EFN115F: Computational Chemistry for graduate students

University of Iceland, fall semester 2023

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

• Teaching assistant: Yorick Schmerwitz (yla1 at hi.is)

• Meetings: Will be held on Tuesday afternoons 15:00-16:00 in the office of the instructor.

• Lab assignments: Students work through roughly weekly assignments and deliver a report by e-mail to the teaching assistant (yla1 at hi.is).

• Computer exercises will make use of student laptops and the 'Elja' computer cluster (elja.hi.is). All students should have their 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. The goal is to make students capable of using research level tools and carry out simple calculations related to their research interests.

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)

Topics Covered:

• Basic concepts of quantum mechanics, variational calculations, Hartree-Fock approximation for electronic systems and basis sets.
• Post Hartree-Fock methods (Moller-Plesset perturbation theory and configuration interaction)
• Density functional theory, DFT (local density approximation, gradient dependent functionals, self-interaction correction).
• Semi-empirical methods.

Lecture Notes (to be updated):

• Ia. Variational method
• Ib. Slater determinants
• Ic. Hartree-Fock approximation
• Id. SCF procedure and basis sets
• Ie. More about basis sets

• IIa. Post-HF: Semi-empirical and CI methods; and (optional) review article on semi-empirical methods.
• IIb. On the side: review of perturbation theory
• IIc. Post-HF:Møller-Plesset perturbation method
• IId. Post-HF: Coupled-cluster approach
• IIe. Density functional theory(DFT) ; and review article by Kohn.

• IIIa. Slides on normal modes of vibration.
• 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 Villi's presentation at ORCA users meeting (optional 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. Short calculations can be carried out on laptops, but longer calculations should be run using the 'Elja' computer cluster. Visualization of the output from ORCA can be done using the Chemcraft or the ASE software packages. 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.

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. Session1

• 2. First Hartree-Fock calculations. Session2
  exemplary report

• 3. Molecular orbitals and potential energy function. Session3
  exemplary report

• 4. Chemical reactions. Session4
  exemplary report

• 5. Methylene molecule. Session5. See article in Science.
  exemplary report

• 6. Configuration interaction and semi-empirical approaches. Session6. Data from Kolos file.
  exemplary report

• 7. MP2 calculations. Session7.
  exemplary report

• 8. DFT calculations. Session8. See article comparing functionals.
  exemplary report

• (9. Coupled cluster calculations. Session9.)

• (10. Transition rates. Session10.)

• (11. Excited states. Session11.)

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 a teaching assistant will be present. Here is a list of example questions that could come up on the exam.