Conformation chemistry

The latter are, indeed, of considerable interest. They have a long history in conformational chemistry [258,259] and deserve attention for the major role they play in the discussion and prediction of stmcmral feamres. Typically, we refer here to gauche interactions exemplified by one of the methyl protons of the axial methylcyclohexane (for instance) interacting with the axial protons at C-3 and C-5 of the ring, or to the three gauche interactions occurring in cw-decalin. ... 

The first two of these roles appear to focus on the conformal chemistry associated with the external profile of the molecules. The latter role focuses on the internal, quantum-mechanical structure of the molecules. While retinol, in its metabolic role as a vitamin participates in the manufacture of components of the disks of the Outer Segment of the Photoreceptor cells, it primary role is the last one. It acts as the critical chromogen, independent of any vitamin or hormonal role, leading to the production of chromophores in the retinal pigment epithelium (RPE) cells of the eye. Morton noted this role specifically In the retina, retinol is indubitably a precursor. ... 

Wang, X., Ellis, J. S., Lyle, E-L., Sundaram, P., Thompson, M. (2006). Conformational chemistry of surface-attached calmodulin detected by acoustic shear wave propagation. Mol Biosyst 2, 184-192. 

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 Web-based graphical user interface permits a choice from numerous criteria and the performance of rapid searches. This service, based on the chemistry information toolkit CACTVS, provides complex Boolean searches. Flexible substructure searches have also been implemented. Users can conduct 3D pharmacophore queries in up to 25 conformations pre-calculated for each compound. Numerous output formats as well as 2D and 3D visuaHzation options are supplied. It is possible to export search results in various forms and with choices for data contents in the exported files, for structure sets ranging in size from a single compound to the entire database. Additional information and down-loadable files (in various formats) can be obtained from this service. 

I. Pettersson, T. Liljefors, Molecular mechanics calculated conformational energies of organic molecules a comparison of force fields, in Reviews in Computational Chemistry, Vbl. 9,... 

D.R. Ripoll, H.A. Scheraga, ECEPP Empirical Conformational Energy Program for Peptides, in The Encyclopedia of Computational Chemistry, Vol. 2,... 

GAs or other methods from evolutionary computation are applied in various fields of chemistry Its tasks include the geometry optimization of conformations of small molecules, the elaboration of models for the prediction of properties or biological activities, the design of molecules de novo, the analysis of the interaction of proteins and their ligands, or the selection of descriptors [18]. The last application is explained briefly in Section 9.7.6. 

There is a lot of confusion over the meaning of the terms theoretical chemistry, computational chemistry and molecular modelling. Indeed, many practitioners use all three labels to describe aspects of their research, as the occasion demands "Theoretical chemistry is often considered synonymous with quantum mechanics, whereas computational chemistry encompasses not only quantum mechanics but also molecular mechaiucs, minimisation, simulations, conformational analysis and other computer-based methods for understanding and predicting the behaviour of molecular systems. Molecular modellers use all of these methods and so we shall not concern ourselves with semantics but rather shall consider any theoretical or computational tecluiique that provides insight into the behaviour of molecular systems to be an example of molecular modelling. If a distinction has to be... 

Smith G D and R L Jaffe 1996. Quantum Chemistry Study of Conformational Energies and Rotational Energy Barriers in u-Alkanes. Journal of Physical Chemistry 100 18718-18724,... 

Volumen and Hydratationswarme der lonen. Zeitschrift filr Physik 1 45-48. aan C M and K B Wiberg 1990. Determining Atom-Centred Monopoles from Molecular Electro-itic Potentials. The Need for High Sampling Density in Formamide Conformational Analysis. imal of Computational Chemistry 11 361-373. 

A R 1991, A Survey of Methods for Searching the Conformational Space of Small and Medium-iized Molecules. In Lipkowitz K B and D B Boyd (Editors) Reviews in Computational Chemistry /olume 2. New York, VCH Publishers, pp. 1-55. 

Gibson K D and H A Scheraga 1987. Revised Algorithms for the Build-up Procedure for Predicting lAotein Conformations by Energy Minimization, journal of Computational Chemistry 8 826-834. 

Goodman J M and W C Still 1991. An Unbounded Systematic Search of Conformational Space. Journaloj Computational Chemistry 12 1110-1117. 

Judson R S, W P Jaeger, A M Treasurywala and M L Peterson 1993. Conformational Searching Methods for Small Molecules. 2. Genetic Algorithm Approach. Journal of Computational Chemistry 14 1407-1414. 

Ripoll D R and H A Scheraga 1989. On the Multiple-Minimum Problem in the Conformational Anal of Polypeptides. IB. An Electrostatically Driven Monte Carlo Method Tests on met-Enkepha journal of Protein Chemistry 8 263-287. 

Jorgensen W L 1983. Theoretical Studies of Medium Effects on Conformational Equilibria, jouniM Physical Chemistry 87 5304-5314. 

Barrows S E, J W Storer, C J Cramer, A D French and D G Truhlar 1998. Factors Controlli Relative Stability of Anomers and Hydroxymethyl Conformers of Glucopyranose. Journal Computational Chemistry 19 1111-1129. 

Jorgensen W L and J K Buckner 1987. Use of Statistical Perturbation Theory for Computing Solven Effects on Molecular Conformation. Butane in Water. Journal of Physical Chemistry 91 6083-6085. 

GeUiaar D K, G M Verkhivker, P A Rejto, C J Sherman, D B Fogel, L J Fogel and S T Freer 1995 Molecular Recognition of the Inhibitor AG-1343 by HFV-l Protease Conformationally FlexibL Docking by Evolutionary Programming. Chemistry and Biology 2 317-324. 

R and M M Hann 2000. The In Silico World of Virtual Libraries. Drug Discovery Today 5 326-336. R and I D Kuntz 1990. Conformational Analysis of Flexible Ligands in Macromolecular eptor Sites. Journal of Computational Chemistry 13 730-748. 

The regioselectivity benefits from the increased polarisation of the alkene moiety, reflected in the increased difference in the orbital coefficients on carbon 1 and 2. The increase in endo-exo selectivity is a result of an increased secondary orbital interaction that can be attributed to the increased orbital coefficient on the carbonyl carbon ". Also increased dipolar interactions, as a result of an increased polarisation, will contribute. Interestingly, Yamamoto has demonstrated that by usirg a very bulky catalyst the endo-pathway can be blocked and an excess of exo product can be obtained The increased di as tereo facial selectivity has been attributed to a more compact transition state for the catalysed reaction as a result of more efficient primary and secondary orbital interactions as well as conformational changes in the complexed dienophile" . Calculations show that, with the polarisation of the dienophile, the extent of asynchronicity in the activated complex increases . Some authors even report a zwitteriorric character of the activated complex of the Lewis-acid catalysed reaction " . Currently, Lewis-acid catalysis of Diels-Alder reactions is everyday practice in synthetic organic chemistry. 

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... 

Rotation around carbon-carbon bonds is one of the fastest processes m chemistry Among the ways that we can describe the rate of a process is by its half life which is the length of time it takes for one half of the molecules to react It takes less than 10 s for half of the molecules m a sample of ethane to go from one staggered conformation to another at 25°C... 

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... 

The conformational features of six membered rings are fundamental to organic chemistry so it is essential that you have a clear understanding of the directional prop erties of axial and equatorial bonds and be able to represent them accurately Figure 3 17 offers some guidance on the drawing of chair cyclohexane rings... 

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