Brief Discussion about How to Determine Crystal Structure Using X-ray Diffraction

Keywords: crystal structure, lattice, unit cell, symmetry, lattice parameter, history of X-rays, production of X-ray, Bragg s law, X-ray powder diffraction Abstracts: Chemistry deals with chemical structures and elements! "raditional ways to determine chemical structure are mainly by imagination and e#periment! But now, with the de$eloped X-ray diffraction crystallography, we can directly %see% the structure! &e discuss the de$elopment of crystallography, including the introduction of crystals and its structure determination using X-ray diffraction! 't last we briefly introduce the ad$anced structure determining method S"( and how it wor)s!

1. Introduction of crystal and its structure

*!*! Definition and general properties of crystals ' crystal +crystalline solid, is a solid material whose constituent atoms, molecules, or ions are arranged in an ordered pattern e#tending in all three spatial dimensions! -n addition to their microscopic structure, large crystals are usually identifiable by their macroscopic geometrical shape, consisting of flat faces with specific, characteristic orientations! 1.2. Introduction of crystal structure &e can always find crystals symmetric! "he symmetry obser$ed in crystals as e#hibited by their crystal faces is due to the ordered internal arrangement of atoms in a crystal structure! "his arrangement pattern of atoms in crystals is called lattice. ' lattice is a periodic array of lattice points! -t is a mathematic abstraction used to describe the translational symmetry of a periodic structure! ' crystal is characteri.ed by both translational and orientational long-range order, which restricts the symmetry of a unit cell! "ranslational symmetry means unit cells repeats in three dimensions, while orientation means there is no rotation or reflection in the unit cell repeating! "o describe the crystal lattice, we build up coordinate system within the crystal! /or 0dimensional space lattices we need 0 or in some cases 1 crystallographic a#es that define directions within the crystal lattices! "he a#es are defined based on the symmetry of the lattice and the crystal! 2ach crystal system has different con$entions that define the orientation of the a#es, and the relati$e lengths of the a#es! 2dges of length a, b, c, angles between three coordinate a#is, are lattice parameters for unit

cells of the lattice! /or each lattice there are multiple possible unit cells! But practically, we often encounter unit cells that contain only one lattice point, which called primiti$e cells! "here are *1 possible uni3ue lattices +fall into 4 lattice systems, in three dimension, called Bra$ais lattices, as shown in the following table!
"he 4 lattice systems +/rom least to most symmetric, *! "riclinic+ , +none,

primiti$e+a5,

6! (onoclinic +* diad,

primiti$e+m5, 0! 7rthorhombic +0 perpendicular diads,

base-centered+mC,

primiti$e+o5, 1! 8hombohedral +* triad,

base-centered+oC,

body-centered+o-,

face-centered+o/,

primiti$e+h8, 9! "etragonal +* tetrad,

primiti$e+t5,

body-centered+t-,

:! He#agonal +* he#ad,

primiti$e+h5, 4! Cubic +1 triads, bod face

primiti$e+c5,

y-centered +c-,

-centered +c/,

"he faces of an alternati$e shaped crystal can always be labeled with respect to the crystal a#es! 2ach face is gi$en with a set of three integers +h ) l,, called (iller indices, in which h, ), l are reciprocals of the fractions of a unit cell edge, a, b and c on the coordinate a#es! "he corresponding plane intercepts the $ector determine by the indices! "he directions in the coordination are also labeled with (iller indices in ; < brac)ets, for the difference response of a crystal to an e#ternal stimulus in different directions! Symmetry can always be found in crystal lattice, as mention at the beginning! /or three-dimensional lattice, there are typically two symmetric operations: reflection and rotation! 8eflection concerns with mirror images, results in chirality or handedness, is denoted m! 8otation should be handled according to a certain a#is! -f the rotation regenerate the initial shape in 0:=>?0 degree, then the corresponding a#is are called a triad a#is or a three-fold a#is! Similarly, there are monad, diad, pentad, he#ad a#is, labeled by *,6,1,9,:! '#is of in$ersion are labeled ! "he collection of symmetry elements of an isolated shape is called the point group and the combination of elements is called the general point symmetry of the shape! "he symmetry elements that characteri.e the point group are collected together into a point group symbol! "hus an e3uilateral triangle has the point symmetry, 0m, in which 0 stands for triad a#is and m stands for mirror! 1.3. Parameters for lattice symmetric determination 'lthough the magnitude of any property is related to the atom types that ma)e up the solid, the e#istence of absence of a property is often controlled by the symmetry of the solid! @eumannAs principle states that the symmetry elements of any physical property

of a crystal must include the symmetry elements of the point group of the crystal! Different symmetry accounts for different physical properties! "hus we can determine the microscopic crystal structure with the macroscopic properties! Directional properties can shows the symmetry! /or e#ample, thermal e#pansion can be used to determine whether there is a center of symmetry! 'nother, which will be discussed later, is the diffraction of X-rays! "he refraction inde# of a material is sensiti$e to crystal structure! X-rays from different direction yields different refraction inde#!

2. A history of X-ray crystallogra hy

2.1. !he in"estigation of crystals -n *4th century, Bohannes Cepler hypothesi.ed in his wor) Strena seu de @i$e Se#angula +*:**, that the he#agonalsymmetry of snowfla)e crystals was due to a regular pac)ing of spherical water particles! "hat is the beginning of the e#ploration into the world of crystal! Crystal symmetry was first in$estigated e#perimentally by Danish scientist @icolas Steno +*::D,, who showed that the angles between the faces are the same in e$ery e#emplar of a particular type of crystal, and by 8enE Bust HaFy +*4G1,, who disco$ered that e$ery face of a crystal can be described by simple stac)ing patterns of bloc)s of the same shape and si.e! Hence, &illiam Hallowes (iller in *G0D was able to gi$e each face a uni3ue label of three small integers, the (iller indices which are still used today for identifying crystal faces! HaFy s study led to the correct idea that crystals are a regular three-dimensional array +a Bra$ais lattice, of atoms and moleculesH a single unit cell is repeated indefinitely along three principal directions that are not necessarily perpendicular! -n the *Dth century, a complete catalog of the possible symmetries of a crystal was wor)ed out by Bohan Hessel, 'uguste Bra$ais, 2$graf /edoro$, 'rthur SchInflies and &illiam Barlow! /rom the a$ailable data and physical reasoning, Barlow proposed se$eral crystal structures in the *GG=s that were $alidated later by X-ray crystallographyH howe$er, the a$ailable data were too scarce in the *GG=s to accept his models as conclusi$e! 2.2. !he disco"ery of X-ray X-rays were disco$ered by &ilhelm Conrad 8Intgen in *GD9, Just as the studies of crystal symmetry were being concluded! 5hysicists were initially uncertain of the nature of X-rays, although it was soon suspected that they were wa$es of electromagnetic radiation! "he X-rays are initially accepted as electromagnetic wa$es! Howe$er, X-rays are composed of photons, and thus are not only wa$es of

electromagnetic radiation but also e#hibit particle-li)e properties! "he photon concept was introduced by 'lbert 2instein in *D=9, but it was not broadly accepted until *D66, when 'rthur Compton confirmed it by the scattering of X-rays from electrons! "herefore, these particle-li)e properties of X-rays, such as their ioni.ation of gases, caused &illiam Henry Bragg to argue in *D=4 that X-rays were not electromagnetic radiation! @e$ertheless, Bragg s $iew was not broadly accepted and the obser$ation of X-ray diffraction in *D*6 confirmed for most scientists that X-rays were a form of electromagnetic radiation! 2.3. !he de"elo ment of X-ray diffraction analysis "he idea that crystals could be used as a diffraction grating for X-rays arose in *D*6 in a con$ersation between 5aul 5eter 2wald and (a# $on Kaue! Lon Kaue de$eloped a law that connects the scattering angles and the si.e and orientation of the unit-cell spacing in the crystal, for which he was awarded the @obel 5ri.e in 5hysics in *D*1! 'fter Lon Kaue s pioneering research, the field de$eloped rapidly, most notably by physicists &illiam Kawrence Bragg and his father &illiam Henry Bragg! -n *D*6M *D*0, the younger Bragg de$eloped Bragg s law, which connects the obser$ed scattering with reflections from e$enly spaced planes within the crystal! "he Braggs, father and son, shared the *D*9 @obel 5ri.e in 5hysics for their wor) in crystallography! "he earliest structures were generally simple and mar)ed by onedimensional symmetry! Howe$er, as computational and e#perimental methods impro$ed o$er the ne#t decades, it became feasible to deduce reliable atomic positions for more complicated two- and three-dimensional arrangements of atoms in the unit-cell! "he potential of X-ray crystallography for determining the structure of molecules and minerals was reali.ed immediately! "he earliest structures were simple inorganic crystals and minerals, but e$en these re$ealed fundamental laws of physics and chemistry! "he first atomic-resolution structure to be determined in *D*1 was that of table salt! "he distribution of electrons in the table-salt structure showed that crystals are not necessarily composed of co$alently bonded molecules, and pro$ed the e#istence of ionic compounds!

3. An insight into X-ray diffraction: demonstrated with an instance

3.1 !he roduction of X-rays "he production of #-rays re3uires a rapidly mo$ing stream of electrons that are suddenly decelerated or stopped! "he source of electrons is the cathode, or negati$e

electrode! 2lectrons are stopped or decelerated by the anode, or positi$e electrode! 2lectrons mo$e between the cathode and the anode because there is a potential difference in charge between the electrodes!

X-rays are produced by two main mechanisms and come in two $arieties NN characteristic and bremsstrahlung #-rays! 3.1.1 #remsstrahlung $-rays Bremsstrahlung% means %bra)ing radiation% and is retained from the original Oerman to describe the radiation which is emitted when electrons are decelerated or %bra)ed% when they are fired at a metal target! 'ccelerated charges gi$e off electromagnetic radiation,and when the energy of the bombarding electrons is high enough, that radiation is in the #-ray region of the electromagnetic spectrum! -t is characteri.ed by a continuous distribution of radiation which becomes more intense and shifts toward higher fre3uencies when the energy of the bombarding electrons is increased! "he cur$es abo$e are from the *D*G data of Ulrey, who bombarded tungsten targets with electrons of four different energies!

3.1.2

%haracteristic $-rays

Characteristic #-rays are emitted from hea$y elements when their electrons ma)e transitions between the lower atomic energy le$els! "he characteristic #-rays emission which shown as two sharp pea)s in the illustration at left occur when $acancies are produced in the nP* or C-shell of the atom and electrons drop down from abo$e to fill the gap! "he #-rays produced by transitions from the nP6 to nP* le$els are called Calpha #-rays, and those for the nP0-Q* transiton are called C-beta #-rays! X-ray production typically in$ol$es bombarding a metal target in an #-ray tube with high speed electrons which ha$e been accelerated by tens to hundreds of )ilo$olts of potential! "he bombarding electrons can eJect electrons from the inner shells of the atoms of the metal target! "hose $acancies will be 3uic)ly filled by electrons dropping down from higher le$els, emitting #-rays with sharply defined fre3uencies associated with the difference between the atomic energy le$els of the target atoms! "he fre3uencies of the characteristic #-rays can be predicted from the Bohr model! (oseley measured the fre3uencies of the characteristic #-rays from a large fraction of the elements of the periodic table and produces a plot of them which is now called a %(oseley plot %! "he #-ray energy is proportional to the atom s R! &here the incident electrons ha$e energies less than the electron binding energy, there will be no characteristic radiation emitted! 's the electron energy increases past the threshold le$el, the ma#imum le$el of characteristic radiation reaches 6=S of total production, and then starts to fall to *=S in the 9=-*== )eL range and 0S in the 6== )eL range! -n the mega$oltage range, characteristic radiation is negligible!

3.2 #ragg&s 'aw

-n physics, Bragg s law gi$es the angles for coherent and incoherent scattering from a crystal lattice! &hen X-rays are incident on an atom, they ma)e the electronic cloud mo$e as does any electromagnetic wa$e! "he mo$ement of these charges reradiates wa$es with the same fre3uency +blurred slightly due to a $ariety of effects,H this phenomenon is )nown as 8ayleigh scattering +or elastic scattering,! "he scattered wa$es can themsel$es be scattered but this secondary scattering is assumed to be negligible! ' similar process occurs upon scattering neutron wa$es from the nuclei or by a coherent spin interaction with an unpaired electron! "hese re-emitted wa$e fields interfere with each other either constructi$ely or destructi$ely +o$erlapping wa$es either add together to produce stronger pea)s or subtract from each other to some degree,, producing a diffraction pattern on a detector or film! "he resulting wa$e interference pattern is the basis of diffraction analysis! "his analysis is called Bragg diffraction! -n Bragg s picture, a number of sets of e3ui-spaced parallel lines are shown which pass through all the scatterers, and the formed plane would act as a partial reflectors for X-rays! &hen a parallel wa$e train falls on a specularly reflecting surface the conditions are such that reflection from any two points of the surface will gi$e rays in phase in the reflected beam! 's $iewed aside in the following diagram:

"he phase difference for rays reflected from ' and B is BC-CD P=! Howe$er this condition could be true for any $alue of T! But actually it is only for special angles that the reflection can occur, as )now from e#periment! Here is the deri$ation:

"he two parallel rays the reflection, thus

are in phase after

where n is an integer! 'pparently, we ha$e

"hen with trigonometry we ha$e adJacent planes! "hen we ha$e where d accounts for the distance between

3.3 #rief introduction of X-ray diffraction in crystal structure determination: ta(ing X-ray owder diffraction as e$am le

-n practice, this would be a time consuming operation to reorient the crystal, measure the angle 3, and determine the d-spacing for all atomic planes! ' faster way is to use a method called the powder method! -n this method, a mineral is ground up to a fine powder! -n the powder, are thousands of grains that ha$e random orientations! &ith random orientations we might e#pect most of the different atomic planes to lie parallel to the surface in some of the grains! "hus, by scanning through an angle 3 of incident X-ray beams form = to D=>, we would e#pect to find all angles where diffraction has occurred, and each of these angles would be associated with a different atomic spacing! "he instrument used to do this is an #-ray powder diffractometer! -t consists of an Xray tube capable of producing a beam of monochromatic X-rays that can be rotated to produce angles from = to D=>! ' powdered mineral sample is placed on a sample stage so that it can be irradiated by the X-ray tube! "o detect the diffracted X-rays, an electronic detector is placed on the other side of the sample from the X-ray tube, and it too is allowed to rotate to produce angles from = to D=>! "he instrument used to rotate both the X-ray tube and the detector is called a goniometer! "he goniometer )eeps trac) of the angle 3, and sends this information to a computer, while the detector records the rate of X-rays coming out the other side of the sample +in units of counts?sec, and sends this information to the computer!

'fter a scan of the sample the X-ray intensity can be plotted against the angle 3 +usually reported as 63 because of the way older diffractometers were made, to produce a chart, li)e the one shown here! "he angle 63 for each diffraction pea) can then be con$erted to d-spacing, using the Bragg e3uation! 7ne can then wor) out the crystal structure and associate each of the diffraction pea)s with a different atomic plane in terms of the (iller -nde# for that plane +h)l,! ' group )nown as the Boint Committee on 5owder Diffraction Standards +BC5DS, has collected data such as this on thousands of crystalline substances! "his data can be obtained as the BC5DS 5owder Diffraction /ile! Since e$ery compound with the same crystal structure will produce an identical powder diffraction pattern, the pattern ser$es as )ind of a %fingerprint% for the substance, and thus comparing an un)nown mineral to those in the 5owder Diffraction file enables easy identification of the un)nown! &e will see how this is done in our laboratory demonstration!

3.) Primary databases (! Lan! Kau using continuous X-rays irradiate single crystal copper sulfate to get diffraction spec)le is the first time XD8 used incrystal research! Kaue also deri$ed Kaue diffraction e3uation to research crystal structure! /rom then on, many physicist and chemists researched inorganic crystal structure Xray diffraction! "he last century 6=s, scientists carry out the wor) of crystal structure determination of organic compounds, in *D0=s begin to study the structure of pepsin, insulin and other proteins and biological crystals using the X-ray! 'fter a lot of scientists efforts, people accumulated a lot of crystal structure data, there are now about 6=====, and the established fi$e main crystallographic database in the world!

Crystallography 7pen Database +C7D, 5rotein Data Ban) +5DB, @ucleic 'cid Databan) +@DB, Cambridge Structural Database +CSD, -norganic Crystal Structure Database +-CSD, Biological (acromolecule Crystalli.ation Database +B(CD,

3.* limitations 's the crystal s repeating unit, its unit cell, becomes larger and more comple#, the atomic-le$el picture pro$ided by X-ray crystallography becomes less well-resol$ed +more %fu..y%, for a gi$en number of obser$ed reflections! "wo limiting cases of Xray crystallographyN%small-molecule% and %macromolecular% crystallographyNare

often discerned! Small-molecule crystallography typically in$ol$es crystals with fewer than *== atoms in their asymmetric unitH such crystal structures are usually so well resol$ed that the atoms can be discerned as isolated %blobs% of electron density! By contrast, macromolecular crystallography often in$ol$es tens of thousands of atoms in the unit cell! Such crystal structures are generally less well-resol$ed +more %smeared out%,H the atoms and chemical bonds appear as tubes of electron density, rather than as isolated atoms! -n general, small molecules are also easier to crystalli.e than macromoleculesH howe$er, X-ray crystallography has pro$en possible e$en for $iruses with hundreds of thousands of atoms!

) +ome ad"anced method to determined crystal structure

"here are many disad$antages in X-ray deflection, li)e one of which is it can not determine the structure of certain area! But ad$anced technics bring possibilities to get insight into the microscopic world! ' scanning tunneling microscope +S"(, is an instrument for imaging surfaces at the atomic le$el! -ts de$elopment in *DG* earned its in$entors, Oerd Binnig and Heinrich 8ohrer +at -B( RFrich,, the @obel 5ri.e in 5hysics in *DG:! /or an S"(, good resolution is considered to be =!* nm lateral resolution and =!=* nm depth resolution! &ith this resolution, indi$idual atoms within materials are routinely imaged and manipulated! "he S"( can be used not only in ultra-high $acuum but also in air, water, and $arious other li3uid or gas ambients, and at temperatures ranging from near .ero )el$in to a few hundred degrees Celsius! "he S"( is based on the concept of 3uantum tunneling! &hen a conducting tip is brought $ery near to the surface to be e#amined, a bias +$oltage difference, applied between the two can allow electrons to tunnel through the $acuum between them! "he resulting tunneling current is a function of tip position, applied $oltage, and the local density of states +KD7S, of the sample! -nformation is ac3uired by monitoring the current as the tip s position scans across the surface, and is usually displayed in image form! S"( can be a challenging techni3ue, as it re3uires e#tremely clean and stable surfaces, sharp tips, e#cellent $ibration control, and sophisticated electronics, but nonetheless many hobbyists ha$e built their own!

8eference:
*! Understanding Single-Crystal X-Ray Crystallography, Dennis &! Bennett 6!An Introduction to X-Ray Crystallography, (ichael ( &oolfson 0!Sturcture of Crystals, B!C!LainshteinUL!(!/rid)inUL!K!-ndenbom 1!Crystals and Crystal Structures, 8ichard "illey 9!&ebsites:

http:??www!tulane!edu?Vsanelson?eens6**?inde#!html http:??www!allaboutgemstones!com?crystalWforms!html http:??en!wi)ipedia!org http:??powertreasuresonline!com? http:??www!chem!o#!ac!u)? http:??www!wi)iradiography!com?page?CharacteristicsXandX5roductionXofXX-rays http:??www!o#ford-instruments!com?products?spectrometers?#-ray-fluorescence-analy.er http:??materials!binghamton!edu?labs?#ray?#ray!html