This document provides an overview of computational chemistry and computational tools used in different fields. It defines computational chemistry and computational quantum chemistry. It discusses the concept of computational models, including ab initio quantum chemistry methods that do not include empirical parameters. It describes different computational models from most to least accurate, including ab initio, semi-empirical, and molecular mechanics methods. It provides details on molecular mechanics and how it estimates molecular energetics without using quantum mechanics. The document also discusses semi-empirical and ab initio methods and levels of theory. It states that high-speed supercomputers and suitable software programs are needed for computational chemistry. It provides examples of commonly used computational chemistry software.

1. Dr. Mazhar Amjad Gilani
COMSATS University Islamabad, Lahore Campus
05-10-2020
Computational Tools and
Applications of
Computational methods
in Different fields of
Chemistry

2. Topics to be covered……..
1. Some more definitions of computational
chemistry
2. Concept of Computational Models
3. Knowledge about Hardware & Software
Topics to be covered……..

3. 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.

4. Computational Models/Tools
 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.

5. Computational Models/Tools
 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

6. 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

8. To predict the energy associated with a given conformation
Molecular mechanics energies have no meaning as absolute quantities
Only differences in energy between two/more conformations have
meaning
A simple molecular mechanics energy equation is given by:
Energy = Stretching Energy + Bending Energy +Torsion Energy + Non-Bonded
Interaction Energy
These equations together with the data (parameters) required to describe the
behavior of different kinds of atoms and bonds, is called a force-field.

9. • Stretching Energy
The stretching energy equation is based on Hooke's law. The "kb" parameter controls
the stiffness of the bond spring, while "ro" defines its equilibrium length. Unique "kb"
and "ro" parameters are assigned to each pair of bonded atoms based on their types
(e.g. C-C, C-H, O-C, etc.). This equation estimates the energy associated with
vibration about the equilibrium bond length. This is the equation of a parabola, as can
be seen in the following plot:

11. • Bending Energy
The bending energy equation is also based on Hooke's law. The "ktheta" parameter
controls the stiffness of the angle spring, while "thetao" defines its equilibrium angle.
This equation estimates the energy associated with vibration about the equilibrium
bond angle:

12. Unique parameters for angle bending are assigned to each bonded triplet of atoms
based on their types (e.g. C-C-C, C-O-C, C-C-H, etc.). The effect of the "kb" and "ktheta"
parameters is to broaden or steepen the slope of the parabola. The larger the value of
"k", the more energy is required to deform an angle (or bond) from its equilibrium value.

13. 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.
Mixing of theory and experiment that makes the method semi-empirical

14. 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

17. Computational Resources
Two fundamental resources are required
•High speed super computers (clusters) etc.
•Suitable software program

19. *Abbreviated Profile of Drugs (APOD) is a web-based decision and prediction program
for drug discovery.
Software's
*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

20. *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.

21. *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
*Gromacs MD 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.

22. 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).

24. Thank You
Thank You