Conformations rotamers

SB. Actually, these tautomeric equilibria are more complex because each of these three forms can exist as two geometric isomers ( and Z for 75A and 75A) or two conformers (rotamers E and Z for 75B). When + H, two diastereomers cis and trans and R ) are possible for the cyclic tautomer 75B. These equilibria have been thoroughly investigated (88TH2) by means of electronic, IR, H-, and C-NMR spectroscopy. The structure of the solid 5-hydroxypyrazoline 74B- (R = Me R = H R = Ph R" = i-Pr) was confirmed by X-ray diffraction (87MI5). An approximate generalization of the influence of the structural factor on these equilibria is shown in Table X. 

Figure 2 Different interpretations of conformers. (A) Exchange of conformers (rotamers) by the strict chemical convention (size of spin set is n = 4 nuclei). (B) Conformers, as sides of a chemical reaction (size of spin set is n = 2 nuclei).

In the gase phase, the infrared bands are broad (50 cm ), due to the rotational structure, overlapping vibrations, and hot transitions. In the solid state, the rotational motions are quenched, but due to intermolecular (hydrogen bond) and correlation field interactions, the band positions are shifted and the bands are even broader. The infrared absorptions of matrix-isolated molecules are close to the gas-phase frequencies and exhibit a sharp line-like character (half-widths 0.1 to 2 cm ). Hence the spectra of matrix-isolated molecules are less complicated, and, in comparison to gas phase or solid state spectra, the sensitivity and selectivity of detection increase by a factor of about 10 to 100. Closely spaced vibrations attributed to mixtures of similar molecules, such as conformers, rotamers, molecular complexes, or isotopic species, e.g., H C104 and H CI04, are easily distinguished. 

The u.v. and c.d. spectra of (364 R = Me, Et, Pr, Bu , or PhCH2) in EtOH and in iso-octane have been reported.The chiroptical properties of the oxaziridine chromophore were generally characterized by a positive pattern at 190—350 nm. The notable exception to this was a clear negative Cotton effect for (364 R = Pr ). The seemingly anomalous behaviour of this compound was interpreted in terms of the possible existence of solvation equilibria and conformational rotamers about the N—CHMe2 bond. The relatively new technique of Liquid-Crystal-Induced Circular Dichroism (LCICD) has been used in the... 

Figure 4-20 Rotamers (rotational conformers ) of 1-butene (Kevins, Chen, and AlliiiceT, 1996 ).

Side chain generation is often a source of error. It will be most reliable if certain rules of thumb are obeyed. Start with structurally conserved side chains and hold them fixed. Then look at the energy and entropy of rotamers for the remaining side chains. Conventional conformation search techniques are often used to place each side chain. 

Quantum chemistry methods allow the prediction of the ultraviolet transitions in good agreement with the experimental values in the case of thiazole and its three methyl derivatives (Table 1-18). A very weak absorption has been indicated at 269.5 nm that could correspond to an n- TT transition given by calculation at 281.5 nm (133). Ultraviolet absorption spectroscopy has been investigated in connection with steric interactions in the A-4-thiazoline-2-thione (74) series (181). It was earlier demonstrated by NMR technique that 4-alkyl-3 isopropyl-A-4-thiazoline-2-thiones exist in solution as equilibrium mixtures of two conformers (75 and 76), the relative populations of which vary with the size of R4 (182) for R4 = rBu the population of rotamer A is 100%, whereas for R4 = Me it is only 28%. Starting from the observed absorption wavelength for... 

Different conformations of the same compound are sometimes called conformers or rotamers... 

Fig. 3. The solid-state conformations of 3- uoro-chloramphenicol (6, R = NO2) showing the corresponding rotamers and schematics of the stabilising...

N-alkylation, 4, 236 Pyrrole, 2-formyl-3,4-diiodo-synthesis, 4, 216 Pyrrole, 2-formyl-1-methyl-conformation, 4, 193 Pyrrole, 2-formyl-5-nitro-conformation, 4, 193 Pyrrole, furyl-rotamers, 4, 546 Pyrrole, 2-(2-furyl)-conformation, 4, 32 Pyrrole, 2-halo-reactions, 4, 78 Pyrrole, 3-halo-reactions, 4, 78 Pyrrole, 2-halomethyl-nucleophilic substitution, 4, 274 reactions, 4, 275 Pyrrole, hydroxy-synthesis, 4, 97 Pyrrole, 1-hydroxy-cycloaddition reactions, 4, 303 deoxygenation, 4, 304 synthesis, 4, 126, 363 tautomerism, 4, 35, 197 Pyrrole, 2-hydroxy-reactions, 4, 76 tautomerism, 4, 36, 198... 

A recent survey analyzed the accuracy of tliree different side chain prediction methods [134]. These methods were tested by predicting side chain conformations on nearnative protein backbones with <4 A RMSD to the native structures. The tliree methods included the packing of backbone-dependent rotamers [129], the self-consistent mean-field approach to positioning rotamers based on their van der Waals interactions [145],... 

FI Schrauber, F Eisenhaber, P Argos. Rotamers To be or not to be An analysis of ammo acid side-chain conformations m globular proteins. J Mol Biol 230 592-612, 1993. 

RL Dunbrack, M Karplus. Pi ediction of protein side-chain conformations from a backbone conformation dependent rotamer library. J Mol Biol 230 543-571, 1993. 

C Wilson, LM Gregoret, DA Agard. Modeling side-chain conformation for homologous proteins using an energy-based rotamer search. J Mol Biol 229 996-1006, 1993. 

Analysis and prediction of side-chain conformation have long been predicated on statistical analysis of data from protein structures. Early rotamer libraries [91-93] ignored backbone conformation and instead gave the proportions of side-chain rotamers for each of the 18 amino acids with side-chain dihedral degrees of freedom. In recent years, it has become possible to take account of the effect of the backbone conformation on the distribution of side-chain rotamers [28,94-96]. McGregor et al. [94] and Schrauber et al. [97] produced rotamer libraries based on secondary structure. Dunbrack and Karplus [95] instead examined the variation in rotamer distributions as a function of the backbone dihedrals ( ) and V /, later providing conformational analysis to justify this choice [96]. Dunbrack and Cohen [28] extended the analysis of protein side-chain conformation by using Bayesian statistics to derive the full backbone-dependent rotamer libraries at all... 

MJ McGregor, SA Islam, MJE Sternberg. Analysis of the relationship between sidecham conformation and secondary stiaicture m globular proteins. J Mol Biol 198 295-310, 1987. RL Dunbrack Jr, M Karplus. Backbone-dependent rotamer library for proteins Application to sidecham prediction. J Mol Biol 230 543-571, 1993. 

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