Exorga, Inc. - Consultants in Chemistry, Molecular Modeling, and the Environment


StruMM3D (Version 8.0.0.X, 2016) © V. G. S. Box, Ph.D.


MOLECULAR MODELING and MOLECULAR GRAPHICS.

Chemistry is a well-developed discipline and is probably the most important area of physical science. Every physical scientific discipline eventually resolves its puzzles by examining their details at the atomic level, from alloys to superconducting composites, to genes. This need to examine the atomic level details of important materials must push molecular modeling into the forefront of the modern scientific modus operandi.

Molecular modeling is one of the areas of modern organic chemistry that will, and must, rapidly develop into an indispensable tool in the lab and in the classroom. However, molecular modeling programs have tended to be expensive, technologically demanding, and single-computer-centered.

Exorga, Inc. wants to change the way students, teachers and researchers routinely do molecular modeling, by providing you with a suite of molecular modeling programs - The StruMM3DMolecular Modelers - that –

1. is powerful, very easy to use, but is very affordable.

2. can be executed even on "low-end" computer system

3. uses small, simple, plain text, structure data files.

4. has the most intelligent set of molecular structure recognition algorithms to be found in ANY molecular modeling program.

In fact, for the first time x-ray Crystallographers can ask themselves the critical question - "Does this structure, derived from my refined data, have plausible and credible patterns of bonding, based on the coordinates of the atoms?" - and receive an explicit answer just by carefully looking at the molecule reconstructed by StruMM3D on the video screen. Every serious crystallographer should use StruMM3D to review their new coordinate data, because they'll 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.

If you associate StruMM3D’s data files with the program, then Internet Explorer will also recognize the StruMM3D data files. This is quite easily done. Then, whenever you are browsing the web and encounter a URL that contains one of the StruMM3D structure data files, just clicking on that data file will launch StruMM3D, and the molecular modeling of the compound encoded in that data file can be performed in YOUR computer. The resulting data is YOURS to keep and use. After you have done an entire molecular modeling exercise on that compound, and saved the data (if you wish) in whatever appropriate form, you can seamlessly return to your web browsing.

Exorga, Inc. will maintain a web page with the data files of many interesting structures, and will add structures that you wish to be included. You could also use your private web-site for this purpose.

Since the WWW is universally available, easy and cheap to access, and can be accessed using a wide variety of computers, this development will have a tremendous impact on the ease with which molecular modeling can be included in the curricula of schools of modest means. The ability to perform molecular modeling exercises via the WWW will truly open the door to all budding and practising chemists. Thus, via the WWW -

1. teachers can set up, and run, molecular modeling exercises for their classes
2. researchers can perform molecular modeling exercises, and
3. anyone can all share their data files with colleagues anywhere.

We all agree that the INTERNET and the World Wide Web - WWW - are important parts of the future. These media will dominate our personal and professional lives in the areas of information transfer, and entertainment, and will become indispensable in teaching and industry.


THE StruMM3DMOLECULAR MODELER

StruMM3D (for computers executing any version of Microsoft’s WINDOWS ®) is a powerful, full-featured molecular modeling and molecular graphics program which has many unique features. The "user-friendliness" is greatly emphasized and the program provides frequent access to informative menus to guide your activity. The powerful features of the StruMM3D Molecular Modeler are therefore easily learned and are very available to the new user.

THE DISPLAY

StruMM3D can display and manipulate two molecular models independently and simultaneously. For StruMM3D, each molecular model can have up to 3000 atoms and lone pairs. Models are shown in several "ball and stick", or "space-filled", formats. The ball and stick models can be customized. For example, bonds (sticks) can have variable sizes, thicker (bolder) bonds can be used in the front and, if desired, "dashed" bonds are in the rear, to enhance the molecule's three dimensional features. Individual atoms can be highlighted to show their positions and are color coded for fast, easy recognition.

SYSTEM REQUIREMENTS

The StruMM3D program size is quite small, about 990 Kbytes, and can be executed in all computers that run Microsoft’s Windows 95/98/ME/NT/2000/XP/Vista/7/8/10 ®. However, more powerful computers will execute these programs much more efficiently because of the math-intensive nature of the software.

StruMM3D does not frequently use the disk drive. This feature, along with the very small memory (RAM) requirements allows the program to be executed nearly as efficiently from a floppy disk, as from a hard disk. More importantly, this small memory requirements releases your system's resources and allows you to do fast, efficient multitasking.

OTHER HARDWARE FEATURES

StruMM3D, like all other WINDOWS programs, use the mouse extensively and the "Windows pointer" is always activated in these versions. The keyboard can also be used for entering data that StruMM3D requires

THE QVBMM FORCE FIELD

The QVBMM force field, a new molecular mechanics force field for the minimization of the structure energy of molecular models, has been developed and implemented in StruMM3D. This force field was based on the principles embodied in VSEPR and VB theories, and was specifically designed to integrate the stereo-electronic and other effects of lone pairs into the process of determining the structural features of heteroatom-bearing molecules. Thus, this new force field is unique, very powerful, and very valuable for the modeling of all biomolecules (sugars, amino-acids, etc) and all other organic molecules.

THE StruMM3D FILES

StruMM3D's coordinate data files are small and simple. The orthogonalized coordinate data for acetone (with single precision data) is shown below:

4.6200, 2.0064, 4.6002E-04, "C", 1
6.0982, 1.9822, -1.2755E-02, "C", 1
6.7633, 3.3004, 6.6053E-02, "C", 1
6.7216, .9405, -8.4324E-02, "O", 1

Users of the StruMM3D molecular modelers know that the StruMM3D structure data files are MUCH SMALLER than the corresponding data files used by any other molecular modeler. This saves lots of hard drive space, makes the "manual - word processor" production of these data files very easy, and results in a rapid loading of the error-free data for most molecules. We have grappled with the challenge of keeping the StruMM3D data files as small as is possible by saving the coordinate data of molecules in single precision mode. This works very well for molecules that do not have lone pairs, but sometimes gives unpredictable reproducibility of energy data for some molecules that have lots of lone pairs in them, like sugars. We have finally decided to save all coordinate data in double precision mode, so removing this final hurdle. This strategy will result in about a 30% increase in the size of StruMM3D's very small structure data files, but these data files still remain the smallest data files for ANY molecular modeler, so you won't really notice this change. Of course, ALL StruMM3D data files are still read by the molecular modelers.

MOLECULE CREATION AND ELABORATION

You never have to create connectivity lists for your molecular models!

Lone pairs and hydrogens can be rapidly added to any structure, like the acetone above, because StruMM3D adds any atoms (hydrogens and/or lone pairs automatically) to valence-incomplete atoms, faithfully reflecting the hybridization state of the atom being elaborated.

StruMM3D facilitates the creation of coordinate data files from X-ray crystallographic data since it will ask for the relevant data, orthogonalize the coordinates, and write files in its desired format, above. Coordinate data files can also be created, from any source of coordinate data, by using a word processor.

StruMM3D was the first molecular graphics program able to evaluate coordinate data and automatically (without input from the user) identify pi-atoms and delocalized, or aromatic, pi-systems. The simplicity of the coordinate data file shown above illustrates the power of the algorithms used in StruMM3D.

StruMM3D can create 3D molecular models using atoms commonly found in organic molecules. Models are made in precisely the conformation desired, with the required configurations at all asymmetric centres, and with bond lengths and angles you wish. Since the model will already be highly realistic it can be used for many purposes. Further, minimal computer time would be required to use the program's structure/energy minimization (QVBMM) module to further refine the model. StruMM3D reads and writes MM2 and MMX files.

MOLECULE MANIPULATION

StruMM3D will rotate, translate, fragment, link, enantiomerize, dock, and perform many other manipulations, on models. It will measure lengths, angles, dihedral angles, and is not confined to measuring parameters between adjacent centers. It will detect and reveal lone pair - lone pair (n-n), steric, torsional and other interactions. It will locate and highlight functional groups and other sub-structural units.

STRUCTURE ENERGY MINIMIZATION

StruMM3D uses the new QVBMM force field to efficiently relax the bond lengths, bond angles and dihedral angles of your molecular model in order to move that molecular structure towards its energy minimum. StruMM3D offers the user total control over the energy minimization process, and you can manipulate and minimize the energies of dihedral angles quite separately from the overall energy minimization process. StruMM3D also offers automatic dihedral angle energy minimizations.

UTILITIES

The FILECONV utility program converts XYZ, PDB, CIF, CSD, MOL, MOP, Schakal, M3D and several other structural data files to StruMM3D files.

Many of StruMM3D's features have not been described here due to space limitations, but they certainly are readily available to the user, and they can be reviewed in the online help file.


For more information about StruMM3D, look HERE

For information on ordering the StruMM3D Molecular modeler, look HERE