نتایج جستجو برای: solvation force
تعداد نتایج: 193555 فیلتر نتایج به سال:
Solvation in 1-ethyl-3-methylmidazolium chloride and in 1-ethyl-3-methylimidazolium hexafluorophosphate near equilibrium is investigated via molecular dynamics computer simulations with diatomic and benzenelike molecules employed as probe solutes. It is found that electrostriction plays an important role in both solvation structure and free energetics. The angular and radial distributions of ca...
We present a method called MOPED for optimizing energetic and structural parameters in computational models, including all-atom energy functions, when native structures and decoys are given. The present method goes beyond previous approaches in treating energy functions that are nonlinear in the parameters and continuous in the degrees of freedom. We illustrate the method by improving solvation...
A historical perspective on the application of molecular dynamics (MD) to biological macromolecules is presented. Recent developments combining state-of-the-art force fields with continuum solvation calculations have allowed us to reach the fourth era of MD applications in which one can often derive both accurate structure and accurate relative free energies from molecular dynamics trajectories...
Using grand-canonical molecular dynamics simulations and free energy calculations of spherical molecular confined films, we investigate the internal energy and entropic origins of density layering and solvation force oscillations. We show that these properties, as well as diffusion and rheological characteristics of such films, depend on interfacial commensurability, with commensurate films exh...
The acidity constants (pKa) of thirty four (34) ;-substituted carboxylic acids in aqueous solution havebeen calculated using conductor-like polarizable continuum (C-PCM) solvation model. The gasphaseenergies at the Density Functional Theory (DFT-MPW1PW91) and solvation energies atHartree Fock (HF) are combined to estimate the pKa values which are very close to the experimentalvalues where, and ...
We have studied the potential of mean force of two peptides, one known to adopt a -hairpin and the other an -helical conformation in solution. These peptides are, respectively, residues 41–56 of the C-terminus (GEWTYDDATKTFTVTE) of the B1 domain of protein G and the 13 residue C-peptide (KETAAAKFERQHM) of ribonuclease A. Extensive canonical ensemble sampling has been performedusing aparallel re...
We employ quantum mechanical/molecular mechanical umbrella sampling simulations to probe the free energy surfaces of a series of increasingly complex reaction models of RNA 2'-O-transesterification in aqueous solution under alkaline conditions. Such models are valuable for understanding the uncatalyzed processes underlying catalytic cleavage of the phosphodiester backbone of RNA, a reaction of ...
The propensity of amyloid-β (Aβ) peptide to self-assemble into highly ordered amyloid structures lies at the core of their accumulation in the brain during Alzheimer's disease. By using all-atom explicit solvent replica exchange molecular dynamics simulations, we elucidated at the atomic level the intrinsic determinants of the pH-dependent dimerization of the central hydrophobic segment Aβ(12-2...
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