method, Mozyme, that can optimize the geometry of large systems — proteins
included — up to 20,000 atoms, with or without a solvent fi eld. CAChe TM can
run and visualize results for Gaussian TM software (requires separate installa-
tion of Gaussian TM ).
Gaussian, Inc. ’ s newest software program, Gaussian 03 TM , is available at
http://www.gaussian.com/. Starting from the basic laws of quantum mechanics,
Gaussian 03 TM predicts the energies, molecular structures, and vibrational fre-
quencies of molecular systems, along with numerous molecular properties
derived from these basic computation types. The program can be used to study
molecules and reactions under a wide range of conditions, including both
stable species and compounds that are diffi cult or impossible to observe exper-
imentally such as short - lived intermediates and transition structures. The
Gaussian 03 TM ONIOM method can treat proteins and other large biological
molecules, traditionally out of the reach of electronic structure methods.
ONIOM fi rst appeared in Gaussian 98 TM , and several signifi cant innovations
in Gaussian 03 TM make it applicable to much larger molecules. The ONIOM
facility in Gaussian 03 TM provides substantial performance gains for geometry
optimizations via a quadratic coupled algorithm and the use of micro - itera-
tions. In addition, the program ’ s option to include electronic embedding within
ONIOM calculations enables both the steric and electrostatic properties of
the entire molecule to be taken into account when modeling processes in the
high - accuracy layer (e.g., an enzyme ’ s active site). These techniques yield
molecular structures and properties results that are found to be in very good
agreement with experiment. Gaussian 03 TM can predict spin – spin coupling
constants in addition to the NMR shielding and chemical shifts available previ-
ously. Computing these constants for different conformations and then com-
paring predicted and observed spectra makes it possible to identify the specifi c
conformations that were observed. In addition, the assignment of observed
peaks to specifi c atoms is greatly facilitated. Gaussian 03 TM also can compute
a very wide range of spectra and spectroscopic properties. The full Gaussian
03 TM program requires a Unix workstation platform. GaussianW TM is available
for PC, Windows 98 or above OS, 300 MHz or higher processor, 256 MB
memory, and 200 MB disk storage available. GaussianM TM is available for
Macintosh machines with G3, G4, or G5 processor, OS X 10.2 or higher oper-
ating system, 256 MB memory, and 200 MB disk storage available.
Hypercube, Inc. at http://www.hyper.com offers molecular modeling pack-
ages under the HyperChem TM name. HyperChem ’ s newest version, Hyper-
Chem Release 7.5, is a full 32 - bit application, developed for the Windows 95,
98, NT, ME, 2000, and XP operating systems. Density Functional Theory (DFT)
has been added as a basic computational engine to complement Molecular
Mechanics, Semiempirical Quantum Mechanics and ab initio Quantum
Mechanics. The DFT engine includes four combination or hybrid functions,
such as the popular B3 - LYP or Becke - 97 methods. The Bio+ force fi eld in
HyperChem represents a version of the Chemistry at HARvard using Molecu-
lar Mechanics (CHARMM) force fi eld. Release 7.5 of HyperChem updates
COMPUTER SOFTWARE FOR CHEMISTRY 177