the molecular dynamics (md) simulation method is used to assess structural details for humanprion protein (hereafter prpn) and its asp178 asn mutant (hereafter prpm) which causes fatalfamilial insomnia disease. the results reveal that the flexibility and instability increase in prpmcould be related to specific amino acids exposed to the solvent. solvation free energy of prpm is 20kjmot1nni2 mor...

A coherent framework is presented for determining the free energy change accompanying ligand binding to protein receptors. The most important new feature of the method is the contribution of the flexibility of the free ligand, and hence its conformational change on binding, to the free energy. Flexibility introduces two additional terms in the free energy difference: the internal energy differe...

some of the adamantane properties were calculated in this study. chemical shift, free energy ofsolvation, free energy of cavity formation, henry's law constant, and other properties ofadamantane in dry phase, three solvents and three temperatures have been calculated with abinitio method base on density functional theory (dft) at b3lyp/6-31g, b31yp/6-31g*, b3lyp/6-31+g* and b3lyp/6-31++g** leve...

this study is about complexes of li doped silicon carbide nanotube with thymine and cytosine ingas phase and aqueous solutions. li doped silicon carbide nanotube and its pyrimidine nucleobasecompounds were first modeled by quantum mechanical calculations in gas phase and in water.calculated binding energies indicated the stronger ability of thymine to functionalize silicon carbidenanotube than ...

Solvation free energy is a fundamental thermodynamic quantity that should be determined to estimate various physicochemical properties of a molecule and the desolvation cost for its binding to macromolecular receptors. Here, we propose a new solvation free energy function through the improvement of the solvent-contact model, and test its applicability in estimating the solvation free energies o...

The molecular dynamics (MD) simulation method is used to assess structural details for humanprion protein (hereafter PrPN) and its Asp178 Asn mutant (hereafter PrPm) which causes fatalfamilial insomnia disease. The results reveal that the flexibility and instability increase in PrPmcould be related to specific amino acids exposed to the solvent. Solvation free energy of PrPm is 20kjmot1nni2 mor...

Estimating protein-protein interaction energies is a very challenging task for current simulation protocols. Here, absolute binding free energies are reported for the complex H-Ras/C-Raf1 using the MM-PB(GB)SA approach, testing the internal consistency and model dependence of the results. Averaging gas-phase energies (MM), solvation free energies as determined by Generalized Born models (GB/SA)...

Accurate experimental values for the free energies of hydration, or the free energies of solvation, of the H+, OH-, and H3O ions are of fundamental importance. By use of the most accurate value for the free energy of solvation of H+, the known value for the free energy of solvation of water, and the known values for the gas phase and aqueous phase deprotonation of water, the corresponding exper...

Computation of the solvation free energy for chemical and biological processes has long been of significant interest. The key challenges to effective solvation modeling center on the choice of potential function and configurational sampling. Herein, an energy sampling approach termed the “Movable Type” (MT) method, and a statistical energy function for solvation modeling, “Knowledge-based and E...

This work introduces a model, solvation model 6 with temperature dependence (SM6T), to predict the temperature dependence of aqueous free energies of solvation for compounds containing H, C, and O in the range 273-373 K. In particular, we extend solvation model 6 (SM6), which was previously developed (Kelly, C. P.; Cramer, C. J.; Truhlar, D. G. J. Chem. Theory Comput. 2005, 1, 1133) for predict...