Exorga, Inc. - Consultants in Chemistry,
Molecular Modeling, and the Environment
Welcome to Exorga,
Incorporated's Web-Site!
Consultants in
chemistry and chemical engineering, actively involved in computational, experimental,
and environmental organic chemistry.
Two molecules of the tetrabenzoate of xylopyranose
in the unit cell of its crystal.
Note that the counter-intuitive axial conformation is favoured in the
solid phase.
Find out about StruMM3D's molecular models, how you can generate them, and how you can use them in your daily tasks, presentations, reports and publications.
StruMM3D, The MOLECULAR
MODELER
StruMM3D
is now tightly integrated with its file importation utility, FileConv, enabling
it to read many structure data file formats, and boasts new structure display
features and options. Starting
with version 4.6.0.1, Str3Di32 had a totally revamped structure-energy
minimization routine, to provide more accurate structure energy minima. New algorithms link your computer’s
performance to the structure energy minimization mode used.
StruMM3D/Str3Di32
was written and developed by a practicing synthetic organic chemist, who
ensured that the simulations generated by StruMM3D/Str3Di32 were consistent
with experimental organic chemistry.
Many of the unique features of StruMM3D were developed because of the
familiarity of the author with the subtleties of organic chemistry, and to
ensure its compatibility with organic chemistry. For example, unlike most other molecular modelers, StruMM3D
always generates a molecular simulation that visually presents the bond length
and bond type data because this data is invaluable.
Str3Di NEWS
·
The series
6, year 2010, version of StruMM3D is now available. This new upgrade of StruMM3D
has -
·
improved user
friendliness
·
improved
molecular analytical and recognition features
·
improved
automated features, you NEVER have to write a connectivity list/table and so
you never have to worry about making mistakes there.
·
improved
structure handling
·
improved
structure energy minimization
·
improved
system memory usage
·
improved file
name recognition (especially for long file names) for atomic coordinate data files, so enabling you to give
these files usefully descriptive names.
·
improved HTML-based
molecule log that enables you to quickly retrieve structures you have saved, by
way of the description of the molecules that you entered.
·
StruMM3D enables you to view
"slices" of large molecules.
An excellent way to review the base pairs in a DNA double helical stack
and other pi-stacked systems.
·
StruMM3D enables you to dock
two, or more, molecules. The
structure energy of the cluster can be minimized, and all interaction energies
can be measured. No other
molecular mechanics based program can do this
·
Internet based, as well as
locally accessible, help files
·
New sound prompts and
flourishes
Rigorously tested under Windows 95/98/ME/NT3.5/NT4/2000/XP/Vista/Windows 7
StruMM3D can automatically recognize and model
allenic systems, carbocations, and interesting systems like vinyl cations,
protonated aldehydes and ketones.
We have increased the number of atoms/lone pairs that will be handled by
the QVBMM force field (in one logical molecular model) to 1000, so enabling the
user to simulate really complex large molecules, like proteins and DNA/RNA
oligomers.
We have developed the StruMM3D into an easy-to-use, very versatile, efficient and dramatically powerful software package. This software can deliver unique, insightful molecular modeling experiences to all organic chemists and crystallographers. Undergraduates, high school teachers, professors, and advanced researchers will enjoy using this software to enhance their understanding, and presentations, of organic molecules. The Str3Di molecular modeler will bring molecular modeling from the World Wide Web into your office, lab., or living room. Find out more about the Str3Di MOLECULAR MODELING PROGRAMS.
StruMM3D has been used to produce data for several scientific publications, in highly regarded refereed scientific journals, thus assuring you of its rigor and acceptability. Indeed, these papers will demonstrate, and validate, the our assertion that the Str3Di molecular modelers can provide solutions to molecular structure-reactivity problems that cannot be addressed by many other molecular modeling programs. Further, StruMM3D's uniquely powerful ability to examine, and extract information from, x-ray crystallographic coordinate data is also highlighted in these papers.
StruMM3D is powered by the new QVBMM MOLECULAR MECHANICS FORCE FIELD - recently described as ".the next generation of molecular mechanics force fields.." will do everything that any modern molecular mechanics, or semi-empirical molecular orbital, program can do. This force field can also do lots of things that other molecular modeling programs cannot do.
If
you are unsure about the benefits of using an advanced molecular mechanics
force field instead of quantum mechanical calculations then read this note on ab initio
calculations to assure yourself that quantum
mechanical calculations are not as "ab initio" as they are touted to
be. These quantum mechanics
calculations are just as approximate as molecular mechanics calculations, and
are often incorrect. Did you know
that ALL of these QM calculations start with molecular mechancis generated
model? None of these QM programs
can generate a viable structure from “scratch”.
For example, StruMM3D will -
- dock molecules under the influence of their stereo-electronic interactions - structure energy minimization and modeling of dimers, trimers, and oligomers is a longstanding problem for other molecular mechanics programs
- predict the selective nucleophilic reactivities of molecules that have several nucleophilic centers - a very valuable feature if you are working with sugars or other complex biomolecules
- thoroughly analyze the structural features of molecules (experimentally determined by the diffraction methods, or generated by other theoretical methods). Many of these structures, which include important biomolecules, are riddled with unrealistic geometrical features that are not detected by the other currently available molecular modeling programs. You really will be surprised by the frequency with which unrealistic geometrical features are present in molecular models that are used by bio-organic chemists for important structure-activity studies. There are several websites that show "pretty pictures" of organic molecules, many of whose bond length and bond angle features are severely flawed.
- generate structure energy minimized molecular models that have more plausible geometrical features than those generated by most other Molecular Mechanics programs - this is possible because of QVBMM uses ALL of the basic stereo-electronic effects that apply to all molecules, all the time.
- rapidly search any molecular structure, even large complex molecules, for instances of unique, or common, structural features and functional groups - you won't understand how valuable this feature is until you try using any other software to search a crystallographic structure for an unusual entity, like a truly non-delocalized example of a pi-system that is "normally delocalized" (such as twisted, non-delocalized, amide units in a large complex structure).
- automatically detect ground-state delocalized pi-systems - a boon to organic chemists, photochemists, and to researchers working with molecules that have extensive pi-systems. There are many molecules whose structures suggest that they should obey Huckel's Rules, but which, in fact, do not. The definitive way to confirm this is to examine the crystal structure data of that molecule, or a close relative, with StruMM3D.
Str3Di SUCCESSES
Small
Data File and program size
We have had some whimsical comments on the very small size of the StruMM3D program (525 K), and its data files (most are less than 2 Kbytes and are also the smallest from any molecular modeling program). The program is small enough to be run from a floppy diskette! The size simply gives you a clue as to the sophistication of the algorithms used in the program. StruMM3D does not need the reams of data the old-styled multi-megabyte molecular modeling programs do (which they also read in from large data files). StruMM3D synthesizes much of the needed data from some basic scientific facts and new relationships, using some elegant algorithms.
Short
Bonds? Weird Data?
One of the real hurdles that remain in modern molecular modeling is the continued use of structure coordinate data files in which bond types are explicitly specified. The creator of these data files can introduce many fatal errors into the structure. For example, a particular carbon - carbon bond in a molecular model can be designated a single bond, even though the length of that bond is less than that of a carbon - carbon triple bond! This type of flawed data is frequently encountered in coordinate data files that are generated by programs that convert 2-dimensional (2D) structures into 3D structures, and, unfortunately, these errors are found, occasionally, in X-ray crystallographic coordinate data files (put there by humans).
StruMM3D is the ONLY molecular modeling program that is sophisticated enough to automatically determine the types of all of the bonds in any molecular model, using only the coordinate data. StruMM3D does not use a connectivity list that is generated externally. StruMM3D cannot be induced to present a bond with an order that is not consistent with that embedded in the coordinate data. StruMM3D will automatically detect these weird bonds in structures that are flawed, and will immediately inform you of the presence of these "short bonds" in your molecular model, so enabling you to take appropriate corrective action.
In contrast, other molecular modeling programs rely
on externally generated connectivity lists (made up by the user) and will not
question that data. They will
simply present to the user the information that is embedded in the (possibly
flawed) data. Rubbish in, rubbish
out! Of course, if your molecular
modeler does not draw your attention to a serious structure flaw, you might
believe that the structure is OK and continue to derive useless data from that
flawed structure.
Visit our Exorga's DownLoadables site to find out how to acquire our molecular modeler for WINDOWS 95/98/ME/NT/2000/XP.