Structural techniques, time scales

Focuses on force field calculations for understanding the dynamic properties of proteins and nucleic acids. Provides a useful introduction to several computational techniques, including molecular mechanics minimization and molecular dynamics. Includes discussions of research involving structural changes and short time scale dynamics of these biomolecules, and the influence of solvent in these processes. 

The LSDA approach requires simultaneous self-consistent solutions of the Schrbdinger and Poisson equations. This was accomplished using the Layer Korringa-Kohn-Rostoker technique which has many useful features for calculations of properties of layered systems. It is, for example, one of only a few electronic structure techniques that can treat non-periodic infinite systems. It also has the virtue that the computational time required for a calculation scales linearly with the number of different layers, not as the third power as most other techniques. 

To date the structure and reactivity of numerous complexes derived from aromatic compounds and nitrosonium cation have been studied (5, 56-63). However, relatively few studies are available on the nitrosonium complexes of cyclophanes (5, 57, 59, 61, 62), cf ref. (63). The interaction of [2.2]paracyclophane with nitrosonium tetrachloroaluminate was studied by H and 13C NMR spectroscopy using deuterium isotope perturbation technique (64). It was found that the resulting nitrosonium complexes containing one (25) or two NO groups (26) are involved in fast interconversion (on the NMR time scale) (Scheme 17). 

Zeolites are the main catalyst in the petrochemical industry. The importance of these aluminosilicates is due to their capacity to promote many important reactions. By analogy with superacid media (1), carbocations are believed to be key intermediates in these reactions. However, simple carbocationic species are seldom observed on the zeolite surface as persistent intermediates within the time-scale of spectroscopic techniques. Indeed, only some conjugated cyclic carbocations were observed as long living species, but covalent intermediates, namely alkyl-aluminumsilyl oxonium ions (2) (scheme 1), where the organic moiety is bonded to the zeolite structure, are usually thermodynamically more stable than the free carbocations (3,4). 

It is for this reason that spectroscopy offers the only experimental method for characterizing the interfacial region that is not automatically destined to run into basic conceptual difficulties. This is not to say that difficulties of a technical nature will not arise (40-48), nor that the conceptual difficulty of differing time scales among spectroscopic techniques will cause no problems (50). Nonetheless, it is to be hoped that future investigations of sorption reactions will focus more on probing the molecular structure of the mineral/water interface than on attempting simply to divine what the structure may be. 

The properties of membranes commonly studied by fluorescence techniques include motional, structural, and organizational aspects. Motional aspects include the rate of motion of fatty acyl chains, the head-group region of the phospholipids, and other lipid components and membrane proteins. The structural aspects of membranes would cover the orientational aspects of the lipid components. Organizational aspects include the distribution of lipids both laterally, in the plane of the membrane (e.g., phase separations), and across the membrane bilayer (phospholipid asymmetry) and distances from the surface or depth in the bilayer. Finally, there are properties of membranes pertaining to the surface such as the surface charge and dielectric properties. Fluorescence techniques have been widely used in the studies of membranes mainly since the time scale of the fluorescence lifetime coincides with the time scale of interest for lipid motion and since there are a wide number of fluorescence probes available which can be used to yield very specific information on membrane properties. 

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