Molecular mechanics computer programs

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.

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. 

When you perform an ah initio calculation, it is not always easy to know which basis set to use. Normally you should not use more complexity than is needed to answer your question or solve the problem. In fact, it may be desirable to determine the approximate geometry of the molecule using molecular mechanics. Many programs will allow you to use the result of a molecular mechanics geometry optimization as a starting point for an ah initio calculation. If possible, you should do so to save computational time. 

The mean residence times, MRT, of water molecules in the immediate vicinity of ions were studied extensively by means of these quantum-mechanical combined with molecular-mechanical computer simulations as reviewed at the time by Hofer et al. [70], The computational program employed has evolved over the years as was the minimal time t, above which a molecule is deemed to have left its position in the immediate vicinity of an ion, from 2ps in the earlier studies to 0.5 ps used in the later ones. The MRT of water molecules in the bulk solvent, r =1.7 ps, is only one-tenth of the time it takes the molecule to diffuse completely away. The relative mean residence times of water molecules in the second hydration shell to that in bulk water, RMRT = /t w (in %) at 25°C, are shown in Table 5.4. The MRT of water in the first hydration shells of multivalent ions are longer than could be studied by the computations. The RMRTs of water molecules near the ions are roughly proportional to the surface density of the charge on the ions, o. RMRT=0.22+l.l4(oJC mrr ), but exceptions are noted. 

This book is an introduction to computational chemistr y, molecular mechanics, and molecular orbital calculations, using a personal mieroeomputer. No speeial eom-putational skills are assumed of the reader aside from the ability to read and write a simple program in BASIC. No mathematieal training beyond ealeulus is assumed. A few elements of matrix algebra are introdueed in Chapter 3 and used throughout. 

Once requiring minicomputers and worksta tions many molecular mechanics programs are avail able for personal computers The information that strain energy calculations can provide is so helpful... 

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