Chemistry 361

CHEM 361
Molecular Modeling

1. Catalog Entry

CHEM 361
Molecular Modeling

Credit hours (3)
Prerequisites: MATH 151, CHEM 302, or instructor approval

The focus of this course is on the theory behind molecular modeling techniques and their application to problems in chemistry and biochemistry research.  Students will apply their knowledge of general and organic chemistry as well as mathematics to the study of computational molecular modeling.

2. Detailed Description of Course

An outline of the topics covered:
    1) Introduction to Molecular Modeling
        a. What is Molecular Modeling?
        b. Visualization and Graphical User Interfaces (GUI)
        c. Molecular mechanics
        d. Electronic structure methods
        e. Introduction to model chemistries
    2) Essential Concepts and Techniques
        a. Single point energy calculations
        b. Geometry optimizations
        c. Frequency calculations
        d. NMR calculations
        e. UV-Vis calculations
        f. Protein ligand docking
        g. Bulk solid, liquid and surface modeling
    3) Model Chemistries
        a. Basis set effects
        b. Selecting an appropriate theoretical method
        c. Applications
        d. Choosing a system of interest to study
    4) Presenting your findings
        a. Paper
        b. Poster
        c. Presentation

3. Detailed Description of Conduct of Course

CHEM 361 is a lecture- and project-based course in which students are encouraged to participate with comments and questions.  The course uses a combination of lectures and notes developed from the literature by the instructor and relevant, current literature in the field as the text for the course.  Homework and/or in-class assignments or quizzes, as well as exams, will be used to evaluate the student’s understanding of the course material.  Students will also complete a research project focused on a topic related to molecular modeling.  A cumulative final will be administered at the end of the semester to evaluate the student’s mastery of the course material.

4. Goals and Objectives of the Course

After successful completion of Molecular Modeling, the student will be able to:
    1) Proficiently apply the topics listed above.
    2) Analyze and interpret scientific literature in the field of molecular modeling.
    3) Communicate course concepts clearly and accurately.

5. Assessment Measures

Assessment of the student’s success in the course is based on examinations and a cumulative final examination, a research project, and other assignments, which may include homework, in-class assignments, and/or quizzes.

6. Other Course Information

The students in Molecular Modeling at Radford University are mainly Chemistry majors interested in careers in medicine, pharmacy, or chemistry research, and the course is designed to meet their needs and interests to the greatest extent possible.  The course can also be of value to any other students, such as some Physics or Biology majors, who might have an interest in modeling the interactions between molecules or between the atoms in molecules.

Review and Approval