Conformational analysis, review

M. Robb, M. Garavelli, M. Olivucci, and F, Bernardi, in Reviews in Computational Chemistry, K. Lipkowitz and D. Boyd, eds., Vol. 15, John Wiley Sons, New York, 2000, pp. 87-146. M. Olivucci, M, Robb, and F. Bernardi, in Conformational analysis of molecules in excited states, Wiley-VCH, New York, 2000, pp. 297-366. 

The stereogenic sulfur atom in sulfoxides is usually configurationally stable at room temperature thus, sulfoxides may be chiral based on this property alone1. In fact, there are many examples of optically active sulfoxides of both synthetic and natural origin. This chapter reviews the important methods for obtaining optically active sulfoxides, and discusses some reactions at sulfur which either leave the coordination number at three or increase it to four, generally with preservation of optical activity. It also describes briefly some recent studies on the conformational analysis and chiroptical properties of sulfoxides. 

For a monograph, see Schill, G. Catenanes, Rotaxanes, and Knots Academic Press NY, 1971. For a review, see Schill, G. in Chiurdoglu Conformational Analysis Academic Press NY, 1971, p. 229. 

For reviews of the conformational analysis of five-membered rings, see Fuchs, B. Top. 

Nuclear magnetic resonance (NMR) spectroscopy is, next to X-ray diffraction, the most important method to elucidate molecular structures of small molecules up to large bio macromolecules. It is used as a routine method in every chemical laboratory and it is not the aim of this article to give a comprehensive review about NMR in structural analysis. We will concentrate here on liquid-state applications with respect to drugs or drug-like molecules to emphasize techniques for conformational analysis including recent developments in the field. 

Applications The general applications of XRD comprise routine phase identification, quantitative analysis, compositional studies of crystalline solid compounds, texture and residual stress analysis, high-and low-temperature studies, low-angle analysis, films, etc. Single-crystal X-ray diffraction has been used for detailed structural analysis of many pure polymer additives (antioxidants, flame retardants, plasticisers, fillers, pigments and dyes, etc.) and for conformational analysis. A variety of analytical techniques are used to identify and classify different crystal polymorphs, notably XRD, microscopy, DSC, FTIR and NIRS. A comprehensive review of the analytical techniques employed for the analysis of polymorphs has been compiled [324]. The Rietveld method has been used to model a mineral-filled PPS compound [325]. 

In addition to the Annual Reports on NMR Spectroscopy monograph reviewing H-NMR and, 3C-NMR spectroscopy of alkaloids in three volumes (305), several books and reviews appeared concerning the 13C-NMR spectroscopy of naturally occurring substances (306-308). Therefore we would like to present only a limited number of examples of the exceptional applicability of these physical methods for structure elucidation and conformational analysis of complex molecules. 

In comparison with other spectroscopic methods, 13C-NMR spectroscopy affords the most valuable information for the stereochemical and conformational analysis of quinolizidine compounds. On the basis of the results, summarized in a review by Tourwe and van Binst (313) as well as in a series of publications (314-318), the steric structure elucidation of indolo[2,3-a]quinolizidine alkaloids has been facilitated. 

Coming back to the experimental methods which can be used for molecular conformational analysis, we include here a brief critical survey of a method much quoted in the literature, i.e. n.m.r. including the VT process. Reviewing our work... 

Aldonolactones are useful starting materials for the synthesis of modified sugars. They have also been used as chiral templates in synthesis of natural products. Some of them are inexpensive, commercially available products or they may be obtained readily from the respective monosaccharides. The purpose of this chapter is to survey the main reactions of aldonolactones. Previous reviews on the subject include articles on gulono-1,4-lactones (1) and D-ribonolactone (2). Methods of synthesis, conformational analysis, and biological properties are not discussed in this chapter. 

The ability of the MM method to calculate accurately potential energies and geometries of molecules is best suited for quantitative conformational analysis (44). Numerical values can readily be given to such terms as strain and stability (45). The topic is extensively covered in Allinger s review (lOd), therefore only some recent developments are mentioned. 

The theoretical and methodological aspects of conformational analysis of macromolecular chains in the disordered state were discussed by Flory in his classic book (155, 187). The literature on the subject includes a large number of books and reviews (37, 39, 188-190) extensive discussions may also be found in general textbooks of macromolecular science (9, 12, 13, 191). 

A few words about conformational analysis are given in Section 7.5.3. In Section 7.5.1 the NMR of peptides in general is discussed. Reviews of NMR spectroscopy of peptides can be found in the literature. 16-18 ... 

The three aromatic amino acids (Phe, Tyr, Trp) have side-chain groups corresponding to the benzene, phenol, and indole chromophores, respectively. The spectroscopic properties of the rat transitions in these chromophores have been reviewed.136-381 Coupling of aromatic transitions among themselves and with peptide transitions can give rise to CD bands in the near and far (k < 250 nm) UV. Near-UV CD bands are useful indicators of the environment of the aromatic chromophores and can frequently be assigned to specific types of side chain, based upon band position, presence of vibrational fine structure, etc. Far-UV CD bands due to aromatic side chains, except for the La band of Tyr (-230 nm) and the Bb band of Trp (-225 nm), are generally difficult to resolve from peptide CD bands and can complicate the conformational analysis of peptides. 

A review of the Journal of Physical Chemistry A, volume 110, issues 6 and 7, reveals that computational chemistry plays a major or supporting role in the majority of papers. Computational tools include use of large Gaussian basis sets and density functional theory, molecular mechanics, and molecular dynamics. There were quantum chemistry studies of complex reaction schemes to create detailed reaction potential energy surfaces/maps, molecular mechanics and molecular dynamics studies of larger chemical systems, and conformational analysis studies. Spectroscopic methods included photoelectron spectroscopy, microwave spectroscopy circular dichroism, IR, UV-vis, EPR, ENDOR, and ENDOR induced EPR. The kinetics papers focused on elucidation of complex mechanisms and potential energy reaction coordinate surfaces. 

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