This course will deal with five general areas, depending on the nature of the project you select:

1. Introduction to LINUX workstations (This area will be covered largely in the form of a handbook.)
   • Directory and file operations

   • Editors

   • Managing processes

   • TCP/IP and file transfer

2. Molecular Mechanics
   • Nature and development of force fields

   • Techniques for searching conformation space; identification of minima

   • The "global minimum problem"

   • Input and output

   • Applications

3. Semi-Empirical Molecular Orbital Methods
   • Huckel theory

   • The AM1 and PM3 Hamiltonians

   • Identification of minima and transition states - vibrational spectra

   • Input and output: the SPARTAN graphical interface, Z-matrices

   • Applications

4. Ab Initio Molecular Orbital Methods, Density Functional Methods
   • Choice of Basis Sets and Functionals

   • Electron Correlation

   • The GAUSSIAN and GAMESS programs

   • Performance and cost issues

   • Applications

5. Biomolecular Modeling
   • Generalities of Protein and Nucleic Acid Structure

   • Force Fields

   • Solvation

   • Molecular Dynamics

   • Docking

   • Homology Modeling

No text will be used, but you will be expected to read extensively in the chemical literature, and the course Web pages.

The Linux workstations we will use are located in 262 Aubert. Undergraduaate students may get keys for this room from Jean in the Department Office; graduate student keys should open the room. If you are the last person out of the room, make sure the door is locked. No food or beverages are permitted in the computer room.

You will also need access to a PC connected to the Internet: your laptop or a computer available in your research group. Our workstations are accessible via the Internet, using secure shell (ssh) applications. Click HERE for instructions regarding this access.

All students will be expected to complete several exercises designed to test their mastery of the operation of the computers and software. You also are expected to complete four small projects using four different computational methodologies of your choice, and one extensive course project. The course project should be chosen in consultation with your research advisor and me and should reflect application of one or more computational tools to your area of research.

Written (word processed) reports are required on all exercises and projects. All reports should be submitted in electronic format. Reports for exercises should be no more than 1-1.5 pages, and should include a molecular graphic when appropriate. The four project reports must be at least 1000 words, in a standard scientific format, and should include appropriate references. In each case, the methodology employed should be described, the data generated presented, and appropriate conclusions drawn. The final course project report must be at least 2500 words. Project reports that are unsatisfactory will be returned for improvement.

Students who complete all five projects in a satisfactory fashion will receive an A. Each uncompleted project reduces your grade by one letter.

I keep no regular office hours. You are welcome to consult me whenever I am in the building. My office is 252 Aubert. You may reach me by e-mail at rcfort@maine.edu.

A Web Page for the course will be found at:

http://chemistry.umeche.maine.edu/CHY550.html