Overview to Molecular Modeling

Computational Chemistry

of a molecular structure Geometry optimization Related properties

vibrational nmr e) density

frequencies

Energy

method / Energy basis set // Geometry method / Geometry basis set

Computational Chemistry

Molecular Mechanics

Atoms

obey laws of classical physics No e) structure MM2, MM3, MM+, others Useful
Large Small

(bio) molecules molecules

NO

energy value

Computational Chemistry

Molecular Mechanics

= 3 Ei Large number of parameters

E
C 2H 6

C-C, 6 @ C-H 6@C-C-H 9@H-C-C-H 6 @ C - H, 6 @ C -/= C (not C - C or C = C) 6 @ C - C - H, 24 torsion

C 6H 6

Parameters

determined empirically

Computational Chemistry

Molecular Mechanics

Quantum Mechanics

structure based on , = E , is known exactly is unknown except for simple systems (H-like atoms, SHO, RR, particles in boxes, etc.)
Electronic

Computational Chemistry

Problems
Molecular Mechanics Quantum Mechanics

Overlap

Integral Exchange Integral

Exchange Functional (HF Correlation Functional

theory)

Computational Chemistry

Molecular Mechanics

Quantum Mechanics

Semiempirical Methods

part of , Hckel molecular orbital theory MOPAC theory ZINDO theory

Ignore

Computational Chemistry

Molecular Mechanics

Quantum Mechanics

Hckel Theory

Semiempirical Methods

HMO

Hckel molecular orbital theory

Applied to conjugated hydrocarbons Assumes ALL overlap integrals are zero

EHT

Extended Hckel theory

to any molecule type

Applied

Useful

for quick and dirty calculations and starting point for more advanced calculations

Computational Chemistry

Molecular Mechanics

Quantum Mechanics

MOPAC Molecular Orbital Package

Semiempirical Methods

CNDO Complete Neglect of Differential Overlap INDO Intermediate Neglect of ... NDDO Neglect of Diatomic ... MINDO Modified INDO
MINDO/3

MNDO Modified Neglect of ...

AM1 Austin Model 1 PM3 Parameterized Model Series 3 AM1/d and MNDO-d (MOPAC 2000,

d e-s)

Useful for ground state energy and geometry

Computational Chemistry

Molecular Mechanics

Quantum Mechanics

ZINDO Zerners INDO

Semiempirical Methods

ZINDO/1, ZINDO/3, ZINDO-d, etc Useful

for

Transition states Energies Spectroscopy Transition elements

Not

useful for optimizations

Computational Chemistry

Molecular Mechanics

Quantum Mechanics

Semiempirical Methods

ab initio Methods

complete , Estimate Variation Principle (Etrial $ Eexperimental)

Use

Computational Chemistry

Molecular Mechanics

Quantum Mechanics

Level of Theory

Semiempirical Methods

ab initio Methods

HF-SCF
Hartree-Fock

Self-Consistent Field

B3LYP
Becke

Density Function Theory (DFT)

Exchange with Lee-Yang-Parr Correlation Order Mller-Plesset perturbation

MP2/MP4
Second/Fourth

theory
QCISD(T)

Quadratic configuration

interaction

Computational Chemistry

Molecular Mechanics

Quantum Mechanics

Semiempirical Methods

ab initio Methods

Trial Wave Functions (Basis Sets)

Computational Chemistry

Molecular Mechanics

Quantum Mechanics

Electron Spin

Semiempirical Methods

ab initio Methods

Open

Shell (unrestricted)

Odd number of electrons Excited states 2 or more unpaired electrons Bond dissociation processes

Closed
Even

Shell (restricted)

number of electrons--all paired

Comparison of ab initio Methods (p 94)

Comparison of Models (F/F p 96)

Comparison of Commercial Software

Basis Sets
Basis Set Criteria

Capable

of describing actual wave function well enough to give chemically useful results Can be used to evaluate Is accurately and cheaply

Basis Functions
Hydrogenlike Orbitals

Hydrogenlike Orbitals

(n - l - 1) nodes

Basis Functions
Slater-type Orbitals (STOs)

Basis Functions
Gaussian-type Orbitals (GTOs)

GTOs

Advantages
Complete Favorable

math properties

Disadvantages
Not mutually orthogonal Poor representation of electron

probability near and far away from nucleus (overcome using large number of GTOs

Use of STOs
One

or more STO on each nucleus Accuracy of calculation increases as

Orbital exponents chosen well Number of STOs used increases

Number of STOs used Minimal Basis Set

Use
H C

STO for occupied AOs Examples

1s 1s 2s 2px 2py 2pz

Number of STOs used Split (Double Zeta ) Basis Set

Linear combination of two similar orbitals with different orbital exponents (different sizes)

2p = a2p,inner + b2p,outer If a > b charge cloud contracted around nucleus If b > a diffuse cloud

Number of STOs used Split (Double Zeta ) Basis Set

Examples: H 1s, 1sN C 1s, 2s, 2sN, 2px, 2py, 2pz, 2pxN, 2pyN, 2pzN

Triple Zeta basis sets are also used

Number of STOs used Diffuse Basis Set

Extra

s and p wave functions included that are significantly larger than usual ones Useful for
Distant electrons Molecules with lone pairs Anions Species with significant negative charge Excited states Species with low ionization potentials Describing acidities

Number of STOs used Polarized Basis Set

Linear

combination of different types of orbitals Examples

H C

1s and 2p 1s, 2s, 2p and 3d

Shifts

charge in/out of bonding regions

Number of STOs used

Other
Place

attempts with increasing number of STOs

STOs in center of bonds instead of on only nuclei

Problems

used
of Is increases as N 4 where N is the number of basis functions As minimization occurs, orbital exponents change thus defining a new basis set to rebegin the calculation
Number

Use of STOs/GTOs
Wrong

shape of GTOs accounted for by

Choosing

several s to get set of primitive gaussians for compact and diffuse Linear combination of primitives (usually 1-7) to get STO Optimize Freeze as contracted gaussian function
Use

minimal, split/double zeta, polarization, diffuse sets

Use of STOs / GTOs

Jargon: minimal basis set

STO-NG where N is the number of primitive gaussians STO-3G 3 primitve gaussians per basis set not the simplest minimal basis set popular

Use of STOs / GTOs

Jargon: split basis set

K-LMG where K is the number of sp type inner shell primitive gaussians L is the number of inner valence s and p primitive gaussians M is the number of outer valence s and p primitive gaussians

Use of STOs / GTOs

Jargon: split basis set

3-21G 3 primitives for inner shell 2 sizes of basis functions for each valence orbital 6-311G 6 primitives for inner shell 3 sizes of basis functions for each valence orbital

Use of STOs / GTOs

Jargon: polarization

* d-type orbital added to atoms with Z > 2 ** d-type orbital added to atoms with Z > 2 and p-type orbital added to H and He ds added: STO-NG are 5 regular 3ds L-KMG are 6 3ds dxx, dyy, dzz, dxy, dyz, dxz (formed by linear combination of 5 regular 3ds and 3s)

Use of STOs / GTOs

Jargon: polarization

6-31G* or 6-31G(d) 6-31G with d added for Z > 2 (FF choice) 6-31G** or 6-31G(d,p) 6-31G with d added for Z > 2 and p added to H 6-31G(2d) 6-31G with 2d functions added for Z > 2

Use of STOs / GTOs

Jargon: diffuse

+ diffuse function included for Z > 2 ++ diffuse function included for Z > 2 and for H 6-31+G(d)
6-31G(d) with diffuse function added for Z > 2

6-31++G(d)
6-31+G(d) with diffuse function added for H

Some Recommended Standard Basis Sets (F/F p 102) ~DZVP

~TZVP

Common Basis Sets