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.

Systematic Study of Different Types of Interactions in α-, ß- and γ-Cyclodextrin: Quantum Chemical Investigation.

In this work, comprehensive ab initio quantum chemical calculations using the DFT level of theory were performed to characterize the stabilization interactions (H-bonding and hyperconjugation effects) of two stable symmetrical conformations of α-, ß-, and γ-cyclodextrins (CDs). For this purpose, we analyzed the electron density using "Atom in molecules" (AIM), "Natural Bond Orbital" (NBO), and energy decomposition method (CECA) in 3D and in Hilbert space. We also calculated the H-bond lengths and OH vibrational frequencies. In every investigated CD, the quantum chemical descriptors characterizing the strength of the interactions between the H-bonds of the primary OH (or hydroxymethyl) and secondary OH groups are examined by comparing the same quantity calculated for ethylene glycol, α-d-glucose (α-d-Glcp) and a water cluster as reference systems. By using these external standards, we can characterize more quantitatively the properties of these bonds (e.g., strength). We have demonstrated that bond critical points (BCP) of intra-unit H-bonds are absent in cyclodextrins, similar to α-d-Glcp and ethylene glycol. In contrast, the CECA analysis showed the existence of an exchange (bond-like) interaction between the interacting O…H atoms. Consequently, the exchange interaction refers to a chemical bond, namely the H-bond between two atoms, unlike BCP, which is not suitable for its detection.

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.

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.

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.

Comparison of the atomic level structure of the plastic crystalline and liquid phases of CBr2Cl2: neutron diffraction and reverse Monte Carlo modelling.

Neutron diffraction results obtained for plastic crystalline dichlorodibromomethane (CBr2Cl2) have been modelled by means of the reverse Monte Carlo method. Comparison with its liquid phase is provided at several levels of the atomic structure (total scattering structure factors, partial radial distribution functions, orientational and dipole-dipole correlations). The results reveal that the relative orientation of neighbouring molecules largely depends on the steric effect. The small dipole moment does not have as strong an influence as the steric effect on the short-range order. Our observations fit well with earlier findings presented for the series CBr(n)Cl(4-n) (n = 0, 1, 2, 4).

Detailed intermolecular structure of molecular liquids containing slightly distorted tetrahedral molecules with C(3v) symmetry: chloroform, bromoform, and methyl-iodide.

Analyses of the intermolecular structure of molecular liquids containing slightly distorted tetrahedral molecules of the CXY(3)-type are described. The process is composed of the determination of several different distance-dependent orientational correlation functions, including ones that are introduced here. As a result, a complete structure classification could be provided for CXY(3) molecular liquids, namely for liquid chloroform, bromoform, and methyl-iodide. In the present work, the calculations have been conducted on particle configurations resulting from reverse Monte Carlo computer modeling: these particle arrangements have the advantage that they are fully consistent with structure factors from neutron and x-ray diffraction measurements. It has been established that as the separation between neighboring molecules increases, the dominant mutual orientations change from face-to-face to edge-to-edge, via the edge-to-face arrangements. Depending on the actual liquid, these geometrical elements (edges and faces of the distorted tetrahedra) were found to contain different atoms. From the set of liquids studied here, the structure of methyl-iodide was found to be easiest to describe on the basis of pure steric effects (molecular shape, size, and density) and the structure of liquid chloroform seems to be the furthest away from the corresponding "flexible fused hard spheres" like reference system.

Extended orientational correlation study for molecular liquids containing distorted tetrahedral molecules: application to methylene halides.

The method of Rey [Rey, J. Chem. Phys. 126, 164506 (2007)] for describing how molecules orient toward each other in systems with perfect tetrahedral molecules is extended to the case of distorted tetrahedral molecules of c(2v) symmetry by means of introducing 28 subgroups. Additionally, the original analysis developed for perfect tetrahedral molecules, based on six groups, is adapted for molecules with imperfect tetrahedral shape. Deriving orientational correlation functions have been complemented with detailed analyses of dipole-dipole correlations. This way, (up to now) the most complete structure determination can be carried out for such molecular systems. In the present work, these calculations have been applied for particle configurations resulting from reverse Monte Carlo computer modeling. These particle arrangements are fully consistent with structure factors from neutron and x-ray diffraction measurements. Here we present a complex structural study for methylene halide (chloride, bromide, and iodide) molecular liquids, as possibly the best representative examples. It has been found that the most frequent orientations of molecules are of the 2:2 type over the entire distance range in these liquids. Focusing on the short range orientation, neighboring molecules turn toward each other with there "H,Y"-"H,Y" (Y: Cl, Br, I) edges, apart from CH(2)Cl(2) where the H,H-H,Cl arrangement is the most frequent. In general, the structure of methylene chloride appears to be different from the structure of the other two liquids.

The liquid structure of haloforms CHCl3 and CHBr3.

New neutron and x-ray diffraction measurements are reported on liquid chloroform, CHCl(3), and bromoform, CHBr(3). Experimental total scattering structure factors have been interpreted by the reverse Monte Carlo method of structural modelling. Partial radial distribution functions, intramolecular bond angle distributions and functions characterizing distance-dependent orientational correlations have been calculated directly from the particle coordinates. It has been found that most of these characteristics of the microscopic structure can be approximated rather well by functions calculated for hard sphere like reference systems. The two liquids show similar features from the point of view of their structure. There are also some distinctive features in terms of orientational correlations: nearest neighbour molecules prefer face-to-face arrangement in chloroform whereas in bromoform, edge-to-face configurations dominate, with a significant occurrence of corner-to-face type correlations.

An approach towards understanding the structure of complex molecular systems: the case of lower aliphatic alcohols.

An extensive study of liquid aliphatic alcohols methanol, ethanol, and propanol, applying reverse Monte Carlo modelling as a method of interpretation of diffraction data, is presented. The emphasis is on the evaluation of several computational strategies in view of their suitability to obtain high quality molecular models via the reverse Monte Carlo procedure. A consistent set of distances of closest approach and fixed neighbour constraints applicable to all three investigated systems was developed. An all-atom description is compared with a united-atom approach. The potentialities of employment of neutron diffraction data of completely deuterated and isotopically substituted samples, x-ray diffraction data, and results of either molecular dynamics or Monte Carlo calculations were investigated. Results show that parallel application of x-ray and neutron diffraction data, the latter being from completely deuterated samples, within an all-atom reverse Monte Carlo procedure is the most successful strategy towards attaining reliable, detailed, and well-structured molecular models, especially if the models are subsequently refined with the results of molecular dynamics simulations.

Orientational correlations in molecular liquid SnI4.

The total scattering structure factor of liquid tin tetraiodide (SnI(4)) has been interpreted by means of reverse Monte Carlo (RMC) modeling. From the sets of particle coordinates provided by RMC, which are consistent with experimental results within errors, partial radial distribution functions as well as correlation functions characterizing mutual orientations of molecules as a function of distance between molecular centers can be calculated. Interestingly and very much in contrast to liquids of symmetric XCl(4) molecules, the corner-to-face (or "Apollo")-type orientation of neighboring molecules has a significant (about 20%) occurrence in liquid SnI(4). Via comparison with a reference system, obtained by hard sphere Monte Carlo simulation, we demonstrate that intermolecular two-body correlations in liquid SnI(4) are determined largely by excluded volume (steric) effects; that is, intermolecular two-body interactions play only a minor role. On the other hand, as it is manifested in the large difference between the reference and "real" systems in terms of the orientational correlations, higher order interactions are indispensable. This feature can explain the extremely rich phase behavior of SnI(4) at high pressures.

The structure of liquid iodomethane, CH(3)I/CD(3)I.

An x-ray diffraction measurement has been performed on liquid iodomethane using the BL04B2 beamline at the SPring-8 synchrotron radiation facility (Japan). The corrected structure factor, together with the results of an earlier neutron diffraction study, has been interpreted by means of reverse Monte Carlo modelling. This approach provides large structural models, containing thousands of atoms that are consistent with the experimental data within their uncertainties. From these models, partial structure factors and radial distribution functions were calculated. It is demonstrated that, for a satisfactory description of the intermolecular correlations, the presence of x-ray data is vital. Orientational correlations between neighbouring molecules have been found to be much better defined than if they were due to excluded volume effects only.