CHEM477/577: Computational Chemistry

The course provides an introduction to computer-based methods in Chemistry.

Methods ranging from continuum mechanics to classical statistical mechanics and quantum descriptions of chemical problems are discussed, with an emphasis on their applicability and limitations. The course has a major applied component: a significant percentage of class time is spent in a computer lab, working with computational chemistry software. Another significant part is dedicated to critical discussions of recent scientific literature in the field of computational chemistry. Evaluation is based on research-type projects, assignments and a presentation/report on a specific aspect within the course's subject matter.

The course is equally suitable to undergraduate and graduate students who have an interest in figuring out how to approach a theoretical/computational research problem, and to undergraduate students interested in seeing where and how their Math, Statistical and Quantum background applies to chemical research. Some comfort with introductory Quantum Chemistry and Thermodynamics is expected. However, the course leaves the rigorous mathematics of Quantum Chemistry and Statistical Thermodynamics to focus on methods and outcomes. As such, in depth knowledge of the Mathematics of Quantum Chemistry is not necessary to follow the course material and successfully complete course requirements. Some of the Physics and Math behind specific computational methods are however discussed in the relevant lectures.

Instructor: Dr. Irina Paci

Syllabus

 

Notes for course

Introduction to Computational Chemistry and the Potential Energy Surface(pdf)

C. David Sherril Brief Review of Quantum Chemistry

From molecular to macroscopic: Brief review of relevant Statistical Mechanics(pdf)

Force fields and Molecular Mechanics(pdf)

Molecular Dynamics calculations(pdf)

September 23 computer lab(pdf)

Paper about Young's modulus calculations(pdf)

Monte Carlo Simulations(pdf)

Hartree Fock and Semiempirical Methods(pdf)

October 21 computer lab(pdf)

Basis sets(pdf)

Density Functional Theory(pdf)

A few correlated methods(pdf)

 

Papers for discussion

Basic questions for paper discussions(pdf)

Hatcher, Guvench, MacKerell, J. Phys. Chem. B 2009, 113(112466) (force fields)

Pelaez and Wilson, Phys. Chem. Chem. Phys. 2007, 9(2968) (molecular dynamics)

Prytkova, Beratan, Skourtis, PNAS 2007, 104(802) (Hartree-Fock)

Schwabe and Grimme Acc. Chem. Res., 2008, 41(569) (DFT and double hybrid methods)

Fink, Pfister, Zhao and Engels, Chem. Phys. 346, 275(2008) (HF and correlation)

 

Assignments

Assignment 1 (pdf) answers (pdf)

Assignment 2 (pdf)

Assignment 3 (pdf)

Assignment 4 (pdf)

Projects

Project 1 (pdf)

Project 2 (pdf)

Py2 S1 (xyz)

Py2 S2 (xyz)

 

Student lectures

Nov. 18 - Elvis - Direct Dynamics

Nov. 22 - Marie - Molecules in external electric fields

Nov. 23 - Sandra - Vibrational Spectra - QC emphasis

Nov. 25 - Shane - Dispersion in QC

Nov. 29 - James - Solvation effects in QC methods

Nov. 30 - Rebecca - Modelling transition states

Dec. 2 - Jia - Basis set issues - BSSE and Effective Core Potentials

Evaluation Scheme (pdf)