1. Case Studies Class 5

2. Computational Chemistry Structure of molecules and their reactivities Two major areas –molecular mechanics –electronic structure theory Basic types of calculation –Computing the energy of molecular structure –Performing geometry optimization (1st derivative) –Computing the vibrational frequency of molecules resulting from interatomic motion (2nd derivative)

3. Molecular mechanics Use laws of classical physics to predict structures and properties of molecules Based on different force fields –Equations defining potential energy and location of components atoms –A series of atom types –Parameter sets define force constants Available in computer programs likes MM3, HyperCHEM, Quanta, Sybyl and Alchemy

4. Electronic structure methods Use laws of quantum mechanics Calculate energy by solving Schrodinger equation Two major class –Semi-empirical methods Use parameters obtained from experimental data Solve approximate form of Schrodinger equation Implemented in MOPAC, AMPAC, HyperCHEM, Gaussian –Ab initio methods Based on solely the law of quantum mechanics Depends on some physical constant such as speed of light, mass and charges of electrons and nuclei, and Planck’s constant

5. Gaussian

6. Description –Starting from the basic laws of quantum mechanics, Gaussian predicts the energies, molecular structures, and vibrational frequencies of molecular systems, along with numerous molecular properties derived from these basic computation types. It can be used to study molecules and reactions under a wide range of conditions, including both stable species and compounds which are difficult or impossible to observe experimentally such as short-lived intermediates and transition structures.

7. VMD

8. VMD – Visual Molecular Dynamics VMD is designed for the visualization and analysis of biological systems such as proteins, nucleic acids, lipid bilayer assemblies, etc. It may be used to view more general molecules, as VMD can read standard Protein Data Bank (PDB) files and display the contained structure. VMD provides a wide variety of methods for rendering and coloring molecule. VMD can be used to animate and analyze the trajectory of molecular dynamics (MD) simulations, and can interactively manipulate molecules being simulated on remote computers (Interactive MD).

9. VMD – Visual Molecular Dynamics

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