Jmol is a Java-based molecule viewer that has been developed as a cross-platform replacement for the Chime plugin. Available as an applet for web pages or as a stand-alone application. It can read multiple file formats, create animations, show molecular vibrations, and supports the Chime scripting language.
JMolEditor is a Java-based molecular viewer for quantum chemistry calculations, with support for Gaussian, GAMESS, ADF and Q-Chem calculations. Molecules can be built, and input files can be prepared and submitted. Calculation results, including isosurfaces from cube files, can be displayed.
JOELib is a Java library for cheminformatics. Among its many features, it can perform SMARTS substructure searches, calculate descriptors, and read and write molecular file formats including Chemical Markup Language.
JSV (Java Structure Viewer) is a crystal structure viewer written in Java. It can also calculate X-ray diffraction intensities. The diffraction viewer module XRDL allows the 3D/2D display of the diffraction pattern. This software is 'Charityware'.
Kalzium is an application which will show you some information about the periodic system of the elements. It is included in KDE 3.1. A balanced equation solver, eqchem, is also part of Kalzium.
Kemistry is a collection of chemistry-related applications written for the KDE2. The Kemistry package provides three applications: KMolCalc - a molecular weight calculator; KDrawStruct - a 2D structures editor; KMolViewer - a 3D molecular renderer. All Kemistry applications are still in their early development stages.
Khimera is a software tool for the estimation of thermodynamic properties and kinetic rate parameters based on results of quantum-chemical calculations (supports GAMESS, Gaussian, Jaguar, ADF). Reactor models included in KHIMERA help to create and test the mechanism of chemical processes.
Kintecus is modeling software to simulate the chemical kinetics of combustion, nuclear, catalyst reactor, and enzyme reactions.
KMovisto is a molecular viewer. It can import GAUSSIAN 94 or 98 files, and XYZ files. 3D view modes (anaglyph or stereo pair) make it possible to enjoy stereoscopic impressions of the molecular structure. In addition, KMovisto can export export POV-Ray files for rendering high quality presentations, as well as VRML files for 3D presentations on the world wide web.
KryoMol is a KDE-based program for visualisation and analysis of several chemistry related file types such as quantum chemistry log files (Gaussian, NWChem, ACESII, GAMESS), molecular mechanics log files (Tinker, Macromodel), 1-D NMR spectra and JCAMP-DX spectra.