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Understanding molecular structure from molecular mechanics

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Abstract

Molecular mechanics gives us a well known model of molecular structure. It is less widely recognized that valence bond theory gives us structures which offer a direct interpretation of molecular mechanics formulations and parameters. The electronic effects well-known in physical organic chemistry can be directly interpreted in terms of valence bond structures, and hence quantitatively calculated and understood. The basic theory is outlined in this paper, and examples of the effects, and their interpretation in illustrative examples is presented.

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Notes

  1. The general problem with DFT methods, and in particular with B3LYP, is that, differing from Schrödinger methods, DFT methods cannot be systematically improved with increasing basis set size, and their accuracy in particular cases is often not known. In general, molecular structures are calculated less accurately by DFT methods than by Schrödinger methods. For energies, this may or may not be true, depending upon the case. There is a general error in B3LYP calculations, because the contribution of dispersion forces is omitted. This error may be small or large, depending upon the particular case, so one must be cautious about the use of such calculated values. There is a common tendency for users to overestimate the accuracy of B3LYP and related methods.

  2. The MM4 program is available to all users from Dr. J.-H. Lii, Department of Chemistry, National Changhua University of Education, No. 1, Jin-De Road, Changhua City 50058, Taiwan, jhrobert.lii@gmail.com.

  3. Bond lengths such as these are somewhat basis set dependent for small basis sets, but the differences between such bond lengths are only slightly so for calculations of this level or higher.

  4. When MM4 is used to study structures, if we learn something useful we may wish to include it in the program. This means that when these studies are being carried out there are two versions of the program. One is the “original” version, called MM4O. The other version, after the improvements have been added, is called MM4 going forward.

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Acknowledgments

The author is indebted to the University of Georgia, and especially to the present and immediate past Department Head’s of Chemistry, Jon Amster and John Stickney, respectively, and also to the Franklin College of Arts and Sciences and Dean Garnett Stokes, for their continuing support.

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  1. Department of Chemistry, Chemistry Annex, University of Georgia, Athens, GA, 30602, USA

    Norman L. Allinger

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  1. Norman L. Allinger
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Correspondence to Norman L. Allinger.

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Throughout this paper “quantum mechanical calculations”, or (QM) means MP2/6-31G++(2p, 2d), unless otherwise stated. Geometric units are in Angstroms or Degrees, and Energies are in kcal/mol unless otherwise specified. The expression MM4O is used to mean the “Original” MM4 program before inclusion of the item under discussion.

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Allinger, N.L. Understanding molecular structure from molecular mechanics. J Comput Aided Mol Des 25, 295–316 (2011). https://doi.org/10.1007/s10822-011-9422-4

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