Theoretical conformational analysis

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. 

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. 

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. 

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. 

Jakobsons, J., and S. M. Shevchenko. 1990. Theoretical conformational analysis of p-quinonemethides as lignin models. Latv. PSR Zinat. Akad. Vestis, Kim. Ser. 1990(2) 186-191. 

Shamovsky IL and Yarovskaya lY (1990) A theoretical conformational analysis of the complex of tocopherol and arachidonic acid molecules. Biol Mem 4 844-852. 

R 64 J. Malicka, C. Czaplewski, M. Groth, W. Wiczk, S. Oldziej, L. Lan-kiewicz, J. Ciarkowski and A. Li wo, Use of NMR and Fluorescence Spectroscopy as well as Theoretical Conformational Analysis in Conformation-Activity Studies of Cyclic Enkephalin Analogues , p. 123 R 65 A. Naito and K. Nishimura, Conformational Analysis of Opioid Peptides in the Solid State and the Membrane Environments by NMR Spectroscopy , p. 135... 

In all our studies so far, the choice of an appropriate molecule was based on model building, considering the coordination geometry of the metal ion and the nature of the coordinating ligands. However, it was considered that it would be of further aid to the molecular design if the conformation of the designed molecule can be predicted before its synthesis. Recent advances in theoretical conformational analysis [11] have laid down the necessary framework for such a prediction. 

Phe-Phe sequence in a He/Ne carrier gas mixture, together with an extensive theoretical conformational analysis, have revealed how specific NH-Jt and it-it interactiOTis stabilise other stmctures than p-tums, namely ji-ji-7 and 5-Jt-7 backbone forms (Fig. 9) [112]. This picture of ancillary interactions governing conformational distribution seems to hold on larger species, as testified by the systematic study of capped tripeptides, Phe-Ala-Ala, Ala-Phe-Ala and Ala-Ala-Phe, which shows how the presence of an NH-jr interaction can guide the backbone overall folding, and in this case control the formation of an incipient heUx [85]. 

At the biologically relevant pH of 7.4, the neurotransmitters are mostly proto-nated. The fraction of the cationic form for the above aminophenols is at least 92.8%, as measured for norepinephrine (23) [83]. Accordingly, most theoretical conformational analysis studies referred to the cationic form [see reviews 52,77]. 

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