II MSC COMPUTATIONAL CHEMISTRY UNIT-III

Syllabus
Syllabus:: Introduction to computational chemistry - quantum mechanics - schrodinger
equation. Types of calculations – single point energy, geometry optimization, frequency
prediction - Brief introduction of computational methods - Ab initio method, semi-empirical
Learn to generate Hirshfeld surfaces, study the interaction energies and draw
method, Density Functional Theory method, Molecular mechanics. Basis Sets - minimal basis
the electrostatic
sets, potential
split valence basis map using
sets, polarized Crystal
basis Explorer
sets, Diffuse Software.
functions, High angular momentum
basis sets.

Introduction

❖ The term theoretical chemistry may be defined as the mathematical description

of chemistry.
❖ Currently, there are two ways to approach theoretical chemistry problems
1. Computational Theoretical Chemistry [CTC]
2. Non-Computational Theoretical Chemistry [NCTC]
❖ Computational theoretical chemistry is primarily concerned with the numerical
computation of molecular electronic structures and molecular interactions
❖ Non-computational quantum chemistry deals with the formulation of analytical
expressions for the properties of molecules and their reactions.
❖ The term computational chemistry is usually used when a mathematical
method is sufficiently well developed that it can be automated for implementation
on a computer.
❖ Computational chemistry is the application of chemical, mathematical and
computing skills to the solution of interesting chemical problems.
❖ It uses computers to generate information such as properties of molecules or
simulated experimental results. Very few aspects of chemistry can be computed
exactly, but almost every aspect of chemistry has been described in a qualitative
or approximate quantitative computational scheme.
❖ The biggest mistake that computational chemists can make is to assume that
any computed number is exact. However, just as not all spectra are perfectly
resolved, often a qualitative or approximate computation can give useful insight
into chemistry
❖ It also helps chemists make predictions before running the actual experiments
so that they can be better prepared for making observations

P.RAM KUMAR ASST PROFESSOR OF CHEMISTRY VOC COLLEGE

II MSC COMPUTATIONAL CHEMISTRY UNIT-III

❖ The quantum and classical mechanics as well as statistical physics and

thermodynamics are the foundation for most of the computational chemistry
theory and computer programs.
❖ Using computational chemistry software you can in particular perform:
1. Electronic structure determinations
2. Geometry optimizations,
3. Frequency calculations
4. Definition of transition structures and reaction paths5protein calculations, i.e.
docking,
5. Electron and charge distributions calculations,
6. Calculations of potential energy surfaces (PES)
7. Calculations of rate constants for chemical reactions (kinetics)
8. Thermodynamic calculations- heat of reactions, energy of activation, etc
9. Calculation of many other molecular and balk physical and chemical
properties.
❖ The most important numerical techniques are Ab-initio, Semi-empirical and
Molecular Mechanics.
❖ Ab-initio (Latin for "from scratch") a group of methods in which molecular
structures can be calculated using nothing but the Schrödinger equation, the
values of the fundamental constants and the atomic numbers of the atoms
present.
❖ Semi-empirical techniques use approximations from empirical (experimental)
data to provide the input into the mathematical models.
❖ Molecular mechanics uses classical physics and empirical or semi-empirical
(predetermined) force fields to explain and interpret the behavior of atoms and
molecules.

Basis set

❖ Models of a chemical system generally consist of the combination of a theoretical

method such as restricted HF and B3LYP with a basis set.
❖ Each such unique pairing of method with basis set represents a different
approximation to the Schrödinger equation.

P.RAM KUMAR ASST PROFESSOR OF CHEMISTRY VOC COLLEGE

II MSC COMPUTATIONAL CHEMISTRY UNIT-III

❖ A basis set is a mathematical description of the orbitals within a system used to

perform the theoretical calculation.
❖ Larger basis sets approximate more accurately the orbitals by imposing fewer
restrictions on the locations of the electrons in space.
❖ Standard basis sets for electronic structure calculations use linear combinations
of gaussian functions to form the orbitals.
❖ Basis sets assign a group of basis functions to each atom within a molecule to
approximate its orbitals.
❖ These basis functions themselves are composed of a linear combination of
Gaussian functions; such basis functions are referred to as contracted functions,
❖ Component gaussian functions are referred to as primitives.
❖ A basis function consisting of a single gaussian function is termed uncontracted.

Minimal basis sets

❖ Minimal basis sets contain the minimum number of basis functions that are

needed for each atom.

❖ Minimal basis sets use fixed size atomic type orbitals.

❖ The STO-3G basis set is a minimal basis set

❖ It uses three gaussian primitives per basis function (“3G”). “STO” stands for

“Slater type orbitals”, and the STO-3G basis set approximates Slater orbitals with

gaussian functions.

❖ Nrn-1e-ξrYlm(θ,φ) Ylm(θ,φ) are spherical harmonic

Split valence basis sets

❖ One way to increase the size of a basis set is to take more basis functions per

atom.

❖ Split valence basis sets, such as 3-21G and 6-31G basis sets, have two (or more)

sizes of basis function for each valence orbital.

❖ For example, in the above 3- 21G and 6-31G basis sets we have:

P.RAM KUMAR ASST PROFESSOR OF CHEMISTRY VOC COLLEGE

II MSC COMPUTATIONAL CHEMISTRY UNIT-III

H: 1s s

C: 1s , 2s , 2s ', 2Px , 2 Px , 2 Py , 2 Pz ', 2 Px ', 2 Py . 2 Pz

❖ Here the primed and unprimed orbitals differ in size.

❖ The double zeta valence basis sets form molecular orbitals from the linear

combinations of two sets of functions for each atomic valence orbital.

❖ Similarly, triple split valence basis sets such as 6-311G, use three sets of

contracted functions for each valence orbital type.

Polarized basis sets

❖ Split valence basis sets could be improved by adding orbitals with different
shapes.
❖ Polarized basis sets add orbitals with angular momentums going beyond of
requirement for the proper description of the ground state of each atom at the HF
level.
❖ For example, polarized basis sets add to carbon atoms and some of them add to
hydrogen atoms.
❖ Examples for polarized basis sets are the 6- 31G(d) and the 6-311G(d, p) basis
sets.
❖ Examples: STO-3G – each occupied atomic orbital is constructed from three
gaussian functions. 3-21G

Diffused functions

❖ Basis sets with additional diffuse functions are large by size versions of s- and p-
type split valence basis sets.
❖ Diffuse orbitals occupy a larger region of space.
❖ Basis sets with diffuse functions are important for systems where electrons may
be far from the nucleus.
❖ One example for diffuse basis function is the 6-311+G(d, p) basis set.

P.RAM KUMAR ASST PROFESSOR OF CHEMISTRY VOC COLLEGE

II MSC COMPUTATIONAL CHEMISTRY UNIT-III

P.RAM KUMAR ASST PROFESSOR OF CHEMISTRY VOC COLLEGE