Theoretical conformation

Wilkes BC, Schiller PW. Theoretical conformational analysis of a p-selective cyclic opioid peptide analog. Biopolymers 1987 26 1431-1444. 

We have presented above some examples in which the theoretical conformational analysis of a molecule had to be supported by — or could help to support — an accurate knowledge of the static geometry in the gas phase. 

The theoretical conformational analysis of a molecule, whatever the quantum technique used, provides quantities related to the free molecule at 0°K and within ideal standard entropy conditions. It follows that such results must be compared with experimental results obtained in conditions as close as possible to these. Obviously, any study in the gas phase will be preferable to corresponding ones performed on liquid or solid states. The most suitable experimental approaches will thus be electron diffraction and microwave spectroscopy. 

The purpose of this brief survey was to demonstrate that, despite the criticisms which may be made of the use of any semi-empirical quantum technique for structural and conformational studies, the CNDO/2 and Extended CNDO/2 formalisms are definitely reliable tools for theoretical conformational analyses in inorganic and coordination chemistry. Moreover, if these tools are combined with the most suitable experimental techniques (i.e. microwave spectroscopy and electron diffraction) in that field, many problems of geometry and conformation can be solved in a way that neither of these approaches could have accomplished alone. 

Tight turns were first recognized from a theoretical conformational analysis by Venkatachalam (1968). He considered what conformations were available to a system of three linked peptide units (or four successive residues) that could be stabilized by a backbone hydrogen bond between the CO of residue n and the NH of residue n + 3. He... 

It should be observed that theoretical conformational analysis refers to an isolated molecule that has no interaction with the adjacent ones. This assumption is appropriate for low molecular weight compounds in the gas phase. For ma-cromolecular compounds particular conditions are known under which the interactions with the environment are minimized. In any case, such interactions are considered to be of higher order, to be introduced into calculations only where necessary. 

These workers proceeded to carry out theoretical conformational analyses of a set of sweeteners, many of which have multiple A-H and/or B sites. The set of compounds analyzed are reported in Table I along with the sweet potency relative to sucrose. A fixed valence geometry molecular mechanics force field was used in the conformational analyses. The conformational search strategy was as follows ... 

The characteristic ratios of poly(pro-gly), poly(hyp-gly), poly(gly-gly-pro-gly), poly(gly-gly-hyp-gly), and poly(pro-ale) are determined in water, The results confirm the main features of the theoretical conformational maps derived by Rory and coworkers for glycine followed by either l-proline or a nonproline residue. Small adjustments, well within the uncertainty described by Schimme and Rory, are suggested In the conformational map for L-proline followed by glycine. The constants for the Lennard-Jones functions of Scheraga and coworkers, as used by Madison and Scheliman, produce a conformational map for L-proline followed by a nonproline residue which is in somewhat poorer agreement with experiment. The two sets of modified constants introduced by Madison and Scheliman fall to predict the conformational properties of these sequential copolypeptides. 

Theoretical conformational analysis provides a basis for understanding the unique features of double-stranded DNA In terms of its chemical architecture. The well-known stiffness of the chain as a whole derives from the sequence of heterocyclic bases, while the local mobility of the constituent nucleotides reflects the structural complexity of the sugar-phosphate backbone. 

By theoretical conformational analysis the me/a-isomer (m-Abz) has been shown to provide distances between the amino and the carboxy functions that are in the range of those accessible to a tram dipeptide.121 22 The conformational flexibility is quite different, however, and turn structures are excluded. 23 ... 

Lehn, J. M. Theoretical Conformational Analysis. Ab initio SCF—LCAO—MO studies of conformations and conformational energy barriers. Scope and limitations. Proceedings of the International Symposium on Conformational Analysis, Brussels, 8—12 September 1969 Academic Press, to be published. 

Y. Paterson, S. M. Rumsey, E. Benedetti, G. Nemethy, and H. A. Scheraga, J. Am. Chem. Soc., 103, 2947 (1981). Sensitivity of Polypeptide Conformation to Geometry. Theoretical Conformational Analysis of Oligomers of a-Aminoisobutyric Acid. 

A comparison has been made(392) between the solution, solid-state, and theoretical conformations of morphine in D20 (+DC1) employing H nmr at 100 MHz and 600 MHz and 13Cnmr at 25.2 MHz. Because of the increased chemical shift separation that occurred at very high field, the proton signals for C-15 and C-16H could be assigned and examined. This, together with data from N-CH3 and NH, and 13C (C-15 and C-16), facilitated a close... 

Theoretical conformational calculations of Birshtein, Gotlib and Grigor eva " are also in favor of the concepts that a great hindrance to rotational isomerization exists in the main PMMA chain and that rotational-isomeric transitions (at (7>6 Kcal/mol) in side groups are possible. 

This conclusion is also confirmed by theoretical conformational calculations of these polymers. 

A similar analysis of the shape of curves Y(Tlrj) for labeled polyamic acid and numberical calculations of the rotatory diffusion coefficients of its units show that the relaxation behavior of a chain is similar to that of a model chain with free internal rotations. This result is in agreement with the data on other conformational and hydrodynamic properties of PAA ° and with theoretical conformational... 

Waterbeemd van de, H., Testa, B. Theoretical conformational smdies of some dopamine antagonistic benzamide drugs 3-pyrrolidyl- and 4-piperidyl derivatives. J. Med. Chem. 1983, 26, 203-207. 

In disaccharides one can also observe a slower secondary P-relaxation. Recently, it was shown that twisting rotation of the monosugar units around glycosidic bond is responsible for occurrence of this relaxation. This supposition was confirmed by theoretical conformational analysis. Additionally, it was proven that the activation energy provides direct information about structural rigidity of the examined disaccharides. 

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