Correlation with internal structure

The trans-activation response (TAR) RNA is a structural motif at the 5Cend of the HIV RNA, which interacts with the Tat protein during HIV transcription. The binding site of the Tat protein is an internal loop in the TAR RNA (Fig. 15.10A). The TAR—Tat interaction assures an efficient transcription and thereby facilitates replication of the HIV virus (Frankel, 1992). Therefore, interference with the TAR—Tat interaction has been pursued as a strategy to combat HIV. Below is a description of how cw-EPR spectroscopy has yielded information about RNA dynamics that are correlated with the structure of the TAR RNA receptor bound to various ligands. 

Free radical addition of HBr to buta-1,2-diene (lb) affords dibromides exo-6b, (E)-6b and (Z)-6b, which consistently originate from Br addition to the central allene carbon atom [37]. The fact that the internal olefins (E)-6b and (Z)-6b dominate among the reaction products points to a thermodynamic control of the termination step (see below). The geometry of the major product (Z)-(6b) has been correlated with that of the preferred structure of intermediate 7b. The latter, in turn, has been deduced from an investigation of the configurational stability of the (Z)-methylallyl radical (Z)-8, which isomerizes with a rate constant of kiso=102s 1 (-130 °C) to the less strained E-stereoisomer (fc)-8 (Scheme 11.4) [38]. 

Diffusion measurements in neat ILs can reveal information on the internal structure of fhese media and on ionic association. But due to the high viscosities of mosf ILs, sfrong gradients or quite long diffusion times are necessary. With this technique, it was found that most IL cations diffuse faster than their corresponding anions [39], but the molecular size of anions and cations did not correlate well with their diffusion coefficients. In addition to this, the diffusion coefficients of the cations were strongly anion-dependent [40]. 

In addition to this influence of the molecular structure, which correlates with the number and the delocalization of -electrons, steric effects resulting from the internal molecular geometry and the nature of the substituents may play an important role in intermolecular charge transfer because of the packing of adjacent molecules in the solid 80>. For instance, the observation that the introduction... 

The crystal structures of fragment D from several recombinant fibrinogens has demonstrated that these mutant molecules are excellent models for the study of structure-function relationships, since the polypeptide chains are folded properly with only local changes (Kostelansky et al., 2002). Moreover, these studies allow testing of hypotheses about the effects of a particular mutation on structure and internal interactions within the molecule, which then can be correlated with the effects on fibrin polymerization or platelet aggregation (Kostelansky et al., 2004a,b). 

N diffuses into the structural pores of clinoptilolite 10 to 10 times faster than does CH4. Thus internal surfaces are kinetically selective for adsorption. Some clino samples are more effective at N2/CH4 separation than others and this property was correlated with the zeolite surface cation population. An incompletely exchanged clino containing doubly charged cations appears to be the most selective for N2. Using a computer-controlled pressure swing adsorption apparatus, several process variables were studied in multiple cycle experiments. These included feed composition and rates, and adsorber temperature, pressure and regeneration conditions. N2 diffusive flux reverses after about 60 seconds, but CH4 adsorption continues. This causes a decay in the observed N2/CH4 separation. Therefore, optimum process conditions include rapid adsorber pressurization and short adsorption/desorp-tion/regeneration cycles. 

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