence (right) of chloride. Adapted with
permission from ref 1310. Copyright 2010 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Liu et al. have developed a [2]pseudorotaxane with a dual stimulus luminescent lanthanide
switch using a diarylper uorocyclopentene as the photochromic component (Figure 46).
(1314) The diarylper uorocyclopentene (114) bears a benzyl ammonium recognition unit
and reacts reversibly to generate its closed form upon absorption of UV irradiation (365 nm).
The open form can be obtained via irradiation at 614 nm. The Eu3+ complex of
terpyridinyldibenzo-24-crown-8 (115) was used to reversibly complex the ammonium moiety
of 114. This Eu3+ center uoresces at 619 nm through intramolecular energy transfer from
an excited terpyridine ligand. Upon complexation of the two compounds through crown
ether–ammonium interactions, a small amount of quenching of the lanthanide uorescence
at 619 nm was observed (ca. 10%) due to the poor spectral overlap between the donor
emission and acceptor absorbance (which is required for resonant energy transfer (RET)).
Upon UV irradiation to form the closed form of compound 114, spectral overlap increased
and uorescence was quenched by 80%, with an accompanying 3-fold decrease in excited-
state lifetime. The pseudorotaxane could be reversibly disassembled by the addition of
potassium cations and regenerated by the addition of 18-crown-6.

Figure 46
   

Figure 46. (a) Chemical structures of 115, and the open and closed forms of 114. (b)
Schematic representation of light modulated switch and K+/18-crown-6-mediated
complexation. (c) Fluorescence quenching of the Eu3+ complex upon UV irradiation in 1:1
CH3CN/CHCl3. Fluorescence before (I) and after (II) excitation at 390 nm (c inset). Reprinted
with permission from ref 1314. Copyright 2013 American Chemical Society.

The responsive nature of induced circular dichroism makes it an interesting phenomenon to

study with the CD response of one species changing upon its interaction with another.
(387, 1315-1319) The transformation of an achiral carbon center to a chiral one upon
hydrogen-bonding-dependent symmetry breaking provided an early example of the in uence
of supramolecular interactions on chirality.(1320) A number of chiral supramolecular
assemblies,(1315, 1316, 1321) chiral spaces (dissymmetric cavities),(1322) and helices
(1323-1325) have been reported. The solvent-dependent rearrangement of a macrocycle
along a thread has been shown to alter the CD response of a rotaxane (section 4.3.1).(715)
The position of a macrocycle has been used to control the reactivity of a secondary alcohol
toward esteri cation in the presence of a chiral catalyst in a chemical information ratchet
(section 4.4.1).(809, 810) Similarly, a chiraloptic switch has been reported based on a
benzylic amide macrocycle and fumaramide/peptide stations (Figure 47).(1285, 1326)
Photoisomerization-dependent relocation of the macrocycle to the peptide station altered
the CD response due to proximity-dependent macrocycle–leucine residue interactions. A
large reversible difference in elliptical polarization response (>1500 deg cm2 dmol–1) was
obtained upon isomerization of the fumaramide station from E to Z.

Figure 47
   

Figure 47. (a) Chiraloptical switching upon photoinduced shuttling of the macrocycle
between fumaramide (green) and peptide (orange) stations; the chiral center of the peptide
station is highlighted by a black circle. (b) Percentage of E isomer calculated using 1H NMR
(left y axis) and induced CD absorption at 246 nm after alternating irradiation between 254
nm (half integer) and 312 nm (integers) (right y axis). Reprinted with permission from ref
1326. Copyright 2003 American Chemical Society.

Li et al. synthesized rotaxane 117 bearing a tetracyanobutadiene (TCBD) stopper, which

tends to form aggregates via intermolecular dipole–dipole interactions, to attempt to control
this clustering behavior (Figure 48).(1327) The position of macrocycle relative to the TCBD
group determined the strength of intermolecular interactions and hence the structure of the
assemblies formed. In a hexane:chloroform mixture (1/1, v/v), the macrocycle rested on the
peptidic station, and the TCBD units were free to interact to generate nano bers (Figure 48b).
In methanol:chloroform (1/1, v/v), the amphiphilic nature of the molecules generated
perforated nanocapsules (Figure 48c). Finally, when DMSO was used as the solvent, the
macrocycle relocated closer to the TCBD group, interfering with aggregation and generating
a worm-like nanostructure (Figure 48d). A similar phenomenon was reported in which a
fumaramide bearing rotaxane displayed different nanostructures when the macrocycle
bound Zn2+ metal in the presence or absence of irradiation.(1328) Anion and acid/base-
dependent control over the formation of an organogel has been achieved using a [2]rotaxane
architecture.(1329) In this system, stimuli-induced shuttling of the macrocycle between urea
and ammonium stations led to sol–gel phase transitions. Polyrotaxane structures have been
formed in a concentration-dependent manner in solution using the interaction of an electron-
de cient macrocycle with a monoanionic species.(1330) Recently, light and acid/base-
dependent threading and dethreading of pseudorotaxane structures embedded in nano bers
was reported to induce a macroscopic change (more than 1.5-fold enhancement of Young’s
modulus upon dethreading).(1331)

Figure 48
   

Figure 48. (a) Solvent-induced shuttling on a tetracyanobutadiene bearing rotaxane 117. (b)
Proposed assembly of rotaxane and SEM images in CHCl3/n-C6H14 (1/1, v/v), (c) in
CHCl3/MeOH (1/1, v/v), and (d) in DMSO. Reprinted with permission from ref 1327. Copyright
2009 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

The concept of a “molecular muscle”, created from doubly threaded rotaxanes or interlocked
daisy chain molecular structures, was developed by Sauvage et al.(1332) In these systems,
submolecular movement drives a relative motion that either contracts or expands the entire
molecule upon metal exchange,(1332) solvent exchange,(1333, 1334) redox reaction,
(1236, 1238, 1335) or acid/base exchange.(18, 1336-1339) Photoinduced
contraction/expansion has also been reported.(1340) The concept has been used to cause
the macroscopic bending of a microcantilever by means of redox-driven shuttling of the
surface-adsorbed macrocycle along a thread (section 8.6.4).(1238, 1341)

The design of enzyme-responsive molecular machines is an emerging area and could nd

applications in biotechnology. Biodegradable polyrotaxanes have been studied as selective
drug and gene delivery systems.(1342-1349) Leigh and co-workers published two
generations of [2]rotaxane-based propeptides (118, 119) where the peptide axle is protected
from degradation from general peptidases by the macrocycle.(1350, 1351) The introduced
glycosidase-cleavable stopper allows the release of the free peptide in a controlled fashion
through treatment with a speci c glycosidase. The sequence of reactions triggered by the β-
galactosidase leading to the decomposition of the stopper is shown in Scheme 39. This
approach offers a promising alternative delivery system for peptide-based therapies,
because many bioactive peptides suffer from in vivo instability and poor bioavailability.
Similar principles have been used to deliver a deactivated cancer drug (acting as a
stoppering moiety in a rotaxane) via the blood before the macrocycle immolates inside a cell.
This releases the thread, and enzyme-mediated hydrolysis furnishes the active drug
molecule. The rate of hydrolysis in cancerous cells versus benign cells was somewhat
enhanced due to their overexpression of the hydrolyzing enzyme.(1352)

Scheme 39
   

Scheme 39. β-Galactosidase-Triggered Release of Triglycyl Peptide 120 from the

[2]Rotaxane Propeptide 118 and 119(1351)

8.3 Synthetic Molecular Walkers

8.3.1 Introduction

Biological motor proteins have evolved a plethora of functionalities. DNA, RNA, and protein
synthesis machineries (DNA polymerases, RNA polymerases, the ribosome) work
cooperatively with helper proteins to “unzip” molecules (helicases,(1353) poly(ADP-ribose)
polymerases),(1354) release strain in a substrate (gyrase,(1355, 1356) topoisomerase),
(1357, 1358) slide over the substrate, and processively synthesize a product (DNA
polymerases, RNA polymerases, the ribosome).(68-70) The ATPase rotary motor is the
energy factory of the cell producing ATP via complex mechanical processes.(1359) Pumps
(1360) and pores(1361) are essential to maintain communication and transportation across
the membranes of different compartments (functioning at organelle, cell–environment, or
cell–cell boundaries). Among these machines, molecular walkers are attracting increasing
attention as their mechanism of action has been revealed. Dynein, myosin, and kinesin are
walker proteins of the ATPase family and differ in their structure, function, and use of energy.
(1362-1365) Proteins such as collagenase and exonucleases, which are not traditionally
viewed as walker proteins, migrate along their substrate tracks by destroying the track via a
“burnt-bridges” mechanism.(1366-1368)
Biological walkers have some important characteristics.(1369) First, they must be supplied
with energy to do work against random Brownian uctuations. ATP hydrolysis normally   
provides this energy. Second, attachment to a track results in a restriction of their degrees of
freedom facilitating directional 1-D or 2-D walking in solution. Inertia and momentum under
conditions of low Reynold’s number are irrelevant, and work is performed under the in uence
of viscous and thermal motions. Third, to drive the walker away from equilibrium, that is, to
generate directional motion, a ratcheting process (either an energy or an information ratchet)
must take place. In addition to the requirements of a Brownian motor, certain additional
characteristics are necessary for a motor to be de ned as a walker.

(i) Processivity is a measure of the integrity of walker–track interactions during its

operation. A walker should remain attached over multiple operations to extract
useful work.

(ii) Directionality is the exclusive or preferential movement of the walker in one

direction along the track.

(iii) Repetitive operation means the motor should be able to carry out similar
mechanical cycles repetitively.

(iv) Progressive operation is the ability of the motor to culmulatively perform work
with each operating cycle.

(v) Autonomous operation allows the motor to function continuously without

external intervention, as long as an energy source (fuel) is available.

Conventional kinesin (kinesin I) meets all of these criteria and was rst isolated by Vale et al.
in 1985.(1370) It is a homodimeric protein with two identical heads that interact with a
microtubule track. Through cyclical binding, hydrolysis, and then release of ATP, it can walk
along the track by an asymmetric hand-over-hand mechanism.(1371-1373) Because at any
time one of the heads remains attached to the track during the walking process, processivity
is high. On average, this walker takes 100 steps before detaching from the track.(1374-1377)
Although walkers with two attachment points or more are common, this is not a requirement
for processivity. The KIF1A kinesin protein processively walks along microtubules using a
single leg.(1378) In contrast, some 2-legged biological walkers such as myosin-II are
nonprocessive.(1365) Even without being processive, myosin-II can still move directionally,
and in a large ensemble it can generate macroscopic motions such as muscle contraction.

DNA has the notable ability to form predictable hydrogen bonds with a complementary
strand and can be synthesized using machine-assisted technologies. Strand displacement
provides a versatile design for walking processes, and the ability to make complex 3-D
structures can be exploited to perform complex physical tasks. The rst arti cial walkers
were made of DNA. Directional walkers,(1379) autonomous walkers,(1380) walkers using the
burnt-bridges mechanism,(1380) cargo-carrying walkers,(1381) and a light-driven walker
 
(1382, 1383) based on DNA have been reported, and will be examined in section 9.4. Aside
from DNA-based walkers, the preferential diffusion of molecules along the higher symmetry
axis of a metal surface has also been observed.(1117, 1127) Huskens et al. reported the
gradient-driven diffusion of molecules bearing two adamantane legs across α-cyclodextrin-
functionalized surfaces.(1384) Processive crown ether migration on an oligoglycine chain
(1385) and migration of metal atoms on aromatic scaffolds(615, 1386, 1387) have also been
explored. Rearrangement reactions enable the migration of a fragment along a molecule
(such as the Claisen(1388, 1389) and Cope(1390-1393) rearrangements). However,
progressive and repetitive operation using sigmatropic rearrangement reactions is generally
challenging.

For the design of processive small molecule synthetic molecular walkers, mechanically
interlocked architectures are good candidates, because the walker (macrocycle) is
mechanically bonded to the track (thread). However, their interlocked-structure prevents
resetting because each resetting process undoes the walking process, by relocating the
walker to its original position.(1369) Moreover, the macrocycle cannot choose a new path
without bond breaking, which would result in detachment from the thread. A two-leg system
operating under orthogonal conditions could provide a viable synthetic molecular walker.
Orthogonal dynamic covalent exchange reactions can provide a suitable balance of
reversibility and kinetic stability. A rigid track can decrease the possibility of overstepping.

8.3.2 Spontaneous Walking of Small Synthetic Molecular Walkers

Reversible and processive migration of a Michael acceptor along a protein was reported in
1979 by Lawton et al.(1394) More recently, Lehn et al. used dynamic imine exchange to
transport a salicylidene walker 125 along an amine bearing track (Figure 49).(1395)
Deprotection of the amine at one side of the track using methoxyamine initiated the dynamic
exchange reactions. The speed of exchange was shown to be modulated when substitution,
composition of the solvent, or temperature was altered. 1H NMR analysis in CDCl3 proved
that the relative intensity of a characteristic signal corresponding to the transported walker
(H6) increased gradually and in 2 days the transported walker was the dominant product in
solution. Recently, the same group reported a modi ed version of their walker with
thermodynamic sinks at each end of the track. These trap the stochastic walker at one end
in acid as an imine, or as a lactone at the other end under basic conditions.(1396)

Figure 49
   

Figure 49. (a) The structure and operation of walker 125, which uses dynamic imine
exchange chemistry. Amine footholds are highlighted in blue and red. Each molecule is
labeled with one or two numbers in parentheses indicating the amine footholds to which the
walker is attached (foothold amines are assigned with numbers starting from the left). (b) 1H
NMR spectra of indicated protons in CDCl3. H7 corresponds to a side product in which the
walker is detached from the track. Reprinted with permission from ref 1395. Copyright 2012
American Chemical Society.

Figure 50

Figure 50. (a) The chemical structure of the model walker 127, and (b) gradual change in 1H
NMR of the model walker in d6-DMSO upon formation of new positional isomer on the track.
Ratio of (1):(2) isomers reaches 1:0.9 after 15 h of operation. (c) Chemical structure of the
walker on a larger track bearing an anthracene moiety, 128. (d) Fluorescence quenching of
anthracene after 6.5 h of walking. Reprinted with permission from ref 1397. Copyright
  2012
Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Figure 51

Figure 51. (a) Chemical structure of walker 129, with each positional isomer labeled in a
different color, and amines numbered. (b) Change in the partial 1H NMR spectra over 48 h of
operation. (c) Occupancy of each foothold over time. Reprinted with permission from ref
1398. Copyright 2013 American Chemical Society.

Leigh et al. reported a spontaneous walking process using a Michael addition reaction
between an α-methylene-4-nitrostyrene walker and a polyamine track (Figure 50).(1397) It
was shown that the walker translocated preferentially through successive 1,4-N,N-migration
rather than by overstepping. After 48 h, no out of sequence N,N-migration was observed with
a model walker (Figure 50a,b). 1H NMR analysis showed that the walking was highly solvent
dependent and accelerated in polar solvents such as dimethylformamide and dimethyl
sulfoxide. In d6-DMSO, the walker reached an equilibrium distribution in 15 h. A ratio of 1:0.9
between the occupancy of initial position and the central amine of the track was achieved
over this time period. Intermolecular exchange of less than 6% took place when the model
walker was mixed with a longer free track for 3 days. This indicates a high processivity (on
average 530 steps taken before detachment). Using a longer track modi ed with an
anthracene at the far end, it was possible to monitor walking via an observed decrease in
uorescence as the walker approached the anthracene. As the nitrostyrene walker
approached the edge of the track, it quenched the uorophore (Figure 50d). Leigh et al. have
since reported an extended system with a naphthalene moiety at one end of the track (Figure
51 a).(1398) In the presence of excess base (iPr2NEt), the walker was “trapped” by the
naphthylmethylamine, which was the thermodynamic sink. 1H NMR analysis showed  that 
the steady-state distribution of the walker was biased and 46% of walker molecules had
reached the nal benzylic foothold in 48 h (Figure 51b,c). When a longer track (with 9
footholds) was used, the percentage at the nal station dropped to 19%.

Scheme 40

Scheme 40. Structure and Operation of a Small Molecule Walker, Walking along a Molecular
Tracka

Scheme a Footholds are shown in blue and green; the walker unit is depicted in red.
Numbering shows the footholds to which the walker is attached.(1399)

A walker with two chemically different legs that labilize under orthogonal conditions has
been reported by Leigh et al. (130, Scheme 40).(1399) The walker unit was attached to the
thread by hydrazone and disul de linkages. Hydrazone exchange took place under acidic
conditions, while under these conditions the disul de bond was stable. Disul de exchange
required basic conditions, which did not affect the hydrazone bond. Successive acid–base
cycles led to a 39:36:19 (1,2:2,3:3,4) distribution of walker, with only 6% forming the
overstepped (1,4) isomer. Changing the length of the walker alkyl chain from 6 carbons to 5
and using oxidation instead of base exchange at the nal step, the distribution could be
biased in favor of the (3,4) isomer, which was attributed to strain in the (2,3) isomer.(1400)

Recently, Bayley et al. monitored an organoarsenic molecule walking along a cysteine

bearing track in a protein pore, by measuring changes in ionic current. The walker “stepped”
by thiol exchange reactions and displayed a limited degree of processivity and directionality
(the latter due to the thermodynamic sink at the track terminus).(1401) An inchworm walker
able to walk on a copper surface has been reported. It could be constrained to one
dimension of motion by the use of oligomeric “fences”.(1402)

8.3.3 Directional Synthetic Small Molecule Walkers

The biased migration of molecules along a track requires either a preference for one isomer
over others under the operating conditions or that strain should be released upon stepping.
An e cient ratcheting step is needed. Recently, the use of metal complexes in a molecular
biped was explored by Leigh et al. (Figure 52).(1403) The track contained three different
pyridine derivatives: 2,6-dialkyl-4-N,N-dimethylaminopyridine (foothold 1, green), 3,5-
  
dialkylpyridine (foothold 2, red), and 2,6-dialkylpyridine (foothold 3, blue). The walker
consisted of pincer ligands able to complex the pyridine foothold via Pd(II) or Pt(II) centers.
Initially, the walker was attached to the track by complexation of Pd(II) with foothold 1, and
Pt(II) with foothold 2. Upon protonation of the free 2,6-dialkylpyridine foothold (foothold 3)
and heating, exchange of the Pd(II) complex between foothold 1 and foothold 3 took place. A
distribution of 15:85 in favor of foothold 3 was observed. The proton on foothold 3 was
captured by the more strongly basic foothold 1 in this process. Migration could be reversed
when the rst foothold was deprotonated and the solution was heated. A ratio of 95:5 in
favor of the initial position was obtained. Even though this example is not truly a walker, the
signi cant directional bias in the stepping process of the metal-based biped could be used to
inform more advanced designs.

Figure 52

Figure 52. Toward directional molecular walkers. (a) Chemical structure and schematic
representation of the walker attached to the track, and (b) operation of walking through
successive acid–base addition and heating cycles. Reprinted with permission from ref 1403.
Copyright 2014 American Chemical Society.

Finally, a small molecule walker displaying all of the desired properties of an arti cial walker,
save autonomy, has been reported by Leigh et al. (Scheme 41).(1404) The walker was based
on the previously published 130 (Scheme 40), but a stilbene moiety now linked footholds 2
and 3 (Scheme 41). The walker operated by the same hydrazone and disul de exchange
reactions, but with photoisomerization of the stilbene moiety driving directionality.
Isomerization led to greater proximity between footholds 2 and 3 (over 1 and 2) in the cis
form of the stilbene, resulted in a steady-state distribution of 40:60 in favor of the (2,3)
positional isomer. During the second hydrazone exchange step, reisomerization to trans
stilbene moved footholds 2 and 3 apart, which led to almost exclusive (5:95) formation of the
(3,4) isomer.

Scheme 41
   

Scheme 41. Light-Driven Transport of a Molecular Walker along a Molecular Tracka

Scheme a Footholds are shown in blue and green; the walker unit is depicted in red. Each
molecule is labeled with two numbers in parentheses indicating the two footholds to which
the walker is attached. (a) (i) hν (365 nm), CD2Cl2, (ii) DBU, DTT, CHCl3; (b) (i) I2, hν (500 nm),
CD2Cl2, (ii) TFA, CHCl3.(1404)

8.3.4 Challenges Yet To Be Overcome

Signi cant progress has been achieved in the synthesis of synthetic molecular walkers with
highly processive, progressive, and in some cases directional walkers being reported. The
exploration of additional, reversible, walker–track interactions may lead to greater control
over the directionality of motion. Autonomous walking remains a challenge to be addressed.
Polymeric tracks could be designed for cargo transport over large distances. The ability to
immobilize walkers on surfaces could lead to future technological applications.

8.4 Switchable Catalysts

In the living cell, many processes and reactions occur in parallel. To make sure that these
reactions and their products do not interfere with each other, these operations must be
rigorously controlled and switched on or off when necessary. In nature, enzymes control the
outcome and rate of the large majority of reactions taking place in a cell. Recently, a number
of biologically inspired systems have been published using molecular machines to control
the outcome of reactions by switching on and off catalytic units or by controlling the
enantioselectivity of the process.(1405-1412) In this section, switchable catalysts controlled
by stimuli such as light, pH change, ion in ux, and redox chemistry will be explored.

8.4.1 Photoswitchable Catalysts

Several examples of photoswitchable catalytic systems have been reported.

(1407, 1413-1415) The reactivity of the catalytic unit is typically controlled through alteration
of the steric shielding of the active site or by bringing the catalytic units into closer proximity.
In these examples, switching between the cis and trans forms of a photochromic group such
as an azobenzene or a stilbene, or the electrocyclization of a diarylethene, provides the
requisite control. An early example of a photoswitchable catalyst was published by Rebek Jr.
and co-workers.(1416) Two adenine receptors capable of forming complexes with purine
bases were linked through a trans azobenzene moiety. When the system was isomerized to
its cis conformation, the rate of reaction between an amine and p-nitrophenyl ester was
markedly increased due to greater proximity between the reactive groups, which increased
the effective molarity of these groups and thus increased the rate of reaction. A switchable
catalyst based on a light-responsive cavitand was published by the same group. The
cavitand was functionalized with an azobenzene switch and the cavity of the trans state 
accessible to a guest molecule, while the cis conformation could not bind guests.
Piperidinium acetate was used as the guest, and it could be shown that the host–guest
complex signi cantly accelerated a Knoevenagel condensation between malononitrile and
an aromatic aldehyde.(1417) Hecht and co-workers described the photoswitchable tertiary
piperidine derivative 133, which could function as a general base catalyst in a Henry reaction
between p-nitrobenzaldehyde and nitroethane (Figure 53). Catalysis was regulated through
the shielding/deshielding of the catalytic site upon irradiation of an azobenzene unit.(1418)
The reversible shielding and deshielding of a catalytic site by photoisomerization has also
been used to control the organocatalytic activity of a thiourea and a guanidine catalyst.
(1419, 1420)

Figure 53

Figure 53. (a) Molecular structure of the photoswitchable piperidine base 133, and (b) X-ray
structure of the photoswitchable piperidine base 133. X-ray crystal structure reprinted with
permission from ref 1418. Copyright 2008 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

The photoswitchable organocatalyst 134 consisting of a photochromic diarylethene (DAE)

unit and an imidazolium salt was reported by Bielawski and co-workers.(1421, 1422) Under
ambient light and in the presence of base, the imidazolium species catalyzed
transesteri cation and amidation. These reactions were considerably slowed upon
photoinduced formation of the ring-closed isomer (Scheme 42).(1421)
Scheme 42
  

Scheme 42. Ring-Opened and Ring-Closed Isomers of the DAE-Modulated Photoswitchable

Organocatalyst 134(1421)

Exploiting the ability of dithienylethene to switch between ring-closed and ring-opened

isomers upon irradiation, Branda et al. designed a photo responsive system mimicking
enzyme cofactor pyridoxal 5′-phosphate 135 (PLP) (Scheme 43). PLP is responsible for
amino acid metabolism and participates in a diverse range of enzymatic reactions such as
transamination, racemization, decarboxylation, and various elimination processes. The
structural features responsible for the action of PLP are the conjugated aldehyde and
pyridinium functional groups. Branda and co-workers replaced the core ring of PLP with a
dithienylethene where, in the ring-open form, the pyridinium and aldehyde units were
electronically isolated from each other preventing catalytic activity (138-inactive). However,
photoirradiation to form the ring-closed (138-active) isomer resulted in a fully conjugated
structure, which restored the connectivity between the pyridinium and the aldehyde groups
and therefore led to catalytic activity.(1423)

Scheme 43

Scheme 43. (a) Reaction of an Amino Acid with PLP Showing the Aldimine 136 Initially
Produced, and the Molecular Structure of the Quinonoid 137 Formed after Removal of the
Amino Acid’s α-Hydrogen, Which Leads to Racemization; and (b) Photoresponsive PLP
Mimic 138(1423)
Feringa et al. used one of their rotary molecular motors based on a chiral overcrowded
alkene, which can perform a directional 360° rotary cycle fueled by light and heat to create
 a
photoswitchable catalyst. During this rotation, the helicity of the motor changes, which
changes the overall chirality of the system. A DMAP (dimethylaminopyridine) Brønsted base
(Figure 54) and a thiourea hydrogen-bonding donor group, which together comprise a
bifunctional organocatalyst, perform Michael additions when in close proximity. As a
consequence, the catalytic activity as well the stereoselectivity can be controlled. Michael
addition of 2-methoxy thiophenol to cyclohexanone was used as a test system. The (P,P)-
trans-140 isomer resulted in a racemic (R,S)-thiol adduct in low yield (7%) after a lengthy
reaction. When the (M,M)-cis-140 isomer was used, the Michael addition proceeded
signi cantly faster furnishing a 50% yield of product, with an er of 75/25 (S/R). Finally, the
(P,P)-cis-140 isomer led an 83% yield with an inversion in enantioselectivity providing an er of
23/77 (S/R).(1424) Recently, the same group reported a bisphosphine derivative of the same
photoswitchable rotary motor. Both product enantiomers of a palladium-catalyzed
desymmetrization reaction could be formed, although in situ switching experiments were
complicated by the photosensitivity of the active palladium complex.(1425)

Figure 54

Figure 54. Schematic representation and molecular structure of a bifunctional

organocatalyst integrated in a directional light-driven molecular motor. A, DMAP; B, thiourea
hydrogen-bonding donor group. (a) A and B are remote. (b) A and B are in close proximity
with M helicity in the (M,M)-cis-140 isomer, preferentially providing the (S) enantiomer of the
reaction product. (c) A and B are in close proximity with P helicity in the (P,P)-cis-140 isomer,
generating (R) enriched product. Step 1: irradiation at 312 nm at 20 °C. Step 2: heating at 70
°C. Step 3: irradiation at 312 nm at −60 °C. Step 4: temperature −10 °C.(1424)
8.4.2 pH-Dependent Switchable Catalysts
  
Several rotaxanes containing a catalytic unit have been reported. However, these cannot
typically be switched on/off.(1318, 1426-1430) Leigh et al. described the rotaxane-based
switchable organocatalyst 141, in which catalytic activity could be controlled by pH-
dependent macrocycle shuttling (Scheme 44). The design consisted of a dibenzo[24]crown-8
macrocycle and an axle containing both triazolium rings and a dibenzylamine/ammonium
moiety. The secondary amine/ammonium group was able to carry out iminium catalysis.
However, when the rotaxane was protonated, the ammonium group was a better binding site
for the macrocycle than the triazolium ring, and so the macrocycle blocked the catalytic
center, preventing the reaction. When the secondary amine of the rotaxane was not
protonated, the triazolium ring provided a better binding site for the macrocycle and the
dibenzylamine group was exposed, and could therefore participate in catalysis. As a model
reaction, the Michael addition of an aliphatic thiol to trans-cinnamaldehyde was performed.
The free thread was found to e ciently catalyze the reaction in both its protonated and its
deprotonated states.(1431) Recently, Leigh and co-workers explored the activation modes of
rotaxane catalyst 141 and published a chiral version of this design, with a chiral center next
to the secondary amine.(1432, 1433) This chiral organocatalyst was able to perform an
asymmetric Michael addition with good stereoselectivity.(1433) The pH-driven shuttling of a
pyridyl-2,6-dicarboxyamide macrocycle between squaramide (hydrogen bond catalyst) and
ammonium (iminium catalyst) stations has been reported.(1434) The macrocycle blocks the
site it is bound to, allowing the selective exposure of catalytic sites and the generation of
different products.

Scheme 44
   

Scheme 44. Acid–Base Switching of the Position of the Macrocycle, Which Conceals or
Exposes the Catalytic Site on the Rotaxane(1431)

8.4.3 Allosteric Regulation of Switchable Catalysts through Ion Addition

A different approach to the regulation of catalytic activity is via the addition of small
molecules such as ions, which can change the supramolecular structure of the catalyst, as is
observed in many enzymatic processes. Mirkin and co-workers reported the synthesis of
triple-layer complex 142 composed of two transition metal hinges, two chemically inert
blocking exterior layers, and a single catalytically active interior Al (III)-salen complex, which
can act as a ring-opening polymerization catalyst for ε-caprolactone (Figure 55). Polymer
growth and molecular weight could be controlled by the addition of Cl– (catalytic layer
exposed) or of the Cl– abstracting agent NaB(ArF)4, which results in the fully closed complex
142.(1435-1437) Recently, the same research group reported an allosterically regulated
photoredox catalyst based on a similar switching mechanism.(1438)

Figure 55
   

Figure 55. (a) Allosteric supramolecular triple-layer complex 142, which regulates the
catalytic living polymerization of ε-caprolactone. (b) Molecular structures of the
components.(1435)

Another ion triggered switch was the self-locking system published by Schmittel and co-
workers (Scheme 45).(1439-1441) Their design consisted of a zinc porphyrin and a 4-aza-
2,2′-bipyridine tether, which either coordinated to the zinc porphyrin or formed a complex
with copper and a shielded phenanthroline. In the presence of copper, the tether was
removed from the zinc porphyrin center, and piperidine was bound at the coordination site.
When copper was removed, piperidine was liberated and able to catalyze Knoevenagel
reactions.(1439)

Scheme 45

Scheme 45. Schematic Representation of the Reversible Locking and Unlocking of

Switchable Catalyst 143(1439)

8.4.4 Redox-Driven Switchable Catalysts

Canary and co-workers have reported a redox-switchable chiral catalyst capable of delivering
either enantiomer of a nitro-Michael addition product depending on the oxidation state
of a 
single copper atom. The design, inspired by previous work carried out in their group and by
others,(1442-1444) is based on complexes derived from methionine, which were shown to
undergo inner sphere ligand rearrangement upon one-electron oxidation or reduction of
copper. The rearrangement is coupled to the orientation of quinolone rings to afford
enantiomeric con gurations. Urea catalysis produced the (S) enantiomer in 72% ee and 55%
yield, and the in situ reduced complex produced the (R) enantiomer in 71% ee and 43% yield.
(1445)

8.5 Synthesis Using Arti cial Molecular Machines

Nature provides us with many examples of biological molecular machines that engage in
sequence-speci c chemical synthesis. For example, the ribosome utilizes sequence
information stored in mRNA to synthesize proteins with excellent delity.(68-70) The various
DNA polymerases provide further examples of sequence-speci c polymer synthesis by
biological molecular machines.(71) The inherently programmable nature of DNA has been
used by synthetic chemists to accomplish sequential oligomer synthesis. A common
strategy is exempli ed by the seminal work of Liu et al.,(1446) where complementary
sequences of DNA capped with different, mutually reactive end groups are annealed to
create an extremely high local concentration of the two reactive species ensuring
intracomplex bond formation predominates. After the rst reaction is complete, a biotin tag
on one strand allows its selective removal, after which a new reactive partner can be
annealed to the existing strand and a second reaction conducted. Peptide,(1446-1448)
carbon–carbon,(1449-1452) carbon–heteroatom bond forming reactions,(1453) and even
cycloaddition reactions have all been reported on the basis of this type of methodology.
(1454) More elaborate DNA systems have been used by Seeman and co-workers to create a
“molecular assembly line” where three gold nanoparticles could be combined to form eight
differently composed products, illustrating the complexity that can be achieved with DNA-
based molecular machines.(1455)

In a seminal example of a synthetic system mimicking some of the properties of an enzyme,

Nolte, Rowan et al. reported a rotaxane-based catalytic system.(1456) A glycoluril clip-based
macrocycle containing a manganese porphyrin catalyst catalyzed the epoxidation of a
butadiene polymer, which formed the thread of the rotaxane. A greatly enhanced proportion
of cis-epoxide was observed in the product, consistent with previous work showing that
when the reaction occurred in the macrocyclic cavity steric constraints favored the cis
product.(1457) This system has been further optimized by substitution of the porphyrin
macrocycle with protective ligand groups, which increase turnover number (TON) and
provide even greater cis selectivity by preventing reaction on the exterior face of the
macrocycle (Figure 56).(1458) The rate of threading of their macrocycle onto polymeric
materials was also studied and found to be highly dependent on interactions between the
thread and the outside of the macrocycle preassociating the two moieties.(1459)
Figure 56
  

Figure 56. Porphyrin-catalyzed epoxidation of a butadiene polymer by 144, utilizing a

rotaxane architecture. Reprinted with permission from ref 1456. Copyright 2003 Nature
Publishing Group.

A cyclodextrin dimer has been used as both a catalyst (for the polymerization of δ-
valerolactone) and a molecular “clamp”, which guides the output of the polymer.(1460) In this
system, an α-cyclodextrin acts as the active site while a β-cyclodextrin acts as the clamp
guiding the growing chain away from the active site (Scheme 46). An additional example was
provided by Takata et al.,(1430) where the cyclization of propargyl or allyl urethane groups in
the rotaxane backbone to oxazolidinones was catalyzed by a palladium center, bound to the
macrocycle.

Scheme 46

Scheme 46. Cyclodextrin Dimer 145 Polymerization Catalyst(1460),a

Scheme a Reprinted with permission from ref 1460. Copyright 2011 Wiley-VCH Verlag GmbH
& Co. KGaA, Weinheim.

Recently, Leigh et al. reported the rst small molecule arti cial molecular machine (146)
capable of sequence-speci c peptide synthesis.(666) The machine is based on a rotaxane
architecture, which is used to ensure processivity in a manner reminiscent of both the
ribosome-mRNA structure and the DNA clamp of DNA polymerases.(68-71) Sequence
information contained in the track is directly converted into the sequence of the peptide
synthesized, and thus the track plays some aspects of the role of mRNA in the ribosomal
system. Reactive phenolic ester groups take the place of tRNA-bound amino acids andare 
sequentially “picked up” by the catalytic arm of the macrocycle. The catalytic arm bears a
cysteine group and operates by native chemical ligation (NCL) chemistry where the thiolate
of the cysteine unit reacts rst with the ester group before transferring the activated amino
acid to the end of the growing chain.(1461) The steric bulk of the loaded amino acid prevents
the macrocycle passing over the barrier unit before this reaction has taken place but allows
free passage of the macrocycle after being cleaved. This prevents the peptide sequence
from being scrambled and allows sequential reaction. Rigid spacing units between each
loaded amino acid minimize the likelihood of the catalytic arm encountering an out of
sequence amino acid. The catalytic unit consists of a cysteine-glycine-glycine motif with the
second two amino acids present to prevent an unfavorable 1,8-S,N-acyl shift transition state
during the second ligation (Figure 57).

Figure 57

Figure 57. Leigh’s small molecule peptide synthesizer, 146.(666)

After the third and nal amino acid has been cleaved from the thread, the macrocycle can
dethread and be isolated. The delity of sequence transfer in this process was demonstrated
by tandem mass spectrometry of the macrocyclic product, identical to an authentic sample
synthesized by conventional methods. No out of sequence or abbreviated products were
observed by HPLC–MS underlining the extremely high level of control afforded by this
system. This molecular machine showed processivity, sequence speci city, and autonomy
and an exceptional level of control at the molecular level. However, several problems remain
with this design. The rate of reaction is vastly slower than that of the ribosome; one peptide
bond takes an average of 12 h to form, whereas the ribosome makes approximately 20
amide bonds every second.(68) Additionally, information is read in a destructive manner;
once the macrocycle has cleaved the ester bonds, there is no way to reload the machine for
a second run. Finally, the NCL reaction used to catalyze peptide formation limits the scope of
amino acids that can be incorporated into the growing peptide chain.

Recently, Leigh et al. reported an extension to this system, creating a four barrier machine
whose nal product is a macrocycle-bound heptapeptide.(661) The sequence speci city of
the product was again con rmed by tandem mass spectrometry and compared to an
authentic sample. Although no problems were encountered in this system, whose nal bond
formation involves a 20-membered ring S,N-acyl transfer, the ever-expanding size of the
required cyclic transition state will at some point limit the length of potential peptide
  
products formed by the current design (Scheme 47).

Scheme 47

Scheme 47. Operation of Leigh’s Peptide Synthesizer(666),a

Scheme a Reprinted with permission from ref 666. Copyright 2013 American Association for
the Advancement of Science (AAAS).

8.6 Controlled Motion on Surfaces, in Solids, and Other

Condensed Phases
8.6.1 Controlled Motion in Solids and Condensed Phases

A major challenge is to use molecular machines for practical applications by utilizing

molecular scale changes to create macroscopic effects. Using molecular machines in the
solid state or other condensed-phase matter could lead to new materials with a higher level
of complexity with controlled cooperative molecular motion leading to changes in the
properties and function of the material on a macroscopic scale. In recent years, several
examples of molecular motion in condensed-phase matter have been described, some of
which show promise for applications in the elds of electronics and optoelectronics.
  
Garcia-Garibay and co-workers have investigated the rotational dynamics and photophysical
properties of the crystalline, linearly conjugated, phenyleneethynylene molecular dirotor 147
(Figure 58). A pentiptycene unit was incorporated as a central stator about which the two
anking ethynylphenylene rotators could adopt various torsion angles. X-ray diffraction
studies showed that in the solid-state structure of molecular dirotor 147 all of the
phenyleneethynylene chromophors are arranged parallel to one another and therefore shared
the same rotation axis. The chromophore displayed signi cant uorescence changes as a
function of interphenylene torsion angles. The authors suggest that with this system external
control of the rotation could be achieved by the application of an electric eld, which would
allow a rapid shift of solid-state uorescence emission and optical properties upon the
application of appropriate stimuli.(1462-1470)

Figure 58

Figure 58. (a) Molecular structure of linear conjugated phenylethynylene molecular dirotor
147. Rotation of the phenylene rotor (shown with an arrow) creates rotamers with varying
degrees of π-conjugation and so wavelengths of emission. (b) X-ray structure of the dirotor
147. X-ray crystal structure reprinted with permission from ref 1462. Copyright 2013
American Chemical Society.
Sozzani and co-workers have published several examples of molecular rotors in crystals with
open porosity, as well as molecular rotors embedded in porous frameworks such as  
aromatic or organosilica frameworks. In some of these systems, the rotational motion can
be actively regulated in response to guest molecules such as CO2, I2, tetraethylammonium
chloride, and water. These responsive materials may nd applications spanning from
sensors to actuators, which could capture and release chemicals on command.(1471-1474)
Recently, Schurko and Loeb published a metal–organic framework (MOF) material
containing dynamically interlocked components.(1475) They used [2]rotaxane 148 as the
organic linker and binuclear Cu(II) units as the nodes (Figure 59). Void spaces inside the rigid
framework allowed the macrocyclic ring of the rotaxane to rotate rapidly. Initially the
macrocycle is locked in place through hydrogen bonding from an ether oxygen atom of the
macrocycle to a copper-bound H2O. Dynamic motion occurs upon removal of the water
molecules by heating to 150 °C under vacuum, destroying hydrogen-bond interactions and
allowing rapid circumrotation about the rotaxane axle. Rotation can be quenched by the
addition of water. This type of material could be useful for the creation of solid-state
molecular switches and machines.(1475) A rotaxane-based molecular shuttle incorporated
into the structure of a MOF has recently been reported.(1476)

Figure 59

Figure 59. (a) Structure of [2]rotaxane 148. (b) Schematic representation of the structural
design components used to create the metal–organic framework. (c) X-ray structure of the
tetra-ester precursor to [2]rotaxane 148. (d) X-ray structure of a single unit of the
mechanically interlocked molecule, coordinated to four Cu(II) paddlewheel clusters. X-ray
crystal structure reprinted with permission from ref 1475. Copyright 2012 Nature Publishing
Group.
8.6.2 Solid-State Molecular Electronic Devices
  
In a series of ground-breaking but controversial experiments interfacing switchable
rotaxanes and catenanes with silicon-based electronics, molecular shuttles have been
employed in solid-state molecular electronic devices.(1146, 1477-1485) Bistable [2]rotaxanes
and [2]catenanes have been the subject of numerous experimental investigations in the
course of the development of such molecular electronic devices.(1233, 1478, 1486-1495)
Here, the bistable [2]catenanes and [2]rotaxanes feature a cyclobis(paraquat-p-phenylene)
(CBPQT4+) macrocycle and two stations, often a tetrathiafulvalene (TTF) site and a
dioxynaphtalene site (DNP). Initially the macrocycle preferentially resides over the TTF site
due to strong aromatic charge-transfer interactions between the components; this is referred
to as the ground-state coconformation (GSCC). Electrochemical oxidation of the TTF station
to form TTF2+ generates Coulombic repulsion between CBPQT4+ and TTF2+, and drives the
translation of the macrocycle to the DNP station, to give the metastable state
coconformation (MSCC). The process can be reversed on reduction of TTF2+ to TTF
followed by either thermal relaxation of the macrocycle to the TTF station, or reduction of the
bipyridinium units in the cyclophane ring to the corresponding radical cations, which reduces
the activation barrier to shuttling, restoring the system to the GSCC. These two mechanically
distinguishable states exhibit different characteristic tunneling currents. On the basis of
quantum mechanical computational studies, the MSCC state is predicted to be the more
highly conducting state. The switching cycle can be detected by a number of experimental
techniques including time- and temperature-dependent electrochemistry and spectroscopy.
Studies have shown that current levels on switching are in uenced by temperature, the
structure of the rotaxane/catenane, and the environment in which the molecular machines
are embedded.(1496-1498) Different environments, including Langmuir–Blodgett (LB) lms,
(1499-1501) self-assembled monolayers (SAMs),(1502-1506) and solid-state molecular-
switch tunnel junctions (MSTJs), have been extensively studied.
(1150, 1151, 1488, 1489, 1507-1512) In one particular MSTJ, a monolayer of switchable
rotaxane 149 was embedded between two conducting electrodes (Figure 60). This MSTJ
acts as a gate, which can be opened or closed in response to an applied voltage by changes
in conductivity and resistance and could be used in molecular logic gate designs. The
reported design showed stable switching voltages of −2 and +2 V, with reasonable on/off
ratios and low switch-closed currents. Nanometer-scale devices have been built using this
approach and connected to form 2-D crossbar circuit architectures.(1144) As a next step, the
authors published the design of a 160-kilobit molecular electronic memory circuit consisting
of 400 silicon-nanowire electrodes (16 nm wide) and crossed by 400 Ti electrodes
sandwiching a monolayer of bistable [2]rotaxanes.(1513) Despite the interesting ndings,
many remain skeptical about the utility of rotaxanes in electronics, and an array of scienti c
and engineering challenges remain to be addressed such as device robustness, improved
etching tools, and improved switching speed.(1514-1516)

Figure 60
   

Figure 60. (a) Rotaxane 149-based molecular switch tunnel junctions and proposed
mechanism for the operation. (i) In the ground state, the tetracationic cyclophane (dark blue)
mainly encircles the TTF station (green) and the junction exhibits low conductance. (ii)
Application of a positive bias results in one- or two-electron oxidation of the TTF units (green
→ pink), and increases electrostatic repulsion causing (iii) shuttling of the macrocycle to the
DNP station (red). (iv) Returning the bias to near −0 V provides a high conductance state, in
which the TTF units have been regenerated, but translocation of the cyclophane has not yet
occurred due to a signi cant activation barrier to movement. Thermally activated decay of
this metastable state may occur slowly ((iv) → (i), in a temperature-dependent manner) or
can be triggered by the application of a negative voltage (v), which temporarily reduces the
cyclophane to its diradical dication form (dark blue → orange), allowing facile recovery of the
thermodynamically favored coconformation (vi). (b) Example of one design of a molecular
switch. The coloring of the functional units corresponds to that used for the structural
diagrams.(1479, 1482, 1483) Reprinted with permission from ref 14. Copyright 2007 Wiley-
VCH Verlag GmbH & Co. KGaA, Weinheim.

8.6.3 Using Mechanical Switches To Affect the Optical Properties of Materials

Molecular machines can in uence the optical properties of materials in the solid state as
well as in solution (section 8.2.2). Numerous molecular-machine-functionalized materials
where changes can be visually monitored have been reported. Some pertinent examples are
discussed below.

Liquid crystals have become widespread in numerous technological applications.

(1517-1520) The photoalignment of liquid crystals has considerable potential for display and
other optoelectronic applications. The reorienting effect of light on nematic liquid crystals is
well-known.(1521-1525) However, the effect can be greatly enhanced by the presence of a
dopant dichroic dye. Studies have suggested that the mechanism of this effect involves the
photoexcited dye molecules acting as Brownian rotors in the nematic liquid crystal.
(1526, 1527) The change in orientation was attributed to a ratchet mechanism operating via
the generation of torque. Feringa and co-workers reported a chiral nematic liquid crystal lm
doped with a previously reported chiral light-driven molecular motor. Irradiation of the  lm 
resulted in directional motion of the molecular motor, which induced a rotation of the rod-like
liquid crystal molecules. This rotation led to the alteration of the color of the lm over a large
part of the visible spectrum (Figure 61).(1528, 1529)

Figure 61

Figure 61. Color changes in a liquid-crystal lm doped with a light-driven rotor. Reprinted with
permission from ref 1528. Copyright 2002 American National Academy of Sciences.

Yamaguchi et al. reported crystalline molecular gyrotop, which showed temperature-

dependent changes in optical properties as a result of structural expansion upon rotor
acceleration (Figure 62).(1530-1532) Utilizing a phenylene moiety as the rotor, they observed
that the orientation of the rotor in the crystal was ordered below 270 K, but became
disordered above this temperature generating a slight deformation of the crystal lattice.
Using the temperature-dependent features of the crystal, the birefringence (Δn) of the crystal
could be controlled. At 280 K, the phenylene moiety undergoes a 180° ipping between two
equilibrium states, which provides an almost constant Δn. Above this temperature, Δn
decreases as the phenylene moiety rapidly rotates, and the cage expands. The dynamic and
optical properties are reversible.(1530)

Figure 62

Figure 62. (a) Molecular structure of gyrotops 150 and 151. The bulkier 151 does not exhibit
rotation. (b) X-ray structure of 150. (c) Single crystal of 150 irradiated with polarized white
light. (d) X-ray structure of 151. (e) Single crystal irradiated with polarized white light. For
150, a continuous change in color was observed, due to thermal expansion. Reprinted with
permission from ref 1530. Copyright 2012 American National Academy of Sciences.
A pseudorotaxane that acts as a thermally driven molecular switch in a crystalline state was
recently published by Horie and co-workers.(1533-1535) Crystals of the pseudorotaxane
  
underwent phase transitions upon heating with accompanying changes in optical properties.

Leigh et al. used [2]rotaxanes to control uorescence by distance-dependent intercomponent

electron transfer both in solution and on a polymer lm. The thread of these rotaxanes
included an anthracene uorophore as a stopper attached to a glycylglycine hydrogen-
bonding station and a C11 alkyl chain that could act as a second station. The macrocycles in
152 and 153·2H2+ contained nitrophenyl and pyridinium moieties, respectively, which are
known to quench the uorescence by distance-dependent electron transfer. Macrocyclic
shuttling could be induced by changes in solvent with strongly hydrogen-bonding solvents
displacing the macrocycle from the glycylglycine station to the alkyl thread. In non-hydrogen-
bonding solvents (e.g., benzene, CH2Cl2, CH3CN), the macrocycle was located on the
glycylglycine station and uorescence was completely quenched. In strongly hydrogen-
bonding solvents (e.g., DMSO and NH2CHO), the macrocycle encapsulated the alkyl chain
and uorescence was restored. Polymer/rotaxane hybrids were used to prepare transparent
lms on quartz slides. Initially, no uorescence was detected when the slides coated with a
154 containing lm were illuminated with UV light (254–350 nm). However, after the slides
were exposed to DMSO vapor, prior to illumination, a characteristic blue uorescence was
observed showing that similar shuttling processes were occurring on the polymer lm as
were observed in solution. Masking regions of the lm from the DMSO vapor allowed the
transitory etching of patterns on the polymeric lms (Figure 63).(1536)

Figure 63
   

Figure 63. (a) Chemical structures of rotaxane initiators 152 and 153 and the corresponding
PMMA-based polymers 154, 155, and 155·2H2+. (b) Images obtained by casting lms of
polymer 154 on quartz slides, then covering the lms with aluminum masks and exposing
the unmasked area to DMSO vapor for 5 min. The photographs were taken while illuminating
the slides with an 8-W UV lamp (254–350 nm). Reprinted with permission from ref 1536.
Copyright 2005 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Polymeric 155·2H2+ lms responded to two different stimuli. Protonation of the macrocycle
by CF3CO2H vapor caused quenching of uorescence, while DMSO vapor induced shuttling
of the macrocycle and subsequently restored uorescence emission. The response of
155·2H2+ to the different combinations of two stimuli (DMSO and protons) corresponds to
an INHIBIT Boolean logic gate (Figure 64).(1536)

Figure 64
   

Figure 64. (a) Aluminum grid used in the experiment. (b) Pattern generated when lms of 155
were exposed to tri uoroacetic acid vapor for 5 min through the aluminum-grid mask. (c)
Mesh pattern obtained by rotation of the aluminum grid by 90° and exposure of the lm
shown in (b) to DMSO vapor for a further 5 min; only regions exposed to tri uoroacetic acid
but not to DMSO were quenched as shown in the magni ed view. Inset: Truth table for an
INHIBIT logic gate. The photographs were taken while illuminating the slides with an 8-W UV
lamp (254–350 nm). Reprinted with permission from ref 1536. Copyright 2005 Wiley-VCH
Verlag GmbH & Co. KGaA, Weinheim.

Hydrosol–gel systems represent another example of a nonsolution media. The effect of

doping these systems with rotaxanes has been studied by various groups.(1208, 1537-1541)
Light-driven rotaxanes based on α-cyclodextrin and cucurbit[7]uril have been dispersed in
thermoreversible hydrogel systems by Tian and co-workers. They observed that when the
rotaxanes were embedded in the hydrogel, their optical performance ( uorescence and
induced circular dichroism) improved. They attributed this observation to the restriction of
movement in the hydrogel system.(1539, 1542)

8.6.4 Using Mechanical Switches To Affect the Mechanical Properties of Materials

Piezoelectric materials provide the most common example of an external stimulus being
converted into a mechanical change in the material. Materials incorporating molecular
machines could provide a far greater level of control over macroscopic properties than is
currently possible, and their development has been the focus of great interest.(1543, 1544)
Conformational changes in polymers leading to macroscopic mechanical changes have
been extensively studied. Hydrogels, consisting of water-swollen cross-linked networks of
neutral or ionic amphiphilic polymers, have been shown to undergo reversible phase   
transitions in response to changes in temperature, solvent, pH, electric eld, or irradiation
with an up to 100-fold expansion on phase change.(1545-1558) Katchalsky et al. rst
exploited these properties to develop devices that converted chemical potential energy into
macroscopic mechanical work.(1559, 1560) A large variety of devices based on the
characteristics of these materials have been proposed(1561-1581) including guest binding
and release,(1582) control of enzyme activity,(1583) and the macroscopic motion of a
polymer gel by selective contraction of alternate sides of a gel.(1571) Finally, guest binding
by built-in recognition sites can lead to large-scale changes in the volume of the host gel.
(1584-1598)

Shape memory materials have also been designed that utilize control at a molecular level.
(1599, 1600) While most of these systems rely on a temperature variation-induced shape
change, a system utilizing a photoinitiated radical reaction to rearrange covalent cross-links
and recover the “memorized” shape has been reported.(1601) A reversible cross-linking [2 +
2] cycloaddition has also been used to achieve this control.(1602)

Conducting polymers have been used to create stimuli responsive mechanical changes.
(1603-1605) Electrochemical oxidation can induce counterion expulsion or inclusion and
thus volume change, although these changes tend to be slow in aqueous solution.
(1606-1609) Solid state,(1610) gel,(1611) and ionic liquid electrolytes have been shown to
accelerate this process.(1612) Conformationally exible calix[4]arenes have been used as
“hinges” to form conducting oligothiophenes where the cone (but not the kite) form of the
calix[4]arene maximizes the desired π–π interactions and switching could be utilized to
provide macroscopic mechanical motion.(1613, 1614)

In the previous examples, a macroscopic change was induced by the sum of multiple,
relatively uncontrolled conformational changes in a polymeric network; that is, the observed
change is not an inbuilt feature of the molecular components. The use of particular
submolecular conformational/con gurational switches to directly trigger macroscopic
changes has numerous bene ts such as overcoming problems caused by slow diffusion of
guests or solvents and ensuring a uniform response in the material. The use of
con gurational switches to control long-range order in liquid crystalline phases has been
discussed elsewhere (section 8.6.3), but a similar application in synthetic polymers often
furnishes a useful result.

Azobenzenes are often used to control reversible contraction in polymers, a process that has
been observed at a molecular level using AFM,(1615) as well as properties such as viscosity
and solubility.(1616, 1617) In the aforementioned AFM experiment, the application of a “load”
to the AFM tip and subsequent isomerization toward the cis isomer provided the rst direct
measurement of the conversion of light to mechanical energy. Chiral azobenzene side chains
can allow control over the screw sense of arti cial helical polymers with isomerization
leading to interconversion of the P and M forms.(1618-1620) Several liquid crystal polymeric
systems have been reported.(209, 1621-1635) Macroscopic motion was induced in liquid
crystal polymer springs devised by Fletcher, Katsonis et al.(1636) Here, a chiral dopant,
 a 
polymerizable liquid crystal, and a polymerizable azobenzene switch were used to generate a
liquid crystal polymeric spring. Irradiation with UV light caused cis–trans isomerization of the
azobenzene switch, which in turn led to coiling/uncoiling or helical inversion of the spring.
More complex behavior such as side to side bending could be induced by careful
manipulation of the initial helical state and directed illumination.(1636)

Light-driven directional rotor 156 has been used to drive the macroscopic motion of a glass
rod.(1637, 1638) When doped at 1 wt % into a liquid crystal, the helicity of the rotor induced a
helical arrangement in the liquid crystal, giving rise to a characteristic “ ngerprint” texture in
the liquid crystal’s surface. Irradiation altered the distribution of isomers of the rotor and thus
caused the liquid crystal’s helical nature to rearrange. This process could be observed by the
clockwise rotation it caused of a glass rod laid on the surface and of the “ ngerprint” pattern.
Eventually, however, rotation stopped as the system reached a photostationary state with the
distribution of molecules between isomers reaching equilibrium. When the light source was
removed, the isomer distribution decayed back to its initial state, with concomitant reverse
rotation. The use of the opposite isomer of the rotor led to inversion of the direction of
rotation (Figure 65).

Figure 65

Figure 65. (a) Rotor 156. (b) Rotation of micrometer scale glass rod on doped liquid crystal
lm. Photos taken at 15 s intervals. Reprinted with permission from ref 1637. Copyright 2001
Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Shuttling in [3]rotaxane 157 has been used to generate a macroscopic mechanical response,
deformation of a microcantilever beam, which had been coated with a monolayer of ca. 6
billion rotaxanes.(1238, 1341) Oxidation of the tetrathiafulvalene (TTF, green) station
decreased the a nity of the macrocycle for this station, and induced shuttling to the
naphthalene (red) station. A deformation of 550 nm was recorded, and the process could be
reversed and repeated (with diminishing amplitude) over several cycles (Scheme  48).  
(1238, 1341) Microcantilever deformation by guest recognition at the surface has been used
by several groups as a “read-out” from molecular detectors.(1639-1646) A polymer has been
reported that contracts upon illumination based on a directional light-driven rotor (Scheme
48).(1647) A photodriven rotary motor has also been used to induce the disassembly of self-
assembled nanotubes.(1648)

Scheme 48

Scheme 48. Molecular Motion Generating a Macroscopic Mechanical Response

(1238, 1341, 1647),a

Scheme a Reprinted with permission from ref 1647. Copyright 2015 Nature Publishing
Group.

8.6.5 Using Mechanical Switches To Affect Interfacial Properties

The ability to easily modify the properties of surfaces in a reversible manner would be
extremely valuable in the design and synthesis of technologically useful devices. Stimuli-
responsive polymer modi cation of surfaces can lead to control over wettability, adhesive
ability, porosity, patterning, and interfacial interactions; this topic has been reviewed
elsewhere.(1649-1663)
Interlocked architectures such as bistable rotaxane 158 have been used to restrict or allow
access to the pores in materials such as mesoporous silica particles.(1664) The  positively
 
charged macrocyclic ring initially prefers the TTF station, and in this conformation, diffusion
into and out of the nanopores of the silica is allowed. Oxidation of the TTF moiety causes
shuttling of the ring to the dioxynaphthalene station, and closure of the nanopores, trapping
a portion of the solvent/solute mixture. Solvent exchange and reduction of the oxidized TTF
station leads to guest release (Figure 66). The aggregation and deaggregation of a polymeric
material has been caused by the formation of pseudorotaxanes between strands. This has
been used to transiently trap nanoparticles in the pores formed upon aggregation.(1665)

Figure 66

Figure 66. (a) Structure of nanopore gate, and (b) controlled release of guest from
nanopores.(1664) Reprinted with permission from ref 14. Copyright 2007 Wiley-VCH Verlag
GmbH & Co. KGaA, Weinheim.

The translation of the macrocyclic ring of 159 has been converted into an electric signal.
(1666-1668) A gold electrode was used in place of one stopper of the rotaxane, and a
cyclodextrin ring with an attached ferrocene was used as the macrocycle. On photoactivated
shuttling, the change in rate of distance-dependent oxidation of the ferrocene moiety allowed
detection of the shuttling motion.(1669) When a glucose oxidase enzyme was attached via a
rotaxane architecture to a gold electrode, the CBPQT4+ macrocycle of the rotaxane acted as
a two-electron shuttle and allowed enzyme operation, which was prevented when the
enzyme was attached solely by the thread.(1670) A similar effect was seen in a system
involving a CdS nanoparticle in place of the enzyme in which the observed photocurrent was
ampli ed 8-fold in the rotaxane over the thread.(1671) In a simpler analogue of these
systems involving a CBPQT4+ macrocycle and a diiminobenzene station (159), electrode-
  
induced shuttling could be directly observed.(1672) The reduction in macrocycle charge on
shuttling was shown to decrease the hydrophilicity of the surface, and thus increased the
contact angle of a drop of water on the surface (Scheme 49).

Scheme 49

Scheme 49. Electrode Controlled Macrocycle Shuttling, Leading to Control of the

Hydrophilicity of the Surface(1672)

This control of wettability has been exploited by many groups to form a wide range of
interesting systems, especially in the development of “self-cleaning” surfaces.(1673-1679)
Surface wettability has been controlled by surface mounted photochromic switches.(1680)
Self-assembled monolayers of carboxylate-terminated alkanethiols on gold have been
switched between hydrophilic (carboxylate exposed, gold electrode at a negative potential)
and hydrophobic (carboxylate surface bound, gold electrode at a positive potential) states by
varying the electric potential.(1681) Bipyridinium groups have been used in place of
carboxylates to similar effect.(1682)

Several methods for the photoswitchable change of surface wettability have been developed.
Systems based on the reversible exposure of hydrophobic groups upon shuttling of a
cyclodextrin ring,(1683) or the release of a hydrophilic guest,(1684) have been successfully
exploited. Feringa and co-workers exploited a tripodal stator to x a molecular directional
rotor to a surface, which upon irradiation exposed or hid a hydrophobic uorinated chain
providing control over surface wettability (Figure 67).(1685)

Figure 67
   

Figure 67. Feringa’s tripodal wettability switch 160.(1685)

Perhaps the most powerful demonstration of the usefulness of control over wettability is in
the macroscopic transport of a liquid across a surface. The earliest example came from
Whitesides and Chaudhury who created a hydrophilicity gradient on a silica wafer by reaction
with a trichloroalkylsilane vapor and observed the motion of a droplet of water up a 15°
incline.(1677) Numerous examples of droplet motion driven by surface energy
gradients/steps have since been reported.(1686-1690) However, remotely controlling
wettability to generate droplet motion has remained challenging.(1691) This remote control
would be particularly useful in “lab-on-a-chip” type applications where it could provide a
gentle and cheap alternative to expensive microscopic pumps and strong electric elds.
(1692)

Azobenzene containing calix[4]resorcinarene 161, when deposited as a monolayer, provided

the rst example of remote control of surface energy and therefore droplet motion by
irradiation.(1693) The monolayer initially consisted of all cis isomers. However, a droplet of
olive oil has more favorable interactions with the extended trans form, where interactions
with the alkyl chain of the calix[4]arene can be maximized. As such, when an asymmetric
light source irradiated the droplet, forming more trans-calix[4]arene on one side of the droplet
than the other, a surface energy gradient was created and the droplet moved away from the
trans enriched area. This movement could be continued if the light source followed the rear
edge of the droplet (Figure 68).
Figure 68
  

Figure 68. Calix[4]arene 161, used to control surface wettability.(1693)

Photoresponsive control of droplet motion has also been achieved using a system based on
bistable rotaxane 162, adsorbed onto a gold surface using a thiol linker.(1245)
Diiodomethane drops could be transported on a millimeter scale across a surface using the
macrocycle of 162 to either hide or expose the uoroalkane region of the rotaxane and thus
modify surface energy. Using this strategy, a microliter droplet could be moved up a 12°
incline. Roughly 50% of the absorbed photon energy was converted into gravitational
potential energy of the drop (Figure 69).

Figure 69
   

Figure 69. Light switchable rotaxane 162, and transport of a microliter drop of CH2I2 across a
at surface (a–d) and up a 12° incline (e–h). Reprinted with permission from ref 1245.
Copyright 2005 Nature Publishing Group.

The above examples of macroscopic control utilizing molecular motion underscore the
potential importance of this concept for technological applications. Similar control of motion
has been achieved with surfaces microscopically patterned with thermoresponsive polymers
(1694-1696) and by amplifying the effect of the photochemical switching of a spiropyran-
functionalized surface.(1697)

9 Arti cial Biomolecular Machines Jump To

9.1 Hybrid Biomolecular Systems

Biological systems make extensive use of motor proteins such as ATPase, kinesin, myosin,
and dynein. These biological motors provide both examples of machines viable at the
nanoscale and useful building blocks for the creation of hybrid systems. The availability of
preformed nanoscale machines has greatly expedited the creation of complex
nanotechnological systems. Although a thorough exploration of this topic is beyond the
purview of this Review and has been covered elsewhere,(15, 47, 1364, 1698-1702) a brief
overview is useful. The initial purpose of these biohybrid experiments was to further probe
the complex mechanisms by which biological machines operate. An early example was
provided by Kinosita et al., who reported a series of experiments exploring the F1-ATPase
rotary motor.(1703-1707) They were able to observe the 360° rotation of the motor, powered
by the hydrolysis of ATP, directly, via microscopy, for individual motors mounted on glass.
Mechanical rotation has also been observed in an F0F1-ATPase, where the rotor domain is
coupled to a proton transporting domain.(1708) Even more remarkably, ATP synthesis has
been driven by rotating a magnetic bead attached to an F1-ATPase with electromagnets.
(1709) This is a stunning example of chemical synthesis driven by an external mechanical
force. ATPase systems have been less exploited in recent years due to the di culties in
using them in synthetic systems.(1710) However, a recent example showed the insertion of
ATP synthases into an arti cial lipid microcapsule and their subsequent use to generate
 ATP 
inside the capsule.(1711)

Kinesin, myosin, and dynein systems have been much more extensively utilized.(1712-1722)
They have been shown to transport cargos in arti cial systems, although cargos must
typically be large to outcompete diffusive forces.(1375, 1723-1727) These biological walkers
have been controlled by the design of appropriate tracks,(1728-1730) or by the application of
external forces. Kinesin has been used to stretch a length of DNA,(1715) and to enable the
detection of nanomolar concentrations of a targeted protein.(1731) Cross-linked actin and
myosin gels were found to move over each other in the presence of ATP.(1732) Microtubule
containing gels combined with kinesin and ATP have been shown to spontaneously generate
autonomous motility.(1733, 1734) As a further bene t to using biological motors, ATPase
motors have been shown to operate at a near 100% e ciency,(1707, 1735-1737) and kinesin
at >50%,(1738) whereas in a typically used polymeric system where phase transitions are
used to generate molecular level forces, an e ciency of 0.0001% was observed. The eld of
biomolecular electronics often uses molecular motion as a switching mechanism,
particularly in systems utilizing photoactive proteins (be they native or engineered).
(1739-1750)

9.2 Hybrid Membrane-Bound Machines

Ionophores and ion channels, both synthetic(1751-1755) and biological,(1756-1766) have
been extensively explored and exploited. Biological ion channels have been inserted into
arti cial membranes and used to sequence single strands of DNA,(1756) to open the pore of
a nonselective e ux channel,(406, 1767, 1768) and to effect the light-driven production of
ATP by F0F1-ATPase.(1769) Feringa et al. reported the switching of the “mechanosensitive
channel of large conductance’ (MscL) of E. coli, which can be opened in response to the
introduction of charged entities at a certain location in the protein channel.(406) Initially, a
light-cleavable group was used to release acetate anions and thus open the channel, with a
reversible version, utilizing a spiropyran switch, also reported (Scheme 50). Ion channel
proteins modi ed postsynthetically to be light switchable have been inserted into living cells,
and successfully opened and closed.(1770-1777) Unnatural, light switchable amino acids
have also been incorporated into ion channel proteins.(400, 1778-1780)

Scheme 50
   

Scheme 50. (a) Irreversible Photocleavage of 163 Leading to Pore Opening; and (b)
Reversible Photoswitching of 164, Leading to Pore Openinga

Scheme a MscL = mechanosensitive channel.(406)

Active transport between aqueous phases across an organic phase,(1781-1783) and lipid
bilayers,(1784) has been observed, driven by differing redox potentials in each aqueous
phase. An electron donor–acceptor molecule has been directionally inserted into a lipid
bilayer, which on irradiation created a redox potential gradient and ferried protons across the
bilayer establishing a pH gradient. However, the quantum yield for the process was only
0.004.(1785) Calcium ions have been transported across a membrane in a similar system.
(1786) Work to establish longer lived photoinduced charge separated states, which might
lead to greater quantum yields and further applications, has continued.(627, 1787-1807)
Alternating currents have been induced in a protein-based photoelectrochemical cell by
irradiation with intermittent light.(1808) An interesting recent example utilized the light-
induced ring-opening of spiropyrans under ultraviolet light and their ring closure under visible
light illumination. When a membrane doped with spiropyran 165 was illuminated with
ultraviolet light on one side and visible light on the other, the differing proton a nities of ring-
opened and ring-closed spiropyran led to proton shuttling across the membrane and the
generation of an electric potential of ca. 210 mV and pH gradient of ca. 3.6 pH units (Figure
70).(1809)

Figure 70
   

Figure 70. Proton gradient established by spiropyran (165) shuttling upon differential
illumination of the two sides of a membrane. Reprinted with permission from ref 1809.
Copyright 2014 Nature Publishing Group.

9.3 DNA-Based Motors and Switches

Biological building blocks have been used to design and create molecular machines by many
research groups.(1810-1828) A large number of DNA-based molecular motors,(1829-1832)
walkers,(1382, 1833-1838) tweezers,(1839) gears,(1840) springs,(1841) robots,(1842, 1843)
transporters,(1844) and interlocked structures such as DNA rotaxanes and catenanes can be
found in the literature.(1845-1850) All are built by self-assembly, exploiting the sequence-
speci c interactions that bind complementary oligonucleotides together to form double helix
or triplex structures.(1851-1870) Beside base-pairing, other structural motifs can be formed
and used in the design of molecular machines such as the pH-induced self-assembly of C-
rich sequences into i-motif con gurations,(1871, 1872) the ion-induced self-organization of
G-rich sequences into G-quadruplexes,(1873-1876) and the metal–ion bridging of duplex
DNA by T–Hg2+–T or C–Ag+–C complexes.(1877, 1878) Various fuels such as single-
stranded oligonucleotide fragments, pH variation, metal ions, and light have been used to
trigger these DNA devices.(1879-1884) These systems have been used in molecular sensing,
drug delivery and other medical applications, the construction of logic gates, the control of
chemical transformations, and for many other purposes.(1874, 1885-1911)
DNA tweezers represent a simple class of DNA machines.(1884, 1912) They are two-armed
constructs bridged by a DNA linker that can undergo transitions between open and closed
 
states in response to external triggers such as the addition of single-stranded DNA or metal
ions, or a change in pH. Willner et al. reported a biomolecular logic gate based on three
different DNA tweezers A, B, and C. These were activated by different inputs: protons, Hg2+
ions, and nucleic acid strands (Figure 71). The output delivered by this machine depends
both on the inputs provided and its initial internal state. Depending on the input, there are
eight possible con gurations of the three tweezers (open or closed for each). The output
could be studied by measuring the Förster resonance energy transfer (FRET) between
different pairs of uorophore and quenching molecules attached to the arms of each of the
three tweezers. The linker unit is common to all three tweezers, meaning that tweezers A and
B can also be opened by the complementary antilinker. Thus, for any pair of tweezers, there
are two different inputs that cause a change in the state of the device. In total, the device can
adopt 16 different states and can furthermore be used as a memory storage system
because each state and output is dependent not only on the most recent input but also on
past states and inputs.(1913, 1914)

Figure 71

Figure 71. (a) Tweezer A: in the closed form the arms are bound to the linker unit (blue) by
Hg2+ ions through T–Hg2+–T bonds. To open the molecular tweezer, Hg2+ is sequestered by
the addition of cysteine. (b) Tweezer B: in acid the arms form an i-motif, thus releasing the
linker unit, whereas at pH = 7.2, the i-motif is destroyed resulting in the stabilization
of 
the 
closed structure. (c) Tweezer C: the linker unit can be released by a complementary strand,
the antilinker that opens the tweezers. Reprinted with permission from ref 1914. Copyright
2010 American National Academy of Sciences.

DNA machines have been used to regulate enzyme cascade reactions.(1890, 1891) Liu and
co-workers reported a machine containing DNA double crossover (DX) motifs, which formed
two rigid arms, joined by an immobile four-way junction (Figure 72).(1915) A DNA motor that
could switch between stem-loop and double-helix structures, driven by a strand
displacement reaction, was incorporated at the center of the machine to cycle between open
and closed states. This design ampli es the small motion generated by the DNA motor into a
much greater change in separation between the ends of the two arms where glucose
oxidase (GOx) and horseradish peroxidase (HRP) were attached. In this biochemical cascade
system, GOx rst catalyzed the oxidation of glucose to generate gluconic acid and hydrogen
peroxide. Hydrogen peroxide is catalytically reduced by HRP into H2O. At the same time, HRP
turns ABTS2– into ABTS–, which allowed the kinetics of the peroxidase to be monitored. HRP
has a much higher turnover rate then GOx, so the distance hydrogen peroxide must diffuse
has a crucial in uence on the rate of reaction. Therefore, when the two enzymes are
attached to the two arms, the diffusion distance of hydrogen peroxide can be changed from
6 to 18 nm by operation of the DNA motor, regulating the rate of enzymatic reaction.
Sequential addition of fuel and antifuel strands showed that this regulation was reversible.

Figure 72

Figure 72. DNA machine reported by Liu and co-workers, which could be used to regulate an
enzyme cascade reaction. Reprinted with permission from ref 1915. Copyright 2013 Wiley-
VCH Verlag GmbH & Co. KGaA, Weinheim.

Willner and co-workers have used catenated DNA machines as carriers of Au nanoparticles.
(1916) Ordered assemblies of nanoparticles with de ned geometries have recently attracted
a great deal of interest as these engineered nanoparticle systems are anticipated to show
unique plasmonic properties.(1917, 1918) The synthesis and structural characterization of
DNA catenanes has been reported previously,(1847, 1849, 1919, 1920) as has a three-station
directional DNA catenane rotary motor.(1921) A three-ring catenated nanostructure has been
used to program the assembly of two Au nanoparticles (of 5 and 10 nm diameter, Figure 73).
One of the nanoparticles was attached to ring α and the other to ring γ (L1). Ring α included
 
two equivalent domains, I and II, which are complementary to domain III on ring γ. While the
initial duplex between rings β and γ in region III is energetically favored, treatment of the
linear catenated system L1 with a fuel strand (Fu) displaces ring γ, which then translocates
through hybridization to either site I or II of ring α (structures M1 or M2). In the presence of
the appropriate blocker units (B), the directional translocation of ring γ proceeds below or
above the central ring β to yield the con gurations M3 or M4, respectively. The changes in
proximity of the nanoparticles led to changes in plasmonic coupling, which was theoretically
modeled. Such systems could have uses in nanomedicine and intracellular diagnostics.
(1916)

Figure 73

Figure 73. (a) Programmed migration of two Au nanoparticles. (b) STEM images
corresponding to the different structures; the bar corresponds to 20 nm. Reprinted with
permission from ref 1916. Copyright 2013 Nature Publishing Group.

9.4 DNA Walkers

The controlled and predictable strand displacement of DNA and RNA has been used to
construct complex devices.(1369, 1869, 1922-1932) Among them, walkers represent a major
subclass. The basic principle behind 1-D walking is illustrated in Figure 74. A relatively rigid
and stable DNA track functionalized with protruding single-stranded anchorage points
(footholds) is typically used.(1369, 1933) Unlike the direct interactions of biological walker
proteins with polymeric tracks, the footholds are attached to the track and bind the walker
unit by base paring. The walker unit consists of regions with different nucleotide sequences
(feet), which are attached to the track via another DNA fragment (the anchor strand), that can
hybridize with both the walker and one of the footholds leaving a “toehold region” unpaired.
Addition of the fuel strand results in base-pairing with an anchor strand, starting from the
protruding toehold, and forms a more thermodynamically favored waste duplex. The removal
of the anchor strand liberates the foothold and one foot of the walker. Walking is processive
because the other foot is still attached to the track by a holding strand, which provides
additional stabilization. The walker can be reattached to the track via the addition of another
anchor strand.   

Figure 74

Figure 74. Schematic representation of a DNA-based walker and track system. Footholds
protrude from the track as single-stranded DNA fragments. Anchor and holding strands
enable the walker unit to bind to the footholds by hybridization. Areas with functional
importance are labeled, and complementary strands are depicted in the same color for
clarity.

Stimuli-dependent positional DNA switches(1934, 1935) and DNA-based devices performing

multistep organic synthesis while migrating along a track have been reported.(1447) An in
silico “tumbleweed” walker design has also been proposed.(1936) The rst DNA-based
walker was nonautonomous and bipedal and was reported by Sherman and Seeman.(1834)
High dilution conditions were used to prevent the walker from scrambling betwen different
tracks. Sequential addition of two different anchor and fuel strands in an aqueous buffer at
16 °C led to the desired walking motion being obtained. The products were characterized by
polyacrylamide gel electrophoresis (PAGE). The energy required for directional walking was
provided by the additional base-pairing in the waste duplex (red toehold region, Figure 74).
Mechanistically, this walker is an inchworm walker because the leading foot remains the
same throughout the operation. A hand-over-hand DNA walker (the mechanism of operation
of kinesin) has been published by Shin and Pierce who used a similar design.(1833)
Transport of a cargo over a DNA origami tile and the synthesis of nanoparticle sequences
have been reported. It used a DNA origami walker unit with four “feet” for controlled
movement, and three “arms” for picking up cargo, each consisting of single strands of DNA
(Figures 75 and 76).(1455, 1937, 1938) Fuel strands (Fi) were used to drive the motion and to
remove the anchor strands (Ai). Each station was loaded with a distinct gold nanoparticle
cargo and could be switched between states where cargo delivery was possible and where it
was not. By manipulating the selective release of each foot from complementary strands of
DNA on the DNA tile, the movement of the walker could be controlled. When coupled to the
ability of the stations to be switched “on” or “off”, this allowed the formation of eight,
differently composed, noncovalently bound products from the full operational sequence. This
remarkable level of control on the nanoscale shows that the forces of Brownian motion can
be exploited to great effect in the synthesis of complex supramolecular products.
Transportation of a DNA cargo on a DNA origami tile over 16 consecutive steps has
 also
 
been reported.(1939)

Figure 75

Figure 75. (a) Structure of the DNA walker with four “feet” (F1–4) and three “hands” (H1–3).
(b) Movement of walker across the DNA origami tile driven by sequentially added DNA “fuel”
strands labeled FA. (c) Loading of cargo onto DNA walker. Reprinted with permission from
ref 1455. Copyright 2010 Nature Publishing Group.

Figure 76
   

Figure 76. (a) Operation of DNA-based walker. (b) AFM images of walker. Reprinted with
permission from ref 1455. Copyright 2010 Nature Publishing Group.

Turber eld, Reif, and Yan have reported autonomous walking in a DNA-based system.(1379)
Three enzymes, the PfIM I and BstAP I restriction enzymes, and T4 ligase, were required for
autonomous operation. Successive cleavage and ligation of the walker-foothold duplex
resulted in directional walking along the track. Two autonomous burnt-bridges walkers have
been reported using either a restriction endonuclease as an additive(1940) or a walker unit
with intrinsic DNAzyme activity.(1380, 1941, 1942) An autonomous DNA motor whose
propulsion was driven by random polymerization has been synthesized.(1829) DNA strands
were propeled at the growing end of the polymer by the energy gained from hybridization. A
number of enzyme-free autonomous DNA walkers have since been published.
(1836, 1943-1945) Autonomous multipedal walkers(1842, 1946) and walkers performing
autonomous and progressive acylation reactions have been disclosed.(1447) Autonomous
DNA walkers that are driven by pyrene-mediated photocleavage of disul de bonds,(1947) or
photoisomerization-dependent hindrance/exposure of a complementary strand,(1383) have
been designed.

A vital requirement for useful cargo transport is the ability to choose the correct path at a
junction point. The walker should be capable of crossing the junction, and the path choice
should be programmable. Turber eld et al. were able to autonomously regulate the transport
of a DNA cargo on a branched track (Figure 77).(1843) Successive Holliday junctions formed
between the selected fuel, foothold, and the cargo as the walker migrated. These led to
strand exchange (equivalent to junction migration), followed by loop opening, which allowed
the controlled migration of the cargo from one foothold to another. The same group have
since used a single nucleoside, adenosine, to control the route taken at the track junction.
(1381)   

Figure 77

Figure 77. Walker with a choice of path at a junction. (a) Initially cargo resides on position W,
and (b) the use of different set of fuels (F) leads to transport of cargo to either position. A
displacing strand (Dz) was used for the fragmentation of the molecular ensemble and
subsequent analysis of the cargo position. Reprinted with permission from ref 1843.
Copyright 2011 American Chemical Society.

10 Conclusion and Outlook Jump To

Perhaps the best way to appreciate the technological potential of controlled molecular-level
motion is to recognize that molecular machines lie at the heart of every signi cant biological
process. Over billions of years of evolution, nature has not repeatedly chosen this solution for
achieving complex task performance without good reason. In stark contrast to biology, none
of mankind’s fantastic myriad of present-day technologies exploit controlled molecular-level
motion in any way at all: every catalyst, every material, every polymer, every pharmaceutical,
and every reagent all function through their static or equilibrium dynamic properties. When
we learn how to build arti cial structures that can control and exploit molecular-level motion,
and interface their effects directly with other molecular-level substructures and the outside
world, it will potentially impact on every aspect of functional molecule and materials
 design.
 
An improved understanding of physics and biology will surely follow.

As indicated by the many examples that appear in this Review, the future for the eld of
arti cial molecular machines is very bright.(1948) After a somewhat di cult period in the
1990s, when chemists struggled to understand the basic differences between machines at
the macroscopic and nanometer length scales, scientists now have the know-how and
synthetic tools available to enable them to make suitable machine architectures (e.g.,
catenanes, rotaxanes, overcrowded alkenes, molecules that walk upon tracks, etc.). They can
switch the position of components (often by clever manipulation of noncovalent interactions
between the various parts), they understand how to use ratchet mechanisms to create
motor-mechanisms, and they are learning how to introduce them into more complex
molecular machine systems.

Yet there are still several basic challenges to overcome for molecular machines to be able to
ful ll their potential:

(i) In contrast to motor proteins, powered by ATP hydrolysis or proton gradients, there are as
yet no chemically driven synthetic small-molecule motors that can operate autonomously
(i.e., move or rotate directionally as long as a chemical fuel is present), the closest counter-
examples being the Feringa overcrowded alkene motors that rotate continuously under
irradiation with light.(429-453)

(ii) Most of the synthetic molecular machines reported to date are based on only a single
functioning part that moves, stops, uoresces, catalyzes a reaction, etc. To perform tasks
that cannot be accomplished by conventional chemical means, it will be necessary to design
systems with multiple integrated parts, each component performing a dedicated role within
the machine ensemble. This will not be straightforward because unlike a watch where the
second hand, say, does not interfere with the components in the escapement mechanism,
the components of a chemical machine are not easily isolated from each other (or the
environment) and interference from one reactive part of a machine with another will be a
signi cant issue as complexity increases beyond the current rather trivial systems.

(iii) The machines we are familiar with in the macroscopic world are generally stable,
operating unchanged through many cycles, and by and large they do not make “mistakes”.
This contrasts with those in the biological world where the stochastic nature of molecular
dynamics mean that motors stall, or step backward, or detach from tracks, or make errors in
synthesis that are spotted or corrected by other machines. These are intrinsic differences
that require fundamentally different philosophies in terms of the way machines carry out
tasks that chemists have not yet started to tackle.

(iv) The “reading” of a sequence of functional groups on a polymer stand (mRNA or DNA) is
how biological molecular machines are programmed to carry out synthesis operations in the
correct sequence. Although it is possible to use biological polymers to do this, molecular
machines made from DNA are obviously far more limited in terms of operating conditions,
chemical stability, and functionality than wholly synthetic systems. As yet there is
no small-
 
molecule “Turing machine”,(1949) that is, a molecular machine that can read information
from a symbol-encoded molecular strand. Programming of small-molecule machines with
an information-rich non-DNA strand (rather than the sequential addition of chemical stimuli,
say) would be a game-changing development.

There are also issues on which protagonists in the eld have differing points-of-view. The
debate continues over whether it will ultimately prove more productive to build molecular
machines based on macroscopic objects (e.g., Stoddart’s “molecular elevator”(730) and
“molecular pistons”(527) and Tour’s “nanocars”,(1129-1132) etc.) or based on biological
machines (e.g., arti cial systems that seek to reproduce aspects of the behavior of kinesin
(1398-1400) or the ribosome(666)). Certainly mimicking biology is not the only way to
achieve complex functionality: computer chips are manufactured from silicon wafers rather
than being wet and carbon-based like our brains. Yet equally machines have to be designed
according to the environment they are intended to operate in, and there may be reasons why
biology uses motors and not switches, and tracks and not wheels, to transport molecular
cargoes. Or it may be that evolution just did not discover these solutions to such problems
and that mankind, with the whole of the periodic table and known synthetic chemistry to
work with, can. Perhaps the most productive approach will ultimately be found by following
neither of these lines of investigation too closely, for example, by using chemical principles
for “molecular robotics” in which ratcheted motions of molecular components (i.e.,
biologically inspired mechanisms) are used to perform tasks that have their origins in
innovations introduced to advance developments in macroscopic technology (e.g., factory
assembly lines).

The environments that molecular machines can most productively operate in also remain an
open question. Efforts to incorporate molecular machines into regular arrays within
crystalline solids (e.g., MOFs) are progressing apace and should allow tethered molecular
machines to interact effectively with solution- or gas-phase substrates. It will be interesting
to see what applications such systems are being tailored for. Molecular machines mounted
on surfaces should allow for surface properties to be changed in a facile and effective
manner using a minimal amount of the high-cost molecular structures. However, whether
monolayers of molecular machines can be su ciently robust will no doubt be an issue for
practical applications. Most biological molecular machines operate while dissolved in
solution, a situation that has no equivalent for macroscopic mechanical machines, and so
chemists will have to consider carefully how to effectively address and utilize such machines
in that environment. Molecular machines have the potential to act productively under each of
these conditions; what is important is that the application is appropriate for which to use
synthetic molecular machines. In most cases, the cost of synthesis will mean that this will
only be the case if there is no way to carry out the task without using a molecular machine.
So rotaxane-based “molecular muscles” have to compete with shape-memory polymers (or
even stilbene-containing polymers) to be effective, and rotaxane-based switches, which work
through the physical displacement of submolecular components, will have to compete with
electron movements in silicon for applications. Chemical synthesis is one area where
arti cial molecular machines may one day be able to perform tasks that are not possible
  to
achieve using conventional chemical methods, a potential “killer app”!

A quarter-of-a-century after chemists made the rst edging molecular protomachines, the
tantalizing prospect of arti cial molecular machines that can perform useful tasks is moving
ever closer to becoming a reality. Molecular machines with multiple integrated parts are in
design terms a fusion of the familiar with the strange. Examples of mechanical engineering
from the world around us provide a conceptual framework for what we want tiny machines
to achieve. Biology shows us how machines cope with the nature of the environment in
performing tasks at nanometer length scales, and physics explains the often counterintuitive
ways that such small objects must behave. Yet ultimately, while drawing on all of these
disciplines for ideas, guidance, and inspiration, such machines have to be designed, built, and
operated through chemistry, the central science.

Special Issue
This paper is an additional review for Chem. Rev. 2015, 115, 15, “Supramolecular Chemistry”.

The authors declare no competing nancial interest.

Acknowledgment Jump To

We thank the ERC and EPSRC for nancial support and the European Union Seventh
Framework Marie Curie Intra-European Fellowship Program and the Swiss National Science
Foundation for Postdoctoral Fellowships (to S.E.-C. and A.L.N., respectively).

Abbreviations

AB azobenzene

ABTS 2,2′-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid)

AFM atomic force microscope

ATP adenosine triphosphate

BODIPY boron-dipyrromethene
Bpy bipyridine
  
CB cucurbituril

CBPQT cyclobis(paraquat-p-phenylene)

CBS Corey–Bakshi–Shibata

CD circular dichroism or cyclodextrin

CuAAC copper-catalyzed azide–alkyne cycloaddition

Cys cysteine

D displacing strand

DAE diarylethene

DBU 1,8-diazabicycloundec-7-ene

DMAP 4-dimethylaminopyridine

DMF dimethylformamide

DMSO dimethyl sulfoxide

DNA DNA

DNP dioxynaphtalene

DTT dithiothreitol

ee enantiomeric excess

ESIPT excited-state intramolecular proton transfer

EXSY exchange spectroscopy
  
F fuel strand

FRET Förster resonance energy transfer

GOx glucose oxidase

GSCC ground-state coconformation

HBT 2-(2-hydroxyphenyl)-benzothiazole

HOMO highest occupied molecular orbital

HPLC high-performance liquid chromatography

HRP horseradish peroxidase

iPr2NEt N,N-diisopropylethylamine

IR infrared

LB Langmuir–Blodgett

LUMO lowest unoccupied molecular orbital

MOF metal organic framework

Mc merocyanine

MS mass spectrometry

MSCC metastable state coconformation

MscL large-conductance mechanosensitive channel

MSTJ molecular switch tunnel junction
  
MV methyl viologen

NCL native chemical ligation

NMR nuclear magnetic resonance

XPS X-ray photoelectron spectroscopy

PAGE polyacrylamide gel electrophoresis

PEO poly(ethylene oxide)

PLP pyridoxal 5′-phosphate

PMB p-methoxybenzyl

PMMA poly(methyl methacrylate)

R Reynolds number

RET resonance energy transfer

RNA ribonucleic acid

SAM self-assembled monolayer

SEM scanning electron microscope

Sp spiropyran

STM scanning tunneling microscope

T temperature
 TBDMSCl tert-butyldimethylsilyl chloride
  
TCBD tetracyanobutadiene

TFA tri uoroacetic acid

TNF 2,4,7-trinitro-9- uorenone

TON turnover number

TTF tetrathiafulvalene

UV ultraviolet

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57. Arshid A. Ganie, Aadil A. Ahangar, Aijaz A. Dar. Sulfonate···Pyridinium Supramolecular Synthon: A Robust
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58. Morgan E. Howe, Miguel A. Garcia-Garibay. Fluorescence and Rotational Dynamics of a Crystalline
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59. Si Yue Guo, Matthew J. Timm, Kai Huang, John C. Polanyi. Electron Attachment Leads to Unidirectional
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60. Zhi-Xu Zhang, Tie Zhang, Ping-Ping Shi, Wan-Ying Zhang, Qiong Ye, Da-Wei Fu. Anion-Regulated Molecular
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61. Nikolai Kh Petrov, Denis A. Ivanov, Michael V. Al mov. Ultrafast Dynamics of Electronically Excited Host–
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62. Haochuan Chen, Hong Zhang, Xueguang Shao, Wensheng Cai. Tumbling of Anisole Units in Calixarene
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63. Paola Franchi, Cecilia Poderi, Elisabetta Mezzina, Chiara Biagini, Stefano Di Stefano, Marco Lucarini. 2-
Cyano-2-phenylpropanoic Acid Triggers the Back and Forth Motions of an Acid–Base-Operated Paramagnetic
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64. Jens Kügel, Tim Zenger, Markus Leisegang, Matthias Bode. On the Impact of Geometrical Factors on Hot
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65. Jiří Kaleta, Guillaume Bastien, Jin Wen, Martin Dračínský, Edward Tortorici, Ivana Císařová, Paul D. Beale,
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66. Yuanyuan Chang, Zhongyu Wu, Qianxin Sun, Ying Zhuo, Yaqin Chai, Ruo Yuan. Simply Constructed and
Highly E cient Classi ed Cargo-Discharge DNA Robot: A DNA Walking Nanomachine Platform for
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68. Zhao Wang. Selective Conduction of Organic Molecules via Free-Standing Graphene. The Journal of
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69. Stefano Corra, Christiaan de Vet, Jessica Groppi, Marcello La Rosa, Serena Silvi, Massimo Baroncini,
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70. Agostino Galanti, Jasmin Santoro, Rajesh Mannancherry, Quentin Duez, Valentin Diez-Cabanes, Michal
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71. Kanagaraj Naveen, Paramasivan Thirumalai Perumal, Deug-Hee Cho. Domino Palladium-Catalyzed Double
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72. Baihao Shao, Hai Qian, Quan Li, Ivan Aprahamian. Structure Property Analysis of the Solution and Solid-
State Properties of Bistable Photochromic Hydrazones. Journal of the American Chemical Society 2019, 141
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73. Habiburrahman Zul kri, Mark A. J. Koenis, Michael M. Lerch, Mariangela Di Donato, Wiktor Szymański,
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74. He-Ye Zhou, Ying Han, Qiang Shi, Chuan-Feng Chen. Directional Transportation of a Helic[6]arene along a
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75. Jing-Jing Yu, Li-Yang Zhao, Zhao-Tao Shi, Qi Zhang, Gabor London, Wen-Jing Liang, Chuan Gao, Ming-
Ming Li, Xiao-Ming Cao, He Tian, Ben L. Feringa, Da-Hui Qu. Pumping a Ring-Sliding Molecular Motion by a
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76. Hong Zhang, Xueguang Shao, Christophe Chipot, Wensheng Cai. pH-Controlled Fluorescence Probes for
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77. Charlie T. McTernan, Tanya K. Ronson, Jonathan R. Nitschke. Post-assembly Modi cation of Phosphine
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78. Noushaba Nusrat Mafy, Yuna Kim, Reji Thomas, Takehito Akasaka, Nobuyuki Tamaoki. Molecular
Crankshaft Effect Converting Piston-like Molecular Motion to Continuous Rotation of Macro Objects. ACS
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79. Arshid A. Ganie, Pratap Vishnoi, Aijaz A. Dar. Utility of Bis-4-pyridines as Supramolecular Linkers for 5-
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80. Tomoyuki Ikai, Takumu Yoshida, Ken-ichi Shinohara, Tsuyoshi Taniguchi, Yuya Wada, Timothy M. Swager.
Triptycene-Based Ladder Polymers with One-Handed Helical Geometry. Journal of the American Chemical
Society 2019, 141 (11) , 4696-4703. https://doi.org/10.1021/jacs.8b13865

81. Yuree Oh, Kyoung Min Lee, Doyoung Jung, Ji Ae Chae, Hea Ji Kim, Mincheol Chang, Jong-Jin Park,
Hyungwoo Kim. Sustainable, Naringenin-Based Thermosets Show Reversible Macroscopic Shape Changes
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82. Soumalya Bhattacharyya, Aniket Chowdhury, Rupak Saha, Partha Sarathi Mukherjee. Multifunctional Self-
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83. Salvador Pérez-Estrada, Braulio Rodríguez-Molina, Emily F. Maverick, Saeed I. Khan, Miguel A. Garcia-
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84. Tainára Orlando, Paulo R. S. Salbego, Carmen L. R. Taschetto, Helio G. Bonacorso, Nilo Zanatta, Manfredo
Hoerner, Marcos A. P. Martins. Polymorphism in a Rotaxane Molecule: Intra- and Intermolecular
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85. Martina Cirulli, Amanpreet Kaur, James E. M. Lewis, Zhihui Zhang, Jonathan A. Kitchen, Stephen M.
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86. Wei Zheng, Wei Wang, Shu-Ting Jiang, Guang Yang, Zhen Li, Xu-Qing Wang, Guang-Qiang Yin, Ying Zhang,
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Metallacycle-linked Star Polymers Driven by Simple Phosphine Ligand-Exchange Reaction. Journal of the
American Chemical Society 2019, 141 (1) , 583-591. https://doi.org/10.1021/jacs.8b11642

87. Kai-Jen Chen, Ann Chen Tan, Chi-Hsien Wang, Ting-Shen Kuo, Pei-Lin Chen, Masaki Horie. Photoinduced
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88. Henry Hess, Gadiel Saper. Engineering with Biomolecular Motors. Accounts of Chemical Research 2018,
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89. Naoki Ousaka, Kaori Shimizu, Yoshimasa Suzuki, Takuya Iwata, Manabu Itakura, Daisuke Taura, Hiroki
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Racemo Isomerization and Ion-Triggered Springlike Motion of the Racemo-Helicate. Journal of the American
Chemical Society 2018, 140 (49) , 17027-17039. https://doi.org/10.1021/jacs.8b08268
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Feringa. Central-to-Helical-to-Axial-to-Central Transfer of Chirality with a Photoresponsive Catalyst. Journal of
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91. Shinji Ikejiri, Yoshinori Takashima, Motofumi Osaki, Hiroyasu Yamaguchi, Akira Harada. Solvent-Free
Photoresponsive Arti cial Muscles Rapidly Driven by Molecular Machines. Journal of the American Chemical
Society 2018, 140 (49) , 17308-17315. https://doi.org/10.1021/jacs.8b11351

92. Aaron Gerwien, Peter Mayer, Henry Dube. Photon-Only Molecular Motor with Reverse Temperature-
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93. Agostino Galanti, Valentin Diez-Cabanes, Jasmin Santoro, Michal Valášek, Andrea Minoia, Marcel Mayor,
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94. Zoran Kokan, Michał J. Chmielewski. A Photoswitchable Heteroditopic Ion-Pair Receptor. Journal of the
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95. Pei Li, Ganhua Xie, Pei Liu, Xiang-Yu Kong, Yanlin Song, Liping Wen, Lei Jiang. Light-Driven ATP
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96. José F. Rodríguez, Katherine I. Burton, Ivan Franzoni, David A. Petrone, Ina Scheipers, Mark Lautens.
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97. Miyako Tsurunaga, Yusuke Inagaki, Hiroyuki Momma, Eunsang Kwon, Kentaro Yamaguchi, Kenji Yoza,
Wataru Setaka. Dielectric Relaxation of Powdered Molecular Gyrotops Having a Thiophene Dioxide-diyl as a
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98. Mark J. Moran, Mitchell Magrini, David M. Walba, Ivan Aprahamian. Driving a Liquid Crystal Phase
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99. Yansong Ren, Sheng Xie, Erik Svensson Grape, A. Ken Inge, Olof Ramström. Multistimuli-Responsive
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100. Reguram Arumugaperumal, Putikam Raghunath, Ming-Chang Lin, Wen-Sheng Chung. Distinct
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101. Youzhi Xu, Ramandeep Kaur, Bingzhe Wang, Martin B. Minameyer, Sebastian Gsänger, Bernd Meyer,
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Synthesis of [10]Cycloparaphenylene–Fullerene [2]Rotaxanes. Journal of the American Chemical Society 2018,
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103. Anouk S. Lubbe, Christian Böhmer, Filippo Tosi, Wiktor Szymanski, Ben L. Feringa. Molecular Motors in
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104. Michele Bruschini, Gianfranco Ercolani, Stefano Gallina, Paolo Mencarelli. Record Rate Enhancements
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105. Jizhuang Wang, Ze Xiong, Jing Zheng, Xiaojun Zhan, Jinyao Tang. Light-Driven Micro/Nanomotor for
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106. Lindsay J. Schafer, Kevin J. Garcia, Andrew W. Baggett, Taylor M. Lord, Peter M. Findeis, Robert D. Pike,
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107. Ming Zhang, Yong-Guang Jia, Lingyan Liu, Jing Li, X. X. Zhu. Soluble–Insoluble–Soluble Transitions of
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108. Jens Kügel, Markus Leisegang, Matthias Bode. Imprinting Directionality into Proton Transfer Reactions
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109. Rashmi J. Das, Kingsuk Mahata. Synthesis, Photophysical, Electrochemical, and Halochromic Properties
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110. Carlos Romero-Muñiz, Denís Paredes-Roibás, Concepción López, Antonio Hernanz, José María Gavira-
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111. Ruizi Peng, Xiaofang Zheng, Yifan Lyu, Liujun Xu, Xiaobing Zhang, Guoliang Ke, Qiaoling Liu, Changjun
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112. Lais S. Matos, Ronaldo C. Amaral, Neyde Y. Murakami Iha. Visible Photosensitization of trans-
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113. Ronaldo C. Amaral, Lais S. Matos, Kassio P. S. Zanoni, Neyde Y. Murakami Iha. Photoreversible
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115. Ruth Dorel, Carla Miró, Yuchen Wei, Sander J. Wezenberg, Ben L. Feringa. Cation-Modulated Rotary
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116. Yoshinori Takashima, Yuki Hayashi, Motofumi Osaki, Fumitoshi Kaneko, Hiroyasu Yamaguchi, Akira
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117. Sergey Simonov, Leokadiya Zorina, Pawel Wzietek, Antonio Rodríguez-Fortea, Enric Canadell, Cécile
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118. Ren-Tsung Wu, Xiaodong Chi, Takehiro Hirao, Vincent M. Lynch, Jonathan L. Sessler. Supramolecular
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119. Jiawen Chen, Jérôme Vachon, Ben L. Feringa. Design, Synthesis, and Isomerization Studies of Light-
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120. Hang Yin, Roselyne Rosas, Didier Gigmes, Olivier Ouari, Ruibing Wang, Anthony Kermagoret, David
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121. Tania Neva, Thais Carmona, Juan M. Benito, Cédric Przybylski, Carmen Ortiz Mellet, Francisco
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122. Christian Petermayer, Henry Dube. Indigoid Photoswitches: Visible Light Responsive Molecular Tools.
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123. Kazuto Takaishi, Makoto Yasui, Tadashi Ema. Binaphthyl–Bipyridyl Cyclic Dyads as a Chiroptical Switch.
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124. Shunsuke Kuwahara, Yuri Suzuki, Naoya Sugita, Mari Ikeda, Fumi Nagatsugi, Nobuyuki Harada, Yoichi
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125. Roland Wilcken, Monika Schildhauer, Florian Rott, Ludwig Alexander Huber, Manuel Guentner, Stefan
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127. Toru Amaya, Hayato Fujimoto, Takahiro Tanaka, Toshiyuki Moriuchi. Synthesis and Isomerization
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128. Nikita Mittal, Merve S. Özer, Michael Schmittel. Four-Component Catalytic Machinery: Reversible Three-
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129. Paul M. Bogie, Lauren R. Holloway, Yana Lyon, Nicole C. Onishi, Gregory J. O. Beran, Ryan R. Julian,
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130. Richard J. Hooley. Rings and Things: The Magic of Building Self-Assembled Cages and Macrocycles.
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131. Jinqiao Dong, Xu Li, Kang Zhang, Yi Di Yuan, Yuxiang Wang, Linzhi Zhai, Guoliang Liu, Daqiang Yuan,
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132. Ian G. Powers, John M. Andjaba, Xuyi Luo, Jianguo Mei, Christopher Uyeda. Catalytic Azoarene
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133. Tomoyuki Ikai, Takumu Yoshida, Seiya Awata, Yuya Wada, Katsuhiro Maeda, Motohiro Mizuno, Timothy
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137. Timothy A. Barendt, Ilija Rašović, Maria A. Lebedeva, George A. Farrow, Alexander Auty, Dimitri
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140. Ning-Ning Yang, Jia-Jia Fang, Qi Sui, and En-Qing Gao . Incorporating Electron-De cient Bipyridinium
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141. Oleksandr Stetsovych, Pingo Mutombo, Martin Švec, Michal Šámal, Jindřich Nejedlý, Ivana Císařová,
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144. Anna Walczak and Artur R. Stefankiewicz . pH-Induced Linkage Isomerism of Pd(II) Complexes: A
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146. Fu Huang, Guangxia Wang, Lishuang Ma, Ying Wang, Xuebo Chen, Yanke Che, and Hua Jiang . Molecular
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147. Laurianne Wojcik, François Michaud, Sébastien Gauthier, Nolwenn Cabon, Pascal Le Poul, Frederic
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148. Hitoshi Ube, Ryo Yamada, Jun-ichi Ishida, Hiroyasu Sato, Motoo Shiro, and Mitsuhiko Shionoya . A
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150. Mariangela Di Donato, Michael M. Lerch, Andrea Lapini, Adèle D. Laurent, Alessandro Iagatti, Laura
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151. Zarina M. Bikbaeva, Daniil M. Ivanov, Alexander S. Novikov, Ivan V. Ananyev, Nadezhda A. Bokach, and
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152. Qi Sui, Ning-Ning Yang, Teng Gong, Peng Li, Ye Yuan, En-Qing Gao, Lin Wang. Impact of Lattice Water on
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154. Antoine Goujon, Thomas Lang, Giacomo Mariani, Emilie Moulin, Gad Fuks, Jesus Raya, Eric Buhler,
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155. Elton Oyarzua, Jens Honore Walther, Constantine M Megaridis, Petros Koumoutsakos, and Harvey A.
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156. Elizabeth Elacqua, Xiaolong Zheng, and Marcus Weck . Light-Mediated Reversible Assembly of
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157. Ting Wang, Cheng Wang, Shuai Zhou, JianHua Xu, Wei Jiang, LingHua Tan, and JiaJun Fu . Nanovalves-
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158. Yuping Wang, Marco Frasconi, and J. Fraser Stoddart . Introducing Stable Radicals into Molecular
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159. Dustin Chen and Qibing Pei . Electronic Muscles and Skins: A Review of Soft Sensors and Actuators.
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160. Ivica Cvrtila, Hugo Fanlo-Virgós, Gaël Schaeffer, Guillermo Monreal Santiago, and Sijbren Otto . Redox
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161. Ruizi Peng, Huijing Wang, Yifan Lyu, Liujun Xu, Hui Liu, Hailan Kuai, Qiaoling Liu, and Weihong Tan .
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164. Christopher J. Martin, Alan T. L. Lee, Ralph W. Adams, and David A. Leigh . Enzyme-Mediated Directional
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165. Chuhan Zong, Michelle J. Wu, Jason Z. Qin, and A. James Link . Lasso Peptide Benenodin-1 Is a
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166. Jiří Kaleta, Jiawen Chen, Guillaume Bastien, Martin Dračínský, Milan Mašát, Charles T. Rogers, Ben L.
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167. Chuan Gao, Zhou-Lin Luan, Qi Zhang, Si-Jia Rao, Da-Hui Qu, and He Tian . A Braided Hetero[2]
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169. Benjamin Doistau, Lorien Benda, Jean-Louis Cantin, Lise-Marie Chamoreau, Eliseo Ruiz, Valérie Marvaud,
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170. Xiang Wang, Barbara Wicher, Yann Ferrand, and Ivan Huc . Orchestrating Directional Molecular Motions:
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172. Timothy A. Barendt, Liliana Ferreira, Igor Marques, Vítor Félix, and Paul D. Beer . Anion- and Solvent-
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174. Qiang Shi and Chuan-Feng Chen . Switchable Complexation between (O-Methyl)6-2,6-helic[6]arene and
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176. Krishna Kanti Dey and Ayusman Sen . Chemically Propelled Molecules and Machines. Journal of the
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179. Liu-Pan Yang, Fei Jia, Jie-Shun Cui, Song-Bo Lu, and Wei Jiang . Light-Controlled Switching of a Non-
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180. Giuseppe Romanazzi, Leonardo Degennaro, Piero Mastrorilli, and Renzo Luisi . Chiral Switchable
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181. Bartosz Krajnik, Jiawen Chen, Matthew A. Watson, Scott L. Cockroft, Ben L. Feringa, and Johan Hofkens
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183. Margherita De Rosa, Carmen Talotta, Carmine Gaeta, Annunziata Soriente, Placido Neri, Sebastiano
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192. Dawei Zhang, Alexandre Martinez, and Jean-Pierre Dutasta . Emergence of Hemicryptophanes: From
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197. Stefano Di Stefano and Gianfranco Ercolani . Statistical Ring Catenation under Thermodynamic Control:
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775. Jan Maciejewski, Adam Sobczuk, Alexis Claveau, Adrien Nicolai, Riccardo Petraglia, Luca Cervini, Emilie
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776. Marianna Rossetti, Simona Ranallo, Andrea Idili, Giuseppe Palleschi, Alessandro Porchetta, Francesco
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794. Salma Kassem, Thomas van Leeuwen, Anouk S. Lubbe, Miriam R. Wilson, Ben L. Feringa, David A. Leigh.
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795. Leilei Xu, Fangzhi Mou, Haotian Gong, Ming Luo, Jianguo Guan. Light-driven micro/nanomotors: from
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796. Merve S. Özer, Anup Rana, Pronay K. Biswas, Michael Schmittel. Four-component zinc-porphyrin/zinc-
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797. Lauren R. Holloway, Paul M. Bogie, Richard J. Hooley. Controlled self-sorting in self-assembled cage
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798. Bryan Lau, Ofer Kedem, James Schwabacher, Daniel Kwasnieski, Emily A. Weiss. An introduction to
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800. Marcos A. P. Martins, Geórgia C. Zimmer, Leticia V. Rodrigues, Tainára Orlando, Lilian Buriol, Mateo
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801. Jijun Yan, Chuanqing Kang, Zheng Bian, Rizhe Jin, Xiaoye Ma, Lianxun Gao. Supramolecular self-
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802. Giacomo Mariani, Antoine Goujon, Emilie Moulin, Michel Rawiso, Nicolas Giuseppone, Eric Buhler.
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804. Asha Brown, Thomas Lang, Kathleen M. Mullen, Paul D. Beer. Active metal template synthesis of a
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805. Tomoyuki Ikai, Yuya Wada, Seiya Awata, Changsik Yun, Katsuhiro Maeda, Motohiro Mizuno, Timothy M.
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806. Ashot Gevorgyan, Satenik Mkrtchyan, Tatevik Grigoryan, Viktor O. Iaroshenko. Disilanes as oxygen
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807. J. Śniechowska, P. Paluch, M. J. Potrzebowski. Structure and dynamics processes in free-base chlorins
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808. Alberto Martinez-Cuezva, Adrian Saura-Sanmartin, Tomas Nicolas-Garcia, Cristian Navarro, Raul-Angel
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809. Kelong Zhu, Giorgio Baggi, V. Nicholas Vukotic, Stephen J. Loeb. Reversible mechanical protection:
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810. Haohao Fu, Xueguang Shao, Christophe Chipot, Wensheng Cai. The lubricating role of water in the
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813. Hendrik V. Schröder, Sebastian Sobottka, Maite Nößler, Henrik Hupatz, Marius Gaedke, Biprajit Sarkar,
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816. Zhong-Liang Gong, Yu-Wu Zhong, Jiannian Yao. Regulation of intra- and intermolecular Pt–Pt and π–π
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