CHM3701

COMPUTATIONAL
CHEMISTRY

Quantum Chemistry
Part 1
 TOPICS

• Quantum chemistry basics

• Schrodinger Equations

• Wave-functions

• Molecular orbitals

• SCF and Hartree-Fock Method

• Born-Oppenheimer Approximation
• The Variational Principal

• Higher order methods & DFT

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 BASICS

Quantum Chemistry Basics

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 BASICS

 Motions in microscopic (atomic) world:

• energy & matter quantized.

• duality of wave & particle

• probabilistic description

• quantum mechanics (Schrodinger Eq.).

• It was born out because of the inability of classical

mechanics to reconcile theory with experiment, such as
blackbody radiation, the photoelectric effect, and heat
capacity.

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 BASICS

• Calculation of Molecular structures and molecular properties by

quantum chemical methods
• Scientists who involved in this new physics (Quantum mechanics):

N.H.D. Bohr M. Planck A. Einstein

Bohr Atomic Energy Quantization Photoelectric effect
model

W. Heisenberg P. A.M. Dirac E. Schrödinger

Uncertainty Principle Quantum Mechanics Schrödinger Eq.

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 SCHRÖDINGER EQUATION

The quantum mechanical (QM) Hamiltonian is constructed from

the classical Hamiltonian by this transformation:

 
ˆ  1 pˆ x2  pˆ 2y  pˆ z2  V( xˆ , yˆ , zˆ )
HClass  H
2m
Classical Quantum Classical Quantum
Mechanics Mechanics Mechanics Mechanics

x Px pˆ x 

i x

y Py pˆ y 

i y

z Pz pˆ z 

i z

H-bar (ℏ) is a modification of Planck constant;

h
 ( 1.05457 1034 J .s )
2
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 SCHRÖDINGER EQUATION

• Erwin Schrodinger proposed an equation to find the wave function of

the system.

• Based on classical mechanics, trajectory is the path in which a moving

object follows through space as a function of time.

• The mathematical representation of the wave in quantum mechanics

(QM) replaces the classical concept of trajectory with a wave function, 𝜓
.

• The general time-independent Schrodinger equation;

Ĥ   

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 SCHRÖDINGER EQUATION

For a three-dimensional system:

𝐻𝜓 𝑥, 𝑦, 𝑧 = 𝐸𝜓 𝑥, 𝑦, 𝑧

ℏ2 𝜕 2 𝜓 𝜕 2 𝜓 𝜕 2 𝜓
− 2
+ 2 + 2 + 𝑉 𝑥, 𝑦, 𝑧 𝜓 = 𝐸𝜓
2𝑚 𝜕𝑥 𝜕𝑦 𝜕𝑧

ℏ2 2
− 𝛻 𝜓 𝑟 + 𝑉 𝑟 𝜓 𝑟 = 𝐸𝜓 𝑟
2𝑚

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 SCHRÖDINGER EQUATION

• The quantity with hat is an operator which plays a special role in QM.

(the energy operator)(wavefunction/eigenfunction)=(eigenvalue)(wavefunction/eigenfunction)

• The Hamiltonian operator (𝐻) corresponds to the total energy of the system.

• (the energy operator/Hamiltonian) 𝜓 = (the total energy)× 𝜓

• An observable is a measurable properties of a system, so:

(an operator corresponding to an observable) 𝜓 = (the value of observable)× 𝜓

• An observable is a property of the system that can be determined by some

sequence of physical operations. For example, Hamiltonian is an observable.

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 SCHRÖDINGER EQUATION
For a particle of mass, m, moving in one dimension with energy, E, which
does not change with time, Schrodinger equation can be written as;
d 2 ( x)
2
 2
 V  x  ( x)   ( x)
2m dx
V(x) is the potential energy of the particle at point x. As you can see the
potential energy, V, depends on the position.

Since Etot=Ek+Ep, the other part must be related to the kinetic energy of the
particle.

Therefore, rather than saying a particle has a specified position and

momentum, we instead describe it by a wavefunction.

Wavefunction is a function of all the coordinates of the particle [𝜓(x,y,z)] .

For example, in one-dimension (x);

 ( x)

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 SCHRÖDINGER EQUATION

For ab initio calculation purposes, the time-independent Schrodinger

equation contains three variables:

• The Hamiltonian – an operator (essentially a function)

• The wave function – a vector that “describes” the electron (also a

function)

• The energy – a number (scalar), a result from the operation of the

Hamiltonian operator on the wave function

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 SCHRÖDINGER EQUATION

• Given an appropriate wave function, the Schrodinger equation

can be solved by expanding the equation in the Hamiltonian,
and applying the operation from the equation to the given wave
function

• However, most of the problems for ab initio calculation for

molecular system involves wave function of the unknown form.

• Thus, the wave function has to be found first before the energy of
the system can be calculated.

• The process of finding the appropriate wave function is the main

focus of the ab initio calculation.

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 SCHRÖDINGER EQUATION

EXAMPLE 1:

Given a particle with the wave function Ψ = e-2x describing its

behavior. Find the energy of the particle, assume the particle is
attracted to a surface with V(x) = 1.

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 SCHRÖDINGER EQUATION

EXAMPLE 2:

Given a particle with the wave function Ψ = 2x2 describing its

behavior. Find the energy of the particle, assume the particle is
attracted to a surface with V(x) = 1.

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 WAVE FUNCTION
The wave function (Ψ) contains all the dynamical information about
the system it describes. Thus, we concentrate on the information it
carries about the location of the particle.

 But Ψ is a complex mathematical equation, so how can it

correspond to real physical measurements?

The Born Interpretation of Wave Function

The interpretation of wave function in terms of location of the

particle is based on a suggestion made by Max Born.

 He made use of an analogy with the wave theory of light, in which

the amplitude of an electromagnetic wave in a region is interpreted
as its intensity and therefore in quantum terms as a measure of the
probability of finding a photon present in the region.

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 WAVE FUNCTION

If the wave function of a particle has the value of 𝜓 at some point,
𝑥 , then the probability of finding the particle between 𝑥 and 𝑥 + 𝑑𝑥 is
proportional to:
probability  
2
dx

1. The square of wave function is the

probability density.

2. So, 𝜓 itself is called the probability

amplitude.

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 WAVE FUNCTION

 
  dx    * dx
2
 

Born interpretation does away with any worry

about the significance of a negative value of ψ
because |ψ|2 is real & never negative.


 
 * d d  dxdydz

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 WAVE FUNCTION

EXAMPLE 3:

The wave function of an electron in the lowest energy state of a H atom is

𝑟
proportional to 𝑒 − 𝑎0 , with 𝑎0 is a constant (Bohr radius=5.29 Angstrom)
and 𝑟 is the distance from the nucleus. Calculate the relative probabilities
of finding the electron inside a region of volume 𝛿𝑉 = 1.0 𝑝𝑚3, located at

(a) nucleus,

(b) a distance 𝑎0 from the nucleus.

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 WAVE FUNCTION

METHOD:

The region of interest is so small on the scale of the atom that we can
ignore the variation of 𝜓 within it & write the probability, P, as
proportional to the probability density (𝜓2; 𝜓 is real) evaluated at the
point of interest multiplied by the volume of interest, 𝜹V. That is ,
−2𝑟
𝑃 ≈ 𝜓 𝜹𝑉, with 𝜓 ≈ 𝑒 𝑎0
2 2

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 WAVE FUNCTION

ANSWER:
In each case 𝜹𝑉 = 1.0 𝑝𝑚3

(a). At the nucleus, 𝑟 = 0, so; 𝑃 ≈ 𝑒0 × (1.0 𝑝𝑚3)

(b). At a distance 𝑟 = 𝑎0 in an arbitrary direction,

𝑃 ≈ 𝑒 −2 × (1.0 𝑝𝑚3) = (0.14) × (1.0 𝑝𝑚3)

Therefore the ratio of probability is 1.0/0.14=7.1. It means that it is more

probable that the electron will be found at the nucleus than in volume
element of the same size located at the a distance a0 from the nucleus.
The negatively charged electron is attracted to the positively charged
nucleus, and it is likely to be found close to it.

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 WAVE FUNCTION

There is a normalization factor, N, such that the proportionality of

Born interpretation becomes one.


  * dx  1
2
N


The process of finding N is called Normalization.

The solution of the Schrödinger equation is a wave function.

• This wave function must be infinite anywhere. Otherwise the normalization
constant would be zero.
• As seen, the Born interpretation puts severe restrictions on the
acceptability of wave functions.
• A wave function must be single-valued & continuous. It means that there
is only one value at each point of space. It requires have continuous slope.
• It must be square-integrable.

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 WAVE FUNCTION

EXAMPLE 4:
consider the following plots. Which one of these plots gives an
acceptable wave function;

 ( x)  ( x)  ( x)

x x x
A B C D

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 WAVE FUNCTION

• As a consequence of the restriction on wave function, the

energy of a particle is quantized.

• Mathematically, when the wave function is not an appropriate

function of the Hamiltonian, the wave function is represents a
state of the quantum particle that has a forbidden energy level.

• If the wave function of a particle is not an eigenfunction of an

operator, the property to which the operator corresponds does
not have a definite value.

• Here, we say that the total wave function is a superposition of

more than one wave function or in another words, superposition
of several wave functions of definite wavelength.

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 WAVE FUNCTION

• Therefore, in a long series of observations, if the particle describe

by a wave function, then there are equal probabilities of find the
particle travelling to each direction. So:

  c1 1  c2 2  ...   ck k

k

• 𝑐𝑘 is a numerical coefficient and 𝜓𝑘 corresponds to different

states.

• It means that when the momentum is measured, you will find

one of eigenvalues corresponding to the 𝜓𝑘 .

• The probability of measuring a particular eigenvalue is

proportional to |𝑐𝑘 |2.

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 WAVE FUNCTION

• An infinite number of waves is

needed to construct the wave
function of a perfectly localized
particle.

• These wave functions interfere

constructively in one place but
destructively elsewhere.

• As more waves are used in the

superposition (as given by the
numbers attached to the curves),
the location becomes more precise
at the expense of uncertainty in
the particle's momentum.

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 WAVE FUNCTION

• In the typical molecular system, the wave functions is used to

described the electrons in the system
• The wave function that describes the electrons are called
molecular orbitals

Next :
QC Part 2: Molecular Orbitals

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 CHM3701

COMPUTATIONAL
CHEMISTRY

Quantum Chemistry
Part 2
 MOLECULAR ORBITALS

• Molecular orbitals (MOs) are typically constructed from atomic

orbitals (AOs) (LCAO-MO method)
• In a typical setup, n number of AOs are needed to construct n
number of MOs
• In ab initio calculation, the set of initial (trial) functions is
described by what is called basis sets

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MOLECULAR ORBITALS

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 MOLECULAR ORBITALS

Types of basis sets

Minimal: One basis function (STO, GTO or CGTO) for each atomic
orbital in the atom

Double-zeta: Two basis functions for each AO

Triple-zeta: Three basis functions for each AO
and etc…for quadruple-zeta (QZ), 5Z, 6Z…

Having different-sized functions allows the orbital to get bigger or

smaller when other atoms approach it.

A split-valence basis uses only one basis function for each AO,
and a larger basis for the valence AOs

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 MOLECULAR ORBITALS
Slater Type Orbitals

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 MOLECULAR ORBITALS

𝜁(zeta) controls the width of the orbitals (large zeta

gives tight function, small zeta gives diffuse function)

Problem: STO’s are more accurate, but it takes longer

to compute integrals using them

Solution: Use a linear combination of enough GTOs to

mimic an STO

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 MOLECULAR ORBITALS
Gaussian Type Orbital (GTO)

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MOLECULAR ORBITALS

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 MOLECULAR ORBITALS
Minimum Basis Set

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 MOLECULAR ORBITALS
Extended Basis Set

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MOLECULAR ORBITALS

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 MOLECULAR ORBITALS
Split-valence Basis Set

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MOLECULAR ORBITALS

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MOLECULAR ORBITALS

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 MOLECULAR ORBITALS

Correlation-consistent Basis Set

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 MOLECULAR ORBITALS
Polarized Functions

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 MOLECULAR ORBITALS

• When polarized basis set is added to a carbon atom, a p -

function is added to each s - orbitals, and a d - function is
added to each p - orbital

• Polarization essentially allows the electrons to “move” to a

higher orbital. This allows better description of the molecular
orbitals.

• Polarization is especially important to heavy atoms.

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MOLECULAR ORBITALS

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 MOLECULAR ORBITALS

Diffuse Functions

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MOLECULAR ORBITALS

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MOLECULAR ORBITALS

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MOLECULAR ORBITALS

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To be continued…
Next: Self-Consistent Field (SCF) and Hartree-Fock Method

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 CHM3701

COMPUTATIONAL
CHEMISTRY

Quantum Chemistry
Part 3
 SCF/HF

• Hartree-Fock (HF) method is designed to solve the electronic

Schrödinger’s equation (time-dependent) after invoking the
Born-Oppenheimer’s approximation
• Solution to many-body (electrons) problems
• Assumption: electrons can be described by an anti-
symmetrized product (Slater determinant)
• Move independently

• Still feel the Coulomb repulsion due to average position of all electrons
(mean field)

• The solutions depends on orbitals

• Guess some initial orbitals – refine iteratively

• Self-Consistent Field (SCF) approach

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 SCF/HF

• The Schrodinger equation is of the form

• The Hamiltonian operator has the form

1st term on the right hand side is the kinetic energy of the electron
2nd term is the kinetic energy of the nuclei
3rd term is the potential energy between the electron and the nucleus
(electron-nucleus interaction)
4th term is the potential energy between the electrons (electron-
electron interaction)
5th term is the potential energy between the nuclei (nucleus-nucleus
interaction)
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 SCF/HF

• The general Schrodinger equation has many sets of acceptable

wave-function (eigenfunction) Ψi, each with gives a different
energy value (eigenvalue) Ei.

• For determining these wave-functions, these wave-functions

have to be orthonormal (or be made orthonormal), where for one
particle system,

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 SCF/HF

• If we multiply the whole equation by Ψi then the equation

becomes:

• Since the energy is a scalar value (a number), and since for

orthonormal wave-function the integration is equals to
kronecker delta, we have

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 SCF/HF
• For a molecular orbital, where more than one atoms are involved, the
wave-function used is the linear combination of the atomic wave-
functions Ψi .
• The molecular wave-function, Φ can be abbreviated as

• The normality of the Φ imposes a constraint

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 SCF/HF
• Thus, the sum of the square of the atomic wave-function coefficient
must be equal to 1.
• Considering the solution to the Schrodinger equation

and replacing the wave-function with our molecular wave-function

• Thus the energy Ei can be determined if the coefficients ci can be

determined.
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 SCF/HF

The Variational Principle

• The variational principle states that the true energy value of the
molecular system is the lowest value of the system.

• Any subsequent energy calculated from the approximation to the

Schrodinger equation is equals to OR higher than the true energy value
of the system.

• If E0 is the true energy value of the system, then Ei where i ≥ 0 is the

energy from the calculated approximation of the Schrodinger equation.

• In other words, our solution to the Schrodinger equation is

CHM3701
 SCF/HF
• If the molecular orbital is written as

• Then the solution to the energy can be written as:

• Here, the resonance integral, Hij and the overlap integral,

Sij has been introduced
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 SCF/HF

• The Hij is the resonance integral, where the value of Hii (the
two subscripts are the same) is the ionization energy.

• The Sij is the overlap integral, where the value describes the
extent of overlap between various molecular wave-function
overlap in space.

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 SCF/HF

• In the energy equation, the desired unknown to be solved are

the coefficients, ai

• In a typical fashion, from calculus, we know that a function is

at a minimum when the first derivative with respect to all
unknown is equals to 0
• i.e. df(x)/dx = 0

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 SCF/HF

• Thus, to solve for the unknown coefficients, ai, the first

derivative of the energy with respect to all coefficients is taken
and set to 0

• Performing these tedious differentiation and rearranging the

equation leads to

• These sets of k equations involves i unknowns. While the

value of Hki and Ski can be solved, the value of E is not
known.

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 SCF/HF

• But, from linear algebra, it is known that a set of linear equations has a
real solution if determinants formed from the unknown coefficients is
equals to 0

• In our case, the molecular orbital wave-function coefficients ai are the

unknowns, and the various (Hki-ESki) terms are the coefficents

• Solving for the equations of the determinant will give the value of the
energy, Ei

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 SCF/HF

• Plugging the value of Ei into the differentiated form of the

equation

allow to solve for the coefficients ai

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 SCF/HF

• In general, the Hartree-Fock algorithm to solve for the

coefficients of the wave-functions are:

1. Select a set of N basis functions

2. Determine the value of all Hij and Sij
3. Using the secular determinant equation, determine the
various energy values Ei
4. From all of the Ei values, solve the ai equations
to solve for the coefficients

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 SCF/HF

EXAMPLE
The Simple Huckel Method applied to Allyl system (C3H5)

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SCF/HF

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SCF/HF

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 SCF/HF

• The number of basis set of the allyl system implies that the secular
equation will be a 3 x 3 form
• Plugging in the Hij and Sij values gives

• Multiply out the determinant gives

where the three energy values are

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 SCF/HF

• Using these energy values, solve for the various coefficients

ai:

• This will result in the value of

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 SCF/HF

• The Hamiltonian used in the previous example is

• Specifically, the electron-electron interaction (repulsion) is not

explicitly described.

• How does the e2 term describes the electrons when all this
while we are trying to find the best description of the
electrons?

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 SCF/HF

• Hartree modified the electron-electron repulsion to:

• In the equation, the electron-electron repulsion term is

replaced by the density of the electrons

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SCF/HF

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SCF/HF

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To be continued…
Next: Higher Order Methods and Density Functional Theory

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 CHM3701

COMPUTATIONAL
CHEMISTRY

Quantum Chemistry
Part 4
 DFT

Density Functional Theory (DFT)

• Hartree-Fock method does not include electron-electron

repulsion exactly.
• This led to incorrect properties.
• DFT is created to overcome this problem.

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 DFT

• In DFT, the energy is a function of the density:

the 1st term is the kinetic energy of non-interacting electron

the 2nd term is the nucleus-electron interaction
the 3rd term is the electron-electron interaction
the 4th term is the correction term to the kinetic energy
the 5th term is the correction to the electron-electron repulsion

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 DFT

• The electron-electron correlation causes an extra term called

the exchange-correlation term

• This necessitate the use of “functionals”

• Functionals are the energy term of the DFT energy equation
that contains “experimental data”

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 DFT

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 DFT

Typical functionals:
1. Local Density Functionals (LDA)
2. Generalized Gradient Approximation (GGA)
3. Hybrid Functionals
4. More advanced functionals

In general, the accuracy of the calculation follows the trend:

LDA < GGA < hybrid functionals

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 DFT

1) LDA Functionals
• SVWN

2) GGA Functionals
• BP86, BLYP, OLYP/TPSS, PBE

3) Hybrid Functionals
• B3LYP, TPSSh, M05, M06, M08, M11, M12

Calculation involving transition metals requires the hybrid

functionals. The Minnesota set of functionals (especially M06)
are known to produce good results for transition metals.

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 DFT

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 DFT

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 DFT

• All of the DFT functionals mentioned failed to take into

account long-range interaction accurately (dispersion
interaction).
• The dispersion affects the long-range interaction between
atoms located about 10 Angstroms apart or further.

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 DFT

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 DFT

While typically, dispersion interaction is considered weak, but

when the number of atoms involve is big, the dispersion
interaction energy can be significant:

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 DFT

• All of the DFT functionals mentioned failed to take into

account long-range interaction accurately (dispersion
interaction). To overcome this problem, Grimme created the
dispersion-correction functions.

• These functions are known as:

• D1 – first generation dispersion correction
• D2 – second generation dispersion correction
• D3 – third generation dispersion correction
• D3(BJ) – improved version of the D3 dispersion correction

The dispersion physically corrects for the long-range interaction

between atoms ~10 Angstroms apart.

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 DFT

Performance of Various DFT Functionals

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 DFT

Practical applications of ab initio method

1. Calculate the energy of atoms & molecules (electron +

nucleus)
2. Perform geometry optimization of molecules
3. Predict the IR spectrum (second derivative, provide
frequency and force constant)
4. Predict mechanism of a reaction
5. Calculate the NMR chemical shift
6. Calculate ‘partial charges’ of atoms in a molecule

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 DFT

2. Perform Geometry Optimization of Molecules

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 DFT

2. Perform Geometry Optimization of Molecules

• Typically, the frequency calculation is performed to conform that

the optimized structure is correct.

• The frequency calculation will produced only 1 negative

frequency if the optimized structure is a reactant or a product,

• and 2 negative frequencies if the optimized structure is a

transition state structure.

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 DFT

2. Perform Geometry Optimization of Molecules

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 DFT

4. Predict mechanism of a reaction

• Involves a few steps

i. Determine the geometry and thus the energy of the
reactants and the products
ii. Determine the geometry and thus energy of the transition
state (the most time consuming steps!!!)
iii. Determine the energy difference between the transition
state and the reactants and products

• The lowest energy transition state(s) is typically the correct

mechanistic pathway for the reaction

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 DFT

4. Predict mechanism of a reaction

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End of Chapter 5

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