4:180
Homework:
Experiment 11: write-up due 9/19
Experiment 34: discuss 9/19
Reading:
|
The Potential Energy surface The Hessian/Stationary points Geometry Optimization Multi-minima Problem/MD/MC/Free energy Thermochemistry Molecular Mechanics Basic QM Basis Sets Semiempirical Methods Electron Correlation DFT Charge Distribution/Spectroscopy Solvation Models |
Chapter 1 (Section 3) Chapter 9 (section 3) Chapter 2 (Section 4) Chapter 3 Chapter 10 Chapter 2 Chapter 4 Chapter 6 Chapter 5 Chapter 7 Chapter 8 Chapter 9 Chapter 11 |
Announcements:
The following books are on reserve in the Chemistry Library:
Alan Hinchliffe "Modeling Molecular Structure"
Frank Jensen "Introduction to Computational Chemistry"
Andrew Leach "Molecular Modeling: Principles and Applications"
David Young "Computational Chemistry"
Atilla Szabo and Neil Ostlund "Modern Quantum Chemistry"
Select titles of previous research projects
Computational Study of Different Catalyst Systems for Ethylene Polymerization
An ab initio Study of Some Urocanic Acids: The Roles of Hydrogen Bonding in the Catalytic Triad of Serine Proteases
Computational Studies on a Myelin Basic Protein Peptide and the Role that Zinc Plays
Study of the Vibrational Frequencies of Adsorbed Sulfite and Sulfate Species on a Metal Oxide Surface
The Effect of Mutations on Protein Backbone Entropy
Stretching the m-N-N Distance in a Novel Ditantalum d0 System
Outside Links
PNNL Gaussian Basis Set Order Form
Instructor: Professor Jan H. Jensen
Office: 331 CB
E-mail: jan-jensen@uiowa.edu
Office Hours: Mondays and Wednedays 4-5 or by appointment
Web Page: http://www.uiowa.edu/~c004180/
Lecture: 10:30-11:20 MWF in C139 CP
Course Material
Required Text: C. J. Cramer "Essentials of
Computational Chemistry: Theories and Models" John Wiley & Sons
Required Text: W.J. Hehre, A.J. Shusterman, W.W. Huang, "A Laboratory
Book of Computational Organic Chemistry," Wavefunction, Inc. 1996.
Most homework problems will be assigned from this text
Manuals can be checked out from the Chemistry Center
Computational Resources
Undergraduate Computer Facility (235 CB)
Spartan, GAMESS, HyperChem (1), Titan (1)
Computational Research Facility (339 CB)
GAMESS, GAUSSIAN
Students are encouraged to find additional computational resources. GAMESS is free of charge and runs on PowerMacs, PCs and almost any UNIX system.
Course Requirements:
Grading will be based on written reports and in-class presentations of
completed projects:
Homework Projects: 40%
Midterm Proposal: 20%
Research Project 40%
Course Content
This course covers the theory and application of ab initio quantum
mechanics, semiempirical molecular orbital theory, and molecular mechanics
force fields to chemical research problems. Lectures will focus on the
underlying theory of these methods (with emphasis on ab initio theory) and their practical application to chemical
problems. Assignments will mainly consist of computational chemistry projects
using modeling software such as Spartan
and GAMESS. In the
first half of the semester computational projects will be assigned from the
text. During this time students also plan a more ambitious computational
project for the second half of the semester and submit a proposal describing
the project. Most of the second half of the semester is spent completing and
presenting this project.
Specific topics will be covered in approximately the order shown below. Topics may be dropped or added depending on how the course progresses.
The Potential Energy Surface
Stationary Points (minima and maxima)
Characterizing Stationary Points (Hessians)
Finding/Connecting Stationary Points
Beyond Stationary Points (Monte Carlo and Molecular Dynamics)
Point Group Symmetry
Molecular Mechanics Forcefields (SYBYL, Amber)
Calculating the Energy
Intro to the Schrdinger Equation/The Born-Oppenheimer Approximation
The Molecular Orbital Approximation (RHF, UHF, ROHF)
The LCAO Approximation (basis sets)
Molecular Orbitals
Dynamic Correlation (MP2, CI)
Density Functional Theory (X-alpha, B3LYP)
Semiempirical Methods (MNDO, AM1, PM3)
Multiconfigurational SCF (CASSCF)
Intepretation and Properties
Canonical/Localized Molecular Orbitals
Density/Density Differences
Electrostatic Potentials
Charges, Dipoles
Localized Charge Distributions
Miscellaneous
Solvent Effects
QM/MM
Effective Core Potentials
Course Policies
Working together on the assigned computational projects is encouraged. However,
anything you hand in must reflect your own thoughts and be in your own words.
Plagiarism and cheating will not be tolerated. (See College of Liberal Arts,
Handbook of Academic Policies and Procedures).
Anyone with disabilities that require special attention should feel free to
contact me to make arrangements.