Relation to Molecular Conformation

Luminescence from the solid slate is strongly subject to packing effects. Some arc related to molecular conformation, some result from electronic interactions be-... 

The Viscosity of Macromolecules in Relation to Molecular Conformation Jen Tsi Yang... 

Terminology relating to molecular conformation within polymer crystals... 

TERMINOLOGY RELATING TO MOLECULAR CONFORMATION WITHIN POLYMER CRYSTALS [9,10]... 

Finally, the model facilitates the accurate measurement of certain separation parameters (S and Z) that are believed to be directly related to molecular conformation. Values of. 5 and Z are required for the nmmal application of the model in predicting retention and band width. Equally important, knowledge of molecular conformation during separation is b eved to be related to soolled nonideal separation effects that d rade HPLC separation in many cases. Hopefully, measurements of S and Z in such cases will provide added insight into the cause and remedy of these nonideal eflb ts. Information of this same type diould fiirther improve the predictive accuracy of our model. 

Thus, identification of all pairwise, interproton relaxation-contribution terms, py (in s ), for a molecule by factorization from the experimentally measured / , values can provide a unique method for calculating interproton distances, which are readily related to molecular structure and conformation. When the concept of pairwise additivity of the relaxation contributions seems to break down, as with a complex molecule having many interconnecting, relaxation pathways, there are reliable separation techniques, such as deuterium substitution in key positions, and a combination of nonselective and selective relaxation-rates, that may be used to distinguish between pairwise, dipolar interactions. Moreover, with the development of the Fourier-transform technique, and the availability of highly sophisticated, n.m.r. spectrometers, it has become possible to measure, routinely, nonselective and selective relaxation-rates of any resonance that can be clearly resolved in a n.m.r. spectrum. 

The remaining problem of the molecular mechanisms of this action was judged to be related to the conformation of the dicarboxylic acid at the interface. This conformation is usually determined directly with the use of a Langmuir trough (16-18). The disadvantage of such a method for the present problem lies with the restrictions of the environment of the molecule to be Investigated. The basic requirement is that the molecule must be virtually insoluble in the liquid substrate on which the monolayer is supported. For the dicarboxylic acid in question, this meant a pH value as low as 2 and also a high electrolyte content in the aqueous substrate. 

The comprehensive manner by which VOA intensities relate to the details of molecular stereochemistry can be appreciated by recognizing that the set of 3N-6 vibrational degrees of freedom is defined in the same space that specifies the parameters of molecular conformation. No other form of molecular spectroscopy is so closely related to molecular stereochemistry. It is literally trae that VOA spectra arise from stereospecific vibrational oscillations of a chiral molecule. A challenge facing VOA spectroscopy at the present is how to fully extract this stractural and conformational information from the spectra. 

The major hurdle to overcome in the development of 3D-QSAR models using steric, electrostatic, or lipophilic fields is related to both conformation selection and subsequent suitable overlay (alignment) of compounds. Therefore, it is of some interest to provide a conformation-ally sensitive lipophilicity descriptor that is alignment-independent. In this chapter we describe the derivation and parametrization of a new descriptor called 3D-LogP and demonstrate both its conformational sensitivity and its effectiveness in QSAR analysis. The 3D-LogP descriptor provides such a representation in the form of a rapidly computable description of the local lipophilicity at points on a user-defined molecular surface. 

A conformational analysis, by NMR and molecular dynamics,116 of a cyclic C-glycosyl analogue of p-GlcNAc-Asn demonstrated some variations in relation to the conformation of the regular A-glycosyl analogue. 

In order to explain the stereospecificity of the thermally induced cyclization of preisocalamendiol (315) to give dehydroisocalamendiol (316), Terada and Yamamura have carried out molecular mechanics calculations on the ground-state conformers and probable transition states of (315). The computed values of the steric energies of the possible transition states are in good agreement with the observed experimental facts. Other studies related to the conformational aspects of germacrane sesquiterpenoids include an examination of the NOE effects in the isofuranodiene (317), which shows the 1,5-diene system to be in a crossed... 

Consider the relation between the correlation function and its spectral density. Slower and faster decays of the correlation function (i.e. slower and faster motions) give narrower and wider distributions of the spectral density, respectively. Figure 11 (a) shows some decay curves of the correlation function for motions with different xc values and (b) indicates the distributions of their respective spectral densities that are obtained by Fourier transform of the decay curves. Here A, B, C in (a) are the decay curves with xca> tcb> and A, B, C in (b) are the distribution of their respective spectral densities. As can be seen, the decay becomes slower and the spectral density distribution becomes narrower as the Xc increases. Assume here that xca cb i cc and the amorphous phase involves two independent motions dictated by xca and xcb whereas the crystalline-amorphous interphase involves two motions dictated by xca and Xcc-Here, xca characterizes a local molecular motion with relation to few carbon atoms in the main molecular chain, and xcb>tcc a somewhat long-ranged motion with relation to a conformational change of ca. 10-20 carbon atoms. In other words, it is assumed that somewhat long-ranged motion is different between the two phases but local motion is the same, the former is dictated by xcb or Xcc and the latter by a common relaxation time xca-... 

Conformational invariance means that molecular descriptor values are independent of the conformational changes in molecules. Conformations of molecules are the different atom dispositions in the 3D space, i.e. configurations that flexible molecules can assume without any change to their connectivity. Usually interest in different conformations of a molecule is related to those conformations where the total energies are relatively close to the minimum energy, i.e. within a cut-off energy value of some kcal/mol. 

These include multipole moments, molecular polarizabilities, ionization potentials, electron affinities, charge distributions, scattering potentials, spectroscopic transitions, geometries and energies of transition states, and the relative populations of various conformations of molecules. Some of these properties are directly related to molecular reactivity (e.g., charge distribution, molecular polarizabilities, scattering potentials), and they can be implemented in QSAR studies. Quantum mechanical methods can therefore be used to obtain reactivity characteristics in order to relate molecular structure to the observed biological activity (183, 230). 

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