11th PhD seminar, Garching, September 12th 2008

Introduction to Computational Chemistry for Experimental Chemists... (Part 1/2)

Dr. Markus Drees, TU Mnchen
Universitt Regensburg Universitt Augsburg

Outline of today A) What is computational chemistry?

Definitions - Methods - Types of calculations

B) From a Formula to calculated Properties

Graphical interfaces - input files - basis sets - calculation - output analysis

C) How to evaluate Mechanisms with Computational Chemistry

Mechanism theorems - energetic evaluation - transition states and kinetics

D) A Word on Costs and Accuracy

Phrases of prejudice - computational costs - accuracy

A) What is computational chemistry?

Definitions - Methods - Types of calculations

A) What is Computational Chemistry? - Definitions

Chemistry, that is investigated in silico

Computational Chem.
- Simulation / Modelling of structural features - Calculation of molecular properties and energies - Ab initio (simulation from the beginning) and molecular mechanics -Quantum / Molecular dynamics ==> related field: theoretical chemistry

Cheminformatics
- Storage and analysis of compound data (databases!) - Virtual screening (identification of targets in pharmacy) - QSAR => quantitative structureactivity relationship ==> related field: statistics

A) What is Computational Chemistry? - Method classes (I)

Molecular Mechanics (force field)
Atoms and bonds as ball and spring Needs parameters for radii, bonds, angles, dihedrals and non-bonding contacts from experiments (force field) Optimizations in reducing bond-streching Seperates nuclei and electrons

Ab initio (Latin: from the beginning)

Deals with Electron density and wave functions as descriptions for the electrons, no data from experiments needed

No treatment of electron densities or wave Optimizations in forces and energies, functions, no direct prediction of properties derived from the electron density Very fast calculations of structures, also for big systems (atoms > 10,000) Also suitable for molecular dynamics (time-dependent structure prediction), but Difficulties in bond-breaking reactions Examples: UFF, MM2 - MM4, CHARMM, AMBER, OPLS Solvation of the Schrdinger equations and determination of the suitable Hamiltonian (H! = E!) High computational costs likely (especially when electron correlation is induced) Examples: HF, MP2-MP4, CI, CC, (DFT) (sometimes also semiempric calculations)

A) What is Computational Chemistry? - Method classes (II) Semiempirics

Mixture of force-field and ab initio calculation Reduction of the system (Hueckel => only valid for "-electrons) Treatment only of valence eletrons (AM1, MNDO, PM3-PM5) Simple Hamiltonian used to solve a simplier Schroedinger equations in combination with force-field parameters ==> not always suitable for all configurations of an element Fast calculations in comparison the ab initio methods Also suitable for molecular dynamics (time-dependent structure prediction), even for reaction prediction

Density functional theory

Correlation between wave function and electron density (Hohenberg-Kohn) => All physical properties derived from wave functions are also predictable by electron density Problem: Exact functional to calculate electron correlation and exchange is not exactly known! => All DFT methods are approximations of this functional Good treatment of electron correlation (better than in HF, while with less cost than in post-HF methods) Problems with intermolecular interactions (dispersion, van der Waals-forces) Examples:B3LYP, PBE, BLYP, BP88, O3LYP, MPW1K, ...

A) What is Computational Chemistry? - Method classes (III) QM/MM (or Hybrid Calculation)
Useful for larger molecules (biochemistry!) or solvent systems: Distribution of the molecule into at least two parts: a QM part and a MM part QM: normally the reaction center (higher accuracy) MM: expresses the sterically more demanding sites that play only the role of spectators. Example: ONIOM

A) What is Computational Chemistry? - Calculation types (I)

- Geometry optimization of a ground state Minimizes the energy, while intramoleculare forces are brought to 0. Needs a structural starting point from the user. Delivers the best structure an its total electronic energy

- Frequency calculation Delivers the force constants and the vibrational frequencies Simulations IR and Raman Spectra Distinguishes a ground state from a transition state (number of negative frequencies) Delivers thermodynamical data (enthalpy, entropy, free energy, heat capacities, ...) - Search for a transition state of a chemical reaction Optimizies the initial structure, while intramoleculare forces are brought to 0. Follows the most negative frequency of the initial structure Some algorithms determine the initial TS structure from the geometry of the educt(s) and product(s) Determination of barrier heights and kinetics (in combination with frequency calculation)

To be co ns id er ed to da y!

A) What is Computational Chemistry? - Calculation types (II)

- Population analysis Determines the distribution of the electrons into the molecular orbitals Delivers dipole moments Creates graphical expressions of orbitals

- NMR calculation Simulates the external field of the NMR source as perturbation for the electron density Delivers chemical shifts (in combination with a standard) and - very time consuming even coupling constants - UV/VIS calculation Calculates the most feasible electron excitations Methods: time-dependent DFT or CIS (configuration interaction - singlets) - Solvation energies Implicit methods (SCRF) via correlation of an external reaction field in relation to the polarity of the solvent, solvent models: PCM, Dipole, ...

Explicit calculations (addition of the solvent molecules to molecular systems) are more time consuming than implicit methods

To be co ns id er ed in pa rt 2!

B) From a Formula to calculated Properties

Graphical interfaces - input files - basis sets - calculation output analysis

B) From a formula to calculated properties - programs Examples for program suites: -GAUSSIAN -NWCHEM -GAMESS -TURBOMOLE -ADF (DFT only) -MOPAC (Semiempric and HF) -TINKER (Molecular mechanics)

B) From a formula to calculated properties - graphical interfaces Graphical interfaces as source for initial geometries:

(GaussView as example) Also possible is the use of programs like Chem3D or the conversion of crystal structure data into xyz coordinates or Z-matrix.

B) From a formula to calculated properties - input files Input files contain: - the level of theory (method and basis sets) - (initial) geometry of the investigated system - system requirements (no. of proceesors, memory) - additional data depending on the type of calculation

Example: Optimization of Ammonia

%chk=nh3_zmat.chk %mem=3800MB %nproc=2 #opt b3lyp/6-311++G** Ammonia as ZMat 0 1 N H H H B1 B2 B3 A1 A2 D1 %chk=nh3_xyz.chk %mem=3800MB %nproc=2 #opt b3lyp/6-311++G** 2 D1 Ammonia in cart coordinates 0 1 N H H H 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 1.00000000 0.94280915 0.00000000 -0.33333304 -0.47140478 -0.81649655 -0.33333304

Z matrix (left) vs. cart. coordinates (right) taken from Gaussian03

1 1 1

B1 B2 B3

2 3

A1 A2

1.00000000 1.00000000 1.00000000 109.47120255 109.47125080 -119.99998525

B) From a formula to calculated properties - basis sets (I) Mathematical functions to describe the electrons (wave character) Mostly used: Linear combinations of gauss functions

Linear combinations of Gauss functions are flexible enough to model s, p, d and f orbitals!

B) From a formula to calculated properties - basis sets (II) Minimal basis: STO-NG (N primitive Gauss functions as linear combination for one orbital each) => Lousy accuracy Often used: Split valence basis set (Inner shell orbitals with other numbers of gauss functions than valence shell orbitals) 3 - 21G Sum of 3 Gauss functions for inner shell orbitals Separation for valence shell orbitals into two basis functions consisting of 2 and 1 Gauss functions (carbon: 1s=3, 2s=3, 2p=3: 9 Gaussian functions) 6 - 31G Sum of 6 Gauss functions for inner shell orbitals Separation for valence shell orbitals into two basis functions consisting of 3 and 1 Gauss functions (carbon: 1s=6, 2s=4, 2p=4: 14 Gaussian functions) 6 - 311G Sum of 6 Gauss functions for inner shell orbitals Separation for valence shell orbitals into three basis functions consisting of 3 and a pair of independent gauss func. (C: 1s=6, 2s=5, 2p=5: 16 Gauss func.)

B) From a formula to calculated properties - basis sets (III) More flexiblity via polarized and diffuse functions 6-31++G** Polarized functions: * add polarized functions per element (except H, He) ** add polarized functions on all elements (incl. H, He) Diffuse functions: + add diffuse functions on all elements (except H,He) ++ add diffuse functions on all elements (incl. H, He)

Polarized functions: add functions for orbitals with higher angular momentum Diffuse functions: add small amounts (small orbital exponent) of (6 d functions summed into p orbitals of elements Li-Ca, 10 f functions are functions of the same angular momentum (distributes electron density far added for Sc to Zn, 3 p functions summed into s orbitals of H and He, ...) away from the nuclei) => Suggested for lone pair compounds, anions, => Required at least for the heavier elements (=*), because of the electric field radicals (+), and hydrogen bridges and transition states with H that is polarizing the calculated AOs in the non-spherical MO environment abstraction(++)

B) From a formula to calculated properties - basis sets (III) More flexiblity via polarized and diffuse functions 6-31++G** Polarized functions: * add polarized functions per element (except H, He) ** add polarized functions on all elements (incl. H, He) Diffuse functions: + add diffuse functions on all elements (except H,He) ++ add diffuse functions on all elements (incl. H, He)

Diffuse functions: add small amounts (small orbital exponent) of functions of the same angular momentum (distributes electron density far away from the nuclei) => Suggested for lone pair compounds, anions, radicals (+), and hydrogen bridges and transition states with H abstraction(++)

B) From a formula to calculated properties - basis sets (IV) What about heavier atoms (transition metals)? Description of metals via ECPs (Effective core potential) #Valence shell orbitals via basis functions #Inner shell electrons summed up into an averaged field #Relativistic effects easily incorporated Examples: LANL2DZ / Hay-Wadt; Stuttgart-Dresden-(Kln)-ECPs

Suggestions for suitable basis sets (number of atoms < 90): 6-31G* is regarded to be the minimum requirement for publications Smaller systems (number of atoms < 20): 6-311+G** might be useful Anions, Radicals: 6-31+G* might be required

B) From a formula to calculated properties - calculations From the basis set to a valid wave function: SCF cycle

Complex evaluation of Integrals!

SCF = self-consistent field

B) From a formula to calculated properties - calculations (II) Geometry Optimization: also a calculation cycle
Initial structure SCF procedure (Determination of the wave function and the energy) Calculation of orbital energies First derivative of the SCF energy with respect to the vector of location For TS searches: also evaluation of the second derivatives (Hessian matrix)

Algorithm for determing the geometry for the next point on energy surface

NO

Check for reaching the thresholds in forces and changes in coordinates and SCF energy down to 0?

YES
Final summary of optimized geometry End of optimzation run

B) From a formula to calculated properties - calculations (III) Geometry Optimization: Minimum versus Transition state Transition state Product(s) (Local Minimum) (1st order saddle point) Reactant(s) (Local Minimum)

Potential Energy Surface (PES)

B) From a formula to calculated properties - calculations (IV) Transition state searches - Strategies The search for transition states is one of the toughest businesses in computational chemistry. => Mostly no automaticity, human interaction is needed Strategies: A) Draw your TS structure guess as accurate as you think. Most negative eigenvector is followed. This might be also an unwanted motion in the molecule (e.g. methyl rotation). B) Pre-optimization Draw the molecule with a reasonable geometry especially at the reaction center. Freeze the reaction coordinate(s) and make a normal geometry optimization (to avoid other unwanted modes). Open the frozen coordinates and search the TS.

B) From a formula to calculated properties - output analysis Analysis of output files: text file or graphical tools (GaussView, MOLDEN) Geometry optimization: Intermediate step:
SCF Done: E(RB+HF-LYP) = -760.849791059 Convg = 0.4573D-08 S**2 = 0.0000 A.U. after 14 cycles -V/T = 2.0696

Item Value Threshold Converged? Maximum Force 0.061492 0.000450 NO RMS Force 0.005240 0.000300 NO Maximum Displacement 0.188036 0.001800 NO RMS Displacement 0.044821 0.001200 NO Predicted change in Energy=-1.175625D-02

B) From a formula to calculated properties - output analysis (II) Optimization accomplished:

Item Value Threshold Converged? Maximum Force 0.000011 0.000450 YES RMS Force 0.000001 0.000300 YES Maximum Displacement 0.001232 0.001800 YES RMS Displacement 0.000269 0.001200 YES Predicted change in Energy=-1.834641D-09 Optimization completed. -- Stationary point found. ---------------------------! Optimized Parameters ! ! (Angstroms and Degrees) ! --------------------------------------------------! Name Definition Value Derivative Info. ! -------------------------------------------------------------------------------! R1 R(1,2) 1.7311 -DE/DX = 0.0 ! ! R2 R(1,3) 1.7724 -DE/DX = 0.0 ! ! R3 R(1,4) 2.3156 -DE/DX = 0.0 ! ! R4 R(1,20) 2.4801 -DE/DX = 0.0 ! ! R5 R(1,21) 2.5229 -DE/DX = 0.0 ! ! R6 R(1,22) 2.5034 -DE/DX = 0.0 ! ! R7 R(1,23) 3.156 -DE/DX = 0.0 ! ! R8 R(1,24) 2.4604 -DE/DX = 0.0 ! ! R9 R(1,25) 3.163 -DE/DX = 0.0 ! ! R10 R(1,26) 2.4485 -DE/DX = 0.0 ! ....

103,-0.4177548259\H,2.9027772668,-1.9957406754,1.1866693856\H,2.109005 4958,-2.5938312578,-0.2920838803\\Version=AM64L-G03RevC.02\State=1-A\H F=-760.883834\RMSD=4.495e-09\RMSF=5.242e-06\Dipole=-1.8589791,0.386761 ,-0.5495466\PG=C01 [X(C10H18Mo1O4)]\\@

Electronic energy! (atomic units: 1 au = 627.50956 kcal/mol)

B) From a formula to calculated properties - output analysis (III)

Graphical analysis of the profile of a geometry optimization (TS search) in MOLDEN (left) and GaussView (right)

B) From a formula to calculated properties - output analysis (IV) Frequency calculations: Summary of vibrational modes

Harmonic frequencies (cm**-1), IR intensities (KM/Mole), Raman scattering activities (A**4/AMU), depolarization ratios for plane and unpolarized incident light, reduced masses (AMU), force constants (mDyne/A), and normal coordinates: 1 2 3 A A A Frequencies -- -540.2082 25.3888 35.6969 Red. masses -8.7207 3.1003 3.7200 Frc consts -1.4994 0.0012 0.0028 IR Inten -79.5409 0.5030 0.7834 Atom AN X Y Z X Y Z X Y Z 1 42 0.00 0.01 0.00 0.00 0.01 0.00 -0.02 0.03 -0.03 2 8 0.02 0.00 -0.01 -0.04 0.03 0.01 -0.04 0.11 -0.06 3 8 -0.04 0.03 0.02 0.03 0.00 0.02 0.02 -0.03 -0.02 4 8 0.39 0.12 -0.11 0.00 0.01 0.05 0.01 0.01 0.05 5 6 -0.05 0.05 0.24 0.00 -0.01 -0.02 0.01 -0.04 0.04 6 6 0.03 0.08 0.08 0.00 -0.04 0.14 0.02 -0.05 0.16 7 6 0.07 0.01 0.13 0.10 -0.13 -0.13 0.04 -0.13 -0.03 8 6 -0.18 -0.03 0.07 -0.08 0.13 -0.11 -0.02 0.05 0.01

One true imaginary frequency => transition state

B) From a formula to calculated properties - output analysis (IV) Frequency calculations: Thermodynamic data
------------------- Thermochemistry ------------------Temperature 298.150 Kelvin. Pressure 1.00000 Atm. Atom 1 has atomic number 42 and mass 97.90550 Atom 2 has atomic number 8 and mass 15.99491 Atom 3 has atomic number 8 and mass 15.99491 Atom 4 has atomic number 8 and mass 15.99491 Atom 5 has atomic number 6 and mass 12.00000 Atom 6 has atomic number 6 and mass 12.00000 Atom 7 has atomic number 6 and mass 12.00000 Atom 8 has atomic number 6 and mass 12.00000 ... Zero-point correction= 0.265624 (Hartree/Particle) Thermal correction to Energy= 0.284234 Thermal correction to Enthalpy= 0.285178 Thermal correction to Gibbs Free Energy= 0.218585 Sum of electronic and zero-point Energies= -760.618210 Sum of electronic and thermal Energies= -760.599600 #H enthalpy Sum of electronic and thermal Enthalpies= -760.598656 #G Gibbs free energy Sum of electronic and thermal Free Energies= -760.665249 E (Thermal) KCal/Mol 178.360 0.000 0.889 0.889 176.582 CV Cal/Mol-Kelvin 68.622 0.000 2.981 2.981 62.661 S Cal/Mol-Kelvin 140.157 0.000 42.993 32.417 64.747

Adjustable isotope pattern, temperature, pressure

Total Electronic Translational Rotational Vibrational

B) From a formula to calculated properties - output analysis (V)

Graphical analysis of the vibrational modes of the transition state

C) How to evaluate Mechanisms with Computational Chemistry

Mechanism theorems - energetic evaluation transition states and kinetics

C) How to evaluate Mechanisms with Computational Chemistry What is a reaction mechanism?

- Collection of elementary processes (also called elementary steps or

elementary reactions) that explains how the overall reaction proceeds. - A proposal from which you can work out a rate law that agrees with the observed rate laws. - Rationalization of a chemical reaction But: Is the explanation of experimental (and computational) results alone a proof of the correctness of a mechanism?

C) How to evaluate Mechanisms with Computational Chemistry

Inductive approach: Formulate hypothesis based on known facts Execute experiments and/or calculations to test this hypothesis Results and hypothesis consistent? Yes! All features tested? Yes! No!

No!

Proven mechanism!!

C) How to evaluate Mechanisms with Computational Chemistry

Case study: Hydrosilylation of benzaldehyde

Possible mechanistic pathways!

Drees and Straner, Inorg. Chem. 2007, 10850-9

C) How to evaluate Mechanisms with Computational Chemistry How to check mechanistic pathways in computational chemistry? Energy evaluation approach: 1. Optimize all structures of the pathways (starting material, intermediates, transition states, products) - be aware of isomers! 2. Frequency calculations in order to distinguish from minima structure and transition state and to obtain the thermodynamical data 3. Choose a point on the PES to scale all the energies to (zero point). Non-catalytic reaction: sum of reactants. Catalytic cycle: starting point or the resting state 4. Substrate the energies of the zero-point from the energy of the desired calculated point 5. Important: Do not loose atoms or fragments, even when compounds are added or eliminated during the reaction!

C) How to evaluate Mechanisms with Computational Chemistry

C) How to evaluate Mechanisms with Computational Chemistry

Further approaches: - If kinetic data is available (rate constants, derived activation energies), a comparison with the calculated barriers of the rate-determining step is useful. - Kinetic isotope effects could also be evaluated computationally (=>isotope pattern at the frequency calculation!)

KIE = e

#G $ ( D )"#G $ ( H ) " RT

derived from

k (H ) KIE = k ( D)

- Simulation of spectroscopy (NMR, IR, UV) and comparison with measurements - although with higher absolute errors than the energy ! approach

C) How to evaluate Mechanisms with Computational Chemistry Excursion: Transition states and kinetics Arrhenius equation

k = A"e

Ea RT

=> Simplest approach to calculate reaction rates or activation barriers

!
Transition state theory (Eyring)

k T k= "e
h

$G % # RT

k T = "e
h

$S % # R

"e

H% # RT

=> Incorporation of the laws of thermodynamics to have access to activation enthalpy and entropy

C) How to evaluate Mechanisms with Computational Chemistry Meaning of the activation energies: Free energy of activation $G

Downside: Temperature- and concentration-dependent But: the easiest parameter for evaluation Correlated via kinetic measurements. A fair comparison: correlation of $G with $G0 in a linear relationship.

#Example: Hammett equation

Correlation between kinetic data from a test reaction and substituent effects
"k% log$ ' = () # k0 &
%>0: substituent more electron withdrawing than H %<0: substituent less electron withdrawing than H &>0: reaction accelerated by electron withdrawing substituent &<0: reaction accelerated by electron donating substituent

Connection to $G:

' #$G% * T .1 ) , #$H % ( #& + "= = / ' #$G * 2.303RT #& ) , ( #& +

C) How to evaluate Mechanisms with Computational Chemistry Meaning of the activation energies: Activation enthalpy $H

Experimental value: from the gradient in the Eyring plot (ln(k/T) vs. 1/T))

"k% " k % 1 H* )S * ln$ $T' ' = ( R + ln$ $h' '( T + R # & # &

!
Temperature independent #Fair comparison between theory and experiment Interpretation as the heat that is needed to reach the reaction barrier

C) How to evaluate Mechanisms with Computational Chemistry Meaning of the activation energies: Activation entropy $S

Sign of $S in unimolecular reactions: $S <0 !loss of degrees of freedom in the transition state (e.g. hydrogen transfer, cleavage of a C-X bond via HX eliminiation, rearrangements, cyclic transition states, system crossings) $S >0 !gain of degrees of freedom in the transition state (e.g. C-C cleavage, peroxide cleavage, biradical formations without system crossings)

D) A Word on Costs and Accuracy

Phrases of prejudice - computational costs - accuracy

D) A Word on Costs and Accuracy Well-known prejudice phrases: Regardless of what the experimental result would be, the computational chemist tries to find the level of theory, where the experiment would be verified. (Or if the computational chemist is not your friend, but your enemy: Regardless of what the experimental result would be, the computational chemist tries to find the level of theory, where the computational approach delivers a more feasible mechanism that also fits the experimental result.) Four computational chemists working on one problem would result in five different computational results for the same experiment. A computational study always needs more computational runs than initially thought. (Murphys law for impossible time-management) A model system (e.g. smaller substituents) always has different behaviors than the desired system, but saves a lot of computer time

D) A Word on Costs and Accuracy Accuracy considerations Comparison of various levels of theory in calculating the G2 test suite. (Hundreds of molecules incl. reaction energies)

Level 2 // Level 1: Geometry optimization at Level 1, Energy calculation at level 2 for the optimized geometry from level1.

taken from the Gaussian manual

D) A Word on Costs and Accuracy Cost considerations

CPU = computer time Memory = RAM memory Disk = Disk space needed

N = number of basis sets O = number of occupied orbitals V = number of virtual orbitals

Direct: solve integrals in the memory without storing data on the hard disk Conventional: solve the integrals using a lot of temporary files on disk

D) A Word on Costs and Accuracy Cost meets accuracy

SCF Cycle for methane

SCF Cycle for pentane

The computational chemist has always to consider the need for a specific accuracy in the focus of the higher computational costs that this might cause.

Further reading....

Computational: I.N. Levine - Quantum Chemistry - Prentice Hall (broad overview) W. Koch, M. C. Holthausen - A Chemists Guide to Density Functional Theory - Wiley-VCH (as the name indicates, focus on DFT ,but also with a lot of physical formulas) A. Szabo, N. S. Ostlund - Modern Quantum Chemistry: Introduction to Advanced Electronic Structure Theory - Dover (partly hardcore derivation of all the theory - HF and post-HF only) Mechanisms: B.K. Carpenter - Determination of Organic Reaction Mechanisms Wiley&Sons (rather old book, focuses on kinetics and thermodynamical values)

... To be continued! Thank you very much for your kindest attention!