Prediction of conformation

Fortunately, conformational analysis provides a variety of independent methods to determine conformations17. Nowadays, a prediction of conformational energies and their minimum is often facilitated by force-field18,19 and quantum-mechanical20 calculations, at least on a semiquantitative level. 

The pioneering applications of molecular mechanics to coordination compounds were conformational analyses127,281. Recent applications involving the computation of conformer equilibria discussed in this chapter are studies of solution structure refinements126,29 1, racemate separations131 3il and the evaluation of reaction pathways11 1,34,3S1. The importance of conformer equilibria in the areas of electron transfer rates and redox potentials is discussed in Chapter 10, and many examples discussed in the other chapters of Part II indicate how important the prediction of conformational equilibria is in various areas of coordination chemistry. 

Bublil EM, Freund NT, Mayrose I et al (2007) Stepwise prediction of conformational discontinuous B-cell epitopes using the Mapitope algorithm. Proteins 68 294-304... 

EHT, iterative EHT, and dispersion bonding calculations, the conformations of prostaglandin E-l were predicted (78). The prominent con-formers were all predicted to have intimate interaction between the side chains, in agreement with crystal studies (79). Finally, predictions of conformation have led to the prediction of a sweet-taste pharmacophore (91). 

Despite the fact that correlations of LIS ratios with the solution geometry of the LSR substrate adduct are now well established and very widely employed, warnings have been given (425, 426) that predictions of conformations of non-rigid molecules must be made with extreme caution. 

The development of the PF method culminated in molecular mechanics, a reliable method of prediction of conformational eneigy and equilibrium structure of nonpolar molecules. For molecules having several heteroatoms, a modified parameterization was developed, with the lone-pair parameters as a part of the force field, and with their inclusion into all types of intramo-... 

Molecular Mechanics calculations can be used (1) in the analysis of disordered structures, (2) in the prediction of known structures, (3) in the prediction of isomer ratios, and (4) in the prediction of conformer ratios. The majority of studies have dealt with Co hexaamine systems,but now force fields are available for amine complexes of Co , Ni , Cu , Zn , Cri , Fe i, and Rh F... 

The quality of rationalization provided by a given theory can be evaluated with relative ease by its applicability to explain all phenomena caused by the anomeric effect and its ability (if possible) to afford quantitative predictions of conformational equilibria. Following this approach, the description of the most important interpretations of the anomeric effect will be presented. 

Sisido M, Ishikawa Y, Harada M, Itoh K. 1991a. Helically arranged azobenzene chromophores along a pol5q)eptide chain. 2. Prediction of conformations and calcula tion of theoretical circular dichroism. Macromolecules 24(14) 3999 4003. 

A simple and popular method for the prediction of conformation is the application of empirical conformational parameters. From the study of numerous protein structures determined by x-ray crystallography it became obvious that certain amino acids are frequent constituents of helical portions while others are more likely to occur in j -sheets and still others are often found in reverse turns. Statistical treatment of such frequencies (Chou and Fasman 1978) produced sets of conformational parameters (Table 5) which were applied for the prediction of conformation in proteins with considerable success. A cluster of four helical residues (P > 1.00) in a six residue stretch of a chain is predictive for a helical region that can be extended in both directions until a... 

If we depict the same Newman projections with bent bonds, as shown in Figure 1.34, we see that conformer II now represents essentially an all-eclipsed conformation. Thus, it is easily predicted to be less stable than I, which is an all-staggered arrangement. If utility is the main criterion for adopting conceptual models, then this result would seem to argue persuasively for using the bent bond formulation. The bent bond model leads directly to a correct prediction of conformational stability, but the G,n model does not. ... 

Results such as these have tended to restrict use of the EH method to qualitative predictions of conformation in molecules too large to be conveniently treated by more accurate methods. However, just as the simple Huckel method underwent various refinements (such as the cjo technique) to patch up certain inadequacies, so has the EH method been rehned. Such refinements have been shown to give marked improvement in numerical predictions of various properties. The EH method has been overtaken in popularity by a host of more sophisticated computational methods. (See Chapter 11.) However, it is still sometimes used as a first step in such methods as a way to produce a starting set of approximate MOs. The EHMO method also continues to be important as the computational equivalent of qualitative MO theory (Chapter 14), which continues to play an important role in theoretical treatments of inorganic and organic chemistries (as, for example, in Walsh s Rules and in Woodward-Hoffmann Rules). 

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