Thermodynamics of conformation

In presented work the analysis of osmotic pressure of the polymeric solutions has been done with taken into account the thermodynamics of conformation state of macromolecules following from the self-avoiding random walks statistics [13, 14],... 

Whereas relaxation experiments to probe biomolecule dynamics have become popular only within the past 10 years, HX experiments have been performed on proteins for many decades. Provided that the experiment is carried out under conditions favoring the native protein state, thermodynamics of conformational flnctnations that lead to exchange of protons with solvent (AGhx) can be determined using the following expression ... 

Olmsted, M. C., C. F. Anderson and M. T. Record. (1991). Importance of oligoelectrolyte end effects for the thermodynamics of conformational transitions of nucleic acid oligomers. Biopolymers. 31 1593-1604. 

Benegas JC, Pantano S, Vetere A, Paoletti S. Polyelectrolytic aspects of the thermodynamics of conformational transitions k carrageenan in formamide. Biopolymers 1999 49 127-130. 

Effect of preferential conformations on base properties and thermodynamics of conformation conversion along with t3q>e of ring fusion on cis-trans conversion of bicycle in pyrrolizidines 06KCS1443. 

THERMODYNAMICS OF CONFORMATION AND DEFORMATION OF THE INTERTWINING POLYMERIC STARS... 

The chapter did not consider the contribution of conformation variation into the change of the process of free energy. In general, case values of limited parameters at which there appears thermodynamic opportunity of reaction initiation decrease at the formation of thermodynamically unstable conformers. 

Thermodynamically it would be expected that a ligand may not have identical affinity for both receptor conformations. This was an assumption in early formulations of conformational selection. For example, differential affinity for protein conformations was proposed for oxygen binding to hemoglobin [17] and for choline derivatives and nicotinic receptors [18]. Furthermore, assume that these conformations exist in an equilibrium defined by an allosteric constant L (defined as [Ra]/[R-i]) and that a ligand [A] has affinity for both conformations defined by equilibrium association constants Ka and aKa, respectively, for the inactive and active states ... 

The thermodynamic analysis of conformational and structural transformations in the melt at high pressures34 showed that the free volume and free energy minimum required for hydrostatic compression is attained as a result of the transition of the molecules in the melt into a more extended conformation (gauche —> trans transitions) since the extended molecules ensure a more compact packing of the chains at compression. Chain uncoiling leads to a decrease in their flexibility parameter f with increasing pressure p ... 

The Pummerer reaction346 of conformationally rigid 4-aryl-substituted thiane oxides with acetic anhydride was either stereoselective or stereospecific, and the rearrangement is mainly intermolecular, while the rate-determining step appears to be the E2 1,2-elimination of acetic acid from the acetoxysulfonium intermediates formed in the initial acetylation of the sulfoxide. The thermodynamically controlled product is the axial acetoxy isomer, while the kinetically controlled product is the equatorial isomer that is preferentially formed due to the facile access of the acetate to the equatorial position347. The overall mechanism is illustrated in equation 129. 

If peptide residues are converted to peptoid residues, the conformational heterogeneity of the polymer backbone is likely to increase due to cis/trans isomerization at amide bonds. This will lead to an enhanced loss of conformational entropy upon peptoid/protein association, which could adversely affect binding thermodynamics. A potential solution is the judicious placement of bulky peptoid side chains that constrain backbone dihedral angles. 

The success of such reactions depends on the intramolecular hydrogen transfer being faster than hydrogen atom abstraction from the stannane reagent. In the example shown, hydrogen transfer is favored by the thermodynamic driving force of radical stabilization, by the intramolecular nature of the hydrogen transfer, and by the steric effects of the central quaternary carbon. This substitution pattern often favors intramolecular reactions as a result of conformational effects. 

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