# CHM 579: Computational Chemistry: Molecular Modeling and Simulations

# Spring 2020

## Instructor: Gaurav Chopra, DRUG 261, gchopra@purdue.edu, (765) 496-6108

## Course Description

**Theoretical basis and practical applications of computational methods relevant to chemical and biochemical research problems.** The objective of the course is learning, developing and using molecular modeling methodologies useful for research work in a variety of areas. The applications of the course range from computational modeling of biomolecules, drug discovery, to nanotechnology, depending on the system of interest. We will learn about theoretical concepts and techniques used in modern computational chemistry and biology that includes modeling of energetic interactions between atoms from polarizable to classical to statistical (knowledge-based) formulations that are applied to areas in drug design and discovery, nanotechnology, and other areas of molecular modeling and simulations taking into account the students background and interest.
## Course Meetings

__Lectures:__ Monday, 9:30am-11:20am in DRUG 182

__Labs:__ Monday, 3:30pm-5:20pm in DRUG 182

__TA office hours:__ Tuesday and Thursday 4:00-5:00 pm in DRUG 269 ; Online office hours: Follow the links separated by date on twitter. The handle for the class is @compchemclass.

__Course notifications and discussion forum:__ Register at Piazza and add CHM 579 class

## Syllabus

- Introduction to molecular modeling theory, applications and machine learning
*Simulation methods*: Monte Carlo, Molecular dynamics, Docking
*Force fields*: Classical physics-based potentials, Statistical knowledge-based potentials
*Environment*: Simple homogenous and complex molecular systems
*Interactions*: Cheical environments - docking and drug design
- Machine learning introduction in the context of drug design
- Course readings: Publications

## Grading

The grading in this class will be on absolute scale. There are 600 points divided as following with an additional 100 points for optional final project as extra credit. So students can earn a maximum of 700 points out of 600 grading scale.
__Individual lab assignments:__ 200 points (TBD)
__Final exam:__ 200 points (TBD)
__Final project presentation and Manuscript with author contributions:__ 200 - Topic to be mutually selected by student and instructor, maximum groups size of 3 permitted

## Assignments

The submission of all assignments and the final project for this course is in form of webpages. The assignments will be made available on the day we will discuss them in the lab sessions. Due dates and times of the assignments are shown as follows. **Monday lab help sessions are mandatory.** Assignments are written in the format of a research publication unless otherwise noted.

Problems? Questions about the Page or the Class?
Contact the instructor