The course will consist of one lecture and one hands-on computational lab per week. There will be one midterm and a final (each worth 20%), 6 computational assignments (30%), 4 reviews of papers from the scientific literature (10%) and a major computational project (20%).
Week 1, Jan. 11,13.
Lecture: Potential energy surfaces, Model Chemistries, Asking the right questions (notes)
Lecture: WSU closed due to snow
Week 2, Jan. 18,20.
Lecture: (no class - Martin Luther King Day)
Lecture: Molecular mechanics - theory and practice (notes, Leach - Ch 3; Grant & Richards, Ch. 3)
Week 3, Jan. 25,27.
Comp. Lab: Molecular mechanics calculations with Chem3D
Comp. Lab: Molecular mechanics calculations with Chem3D
Week 4, Feb. 1,3.
Lecture: Introduction to molecular orbital calculations ( notes , Leach - Ch 2; Grant & Richards, Ch. 2, Exploring Chemistry, Appendix A)
Week 5, Feb. 8,10.
Lecture: Equilibrium geometries ( notes, Leach - Ch 4, Exploring Chemistry, Ch 3), molecular vibrations ( notes , Exploring Chemistry, Ch 4)
Comp. Lab: Geometry optimization and vibrational frequency calculations
Week 6, Feb. 15,17.
Lecture: Gaussian output, population analysis (Exploring Chemistry, Ch 2-4)
Comp. Lab: Visualizing orbitals, Calculating molecular properties.
Week 7, Feb. 22,24.
Lecture: Transition states, reaction paths and reaction rates
Comp. Lab: Exploring potential energy surfaces for chemical reactions
Week 8, Mar. 1,3.
Lecture: Post-SCF methods, model chemistries and thermochemistry
Comp. Lab: Internet resources
Week 9, Mar. 8,10.
Lecture: Solvation. Excited states.
Comp. Lab: Continuum models for solvation. Calculating excited states.
Week 10, Mar. 22,24.
Lecture: Midterm.
Comp. Lab: MM/QM calculations.
Week 11, Mar. 29, 31.
Lecture: Gas phase molecular dynamics.
Comp. Lab: Classical trajectory calculations.
Week 12, Apr. 5,7.
Lecture: Macromolecular modeling.
Comp. Lab: Free energy calculations.
Week 13, Apr. 12,14.
Lecture: Simulation of liquids. Car-Parrinello methods
Comp. Lab: Car-Parrinello calculations.
Week 14, Apr. 19,21.
Student presentations of major projects
Apr. 26. Final exam.