CHEM599: Quantum Chemistry in Real World


    Important dates (2017)

  • August 23: First lecture - Welcome to 599!
  • November 6-13: scheduled HPCC downtime.



Prof. Anna Krylov

Office: SSC 409

Phone: (213)740-4929


To provide working knowledge of advanced molecular electronic structure and to develop skills for practical applications of quantum chemistry methods to real research problems.

Course description

The course is dedicated to learning practical aspects of advanced quantum chemistry. The students are expected to have good understanding of Quantum Mechanics and knowledge of Molecular Orbital Theory and basic Quantum Chemistry tools (Hartree-Fock and Density Functional Theory). The course is build around guided projects addressing the real-world research problems. The course includes lectures on advanced Quantum Chemistry topics expanding on the material covered in Chem545, discussions of the practical aspects of performing calculations using these methods, discussions of the research papers presenting advanced electronic structure calculations, and presentations by students of their projects. The individualized course projects will be summarized in the term paper and presented in the class in the form of research presentation. The paper should contain introductory notes describing chemical problem and outlining the computational part, as well as a brief review of the literature. The bulk of the paper is presentation of results of the computations, followed by a discussion and a critical analysis. The project will be evaluated by the following criteria: (i) relevance the proposed computational experiment to the specific chemical problem; (ii) the completeness of the performed computations and the quality of presentation; (iii) correctness of the reported results; (iv) quality of analyses of the results.

Software and hardware resources

Software. We will be using the Q-Chem electronic structure and its graphical interface IQmol. This page contains detailed instructions of how to install and configure the software, how to submit jobs to HPCC, as well as links to relevant tutorials and manuals. See also introduction to the course software and HPCC.

Computer resources. The main computational resource is USC's HPC cluster. Everyone is added to the Chem599 project, and should be able to run calculations. There are several ways to submit and run a job. The easiest way is to use IQmol interface (it needs to be properly configured for remote submission). Alternatively, you can submit jobs "old-fashioned" way, that is, prepare an input file, either manually or by using IQmol, ftp the input to HPC, and run a job using pbs system. Detailed instructions (for experts) how to access HPC and run jobs using pbs are given here. Simpler instructions will be available soon. To visualize the results of jobs submitted to HPC (or another machine) manually, you need to ftp the output (and the checkpoint file for orbitals) back to your laptop or desktop, where you can visualize the results using IQmol.

Time and place

SSC 604, 10:30–11:50 W Discussion hour: 10:30-11:50 F (will be used occasionaly)

Office hour: 3:00-4:00 F

Main textbook

"Quantum Chemistry" by Ajit Thakkar. Suggested additional reading: ``Modern Quantum Chemistry. Introduction to Advanced Electronic Structure Theory'' by A. Szabo and N.S. Ostlund and "Essentials of Computational Chemistry" by Christopher Cramer. Additional materials will be supplied.

Credit distribution

  • Presentation and critical analysis of the research paper assigned by the instructor 15%.
  • Midterm presentation of the term project: 15%.
  • Final presentation of the term project: 15%.
  • Term paper: 40%.
  • Attendance and participation in the discussions: 15%.

Material covered and downloads

  1. Introduction: Technical setup and introduction to IQmol and HPCC. Computational lab #1 assignment Computational lab #2: Bonding and molecular orbitals of formaldehyde. Homework #1.
  2. Student presentations on their research. HW: Read Chapter 10 from Thakkar.
  3. Finish student presentations on their research. Q/A about homework and computational labs: Please prepare your questions and be ready to be called to blackboard. Please bring laptops (just in case). Begin lecture "Overview of quantum chemistry". Computational lab #3: Koopmans theorem and ionized states of formaldehyde (due 09/20). Homework #2 (due 09/20).
  4. Class meets on Friday, 09/15. Lecture "Overview of quantum chemistry: From Hartree-Fock to exact solution".
  5. Virtual lecture (no class meeting on 09/20): "Quantum Chemistry of Electronically Excited and Open-Shell Species"[View the lecture] Computational lab #4: CIS calculations of formaldehyde.
  6. Class meets on Friday, 09/22. Excited states: Discussion and Q/A. Introduction of density matrices, natural orbitals, and natural transition orbitals. HW: Revisit CIS calculations of formaldehyde and visualize NOs and NTOs of the two lowest excited states. Read papers on wave-function analysis: Theory and examples. Homework and tips on NTOs.
  7. Class meets on Wednesday 10/4. Student presentations on wave-function analysis and NTOs.
  8. Class meets on Wednesday 10/11. Short meeting: Presentation how to execute NTO calculaions and how to visualize NTOs using JMol. Pavel's presentation on NTOs.
  9. Class meets on Wednesday 10/18. Student presentations (Bibek and Ariel) on wave-function analysis and NTOs. Q/A. Home work.
  10. Class meets on Wednesday 10/25. Overview of correlation treatment for ground and excited states: Hierarchy of approximations and Pople's chart. Review basis sets.
  11. Class meets on Wednesday 11/01. Density Functional Theory. Homework (due 11/08): Read 2 papers about DFT theory (A brief oberview of DFT and A recent review with extensive benchmarks).
  12. Class meets on Wednesday 11/08. Density Functional Theory: cont-d. Homework (due November 15). NBO analysis of formaldehyde. Pages to read from Szabo. Pages to read from Cramer.
  13. Class meets on Wednesday 11/15. Molecular properties and population analysis (Mulliken, Lowdin, NBO, etc).
  14. Class meets on Wednesday 11/29. Dyson orbitals. Koopmans theorem versus density differences in Kohn-Sham DFT. Ryan and Michael will present examples. Homework: Read JPCL 6, 4532 and JCP 127, 234106.
  15. Class meets on Wednesday 12/06. Project presentations (10 min + 5 min questions): Ariel, Michael, Ryan, Tirthendu, Sahil.