Computational Tools

Mechanics is used by SCIGRESS to optimize molecular structures using an augmented version of Allinger's standard MM2 and MM3 classical force field.

Dynamics methods use classical, empirical force fields to approximate the movement of atoms. The dynamics application uses the same force fields (MM2 and MM3) as the Mechanics application. Use dynamics to visualize conformations that occur as a result of molecular motion; discover information regarding the structure-energy relationships of the molecule; investigate conformational space occupied by the system at varying temperatures.

MD-ME is an advanced molecular dynamics module that can be used to study the molecular dynamics of model systems including crystals, polymers, dendrimers, etc. MD-ME implements a wide variety of force fields that can be used with organic and non-organic models.

MO-G is a general-purpose semi-empirical molecular orbital package. Use MO-G to calculate the vibrational spectra, thermodynamic quantities, isotopic substitution effects and force constants for molecules, radicals, ions, and polymers. For studying chemical reactions a transition state location routine is also available.

CONFLEX generates low energy confomers of a molecule of any shape. Use CONFLEX to compute optimum geometries, conformations and potential energy maps.

ZINDO computes semi-empirical quantum mechanical values for molecular properties and spectra of molecules. ZINDO uses theoretically-based INDO parameterization and therefore contains parameters for more elements than does the experimentally-based MO-G or MO-S. However, because MO-G has been specifically parameterized for ground-state heats of formations MO-G is the better method for computing molecule structures and energetics. Use ZINDO to carry out calculations of electronic UV-visible absorptions spectra.

MO-S is a semi-empirical program with advanced methods (configuration interactions and random phase approximation) for evaluation of UV-visible electronic absorption spectra. Use MO-S for he evaluation and interpretation of electronic structure transitions.

Extended Hückel is a semiempirical quantum mechanical method used for calculating the electronic wavefunction to determine electron densisties, molecular orbitals, electrostatic potentials, partial charges and bond orders.

SCIGRESS combines experimental data with over 100 descriptors to develop QSAR protocols, and additional descriptors can be defined within the system.

ADF is developed and released by Scientific Computing & Modelling NV (SCM). Please refer to www.scm.com for more information.

GAMESS is developed and released by the Gordon Group at Iowa State University. Please refer to www.msg.chem.iastate.edu/gamess for details on how to obtain the program.

Scigress Explorer can transparently run and visualize results from the third party program Gaussian. Gaussian is not included in the package. Scigress Explorer works with Gaussian 03W revision B.03 or higher.

Advance/PHASE is developed and released by AdvanceSoft Corporation. Please refer to www.advancesoft.jp for more information.

MOPAC2009 is developed and released by Stewart Computational Chemistry. Please refer to www.openmopac.net for details on how to obtain the program.

CONFLEX is developed and released by CONFLEX Corporation. Please refer to www.conflex.us for details on how to obtain the program.