BobScript is a program to facilitate the production of publication quality molecular graphics. It is a further development of the program MolScript, but has extensions that make it particularly suited to protein crystallography. Output can be in PostScript format or as a file suitable for rendering with <a href=http://www.bmsc.washington.edu/raster3d/raster3d.html>Raster3D</a>. A conversion program also enables POV-Ray to be used as the rendering engine.

Bodil is a modular, multi-platform software package for biomolecular visualization and modeling. Bodil aims to provide easy three-dimensional molecular graphics closely integrated with sequence viewing and sequence alignment editing.

BOSS (Biochemical and Organic Simulation System) is a general purpose molecular modeling system that performs molecular mechanics (MM) calculations, Metropolis Monte Carlo (MC) statistical mechanics simulations, and semiempirical AM1, PM3, and PDDG/PM3 quantum mechanics (QM) calculations.

CACTVS is a distributed client/server system for the computation, management, analysis and visualisation of chemical information of any, even dynamically and ad-hoc defined type. CACTVS Tools is a visualization package for chemist.

CAMEO is a modular expert system, a computer program that predicts the products of organic reactions given starting materials, reagents and conditions. Online demo - WebCAMEO available.

Cantera is a suite of object-oriented software tools for problems involving chemical kinetics, thermodynamics, and/or transport processes. You can use Cantera from Python or Matlab to handle problems in areas such as combustion, flame structure, detonations, electrochemical energy conversion, fuel cells, aqueous electrolytes, plasmas and thin-film deposition.

A fully-featured first principles electronic structure code based on density functional theory and using a plane-wave basis set with pseudopotentials. It uses periodic boundary conditions and is therefore highly suited to modelling solids, liquids, and surfaces using slab geometry. Available for free to UK academics.

cclib (computational chemistry library) allows users to easily implement computational chemistry algorithms that use the results from calculations from any of a large number of popular computational chemistry packages (incl. GAMESS, GAMESS-UK, Jaguar, Gaussian, Molpro and ADF).

CCP1GUI is a free, extensible Graphical User Interface (GUI) developed for GAMESS-UK, but also supporting other packages. The GUI has been built around the Python open-source programming language and the VTK visualisation toolkit. It has support for conventional formats such as Z-matrix and PDB, as well as programme-specific formats for CHARMM, ChemShell, XMol and Gaussian.

CDA (Charge Decompositional Analysis) has been devised to analyze chemical systems which can be described as donor-acceptor complexes. The electronic and energetic changes associated with the formation of a complex consisting of two fragments A and B are partitioned in terms of the familiar Dewar-Chatt-Duncanson model. The energy analysis is feasible within the Hartree-Fock approximation, while the charge decomposition analysis can also be carried out at correlated levels. Requires Gaussian output files.