Rotamer

Figure 2-53. Tolane rotamers a) one with the two aromatic rings in the same plane, and b) one with the two rings perpendicular to each other.

Figure 2-54. Using RAMSES, the two rotamers oftolane can be distinguished the planar rotamer is shown on the left-hand side, and the rotamer with the ring planes perpendicular to each other is on the right.

VViberg K B and M A Murcko 1988. Rotational Barriers. 2. Energies of Alkane Rotamers. An Examination of Gauche Interactions. Journal of the American Chemical Society 110 8029-8038. 

Dunbrack R L Jr and M Karplus 1993. Backbone-dependent Rotamer Library for Proteins. Applic to Side-chain Prediction. Journal of Molecular Biology 230 543-574. 

Minimize the cis rotamer in the MM3 force field starting from the skeleton... 

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

What enthalpy difference would lead to a 25-75% mixture of syn and skew rotamers of 1-butene Neglect any entropy change. 

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...

The small optical rotations of the alditols arise from the low energy barrier for rotation about C—C bonds, permitting easy iaterconversion and the existence of mixtures of rotational isomers (rotamers) ia solution (12). 

Acrylic acid, -(3-benzo[f>]thienyl)-a -mercapto-reaction with iodine, 4, 764 Acrylic acid, o -cyano-y3-(2-thienyl)-ring opening, 4, 807 Acrylic acid, -formyl-in pyridazinone synthesis, 3, 46 Acrylic acid, furyl-rotamers, 4, 545 synthesis, 4, 658 Acrylic acid, 2-hydroxybenzoyl-chroman-4-one synthesis from, 3, 850 Acrylic acid, 5-(l-propynyl)-2-thienyl-methyl ester occurrence, 4, 909 Acrylonitrile... 

Furan, 3-acetoxy-2,4,5-triphenyl-synthesis, 4, 659 Furan, 2-acetyl-isopropylation, 4, 607 rotamers, 4, 544 synthesis, 4, 665 toxicity, 1, 136 Furan, 3-acetyl-bromination, 4, 604 Furan, 3-acetyI-2-amino-reactions, 4, 74 Furan, 2-acetyl-3,5-dimethyl-synthesis, 4, 691 Furan, 2-acetyl-5-ethyl-synthesis, 4, 691 Furan, 2-acetyl-3-hydroxy-synthesis, 4, 649... 

Furan, perfluoro-2-butyltetrahydro-mass spectrometry, 4, 584 Furan, perfluorotetramethyl-synthesis, 4, 676 Furan, 2-phenyl-rotamers, 4, 545 Furan, 3-phenyl-rotamers, 4, 545 synthesis, 4, 663 Furan, 2-styryl-rotamers, 4, 545 Furan, tetraoyano-mass spectrometry, 4, 583 Furan, tetrahydro-applioations, 4, 707 basicity, 4, 554... 

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. 

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