SHAPES force field

The SHAPES force field" has been implemented in CHARMM and used to examine the structures of several square planar rhodium complexes. This force field is based on angular overlap considerations and treats angular distortions for a variety of geometries. Spherical internal coordinates and Fourier potential functions form the basis for the description of these molecular shapes. The parameters for this force field were derived from normal coordinate analysis, ab initio calculations, and structure-based optimizations. The average rms deviation for bond lengths was 0.026 A, and the average rms deviation for bond angles was 3.2°. 

In a recently published application of the SHAPES force field, MM and NOE investigations were combined to determine the solution structures of... 

Separability theorem, 309 SHAKE algorithm, 385 SHAPES force field, 40 Simulated Annealing (SA), global optimization, 342 Simulation methods, 373 Supidfiidiil, iulcs, 3j6 Susceptibility, 237 Symbolic variables, for optimizations, 416 Symmetrical orthogonalization of basis sets, 314 Symmetry adapted functions, 75 Symmetry breaking, of wave functions, 76 ... 

The picture of molecules being composed of structural units, functional groups , which behave similarly in different molecules forms the very basis of organic chemistry. The drawing of molecular structures where alphabetic letters represent atoms and lines represent bonds is used universally. Organic chemists often build ball and stick, or CPK space-filling, models of their molecules to examine their shapes Force, field methods are... 

This situation, despite the fact that reliability is increasing, is very undesirable. A considerable effort will be needed to revise the shape of the potential functions such that transferability is greatly enhanced and the number of atom types can be reduced. After all, there is only one type of carbon it has mass 12 and charge 6 and that is all that matters. What is obviously most needed is to incorporate essential many-body interactions in a proper way. In all present non-polarisable force fields many-body interactions are incorporated in an average way into pair-additive terms. In general, errors in one term are compensated by parameter adjustments in other terms, and the resulting force field is only valid for a limited range of environments. 

The fifth and final chapter, on Parallel Force Field Evaluation, takes account of the fact that the bulk of CPU time spent in MD simulations is required for evaluation of the force field. In the first paper, BOARD and his coworkers present a comparison of the performance of various parallel implementations of Ewald and multipole summations together with recommendations for their application. The second paper, by Phillips et AL., addresses the special problems associated with the design of parallel MD programs. Conflicting issues that shape the design of such codes are identified and the use of features such as multiple threads and message-driven execution is described. The final paper, by Okunbor Murty, compares three force decomposition techniques (the checkerboard partitioning method. 

V S, C M Kelly and C R Landis 1991. SHAPES Empirical Force-Field - New Treatment of igular Potentials and Its Application to Square-Planar Transition-Metal Complexes. Journal of American Chemical Society 113 1-12. 

Terms in the energy expression that describe a single aspect of the molecular shape, such as bond stretching, angle bending, ring inversion, or torsional motion, are called valence terms. All force fields have at least one valence term and most have three or more. 

Molecular mechanics force fields are sometimes parameterized to describe lanthanides and actinides. This has been effective in describing the shape of the molecule, but does not go very far toward giving systematic energies. A few semiempirical methods have been parameterized for these elements, but they have not seen widespread use. 

ChemSketch has some special-purpose building functions. The peptide builder creates a line structure from the protein sequence defined with the typical three-letter abbreviations. The carbohydrate builder creates a structure from a text string description of the molecule. The nucleic acid builder creates a structure from the typical one-letter abbreviations. There is a function to clean up the shape of the structure (i.e., make bond lengths equivalent). There is also a three-dimensional optimization routine, which uses a proprietary modification of the CHARMM force field. It is possible to set the molecule line drawing mode to obey the conventions of several different publishers. 

Most drug-like molecules adopt a number of conformations through rotations about bonds and/or inversions about atomic centers, giving the molecules a number of different three-dimensional (3D) shapes. To obtain different energy minimized structures using a force field, a conformational search technique must be combined with the local geometry optimization described in the previous section. Many such methods have been formulated, and they can be broadly classified as either systematic or stochastic algorithms. 

The first-principles calculation of NIS spectra has several important aspects. First of all, they greatly assist the assignment of NIS spectra. Secondly, the elucidation of the vibrational frequencies and normal mode compositions by means of quantum chemical calculations allows for the interpretation of the observed NIS patterns in terms of geometric and electronic structure and consequently provide a means of critically testing proposals for species of unknown structure. The first-principles calculation also provides an unambiguous way to perform consistent quantitative parameterization of experimental NIS data. Finally, there is another methodological aspect concerning the accuracy of the quantum chemically calculated force fields. Such calculations typically use only the experimental frequencies as reference values. However, apart from the frequencies, NIS probes the shapes of the normal modes for which the iron composition factors are a direct quantitative measure. Thus, by comparison with experimental data, one can assess the quality of the calculated normal mode compositions. 

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