Modern biology is increasingly about molecules and their interactions---the stuff of chemistry. In this section of the Biology Student Workbench, we introduce you to materials developed for our sister NCSA project, the Institute for Chemistry Literacy through Computational Science. These materials will provide an introduction to core computational chemistry tasks that are useful in the study of all molecules, of biological origin or not.
1) Building and Visualizing Molecules
The tutorial is developed to get students familiar with ACD/ChemSketch and 3DViewer, which is a power tool for building and visualizing the structure of a molecule. It can produce publication-quality graphics. Structures can be minimized using molecular mechanics based on CHARMM, and various molecular properties can be determined. A variety of biochemical templates are available for rapid structure generation.
2) Exploring Molecules Using WebMO
The tutorial is developed to get students familiar with WebMO, which is a free World Wide Web-based interface to computational chemistry packages. It improves the accessibility and usability of computational chemistry software. Users can access and use your software from their web browser.
3) Further Explorations of Molecules Using WebMO
The tutorial is developed to introduce users further advanced explorations of molecules by using WebMO .
4) Virtual Exploration of Acids and Bases
The tutorial is developed to introduce Virtual Lab Simulator, which allows us conduct a virtual experimention. Here this unit take a pH titration on hydrofluoric acid (HF) for example. Furthermore, data collected by the simulator (mL NaOH added and pH) will be plotted in OpenOffice Calc. You will also use Virtual Lab Simulator to investigate the heat of neutralization. This unit also includes basic techniques of using spreadsheets(ex. Microsoft Excel, OpenOffice Calc).
5) Ideal Gas Law
The tutorial is developed to use an applet that simulates the behavior of an ideal gas, users will explore the relationship between
volume and each of the following variables: (1) Number of gas particles; (2) Velocity of the gas
particles, and (3) Pressure. Several gas laws will be discovered by collecting and analyzing data to
determine mathematical relationships.
6) Explorations of Chemical Kinetics
The tutorial is developed to explore chemical kinetics by using spreadsheet softwares. We can calculate the concentrations of chemicals as a function of time using both
the analytically integrated rate law and by numerical integration of the differential rate law using
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