نتایج جستجو برای: linear solvation energy relationship lser
تعداد نتایج: 1618683 فیلتر نتایج به سال:
A variety of analytical and computational models have been proposed to answer the question of why some protein structures are more ‘‘designable’’ ~i.e., have more sequences folding into them! than others. One class of analytical and statistical-mechanical models has approached the designability problem from a thermodynamic viewpoint. These models highlighted specific structural features importa...
An algorithm is developed for performing calculations for the nonlocal electrostatic solvation theory of an ion in a cavity, accounting for electrostatic boundary conditions. The latter implies an induced charge distribution on the cavity surface as well as an induced volume charge distribution in the medium. This approach is validated by a variational derivation which also provides a general e...
RNA cleavage transesterification is of fundamental reaction in biology that is catalyzed by both protein and RNA enzymes. In this work, a series of RNA transesterification model reactions with a wide range of leaving groups are investigated with density-functional calculations in an aqueous solvation environment in order to study linear free energy relationships (LFERs) and their connection to ...
The linear pentapeptide, Ala-Tyr-cis-Pro-Tyr-Asp-NMA (AYPYD) is known to have a significant population of type VI turn conformers in aqueous solvent. We have carried out theoretical studies of the conformational energetics of this peptide using a potential of mean force (PMF) consisting of the AMBER/OPLS empirical potential energy function, a macroscopic electrostatic model of polar solvation, ...
A nonlocal continuum theory of solvation is applied using an oscillating dielectric function with spatial dispersion. It is found that a convergent solution cannot be calculated using a model of a fixed solute cavity inside the solvent continuum. This is attributed to the fact that the dielectric oscillations appear as a result of coupling between polarization and density fluctuations, contradi...
We analyze de ciencies of commonly used Coulomb approximations in Generalized Born solvation energy calculation models and report a development of a new fast surface-based method (FSBE) for numerical calculations of the solvation energy of biomolecules with charged groups. The procedure is only a few percents wrong for molecular con gurations of arbitrary sizes, provides explicit values for the...
Thermochemical cycles that involve pKa, gas-phase acidities, aqueous solvation free energies of neutral species, and gas-phase clustering free energies have been used with the cluster pair approximation to determine the absolute aqueous solvation free energy of the proton. The best value obtained in this work is in good agreement with the value reported by Tissandier et al. (Tissandier, M. D.; ...
The division of thermodynamic solvation free energies of electrolytes into contributions from individual ionic constituents is conventionally accomplished by using the single-ion solvation free energy of one reference ion, conventionally the proton, to set the single-ion scales. Thus, the determination of the free energy of solvation of the proton in various solvents is a fundamental issue of c...
Differential geometry (DG) based solvation models are a new class of variational implicit solvent approaches that are able to avoid unphysical solvent-solute boundary definitions and associated geometric singularities, and dynamically couple polar and non-polar interactions in a self-consistent framework. Our earlier study indicates that DG based non-polar solvation model outperforms other meth...
A dielectric continuum theory for the solvation of a polar molecule in a polar, polarizable solvent is tested using computer simulations of formaldehyde in water. Many classes of experiments, for example those which measure solvent-shifted vertical transition energies or electron transfer rates, require an explicit consideration of the solvent electronic polarization. Due to the computational c...
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