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CHEMISTRY 164, MOLECULAR STRUCTURE AND MODELING
SPRING, 2008

comparison of structures generated by instrumental and modeling methods (Exercise 1)
stereochemistry of neopeltolide (2008 version of Exercise 2)
conformational analysis of amphetamine (2007 version of Exercise 2)
You will need the structure of octopamine bound to the enzyme PNMT. It has been extracted from the pdb file 2an4 for the protein-substrate complex and can be downloaded from this site in Spartan, pdb, and SYBYL mol2 format.
search of conformers of NATMA (2003 version of Exercise 2)
beryllium borohydride (2008 version of Exercise 4)
dimerization of phosphorus (2007 version of Exercise 4)
To complete Exercise 4, you need the structure of the problem child in pdb format.
dimerization of nitric oxide (2003 version of Exercise 4)
development of a teaching module using modeling (Exercise 3)

CCL, the Computational Chemistry List, is maintained by Jan Labanowski at The Ohio State University. It is the premier clearing house for software and documents on all aspects of modeling and computational chemistry. The software archive covers all types of computers and operating systems.
QCPE, the Quantum Chemistry Program Exchange at Indiana University, has been a source of software developed at colleges and universities for decades. Many groups have deposited their code with QCPE. There is normally a modest charge for downloading software.
Soaring Bear is a Web site with links to a large array of modeling software. Much of it is freeware.

Pomona has a site license for Spartan and Gaussian and these products should be installed on all computers in Seaver North.
The Linux workstation sybyl.dci.pomona.edu in Seaver North 205 has a copy of SYBYL. You have to sign up for an account and password through the DCI Web site. When you request the password, request a csh (C shell) environment.
ORCA is a very sophisticated ab initio program written and maintained by Professor Frank Neese at the University of Bonn. It includes a wide array of basis functions and ZINDO. The free software runs on a PC. However, note that it does not have a sophisticated GUI like Spartan and SYBYL and you have to learn its command language in order to run it.

Executables for Babel can be downloaded from the CCL site. Babel is a DOS program that allows one to convert a structure file from one format, e.g. pdb, to another. Windows users need to download the babel106.zip file, the DOS executable, and babelwin.zip, the Windows GUI. Executables for other machines are also available.
Mercury, a product of the CCDC, is the best software for displaying crystallographic data. It has routines for converting structure files from one format to another.
Rasmol is a venerable but popular visualization program that was originally written to display protein structures. It runs on a number of platforms.
Accelrys, a major vendor of modeling software, provides DS Visualizer, its successor to WebLab Viewer Lite. DS Visualizer allows one to display structures, convert between formats, and perform a number of functions. You have to register at the Accelrys site in order to download the software.
Chem Office software which requires a license should be installed on all computers in Seaver North. Pomona has a site license for ChemBioOffice Ultra. You should be able to download a copy from the Cambridge Soft site. You may need some special codes to install the software.

The Molecular Zoo is a Web library of molecular structures generated by instrumental and modeling methods. You will add to the library as one of the graded exercises.
Annotated Bibliography on Modeling

last updated 17 February 2008, WES