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Recommended Textbooks
These books are not required for the course, but you may find them useful.
1) Guy H. Grant and W. Graham Richards, Computational Chemistry (amazon).
2) Press et al, Numerical Recipes in C : The Art of Scientific Computing (amazon).
General Support
Adobe Acrobat Reader A plug-in that enables your browser to view Adobe PDF files.
CTC information Using the CTC
ctc.chsrc configuration file for CTC accounts. 
Mathworks   The company that develops Matlab. (Student editions available for $99.)
Matlab Tutorial  HTML version of the tutorial distributed in class. (pdf version) (Also check  here for other online tutorials.)
Online Manuals PDF files of the complete manuals are available at Mathworks. Since these are large files, local copies of the most useful manuals are provided here:
     Getting Started with Matlab (1.2Mb, 99 pgs.) 
     Using Matlab (4Mb, 585pgs.)
     Using Matlab Graphics (13Mb, 488pgs.)


Accelrys The company that develops Cerius2.
Online Manuals Modeling Environment User environment and molecule builder.
Cerius˛ˇForcefield Engines
Cerius2 OFF  
Cerius2 Forcefield Based Simulations 
Quantum 1 Modules
Crystal and Surface Builder

Suggested papers for Molecular mechanics calculations

Here, Vardeny has made a very highly substituted polyacetylene. See if you can use molecular mechanics to determine the structure. (If done well, this result is publishable.)

Dendrimers are a class of highly branched macromolecules. In this paper, Percec and coworkers consider the structure of various dendrimers. You can use molecular mechanics to examine these structures, and calculate the amount of steric strain. 

In this paper, Frechet and co-workers put rotaxanes on a oligomer, sort of like putting beads on a piece of thread. Dendrimers serve as caps to keep the beads from falling off the end. You can use molecular molechanics to determine the size dendrimer needed to confine the rotaxanes.

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Questions or comments:  Last updated: Tuesday, August 28, 2001