Introduction
Dr. Vipin Kumar Mishra
Overview of the course
• Course Name: Introduction to Computational Chemistry
• Course Code: CHY1005
• LTP Course: Lecture, Tutorial, and Practical
• 4 Credits; 3 Sessions per week
Course structure
•Module 1: Introduction: Overview of the course, history and promises of
computational chemistry, tools for computational chemistry, units, errors in
computed quantities.
•Module 2: Quantum Chemistry: Historical development, Bohr’s atomic model,
de Broglie wavelength, Heisenberg uncertainty principle, Schrodinger equation,
Wave function, particle in a box, Hydrogen atom, radial and angular solution to
hydrogen atom, applications and limitations.
•Module 3: Thermodynamics: Intensive and extensive variables, state and path
functions, Laws of Thermodynamics (First law and enthalpy; second law and
entropy, spontaneity, and equilibrium; third law and absolute entropy) free energy,
Gibbs and Maxwell's relations, Ideal and real gases.
Course structure
•Module 4: Potential Energy Surfaces: Chemical bonds and intermolecular
interactions, Types of intermolecular interactions (charge distribution of isolated
molecules, electrostatic interaction, induction interaction, London or dispersion
forces, hydrogen bonding, repulsive interaction, relative contribution of different
terms), representing the potential energy surfaces (pair additivity, rare gas),
intramolecular interactions (bond stretching, angle bending, torsional and improper
terms).
•Module 5: Molecular Dynamics: Introduction to ensembles, force fields,
integration of Newton’s laws of motion, force calculation, energy minimization,
periodic boundary conditions, choice of input configuration, velocities, and
time-step, applications, and calculation of simple thermodynamic variables.
•Guest Lectures
Physics:
Behaviour of Matter When it is
motion.
Physics: Classical Physics (Before 1900)
Classical mechanics deals with the
motion of bodies under the influence of
forces or with the equilibrium of bodies
when all forces are balanced.
Newton
Huugen
Young
Nature of Light:
❖ Newton: Beam of Particles
❖ Huygens: Wave
❖ Young: Wave and Energy Continuous
❖ 1900: Max Planck: Black body Radiation: Energy is Quantized
❖ 1905: Albert Einstein: Photo Electric Effect: Light is Particle:
Energy Quantized
❖ 1924:De-broglie: wave particle Duality nature :
Quations
Question 1: Find the wavelength of an electron
moving with a speed :
Given:
Velocity of the electron, v =2×106 ms-1
Mass of electron, m =9.1×10-31 Kg
Planck’s Constant, h = 6.62607015×10−34 Js
Question 2: Find the wavelength of an Elephant
moving with a speed :
Given:
Velocity of the electron, v =20 ms-1
Mass of electron, m =1000 Kg
Planck’s Constant, h = 6.62607015×10−34 Js
Overview of Computational Science
• Computational science is the application of computational and
numerical techniques to solve large and complex problems.
Overview of Computational Chemistry
• Computational chemistry is simply the application of chemical,
mathematical and computing skills to the solution of interesting
chemical problems.
• Useful way to investigate materials that are too difficult to find or too
expensive to purchase.
• Make predictions before running the actual experiments.
• Schrödinger equation is the basis.
Questions commonly investigated
computationally are
• Molecular geometry: the shapes of molecules – bond lengths, angles
and dihedrals.
• Energies of molecules and transition states: this tells us which
isomer is favored at equilibrium, and (from transition state and
reactant energies) how fast a reaction should go.
Questions commonly investigated
computationally are
Grambow, C.A.,
Pattanaik, L. &
Green, W.H.
Reactants, products,
and transition states
of elementary
chemical reactions
based on quantum
chemistry. Sci
Data 7, 137 (2020).
• Chemical reactivity: for example, knowing where the electrons are
concentrated (nucleophilic sites) and where they want to go
(electrophilic sites) enables us to predict where various kinds of
reagents will attack a molecule.
Questions commonly investigated
computationally are
• IR, UV and NMR spectra: these can be calculated, and if the
molecule is unknown, someone trying to make it knows what to look
for.
Questions commonly investigated
computationally are
• The interaction of a substrate with an enzyme: seeing how a
molecule fits into the active site of an enzyme is one approach to
designing better drugs.
Drug discovery to fight COVID-19: Deep learning paired with drug docking and
molecular dynamics simulations.
Questions commonly investigated
computationally are
• The physical properties of substances: these depend on the properties of individual
molecules and on how the molecules interact in the bulk material. For example, the
strength and melting point of a polymer (e.g. a plastic) depend on how well the
molecules fit together and on how strong the forces between them are.
Tools of Computational Chemistry
• Two approaches (general):
(a) Quantum Mechanical Methods: numerical computation of
molecular electronic structures by density functional methods, ab
initio and semi-empirical techniques.
(b) Classical Computational Methods: formulation of analytical
expressions for the properties of molecules and their reactions.
Molecular Mechanics/Molecular Dynamics/Monte – Carlo Methods.
Tools of Computational Chemistry
Advantages Disadvantages Best for
Hybrid Methods: QM/MM
Tools of Computational Chemistry
• Ab initio methods – based on approximate solutions of the Schrodinger
equation without appeal to fitting to experiment.
• Semiempirical methods – based on approximate solutions of the
Schrodinger equation with appeal to fitting to experiment (i.e. using
parameterization).
• Density functional theory (DFT) methods – based on approximate
solutions of the Schrodinger equation, bypassing the wavefunction that is a
central feature of ab initio and semiempirical methods.
• Molecular mechanics – based on a ball-and-springs model of molecules.
• Molecular dynamics methods study molecules in motion.
Revision: Introduction to Computational
Chemistry
Length and time scales
Conducting a computational project
These questions should be answered
● What do you want to know?
● How accurate does the prediction need to be?
● How much time can be devoted to the problem?
● What approximations are being made?
The answers to these questions will determine the type of calculation,
model to be used.
History and evolution of Computational
Chemistry
• 1925: Heisenberg publishes his first paper on quantum mechanics (Z.
Phys., 1925, 33, 879).
• 1926: Schrödinger publishes his first paper on the theory of quantum
mechanics (Ann. Phys., 1926, 79, 361).
• 1931: Pi electron theory postulated by Hückel (Z. Phys., 1931, 70,
204).
• 1943: The first computer, the ENIAC (Electronic Numerical Integrator
and Computer) is built for the US Army Ordnance Department.
• 1951: The first UNIVAC (Universal Automatic Computer) is delivered
to the Census Bureau.
• 1953: Metropolis and co-workers describe the application of the Monte
Carlo method of simulation to physical chemistry problems (J. Chem.
Phys., 1953, 1087, 21).
History and evolution of Computational
Chemistry
• 1955: Scherr reports the first ab initio calculation for a large system, N2.
• 1956: Alder and Wainwright –molecular dynamics (MD) simulation of hard
spheres.
• 1957: Pople publishes details on the application of self-consistent molecular
orbital methods to pi electrons (J. Phys. Chem., 1957, 61, 6).
• 1958: The first integrated circuit board is constructed by Jack Kilby at Texas
Instruments.
• 1961: Hendrickson publishes the results of calculations of relative conformational
stabilities of cyclohexane (J. Amer. Chem. Soc., 1961, 83, 5537).
• 1964: Hansch and Fujita describe a new approach to analyzing drug actions:
QSAR, a quantitative structure activity relationship (Hansch, C and Fujita, T., J.
Amer. Chem. Soc., 1964, 86, 1616).
• 1964: Rahman–MD simulation of liquid Ar
History and evolution of Computational
Chemistry
• 1966: Cyrus Levinthal, et. al. publish paper on the use of molecular graphics and computer
simulation (Levinthal, C.; Scientific American, 1966, 214: 42).
• 1969: Levitt and Lifson report the use of force fields to refine protein conformations derived
from experimental data (Michael Levitt and Shneior Lifson; J. Mol. Biol., 1969, 46,
269-279).
Ken Thompson, Dennis Ritchie and Joseph Ossanna develop a new operating system,
UNIX, for the DEC PDP-7.
Dennis Ritchie and Brian Kernighan create “C” at Bell Labs.
• 1971: Rahman and Stillinger–MD simulation of water.
• 1973: The Brookhaven Protein Data Bank is announced (Acta. Cryst. B, 1973, 29: 1746);
N.L. Allinger describes the modeling of hydrocarbons with a new force field, MM1
(Allinger, N.L.; Sprague, J.T.; J. Amer. Chem. Soc., 1973, 95: 3893).
History and evolution of Computational
Chemistry
• 1975: Microsoft is founded by Bill Gates and Paul Allen.
• 1977: Martin Karplus, et. al. publish the first molecular
dynamics study of a protein (McCammon, J.A.; Gelin, B.R.;
Karplus, M.; Nature, 1977 267: 585-590).
• 1980: The first issue of the Journal of Computational
Chemistry is published.
• 1981: AMBER Force-field for proteins/DNA calculations;
IBM introduces its Personal Computer to the market.
• 1982: An algorithm for docking small molecules to receptors
(later to become the DOCK program) is published by Irwin
Kuntz and colleagues (Kuntz, I.D.; Blaney, J.M.; Oatley, S.J.;
Langridge, R.; Ferrin, T.E.; J. Mol. Biol., 1982, 161, 269).
History and evolution of Computational
Chemistry
• 1983: Martin Karplus, et. al. publish description of the CHARMM program (Brooks,
B.R.; Bruccoleri, R.E.; Olafson, B.D.; States, D.J., Swaminathan, S. and Karplus, M.; J.
Comp. Chem., 1983, 4:187-217); W. F. van Gunsteren, et. al. publish description of
molecular dynamics of proteins using GROMOS program (van Gunsteren, W. F.;
Berendsen, H. J. C.; Hermans, J.; Hol, W. G. J.; Postma, J. P. M.; Proc. Natl. Acad. Sci.,
1983, 80: 4315); The Compact Disk (CD) is launched.
• 1983 – Till now: A lot of developments!! (Not mentioned here.)
• NOBLE PRIZES:
• 1998: Walter Kohn, "for his development of the density-functional theory", and John
Pople, "for his development of computational methods in quantum chemistry", received
the 1998 Nobel Prize in Chemistry.
• 2013: Martin Karplus, Michael Levitt and Arieh Warshel received the 2013 Nobel
Prize in Chemistry for "the development of multiscale models for complex chemical
systems".
Severe Acute Respiratory Syndrome
Coronavirus 2 (SARS-CoV-2)
Severe Acute Respiratory Syndrome
Coronavirus 2 (SARS-CoV-2)
Introduction: Measurements
Dr. Arindam Ghosh
Measurements in everyday life
Physical quantity
Types of physical quantities
Units of measurement
Seven fundamental & two supplementary
units
SI prefixes and some practical units for
measuring length
Dimensions of a physical quantity
Question
•
Question
•
Question
(1st person to do the question properly gets a Galaxy milk chocolate)
3. The force F acting on a body moving in a circular path
depends on mass of the body (m), velocity (v) and radius (r) of
the circular path. Obtain the expression for the force by
dimensional analysis method. (Take the value of k=1)
Accuracy and precision of measurement
Significant figures
Rules for counting significant figures
Exact numbers
Rules for rounding off a measurement
Significant figures in calculations
Questions
1. How many Significant figures in each term?
a. 34.6209 b. 0.003048 c. 5010.0 d. 4032.090
2. Solve the following equations using the correct number of
significant figures.
a. 0.003 + 3.5198 + 0.0118 b. 6.90 / 2.8952
c. 98.1 x 0.03
3. A meter has 1000 millimeters in it. How many significant figures
does this number have?
Errors in measurement
Error analysis
Error analysis
Combination of errors
When X = A ± B When X = A × B or A / B When X = An
Standard deviation and standard error of
the mean
• The standard deviation is a statistic that measures the dispersion of a
dataset relative to its mean and is calculated as the square root of
the variance.
Question
1) The marks of a class of eight students (that is, a statistical
population) are the following eight values: 2, 4, 4, 4, 5, 5, 7, 9.
Calculate mean, absolute error, mean absolute error, relative error,
percentage error, variance, standard deviation, and standard error.
2) 5.74 g of a substance occupies 1.2 cm3. Express its density by
keeping the significant figures in view.
3) The radius of a circle is measured to be 10.5 ± 0.2 m. Calculate the
(a) area and (b) circumference of the circle and give the uncertainty
in each value.
Thank you