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).
11
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, ....
17
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.
20
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
28
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
31
Fundamental Principles
Statistical Mechanics
Another way of formulating this problem is to use derivatives of the
partition function without a weight function
32
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
34
The End
Q&A
35
Thermodynamic properties and their characteristics
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36
