Conformation, environmental influences

In the study of the four conformational polymorphs of a cobaloxime complex, Sawada et al. (1996) were able to establish a quantitative relationship between the size of the reaction cavity for an intramolecular photoisomerization reaction and the rate constant for the process in three of the modifications. Such studies provide a great deal of direct detailed information about the relationship between the environmental influences on the mechanism of a reaction at essentially the atomic level, information which is much more difficult to obtain from studies on a single crystalline form. 

Macromolecules are intricate physical-chemical systems whose properties vary as a function of environmental influences such as temperature, pH, ionic strength, contaminants, and solvent composition, to name only a few. They are structurally dynamic, often microhetero-geneous, aggregating systems, and they change conformation in the presence of ligands. Superimposed on this is the limited nature of our current understanding of macromolecular crystallization phenomena and the forces that promote and maintain protein and nucleic acid crystals. 

Figure 4 Indicates that CD can be employed to determine com-plexatlon Kjj s (see Table I). The ratio of the Na K+Kjj s, l.e. K+ Na+ selectivity, also shows a sharp shift between Z values of 80 and 83 (cf. Figure 6). Thus, the ability of the complexlng form of the lonophore to discriminate between ions depends strongly upon environmental Influences on conformation. Changes In inter-ligand distances and ligand orientations effected by changes In lonophore conformation manifest themselves by a determinative alteration of the free energy of complexatlon.

Clearly this test of environmental influence requires a well chosen test case. The limited conformational sampling seen in RNA simulations rules this system out as a candidate. In a similar manner, any conformational change which requires overcoming a significant conformational barrier, such as a B-DNA to Z-DNA transition, cannot reasonably be represented in nanosecond length simulations without methods applied to artificially boost the conformational sampling. Since we were able to see spontaneous B-DNA to A-DNA transitions within a nanosecond time period, since the DNA is very flexible and dynamic, and since the equilibrium between A-DNA to B-DNA is very strongly influenced by the environment, this seemed like a reasonable test case. 

The research is still in progress and every year even more data is published. Among the available works an attentive reader can find a very interesting pieces of research. For example Vivas et al. published the research on the influence of solvent on the induction of coil to helix conformational change generating the modification of the a2PA valnes." Kavitha et have presented the solvent effect on the 2PA of ZnO nanoparticles. Also, other than solvent types of environmental influences attract attention of scientists. Woo et al. and, more recently, Bairn et al. ° have demonstrated that the micellar systems, in... 

Simulations of the dynamic motion of proteins aim at sampling relevant portions of the conformational space accessible to the proteins under the influence of environmental variables such as temperature, pressure, and pH. We... 

The balance of electrostatic and delocalization interactions in an isolated molecule may be perturbed by the influence of the solvent. In calculations based on Eq. 7, the analysis of solvation-energy terms suggested that the electrostatic contribution stabilizing the ap orientation of the acetal s ment is the conformationally dominant term. For example, in 2-methoxyoxane, the difference in energy of the (ap, ap) and (ap, sc) conformers in water, compared to that in the isolated molecule, caused by solute-solvent electrostatic interactions alone, amounts to 4 kJ.mor. Accordingly, the inter-and intra-molecular, electrostatic interactions operate in reverse directions in acetals. Whereas the intramolecular, electrostatic interactions are responsible, together with delocalization interactions, for the aiq)earance of the anomeric, reverse anomeric, and exo-anomeric effects, the solute-solvent electrostatic interactions lessen their im nitude, and may even cancel them. Of course, the solvent may also influence the electron distribution and energy of MO s in a molecule. In this way, the orbital interactions of lone-pairs and delocalization contributions to the anomeric effect may be scaled by the solvent, but this mechanism of the environmental effect is, in most cases, of only minor importance. 

Plasma proteins organize on polymer substrates in different ways. Adsorbates are influenced by substrate physicochemical properties and by environmental factors, especially fluid shear and bulk protein distribution. Different types of binding interactions and more than one conformation for adsorbed protein are observed. In the case of albumin, the irreversibly adsorbed conformation, as measured by pulse intrinsic fluorescence, appears to be substantially altered from that of bulk albumin. Microaggregated albumin and undenatured forms are seen at the polymer interface, which are readily desorbed by viscous drag. 

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