Chem 126
Computational Chemistry
Fall 2008
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Chem 126
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Dr. Kalju Kahn
Office: PSB-N 2623, Phone: 893-6157
E-mail: kalju@chem.ucsb.edu, Website: http://www.chem.ucsb.edu/~kalju
The course focuses on learning the principles of computational chemistry and computer-based molecular design. Both molecular mechanical and quantum mechanical models are covered. Students will learn a variety of commonly used techniques, such as geometry optimization, location of transition states, conformational analysis, and prediction of molecular and spectroscopic properties. Students will learn basics of implementing key algorithms, such as Newton-Rhapson minimization, and normal mode analysis of vibrational motions. Students also will become familiar with different software packages, including MOLDEN for general model building, Gaussian, PC GAMESS, and Dalton for quantum chemical calculations, and BOSS for liquid simulations. Students who complete the course are expected to be able to ask questions that can be solved with modern computational approaches and choose right computational tools to assist in their current or future research.
| Syllabus | General information about the course | |
| Last Years | Computational Chemistry 126 by Dr. Kirtman: 2007 | Link |
| Last Years | Computational Chemistry 126 by Dr. Kahn: 2006 | Link |
| Last Years | Computational Chemistry 126 by Dr. Aue: 2005 | Link |
| Textbook | Suggested: Intoduction to Computational Chemistry : Theories and Models | Amazon |
| Textbook | Alternative: Essentials of Computational Chemistry : Theories and Models | Amazon |
| Upload | Submit your assignments as MS Word or PDF files | Link |
| Exam | Sample Exam from 2006 | |
| Exam | Midterm Preparation Guide | |
| Exam | Final Preparation Guide |
| Literature | Required or optional reading in PDF | Acrobat |
| Required | "Biomolecular simulation and modelling: Status ..." by van der Kamp et al | |
| Required | "Potential energy functions for atomic-level simulations of water and organic and biomolecular systems" by Jorgensen and Tirado-Rives | |
| Optional | "Molecular Modeling of Organic and Biomolecular Systems Using BOSS and MCPRO" by Jorgensen and Tirado-Rives | |
| Optional | Manual for the BOSS program | |
| Optional | The Many Roles of Computation in Drug Discovery | |
| Required | Intro Quantum Mechanics: MO Theory | |
| Optional | Basis Sets for Ab Initio MO Calculations ... | |
| Required | DFT: Performance and Problems | |
| Optional | "Performance of B3LYP Density Functional Methods ..." by Tirado-Rives and Jorgensen | |
| Optional | "Solvent Effects and Mechanism ... from QM/MM Simulations" by Acevedo and Jorgensen | |
| Required | "Modeling Enzyme Reaction Mechanisms, Specificity and Catalysis" by Adrian Mulholland |
The assignments are posted one week before the due date. Answers shall be submitted electronically no later than the midnight of the due date.
| Assignments | Submit Your Work | Link |
| 1 | Minimization: Tutorial and Assignments | Link |
| 2 | Molecules: Building, Minimization, and Conformational Analysis | Link |
| 3 | Monte Carlo Simulations | Link |
| 4 | Introduction to QM and Semiempirical Methods | Link |
| 5 | Introduction to An Initio Methods | Link |
| 6 | An Initio Methods: Practical Considerations | Link |
| 7 | Molecular Vibrations | Link |
| 8 | Electronic Spectra and Solvent Effects | Link |
| 9 | QM/MM Modeling of Reactions: Free Energy Perturbation | Link |
The answer keys are posted one week after the due date.
| 1 | Minimization | Link |
| 2 | Conformational Analysis and Monte Carlo | Link |
| 3 | Semiempirical Methods in Quantum Chemistry | Link |
| 4 | Ab Initio Calculations and Basis Sets | Link |
| E | Midterm Take-home | Link |
| 5 | Reaction Paths and Transition States | Link |
| 6 | Molecular Vibrations, Spectra and Solvent Effects | Link |
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