Conformation angle

In terms of the refinement illustrated here, the function Y is the function Fix], The first point, Xj, is represented by all variable bond lengths, bond angles, conformation angles, chain position parameters, coordinates of the solvent of crystallization, etc., of the initial model. All other points X2,. .., Xj, represent trial values for the same n variables within the desired interval limits and subject to any other constraints, such as coupling of variables or hydrogen bond formation. Clearly, the number and type of variables, and their limits and constraints are easily changed in this procedure, as is the form of the function. The search procedure is also relatively rapid and does not suffer from a slowdown in the vicinity of the minimum, as may occur in steep-est-descent methods. 

Microwave spectroscopy allows the determination of precise bond lengths and angles, conformations, and dipole moments. Table 4 summarizes some molecular geometries deduced from microwave spectra. A disadvantage is that measurements have to be made in the gas phase and studies are limited to relatively small volatile molecules. 

The lactam restriction of peptide conformation (20) (Ci -o-Ni+i) was proposed first by Freidinger et al. (58) with the aim at forcing the peptide bond (coi) to be trans and placing a severe constraint on the rj/i torsion angle. Conformational... 

Lastly it is noted that an effective potential of a form similar to Eq. (2.19) appiears when use is made of holonomic constraints in Brownian dynamics simulations, that is, in the use of fixed bond lengths and bond angles in studies of dihedral angle conformational relaxation in polymer systems. In fact the two potentials represent different physical phenomena, but each acts so as to yield the correct equilibrium distribution in the coordinates of interest. The two approaches, of thermalization and constraint, have been compared for the case of the four-particle chain. ... 

Much effort has been expended on the formulation of more quantitative approaches, including the deduction of precise distances, bond angles, conformations, and potential energy surfaces for internal motions. These approaches may rely on a priori calculation of expected spectral parameters from hypothesized structures, or empirical correla-... 

A gauche conformation with a positive dihedral angle of -f- 60° can be denoted g, while a gauche conformation with a dihedral angle of -60° (i.e., -I- 300°) can be denoted g. The anti conformer can be denoted a. The anti conformer may also be denoted t, because the 180° dihedral angle conformation is often called "trans" in the physical chemistry literature. Organic chemists usually reserve the term trans for cis, trans isomers, however. This compact notation is particularly useful for representing several consecutive conformations in concise fashion. For example, three conformations of... 

MSA usually begins with a fixed-valence (frozen bond lengths and bond angles) conformational search and energy minimization on each compound to produce a set of candidate conformations. If the data set consists of congeners, the molecules are superimposed on their common skeleton otherwise, they are superimposed by a pharmacophore hypothesis as discussed in the section on molecular alignment. 

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