This document discusses computational chemistry and its applications. It begins by defining computational chemistry as the application of mathematical models and simulations to chemical problems using computers. It then lists some common applications of computational chemistry, such as determining molecular energies, geometries, and spectroscopic properties. The document also discusses some commonly used computational tools and software programs. It provides an example application of using computational chemistry to study the antioxidant vitamin E.

1. Dr. Mazhar Amjad Gilani
COMSATS University Islamabad, Lahore Campus
28-09-2020
Computational Tools and
Applications of
Computational methods
in Different fields of
Chemistry

2. Topics to be covered……..
1. What is Computational Chemistry???????
2. Significance of Computational Chemistry
3. Some Know-how about Computational tools
Topics to be covered……..

3. “Anyone can do calculations
nowadays.
Anyone can also operate a scalpel.
That doesn’t mean all our medical
problems are solved.”

5. What is Computational Chemistry

6. Wet Versus Dry

7. application of mathematical
models and simulations to
chemical problems using
computers

8. Introduction
Computational chemistry is a branch of chemistry
concerned with theoretically
Optimizing geometry of molecules
determining properties of molecules
Building structure activity relationship

9.  Can predict molecular properties for comparison with experiment
 To elucidate ambiguous or otherwise unclear experimental data
 To model short-lived, unstable intermediates and transition states
 Can predict properties of molecules and potential applications before their
birth

10. application of mathematical models and simulations
to chemical problems using computers

12. 12
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

13. 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

14. A Case study of Vitamin E
• Fat soluble antioxidant
• Discovered in 1922, isolated in 1936 and first synthesized in 1938
• Popular for anti-aging
• Over the counters of health care and cosmetics
Physiological role of vitamin E---antioxidant
14
Participation in cellular signaling mechanisms related to
•hormonal responses,
•cell growth
•and even memory

15. Tocotrienols
15

16. Physiological role of vitamin E---antioxidant
involve oxidized form of alpha-tocopherol-interest in
oxidation of this compound
16
Calculations can predict
Thermodynamic preference of up form over down
form
Change in structure might alter preference
Role of side chain

17. 17

18. Acc. Chem. Res. 2016, 49,6, 1311-1319
18

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

27. *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

28. *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.

29. *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.