STR3DI32

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[edit] STR3DI32

STR3DI32 (an acronym for STRuctures in 3 DImensions) is a modern Molecular Mechanics (MM) based molecular modeling program that was developed by Vernon G. S. Box (an organic chemistry professor at the City College, City University of New York). STR3DI32 can be regarded as a quantitative implementation of VSEPR (Valence Shell Electron Pair Repulsion) theory, coupled with a framework of extremely intelligent structure-analytical algorithms. The program can be executed on computers running the Microsoft Windows operating systems.

STR3DI32 input consists only of a list of atom coordinates, and atom types, for the molecular model. Unlike most other molecular modeling programs, STR3DI32 automatically assembles the atom connectivity list for the molecular model, automatically recognizes π-systems (including allenes etc.), and any instances of delocalized π-bonds. By using a sophisticated algorithm, based on atom electronegativities, STR3DI32 calculates the charges on all of the atoms in the molecule, which obviously depends on the molecule's atomic connectivity. Thus, STR3DI32 will automatically recognize all of the dipolar interactions, including the full range of hydrogen bonds (including C-H hydrogen bonds), present in the molecule. The ability of STR3DI32 to recognize these structural features ensures that any subsequently performed structure-energy minimization calculations will not be marred by a user’s unintended omission of a hydrogen bond, or any other similarly important stereo-electronic effect, from a flawed user-generated connectivity list.

The structure-analytical prowess of STR3DI32, and its ability to recognize bond type and plausible bond lengths, has proven to be of great help in examining structures generated from x-ray crystallographic, and other diffraction, studies. It is quite common to find molecular structures, generated from x-ray crystallographic studies, that contain erroneous bond lengths, which are due to human error in processing the diffraction data. If these flawed structures are reviewed using programs that require a user-generated atom connectivity list, then these common bond length errors will normally go undetected. While STR3DI32 is generating the atom connectivity list for a molecular model, and performing the associated structure analysis, bond lengths that are not congruent with their bond type are flagged as possible errors, and are made obvious to the user.

STR3DI32 uses the QVBMM (Quantized Valence Bonds Molecular Mechanics) force field, which, while similar to the traditional MM force fields, is significantly more advanced, and integrates lone pair interactions into all of its calculations. The QVBMM force field recognizes, and uses, all n-n, n-σ, n-π interactions, and all of the dipolar interactions present in any molecular model. The QVBMM force field also recognizes intermolecular interactions, and that has allowed STR3DI32 to be used for studies involving molecular clusters (including solvation models), and the docking of molecules.

There are considerable challenges in integrating lone pair interactions into MM calculations and so STR3DI32 does a very careful, and detailed, search of the energy profile of the nearest local energy minimum of the molecular model during a structure-energy minimization exercise. Often, these energy minima are more similar to shallow bowls with bumpy bottoms, than to cones, and several conformations can often be found with similar energies. Thus, a structure-energy minimization exercise does take a bit longer when using STR3DI32, but should be more reliable than that done with most other MM programs.

[edit] References

Vernon G. S. Box, The Molecular Mechanics of Quantized Valence Bonds, J. Mol. Model., 3, 124, 1997
Vernon G. S. Box, The anomeric effect of monosaccharides and their derivatives. Insights from the new QVBMM molecular mechanics force field, Heterocycles, 48, 2389 1998
Vernon G. S. Box, Explorations of the Origins of the Reverse Anomeric Effect of the Monosaccharides using the QVBMM (Molecular Mechanics) Force Field, J. Mol. Struct., 522, 145 2000
Vernon G. S. Box, Stereo-electronic effects in polynucleotides and their double helices, J. Mol. Struct., 689, 33-41 2004