CHEM 749 Computational Chemistry
Instructor: Sophya Garashchuk
Dept of Chemistry and Biochemistry, University of South Carolina, Columbia
(Dated: August 23, 2017)
I. SYLLABUS
Learning Outcomes:
(i) the students will learn basic concepts and gain computer skills enabling them to use electronic structure
codes and simulations with confidence and intelligence for better understanding of the chemical processes (such
as computation of stationary geometries, barriers, electrostatics and polarizability, properties in solutions, IR
and UV spectra)
(ii) the students will be able to set up their own input files and interpret/visualize output files for standard
quantum chemistry programs/packages that might be relevant to their research
(iii) the students will improve general critical thinking and problem-solving skills as well as improve their skills
of independent computer-aided research through extensive use of electronically available resources.
Prerequisites: CHEM 112/142, MATH 142, PHYS 211 and 212 or equivalents, i. e. general chemistry,
calculus, classical mechanics and electrostatics
Logistics:
Classes will take place T,Th 11:40 am-12:55 pm in the linux computer lab PSC Jones 101
where we will work with Q-Chem, Spartan and molecular dynamics program packages
Class materials and assignments or links to them will be posted on Blackboard
Computer and software support:
Myk Milligan
[email protected] Jun Zhou
[email protected] Ph: (803) 777-5492
College of Arts & Sciences
Sumwalt College 228
Office hours: W 9:00-11:00 am, GSRC 407. I am generally available Mon-Fri 9:00 AM 5PM. You can just
drop by, call or e-mail to check if I am available; if you have difficulties reaching me, make an appointment.
Suggested textbooks:
Molecular Modeling Basics by Jan H. Jensen
Frank Jensen, Introduction to Computational Chemistry Quantum Chemistry 2nd edition
Christopher Cramer, Essentials of Computational Chemistry 2nd editions
Other resources:
There are many useful guides and texts on the web, particularly with respect to UNIX, linear algebra, and
general aspects of computational chemistry. On-line manuals for all software packages are very useful and often
outline the theory. In addition, electronic wiki-book is a useful resource:
http://en.wikipedia.org/wiki/Book:Electronic structure methods
Quantum Chemistry libguide http://guides.library.sc.edu/qchem has various electronic resources and
applets. Let me know about any other useful/interesting stuff that can be added
Required work: labs/assignments (25% ), quizzes (5%), midterm exam (20% ), independent project (50%).
Attendance above 80% is expected.
Grading scale: A 90 > B+ 85 > B 77 > C+ 69 > C 60 > D 40
[email protected]
631 Sumter Street, GSRC 407, (803)-777-8900
2
Requirements for graduate students:
the independent projects have to be formulated by a student and should include a thorough literature search
and test calculations to validate of the chosen computational methodology. Graduate students are expected to
become proficient in the linux command-line interface (CLI) (in addition to the Graphical User Interface (GUI));
they will be required to use CLI-based Q-Chem for the electronic structure calculations related to assignments.
Academic Academic Integrity:
You are expected to practice the highest possible standards of academic integrity. Any deviation from this
expectation will result in a minimum academic penalty of your failing the assignment, and will result in additional
disciplinary measures including referring you to the Office of Academic Integrity. Violations of the Universitys
Honor Code include, but are not limited to improper citation of sources, using another students work, and any
other form of academic misrepresentation. For more information, please see the Honor Code.
Accomodating Disabilities:
Reasonable accommodations are available for students with a documented disability. If you have a disability and
may need accommodations to fully participate in this class, contact the Office of Student Disability Services: 777-
6142, TDD 777-6744, email
[email protected], or stop by LeConte College Room 112A. All accommodations
must be approved through the Office of Student Disability Services.
II. EXAMPLES OF THE ASSIGNMENTS
A. Labs/Assignments
Compute the inversion barrier (so called umbrella motion) for NH3 . Convert your answer into kcal/mol.
What isomer, LiCN or LiNC is more stable, and by how much?
Convert the value of 2 kcal/mol to atomic units, eV, and cm1 .
B. Midterm
1. Is C2 O2 stable molecule? What is its geometry? What is the dissociation energy of C2 O2 into two CO molecules?
2. What is the ground spin state of SiH?
3. Using diatomic molecules, find if Li and Na form an alloy (Hint: compare Li-Li, Na-Na, and Li-Na bond
strengths.
4. List desirable properties of a basis set for quantum chemical calculations. Give example of a widely used basis
set and explain its structure.
5. What is a size of a Fock matrix for calculation on C2 H5 OH with 6-311+G basis set?
6. How many basis functions are in the NaOH molecule with 6-31G** basis set?
7. Write in atomic units a Hamiltonian for CO+ 6
2 molecule (r(CO) = 1.3 A, OCO = 180 )
C. Independent project
The independent project can be related to your research area or chosen from the instructors list; full information
will be given in class. Some examples are:
Isomers of triatomic molecule made of Li, C, and N. Find the absolute minimum and the metastable isomer(s)
in linear configuration. Calculate force constants for each minimum, and calculate the isomerization barrier.
Compare your results using different levels of theory.
Study of valency. Calculate bond energies of the XHn1 -H bond in molecules where X is Be, C, O, and n takes
all possible values yielding stable molecules. Use different levels of theory and different basis sets. Find the
average bond energy for each X.
3
How does benzene crystallize? Examine the benzene dimer to predict the arrangement of molecules in the solid
state. Explain your choice of the computational method.
III. TENTATIVE TIMELINE
08/24 First class
10/19 Fall break, no classes
10/24 Midterm exam
10/26 Verify your project selection with the instructor
12/07 Last class
12/14 All projects are due
IV. CONTENT BY WEEK
1. Preliminaries and computer accounts. Linux OS.
2. Classical mechanics, electrostatic interactions; potential energy surfaces.
3. Force fields; minimum energy search; molecular mechanics and dynamics.
4. Quantum Mechanics: wavefunction, Hamiltonian, electronic spin.
5. Chemical bonding; atomic and molecular orbitals; basis sets.
6. Basic models the Hartree-Fock and Density Functional Theory.
7. Energy calculation, geometry optimization, technical issues (initial guess, convergence).
8. Molecular properties: electrostatic potential/charges, barriers and energy profiles.
9. Midterm. Choice and set up of the projects.
10. Molecular properties (cont): polarizability/properties in solutions.
11. Beyond the basics electron correlation, perturbation theory.
12. Microwave and IR/Raman spectroscopy.
13. Electronic spectroscopy, UV-vis, excited electronic states.
14. Elements of statistical mechanics; temperature.
15. In-class work on the projects.
16. Finals week: independent projects are due.
