Outstanding Properties of the Hydration Shell around ß-d-Glucose: A Computational Study.

Ab initio molecular dynamics (AIMD) simulations have been performed on aqueous solutions of four simple sugars, α-d-glucose, ß-d-glucose, α-d-mannose, and α-d-galactose. Hydrogen-bonding (HB) properties, such as the number of donor- and acceptor-type HB-s, and the lengths and strengths of hydrogen bonds between sugar and water molecules, have been determined. Related electronic properties, such as the dipole moments of water molecules and partial charges of the sugar O atoms, have also been calculated. The hydrophilic and hydrophobic shells were characterized by means of spatial distribution functions. ß-d-Glucose was found to form the highest number of hydrophilic and the smallest number of hydrophobic connections to neighboring water molecules. The average sugar-water H-bond length was the shortest for ß-d-glucose, which suggests that these are the strongest such H-bonds. Furthermore, ß-d-glucose appears to stand out in terms of the symmetry properties of both its hydrophilic and hydrophobic hydration shells. In summary, in all aspects considered here, there seems to be a correlation between the distinct characteristics of ß-d-glucose reported here and its outstanding solubility in water. Admittedly, our findings represent only some of the important factors that influence the solubility.

Connecting Diffraction Experiments and Network Analysis Tools for the Study of Hydrogen-Bonded Networks.

A self-consistent scheme is presented that is applicable for revealing details of the microscopic structure of hydrogen-bonded liquids, including the description of the hydrogen-bonded network. The scheme starts with diffraction measurements, followed by molecular dynamics simulations. Computational results are compared with the experimentally accessible information on the structure, which is most frequently the total scattering structure factor. In the case of an at least semiquantitative agreement between experiment and simulation, sets of particle coordinates from the latter may be exploited for revealing nonmeasurable structural details. Calculations of some properties concerning the hydrogen-bonded network are also described, in the order of increasing complexity: starting with the definition of a hydrogen bond, first and second neighborhoods are described via spatial correlations functions. Attention is then turned to cyclic and noncyclic hydrogen-bonded clusters, before cluster size distributions and percolation are discussed. We would like to point out that, as a result of applying the novel protocol, these latter, rather abstract, quantities become consistent with diffraction data: it may thus be argued that the approach reviewed here is the first one that establishes a direct link between measurements and elements of network theories. Applications for liquid water, simple alcohols, and alcohol-water liquid mixtures demonstrate the usefulness of the aforementioned characteristics. The procedure can readily be applied to more complicated hydrogen-bonded networks, like mixtures of polyols (diols, triols, sugars, etc.) and water, and complex aqueous solutions of even larger molecules (even of proteins).

Properties of Hydrogen-Bonded Networks in Ethanol-Water Liquid Mixtures as a Function of Temperature: Diffraction Experiments and Computer Simulations.

New X-ray and neutron diffraction experiments have been performed on ethanol-water mixtures as a function of decreasing temperature, so that such diffraction data are now available over the entire composition range. Extensive molecular dynamics simulations show that the all-atom interatomic potentials applied are adequate for gaining insight into the hydrogen-bonded network structure, as well as into its changes on cooling. Various tools have been exploited for revealing details concerning hydrogen bonding, as a function of decreasing temperature and ethanol concentration, like determining the H-bond acceptor and donor sites, calculating the cluster-size distributions and cluster topologies, and computing the Laplace spectra and fractal dimensions of the networks. It is found that 5-membered hydrogen-bonded cycles are dominant up to an ethanol mole fraction xeth = 0.7 at room temperature, above which the concentrated ring structures nearly disappear. Percolation has been given special attention, so that it could be shown that at low temperatures, close to the freezing point, even the mixture with 90% ethanol (xeth = 0.9) possesses a three-dimensional (3D) percolating network. Moreover, the water subnetwork also percolates even at room temperature, with a percolation transition occurring around xeth = 0.5.

Pressure-Dependent Structure of Methanol-Water Mixtures up to 1.2 GPa: Neutron Diffraction Experiments and Molecular Dynamics Simulations.

Total scattering structure factors of per-deuterated methanol and heavy water, CD3OD and D2O, have been determined across the entire composition range as a function of pressure up to 1.2 GPa, by neutron diffraction. The largest variations due to increasing pressure were observed below a scattering variable value of 5 Å-1, mostly as shifts in terms of the positions of the first and second maxima. Molecular dynamics computer simulations, using combinations of all-atom potentials for methanol and various water force fields, were conducted at the experimental pressures with the aim of interpreting neutron diffraction results. The peak-position shifts mentioned above could be qualitatively reproduced by simulations, although in terms of peak intensities, the accord between neutron diffraction and molecular dynamics was much less satisfactory. However, bearing in mind that increasing pressure must have a profound effect on repulsive forces between neighboring molecules, the agreement between experiment and computer simulation can certainly be termed as satisfactory. In order to reveal the influence of changing pressure on local intermolecular structure in these "simplest of complex" hydrogen-bonded liquid mixtures, simulated structures were analyzed in terms of hydrogen bond-related partial radial distribution functions and size distributions of hydrogen-bonded cyclic entities. Distinct differences between pressure-dependent structures of water-rich and methanol-rich composition regions were revealed.

Chloride ions as integral parts of hydrogen bonded networks in aqueous salt solutions: the appearance of solvent separated anion pairs.

Hydrogen bonding to chloride ions has been frequently discussed over the past 5 decades. Still, the possible role of such secondary intermolecular bonding interactions in hydrogen bonded networks has not been investigated in any detail. Here we consider computer models of concentrated aqueous LiCl solutions and compute the usual hydrogen bond network characteristics, such as distributions of cluster sizes and of cyclic entities, both for models that take and do not take chloride ions into account. During the analysis of hydrogen bonded rings, a significant amount of 'solvent separated anion pairs' have been detected at high LiCl concentrations. It is demonstrated that taking halide anions into account as organic constituents of the hydrogen bonded network does make the interpretation of structural details significantly more meaningful than when considering water molecules only. Finally, we compare simulated structures generated by 'good' and 'bad' potential sets on the basis of the tools developed here, and show that this novel concept is, indeed, also helpful for distinguishing between reasonable and meaningless structural models.

Structural, rheological and dynamic aspects of hydrogen-bonding molecular liquids: Aqueous solutions of hydrotropic tert-butyl alcohol.

HYPOTHESIS: The structural details, viscosity trends and dynamic phenomena in t-butanol/water solutions are closely related on the molecular scales across the entire composition range. Utilizing the experimental small- and wide-angle x-ray scattering (SWAXS) method, molecular dynamics (MD) simulations and the 'complemented-system approach' method developed in our group it is possible to comprehensively describe the structure-viscosity-dynamics relationship in such structurally versatile hydrogen-bonded molecular liquids, as well as in similar, self-assembling systems with pronounced molecular and supramolecular structures at the intra-, inter-, and supra-molecular scales. EXPERIMENTS: The SWAXS and x-ray diffraction experiments and MD simulations were performed for aqueous t-butanol solutions at 25 °C. Literature viscosity and self-diffusion data were also used. FINDINGS: The interpretive power of the proposed scheme was demonstrated by the extensive and diverse results obtained for aqueous t-butanol solutions across the whole concentration range. Four composition ranges with qualitatively different structures and viscosity trends were revealed. The experimental and calculated zero-shear viscosities and molecular self-diffusion coefficients were successfully related to the corresponding structural details. The hydrogen bonds that were, along with hydrophobic effects, recognized as the most important driving force for the formation of t-butanol aggregates, show intriguing lifetime trends and thermodynamic properties of their formation.

Molecular Dynamics Simulation Studies of the Temperature-Dependent Structure and Dynamics of Isopropanol-Water Liquid Mixtures at Low Alcohol Content.

Series of molecular dynamics simulations for 2-propanol-water mixtures, as a function of temperature (between freezing and room temperature) and composition (xip = 0, 0.5, 0.1, and 0.2), have been performed for temperatures reported in the only available experimental structure study. It is shown that when the all-atom optimized potentials for liquid simulations interatomic potentials for the alcohol are combined with the TIP4P/2005 water model, then the near-quantitative agreement with measured X-ray data, in the reciprocal space, can be achieved. Such an agreement justifies detailed investigations of structural, energetic, and dynamic properties on the basis of simulation trajectories. Here, we focus on characteristics related to hydrogen bonds (HB): cluster-, and in particular, ring formation, energy distributions, and lifetimes of HB-s have been scrutinized for the entire system, as well as for the water and isopropanol subsystems. It is demonstrated that similar to ethanol-water mixtures, the occurrence of 5-membered-hydrogen-bonded rings are significant, particularly at higher alcohol concentrations. Concerning HB energetics, an intriguing double maximum appears on the alcohol-alcohol HB energy distribution function. HB lifetimes have been found significantly longer in the mixtures than they are in pure liquids.

Variations of the Hydrogen Bonding and Hydrogen-Bonded Network in Ethanol-Water Mixtures on Cooling.

Molecular dynamics computer simulations have been conducted for ethanol-water liquid mixtures in the water-rich side of the composition range, with 10, 20, and 30 mol % of alcohol, at temperatures between room temperature and the experimental freezing point of the given mixture. All-atom-type (optimized potential for liquid simulations) interatomic potentials have been assumed for ethanol, in combination with two kinds of rigid water models (SPC/E and TIP4P/2005). Both combinations have provided excellent reproductions of the experimental X-ray total structure factors at each temperature; this yielded a strong basis for further structural analyses. Beyond partial radial distribution functions, various descriptors of hydrogen-bonded assemblies, as well as of the hydrogen-bonded network have been determined. A clear tendency was observed toward that an increasing proportion of water molecules participate in hydrogen bonding with exactly two donor and two acceptor sites as temperature decreases. Concerning larger assemblies held together by hydrogen bonding, the main focus was put on the properties of cyclic entities: it was found that, similarly to methanol-water mixtures, the number of hydrogen-bonded rings has increased with lowering temperature. However, for ethanol-water mixtures, the dominance of 5-fold rings, and not 6-fold rings, could be observed.

Decreasing temperature enhances the formation of sixfold hydrogen bonded rings in water-rich water-methanol mixtures.

The evolution of the structure of liquid water-methanol mixtures as a function of temperature has been studied by molecular dynamics simulations, with a focus on hydrogen bonding. The combination of the OPLS-AA (all atom) potential model of methanol and the widely used SPC/E water model has provided excellent agreement with measured X-ray diffraction data over the temperature range between 298 and 213 K, for mixtures with methanol molar fractions of 0.2, 0.3 and 0.4. Hydrogen bonds (HB-s) have been identified via a combined geometric/energetic, as well as via a purely geometric definition. The number of recognizable hydrogen bonded ring structures in some cases doubles while lowering the temperature from 298 to 213 K; the number of sixfold rings increases most significantly. An evolution towards the structure of hexagonal ice, that contains only sixfold hydrogen bonded rings, has thus been detected on cooling water-methanol mixtures.

Reverse Monte Carlo modeling of liquid water with the explicit use of the SPC/E interatomic potential.

Reverse Monte Carlo (RMC) modeling of liquid water, based on one neutron and one X-ray diffraction data set, applying also the most popular interatomic potential for water, extended simple point charge (SPC/E), has been performed. The strictly rigid geometry of SPC/E water molecules had to be loosened somewhat, in order to be able to produce a good fit to both sets of experimental data. In the final particle configurations, regularly shaped water molecules and straight hydrogen bonding angles were found to be consistent with diffraction results. It has been demonstrated that the explicit use of interatomic potentials in RMC has a role to play in future structural modeling of water and aqueous solutions.

Investigation of the structure of ethanol-water mixtures by molecular dynamics simulation I: analyses concerning the hydrogen-bonded pairs.

Series of molecular dynamics simulations for ethanol-water mixtures with 20-80 mol % ethanol content, pure ethanol, and water were performed. In each mixture, for ethanol the OPLS force field was used, combined with three different water force fields, the SPC/E, the TIP4P-2005, and the SWM4-DP. Water potential models were distinguished on the basis of deviations between calculated and measured total scattering X-ray structure factors aided by ethanol-water pair binding energy comparison. No single water force field could provide the best agreement with experimental data at all concentrations: at the ethanol content of 80% the SWM-DP, for 60 mol % the SWM4-DP and the TIP4P-2005, whereas for the 40 and 20 mol % mixtures TIP4P-2005 water force field provided the closest match. Coordination numbers and hydrogen bonds/molecule values were calculated, revealing that the oxygen-oxygen first coordination numbers strongly overestimate the average number of hydrogen bonds/molecule. The center-of-molecule distributions indicate that the ethanol-ethanol first coordination sphere expands with increasing water concentration while the size of the first water-water coordination sphere does not change. Various two and three-dimensional distributions were calculated that reveal the differences between simulations with different water force fields. Detailed conformational analyses of the hydrogen-bonded pairs were performed; drawings of the characteristic molecular arrangements are provided.

The structure of PX3 (X = Cl, Br, I) molecular liquids from X-ray diffraction, molecular dynamics simulations, and reverse Monte Carlo modeling.

Synchrotron X-ray diffraction measurements have been conducted on liquid phosphorus trichloride, tribromide, and triiodide. Molecular Dynamics simulations for these molecular liquids were performed with a dual purpose: (1) to establish whether existing intermolecular potential functions can provide a picture that is consistent with diffraction data and (2) to generate reliable starting configurations for subsequent Reverse Monte Carlo modelling. Structural models (i.e., sets of coordinates of thousands of atoms) that were fully consistent with experimental diffraction information, within errors, have been prepared by means of the Reverse Monte Carlo method. Comparison with reference systems, generated by hard sphere-like Monte Carlo simulations, was also carried out to demonstrate the extent to which simple space filling effects determine the structure of the liquids (and thus, also estimating the information content of measured data). Total scattering structure factors, partial radial distribution functions and orientational correlations as a function of distances between the molecular centres have been calculated from the models. In general, more or less antiparallel arrangements of the primary molecular axes that are found to be the most favourable orientation of two neighbouring molecules. In liquid PBr3 electrostatic interactions seem to play a more important role in determining intermolecular correlations than in the other two liquids; molecular arrangements in both PCl3 and PI3 are largely driven by steric effects.

The liquid structure of tetrachloroethene: molecular dynamics simulations and reverse Monte Carlo modeling with interatomic potentials.

The liquid structure of tetrachloroethene has been investigated on the basis of measured neutron and X-ray scattering structure factors, applying molecular dynamics simulations and reverse Monte Carlo (RMC) modeling with flexible molecules and interatomic potentials. As no complete all-atom force field parameter set could be found for this planar molecule, the closest matching all-atom Optimized Potentials for Liquid Simulations (OPLS-AA) intra-molecular parameter set was improved by equilibrium bond length and angle parameters coming from electron diffraction experiments [I. L. Karle and J. Karle, J. Chem. Phys. 20, 63 (1952)]. In addition, four different intra-molecular charge distribution sets were tried, so in total, eight different molecular dynamics simulations were performed. The best parameter set was selected by calculating the mean square difference between the calculated total structure factors and the corresponding experimental data. The best parameter set proved to be the one that uses the electron diffraction based intra-molecular parameters and the charges qC = 0.1 and qCl = -0.05. The structure was further successfully refined by applying RMC computer modeling with flexible molecules that were kept together by interatomic potentials. Correlation functions concerning the orientation of molecular axes and planes were also determined. They reveal that the molecules closest to each other exclusively prefer the parallel orientation of both the molecular axes and planes. Molecules forming the first maximum of the center-center distribution have a preference for <30° and >60° axis orientation and >60° molecular plane arrangement. A second coordination sphere at ∼11 Å and a very small third one at ∼16 Å can be found as well, without preference for any axis or plane orientation.

Conformational analysis of bis(methylthio)methane and diethyl sulfide molecules in the liquid phase: reverse Monte Carlo studies using classical interatomic potential functions.

Series of flexible molecule reverse Monte Carlo calculations, using bonding and non-bonding interatomic potential functions (FMP-RMC), were performed starting from previous molecular dynamics results that had applied the OPLS-AA and EncadS force fields. During RMC modeling, the experimental x-ray total scattering structure factor was approached. The discrepancy between experimental and calculated structure factors, in comparison with the molecular dynamics results, decreased substantially in each case. The room temperature liquid structure of bis(methylthio)methane is excellently described by the FMP-RMC simulation that applied the EncadS force field parameters. The main conformer was found to be AG with 55.2%, followed by 37.2% of G(+)G(+) (G(-)G(-)) and 7.6% of AA; the stability of the G(+)G(+) (G(-)G(-)) conformer is most probably caused by the anomer effect. The liquid structure of diethyl sulfide can be best described by applying the OPLS-AA force field parameters during FMP-RMC simulation, although in this case the force field parameters were found to be not fully compatible with experimental data. Here, the two main conformers are AG (50.6%) and the AA (40%). In addition to findings on the actual real systems, a fairly detailed comparison between traditional and FMP-RMC methodology is provided.

Inter-molecular correlations in liquid Se2Br2.

The structure of molecular liquid Se2Br2 was analyzed by means of reverse Monte Carlo structural modeling, using a calculation based on high-energy x-ray diffraction data. It was found that, between the optical isomers of L and D types, the number of L-D neighboring molecular pairs increases, while that of the L-L and D-D pairs decreases with increasing temperature. From this temperature dependence and from the relaxation mode analysis of quasi-elastic neutron scattering spectra, it is reasonable to assume that the presence of L-D pairs relates to genuine inter-molecular interactions while the L-L and D-D pairs appear due to geometrical packing of the gauche-shaped molecules.

Molecular conformations and the liquid structure in bis(methylthio)methane and diethyl sulfide: diffraction experiments vs molecular dynamics simulations.

Molecular dynamics computer simulations with the OPLS-AA and EncadS all-atom force fields have been performed for liquid bis(methylthio)methane and diethyl sulfide. For bis(methylthio)methane, additional simulations using gas electron diffraction and ab initio bond length and bond angle parameters were also performed. Although there were small differences between the structures provided by the different molecular dynamics simulations of bis(methylthio)methane, the main conformer was found to be the AG one (54%), followed by the G(+)G(+) one (31%) in all the calculations. This is in contrast with gas phase electron diffraction and ab initio calculations, where the main conformer was G(+)G(+) (70%; beside that, 30% AG was assumed). For diethyl sulfide, no experimental data was present for the gas phase and the different interatomic potential sets produced different conformer ratios: applying OPLS-AA resulted in 51% AG and 40% AA, while from EncadS the main conformer was G(+)G(+), with an occurrence of 69.5% (AG was present with 29.6%). Comparing the MD calculated structure factors to results of X-ray diffraction experiments, some differences could be found at Q < 5 Å(-1) in all cases. For bis(methylthio)methane, the EncadS potential produced the X-ray structure factor with the smallest difference to the experimental one, whereas for diethyl sulfide the OPLS-AA parameter set proved to be the more successful. The EncadS force field provided a better approximation to the experimental value of the enthalpy of vaporization for bis(methylthio)methane; for diethyl sulfide, the two different force fields gave similar results.

RMC_POT: a computer code for reverse Monte Carlo modeling the structure of disordered systems containing molecules of arbitrary complexity.

An approach has been devised and tested for preserving the molecular dynamics molecular geometry taking into account energetic considerations during Reverse Monte Carlo (RMC) modeling. Instead of the commonly used fixed neighbor constraints, where molecules are held together by constraining distance ranges available for the specified atom pairs, here molecules are kept together via bond, angle, and dihedral potential energies. The scaled total potential energy contributes to the measure of the goodness-of-fit, thus, the atoms can be prevented from drifting apart. In some of the calculations (Lennard-Jones and Coulombic) nonbonding potentials were also applied. The algorithm was successfully tested for the X-ray structure factor-based structure study of liquid dimethyl trisulfide, for which material now significantly more sensible results have been obtained than during previous attempts via any earlier version of RMC modeling. It is envisaged that structural modeling of a large class of materials, primarily liquids and amorphous solids containing molecules of up to about 100 atoms, will make use of the new code in the near future.