Fragments conformational analysis

Ab initio calculations at the MP2 level of theory of a collection of substituted 1,3-dioxanes, 1,3-oxathianes, and 1,3-dithianes have been employed to study both the position of the conformational equilibria and the validity of the Perlin effect <2005T7349>. The 7h,c coupling constant proved to be a valuable tool in conformational analysis both twist conformers, in addition to the chair and alternative chair forms, could be readily identified simply by comparing experimental Vh,c coupling constants to the corresponding calculated values in the particular forms. In addition, the Perlin and reversed-Perlin effects of the C2-H fragments, c in 1,3-dioxanes,... 

The conformational analysis of cyclic molecular fragments is based on the original idea of Kilpatrick, Pitzer and Spitzer [200], as subsequently developed by various workers [201, 202, 203, 204, 205, 206, 207, 208]. 

P. P. Lankhorst, C. A. G. Haasnoot, C. Erkelens, and C. Altona, Carbon-13 NMR in conformational analysis of nucleic acid fragments. 2. A reparametrization of the Karplus equation for vicinal NMR coupling constants in CCOP and HCOP fragments, J. Biomol. Struct. Dyns., 1 (1984) 1387-1405. 

Distinct from these are automatic methods that directly transform 2D input information on atoms, bonds, and stereochemistry into 3D atomic coordinates. The automatic methods are classified into rule-based and data-based, fragment-based, conformational analysis, and numerical methods (Fig. 5). These classes of methods overlap more or less with each other and belong more or less to the domain of automatic 3D structure generation ... 

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