NEWS & EVENTS
Chemistry Modules
  •  

    Chemistry Modules


    Electronic Structure Methods
    Electronic Structure Methods -- For Instructors

    Module Author: Sheryl Hemkin
    Author Contact: hemkins@kenyon.edu
    Funded By: National Science Foundation

    This module was created to enhance a student‟s comprehension of several topics: the relationship between molecular structure and potential energy, the relation between potential energy and its derivative properties, and how simulations can be used to advance the understanding of the reaction pathway and activated complex, etc. As such, the problem sets at the end of each section reflect a variety of themes and a range of difficulties. Therefore, the instructor is encouraged to examine the questions ahead of time to determine which suit the purpose of the target audience.

    Molecular Structure and Interaction
    Molecular Structure and Interaction: Instructor Notes

    Module Author: Sheryl Hemkin
    Author Contact: hemkins@kenyon.edu
    Funded By: W. M. Keck Foundation


    Today we realize that a molecule’s structure can give us many clues as to how it will react and interact with its environment, and now that we have methods to allow us to “see” this three-dimensional structure it is being used extensively in the biochemical realm, especially in drug development. For example, a key molecule in the life cycle of HIV-1 is HIV-1 protease (represented by the lines in the illustration above). Scientists determined that if the active site of this protease was blocked, they could stop the virus from replicating as normal. To that end, knowledge gained from 3-D molecular structures, such as those you will view, was combined with experimental evidence to create a variety of HIV-1 protease inhibitors (represented by the spacefilling structure above). The insight provided by the computational rendering of molecular structures has greatly improved our understanding of how chemical structure and function are interrelated, and on a larger scale, it has increased our ability to understand the body and develop the drugs needed to combat its diseases. In these exercises you will explore a several bio-molecules with the purpose of gaining an understanding as to how structural features, small and large, can have profound influence on life.

    Chemical Kinetics

    Module Author: Kim Baldridge
    Author Contact: kimb@sdsc.edu
    Funded By: W. M. Keck Foundation


    The primary goal of this module is to help beginning chemistry students understand the mathematical models encountered in chemical kinetics. It was designed to accompany the discussion of kinetics presented in undergraduate general chemistry and assumes that have started to take the first semester of Calculus. Secondarily, this module hopes to give students a better sense of the role computational chemistry plays in the science and society by examining the context of the multi-disciplinary research surrounding nitrogen dioxide and ozone pollution. The students use experimental data and models from chemical kinetics to determine a possible reaction mechanism and analyze what the model predicts about concentrations over time. Numerical methods and tools (such as programs like Maple, Matlab or Mathmateica) are introduced. The final project in this module involves modeling the reactions using a stochastic chemical simulation.

    Quantum Chemistry in the Environment

    Module Author: Kim Baldridge
    Author Contact: kimb@sdsc.edu
    Funded By: W. M. Keck Foundation

    This unit introduces how quantum mechanical calculations can be used to investigate chemical problems. An online computational chemistry portal to GAMESS is used to run calculations and explore the major common computational methods and calculations used in computational chemistry. These methods are used to investigate several molecules that are important in the environment. The module is designed to be accessible to undergraduates taking General Chemistry when they encounter quantum theory for the first time. The goal of this module is to familiarize students with computational chemistry so that they will be able to run calculations and determine if the results are reasonable. To accomplish this, the module starts out with a background section (entitled 'learn' in the on-line module) to get students acquainted with the basic background of quantum mechanics used in computational chemistry software packages. There is a tutorial section (entitled 'apply' in the on-line module) that is meant to be a guide to how to complete a computational analysis using the GAMESS portal. Finally, the students apply their knowledge (entitled 'solve' in the on-line module) to a computational chemistry project that uses an on-line web portal to GAMESS and allow students to run calculations on their own and interpret the results.

    Molecular Mechanics

    Module Author: Wayne Becktel
    Author Contact: wbecktel@capital.edu
    Funded By: National Science Foundation (9952806)


    This module introduces the technique of Molecular Mechanics in calculating optimum geometries and interactions of molecules. Solvent approximations and the use of re-entrant boundary conditions are also described.

    Introduction to Computational Chemistry

    Module Author: Wayne Becktel
    Author Contact: wbecktel@capital.edu
    Funded By: National Science Foundation (9952806)


    This module will introduce the student to the fundamental concepts of Computational Chemistry. It prepares the student for more detailed explanations of specific techniques.

    Kinetics of Reaction Systems

    Module Author: Sheryl Hemkin
    Author Contact: hemkins@kenyon.edu
    Funded By: National Science Foundation (0618252)


    This module was designed to give students an understand of the kinetics associated with reaction systems. To that end, the module will also introduce the students to a low cost molecular visualization program, Berkeley Madonna. By learning how to translate rate equations into the coding structure of Berkeley Madonna the students will be able to independently simulate how the reactions' chemical concentrations will change with time.