1. Briefly discuss the differences between Molecular Mechanics, semi-empirical, and ab initio calculations. Where do basis sets and force-fields fit in? Name three methods that youíve used that fall into the three categories of calculations named above. (20 pts)

Molecular Mechanics is based on Classical Laws (or Newtonian Laws of Mechanics) and treat molecules as balls connected with springs of different stiffness. Semi-empirical and ab initio calculations are based on Quantum Mechanical principles. Semi-empirical calculations rely on experimental data such as ionization potentials but ab initio calculation do not make use of any experimental data.

Typical bases sets are combinations of gaussian functions used to simulate atomic orbitals. Linear combinations of atomic orbitals are used to build molecular orbitals. Basis sets are only used in Quantum Mechanical calculations. Force-fields are parameter sets that define ëstrain-freeí or ideal bond lengths, bond angles, etc. for a variety of interconnected atoms. Force-fields are only used in Molecular Mechanics calculations that are sometimes called Force-field calculations.

Molecular Mechanics - MM3 or Sybil; Semi-empirical - PM3; ab initio - HF/STO3G

2. How would you go about finding information on Molecular Modeling program such as Macromodel? (5 pts)

One way is search on the Internet using a site like Yahoo or AltaVista. A better way is to visit the NIH site and look at their collection of Molecular Modeling programs and associated links.

3. What are some of the obvious differences between Spartan and MOPAC packages ? (10 pts)

Spartan has a Graphical User Interface that makes it easier to input target molecular structures and setup calculation jobs, and visualize the results. Spartan allows to setup Molecular Mechanics, semi-empirical, and ab initio calculations.

MOPAC has a standard FORTRAN input/output interface with the first several lines of the input file used to specify the type of calculation to be performed and the target molecule specified via a Z-matrix. MOPAC package handles only semi-empirical calculations.

4. When would be a program such as ChemDraw of use ? (5pts)

Whenever one needs to generate structural formulas for inclusion in papers, diagrams, Web pages, etc.

5. What is Chemical MIME and how it relates to Rasmol and Netscape ? How does PDB file format fit in ? (10 pts)

Chemical MIME (Multipurpose Internet Mail Extension) is a standard way of delivering and manipulating chemical information on the Internet. Main MIME type ëchemicalí and a number of subtypes (such as ëx-pdbí) corresponding to different file formats are defined.
By configuring Netscape (or IE) to recognize Chemical MIME type/subtype, information contained in files such as PDB (specifying molecular structure) can be conveniently viewed using helper programs like Rasmol.