SketchEl is an interactive chemical molecule sketching tool, designed for quick and simple entry of structures. The feature set is limited to those necessary to enter a single chemical species, in a form that might be used in a cheminformatic database, representing each atom and bond as a part of a labelled graph.

SnB is a program based on the Shake-and-Bake algorithm, a dual-space direct-methods procedure for determining crystal structures from X-ray diffraction data.

SNF has been developed for the calculation of Infrared, Raman, and VROA spectra using the harmonic approximation for the frequencies and the double harmonic approximation for the intensities. Vibrational frequencies are determined using numerical differentiation of analytical gradients of the total electronic energy, while infrared, Raman, and VROA intensities are obtained by numerical differentiation of dipole moments and (generalized) polarizability tensor components with respect to nuclear coordinates. Single point calculations are carried out using ADF, Dalton, Gaussian, Molpro or Turbomole.

SODIUM can be used to arrange ions around biological macromolecules.

Sparkle/AM1 is a computational chemistry model which exploits the lanthanide series characteristics to accurately predict geometries of the coordination polyhedra of complexes of ions of the rare earth metals. It is distributed as an external file for MOPAC 93r2, and as the default model for a modified version of the public domain MOPAC 6.

Sparky is a graphical NMR assignment and integration program for proteins, nucleic acids, and other polymers.

Spartan is Wavefunction's flagship modeling software. It combines the versatility of Wavefunction's famous user interface and the power of Q-Chem's computational tools. It can carry out molecular mechanics, semi-empirical, ab initio Hartree Fock, DFT, Moller-Plesset, advanced correlated and excited state calculations. Available as a server or as a workstation edition.

SPIN calculates NMR spectra for systems of up to 9 spin 1/2 nuclei, given chemical shifts and coupling constants as inputs.

Spock is a molecular visualisation program which can display and manipulate atoms, bonds, hydrogen bonds, solid and surfaces, CA traces, electrostatic potential contours, backbone worms, and even electron density maps. Spock can also be used for real-time conferencing over the internet. Spock is free for use in academic courses and for academics without sufficient funding.

SPROUT is a de-novo ligand design system for developing novel active lead compounds. SynSPROUT uses synthetic rules to join fragments, and SPROUT-LeadOpt is designed for lead optimization.