This page will provide a brief listing of the topics mentioned at each discussion section. If you are uncomfortable with your knowledge of any of these topics, seek help from any of the resources available to this class.
| Wed, Jan 17 | Introduction to the course. Review of web pages describing philosophy of the course, mechanisms for teaching, grading. Description of computations as a tool to be used like any other tool (i.e. spectroscopy) that is available to chemists. Information sheets obtained from students. Instructor and TAs described their backgrounds in computing and computational chemistry. |
| Wed, Jan 22 | Survey of the topics representative of computational chemistry. Discussion of the rate of change of computing hardware and the change of computational chemistry from the realm of expert specialists to commercial "user-friendly" packages. Students described their backgrounds in computing and computational chemistry. |
| Fri, Jan 24 | Tour of the Computer and Graphics Facility. Logging on and off the IRIS machines. Starting Netscape and modeling applications. Demonstration of building and optimizing molecules. Introduction to UNIX, FTP and Telnet. |
| Mon, Jan 27 | Demonstration of Macromodel. Molecule building for large organic molecules. Different force fields, different geometry optimization and conformational searching options, Monte Carlo and molecular dynamics examples. Example of cyclooctatetraene. |
| Wed, Jan 29 | Demonstration of SPARTAN. Molecule building for transition metal complexes. Symmetry aspects. Vibrational analysis. Electronic structure calculations. Orbital displays. Electron distribution analysis. |
| Mon, Feb 3 | Beginning survey of computational chemistry - reality, measurable properties, complete wavefunction including time dependence and all excited states. Examples of requirements for exact NMR chemical shifts, exact ionization energies. Exact equations are known, exact solutions are presently not possible. Separation (approximately) of complete problems into smaller parts. Born-Oppenheimer approximation, Jahn-Teller effects, relativistic effects, spin-orbit coupling. Time-independent, steady-state, nonrelativistic Schrodinger wave equation. Molecular modeling in terms of evolution from atomic composition, functional groups and atom connectivity, three-dimensional drawing, physical modeling, molecular graphics. Addition of quantitative features through databases and development of molecular mechanics. Introduction to electronic structure methods - valence bond, molecular orbital, and scattered wave methods are all different approaches to the problem of electron correlation. |
| Wed, Feb 5 | Different approaches to electron correlation/configuration intereaction for solution of the Schrodinger wave equation. List of advantages, disadvantages and improvements to valence bond theory, molecular orbital theory and scattering theory. Expression for single determinant wavefunction. The Hartree-Fock limit. Expansion of molecular orbitals in terms of basis functions. The LCAO-MO approximation. The Hartree-Fock-Roothaan equation FC=SCE. Branching of methods into Huckel, ZDO, Fenske-Hall, and ab initio type approaches. |
| Mon, Feb 10 | Introduction to creation of web pages given in room 311 of CCIT. Browsers, editors, creating links, e-mail, saving and publishing for web pages. |
| Wed, Feb 12 | General discussion of basis functions. The complete set and the best first approximation, which is the atomic orbitals. Discussion of FC=SCE. Definition of the diagonal and off-diagonal elements of the overlap matrix and the Fock matrix. Meaning of the coefficient matrix and the energy matrix. General methods by which the Huckel, ZDO, Fenske-Hall and ab initio approaches treat the Fock and overlap matrices. |
| Mon, Feb 17 | Presentation of extended Huckel method and the information that can be obtained from it by Davide Proserpio. Assumptions for diagonal Fock matrix elements from VOIE (sometimes called VOIP, VSIE, VSIP). Assumptions for the off-diagonal elements from the Wofsberg-Helmholz approximation. Overlap integrals are calculated for the Slater-type orbitals. The total energy is calculated as the sum of the one-electron molecular orbital eigenvalues. Mulliken population analysis is used to evaluate the charge distribution. |
| Wed. Feb 19 | Demonstration of the extended Huckel method through the program CACAO. Generation of orbital pictures and molecular orbital diagrams. Orbital energies as a function of bond rotations. |
| Mon. Feb 24 | Discussion of how to plan and carry out an investigation using computational techniques. Factors involved in selecting a problem, defining the questions, determining what is known or expected before the computations, choosing a computational method, simplifying the problem and adapting it to the method, carrying out the computation, analyzing the results, determining the confidence in the results, looping back through the process. In general, start with the simplest method that is capable of providing information. |
| Wed. Feb 26 | Introduction to force fields in molecular mechanics. Discussion of parameterization. |
| Mon. Mar 3 | Discussion of applications of molecular mechanics by Mark Shenderovich. Practical aspects of geometry minimizations and conformational searching. |
| Wed. Mar 5 | Student presentations of Web materials. Julia Moberg, Brian Drouin, Edward Lorance. |
| Mon Mar 10 | Student presentations of research. Cheryl North display of X-windows. |
| Wed Mar 12 | Student presentations of research. Dayle Smith, William Wehbi |
| Mon Mar 24 | Sandra Blumhorst research presentation. Mulliken population analysis, normalization of LCAO-molecular orbitals. Overlap populations, bonding, non-bonding and anti-bonding situations. Atomic charges. Per cent characters of molecular orbitals. |
| Wed Mar 26 | Kristie Winfield research presentation. Examination of results from a molecular orbital calculation. The calculation of CO by the CACAO programs. Input file and parameters, overlap matrix, Huckel matrix, orbital energies, orbital eigenvectors and approximate visualization of the orbitals. Mulliken charge distribution analysis, pi overlap population analysis. |
| Mon Mar 31 | Introduction to quantum mechanics. Description of the wavefunction as a 'database'. Definition of the electron density. |
| Wed Apr 2 | Additional illustration of Mulliken Population Analysis using the CACAO programs as an example. Short survey of the history of theoretical chemistry. Discussion of lack of direct correlation between amount of computational effort and the quality of results. Fundamental characteristics of wavefunctions - normalized, finite, single-valued, and smoothly varying (except for cusp conditions and spin quanta). |
| Mon Apr 7 | Fundamental characteristics of wavefunctions continued - antisymmetry principle, spatial and spin symmetry, variation principle, orthogonality. Fundamentals of operator mechanics. Eigenvalues and eigenfunctions, expectation values and expansion of wavefunctions in terms of eigenfunctions. Examples of operators, kinetic energy, potential energy, derivation of the Schrodinger wave equation for the one-electron atom. Introduction of the problem of the one-electron atom - assumptions, 6-dimensional wavefunction from coordinates of nucleus and electron. |
| Wed Apr 9 | Complete mathematical solution of the one-electron atom. Separation of center-of-mass, translational wavefunctions, spherical polar coordinates, separation of angular solutions, solutions in phi, m quantum number, solutions in theta, l quantume number, spherical harmonics in imaginary form, spherical harmonics in real form, radial solutions, n quantum number, nodal properties. |
| Mon Apr 21 | Summary of computational chemistry related activities at the national ACS meeting. Discussion of Brian Drouin's question related to conformational searching with ab initio methods. Review of one-electron atomic orbitals. Displays of solutions in phi. |
| Wed Apr 23 | Displays of atomic solutions in theta and r variables. Summary of different ways of displaying atomic orbital wavefunctions and densities. Introduction to many-electron atomic functions and basis sets. Minimum basis sets, extended basis sets, polarization functions, balanced basis sets. Relationships between STO's and GTO's. Contracted basis sets. STO-3G basis sets. |
| Frida Apr 25 | Introduction to algorithms for calculating and displaying electron wavefunctions and densities. Tutorial on running the MOPLOT2 suite of programs. |
| Mon Apr 28 | Development of Hartree-Fock-Roothaan equations. One-electron and two-electron integrals and energies. Coulomb and exchange integrals. Application of variation principle. Hartree-Fock-Roothaan equations in matrix form. Slater-type orbitals for many-electron atoms. Virial theorem. Russell-Saunders states. Exponents and coefficients of basis functions in describing atomic functions. |
| Wed Apr 30 | Gaussian basis sets. Cartesian Gaussians, definitions of "shells", redundancies in "d" and "f" shells, lack of principle quantum number shells. Criteria for generation of basis sets. Contractions, STO-nG basis sets, notations for basis set contractions. Diffuse functions, polarization functions. |
| Fri May 2 |
Fenske-Hall equatiions. Hartree-Fock-Roothaan equations, overlap matrix, Fock matrix elements in atomic basis, density marix expression. Definition of Fenske-Hall basis sets in terms of STO one-electron orbitals. Diagonal terms in Fock matrix. Mulliken coulomb integral approximation, Richardson exchange integral approximation. Calculation of one-center terms, average configuration interaction energies. All two-center terms approximated as point charges. Combination of one-center self-exchange and two-center exchange interactions. Consequences of symmetric potential approximations at the atom. One-center off-diagonal Fock matrix elements assumed to be zero. Two-center off-diagonal Fock matrix elements set to an overlap combination of the one-center diagonal energies, corrected for counting the kinetic energy twice, and a Wolfsberg-Helmholtz combination of the two-center point charge contributions. Discussion of the value and limitations of the method. |
| Mon May 5 | Zero Differential Overlap Methods. CNDO/1, CNDO/2, INDO, SPINDO, MINDO, MINDO/3, AM1, PM3. Unitary overlap matrix. ZDO approximation in coulomb and exchange integrals. Parameterization of one-center and two-center terms. Example parameterizations and comparisons to experiment. |
| Wed May 7 | Density Functional Theory. Hartree-Fock method and static electron correlation vs dynamic correlation. Configuration interaction and perturbation theory. Slater exchange approximation. Alpha values. Local density approximation. Non-local approximations. Examples for transition metal systems. |
| Mon May 12 | Final project presentations. |
Last Updated on January 22, 1997 by Dennis L. Lichtenberger