programs suitable for use with desktop PCs and Macintosh computers. This
author suggests that prospective users evaluate as many programs as possible
by visiting websites or vendor booths at professional society meetings. Many
vendors offer useful software demonstrations at professional meetings and
provide online demonstration software or evaluation CDs for further evalua-
tion. Many other programs not discussed here are available for drawing,
visualization, computation, conformational analysis, combinatorial chemistry
analysis, quantitative structure – activity relationship (QSAR) searching, and
other database searching. Not all capabilities of the software programs dis-
cussed here are mentioned. The idiosyncratic nature of the information
below arises from its accessibility on various software company websites. Some
product description pages were well - organized and very accessible, while
others were diffi cult and required unnecessarily long download times for
complex visualizations better left to demonstration downloads or CDs. In the
listing below, each software supplier or program mentioned will list a website
that should be consulted for the most accurate and up - to - date information.
Most software operating in Microsoft Windows environment will require, at a
minimum, Windows 2000, XP Home or Professional, 1 GB of available disk
space, 256 MB of system memory, a 1024 × 768 resolution - capable display
monitor, and a 1 - GHz Pentium or AMD equivalent CPU. For modeling and
calculations involving proteins, double all of the above. A useful website with
a plethora of information about scientifi c software is found at http://www.
ks.uiuc.edu/Development/biosoftdb/. The category that gives short description
of many of the programs described below, and more, is “ Quantum Chemistry
Calculation. ”
An interesting research article published in 2005 compared a number of
different quantum mechanical and molecular mechanics methods — the pro-
grams and methods to be described in the following paragraphs.^43 The test
molecule, analyzed by the different methods, which were then compared to
known experimental results, was (2 - amino - 5 - thiazolyl) - alpha - (methoxyimino) -
N - methylacetamide, a model of the aminothiazole methoxime (ATMO) side
chain of third - generation cephalosporin antibacterial agents. Among the
quantum methods examined were the semiempirical MNDO, AM1, and PM3
methods, Hartree – Fock (ab initio) at a range of basis set levels, density func-
tional theory (DFT) at a range of basis sets, and a post - Hartree – Fock method,
local M ö ller – Plesset second - order perturbation theory (LMP2). Among the
force fi elds compared were AMBER, MMFF94, MMFF94s, OPLS/A, OPLS -
AA, Sybyl, and Tripos. Programs used were Spartan, MacroModel, SYBYL,
and Jaguar. For the computational versus experimental comparisons made, the
MMFF94 force fi eld such as implemented in MacroModel was the best overall
computational chemistry method at reproducing crystallographic data and
conformational properties of the ATMO moiety. This work demonstrates that
going to a higher level of quantum theory does not necessarily give better
results and that quantum mechanical results are not necessarily better than
molecular mechanics results, at least for small organic molecules.
COMPUTER SOFTWARE FOR CHEMISTRY 175