StruMM3D © V. G. S. Box, Ph.D.
StruMM3D is a fast 32-bit, native-code-compiled, program that runs under the 32 bit operating systems of Windows® 95/98/ME/NT/XP/Vista/7/8/8.1/10.
StruMM3D is probably the MOST intelligent molecular modeler for organic chemists who are interested in the reality of organic chemistry AT THE ATOMIC LEVEL. The user can measure every geometric parameter, and examine each atom, bond, bond length, bond angle, torsional angle, and their accompanying stereo-electronic effects, in any organic molecule.
StruMM3D is not only powerful and very versatile, but its ease of use ensures that this power is accessible to organic chemists at all levels - from advanced high school students to top-flight researchers.
Many molecular modeling programs are written by non-chemists who have little feel for the reality of organic chemistry, but StruMM3D and its supporting programs were written by an experimental organic chemist, who has done many years of research in natural products and synthetic organic chemistry.
StruMM3D does require a fast processor for its execution and most modern computers are more than adequate for the task (if their CPU speeds are greater than 200 MHz). All screen graphics resolution modes are supported, in multiple colors. The "ball and stick" models look like these Helicenes, and other display formats are available.
StruMM3D is unsurpassed in its ability to reconstruct organic molecules from their x-ray crystallographic coordinate data because it uses powerful new algorithms to automatically identify bond types and delocalized pi-systems, all without any input from the user. Its structure analytical features are second to none. These new algorithms give StruMM3D the power and sophistication to even identify errors in coordinate data generated by x-ray crystallographers, or by other molecular modeling programs.
In fact, for the first time x-ray Crystallographers can now ask themselves the critical question - "Does this structure, derived from my data, have plausible and credible patterns of bonding, based on the locations of the atoms?" - and receive an explicit answer just by carefully looking at the molecule reconstructed by StruMM3D from their postulated atomic coordinate data. Every serious crystallographer should use StruMM3D to review their new coordinate data, because they can then be sure that other scientists will use this data with confidence. Obviously, every serious organic chemist should also use StruMM3D to review x-ray, and other, coordinate data to ensure that this data is scientifically meaningful.
StruMM3D uses the NEW QVBMM molecular mechanics force field. This is the ONLY molecular mechanics force field truly designed for modeling molecules which contain lone pair bearing hetero-atoms. The unique features of the QVBMM force field allow us to assert that this force field is the most modern and most suitable force field for the molecular modeling of the important bio-organic molecules - like saccharides, amino-acids, nucleosides and their polymers (among many others). StruMM3D can be run in batch mode. The powerful QVBMM force field enables StruMM3D to identify ALL of the stereo-electronic interactions being experienced by any atom in any organic molecule, and the data will be displayed quantitatively. This analysis can be performed on all small (1024 atoms and lone pairs) organic molecules, and similarly sized fragments which are easily excised from larger molecules.
We also supply a utility program, FILECONV, for the conversion of most popular molecular data file formats into the very much smaller files usable by StruMM3D, so giving you real access to the major sources of x-ray crystallographic data, and saving your valuable hard-drive storage space. StruMM3D can also be coupled to DBOX32, the three-dimensional database management program, to generate and maintain your own structural databases which can store textual information and simultaneously provide you with seamless access to the molecular modeling of the featured molecules.
For a listing of some of StruMM3D's features look here.