Computational Tools and

Applications of
Computational methods
in Different fields of
Chemistry

Dr. Mazhar Amjad Gilani

COMSATS University Islamabad, Lahore Campus

6-09-18
Learning Objectives:

1. What is Computational Chemistry???????

2. Significance of Computational Chemistry

3. Some Know-how about Computational tools

“Anyone can do calculations nowadays.
Anyone can also operate a scalpel.
That doesn’t mean all our medical
problems are solved.”
Karl Irikura
application of mathematical
models and simulations to
chemical problems using
computers
 Introduction

 Computational chemistry is a branch of

chemistry concerned with theoretically
determining properties of molecules.

 Because of the difficulty of dealing with

nanosized materials, computational modeling has
become an important characterization tool in
nanotechnology.
application of mathematical models and simulations
to chemical problems using computers
 application of mathematical models and simulations
to chemical problems using computers

Includes (list is not exhaustive):

• molecular energies  reaction energies, barriers
• molecular geometries
• electron distributions  reactivities
• spectroscopic properties: e.g. UV/VIS, IR/Raman, NMR, etc.
• molecular dynamics  reaction rates, mechanisms & protein folding
• physical properties: e.g. mechanical hardness
• quantitative structure-activity relationships

8
 application of mathematical models and simulations
to chemical problems using computers

Computations can be carried out

 Gas Phase

 in Solution

 Ground state

 Excited state

 Substituent effect

 Reaction mechanism

 PES

 Excitation energies
 Computational tools

Two fundamental tools are required

• High speed super computers (clusters) etc.

• Suitable software program
Software's
*Abbreviated Profile of Drugs (APOD) is a web-based decision and prediction program
for drug discovery.
*ADF (The Amsterdam Density Functional package).
It is a software for first-principles electronic structure calculations (A first-principles
embedding theory that combines the salient features of density functional theory (DFT) and
traditional quantum chemical methods). It is used in the research areas of homogeneous and
heterogeneous catalysis, inorganic chemistry, heavy element chemistry, various types of
spectroscopy, and biochemistry
*ADMEWORKS DDI Simulator -- ADMEWORKS DDI Simulator is a software
application for assessing the risk of potential drug-drug interactions, allowing the user to
perform both quantitative simulations of Competitive and Mechanism-based inhibitions

*AMBER -- Molecular Dynamics Program

*AMSOL -- Semiempirical quantum chemistry program (gas phase and solvation)

*APBS: Adaptive Poisson-Boltzmann Solver -- Software for evaluating the

electrostatic properties of nanoscale biomolecular systems

*ArgusLab 3.0 -- Molecular Modeling Software

*BioSolveIT -- Software solutions for structure and ligand-based molecular design

*Chemissian: quantum chemistry program for visualizing electron/spin density

distribution and UV-VIS spectra, plotting molecular orbital energy level diagrams,
calculating atomic orbital populations, contributions of atoms and fragments to MOs.

*COSMOlogic -- Software for Life Sciences, Chemical Engineering.

*GAMESS ab initio program.

 *Gromacs MD Software
*LiqCryst -- LiqCryst is a MS-Windows-based application, covers all aspects of liquid
crystal research: material properties, display technology, theory, basic research and
applications

*MDL QSAR - Comprehensive QSAR modeling system

*MOLCAS -- quantum chemistry software package

*Polar -- electrochemical simulation and data

analysis
Q-chem -- ab initio and DFT molecular modeling package

*Schrodinger, Computational Chemistry Software

*SCIGRESS -- SCIGRESS is a unique desktop molecular modeling software package that can
apply a wide range of computational models to all types of molecular systems, from small
organic molecules.
Definition of Computational Chemistry

• Computational Chemistry: Use mathematical approximations

and computer programs to obtain results relative to chemical
problems.
• Computational Quantum Chemistry: Focuses specifically on
equations and approximations derived from the postulates of
quantum mechanics. Solve the Schrödinger equation for
molecular systems.
• Ab Initio Quantum Chemistry: Uses methods that do not include
any empirical parameters or experimental data.
 Computational Models

 A model is a system of equations, or computations used

to determine the energetics of a molecule
 Different models use different approximations (or levels
of theory) to produce results of varying levels of
accuracy.
 There is a trade off between accuracy and computational
time.
 There are two main types of models; those that use
Schrödinger's equation (or simplifications of it) and those
that do not.
 Computational Models

 Types of Models
(Listed in order from most to least accurate)

 Ab initio
• uses Schrödinger's equation, but
with approximations
 Semi Empirical
• uses experimental parameters and
extensive simplifications of
Schrödinger's equation
 Molecular Mechanics
• does not use Schrödinger's
equation Simulated zigzag carbon
nanotube
 Molecular Mechanics
 Simplest type of calculation

 Used when systems are very large and approaches that are
more accurate become to costly (in time and memory)

 Does not use any quantum mechanics instead uses parameters

derived from experimental or ab initio data

 Uses information like bond stretching, bond bending,

torsions, electrostatic interactions, van der Waals forces
and hydrogen bonding to predict the energetics of a system

 The energy associated with a certain type of bond is

applied throughout the molecule. This leads to a great
simplification of the equation
 Semi Empirical

 Semi empirical methods use experimental data to

parameterize equations

 Like the ab initio methods, a Hamiltonian and wave

function are used
 much of the equation is approximated or eliminated

 Less accurate than ab initio methods but also much faster

 The equations are parameterized to reproduce specific

results, usually the geometry and heat of formation, but
these methods can be used to find other data.
 Ab Initio
 Ab initio translated from Latin means “from first principles.” This
refers to the fact that no experimental data is used and computations
are based on quantum mechanics.

 Different Levels of Ab Initio Calculations

 Hartree-Fock (HF)
• The simplest ab initio calculation
• The major disadvantage of HF calculations is that electron
correlation is not taken into consideration.
 The Møller-Plesset Perturbation Theory (MP)
 Density Functional Theory (DFT)
 Configuration Interaction (CI)
Take into consideration
electron correlation
 References

 Chem Viz at
http://www.shodor.org/chemviz/basis/students/introduction.html

 D. YOUNG, in “Computational Chemistry, A Practical Guide for

Applying Techniques to Real World Problems” (Wiley-Interscience,
New York, 2001).

 J. SIMMONS, in An Introduction to Theoretical Chemistry”

(Cambridge Press, Cambridge, 2003).

 J. B. FORESMAN AND Æ. FRISCH, in “Exploring Chemistry with

Electronic Structure Methods, 2nd Edition” (Gaussian, Inc.,
Pittsburgh, PA, 1996).
Thank You