Conformation effects

One limitation of clique detection is that it needs to be run repeatedly with differei reference conformations and the run-time scales with the number of conformations pt molecule. The maximum likelihood method [Bamum et al. 1996] eliminates the need for reference conformation, effectively enabling every conformation of every molecule to a< as the reference. Despite this, the algorithm scales linearly with the number of conformatior per molecule, so enabling a larger number of conformations (up to a few hundred) to b handled. In addition, the method scores each of the possible pharmacophores based upo the extent to which it fits the set of input molecules and an estimate of its rarity. It is nc required that every molecule has to be able to match every feature for the pharmacophor to be considered. 

B. Bom, H. W. Spiess, Ah Initio Calculations of Conformational Effects on NMR Spectra of Amorphous Polymers Springer-Verlag, New York (1997). 

B pole opposite in sign, to that produced by the — NH3 group at the appropriate distance. In this way (when allowance was made for conformational effects)... 

Hassel shared the 1969 Nobel Prize in chemistry with Sir Derek Barton of Imperial College (London) Barton demonstrated how Hassel s structural results could be extended to an analysis of conformational effects on chemical reactivity... 

In the main, the physical and chemical properties of saturated and partially unsaturated alicyclic compounds closely resemble those of the analogous acyclic compounds formally derived by cleavage of the carbon ring at a point remote from any functionality. Relatively small, but often significant, differences in properties arise from conformational effects, and from strain effects in small rings, and these differences can be striking in properties which are particularly sensitive to molecular shape. 

AcOH, H2O, 89% yield. ° A factor of 400 in the relative rate of hydrolysis is attributed to a conformational effect where the lone pair on oxygen in the silyl ketals does not oveilap with the incipient cation during hydrolysis. 

The decalin (bicyclo[4.4.0]decane) ring system provides another important system for study of conformational effects in cyclohexane rings. Equilibration of the cis and trans isomers reveals that the trans isomer is favored by about 2.8 kcal/mol. Note that this represents a change in configuration, not conformation. The energy difference can be analyzed by noting that the cis isomer has three more gauche butane interactions that are... 

The selectivity observed in most intramolecular functionalizations depends on the preference for a six-membered transition state in the hydrogen-atom abstraction step. Appropriate molecules can be constmcted in which steric or conformational effects dictate a preference for selective abstraction of a hydrogen that is more remote from the reactive radical. 

However, the possibility of obtaining undesired results due to long-range conformational effects as substituents on far removed sites are changed requires careful analysis. 

Morpholinosulfur trifluoride is more thermally stable and therefore safer to handle than DAST and gives a slightly higher yield of the fluoride in the fluorination of cyclohexanol [95, ISO] Both solvent and conformational effects are pronounced in the fluorination of cyclohexanols [550] The chiral (S)-2-(methoxymethyl)pyr-rolidin-l-ylsulfur tnfluonde is an effective enantioselective fluorodehydroxylating agent [ISI]... 

Conformational effects appear to be important in determining which tertiary a-hydrogen is removed. For example, 4-phenyl-, 4-p-nitrophenyl-, and 4-/)-methoxyphenylquinolizidine (83) all are oxidized to the corresponding /j < -iminium salts (84) and not to the conjugated zJ -iminium salts (85) (86). The authors Judged that steric hindrance was responsible or that the conformation of the 4-sabstituted quinolizidines did not contain ideal... 

The x-ray crystal structures of the hexaethyl- and hexabutenylbenzene complexes show noteworthy conformational effects [78] (Fig. 6). The hexaethylbenzene complex has four distal chains [76] contrary to all the previous conformations of C6Et6 and (M)C6Et6 of C3 symmetry. This conformation also depends on the counter-anion as the three conformations with four, five, and six distal ET groups have close energies and can be observed by low-temperature 1H NMR. The hexabutenyl benzene complex has five distal chains [77]. 

The 1H NMR spectra of the epimeric cyclohexanols in DMSO reveal that the hydroxyl proton in the axial alcohol shows a resonance absorption at a higher field than in the equatorial one, indicating that the conformational effect of the hydrogen bond influences the XH NMR chemical shifts128. 

Conformational shift effects could be discussed in terms of discrete rotational isomeric states. Mainly two effects could be derived empirically to explain the shift differences due to conformational isomerism they-gauche and the Vg effect. However the spectra also indicate that the y-gauche effect is not a quantity with a universal numerical value. Furthermore the spectra of the cycloalkanes show that the conformational effects do not obey simple rules of additivity. With concern to our present knowledge great care has to be taken for the interpretation of NMR-spectra on the base of conformational shift increments which were not determined for the specific molecular structures. 

Syn elimination and the syn-anti dichotomy have also been found in open-chain systems, though to a lesser extent than in medium-ring compounds. For example, in the conversion of 3-hexyl-4-d-trimethylammonium ion to 3-hexene with potassium ec-butoxide, 67% of the reaction followed the syn-anti dichotomy. In general syn elimination in open-chain systems is only important in cases where certain types of steric effect are present. One such type is compounds in which substituents are found on both the P and the y carbons (the unprimed letter refers to the branch in which the elimination takes place). The factors that cause these results are not completely understood, but the following conformational effects have been proposed as a partial explanation. The two anti- and two syn-periplanar conformations are, for a quaternary ammonium salt ... 

Davies [30] studied the PyBOx-induced conformational effects by testing several ligands sterically hindered on the oxazoUne moieties (Scheme 11, structures 18 and 19). However, these new ligands gave poorer results in terms of yields and enantioselectivities than ligand 16 for the Ru-catalyzed cyclopropanation reaction, indicating unfavorable steric interactions between styrene and the carbene complex. 

N.m.r. spectroscopy has played an important part in determining the stereochemistry of the 1,3-dioxaphosphorinanes (52). The presence of the saturated six-membered ring means that there are usually conformational effects to be unravelled before configurational assignments can be made. The chair conformation is generally dominant. Phosphorus substituents which exhibit shielding effects show that in many P " phosphorinanes this substituent occupies an axial position and Sis( has been used to establish the equatorial conformation of a t-butyl substituent at C(5). Even in P" derivatives the isomer possessing the bulkiest P-substituent in an axial... 

Rovis and co-workers have also extended the intermolecular Stetter reaction to inclnde nitroaUcenes as the electrophilic component. Fluorinated triazolinm precatalyst 155 was effective in catalysing the reaction of a variety of heteroaromatic aldehydes 153 with nitroalkenes 154 to generate P-nitroketones in excellent yields and enantioselectivities. The authors propose that stereoelectronically induced conformational effects on the catalyst skeleton are key to the high selectivities observed with flnorinated catalyst 155 (Scheme 12.33) [69],... 

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