EFN510G and EFN115F: Computational Chemistry, University of Iceland fall 2023

EFN510G and EFN115F: Computational Chemistry Course

University of Iceland, fall semester 2025

Teaching assistant: Magnus A. H. Christiansen, office in room 215 in VR-III (mah107@hi.is)

Lectures:
Wednesdays at 10:30-12:00 (in Skjálfti up to and including Sept. 24, after that in Geysir)
Thursdays at 13:00-14:30 (in Geysir)
Lab sessions: Thursdays at 14:30-16:00 (in Geysir)

Lab assignments: Students work through weekly assignments and deliver a report by e-mail to Magnus (mah107@hi.is).
Computer exercises will make use of each student's laptop and the 'Elja' computer cluster (elja.hi.is). All students should have an account on Elja and be able to log on remotely using secure key.

Course Description:

Introduction to methodology and tools for studying the structure of molecules, chemical bonding and chemical reactions. A survey of computational approaches for calculating electron distribution such as ab initio methods (Hartree-Fock, configuration interaction, perturbation theory), density functional theory (various functional approximations) and semi-empirical methods will be given. The focus will mainly be on the electronic ground state, but also some excited state calculations. Furthermore, methods for identifying the mechanism and estimating the rate of transitions will be covered. The goal is to make students capable of using research level tools and carry out simple calculations related to their research interests.

Topics Covered:

Basic concepts of quantum mechanics, variational calculations, Hartree-Fock approximation for electronic systems and basis sets.
Post Hartree-Fock methods (Möller-Plesset perturbation theory and configuration interaction)
Density functional theory, DFT (local density approximation, gradient dependent functionals, self-interaction correction).
Excited electronic states.
Semi-empirical methods.
Methods for identifying the mechanism and estimating the rate of transitions.

Reference books:

A Chemist's Guide to Density Functional Theory, 2nd ed. by W. Koch, M.C. Holthausen (Wiley-VCH Verlag GmbH).
Molecular Modeling: Principles and Applications, 2nd ed. by Andrew R. Leach (Pearson Education Limited).
Szabo and Ostlund: 'Modern Quantum Chemistry' (Dover).
Klaus Capelle, 'A bird's-eye view of density-functional theory', (http://arxiv.org/pdf/cond-mat/0211443.pdf)

Lecture Notes (to be updated):

Part I: Hartree-Fock (or rather SCF)

Ia. Variational method
Ib. Slater determinants
Ic. Hartree-Fock approximation
Id. Basis functions and SCF procedure
Ie. More on basis sets
If. Semi-empirical approximations; and (optional) review article on semi-empirical methods.

Part II: Post-HF and DFT methods:

IIa. Configuration Interaction method; and (optional) slides on neural network selected CI method.
IIb. Perturbation theory and MPn method
IId. Coupled-cluster approach
IIe. Density functional theory(DFT) ; and review article by Kohn.

Part III: Dynamics of atoms and transition rates:

IIIa. Slides on molecular vibrations.
IIIb. Article on an exercise about normal modes of vibration.
IIIc. Slides on rate calculations, part A.
IIId. Slides on rate calculations, part B.
IIIe. Slides on rate calculations, part C.
IIIf. Book chapter on saddle point searches (optional material).
IIIg. Link to a presentation by Villi at an ORCA users meeting (optional material).

Part IV: Excited electronic states:

IVa. Excited electronic states.

Software:

Instructions for installing the needed software on your laptop are given in the document: software installation. An introduction to the most important commands for the Unix operating system are here: unix commands. A summary of instructions for doing calculations with ORCA are given in the document ORCA calculations.

Lab exercises:

1. Getting started. Session 1.
2. Approximate Hartree-Fock calculations of H2, HF and LiH. Session 2.
3. Molecular orbitals and potential energy function. Session 3.
Additional material, OnMOsForH2andDissociation.pdf
4. Chemical reactions. Session 4.
5. The methylene molecule. Session 5. See article in Science.
6. Configuration interaction. Session 6. Data from Kolos file. Article on the Q-correction.
7. Perturbation calculations, MP2. Session 7.
8. Density functional theory. Session 8.
9. Vibrations of molecules. Session 9.
9. Reaction mechanism and rate. Session 10.

Special projects:

Students enrolled in the 10 ECTS version of the course (EFN115F) carry out a special project corresponding to one full week's worth of work. A good option is to work with some published research article and to redo some of the calculations presented there, test for convergence with respect to various parameters and finally expand on the calculations in the article, either by choosing slightly different molecule or going to higher level of theory. The choice of topic and article needs to be made in consultation with the instructor no later than the 10th week of the semester.

Final exam:

example questions