Exorga, Inc. - Consultants in Organic Chemistry and Molecular Modeling



The Uniqueness of The QVBMM Force Field and StruMM3D

We have gotten lots of comments and enquiries about the unique features of the StruMM3D molecular modelers, but the most interesting are usually about the new QVBMM molecular mechanics force field (used for structure energy minimizations) that we developed. This force field is fully integrated into, and used by, our StruMM3D molecular modeler.

The QVBMM force field is based on the principles of a customized and enhanced VSEPR theory, along with elements from VB theory. It intimately integrates bond polarization and lone pair interactions into the molecular mechanics process, in ways that have never been implemented in MM2, MM3, MM4, MMX, PCMODEL, or any other molecular mechanics program.

The user does not have to "set up" the force field, or the molecular model, in order for QVBMM to recognize hydrogen bonds and other dipole - dipole interaction, the way you have to do with other molecular modeling programs, because StruMM3D and the QVBMM Force Field do that automatically.

In fact, the problem of parameterizing a molecular modeling program for the hydrogen bonds that are present in the molecule under examination is an exercise that is designed to confound any researcher, especially if low-energied, but extremely important, C-H hydrogen bonding is not recognized. We have shown that these C-H hydrogen bonds are critically important in almost every type of biomolecule that contains heteroatoms.

Indeed, in 1997 we showed, with the pivotal assistance of the QVBMM Force Field, that C-H hydrogen bonding played an integral role in the molecular simulations of sugar, acetals, and other molecules that showed the Anomeric Effects. We also showed that there were other situations in which very complex and subtle dipolar contributions dictated molecular geometry. These results were suppressed and censored by the Quantum Mechanics (QM) community, largely because the QM tools available were incapable of performing these simulations satisfactorily, but this group has now, more than 18 years after, embraced these views.

Thus, the QVBMM force field recognizes all of the important stereo-electronic interactions, and produces accurate simulations of all kind of molecules, including dimers, trimers and complex hetero-atom laden biomolecules. The StruMM3D molecular modeler uses these QVBMM-generated data to reveal startling, and sometimes previously unrecognized, insights into the stereo-electronic features of many molecules. Suffice it to say that the QVBMM/StruMM3D package can produce data that are not easily available from MM2, MM3, or any other molecular mechanics program.

Although the QM ab initio Molecular Orbital programs are widely used, and are seen by some as the molecular modelers of the future, these methods still cannot handle electron pair interactions properly. Since these electron pair interactions are critically important in the chemistry of nucleophiles, in conformational analysis, and in a host of other scenarios, you should understand that the ab initio methods are still not as mature as they can be. Most QM theoreticians have tried to persuade naïve people that their calculations represent exact solutions to the Schroedinger Wave equations for the molecules being studied, but that is totally untrue. The only atomic system that can yield an exact solution to its Schroedinger Wave equation is that hydrogen atom. For all other molecular, or atomic, systems, only yield VERY APPROXIMATE solutions can be obtained, and these data are often not as good as data obtained from molecular mechanics. A note on ab initio calculations.

The QVBMM force field is the ONLY molecular modeling program that treats lone pair interactions as native parts of its routines. It must therefore be clear that the QVBMM force field offers features and insights that are not available elsewhere, even from ab initio calculations (that are WELL known to not handle electron repulsions well).

The algorithmic and philosophical bases of the QVBMM molecular mechanics force field can be found in a peer-reviewed scientific publication in the Journal of Molecular Modeling. This paper should answer many of the questions often asked about this unique force field.

The fact that StruMM3D has structure recognition capabilities that are unparalleled in molecular modeling, already indicates that StruMM3D is an exceptionally powerful, and unique, molecular modeling tool.

Further, the extraordinary capabilities of StruMM3D ensure that you don’t have to write connectivity lists/tables for molecules displayed by StruMM3D. StruMM3D does this automatically, without your help! So the subsequent calculations by QVBMM simply CANNOT be flawed by the common errors that we find in most “human-generated” connectivity lists, like misses hydrogen bonds, or incorrect bond types.

We regret to inform you that the QVBMM module is no longer available as a stand-alone program. However, StruMM3D can now be run in batch mode (you can minimize the structure energies of a directory full of files while you go fishing!).

Why use Molecular Mechanics, rather than QM ab initio Molecular Orbital calculations?

Just in case you hesitate to give credence to the views below, you should note that these views are also expressed in a different forum, an article displayed at the ChemWeb website, that actually tries to promote ab initio calculations.

Many of us mistakenly assume that the molecular orbital calculations are truly ab initio and are done without any assumptions. This is entirely incorrect!

Indeed, it is quite heartbreaking to hear theoreticians that use the QM/MO methods ardently profess that the ab initio methods are the ultimate methods for performing molecular structure calculations. Many "theoreticians" simply use software that they obtain, rather than create, and so they do not know much about the algorithmic assumptions and limitations of the software. They discover these limitations after using the software. These "theoreticians" are often the most fanatical adherents to, and proponents of, the usage of the QM/MO methods.

To begin with, you must be aware that Quantum Mechanics, and the MO methods, cannot generate an exact solution to the wave equation of the hydrogen molecule, its radical cation, or even the helium atom. It is widely known that the mathematical treatment of "three mutually interacting orbiting bodies” is technically insoluble, unless many basic assumptions and approximations are made to restrict parts of the system. This is also the case in quantum mechanics, and the ab initio solutions for the wave equations of these systems must also involve several approximations and restrictions of parts of the system.

When we move on to more complex molecular systems, more "bodies", the number and extent of the assumptions increase dramatically. Hence, the exact solutions to the wave equations of very simple atoms, like carbon, or simple molecules, like carbon monoxide and formaldehyde, are not possible, and the current calculation methods are loaded with many assumptions (heavily parameterized) that enable some kind of acceptable solution to be arrived at. Indeed, using the currently most sophisticated basis sets available in ab initio calculations, the simulation of carbon monoxide requires the "minor" participation of carbon and oxygen d-orbitals in the bonding. Carbon and oxygen d-orbitals? However, since the simulation of carbon monoxide is "better" by using a "fuller" basis set that involves d-orbital involvement, then that basis set is embraced by the ab initio users. How do we explain the bonding in carbon monoxide to undergraduates and still cling to the widely accepted PMO theory?

More sophisticated organic molecules, like methane and anything larger, require even more elaborate parameterization of the ab initio calculations. Further, these calculations have been known not to handle electron repulsions properly. This explains, in part, the recent development of the Density Functional Theoretical (DFT) methods.

The realistic organic chemist will use a variety of theoretical methods to perform the simulations of selected organic molecules. Some molecules will best be simulated by some methods, rather then others, but no single method does a perfect job with all molecules. Molecular mechanics offers rapid calculations on large molecules, while ab initio calculations, even on small molecules, can sometimes be painfully slow, without additional benefits.

In the 1960s, the quantum mechanics theoreticians had proclaimed that organic chemistry would cease to exist as a discrete discipline, since all of the properties and reactivities of organic molecules should be available from Molecular Orbital calculations. However, the molecular orbital methods developed from quantum mechanics are still very primitive and often yield data that are inconsistent with experimental results.

As unpalatable as it might be to some people, the fact of the matter is that the ONLY molecular structural prediction method that has been thoroughly tested, and that has consistently given the correct, though qualitative, answers is the VSEPR theory. No other molecular structural prediction method can make such a claim. It is quite logical therefore to develop and use a molecular mechanics method that is based on VSEPR theory. The QVBMM force field was designed and developed to be a quantitative expression of the VSEPR theory, while also embracing some very modern concepts on bonding and structural relationships.

Did you know that ALL calculations done by MO theoreticians start with molecular mechanics generated models, since their MO calculations cannot generate plausible models from “scratch”?

EXORGA INC. - Consultants in ALL areas of organic chemistry and Custom chemistry software producers!