Equivalent potential of water for electronic structure of asparagine

The equivalent potential of water for the electronic structure of asparagine(Asn) is constructed by using the first‐principles, all‐electron, ab initio calculation. The process is composed of three steps. The first step is to determine the geometric structure of Asn+nH₂O system with a minimum energy. The second step is to calculate the electronic structure of Asn with the potential of water molecules by using the self‐consistent cluster‐embedding (SCCE) method, based on the result obtained in the first step. The last step is to calculate the electronic structure of Asn with the potential of dipole after replacing water molecules with dipoles. The results show that the major effect of water molecules on Asn' electronic structure be raising the occupied electronic states by 0.034 Ry on average and narrowing energy gap by 0.91%. The effect of water on the electronic structure of Asn can be well simulated by using dipole potential. The obtained equivalent potential can be applied directly to the electronic structure calculation of protein in solution by using the SCCE method. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010     

Equivalent potential of water molecules for electronic structure of glutamic acid

The fundamental importance of the electronic structure of molecules is widely recognized. To get reliable electronic structure of protein in aqueous solution, it is necessary to construct a simple, easy-use equivalent potential of water molecules for protein's electronic structure calculation. Here, the first-principles, all-electron, ab initio calculations have been performed to construct the equivalent potential of water molecules for the electronic structure of glutamic acid, which is a hydrophilic amino acid and is negatively charged (Glu(-)) in neutral water solution. The main process of calculation consists of three steps. Firstly, the geometric structure of the cluster containing Glu(-) and water molecules is calculated by free cluster calculation. Then, based on the geometric structure, the electronic structure of Glu(-) with the potential of water molecules is calculated using the self-consistent cluster-embedding method. Finally, the electronic structure of Glu(-) with the potential of dipoles is calculated. Our calculations show that the major effect of water molecules on Glu(-)'s electronic structure is lowering the occupied electronic states by about 0.017 Ry, and broadening energy gap by 12%. The effect of water molecules on the electronic structure of Glu(-) can be well simulated by dipoles potential.     

A Computer Simulation of the Electronic Structure of Leucine in Aqueous Solution

In order to obtain the electronic structure of leucine (Leu) in aqueous solution, we studied three systems: Leu+7H₂O, Leu+8H₂O and Leu+9H₂O. The results indicated that the system Leu+8H₂O was the only choice which was both acceptable and doable: its computational effort was affordable, and it could simulate a main part of the solvent effect on the electronic structure of Leu in solution. Based on the system Leu+8H₂O, all-electron, ab initio calculations were performed to construct an equivalent potential of water for the electronic structure of Leu with dipoles. The results showed that the main effect of water on the electronic structure of Leu was raising the occupied states about 0.0824 Ry on average, and broadening the energy gap by 11%. The water effect on the electronic structure of Leu could be well simulated by the dipole potential. The obtained equivalent potential can be applied directly to the electronic structure calculation of proteins in solution.     

Liquid structure of benzene and its derivatives as studied by means of X-ray scattering

The liquid structures of benzene, toluene, aniline, benzaldehyde and nitrobenzene were investigated by the X-ray scattering method. The X-ray scattering data were analysed by a method without constructing any structure models. The obtained liquid structure of benzene is different from the previous X-ray scattering results which were derived from the quasi-lattice structure for the liquid based on the crystal structure of benzene. This is because a molecular arrangement which is not found in the crystal structure is left out of consideration. In liquid toluene, benzaldehyde and nitrobenzene, two molecules are associated with the dipole–dipole interaction in the antiparallel fashion. Two aniline molecules are hydrogen-bonded in liquid aniline. The third molecule weakly interacts with the other two in liquid toluene, aniline and benzaldehyde. In liquid nitrobenzene, the parallel dipole–dipole interaction of the third molecule with another one is present in the coplanar form. The substituent effect on the liquid structures is discussed.     

The equivalent potential of water for electronic structure of aspartic acid

The equivalent potential of water for the electronic structure of aspartic acid (Asp(-)) in solution is constructed by the first-principles, all-electrons, ab initio calculations. Aspartic acid is a hydrophilic amino acid which is negatively charged in neutral water solution. The main process of calculation consists of three steps. Firstly, the geometric structure of the cluster containing Asp(-) and water molecules is calculated by the free cluster calculation. Then, based on the obtained geometric structure, the electronic structure of Asp(-) with the potential of water molecules is calculated using the self-consistent cluster-embedding method. Finally, the electronic structure of Asp(-) with the potential of dipoles is calculated. The results show that the major effect of water on Asp(-)'s electronic structure is lowering the occupied molecular orbitals by about 0.02 Ry on average, and narrowing energy gap by 10.8%. The effect of water on the electronic structure of Asp(-) can be simulated by dipoles potential.     

Importance of the single amino acid potential in water for secondary and tertiary structures of proteins

The structure of a protein molecule is considered to be primarily determined by the inter-amino-acid nonbonded interactions, such as hydrogen bonds. However, the conformational space of the polypeptide chain should be simultaneously restricted by the intrinsic conformational preferences of the individual amino acids. We present here precise single amino acid potential (SAAP) surfaces for glycine (For-Gly-NH(2)) and alanine (For-Ala-NH(2)) in water (epsilon = 78.39) and ether (epsilon = 4.335), which were calculated at the HF/6-31+G(d,p) level applying the self-consistent isodensity polarizable continuum model (SCIPCM) reaction field with geometry optimization in the corresponding solvents. The obtained Ramachandran potential surfaces in water showed distinct potential wells in the alpha- and beta-regions. The profiles were in almost perfect agreement with the Ramachandran plots of glycine and alanine residues in folded proteins, suggesting the Boltzmann distributions on the SAAP surfaces. Molecular simulations of polyalanines (For-Ala(n)-NH(2); n = 3-5) by using the SAAP force field equipped with the SCIPCM potentials revealed that the polyalanines readily form 3(10)-helical structures in water but not in vacuo. In ether (hydrophobic environments), the helical structures were relatively stable, but the most stable structure was assigned to a different one. These results indicated that the intrinsic conformational preferences of the individual amino acids (i.e., the SAAPs) in water are of significant importance not only for describing conformations of a polypeptide chain in the random coil state but also for understanding the folding to the secondary and tertiary structures.     

A new model for predicting activity coefficients in aqueous solutions of amino acids and peptides

A new two-parameter model based on the perturbation of a hard-sphere reference has been developed to correlate the activity coefficients of several amino acids and simple peptides in aqueous solutions. The hard-sphere equation of state used as the reference in the model was proposed recently by Ghotbi and Vera. The perturbation terms coupled with the reference hard-sphere equation of state are attributed to the dispersion forces and the dipole–dipole interactions. The Lennard-Jones and Keesom potential functions are used to represent the dispersion and dipole–dipole interactions, respectively. The results of the new model are compared with those obtained by other models. It is shown that the new model can more accurately correlate the activity coefficients of amino acids and peptides in comparison with the other available models in the literature. The model was also used to correlate the solubility of several amino acids in aqueous solutions. The results show that the model can accurately correlate the solubility of the experimental data over a wide range of temperatures with only two adjustable parameters. New values for Gibbs free energy change, Δg, and enthalpy change, Δh, of the solute, i.e., amino acid for transferring one mole of solute from a saturated solution to a hypothetical aqueous solution with an activity of one molal at temperature 298.15 K are also reported.     

Soft sticky dipole-quadrupole-octupole potential energy function for liquid water: an approximate moment expansion

A new, efficient potential energy function for liquid water is presented here. The new model, which is referred here as the soft sticky dipole-quadrupole-octupole (SSDQO) model, describes a water molecule as a Lennard-Jones sphere with point dipole, quadrupole, and octupole moments. It is a single-point model and resembles the hard-sphere sticky dipole potential model for water by Bratko et al. [J. Chem. Phys. 83, 6367 (1985)] and the soft sticky dipole model by Ichiye and Liu [J. Phys. Chem. 100, 2723 (1996)] except now the sticky potential consists of an approximate moment expansion for the dimer interaction potential, which is much faster than the true moment expansion. The object here is to demonstrate that the SSDQO potential energy function can accurately mimic the potential energy function of a multipoint model using the moments of that model. First, the SSDQO potential energy function using the dipole, quadruple, and octupole moments from SPC/E, TIP3P, or TIP5P is shown to reproduce the dimer potential energy functions of the respective multipoint model. In addition, in Monte Carlo simulations of the pure liquid at room temperature, SSDQO reproduces radial distribution functions of the respective model. However, the Monte Carlo simulations using the SSDQO model are about three times faster than those using the three-point models and the long-range interactions decay faster for SSDQO (1/r(3) and faster) than for multipoint models (1/r). Moreover, the contribution of each moment to the energetics and other properties can be determined. Overall, the simplicity, efficiency, and accuracy of the SSDQO potential energy function make it potentially very useful for studies of aqueous solvation by computer simulations.     

Dielectric spectroscopy in the GHz region on fully hydrated zwitterionic amino acids

The complex dielectric permittivity of eight different amino acids in water solutions was determined in the frequency range from 0.2 to 20 GHz at room temperature, trying to span the whole range of solubility in each case. Two relaxations were observed at room temperature in this frequency range, which can be mainly assigned to the rotation of amino acids in the aqueous environment, and the reorientational motion of water molecules, respectively. Although the amino acids have a charged (zwitterionic) nature with huge dipole moments, the tendency towards dipolar alignment seems to be very weak, over the investigated concentration ranges. For these small bio-molecules, water screens solute-solute interactions and amino acids remain typically as isolated hydrated monomers. The dielectric results were used to estimate the number of water molecules restrained by each solute molecule. Finally, the comparison between the amino acid relaxation times made it possible to discuss the relationship between rotational dynamics and the structure and hydrodynamic coupling of the amino acid studied.     

Tafel Slopes in Relation to the Replacement of Adsorbed Water by Organic Molecules

Abstract

In the lecture presented by Prof. Reddy the role of water in determining the potential dependence of electrosorption of neutral organic molecules has been discussed. The process one considers is that of the replacement of a number of water molecules n by each organic molecule adsorbed. The dipole moments of the adsorbed water molecules interact with the electrical field in the double layer and hence cause a potential (or charge) dependent adsorption of the neutral organic molecule, even if the latter possesses no permanent dipole moment. The theory of this phenomenon has been worked out by Bockris, Devanathan and Muller. Corrections for lateral interactions between the adsorbed water molecules and for the permanent dipole moment of the electrosorbed neutral organic molecule have been made.^1,2     

Monolayers of Chiral Calix[4]Resorcinarenes: Surface Pressure and Surface Potential Studies

Abstract

Chiral amphiphilic C-undecylcalix[4]resorcinarenes substituted with phenylethyl group or L(-)nore-phedrine were found to form well-organized mono-layers at the aqueous solution-air interface. The substituents, L(-)norephedrine and phenylethyl group, determined the area occupied by the molecule on the water subphase. Introduction of these substituents lead also to perpendicular dipole moments of the molecules in the monolayers ca. 6 times larger than those of the parent amphiphilic calixresorcinarene, CAL11. Interactions of the compounds with K⁺ were detected by the increase of the surface potential values measured at maximum packing of the monolayer. Addition of amino acids to the subphase lead to conformational changes in the monolayers evidenced by increased surface mean molecular area of the unmodified C-undecyl-calix[4]resorcinarene. These changes were explained by the formation of hydrogen bonds with the amino acids at the expense of hydrogen bonding between the calixarene molecules in the monolayer. In contrast to unsubstituted calixresorcinarenes, interactions of the L(-)norephedrine-and phenylethyl-substituted molecules with amino acids could be easily recognized by the decrease of surface potential and dipole moment in monolayers formed by these calixarenes on subphases containing amino acids. A significant drop in the surface potential and an increased area per molecule demonstrated more specific interactions with selected amino acids: L(-)norephedrine-substituted calixarene interacted with D-valine and the phenylethyl-substituted, with D-tryptophan.     

The effect of the protein environment on the structure and charge distribution of the retinal Schiff base in bacteriorhodopsin

The effects of the amino acid side chains of the binding pocket of bacteriorhodopsin (bR) and of a water molecule on the structure of the retinal Schiff base have been studied using Becke3LYP/6-31G* level of density functional theory. A model protonated Schiff base structure including six conjugated double bonds and methyl substituents was optimized in the presence of several amino acid side chains and of a water molecule, separately. The Schiff base structure was also calculated in the form of a neutral species. At each optimized complex geometry the atomic charges of the model Schiff base were calculated using Mulliken population analysis. In agreement with previously proposed counterion(s) of the protonated retinal Schiff base in bR, the results show that Asp₈₅ and Asp₂₁₂, which are present in the form of negatively charged groups, have significantly large effects on the structure and electronic configuration of both unprotonated and protonated model Schiff bases. The presence of a water molecule in the vicinity of the Schiff base demonstrates significant effects which are comparable to those of aspartate groups. Other side chains studied did not show any significant effect in this direction. Apart from the aspartate groups and the water molecule, in none of the other complexes studied are the atomic charges and the bond alternation of the model Schiff base significantly influenced by the presence of the neighboring amino acids. Received: 24 March 1998 / Accepted: 3 September 1998 / Published online: 10 December 1998     

A DFT study on the relative affinity for oxygen of the alpha and beta subunits of hemoglobin

DFT calculations are carried out on computational models of the active center of the alpha and beta subunits of hemoglobin in both its oxygenated (R) and deoxygenated (T) states. The computational models are defined by the full heme group, including all porphyrin substituents, and the four amino acids closer to it. The role of the protein environment is introduced by freezing the position of the alpha carbon atom of each of the four amino acids to the positions they have in the available PDB structures. Oxygen affinity is then evaluated by computing the energy difference between the optimized structures of the oxygenated and deoxygenated forms of each model. The results indicate a higher affinity of the alpha subunits over the beta ones. Analysis of the computed structures points out to the strength of the hydrogen bond between the distal histidine and the oxygen molecule as a key factor in discriminating the different systems.     

Molecular models for the structure of solvent in an interphase

In view of the difficulties encountered in the discussion of interfacial solvent structure in terms of simple dipolar molecules in a small number of orientations, an attempt is made here to investigate more realistic models for this region. A new technique of searching for minimum energy configurations is developed. The results confirm that even with a more realistic point charge model of the water molecule the dipole tends to be oriented in the plane of a two-dimensional array.     

Electron correlation described by extended geminal models: The EXGEM4 and EXGEM5 models

Within the framework of the general extended geminal model, two new approximate models EXGEM 4 and EXGEM 5 are introduced. The models are tested against full CI calculations on the water molecule for three different nuclear configurations and a full CI potential energy curve for the LiH molecule in the ground state. On the basis of these calculations, it is suggested that the models will yield electronic correlation energies with an accuracy of 1–2% of the corresponding full CI result.