Spring 2006

Administrative Information

Class meets: MW 12:20-1:15pm in ST 349, and MW 1:15-2:45pm in ST 383
Class Text: Molecular Modelling: Principles and Applications by Andrew Leach (an older edition is on reserve)
Instructor: Dr. Jeremy Kua
Office: SCST 381
Phone: x7970 or (619) 260-7970
E-mail:
Office hours: M 3-4pm, Tu: 2:30-4pm, W 10-11am, Th 10:30am-noon
Class web site:  http://home.sandiego.edu/~jkua/chem494spr06.html
Class handouts web site:  Click here

Course goals: To learn the basics of computational chemistry. We will briefly cover a variety of methods  including electronic structure theory methods  (ab initio, semiempirical, DFT), molecular mechanics, molecular dynamics, Monte Carlo simulations, ligand-receptor docking. The best way to learn computational chemistry is to do it! Hence, your grade in the class will be dependent on computer-problem exercises and an independent project in computational chemistry.

Course requirements:
1. There will be nine computer-based exercises. There will not be any exams on the theory parts covered in the lectures.

2. Approximately half the grade is the independent project. The bulk of this will be from the written final report. The proposal (turned-in earlier) and oral presentations will also count for part of the grade. Instead of a final exam, you will turn in the final report and give a 30-minute oral presentation on your project at the end of the semester.

3a. Grade breakdown is as follows:
                9 Exercises @ 6% each              54%
                Independent Project Proposal       5%
                Written Final Report                   25%
                Oral Presentations                       16%

3b. Tentative Grading Scale (subject to change by the instructor at any time)
                A        85-100%
                B        70-84%
                C        55-69%
                D        40-54%
                F         0-39%

4. Late problem sets will receive no credit.

5. Students are most welcome to come in during office hours. Outside of my office hours, if I'm in my office and not swamped with work, I will be happy to answer questions and discuss coursework. Most of the time, if I'm in my office and the door is open, you're welcome to stop by. I check my e-mail reasonably often during working hours so you can contact me that way too. (Don't expect replies on weekends and evenings.)

6. All students are expected to adhere strictly to the Academic Integrity policy. Violations will be dealt with through the Dean of College of Arts and Sciences, in accordance with the University of San Diego policy on academic integrity.

Approximate associated sections of the text are in parenthesis.
Blank lines delimit separate weeks.

30 Jan   Introduction, Solving the Schrodinger Equation (2.1 to 2.5)
01 Feb  Solving the Schrodinger Equation (2.1 to 2.5)

06 Feb  Basis Sets (2.6)
08 Feb  Calculating Molecular Properties (2.7)

13 Feb  The Huckel and Extended Huckel methods (2.10)
15 Feb  Semi-empirical Molecular Orbital Theory

20 Feb  Electron correlation: Configuration Interaction and Perturbation Theory (3.2, 3.3)
22 Feb  Other electronic structure theories: Valence Bond Theory, Density Functional Theory (3.6 to 3.8)

27 Feb  Practical Considerations in Electronic Structure Theory (3.4)
01 Mar  Molecular Mechanics: Force Fields (4.1 to 4.7)

06 Mar  Nonbond interactions (4.8 to 4.13)
08 Mar  Minimization Methods (5.1 to 5.7)

Spring Break (If you haven't started researching an independent project, you had better do so now!)

20 Mar  Applications of Minimization (5.1 to 5.7)
22 Mar  Practical Considerations in Molecular Mechanics

27 Mar  Molecular Dynamics (6 to 7)
29 Mar  Monte Carlo Simulations (8)

03 Apr  Ligand-Receptor Docking
05 Apr  Mixed QM/MM Methods, Solvation Models

10 Apr  Current Issues in Computational Chemistry
12 Apr  Oral Presentation of Proposed Independent Project (10 min presentations)

Easter Monday
19 Apr  Written Proposal Due

24 Apr  Independent Project
26 Apr  Independent Project

01 May  Independent Project
03 May  Oral Presentation of Progress in Independent Project (15 min presentations)

08 May  Independent Project
10 May  Independent Project

15 May  Independent Project
17 May  Final Oral Presentation of Independent Project (30 min presentations) during scheduled Final Exam
19 May  Written Final Report Due at noon