| 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. |
| Matlab |
| 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.) |
|
Cerius2 |
| 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
Builders
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. |
