Lecture_No._1_Computational_Chemistry_Tools___Application_of_computational_methods.ppt.pdf
- 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
- 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.