Computational Chemistry: Basics to
Applications.
Introduction-Quantum mechanical calculations
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What Is Computational Chemistry?
➢ The study, prediction, and comprehension of chemical reactions,
molecular structures, and material properties through the use of
computers is known as computational chemistry.
➢ Chemists investigate molecular behavior using simulations based
on the principles of quantum mechanics, classical physics, and
statistical mechanics rather than carrying out actual experiments
in a lab.
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Lewars, Errol G. "Computational chemistry." Introduction to the theory and applications of molecular and quantum
Computational chemistry is the use of computers to
solve the equations of a theory or model for the
properties of a chemical system.
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Three “Pillars” of Scientific Investigation
⮚ Experiment
⮚ Theory (analytical equations)
⮚ Computational Simulation
⮚ (“theoretical experiments”)
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⮚Simulation is becoming a third pillar of science, along
with theory and experiment.
⮚Using theory, we develop models: simplified
representations of physical systems.
⮚We test the accuracy of these models in experiment,
and use simulation to help refine this feedback loop.
⮚Anything that can be measured can be simulated,
including properties related to energetics, structures,
and spectra of chemical systems.
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The Nobel Prize in Chemistry 1998
John A. Pople Walter Kohn
The Nobel Prize in Chemistry 1998 was divided equally between
Walter Kohn "for his development of the density-functional
theory" and John A. Pople "for his development of
computational methods in quantum chemistry".
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2013 Nobel Prize In Chemistry
"for the development of multiscale models for complex chemical systems”
• Martin Karplus, Université de Strasbourg, France, and Harvard University,
Cambridge, MA, USA
• Michael Levitt, Stanford University, Los Angeles, CA, USA
• Arieh Warshel, University of Southern California (USC), CA, USA 7
Computational Chemistry
WHY
do theoretical calculations?
WHAT
do we calculate?
HOW
are the calculations carried out?
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Why computational
Why computational chemistry?
chemistry?
Used by Top
Research No Safety Risks: No
Reduces Experimental Costs
Institutions & Explosions, No Toxic Exposure
Industries
Saves Time: Faster Than Describes Atomic Chemical
Traditional Experiments Reactions in Detail
Works for Systems That Are Predicts the Future of
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Difficult to Study Facilitates New Material and Drug Design
Chemistry & Materials
Chemistry On Computer. Why?
Advantages:
➢ Calculations are easy to perform whereas experiments are difficult.
➢ Calculations are safe where many experiments are dangerous.
➢ Calculations are becoming less costly whole experiments are becoming
more expensive.
➢ Calculations can be performed on any chemical system, whereas
experiments are relatively limited.
➢ Calculations give direct information whereas there is often uncertain
in interpreting experimental observation.
➢ Calculations give fundamental information about isolated
molecules without the complicating solvents
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Lewars, Errol G. "Computational chemistry." Introduction to the theory and applications of molecular and quantum
What Does Computational Chemistry
Calculate?
Energy, structure, and properties
➢ What is the energy of the given geometry?
➢ How does energy vary when geometry changes?
➢ Which geometries are stable?
➢ How do atoms rearrange to form new molecules?
➢ How do structure, energy, and properties change over time?
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Lewars, Errol G. "Computational chemistry." Introduction to the theory and applications of molecular and quantum
Properties that can be calculated with
computational chemistry are:
◆ Geometry Optimization
◆ Stability and Reaction Mechanism
◆ Transition-state structures
◆ Dipole moments and polarizabilities
◆ Electron and Hole Density Distribution Maps
◆ Vibrational frequencies, IR and Raman Spectra
◆ NMR spectra
◆ Electronic excitations and UV spectra
◆ Thermochemical data
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Lewars, Errol G. "Computational chemistry." Introduction to the theory and applications of molecular and quantum
Computational Chemistry Methods
Methods that make use of
Quantum mechanics to
Methods that use Newton model the molecular
mechanics to design system. This method uses
molecular system different types of
approximation to solve
Schrodinger’s equation.
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Computational Methods
Computational Methods
Quantum Mechanics Classical Mechanics
Semi-empirical Method Ab initio methods Molecular Mechanics (MM)
Molecular Dynamics (MD)
Density Functional Theory (DFT)
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Classical Physics Approach
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Molecular Mechanics:
◆ This method treats molecules as a collection of atoms (balls)
connected by bonds that behave like springs. It uses classical
mechanics (the physics of everyday objects) to calculate the
potential energy of a molecule.
◆ The energy of a molecule is calculated based on how much its
actual geometry deviates from these ideal values.
◆ Geometry optimization involves adjusting the atom positions until
the lowest possible energy is found.
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Lewars, Errol G. "Computational chemistry." Introduction to the theory and applications of molecular and quantum
Molecular Dynamics:
▪ MD simulations apply the laws of classical mechanics to simulate
the movement of atoms and molecules over time.
▪ These calculations apply the laws of motion to molecules, which
change shape or move.
▪ MM is not an electronic structure method; covalent bond-breaking
and bond-making (in contrast to conformational changes) cannot be
studied with molecular dynamics programs that use this method.
▪ For the study of chemical reactions, forces generated with
semiempirical, ab initio, or density functional methods can be used.
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Lewars, Errol G. "Computational chemistry." Introduction to the theory and applications of molecular and quantum
Quantum Mechanics Approach
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Quantum
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• Black Body radiation : Spectral distribution of
intensity of black body radiation Vs frequency.
• As T , maximum shifts to higher freqs and total
radiated energy
• Dashed line in diagram shows prediction of Rayleigh-Jeans law. This
law reproduces exptal data at low freqs.
Expression acc to laws of 19th century physics is
𝑑𝜌(,T) = 𝜌 𝑇 𝑑= 8kb 2 d /c3
• At higher freqs, Rayleigh-Jeans law predicts that radiant energy
diverges as 2 (freq).
• Bcoz freq as radiation enter U.V. region, this divergence was called
Ultraviolet catastrophe.
• People struggled to find theoretical explanation of black body
radiation
• Max Planck : assumed that radiation by black body was caused by
oscillation of electrons of constituent particles.
• Electrons as oscillating in an atom
• E = nh , is freq, n- integer
1
• 𝜌 𝑇 𝑑 = 8 h 3 d /c3 𝑒 ℎ/𝑇𝑘𝑏 −1 - (1)
• Excellent agreement for all freqs and with exptal data if h is Planks
const = 6.626 x 10-34 Js
• Theory of black body radiation : used to estimate surface temps of
stars
• Eqn (1) can be used to derive Stefan-Boltzmann Law.
• Planck : Energies of oscillators have to be an integral multiple of h.
• Einstein explained photoelectric effect with Quantum theory
Photoelectric effect :
• Classical theory : Intensity of radiation proportional
to square of the amplitude of electric field.
• Intensity of radiation increases, so does the
amplitude of electric field
• Disagreement of classical theory with expt
• Exptally, K.E. of ejected electrons is independent of
intensity of incident radiation.
• Classical pic : P.E. effect should occur for any freq of
light as long as intensity is sufficiently high.
• Expts : there is threshold frequency characteristic of
metallic surface, below which no electrons are
ejected, regardless of intensity of radiation.
• Above 0 , K.E. of ejected electrons varies linearly
with freq. These observations were contradicting
the classical theory.
• Planck : E = nh
• Using this, Einstein proposed radiation existed as
small packets of energy called photons.
• K.E. of ejected electron is equal to energy of
incident photon minus minimum energy required to
remove an electron from surface of metal.
• K.E. = ½ mv2 = h - , - Work function
• Threshold freq h 0 =
• K.E. = ½ mv2 = h - h 0
• Plot of KE Vs should be linear and slope should be
h, in complete agreement with data is shown below
Schrodinger Equation
Ab Initio Calculations
◆ These methods attempt to solve the Schrödinger equation from "first principles" (ab
initio means "from the beginning" in Latin) without relying on experimental data.
The Schrödinger equation describes the behavior of electrons in a molecule.
◆ Starts with only the fundamental physical constants and the atomic numbers and
positions of the atoms in the molecule.
◆ The ab initio method solves the Schrödinger equation for a molecule and gives us an
energy and a wavefunction.
◆ The wave function is a mathematical function that can be used to calculate the
electron distribution.
◆ From the electron distribution, we can tell things like how polar the molecule is and
which parts of it are likely to be attacked by nucleophiles or by electrophiles.
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Lewars, Errol G. "Computational chemistry." Introduction to the theory and applications of molecular and quantum
Semi Empirical Calculations
❖ Semiempirical calculations offer a balance between accuracy and computational
speed by simplifying ab initio methods with approximations and experimental
parameters. They are based on the Schrödinger equation but use more
approximations to solve it.
❖ Semiempirical methods start with the ab initio Hartree-Fock calculations but
simplify them by approximating or omitting certain integrals.
❖ This plugging of experimental values into a mathematical procedure to get the
best calculated values is called parameterization (or parametrization).
❖ Semiempirical calculations are slower than molecular mechanics (molecular
mechanics, too, is parameterized) but much faster than ab initio calculations.
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Lewars, Errol G. "Computational chemistry." Introduction to the theory and applications of molecular and quantum
Schrödinger equation
The Schrödinger equation is the foundational equation of quantum
mechanics. It describes how the quantum state (wavefunction) of a
physical system evolves.
Time-Independent Schrödinger Equation (TISE)
This form is used to describe systems with fixed energy (e.g., electrons
in atoms):
Ĥ𝜓 = 𝐸𝜓
Ĥ is the Hamiltonian operator (total energy operator: kinetic +
potential)
𝜓 is the wavefunction of the system
E is the energy eigenvalue of the state
For a single particle in one dimension:
ℏ is the reduced Planck's constant
V is the potential energy function and m= massof the particle
Time-Independent Schrodinger’s Equation
➢ The Schrodinger equation is the basis of quantum
mechanics and gives a complete description of the
electronic structure of a molecule. If the equation
could be fully solved, all information pertaining to a
molecule could be determined.
Rigid
Rotor
➢ Schrodinger Equation can only be solved exactly for
simple systems.
Rigid Rotor, Harmonic Oscillator, Particle in a box,
Hydrogen Atom.
➢ For more complex systems (i.e. many electron atoms/
molecules) need some simplifying assumptions /
approximations and solve it numerically.
➢ However, it is still possible to get accurate results.
Harmonic
➢ In general, the cost of the calculation increases with the Oscillator
accuracy of the calculation and the size of the system.
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Density Functional Calculations
➢ Density function calculation is a mathematical entity related to a function, such as ab
initio and semiempirical calculations, based on the Schrödinger equation.
➢ DFT is based on the idea that the electronic structure of a molecule is completely
determined by its electron density (the probability of finding an electron at a given
point in space).
➢ Instead of calculating the wavefunction (as in ab initio methods), DFT directly
calculates the electron density.
➢ DFT uses functionals (mathematical functions of functions) to approximate the
relationship between the electron density and the energy of the molecule.
➢ Generally more accurate than Hartree-Fock theory and often comparable to more
advanced ab initio methods, but at a significantly lower computational cost.
➢ Can be applied to a wide range of molecules and properties.
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Lewars, Errol G. "Computational chemistry." Introduction to the theory and applications of molecular and quantum
Overview
❑ Computational chemistry allows one to calculate molecular
geometries, reactivities, spectra, and other properties. It
employs:
❑ Molecular mechanics – based on a ball-and-springs model of
molecules
❑ Ab initio methods – based on approximate solutions of the
Schrödinger equation without appeal to fitting to experiment.
❑ Semiempirical methods – based on approximate solutions of
the Schrödinger equation with appeal to fitting to experiment
(i.e., using parameterization).
❑ Density functional theory (DFT) methods – based on
approximate solutions of the Schrödinger equation, bypassing
the wavefunction that is a central feature of ab initio and
semiempirical methods.
❑ Molecular dynamics methods study molecules in motion
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Lewars, Errol G. "Computational chemistry." Introduction to the theory and applications of molecular and quantum
Molecular Orbital Theory
❖ The molecular orbital theory is a theory on chemical bonding developed at
the beginning of the twentieth century by F. Hund and R. S. Mulliken to
describe the structure and properties of different molecules.
❖ In Molecular Orbital Theory, the bonding between atoms is described as a
combination of their atomic orbitals.
❖ The Molecular Orbital Theory allows one to predict the distribution of
electrons in a molecule, which in turn can help predict molecular properties
such as shape, magnetism, and bond order.
❖ Molecular orbital theory revolutionized the study of chemical bonding by
approximating the states of linear combination of atomic orbitals (LCAO).
❖ These approximations are made by applying the density functional theory
(DFT) or Hartree-Fock (HF) models to the Schrödinger equation.
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Molecular Orbital Theory
Linear Combination of Atomic Orbitals (LCAO) Figure. Molecular
Orbitals for the
H2 Molecule. (a)
This diagram shows
the formation of a
bonding
σ1s molecular orbital
for H2 as the sum of
the wave functions
(Ψ) (b) This plot of
the square of the
wave function (Ψ2)
for the bonding
σ1s molecular orbital
(c) This diagram
shows the formation
of an
antibonding σ∗1s mol
ecular orbital (d)
This plot of the
square of the wave
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function (Ψ2)
Molecular Orbital Theory
Linear Combination of Atomic Orbitals (LCAO)
❖ Molecular orbitals can generally be expressed through a linear combination of atomic
orbitals. These LCAOs are useful in the estimation of the formation of these orbitals in
the bonding between the atoms that make up a molecule.
❖ The Schrödinger equation is used to describe the electron behavior for molecular orbitals
❖ It is an approximate method for representing molecular orbitals. It’s more of a
superimposition method where constructive interference of two atomic wave functions
produces a bonding molecular orbital, whereas destructive interference produces a non-
bonding molecular orbital.
Conditions for Linear Combination of Atomic Orbitals
1. Same Energy of Combining Orbitals
The atomic orbitals combining to form molecular orbitals should have comparable
energy. This means that the 2p orbital of an atom can combine with another 2p orbital of another
atom. 36
Molecular Orbital Theory
2. Same Symmetry about Molecular Axis
❖ The combining atoms should have the same symmetry around the
molecular axis for proper combination; otherwise, the electron density
will be sparse.
❖ For e.g., all the sub-orbitals of 2p have the same energy, but still, the
2pz orbital of an atom can only combine with a 2pz orbital of another
atom, but cannot combine with 2px and 2py orbitals, as they have a
different axis of symmetry.
3. Proper Overlap between Atomic Orbitals
For proper energy, the two atomic orbitals should have the same
energy, and the proper orientation, the atomic orbitals should have proper
overlap, and the same molecular axis of symmetry. 37
Molecular Orbitals
❖ Molecular orbitals are basically mathematical functions that describe the wave
nature of electrons in a given molecule. Introduced by R. S. Mulliken in 1932, to
mean one-electron orbital wave functions that describe the Schrödinger wave
equation.
Formation of Molecular Orbitals
The waves of the two atomic orbitals may be in phase or out of phase.
When the two waves are out of phase, the
When the two waves are in phase so that waves are subtracted from each other so
they add up and the amplitude of the that the amplitude of the new wave is Φ
wave is Φ= ΨA + ΨB ´= ΨA – ΨB
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Orbital Interactions
• Orbital interactions are the overlap and coupling
of atomic and molecular orbitals, which
influence a molecule's electronic structure,
reactivity, and properties.
• These interactions are fundamental to concepts
like molecular bonding, chemical reactivity
through frontier molecular orbital theory, and
the magnetic properties of materials.
• Interactions can be stabilizing (bonding) when
filled and empty orbitals overlap to form lower
energy molecular orbitals, or destabilizing
(antibonding) when orbitals with opposite
phases interfere.
• The H₂ molecule forms when two hydrogen atoms
Molecular Orbital in H₂ overlap their 1s atomic orbitals.
and Bond Formation
• The overlapping 1s orbitals create a bonding molecular
orbital that contains the shared electrons.
• The bonding molecular orbital encompasses both
nuclei, holding them together.
• Hydrogen nuclei are separated by an optimum
distance called the bond length.
• Bond length arises from a balance between attractive
and repulsive forces:
• Attractive forces: nuclei attract the shared electrons
between them.
• Repulsive forces: nuclei repel each other due to
Energy vs. Internuclear Separation positive charges.
in H₂
• As atoms approach: Electron density between nuclei
increases, enhancing attraction and lowering potential
energy.
Orbital Interaction upon H2 molecule formation
Bonding orbital (σ):
Constructive combination of atomic orbitals.
Lower in energy than the atomic orbitals → energy
released during bond formation.
Antibonding orbital (σ*):
Results from this destructive interaction.
Higher in energy than the atomic orbitals →
destabilizes the molecule if occupied. Destructive
combination of wave functions:
Adding two wave functions with opposite signs is
like subtracting them. Causes destructive
interference → electron density cancels between
σ (bonding) < atomic 1s levels < σ* nuclei.
(antibonding). Node formation:
A nodal plane (region of zero electron density)
appears between the two atoms.
Molecular hydrogen (H2) is more stable than two isolated
hydrogen atoms by 104 kcal/mol.
p- orbital Interaction
p- orbital Interaction
p orbitals have two lobes with opposite phases (like a 2D wave above and
below zero).
Phase indication: Different lobes are often shown in different colors.
Constructive interference:
Lobes of the same phase overlap → electron density increases → bonding.
Destructive interference:
Lobes of opposite phase overlap → electron density decreases → nodes form
→ antibonding.
End-to-end overlap of p orbitals:
Forms σ (bonding) and σ (antibonding) orbitals*.
Formation of π and π Orbitals from p Orbitals*
Formation of π and π Orbitals from p Orbitals*
Side-by-side overlap of p orbitals forms:
π bonding orbital:
• Electron density above and below the internuclear axis
• Contains electrons that interact with both nuclei → holds atoms
together
π antibonding orbital*: Out-of-phase combination
Contains two nodal planes:
• Along the internuclear axis
• Perpendicular between the nuclei
• Higher in energy, weakens bonding if occupied
Methane Formation
Methane Formation
The formation of a carbon–hydrogen bond through the overlap of an
sp3 hybrid orbital with a hydrogen 1s atomic orbital. Note the formation of
both the bonding (σ) molecular orbital and the antibonding (σ*) molecular
orbital.
Methane Formation
• Carbon needs four equivalent orbitals to bond with four hydrogen atoms.
• The 2s, 2pₓ, 2pᵧ, and 2p_z orbitals of carbon mix to form four sp³ hybrid
orbitals.
• Each sp³ orbital has 25% s-character and 75% p-character.
• These orbitals are oriented toward the corners of a tetrahedron, keeping
electrons as far apart as possible.
• Each sp³ orbital overlaps with a hydrogen 1s orbital to form a σ (sigma)
bond.
• The H–C–H bond angle is 109.5°.
• The C–H bond length in methane is 1.09 Å.
• The geometry of methane is tetrahedral.
Potential energy curve/surface
➢ PEC = relationship between
➢ Energy a object has due to its molecule energy & geometry
relative position (position of atoms)
➢ When the object position ➢ Mathematical / graphical
changes = Potential energy representation
also change
Potential energy curve
➢ Chemical potential energy – ➢ Uses – understanding molecular
energy stored in bonds interactions & chemical reactions
➢ In quantum chemistry context ➢ Predicting reaction rate
– energy associated with ➢ Optimizing molecular structure
position of atoms and ➢ Molecular dynamics simulations
molecules 50
Potential energy curve
Potential energy Harmonic oscillator model
curve ➢ Potential energy is parabolic function
of displacement of R from
equilibrium position
➢ V (vibrational energy) = ½ k (R – Re)2
➢ Re = equilibrium position
➢ Diatomic molecule (AB)
➢ Molecule = balls & bond =
➢ Real molecule deviate from perfect
spring parabola
➢ Bond stretch's & compress – ➢ V = De (1 – e-a(R-Re))2
potential energy change
➢ As bond length changes = PE
decrease
➢ qe = equilibrium value
➢ A molecule can never be stationary at zero
potential energy 2
Potential energy surface
➢ Surface = top layer of material / Why we need ?
object
➢ Understand how energy
changes based on atom position
➢ Identifying transition state and
➢ Potential energy surface = intermediates of reaction
based on atomic position
➢ Predicting reaction rate
and energy
➢ Graph created with hills ➢ Finding most stable
and valleys
configuration
➢ Energy pathway
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Potential energy surface
2D -Potential
What if I take a water
energy curve molecule?
➢ One bond length
(both O-H distance
same) + 1 bond angle
= 2 parameter
➢ 2D object but needs
3D graph (including
energy)
➢ Represented by 2D graph
➢ Example – H2 gas
➢ only one bond length is ➢ A 3D graph is a potential energy
available surface (PES) 53
Potential energy hypersurface
What if I take HOF Can not be used!
molecule ?
➢ Parameter
1. O-H bond length ➢ 3 parameter needs 4D graph
2. O-F bond length ➢ Called potential energy
3. H-O-F bond angle hypersurface
➢ Potential energy ➢ For higher dimensions E =
54
f(q1, q2, q3….qn)
Potential energy surface
Determining transition state
energy
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Potential energy surface
Determining transition state
energy ➢ Lowest energy path
connecting ozone, isoozone &
transition state
➢ Stationary point = point
where surface is flat
➢ Two types
1. Energy minima
2. Saddle point
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Application of Potential Energy Surface
Electrostatic Potential (ESP)
Electrostatic potential (ESP) analysis uses the calculated electron
density of a molecule to map the potential energy of a positive
point charge placed at various locations around the molecule.
This mapping helps understand and predict molecular
interactions, reactivity, and other properties related to charge
distribution.
Molecular electrostatic potential
In essence, electrostatic potential maps in
quantum chemistry offer a way to visualize and
understand the "electrostatic fingerprint" of a Red - negative charge.
molecule, providing insights into its reactivity, Blue- positive charge
potential for noncovalent interactions, and
overall behavior.
Key Concepts and Uses
Molecular Electrostatic Potential (MEP) Maps:
These maps visualize the electrostatic potential around a molecule, typically using color
coding to represent positive (e.g., blue) and negative (e.g., red) regions.
Identifying Reactive Sites:
Regions of high negative potential (red/orange) indicate potential sites of
electrophilic attack, while regions of high positive potential (blue) suggest potential
sites for nucleophilic attack.
Understanding Noncovalent Interactions:
MEP maps help visualize how molecules interact, particularly through hydrogen
bonding and other noncovalent interactions.
Charge Distribution:
MEP maps offer a visual representation of how the electronic charge is distributed
within a molecule, which is crucial for understanding its chemical behavior.
Predicting Interactions:
By understanding the electrostatic potential distribution, one can predict how a
molecule might interact with other molecules or reagents, leading to a better 62
understanding of chemical reactions and processes.
Geometry optimization
• Geometry optimization in computational chemistry is the
process of finding the most stable, lowest-energy arrangement
of atoms in a molecule or system.
• This involves adjusting the positions of atoms to minimize the
total energy and identify stable structures like local minima or
transition states.
Geometry Optimization
• Geometry optimization finds the lowest energy structure of a molecule.
• The bond lengths and angles are stabilized to minimize total energy.
• The graph shows energy decreasing with each optimization step.
• Final structure represents the most stable geometry of water.
Geometry optimization
Purpose:
Geometry optimization is a crucial step in many computational chemistry studies,
as it helps determine the most stable and likely conformation of a molecule or
system.
Methods: Various methods are used for geometry optimization, including:
Energy Minimization: Algorithms like Newton's method or quasi-Newton
methods are employed to iteratively adjust atomic positions until the energy is
minimized.
Output: The result of a geometry optimization is a stable molecular geometry that
represents a local minimum on the potential energy surface. This optimized
geometry can then be used for further calculations, such as electronic structure
calculations or vibrational analysis.
Importance:
Accurate molecular geometries are essential for reliable calculations of electronic
structures, spectroscopic properties, and reactivity.
Frequency Calculation
• Molecular frequency calculation determines the vibrational
modes of a molecule.
• It helps confirm whether the optimized structure is a true
minimum or a transition state.
• Positive frequencies indicate a stable structure, while one
imaginary frequency indicates a transition state.
• These calculations provide IR and Raman active modes,
useful for spectroscopic analysis.
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Frequencies of Water Molecules
Calculated Results 3810cm-1 3907 cm-1 1639 cm-1
• Quantum calculations use ideal and simplified models, while experiments involve real-
world conditions.
• Differences arise due to temperature, environment, and measurement effects not
included in theory.
The comparison between the experimental and the theoretical IR
spectrum of the studied ninhydrin-glycine Schiff base complexes
Excited State
Computational chemistry investigates excited states by simulating how
electrons move to higher energy levels after a molecule absorbs energy,
typically from a photon
IMPORTANCE
Excited states are fundamental to photochemistry,
photophysics, photobiology, and material science. They are
involved in processes like light absorption, emission, and
chemical reactions.
Calculating excited states is computationally intensive due to
the need for accurate quantum mechanical calculations.
Excited states are relevant in various fields, including solar
energy conversion, photocatalysis, and biological systems.
70
Excited State
• In a molecule, electrons occupy molecular orbitals according to their
energy.
• The HOMO contains the electrons in the ground state.
• The LUMO is the next available empty orbital.
• When the molecule absorbs energy (like light or heat), an electron from
the HOMO is promoted to the LUMO.
• This process is called excitation, and the molecule is now in an excited
state.
• The energy difference between the HOMO and LUMO (ΔE) corresponds
to the excitation energy or the wavelength of absorbed light.
• In quantum chemical calculations, this energy gap helps us understand
optical properties, color, and reactivity of the molecule.
Excited State
• When a molecule is excited, one of its
electrons moves to a higher energy
orbital.
• The two unpaired electrons can have
either antiparallel or parallel spins:
• If the spins are antiparallel, the total
spin quantum number is S = 0.
• This is called a singlet state
(multiplicity = 2S + 1 = 1).
The ground state of most molecules is a singlet • If the spins are parallel, the total spin
state, while the first excited state may be either quantum number is S = 1.
singlet (S₁) or triplet (T₁) depending on the spin
orientation. • This is called a triplet state
(multiplicity = 2S + 1 = 3).
Exctied State - Ethene • In ethylene, an electron from the
HOMO (π orbital) can be promoted to
the LUMO (π* orbital).
• The excitation occurs with UV light (≈
200–400 nm).
• The excited state formed has paired
spins (singlet state).
• Energy is absorbed during excitation
and emitted when the electron returns to
the ground state.
• Higher homologs like 1,3-butadiene,
1,3,5-hexatriene, and 1,3,5,7-
octatetraene show similar π → π*
transitions.
Experimental and Calculated Electronic Transitions, Excitation
Energy, and Their Assignments for the PVPP−Phenol Complex,
PVPP, and Phenol
Excitatio Excitatio Major
Compoun λmax λmax Charact
n Energy n Energy Contributio
d (nm) (nm) er
(eV) (eV) n (>20%)
Expt. Theory
PVPP– 99%
phenol 338 3.78 325 3.81 (HOMO → π → π*
complex LUMO)
73.3%
PVPP 278 4.46 280 4.43 (HOMO → π → π*
LUMO + 1)
24%
(HOMO → π → π*
LUMO)
82.4%
Phenol 289 4.29 269 4.61 (HOMO → π → π*
HOMO-LUMO of (a) phenol, (b) PVPP, LUMO)
and (c) PVPP− phenol.
DOI: 10.1021/acsomega.1c02699
Frontier molecular orbital’s (HOMO
and LUMO) of the complexes
Reaction Mechanism
In computational chemistry, a reaction mechanism describes how reactants transform into
products at the molecular level, including all intermediates, transition states, and energy
changes.
Quantum chemical calculations allow us to model experimental observation steps and
understand:
• Which bonds break/form
• The energy profile along the reaction pathway
• The most favorable pathway (kinetics and thermodynamics)
Steps to Study a Reaction Mechanism
Computationally
I. Structure Optimization of Reactants and Products
II. Use methods like DFT, Hartree-Fock, or semi-
empirical methods to get stable geometries.
III. Confirm they are energy minima via frequency
calculations (all vibrational frequencies positive).
⚫ Identifying Transition States (TS)
• Transition states are the highest energy point along the
reaction path
⚫ Energy Profile / Reaction Pathway
• Calculate relative energies of reactants, TS, intermediates, and
products.
• Construct a potential energy surface (PES) showing activation
barriers and reaction exothermicity/endothermicity.
Frequency Analysis
For TS, there should be exactly one imaginary frequency
corresponding to the reaction coordinate.
For reactants/products, all frequencies must be real.
Mechanistic Insights
Examine bond distances, charges, and electron density
changes along the pathway.
Analyze transition state geometries to understand which
bonds are forming/breaking
Potential Energy Diagram (Reaction Coordinate Diagram) showing the
energy pathway for a chemical reaction.
• The diagram represents an SN2
reaction, where bond-breaking and
bond-forming occur simultaneously
in a single step.
• The transition state shows partial
bonds — the C–Br bond is partially
broken, and the C–Cl bond is
partially formed.
• The transition state resembles the
reactant more than the product,
indicating an early transition state.
• As the reaction proceeds, the C–Br
bond lengthens and the C–Cl bond
shortens, leading to the formation
of the product.
Potential Energy Diagram (Reaction Coordinate Diagram)
showing the energy pathway for a chemical reaction.
• The diagram shows how energy changes
as reactants convert into products
during a chemical reaction.
• The peak represents the transition state,
where the system has maximum energy.
• The activation energy (Ea) is the energy
barrier that must be overcome for the
reaction to proceed.
• The energy difference (ΔE) between
reactants and products indicates
whether the reaction is exothermic or
endothermic.
Geometries of Formaldehyde reactants,
TS and product in the formation of glycolaldehyde
*RC - Reaction Complex
*TS- Transition State
Computational Study of Gold-catalyzed
cycloisomerization of functionalised allenes
Study of transition metal
catalyzed mechanisms
using computational
Global maxima methods and appropriate
algorithms for transition
states investigation in the
potential energy surface.
Global minima
Calculated energy profile for the reaction pathway R1
of Trimethy Amine(TMA) interacting with
4Hydroquinone.
[Link]
Advantages of Computational Mechanistic
Studies
• Can predict reaction pathways before experiments.
• Identify hidden intermediates or TS that are hard to observe.
• Quantify activation barriers and rate constants.
• Explore solvent and substituent effects systematically.
Application of Artificial Intelligence to Screen
Semiconductors
• AI accelerates the discovery of new semiconductor
materials by predicting their key properties without costly
synthesis or simulations.
• Traditional computational screening (like DFT) is time-
consuming — AI models can instantly estimate bandgap,
stability, and mobility.
86
AI-Driven Screening of
Semiconductor Materials
87
Introduction to AI and ML
➢ Artificial intelligence - Simulation of human intelligence in machines that
are programmed
➢ Machine learning – subset of AI that enables systems to learn from data
and improve over time without being explicitly programmed
➢ Make predictions or decisions based on data
➢ Types of machine learning
1. Supervised learning – Labeled data
2. Unsupervised learning – Unlabeled data
3. Reinforcement learning – learning by rewards and penalties 88
Application
➢ Prediction – material properties – conductivity and stability
➢ Classification – classifies huge number of materials based on the
requirement
➢ Accelerate identification of drug design
➢ Generative models to design novel compounds
➢ Reaction prediction and optimization
➢ Spectroscopy and structural analysis
➢ Predict pollutant behavior and degradation
89
AI-Driven Screening of Semiconductor
Materials
➢ Screening and identification of optimal semiconductor material
➢ Data – Formation energy, lattice constants, density, and total magnetization
➢ Target – Band gap (eV)
➢ Model is trained for classification, regression and clustering
➢ Hyperparameter is used to optimize the best model
➢ Top semiconductor with band gap is predicted
90
AI-Driven Screening of Semiconductor
Materials
Figure 1. a) Feature importance plot for XGBoost model and b) Predicted top 10 materials 91
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