Transcript Case Studies

Case Studies
Class 5
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)
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
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
Gaussian
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.
VMD
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).
VMD – Visual Molecular Dynamics
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