Molecular mechanics, computation

The classical introduction to molecular mechanics calculations. The authors describe common components of force fields, parameterization methods, and molecular mechanics computational methods. Discusses th e application of molecular mechanics to molecules comm on in organic,and biochemistry. Several chapters deal w ith thermodynamic and chemical reaction calculations. 

The semi-empirical methods of HyperChem are quantum mechanical methods that can describe the breaking and formation of chemical bonds, as well as provide information about the distribution of electrons in the system. HyperChem s molecular mechanics techniques, on the other hand, do not explicitly treat the electrons, but instead describe the energetics only as interactions among the nuclei. Since these approximations result in substantial computational savings, the molecular mechanics methods can be applied to much larger systems than the quantum mechanical methods. There are many molecular properties, however, which are not accurately described by these methods. For instance, molecular bonds are neither formed nor broken during HyperChem s molecular mechanics computations the set of fixed bonds is provided as input to the computation. 

Intermolecular Energetics. Molecular calculations have long been criticized as unrealistic in considering only isolated molecules. Many examples now appear in the literature with molecular mechanics computations on two or more molecules (5). These types of calculations are very time consuming and difficult to analyze. Still, some excellent progress has been made on two or more interacting molecules using techniques such as those available in CHEMLAB. 

The next section in this chapter provides a brief comparison of the dipole moment (magnitude and direction) for a set of simple alcohols. Experimental gas phase dipole moments45 are compared to ab initio and as molecular mechanics computed values. It is important to note that the direction of the vector dipole used by chemists is defined differently in classical physics. In the former definition, the vector points from the positive to the negative direction, while the latter has the orientation reversed. 

Solid-state structure of bicyclic 1,3,5-trioxocane 4 was studied and supported with molecular mechanics computational data to determine its ring-chain tautomerism with keto acetal 5 (see Section 14.08.2.2.1 <1998J(P1)2353>). 

This chapter comprises three sections. The first section briefly discusses the existing reviews of molecular mechanics computations of inorganic systems, the problems intrinsic in the application of molecular mechanics force fields to inorganic molecules and materials, and the current, state-of-the-art force fields. The remaining two sections review the recent literature concerning transition metal complexes and main group compounds. 

The Valence Force Field and Organic Molecular Mechanics Computations... 

Figure 31. Gauche and trans conformations of p-propyl aniline. These illustrations are the result of structural optimization using a molecular mechanics computer program. Atoms were drawn (not to scale) in order to improve spatial perspective.

D. J. Brecknell, D. J. Raber, and D, M. Ferguson,/. Mol. Struct., 124, 343 (1985). Structures of Lanthanide Shift Reagent Complexes by Molecular Mechanics Computations. 

Then you will need to decide what type of calculation to do. You may have a large molecule such as a protein and want to choose molecular mechanics. Computer power has been, and is, increasing rapidly so that even quite large molecules such as metal complexes and organic molecules of a few hundred atoms can be treated quantum mechanically. Even with very large systems it is becoming increasingly common to treat part of the molecule such as an active site on an enzyme by quantum mechanics and the rest by molecular mechanics. 

By the early 1970s, molecular mechanics computer programs such as MMI and MM2 were available, running on the IBM 360. For proteins, ECEPP was developed by Harold A. Scheraga. - Countering the molecular mechanics approach, Michael J. S. Dewar modified John A. Pople s (complete) neglect-of-differential-overlap semiempirical quantum mechanical method (CNDO/2) to calculate quantities such as conformational stability and heats of formation. Such programs (MNDO) were necessarily slower than the empirical force field methods such as MM2 and ECEPP but still had fewer parameters and could account for the effects of polarization in aromatic systems. 

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