EFN510G and EFN115F: Computational Chemistry Course

University of Iceland, fall semester 2026

Instructor: Hannes Jónsson , office in room 212 in VR-III (hannes_jonsson at brown.edu).

Teaching assistants: Raphael Rullan (raphael.rullan@ens-lyon.fr) and Magnus A. H. Christiansen (mah107@hi.is), office in room 215 in VR-III.

• Lectures: Tuesdays 13:30-15:00 and Thursdays 11:00-12:30, in the conference room Skjalfti in Taeknigardur.

• Lab sessions: Fridays 10:30-12:00 in Skjalfti conference room. These sessions serve to help students get going on the exercise of the week. After completing the exercise (typically later, after more work after the lab session, in any case within a week of the assignment) a report should be prepared as a PDF file with answers to the questions raised in the handouts and e-mailed to the instructor. The computer exercises will make use of the 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 using atomic basis sets.
• Post Hartree-Fock methods (Möller-Plesset perturbation theory, configuration interaction, coupled cluster theory)
• 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, such as chemical reactions and diffusion events, in particular transition state theory.

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)
• T. Helgaker, P. Joergensen and J. Olsen, 'Molecular Electronic-Structure Theory', (Wiley, 2000).

Lecture Notes (will be updated as we go along):

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

• 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).

• IVa. Excited electronic states.
• IVb. Additional material.

Software:

The main software used in this course is called 'ORCA'. It is a commonly used quantum chemistry software package. In the latter part of the course, students can also choose to use other software, such as VASP. Short calculations can be carried out on laptops, but longer calculations should be run using the 'Elja' computer cluster. Laptops using Linux or MacOS operating systems can use the Terminal window to connect with the computer cluster, while those using Windows will need to use Putty and/or Mobaxterm software. Visualisation of the output from electronic and molecular structure calculations can be done using the Chemcraft or the ASE software packages.

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.

• 10. Reaction mechanism and rate. Session 10.

• 11. Excited electronic states. Session 11.
  

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:

There will be an oral final exam based on the lab reports and lecture notes. The exam takes half an hour and two labs will be discussed based on a random selection. Students should bring their laptop and be prepared to show their lab reports, possibly corrected from the time they were handed in, and be prepared to carry out calculations, answer questions about the results obtained and the theory/methodology used. The exam will take place in the instructor's office (VR-III, room 212) and another examiner will be present in addition to the instructor. Here is a list of example questions that could come up on the exam.