In this article, we develop goal-oriented error indicators to drive adaptive refinement algorithms for the Poisson-Boltzmann equation. Empirical results for the solvation free energy linear functional demonstrate that goal-oriented indicators are not sufficient on their own to lead to a superior refinement algorithm. To remedy this, we propose a problem-specific marking strategy using the solva...

Simplified models and empirical potentials are being increasingly used for the analysis of proteins, frequently augmenting or replacing molecular mechanics approaches. Recent folding simulations have employed potentials that, in addition to terms assuring proper polypeptide geometry, include only two noncovalent effects-hydrogen bonding and hydrophobicity, with extremely simple approximations t...

A validation based on solvation energies (vacuum to water transfer) is not sufficient to justify the use of approximated models of electrostatics to rank ligand/protein complexes. A full validation should be based on energies in solution, i.e., solvation plus vacuum Coulomb energies, because of the anticorrelation between solvation and vacuum energies. The energy in solution is the relevant qua...

Quantum mechanical calculations of different energies components of 1,10-phenanthroline in ground state were carried out by DFT method , in isolated state and in various solvents to study the effects of solvents on various energy components and global properties. The solvation energy, chemical potential, hardness, electrophilicity of 1,10-phenanthroline were calculated with the help of computed...

We present a new methodology for computing solvation free energy, which is based upon the reference interaction site model (RISM)/hypernetted chain (HNC) solvation free energy expression, but which substitutes radial distribution functions taken from simulations for those calculated by simultaneous solution of the RISM and HNC equations. Consequently, solvation free energy can be obtained from ...

Using a conception given in [1, 3] for single ionic solvation and redox reactions the electron affinities (EA) of halogens are calculated from calorimetric data of their reactions with methyleneblue radical giving the values 8.81 eV; 8.23 eV; and 7.16 eV for Cl, Br and I, respectively. For iodine EA is also obtained from the reaction enthalpy of the reaction between iodide and Mg-porphyrine cat...

Knowing the structure of proteins is an essential step in developing new medicines. This is a very time consuming and expensive process. Researchers from many different areas are trying to find new and efficient ways to discovery protein structures. This is known as the Protein Structure Prediction (PSP) problem and it is divided into experimental and in silico methods [3]. In this work, we use...

Does aqueous solvent discriminate among peptide conformers? To address this question, we computed the solvation free energy of a blocked, 12-residue polyalanyl-peptide in explicit water and analyzed its solvent structure. The peptide was modeled in each of 4 conformers: alpha-helix, antiparallel beta-strand, parallel beta-strand, and polyproline II helix (P(II)). Monte Carlo simulations in the ...

This paper applies the Bayesian Model Averaging statistical ensemble technique to estimate small molecule solvation free energies. There is a wide range of methods available for predicting solvation free energies, ranging from empirical statistical models to ab initio quantum mechanical approaches. Each of these methods is based on a set of conceptual assumptions that can affect predictive accu...

The H-bond inventory approach is used commonly to interpret data involving changes in the number or types of protein hydrogen bonds. I point out here that this approach gives an incorrect answer either for the standard free energy or enthalpy of the reaction between simple amides and water. On the other hand, an electrostatic solvation approach fits almost within error the polar solvation free ...