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Using StruMM3D to look along the axis of a DNA double helix fragment

Exorga, Inc. - We are experts in organic chemistry.

Exorga, Inc. will provide you with expert consultants in every area of organic chemistry, including chemical engineering and environmental matters. We also specialize in the development of nvironmentally benign organic chemistry processes, and in the redirection of organic chemical by-products into mainstream, valuable, "fine" chemicals.

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Exorga, Inc. - We are developers of advanced chemistry software.

Have you StruMM3D a molecule today?


We pronounce StruMM3D like “strumm 3D”, or, better still, “strummed”. Indeed, we use it to reveal, display, and examine, the sweet molecular music that nature plays.

StruMM3D, developed from Str3Di32 and the QVBMM Force Field, is a quantitative implementation of an updated and advanced version (developed by Vernon G. S. Box) of Valence Shell Electron Pair Repulsion (VSEPR) theory, with some influences from Valence Bond (VB) and Molecular Orbital (MO) theories. As such, it is a Molecular Mechanics program and does not use Quantum Mechanics (QM), or any of its many derivatives, but is orbital aware.

StruMM3D has long been able to generate a complete simulation of any organic molecule from only its atom types and their X, Y, and Z coordinate data. StruMM3D automatically detects, and simulates all the connectivity and interatomic interaction features of the molecule. With recent refinements to it's structure recognition algorithms, StruMM3D can now generate a complete simulation of any metal complex, including predicting the covalent radius that is best suited for the metal, and the oxidation state, from only the complex's atom types and their coordinate data. No other currently available molecular modeling program has this capability.

An Important StruMM3D Milestone!

The Quantized Valence Bond Molecular Mechanics (QVBMM) force field is founded on the notion that all bond types are quantized, and that the length of any bond must be indicative of it's quantized bond type and hence bond order. StruMM3D uses this force field, and has facilitated the reviewing of the bond type/bond length data for tens of thousands of x-ray crystallographically determined structures, organic, organometallic and inorganic.

Nearly 40 years after the creation of the QVBMM force field, for every high resolution diffraction determined structure (excluding those with disordered atoms) examined using StruMM3D, there has never been found one case of a violation of the quantized bond type/bond length idea. StruMM3D has empirically verified that the quantized bond type/bond length notion has been upheld. Indeed, recently this bond length, bond type relationship was verified mathematically and shown to be quantized, or non-contimuous.


The rational starting point in the molecular modeling of any organic molecule ought be the process of ascertaining how well the known (experimentally determined) properties of that molecule (physical and chemical) can be simulated by considering, initially, only its the bond length, bond angle, stereo-electronic, and dipolar features.

Only if this initial simulation of the dipolar/stereo-electronic features of any molecule proves to be inadequate, can one truly begin to understand the contributions that are being made to the molecule's structure and properties by delocalization and quantum mechanical (QM) effects.

This notion is especially important since it is well known that QM programs cannot reliably simulate electron pair repulsions, routinely suggest that any bond can be indefinitely long, and offer poor simulations of dipolar effects in general, unless an additional multitude of assumptions are made. Hence, dipolar/stereo-electronic simulations are best done with molecular mechanics (MM) programs.

Regardless of the hype that is bandied about by users of QM programs, most of whom know little about the design and assumptions embedded in these programs, the reality is that QM calculations are far from being “ab initio”. It is impossible to generate an exact solution to the wave equation of the helium atom, and any solution requires a host of approximations. Imagine, then, the multitude of approximations needed for the “ab initio” solution of the wave equation for a simple, small molecule, like methanol.

Your molecular modeling program MUST allow you to examine all of the molecule's potential energy data. Indeed, these data, for each, and every bond, bond angle, and lone pair interaction, can give invaluable insight into the most subtle and important features of the molecule. Only after examining all this data will you truly UNDERSTAND the real roles of these dipolar effects. Most QM programs, and many MM programs, CANNOT give you this data, and so you will be unable to understand how these molecular modelers arrived at their reported molecular energy.

StruMM3D does give access to all the molecular dipolar and other strain data, routinely, without special effort.

Is it surprising that most QM investigations begin with MM generated molecular models?


The important contributions of the StruMM3D/Str3Di molecular modeler and the QVBMM molecular mechanics force field to the understanding of many subtle structural stereo-electronic, and structural features, in organic chemistry have been established by StruMM3D's track record of achievements. Indeed, no other currently available molecular modeling program can mine the weath of data about a molecule using only the molecule's X, Y, and Z atomic coordinate data.

In a series of papers, published in the Japanese chemistry journal Heterocycles, before, during, and after 1998, Vernon G. S. Box used the QVBMM molecular mechanics force field to show that C-H...O hydrogen bonding was pivotal to the full understanding of complex stereo-electronic effects in sugars, like the Anomeric Effects. Nearly 25 years later, ab initio and Quantum Mechanics (QM) theoreticians rushed to claim primacy for this idea. None of these QM theoreticians seemed to have encountered Box's works.

Similarly, in a seminal paper entitled "Pi-Electron Delocalization in Organic Molecules With C-N Bonds", J. Chem. Educ., 1997, 74, 1293-1296, by Vernon G. S. Box and Hing W. Yu, the Str3Di molecular modeling program clearly showed that the nitro-group of many arylnitro compounds were not delocalized into the aryl ring. 19 years later, QM theoreticians were just realizing this truth, but have also not yet encountered Box's work.

As usual, QM theory lags significantly behind, and it's users chose to remain unaware of the "older" literature. Many QM theoreticians often re-investigate old ideas, come to the same conclusions as were developed by using Molecular Mechanics, and then present their work as being original. It didn't help when respected scientists, in 2017, reveal that many DFT calculations often got the correct answers by using "wrong", unsupportable, reasons.

The Uncertainty Principle has correctly suggested that, because we are immensely clumsy and puny, as are our machines, we cannot simultaneously and accurately measure the position and velocity of any atom or subatomic entity. We obviously should resist interpreting this to mean that the probability of encountering these entities must be finite even to infinity, which is just doublespeak itself.


One thing became painfully obvious during our testing of StruMM3D in the Windows 7, 8, 10 environments, is that the UAC feature of these operating systems is of questionable utility, significantly impedes one's use of one's PC, and might simply be ill-intentioned.

Microsoft has now made it almost impossible for third-party programs to function fully when they are installed into the "Program Files" folder on drive C:. Microsoft has severely restricted "write" capabilities to most folders on drive C: by third-party programs. Indeed, even the PC administrator, that uses the PC with the highest system privileges, often cannot simply copy files from one place to another on the PC's hard disk drive, with ease. Worse, even some of Microsoft's system utilities run afoul of the UAC big brother, especially when invoked through the command prompt.

The UAC feature of Windows 10 is dysfunctional, and will remain so until it allows PC administrators the ability to mark, or register, programs as safe to use without the OS's interference, and allows the PC adminstrators to perform simple housekeeping tasks on their machines.

So, unless you go clicking everywhere your anti-malware/anti-virus programs tell you not to, for a smoother, more pleasing experience using your computer (and to re-assert your independence from the big brothers at Microsoft) just turn off the UAC feature and install your programs into your own "user-created" folders. There are excellent anti-virus and anti-malware programs around, especially within (native to) the Windows 7/8/10 OSes, and so the chances of a careful computer user unintentionally executing malware are miniscule in today's computing environment, unless you habitually ignore your computer's anti-virus and anti-malware programs warnings.

The Microsoft security protocols prevent many third party programs, and even some of Microsoft's own programs, from running as they should. This is a permissions problem. We advise all users of StruMM3D to launch Windows Explorer, open the \Str3Di folder, right click on the StruMM3D.Exe file, select properties, then select Compatibilty, and then check the box that says "Run this program as an administrator". Repeat this sequence for all of the Str3Di Exe files whose names start with "str". You should also always use StruMM3DX to launch StruMM3D.Exe.


The use of the StruMM3D (© Vernon. G. S. Box, Ph.D.) downloadable versions and newer are now unrestricted, but the program is still subject to our copyright, and our right to restrict access to registered users.


Update Your StruMM3D program

StruMM3D tells you when a newer version is available so that you can get it, and the most recent versions of StruMM3D will automatically download and install these updates for you. However, if you haven't updated your StruMM3D recently, go download and try the newest version of StruMM3D. It will be faster and just awesome! Remember to visit the StruMM3D FAQ for hints, user/program tips and additional help. The FAQ is updated frequently and always has new information.

Users of versions of Str3Di32 must update to StruMM3D, which has total backward compatibility with all Str3Di structure files. Current users of StruMM3D should visit the StruMM3D download site and get the StruMM3D update file (a self unzipping EXE file). Just execute it in their Str3Di folder/directory to apply all recent updates.


If you're not using StruMM3D, then why not?

If you regularly review structures that have been determined by the diffraction methods (x-ray crystallography etc.), then you simply MUST use StruMM3D to visualize your data. StruMM3D is the ONLY molecular modeler that enables you to spot (visually) weird bond lengths, among other oddities that find their way into diffraction studies. Serious crystallographers always use StruMM3D.

Do you want to see how good your current molecular modeling program is? Or isn’t. Then we dare users of other molecular modelers to see how quickly they can complete one of our very routinely done molecular modeling tasks. This one involves using your current molecular modeling program to spot flaws in the coordinate data of published x-ray crystallographic investigations.Try it.

For more information about our services and other products - Write to us

Visit our Exorga's Web Goodies site for some links a variety of websites that we have found to be both interesting and entertaining. You will be delighted by these sites.

Visit our Exorga's DOWNLOADABLES site for access to StruMM3D, and to some utilities we have found to be very useful..

We offer unsurpassable, confidential consultation in organic chemistry, environmental chemistry, molecular modeling, and in the development of custom chemistry software. We can provide you with expert advice in the construction of molecular databases, and in the conversion of your industrial organic chemical by-products into valuable materials.


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Last updated - 06/06/2024