An efficient approach that combines the electrostatically embedded generalized molecular fractionation with conjugate caps (EE-GMFCC) method with conductor-like polarizable continuum model (CPCM), termed EE-GMFCC-CPCM, is developed for ab initio calculation of the electrostatic solvation energy of proteins. Compared with the previous MFCC-CPCM study [Y. Mei, C. G. Ji, and J. Z. H. Zhang, J. Che...

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 . The solvation energy, chemical potential, hardness, electrophilicity of 1,10-phenanthroline were calculated with the help of computed HOMO-LUMO gap of 1,1...

An empirical continuum solvation model, solvation free energy density (SFED), has been developed to calculate solvation free energies of a molecule in the most frequently used solvents. A generalized version of the SFED model, generalized-SFED (G-SFED), is proposed here to calculate molecular solvation free energies in virtually any solvent. G-SFED provides an accurate and fast generalized fram...

      In this study, the interaction between NO2+ cation and Hen (n = 1-7) clusters is investigated by means of ab initio calculations at MP2/aug-cc-pVTZ and QCISD/aug-cc-pVTZ computational levels. The first and second solvation shells were obtained while N atom of NO2+ interacts with five and two He atoms, respectively. Stabilizat...

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 general expression for the distribution of the fluctuating 2(l)-pole moment M(l) of a spherical sample of dielectric material is derived on the basis of dielectric theory combined with statistical mechanics. The formulas are compared with results from computer simulations of a weakly coupled Stockmayer fluid and the agreement is shown to be excellent. Furthermore, we calculate the size of the...

The highly anisotropic environment of the lipid bilayer membrane imposes significant constraints on the structures and functions of membrane proteins. However, NMR structure calculations typically use a simple repulsive potential that neglects the effects of solvation and electrostatics, because explicit atomic representation of the solvent and lipid molecules is computationally expensive and i...

As the field of structural genomics matures, new methods will be required that can accurately and rapidly distinguish reliable structure predictions from those that are more dubious. We present a method based on the CHARMM gas phase implicit hydrogen force field in conjunction with a generalized Born implicit solvation term that allows one to make such discrimination. We begin by analyzing pair...

Previous work describes a computational solvation model called semi-explicit assembly (SEA). The SEA water model computes the free energies of solvation of nonpolar and polar solutes in water with good efficiency and accuracy. However, SEA gives systematic errors in the solvation free energies of ions and charged solutes. Here, we describe field-SEA, an improved treatment that gives accurate so...

     In this study, the effect of the secondary structure of the protein on the acid strength of three structures of random (R), alpha helix (α) and beta sheet (b) were investigated theoretically. These structures are related to the cationic amino acids of histidine and lysine in the polypeptide chain of eight-glycine residue. Computational methods at the HF, B3LYP, X3LYP and M05-2X levels in t...