Molecular structure conformational changes

Norregaard, L. and Gether, U. (2001) The monoamine neurotransmitter transporters structure, conformational changes and molecular gating. Curr. Opin. DrugDiscov. Dev. 4,591-601. 

More advanced semiempirical molecular orbital methods have also been used in this respect in modeling, e.g., the structure of a diphosphonium extractant in the gas phase, and then the percentage extraction of zinc ion-pair complexes was correlated with the calculated energy of association of the ion pairs [29]. Semiempirical SCF calculations, used to study structure, conformational changes and hydration of hydroxyoximes as extractants of copper, appeared helpful in interpreting their interfacial activity and the rate of extraction [30]. Similar (PM3, ZINDO) methods were also used to model the structure of some commercial extractants (pyridine dicarboxylates, pyridyloctanoates, jS-diketones, hydroxyoximes), as well as the effects of their hydration and association with modifiers (alcohols, )S-diketones) on their thermodynamic and interfacial activity [31 33]. In addition, the structure of copper complexes with these extractants was calculated [32]. 

Only a few molecular orbital calculations regarding the structures, conformational changes and bonding of S molecules have been published. Fimdamental reactions of sulfur rings like interconversions are only poorly understood, and more examples for the formation of homocyclic derivatives directly from the corresponding S parent molecules are likely to be found. These few comments show that much more work has to be done before the chemistry of elemental sulfur can be regarded as well known . 

Abstract. Recent years have seen a growing interest in the use of Raman-based spectroscopy as an analytical tool for the chemical analysis of biological samples. Raman spectroscopy has found many applications in cellular and structural biology, biomedicine, and biodetection. Its attractiveness for live biological studies lies mainly in its hi sensitivity to molecular interactions and small molecular scale conformational changes. In addition, the noninvasiveness of this s roach permits both in-vitro and in-vivo studies. This increased interest has been a result of advances in both instrumentation and techniques that have enabled improved data acquisition and data interpretation. This chapter addresses recent advances in Raman-based techniques and highlights their uses in specific biological studies. 

Up to this point, we have emphasized the stereochemical properties of molecules as objects, without concern for processes which affect the molecular shape. The term dynamic stereochemistry applies to die topology of processes which effect a structural change. The cases that are most important in organic chemistry are chemical reactions, conformational changes, and noncovalent complex formation. In order to understand the stereochemical aspects of a dynamic process, it is essential not only that the stereochemical relationship between starting and product states be established, but also that the spatial features of proposed intermediates and transition states must account for the observed stereochemical transformations. 

This is, for instance, the case of PTFE, which at atmospheric pressure presents two reversible first-order transitions at 19 °C and 30 °C [67], In the transition at 19 °C the molecular conformation changes slightly, from a 13/6 to a 15/7 helix and the molecular packing changes from an ordered structure with a triclinic unit cell (corresponding to a positioning of the chain axes nearly hexagonal) toward a partially disordered structure (partial intermolecular rotational disorder) with a... 

---