Molecular conformation comparisons

Gresh N, Claverie P, Pullman A (1984) Theoretical studies of molecular conformation. Derivation of an additive procedure for the computation of intramolecular interaction energies. Comparison with ab initio SCF computations. Theor Chim 66(l) l-20... 

Culberson, J.C., Nachbar, R.B., and Kearsley, S.K. Comparison of knowledge-based and distance geometry approaches for generation of molecular conformations./. Chem. Inf. Comput. 

The half-widths of 37-39 and 78-88 Hz, respectively, for the crystalline and amorphous phases are significantly larger than 18 and 38 Hz for those of the bulk-crystallized linear polyethylene (cf. Table 1). This is caused by incorporation of minor ethyl branches. The molecular alignment in the crystalline phase is slightly disordered, and the molecular mobility in the amorphous phase will therefore be promoted. With broadening of the crystalline and amorphous resonances, the resonance of the interphase also widens in comparison to that of bulk-crystallized linear polyethylene samples. This shows that the molecular conformation is more widely distributed from partially ordered trans-rich, conformation to complete random conformation, characteristic as the transition phase from the crystalline to amorphous regions. 

Molecular Conformation of sPP gel. Figure 27 shows the DD/MAS 13C NMR spectrum of sPP gel. This spectrum was obtained by a single-pulse sequence (tt /2—FIDdd-tt)ii with the repetition time ty more than 5 times the longitudinal relaxation time Tic. Hence, this spectrum reflects the thermal equilibrium state of the gel. For comparison, the spectrum of the bulk ttgg crystal of this sample... 

The comparison of the Mfiu values with those of Mabs allows one to obtain information about the changes in the electronic structure and molecular conformation between the Franck-Condon excited state initially reached upon excitation and the solvent-equilibrated fluorescent state [14]. Electronic transition dipole moments are mainly determined by the direct interactions between the lowest CT state and the ground state (So), and by the contributions from the locally excited configurations [14, 54, 56, 57]. For example, for the fluorescent CT state one can obtain... 

N. Gresh, P. Glaverie, and A. Pullman, Theor. Chim. Acta, 66,1 (1984). Theoretical Studies of Molecular Conformation. Derivation of an Additive Procedure for the Computation of Intramolecular Interaction Energies Comparison with Ab Initio SCF Computations. 

Holzgrabe, U. and Hopfinger, A.J. (1996). Conformational Analysis, Molecular Shape Comparison, and Pharmacophore Identification of Different Allosteric Modulators of Muscarinic Receptors. J.Chem.lnfComput.ScL, 36,1018-1024. 

The VCD study of the 1,1 -binaphthyl derivatives [110] serves as an example of other structural information that can be obtained by the comparison of experimental and computed VCD. This method allows monitoring not only of absolute chirality of the molecule, but also of the contributions of individual functional groups to the spectra, molecular conformations or some important structural parameter. As an example, we discuss chiral binaphthyls which represent popular building blocks, chiral recognition receptors and catalyst. Controlling the angle between naphthyl planes is important when supramolecular complexes based on these compounds are built. 

The molecules Se and Sio in Se-Sio exhibit the same molecular conformations as in the pure crystals of (D i) and of Sio D2). However, the molecular parameters of Se in Se-Sio show a slight variation of less than 1% of the mean values in the case of the bond and torsion angles and less than 0.1% in the case of the internuclear distances. As in pure Sio both enantiomorphic molecules are present in Ss-Sio in equal amounts. The site symmetry of Sio in Se-Sio is C2 as in pure Sio. However, the site symmetry of the Se molecules in Ss-Sio is reduced to C in comparison with Csi in pure S. The mean bond parameters of S and Sio are almost identical in Se-Sio compared to the pure components (Table 10). 

Figure 3.3.8 Molecular conformation of the four forms of MNPU. For ease of comparison of molecular conformation, all molecules are plotted on the place of the N-C(0)-N with the C=0 bond vertical.

Holzgrabe, U., Hopfinger, A.J., 1996. Conformational analysis, molecular shape comparison and pharmacophore identification of different allosteric modulators of muscarinic receptors. J. Chem. Inf. Comp. Sci. 36, 1018-1024. 

The influence ofthe molecular conformation on the resonance Raman spectra of /3-carotene was systematically determined for 14 different cis-trans isomers in the early 1980s (Koyama et al, 1982, 1983, 1988a). The conformation of 8 of these 14 isomers was determined by NMR spectroscopy, allowing the comparison ofresonance Raman spectra... 

The valinomycin study just described illustrates the value of close comparison of NMR and X-ray diffraction data. Correlation of NMR assignments with X-ray data for known structures may allow the subsequent elucidation of conformational features for related materials on the basis of NMR data alone. It is notoriously difficult to relate solid-state structures determined by X-ray diffraction to the solution conformation observed by conventional NMR spectroscopy, although data from the former technique are often the only type available for work on receptor recognition. However, solid-state NMR may provide a link between these two techniques by indicating whether molecular conformation changes do occur when the physical state is altered. In contrast to the valinomycin complexes discussed above, it has been found that significant differences in the solution and solid-state spectra of morphine... 

Goudreau, N., Weng, J.H. and Roques, B.P. (1994) Conformational analysis of CCK-B agonists using H-NMR and restrained molecular dynamics comparison of biologically active Boc-Trp-(N-Me)Nle-Asp-Phe-NH2 and inactive Boc-Trp-(N-Me)Phe-Asp-Phe-NH2. Bio-polym. 34 155-169. 

Another difficulty is that sublimation energies are known only for about 1000 organic crystals [41], for most of which the crystal structure has never been determined. Even when the crystal structure and sublimation energy of an organic compound are both known, there is the question of whether the compound is polymorphic, and, if so, whether the same polymorph was used for the two kinds of experiment. Another source of uncertainty in the comparison is that for non-rigid molecules the molecular conformation in the crystal may be different from that in the vapour where, indeed, a mixture of conformations can well occur. One authority has come to the somewhat disappointing but realistic conclusion that the discrepancy between observed and calculated quantities cannot be expected to be less than a few kilocalories per mole, i.e. around 10% of the experimental sublimation energy [36]. 

The molecular conformation of the tartaric acid is not significantly different in the tartrate and racemate structures, but the different modes of molecular packing lead to the existence of the two very different crystal structures (see Fig. 4 for a comparison). For the tartaric acid anhydrate crystal, the molecular planes are held directly together by a complicated network of intermolecular hydrogen bonds [25], The hydrogen bonding pattern in the racemic acid monohydrate crystal is very different the molecules are bound into columns that are linked up to form sheets [26]. 

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