Intramolecular conformations

Norton, I. T., Goodall, D. M., Morris, E. R., and Rees, D. A. Kinetic evidence for intramolecular conformational ordering of the extracellular polysaccharide (xanthan) from Xanthomonas campestris,. Chem. Soc. Chem. Comm., 545,1980. 

Intramolecular conformation-locking Si...F coordination in non-coordinating solvents ==> rigid diastereomeric helices... 

Figure 5.3 (a) Structure-determining factors in SAMs. Chemisorption of molecule onto substrate (1), intermolecular interactions (2) intramolecular conformational degrees of freedom (3) and interactions of SAM with the environment (4). 

In the case of crystals, both intramolecular (conformational) and packing energies should be taken into account simultaneously. Such a total energy minimization method, with suitable crystallographic constraints, has been applied in different steps of the analysis of crystalline structures of three different synthetic polymers. Structures of these molecules, namely, isotactic trans-1,4-poly-penta-1,3-diene (ITPP), poly-pivalolactone (PPVL), and isotactic cis-1,4-poly(2-methyl-penta-1,3-diene)(PMPD), do not have troublesome features such as charged groups, counterions, and solvent molecules. 

The unproven, but reasonable, assumption implicit to SAR-directed conformational studies, both experimental and theoretical, is that one of the stable intramolecular conformers is the "active conformation, A difficulty to applying conformational data in quantitative drug design is selection of conformational features for QSAR development. Moreover, molecular shape properties are preferable features to have available in design studies. Conformation is a component of shape. The properties of the atoms, most notably their "sizes," comprise an additional set of factors needed to specify molecular shape. 

For POM, a matrix algorithm for the statistical mechanical treatment of an unperturbed -A-B-A-B- polymer chain with energy correlation between first-neighboring skeletal rotations is described. The results of the unperturbed dimensions are in satisfactory agreement with experimental data. In addition, if the same energy data are used, the results are rather close to those obtained by the RIS scheme usually adopted. The RIS scheme is shown to be also adequate for the calculation of the average intramolecular conformational energy, if the torsional oscillation about skeletal bonds is taken into account in the harmonic approximation. 

These expressions demonstrate that the change of entropy and internal energy on deformation under these conditions is both intra- and intermolecular in origin. Intramolecular (conformational) changes, which are independent of deformation, are characterized by the temperature coefficient of the unperturbed dimensions of chains d In intermolecular changes are characterized by the thermal expansivity a and are strongly dependent on deformation. The difference between the thermodynamic values under P, T = const, and V, T = const, is vefy important at small deformations since at X - 1 2aT/(/,2 + X — 2) tends to infinity. 

Molecular self-assembly will not be considered here (see [9.2]) in fact, it is a special type of synthetic procedure where several reactions between several reagents occur in one experimental operation to yield the final covalent structure it is subject to control by the intramolecular conformational features of intermediates and by the stereochemistry of the reaction(s) the efficient assembly of a covalent structure may require that the connecting reaction(s) be reversible so as to allow searching for the final structure. Examples are found in the generation of macropolycyclic structures by multiple (amine-aldehyde) condensations (see Section 4.1) or of porphyrinogens, porphyrins and phthalocyanins (see also in [9.13a]. 

Fig. 4.76 A dendrimer with flat dendrons with a propeller-like arrangement, in which correlated intramolecular conformational motion leads to inversion of the sense of chirality Owing to a partial steric intermeshing, when one of the dendrons is inverted the other three are also constrained to un-...

It seems to be important to study the intramolecular conformation of the LPS and lipid A molecules within the aggregate. In this way one might understand the way the molecule is arranged, which may be necessary for an understanding of the interaction with target molecules such as binding and receptor proteins. 

K. A. Olszewski, L. Piela, and H. A. Scheraga, J. Phys. Chem. 96,4672 (1992). Mean-Field Theory as a Tool for Intramolecular Conformational Optimization. I. Tests on Terminally-Blocked Alanine and Met-enkephalin. 

The thermochromic effect in solutions of poly(3-alkylthiophene)s has been attributed to an intramolecular conformational transition to an extended chain conformation, principally on the basis of an observed isosbestic point <1987PSB1071, 1992MM2141>, but evidence for supramolecular aggregates was noted <1987PSB1071>. 

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