CHEMISTRY

Chemsketch

ACD/ChemSketch Freeware is a drawing package that allows you to draw chemical structures including organics, organometallics, polymers, and Markush structures. It also includes features such as calculation of molecular properties (e.g., molecular weight, density, molar refractivity etc.), 2D and 3D structure cleaning and viewing, functionality for naming structures (fewer than 50 atoms and 3 rings), and prediction of logP.

Website to download: http://www.acdlabs.com/resources/freeware/chemsketch/

MOPAC

MOPAC is a general-purpose semiempirical quantum mechanics research package for the study of chemical properties and reactions in gas, solution or solid-state. MOPAC directly predicts numerous chemical and physical properties such as Gibbs free energies, activation energies, reaction paths, dipole moments, non-linear optical properties and infrared spectra. It is also used as the basis of quantitative structure-property (or activity) relationships (QSAR), to predict a wide variety of biological and other properties such as carcinogenicity, vapor pressure, water solubility, and reaction rates.

Website to download: http://www.chemsoft.ch/qc/mpc.html

The Open Babel GUI

Open Babel converts chemical objects (currently molecules or reactions) from one file format to another. They are cross-platform programs designed to interconvert between many file formats used in molecular modeling and computational chemistry and related areas. They can also be used for filtering molecules and for simple manipulation of chemical data.

Website to Download: http://openbabel.org/wiki/Instal

Gamess

GAMESS is a research software for ab initio molecular quantum chemistry. Briefly, GAMESS can compute SCF wavefunctions ranging from RHF, ROHF, UHF, GVB, and MCSCF. Correlation corrections to these SCF wavefunctions include Configuration Interaction, second order perturbation Theory, and Coupled-Cluster approaches, as well as the Density Functional Theory approximation. Nuclear gradients are available, for automatic geometry optimization, transition state searches, or reaction path following. Computation of the energy hessian permits prediction of vibrational frequencies, with IR or Raman intensities. Solvent effects may be modeled by the discrete Effective Fragment potentials, or continuum models such as the polarizable Continuum Model. Numerous relativistic computations are available, including third order Douglas-Kroll scalar corrections, and various spin-orbit coupling options. The Fragment Molecular Orbital method permits use of many of these sophisticated treatments to be used on very large systems, by dividing the computation into small fragments. Nuclear wavefunctions can also be computed, in VSCF, or with explicit treatment of nuclear orbitals by the NEO code.

A variety of molecular properties, ranging from simple dipole moments to frequency dependent hyperpolarizabilities may be computed. Many basis sets are stored internally, together with effective core potentials or model core potentials, so that essentially the entire periodic table can be considered.

Most computations can be performed using direct techniques, or in parallel on appropriate hardware. Graphics programs, particularly the MacMolplt program (for Macintosh, Windows, or Linux desktops), are available for viewing of the final results, and the Avogadro program can assist with preparation of inputs.

Website to Download: http://www.msg.chem.iastate.edu/gamess/download.html

Tinker

The TINKER molecular modeling research software is a complete and general package for molecular mechanics and dynamics, with some special features for biopolymers. TINKER has the ability to use any of several common parameter sets, such as Amber (ff94, ff96, ff98, ff99, ff99SB), CHARMM (19, 22, 22CMAP), Allinger MM (MM2-1991 and MM3-2000), OPLS (OPLS-UA, OPLS-AA), Merck Molecular Force Field (MMFF), Liam Dang's polarizable potentials, and our own AMOEBA polarizable atomic multipole force field. Parameter sets for other standard force fields such as GROMOS, UFF, ENCAD and MM4 are under consideration for future releases.

Website to Download: http://dasher.wustl.edu/tinker/