Semester II, 2023-2024

Computational Chemistry
Lecture 1
Introduction and
Fundamental Principles
Lam K. Huynh
School of Chemical and Environmental Engineering
International University

1
Overview

2
 Overview

Real
Complex
Multi-scale
Interdisciplinary
challenges

• Predictive: to model a molecular system prior to synthesizing that

molecule in the laboratory

• Descriptive: to understand a problem more completely

3
Overview

Computational Science

Computational
Chemistry
(Science)

Ref: President’s Information Technology Advisory Committee “Report

to the President - Computational Science: Ensuring America’s
Competitiveness” June 2005.
4
 Overview

Experiments

Fundamental Detailed Kinetics

Chemistry & Modeling[3]
Physics to
Validation
Reaction
Engineering

Reactor modeling[3,4]
(CFD Simulations)

Complex Mechanism[2]

Computational tools

Thermodynamics [1] Gaussian09

Kinetics & Dynamics[2]
[2] Home-made codes:
MSMC & SurfKin
[3] CHEMKIN-PRO
Quantum Chemistry[1] [4] KIVA-3V | Fluent code
5
Overview

“Theoretical chemistry”
≡ the mathematical description of chemistry

“Computational chemistry”
generally used when a
mathematical method is sufficiently
well developed that it can be
automated for implementation on a
computer

Physical chemistry
6
Overview

Scientific method
• A hypothesis: an educated guess or logical conclusion
from known facts.

• If the hypothesis is found to be consistent with known

facts → a theory
– explain observed phenomena,
– predict the results of future experiments
– presented in mathematical form.

• When a theory is found to be always correct for many

years → a scientific law.
7
Overview

Practical approach

• A model (e.g., Lewis dot structure, VSEPR model)

– A simple way of describing and predicting scientific
results, either incorrect or incomplete description.
– Models might be
• simple mathematical descriptions or
• completely nonmathematical
– Models are very useful
• allow us to predict and understand phenomena without the work
of performing the complex mathematical manipulations dictated
by a rigorous theory.
• Approximations are introduced (not feasible to solve
problem exactly) => an average
8
Overview

Real
Complex
Multi-scale
Interdisciplinary
challenges

How?

Computational Chemistry
• Predictive: to model a molecular system prior to synthesizing that
molecule in the laboratory

• Descriptive: to understand a problem more completely 9

Overview
Chemistry
> Physical chemistry
> Theoretical Chemistry
> Computational Chemistry (Quantum Chemistry)

(classical thermodynamics)

10
 Overview
Quantum mechanics (QM) gives a mathematical description of the
behavior of electrons (always correct)

• The QM equations have never been solved exactly (except for

the hydrogen atom).

→ The entire field of computational chemistry is built around

approximate solutions.

NOTES
• Require a knowledge of each approximation being used and how accurate the results
are expected to be
• Obtaining very accurate results requires extremely powerful computers
• Much of the work now done on supercomputers could be performed faster and more
accurately on a PC (if the problem is solvable).
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Fundamental Principles

Energy
• Kinetic: vibrational, translational and rotational motions (of what?)
• Potential: Coulomb's law or bond stretching, bond bending,
conformational energy, hydrogen bonds, …
Absolute energy vs. relative energy

Note:

• The system with the lowest energy is the most stable → the shape of a molecule

12
Fundamental Principles

Chemical processes

• Adiabatic processes: the system does not change electronic state

throughout the process

• Diabatic (or nonadiabatic): a change in the electronic state is part

of the process, usually follow the lowest energy path, changing
state as necessary.

13
 Fundamental Principles

Electrostatics
• The study of interactions between charged objects
• Described by Coulombs law
𝒒𝒒𝟏𝟏 𝒒𝒒𝟐𝟐
𝑬𝑬 =
𝒓𝒓𝟏𝟏𝟏𝟏
𝒒𝒒𝟏𝟏 𝒒𝒒𝟐𝟐
F= − 𝟐𝟐
𝒓𝒓𝟏𝟏𝟏𝟏

• No constants appear! → Atomic unit

14
Fundamental Principles

Atomic Units

• Many of the fundamental constants are defined as having a value of 1

15
 Fundamental Principles
Thermodynamics vs. Kinetics

Elementary
reactions

Sum

Overall
reaction

An elementary reaction is a single molecular event, such as a collision of molecules, resulting in a reaction.
The set of elementary reactions whose overall effect is given by the overall chemical reaction
16
Fundamental Principles
𝑘𝑘 𝑇𝑇 = 𝐴𝐴 × 𝑇𝑇𝑛𝑛 × 𝑒𝑒 −𝐸𝐸𝐸𝐸/𝑅𝑅𝑅𝑅
Thermodynamics vs. Kinetics
Net chemical reaction
H2 + 1/2O2 = H2O

Elementary reactions A n Ea
H+H+M=H2+M 7.000E+17 -1.0 0.0
O+O+M=O2+M 1.000E+17 -1.0 0.0
O+H+M=OH+M 6.750E+18 -1.0 0.0
H2O+M=H+OH+M 6.06E+27 -3.3 120770.
H2O+H2O=H+OH+H2O 1.E+26 -2.4 120160.
H+O2 (+M) =HO2 (+M) 4.660E+12 0.44 0.0
H+O2(+AR)=HO2(+AR) 4.660E+12 0.44 0.0
H+O2(+O2)=HO2(+O2) 4.660E+12 0.44 0.0
H+O2(+H2O)=HO2(+H2O) 9.060E+12 0.2 0.0
OH+OH(+M)=H2O2(+M) 1E+14 -0.37 0.0
OH+OH(+H2O)=H2O2(+H2O) 1E+14 -0.37 0.0
O+H2=OH+H 5.060E+04 2.67 6290.0
H+O2=OH+O 2.06E+14 -0.097 15022.
H2+OH=H2O+H 2.140E+08 1.52 3450.0
OH+OH=H2O+O 3.34E+04 2.42 -1930.
HO2+O=OH+O2 1.630E+13 0.0 -445.0
H+HO2=OH+OH 1.900E+14 0.0 875.0
H+HO2=H2O+O 1.45E+12 0. 0. 0.0
H+HO2=H2+O2 1.05E+14 0.0 2047.
H2+O2=OH+OH 2.040E+12 0.44 69155.0
HO2+HO2+M=H2O2+O2+M 6.84E+14 0.0 -1950.
H2O2+H=HO2+H2 1.700E+12 0.0 3755.0
H2O2+H=H2O+OH 1.000E+13 0.0 3575.0
H2O2+O=HO2+OH 9.55E+6 2.0 3970
H2O2+OH=HO2+H2O 2.000E+12 0.0 427.0

Intermediate
O, H, HO2, ....
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Fundamental Principles
Thermodynamics vs. Kinetics

Lin KC, Wang H-Y, Huynh LK, Han M-X. Industrial &
Engineering Chemistry Research 2020;59(38):16822-
31.

18
Fundamental Principles
Thermodynamics vs. Kinetics

(I)
Energy

Reactants
(II)

Products
For an elementary reaction
(If being the rate limiting step ⇒ applicable for overall reaction) 19
Fundamental Principles

Quantum Mechanics (QM)

• The correct mathematical description of the behavior of electrons
and thus of chemistry
• In theory, QM can predict any property of an individual atom or
molecule exactly.
• In practice, the QM equations have only been solved exactly for one
electron systems
• The Schrodinger equation

� = 𝐸𝐸Ψ
𝐻𝐻Ψ

• The wave function (Ψ) is also called a probability amplitude because it is

the square of the wave function that yields probabilities
• The wave function must be continuous, single-valued, normalizable, and
antisymmetric with respect to the interchange of electrons.

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 Fundamental Principles

Quantum Mechanics (QM)

Hamiltonian operator

Laplacian operator acting on particle i:

Time independent, nonrelativistic Schrodinger equation

� = 𝐸𝐸Ψ;
𝐻𝐻Ψ
Ψ 𝑥𝑥, 𝑦𝑦, 𝑧𝑧

𝑖𝑖𝑖𝑖𝑖𝑖
Time-dependent Schrodinger equation: Ψ 𝑥𝑥, 𝑦𝑦, 𝑧𝑧, 𝑡𝑡 = Ψ 𝑥𝑥, 𝑦𝑦, 𝑧𝑧 𝑒𝑒𝑒𝑒𝑒𝑒 − 21
ℏ
Fundamental Principles

Quantum Mechanics (QM)

Born-Oppenheimer approximation: separating the nuclear and electron motions

(stationary nuclei)

Still challenging to solve

� = 𝐸𝐸Ψ
𝐻𝐻Ψ • Approximate Ψ ⇒ Variational methods: E ≥ Eexact
• Approximate 𝐻𝐻 � ⇒ Perturbation methods

• By substituting different operators, it is possible to obtain different observable properties,

such as the dipole moment or electron density.
• Properties other than the energy are not variational

Another way of obtaining molecular properties is to use the Hellmann-Feynman theorem.

P: some property

(often used for computing electrostatic properties) 22

 Fundamental Principles

Quantum Mechanics (QM)

Z

Ground-state electron configuration (Z = 8): 1s2 2s2 2p4

O atom

X Y

Method: (1s) (2s) (2p-1) (2p-0) (2p+1)

Triplet: 2S+1 = 3 ROHF/6-31g(d)
Energy = -74.7789661 hartrees. What does it mean?
(1 Hartree = 627.5 kcal/mol) 23
 Fundamental Principles

Quantum Mechanics (QM)

Ground-state electron configuration (Z = 8): 1s2 2s2 2p4

O atom

Method:
Triplet: 2S+1 = 3 ROHF/6-31g(d)

24
 Fundamental Principles

Quantum Mechanics (QM)

Ground-state electron configuration (Z = 8): 1s2 2s2 2p4

O atom

Energy = -74.6566041 hartrees (singlet)

Energy = -74.7789661 hartrees (triplet)

Method:
Singlet: 2S+1 = 1 ROHF/6-31g(d)

25
Fundamental Principles

Quantum Mechanics (QM)

26
Fundamental Principles

Quantum Mechanics (QM)

27
Fundamental Principles

Statistical Mechanics
• Is the mathematical means to calculate the thermodynamic properties of
bulk materials from a molecular description of the materials.

• V, P or T
• N individual rigid molecules
• 6N dimensional space (called phase space): translation &
rotation
• An individual point in phase space (denoted by ᴦ)
corresponds to a particular geometry of all the molecules in
the system.

→ The probability of a configuration occurring is a function

of the energy (kinetic & potential) of that configuration.

Energy of bulk materials (temperature of the system) ≠ energy of the individual molecules

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Fundamental Principles
Statistical Mechanics
There is some probability of finding molecules with any given energy. This probability
depends on the temperature T of the system

Boltzmann distribution: the ratio of the number of molecules, Ni, with various
energies, Ei, to the number of molecules in state j

kB is the Boltzmann constant

29
Fundamental Principles

Statistical Mechanics
When some property of a system is measured experimentally, the result is an
average for all of the molecules with their respective energies.
=> This observed quantity is a statistical average, called a weighted average 𝐴𝐴 .

This weighted average must be normalized by a partition function Q

30
Fundamental Principles

Statistical Mechanics

Not a convenient way to design computer simulations for real gas or

condensed-phase systems (determining every possible energy state
is by no means a trivial task)

A result can be obtained from a reasonable sampling of states.

=> a statistical uncertainty σ that is related to the number of states
sampled M by

1
𝜎𝜎 ~
𝑀𝑀

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Fundamental Principles

Statistical Mechanics
Another way of formulating this problem is to use derivatives of the
partition function without a weight function

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Fundamental Principles

Statistical Mechanics

There are equivalent ways to obtain a statistical average:

• A time average
• A calculation is designed to simulate the motion of molecules
• At every step in the simulation, the property is computed for one
molecule and averaged over all the time steps equally

• An ensemble average

• The geometric orientation of molecules.

• This statistical description of geometry is given by a radial distribution
function, also called a pair distribution function

33
Fundamental Principles

Statistical Mechanics

a hard sphere fluid a real gas

a crystal
a liquid

Radial distribution functions

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The End

Q&A

35
 Thermodynamic properties and their characteristics

https://en.wikipedia.org/wiki/List_of_thermodynamic_properties#:~:text=I
n%20thermodynamics%2C%20a%20physical%20property,of%20specify
ing%20the%20system's%20state.
36