MolecularModelingPartIMolecularMechanicsand.pptVIP

Molecular Modeling Part IMolecular Mechanics and Conformational Analysis ORG I Lab William Kelly * Molecular Modeling Molecular modeling in the broadest sense is the use of: a) Physical representations: I.e. Plastic Molecular Models b) Graphical representations: c) Mathematical representations Space Filling Model Ball and Spoke Model Electrostatic Potential Map, Solve Quantum Mechanical equations to determine electron position and atomic charge Molecular Orbital Representation Solve Quantum Mechanical equations to determine molecular orbital appearance Molecular Mechanics Simulation of Dynamic Motion in Ethane Combination of Mathematical and Graphic Model Animation obtained from the solution of molecular mechanics equations of atomic motion for atoms of ethane. Dynamic motion followed for 1 picosec (10-9 sec). Each frame represents a 3 femtosec (3 x 10-12 sec) window. With the development of fast, easy to use computers within the last 15 years computer modeling of molecules has become an important tool for the practicing chemist. There are many approaches to this subject, and a gradation of levels of theory in the understanding of molecules through computer modeling. The subject of this experiment is a technique called Force Field Molecular Modeling or Molecular Mechanics. Molecular Mechanics Background The mechanical molecular model was developed out of a need to describe molecular structures and properties in as practical a manner as possible. ?The great computational speed of molecular mechanics allows for its use in molecules containing thousands of atoms. Molecular mechanics methods are based on the following principles: ?Nuclei and electrons are lumped into atom-like particles. ?Atom-like particles are spherical (radii obtained from measurements or theory) and have a net charge (obtained from theory). ?Interactions are based on springs and classical potentials. ?Interactions must be