Fall 2022

Computational Chemistry and Biochemistry

CHE 400/600 (Fall 2022) – 3 credits

Dr. Atanu Acharya | Office: 4-010 CST or 4-007 CST | | email: achary01@syr.edu

Lecture: 11:40 am -12:35 pm on Monday, Wednesday, and Friday in LSB 215

Office hours: by appointment or whenever you catch me!

Course Description:

This course introduces computational techniques employed to solve problems in chemistry and biochemistry with an emphasis on computational research problems. The students will gain hands-on experience with computational chemistry, molecular dynamics, visualization, and analysis software packages. This course does NOT require previous experience with computational techniques or quantum chemistry – it just warrants a zeal to learn new tools to complement chemical and biochemical. The content of this course is not math-heavy. However, the students should understand simple matrix operations and basic differential equations. Students will also learn rudimentary python and tcl scripting to post-process and analyze the output.

Learning Objectives:

After taking this course, students will be able to:

(1) Represent a molecule in a computer. Calculate and analyze molecular orbitals. Calculate properties of molecules such as redox potential, vibrational spectra, electrostatic potentials, partial atomic charges, and spin densities.

(2) Calculate the optical excitation energy of molecules and UV-Vis spectra.

(3) Calculate the transition states of a chemical reaction.

(4) Model biochemical systems in computers and run molecular dynamics simulations.

(5) Visualize and analyze simulation results.

(6) Run multiscale QM/MM calculations and analyze results.

(7) Understand scientific papers on computational chemistry and biochemistry.

(8) Communicate computational results in publication and presentation formats.

Suggested Textbooks:

The material taught in this course will pull from many sources, including a few textbooks:

• Molecular Modelling: Principles and Applications, Andrew Leech, 2^nd edition

• Introduction to Computational Chemistry, Frank Jensen, 3^rd edition

These books are not required for the course. However, it may be a good investment for learning computational chemistry techniques. In addition, we will refer to peer-reviewed scientific articles/reviews to discuss some topics. References to those articles/reviews will be provided during discussions in the class.

Grading:

Class participation: 15%

Students are expected to participate in discussions actively. The instructor will observe and note the level of participation. Since absence from a class means absence from class participation, non-attendance will lead to reduced points unless verifiable institute-approved excuses are attained. More than three absences will count as zero in this category.

Homework: grad 25%, undergrad 35%

Five homework problems will contribute 25% of the final grade. The chemistry department will provide all required software licenses and tools. The student will need to install the required software, as instructed. The student may consult the instructor during office hours to troubleshoot any installation issue. Homework will be due at the beginning of class on the due date. The student will incur a 15% penalty per day for turning in late homework. An exception may be made to the penalty under extremely extenuating circumstances with a valid and verifiable excuse. For example, a doctor’s note is a verifiable excuse. However, these exceptions should be negotiated beforehand or requested within three days of the posted due date.

Critique: 10%

The course will help students assimilate scientific literature on computational techniques. The students will be assigned a peer-reviewed paper or communication or letter and will be asked to write a critique of the peer-reviewed work. Copying and pasting the abstract/significance from the assigned scientific literature will result in a zero for this work. The written critique should clearly demonstrate the understanding of the material, and the student should make some comments about any limitations of the study. The student may also suggest viable ways to circumvent those limitations. The student will incur a 25% penalty per day for turning in a late critique. An exception may be made to the penalty under extremely extenuating circumstances with a valid and verifiable excuse. The student will receive a zero if the critique is submitted four days late. For example, a doctor’s note is a verifiable excuse. However, these exceptions must be negotiated beforehand or requested within three days of the posted due date. A higher level of sophistication is expected from graduate students.

Design project: grad - 10%, undergrad - 5%

Designing a scientific project requires constructing the correct scientific question that can be tested. Project design skills are required for every scientific endeavor. The student will be assessed on how well the final project is designed from the two-slide class presentations. The student needs to get their project approved by the instructor on the feasibility before preparing the presentation. The student must attend the class for the presentation. The make-up presentation can only be requested under extremely extenuating circumstances and must be negotiated beforehand or requested within three days of the assigned date. A higher level of sophistication is expected from graduate students.

Final project presentations: 20%

The student will work on their project and be continuously advised by the instructor. They will present 1-2 slides on an assigned date to present the project’s progress. Additionally, the students will prepare an 8-minute class presentation summarizing their project, strategy, computational details, results, and conclusion. The dates for the student presentations will be during regular class hours. The student must attend the class to present and answer any follow-up questions. If a student fails to present, they will receive a zero in this category. The grade in this category reflects the combination of both presentations. A higher level of sophistication is expected from graduate students.

Final project report: grad - 20%, undergrad – 15%

One of the major aspects of scientific research is presenting scientific results in written format for publications. The student will write a 2-3 page final report on their project. The written report will have the following sections: introduction, computational methods, results, and discussion. The results and discussions section may be combined if required. The students are encouraged to add graphics and tables to their reports as needed. A higher level of sophistication is expected from graduate students.