Case Studies

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 Plancks constant

5
Gaussian
6
Gaussian

• 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).

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VMD Visual Molecular Dynamics
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End