Individual degrees of freedom and the solvation properties of water

Using molecular dynamics simulations in conjunction with home-developed Split Integration Symplectic Method we effectively decouple individual degrees of freedom of water molecules and connect them to corresponding thermostats. In this way, we facilitate elucidation of structural, dynamical, spectral, and hydration properties of bulk water at any given combination of rotational, translational, and vibrational temperatures. Elevated rotational temperature of the water medium is found to severely hinder hydration of polar molecules, to affect hydration of ionic species in a nonmonotonous way and to somewhat improve hydration of nonpolar species. As proteins consist of charged, polar, and nonpolar amino-acid residues, the developed methodology is also applied to critically evaluate the hypothesis that the overall decrease in protein hydration and the change in the subtle balance between hydration of various types of amino-acid residues provide a plausible physical mechanism through which microwaves enhance aberrant protein folding and aggregation.     

Structural properties of liquid water

Monte Carlo simulations of molecular configurations of liquid water in theNVT-ensemble atT=298 K using unit cells containing 125 and 1000 molecules were, carried out. Comparison of experimental and calculated radial distribution functions suggests the existence of two types of spatial ordering in water. Structural properties of low-energy molecular clusters and associates of closed cycles of H-bonds were determined. The properties of the network of H-bonds can be described by a set of fundamental constants and one free parameter,viz., the probability of bond formation. The existence of long-range correlations in spatial arrangement of both the molecules and the cycles of bonds was established. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 5, pp. 841–851, May, 1999.     

Structural and dynamic features of water and amorphous ice

Structural properties and microscopic dynamics of water and amorphous ice have been studied by the molecular dynamics method. It has been found that the distribution function of the tetrahedricity parameter exhibits two ranges, which correspond to local molecular formations with low and high degrees of tetrahedricity. The number of molecular clusters with a high degree of tetrahedricity grows as temperature decreases. It has been shown that the vibrational density of states comprises two vibrational modes. A low-frequency vibrational mode strongly depends on pressure and is almost independent of temperature, while a high-frequency mode is relevant to the pressure-independent heat motion of molecules. The geometric criterion of hydrogen bonds has been used to evaluate their continuous lifetime as depending on temperature for molecules with different coordination values. The average lifetime of a hydrogen bond substantially depends on the coordination of molecules, with the temperature dependence of the coordination obeying the activation dynamics.     

Thermodynamic anomalies in a lattice model of water: solvation properties

We investigate a lattice-fluid model of water, defined on a three-dimensional body-centered-cubic lattice. Model molecules possess a tetrahedral symmetry, with four equivalent bonding arms. The model is similar to the one proposed by Roberts and Debenedetti [J. Chem. Phys. 105, 658 (1996)], simplified by removing distinction between "donors" and "acceptors." We focus on the solvation properties, mainly as far as an ideally inert (hydrophobic) solute is concerned. As in our previous analysis, devoted to neat water [J. Chem. Phys. 121, 11856 (2004)], we make use of a generalized first-order approximation on a tetrahedral cluster. We show that the model exhibits quite a coherent picture of water thermodynamics, reproducing qualitatively several anomalous properties observed both in pure water and in solutions of hydrophobic solutes. As far as supercooled liquid water is concerned, the model is consistent with the second critical-point scenario.     

An inflection point in the solvation number around Sm3+ in the mixed system of methanol and water

The stability constants (β₁) of the monofluoro complex of Sm(III) have been determined in mixed solvents of methanol and water at a 0.10 mol·dm⁻³ ionic strength using the solvent extraction technique. The values of lnβ₁ increase as the mole fraction of methanol (X _s) in the mixed solvent system increases. The variation in the stability constants can be correlated with both the large effect due to the solvation of F⁻ and the small effect due to both (1) the solvation of cations in connection with the complexation of SmF²⁺ and (2) the electrostatic attraction of Sm³⁺−F⁻. Based on the variation in the sum of (1) and (2) in H₂O and the mixed solvent solutions, it was determined that the coordination number (CN) of Sm(III) varied from a mixture of CN=9 and 8 to CN=8 for about a 0.06 mole fraction of methanol (X _s) in the mixed solvent. TheX _s value of the inflection point of the CN for Sm(III) is slightly higher thanX _s=0.03 for Eu(III) previously determined by us.     

Structural and dynamic properties of the polyanionic hydrides SrAlGeH and BaAlGeH

The quaternary aluminium hydrides SrAlGeH and BaAlGeH were synthesized from either hydrogenating the intermetallic AlB₂-type precursors SrAlGe and BaAlGe or reacting SrH₂ with a mixture of Al and Ge in the presence of pressurized hydrogen. Their structures were characterized by X-ray and neutron powder diffraction of the corresponding deuterides. The compounds crystallize with the trigonal SrAlSiH structure type (space group P3m1, Z = 1, a = 4.2435(2) and 4.3450(2) Å, c = 4.9710(3) and 5.2130(4) Å for SrAlGeH and BaAlGeH, respectively) and feature a two-dimensional polyanion [AlGeH]²⁻ which represents a corrugated hexagon layer built from three-bonded Al and Ge atoms. H is terminally attached to Al. Polyanions [AlGeH]²⁻ are electron precise and, according to electronic structure calculations, the quaternary hydrides display band gaps with sizes between 0.7 and 0.8 eV. Infrared and inelastic neutron scattering spectroscopy show Al–H stretching and bending mode frequencies at around 1250 and 870 cm⁻¹, respectively. SrAlGeH and BaAlGeH are thermally stable up to at least 500 °C. When exposed to air the hydrides decompose rapidly to amorphous, orange colored materials.     

Prediction of the solvation and structural properties of ionic liquids in water by two-dimensional correlation spectroscopy

Two-dimensional vibrational spectroscopy is applied to investigate the dilution process of 1-ethyl-3-methyl-imidazolium tetrafluoroborate ([Emim][BF4]) in water. With increasing water content in ionic liquid (IL)/water mixtures, the C-H stretching vibration of the imidazolium cation showed systematic blue-shifts, which reflect the weakening of the cohesion between the cation and anion of ILs. The two-dimensional IR results reveal that the ILs sense quite different environments during the whole dilution process. First, the three-dimensional network structure of pure ILs was destroyed gradually into ionic clusters, then the clusters were further dissociated into ionic pairs surrounded by water molecules, and finally the latter became the dominant form in bulk water. Within the concentration range we investigated (0.02相似文献   

Predicting conformations and orientations of guests within a water soluble host: a molecular docking approach

In this study we have examined conformations and orientations of guests within a water-soluble host known by the trivial name Octa Acid (OA). Docking program Vina, which was originally developed for screening drug-like molecules, has been used to identify binding modes and affinities of select guest molecules with OA. Hydrophobic guests were encapsulated into the nonpolar cavity of OA capsule owing to solvophobic interactions. Amphiphilic guests were bound by keeping the nonpolar part within the cavity of OA, while pointing the polar anionic group out of the cavity. All these results obtained from the docking study were in accord with experimental findings. The post-complexation attributes of the guests were regulated by available free space and the specific interactions between guest–OA pair, which led to unusual conformations and orientations. This study showed that scoring function available with Vina, which was derived from protein–ligand data set, could successfully predict post-complexed structural features of guests within OA, thus opening opportunities to modulate physical and chemical behavior of guest molecules.     

Structural and atoms-in-molecules analysis of hydrogen-bond network around nitroxides in liquid water

In this study, we investigated the hydrogen-bond network patterns involving the NO moieties of five small nitroxides in liquid water by analyzing nanosecond scale molecular dynamics trajectories. To this end, we implemented two types of hydrogen-bond definitions, based on electronic structure, using Bader's atoms-in-molecules analysis and based on geometric criteria. In each definition framework, the nitroxide/water hydrogen-bond networks appear very variable from a nitroxide to another. Moreover, each definition clearly leads to a different picture of nitroxide hydration. For instance, the electronic structure-based definition predicts a number of hydrogen bonds around the nitroxide NO moiety usually larger than geometric structure-based ones. One particularly interesting result is that the strength of a nitroxide/water hydrogen bond does not depend on its linearity, leading us to question the relevance of geometric definition based on angular cutoffs to study this type of hydrogen bond. Moreover, none of the hydrogen-bond definitions we consider in the present study is able to quantitatively correlate the strength of nitroxide/water hydrogen-bond networks with the aqueous nitroxide spin properties. This clearly exhibits that the hydrogen-bonding concept is not reliable enough to draw quantitative conclusions concerning such properties.     

Determination of synthetic polypeptide conformations and molecular geometrical parameters by nonaqueous CE

The aim of this work was to study changes in homopolypeptide chain conformation as a function of the number of residues by the modeling of the electrophoretic mobility. For this purpose, the frictional coefficients of poly(N(epsilon)-trifluoroacetyl-L-lysine) with different number of residues (up to 11) were determined from the absolute ionic mobilities and modeled by the hydrodynamic frictional coefficient of an equivalent cylinder. This approach allowed determination of geometrical parameters of the polypeptide chain in a liquid phase (nonaqueous solution of the BGE). The fact that the BGE and analyte are dissolved in mixed (methanol-ACN) organic solvent implied to take into account different effects and corrections that are generally not considered in aqueous solvent: namely, the effect of ion-pairs between constituents of the BGE for the calculation of the ionic strength, the effect of ion-pairs between the solutes and the electrolyte counterions and the correction due to the dielectric friction (Hubbard-Onsager equations). In addition, the influence of the ionic strength on the electrophoretic mobility was corrected using the Pitts equation, and the effect of lateral charges due to a slight deprotonation of the -NH- group in the lateral chain was also considered. From this modeling, molecular geometrical parameters relative to the linear and helico?dal conformations were obtained with very good correlation coefficients. Interestingly, this work also points out that the use of ionic mobility modeling for extracting molecular geometrical parameters can also be applied to end-charged polypeptides with slightly charged lateral chains (3% of elementary charge per residue).     

On the van der Waals interactions and the stability of polypeptide chains in helical conformations

In this work, we aim to investigate the contribution of van der Waals (vdW) interactions to the stability of polypeptides in helical conformations studying infinitely long chains of alanine and glycine with density functional theory. To account for vdW interactions, we have used the interatomic pairwise dispersion approach proposed by Tkatchenko–Scheffler (TS), the TS approach with self‐consistent screening (SCS) that self‐consistently includes long‐range electrostatic effects (TS + SCS), the D2 and D3 methods of Grimme et al., and the Langreth–Lundqvist procedure that treats nonlocally the correlation part of the approximation to the exchange‐correlation (xc) functional (called DF). First, we have tested the performance of these strategies studying a set of representative hydrogen bonded dimers. Next, we have studied polyalanine and polyglicine in π‐helix, α‐helix, ‐helix, 2₇, and polyproline‐II conformations and in a fully extended structure. We have found that the DF methodology in combination with a modified version for the Becke approximation to the exchange (optB86b), the D2, D3, TS, and TS + SCS strategies in combination with the Perdew–Burke–Ernzerhof approximation to the xc functional, describe fairly well dimer association energies. Furthermore, the DF method and the D2, D3, TS, and TS + SCS strategies predict very similar helical stabilities even though the approximation used in DF for describing the long‐range dispersion interactions is different that the one used in D2/D3 and TS/TS + SCS. We found that the stability doubles for π and α helices if vdW interactions are taken into account. © 2015 Wiley Periodicals, Inc.     

A simple model of solvation within the molecular orbital theory

A simple model of solvation within the molecular orbital method is proposed whereby the effect of solvent molecules is simulated by the inclusion of fractional point charges at the solvent atomic centers. The method is applied to three solvation problems: the hydration of Li⁺ and F^? and the solvation effect on the interaction between NH₃ and HF. The results of the first two calculations indicate that the point charge model is capable of reliably predicting solvation energies. The calculations for H₃N···HF demonstrate that the hydration has a profound effect on the potential energy surface favoring a proton transfer structure H₃NH⁺···F^?.     

Theoretical studies on the conformations and properties of phenylazonaphthalenes

The conformations of phenylazo‐2‐naphthalene (I) and phenylazo‐1‐naphthalene (II) have been studied using ab initio methods and density functional theory. The rotational potential energy surfaces about the C N bonds were calculated for both the trans and the cis forms at the PM3 and HF/STO‐3G levels. The PM3 method was found to be incapable for locating the energy minima correctly. The geometries of rotamers obtained from the HF/STO‐3G surface were fully optimized at the HF/6‐31G* and B3LYP/6‐31G* levels. Single‐point MP2/6‐31G* calculations have also been carried out at the HF/6‐31G* geometries. The vibrational spectra, standard thermodynamic functions, heats of formation, and equilibrium molar fractions have been obtained. According to the calculated results, I is comparatively more stable than II. The trans forms have much lower energies than the cis forms, implying that I and II mainly exist in the trans planar forms. The energy gap (ΔE) between the frontier molecular orbitals (MOs) of the cis forms are about 0.7 eV higher than those of the trans ones, indicating that change in geometry from trans to cis form will cause a hypsochromic effect. © 2000 John Wiley & Sons, Inc. Int J Quant Chem 79: 25–33, 2000     

Structural properties of nonionic cyclodextrin colloids in water

The amphiphilic character in water of a novel class of chemically modified cyclodextrins has been investigated by means of small-angle X-ray scattering and light scattering. The introduction ofhydrophilic oligo(ethylene glycol) onto the secondary side of heptakis[6-alkylthio-6-deoxy-2-oligo(ethylene glycol)]-beta-cyclodextrins produces an enhanced water solubility of these molecules. Shape and dimensions of the generated micellar aggregates, analyzed in terms of a suitable core-shell model, remain stable in the wide concentration range explored. The highly associative behavior of these macromolecules is evidenced by the very low value of the critical micelle concentration (cmc), which is about 2 orders of magnitude smaller than the cmc usually obtained for traditional surfactant. Despite the complex geometry of this novel macromolecule, shape and dimensions of generated micellar aggregates can be properly described according to the thermodynamic approaches generally used for amphiphilic molecules and block copolymers. Results show how the modulation of hydrophobic and hydrophilic components sensitively influence the structural features of the generated aggregates thus offering the possibility to control molecular organization in a manner similar to that for traditional colloids. For all the classes of the investigated systems, the small micelles have been found in equilibrium with polydisperse large aggregates of entangled micelles. These novel nonionic colloidal systems combine inclusion and transport properties of host macrocycles, such as cyclodextrin, together with the increased stability of colloidal aggregates, and may be of interest for their potential application as innovative drug delivery systems.     

Spectral properties and conformations of nonlinear ketocyanines

The electronic transitions in molecules of the ketocyanine dyes (polyenic ω,ω′-bisamino ketones) were calculated by quantum chemical methods. Satisfactory agreement was obtained between the experimental bands of the S-S absorption spectra and calculated electronic transitions for the ketocyanine with the central pyranone moiety and the corresponding salt assuming an acute angle between the chromophores and for the ketocyanine with the central pyridone moiety assuming an obtuse angle between the chromophores. Such molecular conformations were confirmed by the gNOESY ¹H NMR data for these dyes. The difference in the conformations of the dyes with the pyranone and pyridone moieties is due, most likely, to steric hindrance created by the central methyl groups in the molecules of the latter. The salts corresponding to these dyes have similar conformational differences. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 10, pp. 1954–1958, October, 2007.     

Structural properties and state of the surface layer of zirconium dioxide modified by tungstate anions

A tetragonal metastable phase of zirconium dioxide formed after the addition of tungstate anions (>13 mol %) to the hydroxide precursor by different methods with heating (600–700°C), as revealed by X-ray diffraction analysis and X-ray photoelectron and IR spectroscopy. The W⁶⁺ and W⁵⁺ cations formed a solid solution with ZrO₂. On the surface of the solid solution, the tungsten cations formed tungstate clusters (?WO _x ?)n. The formation of the WO₃ phase was observed at concentrations of tungstate anions higher than 17.6 mol % or at temperatures of 850–870°C.