Chemistry 245: Computational Chemistry

 

Lecture Schedule

 

Notes:

  1. This schedule is tentative and subject to change.  However, the date of the midterm exam will remain fixed.
  2. Reading posted for a given day should be completed prior that class period.

 

20BDetailed class schedule

 

24BAugust 30:

            1) course introduction; syllabus

            2) introduction to theory; examples of applications

            3) in-class exercise: introduction to Spartan ‘08 (in-class assignment #1)

 

25BSeptember 6:

            1) classical mechanics overview

            2) force field terms

            3) comparison of different force fields

            4) in-class exercise: molecular mechanics in Spartan (in-class assignment #2)

* HW #1(a) assigned

 

25BSeptember 13:

            1) quiz #1 and literature application discussion (J. Phys. Chem. A, 2004, 108, 621-627)

            2) classical dynamics overview

            3) MD and Monte Carlo simulations

            4) applications:  protein folding, NMR determination of protein structure

            5) in-class exercise: simulating MD in Excel (in-class assignment #3)

* HW #1(a) due; HW #1(b) assigned

 

25BSeptember 20:

            1) Schrödinger equation, Born-Oppenheimer approximation

            2) LCAO approach

            3) Hückel theory

            4) in-class exercise: Hückel theory (in-class assignment #4)

5) Hartree-Fock theory introduction and Self-consistent field method

* HW #1(b) due

 

25BSeptember 27:

            1) finish Hartree-Fock theory

2) semi-empirical methods overview

            3) comparison of CNDO, INDO, NDDO formalisms and performance

            4) geometry representations: Cartesian coordinates, z-matrices, symmetry

5) in-class exercise: writing z-matrices (in-class assignment #5)

* HW #2(b) assigned

 

29BOctober 4:

            1) quiz #2 and literature application discussion (J. Am. Chem. Soc., 1996, 118, 8920-8924)

2) basis sets (Gaussian functions, polarization & diffuse functions, effective core potentials)

            3) practical issues: SCF convergence, symmetry

            4) Hartree-Fock theory accuracy

5) in-class exercise: electrophilic aromatic substitution of toluene and nitrobenzene – verification of

    substitution patterns via semi-empirical and Hartree-Fock calculations (in-class assignment #6)

* HW #2(b) due; HW #2(a) assigned

 

October 11:

            Molecular properties:

            1) multipole moments and molecular electrostatic potential

            2) partial atomic charges and atomic spin

            3) ionization potentials; electron affinities

            4) infrared spectra

            5) in-class exercise: organometallic metal-carbonyl half-sandwich complexes (in-class assignment #7)

* final project assigned; HW #2(a) due

 

October 18:

            1) computing enthalpy, entropy, and free energy changes for reactions

            2) isodesmic reactions

            3) application: calculating heats of formation and relative stability of species

            4) determining transition states

            5) transition state theory, rate constants

            6) kinetic isotope effects, transmission coefficients

            7) in-class exercise: hydrogen atom transfer between organic molecules (in-class assignment #8)

* group sign-up for final project; HW #3 assigned

 

29BOctober 25: MIDTERM EXAM

 

29BNovember 1:

            1) density functional theory overview

            2) Hohenberg-Kohn theorems, Kohn-Sham methodology

            3) exchange & correlation functionals

            4) DFT performance and comparison with MO theory

            5) application discussion: transition metal complexes (J. Phys. Chem. A, 2004, 108, 5479-5483)

 

29BNovember 8:

1) quiz #3 and literature application discussion (Phys. Chem. Chem. Phys., 2005, 7, 2701-2705)

2) the process of solvation and solvation effects on reactions

            3) continuum solvation models

            4) mixed explicit/implicit solvation models

5) standard-state corrections

* HW #3 due; HW #4 assigned

 

29BNovember 15:

1) calculation of pKa values and reduction potentials

2) calculation of partition coefficients

3) application discussion: pKa values with different solvation models (J. Phys. Chem. A, 2006, 110, 2493-

     2499)

            4) in-class exercise: determining pKa values with different solvation models (in-class assignment #9)

 

29BNovember 22:

1) NMR spectra

2) application discussion: empirical corrections to computed NMR spectra (J. Chem. Theory Comput.,

    2006, 2, 1085-1092)

3) UV-Vis spectra and TD-DFT methods

4) open-shell molecules and unrestricted wave functions

5) in-class exercise: NMR spectra at different levels of theory (in-class assignment #10)

 

November 29:

            1) quiz #4 and literature application discussion (J. Org. Chem., 2003, 68, 6375-6386)

2) overview of QM/MM methods

            3) QM/MM boundaries between space and atoms

            4) application discussions (J. Am. Chem. Soc., 2004, 126, 7652-7664;

J. Am. Chem. Soc., 2005, 127, 1025-1037)

* HW #4 due

 

38BDecember 6:  final project oral presentations & final papers due

 

39December 13: FINAL EXAM