High-pressure neutron diffraction study of superhydrated natrolite

Neutron powder diffraction data were collected on a sample of natrolite and a 1:1 (v/v) mixture of perdeuterated methanol and water at a pressure of 1.87(11) GPa. The natrolite sample was superhydrated, with a water content double that observed at ambient pressure. All of the water deuterium atoms were located and the nature and extent of the hydrogen bonding elucidated for the first time. This has allowed the calculation of bond valence sums for the water oxygen atoms, and from this, it can be deduced that the key energetic factor leading to loss of the additional water molecule upon pressure release is the poor coordination to sodium cations within the pores.     

Structure and dynamics of methanol in water: a quantum mechanical charge field molecular dynamics study

An ab initio quantum mechanical charge field molecular dynamics simulation was carried out for one methanol molecule in water to analyze the structure and dynamics of hydrophobic and hydrophilic groups. It is found that water molecules around the methyl group form a cage-like structure whereas the hydroxyl group acts as both hydrogen bond donor and acceptor, thus forming several hydrogen bonds with water molecules. The dynamic analyses correlate well with the structural data, evaluated by means of radial distribution functions, angular distribution functions, and coordination number distributions. The overall ligand mean residence time, τ identifies the methanol molecule as structure maker. The relative dynamics data of hydrogen bonds between hydroxyl of methanol and water molecules prove the existence of both strong and weak hydrogen bonds. The results obtained from the simulation are in excellent agreement with the experimental results for dilute solution of CH(3)OH in water. The overall hydration shell of methanol consists in average of 18 water molecules out of which three are hydrogen bonded.     

Pressure-induced volume expansion of zeolites in the natrolite family

Powder diffraction patterns of the zeolites natrolite (Na(16)Al(16)Si(24)O(80).16H(2)O), mesolite (Na(5.33)Ca(5.33)Al(16)Si(24)O(80).21.33H(2)O), scolecite (Ca(8)Al(16)Si(24)O(80).24H(2)O), and a gallosilicate analogue of natrolite (K(16)Ga(16)Si(24)O(80).12H(2)O), all crystallizing with a natrolite framework topology, were measured as a function of pressure up to 5.0 GPa with use of a diamond-anvil cell and a 200 microm focused monochromatic synchrotron X-ray beam. Under the hydrostatic conditions mediated by an alcohol and water mixture, all these materials showed an abrupt volume expansion (ca. 2.5% in natrolite) between 0.8 and 1.5 GPa without altering the framework topology. Rietveld refinements using the data collected on natrolite show that the anomalous swelling is due to the selective sorption of water from the pressure-transmission fluid expanding the channels along the a- and b-unit cell axes. This gives rise to a "superhydrated" phase of natrolite with an approximate formula of Na(16)Al(16)Si(24)O(80).32H(2)O, which contains hydrogen-bonded helical water nanotubes along the channels. In mesolite, which at ambient pressure is composed of ordered layers of sodium- and calcium-containing channels in a 1:2 ratio along the b-axis, this anomalous swelling is accompanied by a loss of the superlattice reflections (b(mesolite) = 3b(natrolite)). This suggests a pressure-induced order-disorder transition involving the motions of sodium and calcium cations either through cross-channel diffusion or within the respective channels. The powder diffraction data of scolecite, a monoclinic analogue of natrolite where all sodium cations are substituted by calcium and water molecules, reveal a reversible pressure-induced partial amorphization under hydrostatic conditions. Unlike the 2-dimensional swelling observed in natrolite and mesolite, the volume expansion of the potassium gallosilicate natrolite is 3-dimensional and includes the lengthening of the channel axis. In addition, the expanded phase, stable at high pressure, is retained at ambient conditions after pressure is released. The unprecedented and intriguing high-pressure crystal chemistry of zeolites with the natrolite framework topology is discussed here relating the different types of volume expansion to superhydration.     

Dimerisation of urea in water solution: a quantum mechanical investigation

The effect of water solvation on the structure and stability of cyclic dimers of urea has been investigated with the aid of density functional theory at the B3LYP/6-311++G** level. Several hydration models have been discussed. Specific solvent effects have been simulated through single and multiple water-urea interactions involving all the hydration sites of urea. The bulk solvent effects have been estimated through polarised continuum models. Under all the hydration patterns cyclic dimers continue to be stable structures although the solvent weakens the urea-urea interaction. Single and multiple specific urea-water interactions are competitive with urea dimerisation. The anticooperative nature of the two intermolecular interactions is largely due to the changes on sigma- and pi-electron density of urea caused by hydrogen bonding with water. The stability of the dimer is however, lost within a few ps when the hydrated dimer is described by a quantum mechanical molecular dynamics approach (ADMP). The cyclic dimer evolves towards structures where urea molecules are linked not more directly but through water molecules which have a bridge function.     

Coherent molecular motion in aquatic environment. Extraction of correlation from noise

Molecular dynamics simulation of liquid water and system “argon-thin water film” has been performed. In was shown that time dependence of distances between oxygen atoms of water molecules, connected by hydrogen bonds, looks like random noise and these molecules are doomed to move concertedly. The average distance between the argon atoms dissolved in water is retained for some time, so the argon atoms included in the hydrogen bond networks, but not capable to participate in hydrogen bonds are involved in concerted motions. The problem of revealing the correlations in the motion of molecules and atoms is discussed.     

Solvation free energies and hydration structure of N-methyl-p-nitroaniline

Solvation Gibbs energies of N-methyl-p-nitroaniline (MNA) in water and 1-octanol are calculated using the expanded ensemble molecular dynamics method with a force field taken from the literature. The accuracy of the free energy calculations is verified with the experimental Gibbs free energy data and found to reproduce the experimental 1-octanol∕water partition coefficient to within ±0.1 in log unit. To investigate the hydration structure around N-methyl-p-nitroaniline, an independent NVT molecular dynamics simulation was performed at ambient conditions. The local organization of water molecules around the solute MNA molecule was investigated using the radial distribution function (RDF), the coordination number, and the extent of hydrogen bonding. The spatial distribution functions (SDFs) show that the water molecules are distributed above and below the nitrogen atoms parallel to the plane of aromatic ring for both the methylamino and nitro functional groups. It is found that these groups have a significant effect on the hydration of MNA with water molecules forming two weak hydrogen bonds with both the methylamino and nitro groups. The hydration structures around the functional groups in MNA in water are different from those that have been found for methylamine, nitrobenzene, and benzene in aqueous solutions, and these differences together with weak hydrogen bonds explain the lower solubility of MNA in water. The RDFs together with SDFs provide a tool for the understanding the hydration of MNA (and other molecules) and therefore their solubility.     

Water-induced folding of 1,7-diammoniumheptane

Effects of hydration on the gaseous structures of diprotonated 1,7-diaminoheptane and protonated heptylamine are investigated by infrared photodissociation (IRPD) spectroscopy and computational chemistry. IRPD spectra in the hydrogen bond stretching region (2800-3900 cm(-1)) indicate that 1,7-diammoniumheptane is linear and that hydration occurs predominantly by alternate solvation of the two protonated amine groups for clusters with up to 10 water molecules. The relative intensities of bonded versus free hydroxyl (OH) stretches are greater in the spectra of 1,7-diammoniumheptane with more than 12 water molecules attached than the corresponding reference spectra of heptylammonium. This indicates that in the larger clusters, 1,7-diammoniumheptane adopts a more folded conformation in which the two protonated amine groups are solvated by a single water nanodrop. These results are supported by molecular dynamics simulations which show more hydrogen bonds in representative folded structures of hydrated 1,7-diammoniumheptane versus those with linear structures. These results indicate that the increase in Coulomb energy as a result of bringing the two positive charges closer together in the folded structures is compensated for by the additional hydrogen bonds that are possible when a single nanodrop solvates both protonated amine groups.     

X-ray absorption spectra of hexagonal ice and liquid water by all-electron Gaussian and augmented plane wave calculations

Full potential x-ray spectroscopy simulations of hexagonal ice and liquid water are performed by means of the newly implemented methodology based on the Gaussian augmented plane waves formalism. The computed spectra obtained within the supercell approach are compared to experimental data. The variations of the spectral distribution determined by the quality of the basis set, the size of the sample, and the choice of the core-hole potential are extensively discussed. The second part of this work is focused on the understanding of the connections between specific configurations of the hydrogen bond network and the corresponding contributions to the x-ray absorption spectrum in liquid water. Our results confirm that asymmetrically coordinated molecules, in particular, those donating only one or no hydrogen bond, are associated with well identified spectral signatures that differ significantly from the ice spectral profile. However, transient local structures, with half formed hydrogen bonds, may still give rise to spectra with dominant postedge contributions and relatively weaker oscillator strengths at lower energy. This explains why by averaging the spectra over all the O atoms of liquid instantaneous configurations extracted from ab initio molecular dynamics trajectories, the spectral features indicating the presence of weak or broken hydrogen bonds turn out to be attenuated and sometimes not clearly distinguishable.     

蛋白折叠中的暂态结构与表面水分子慢尺度动力学

蛋白表面水的慢尺度动力学行为往往被认为与蛋白的结构稳定性、功能以及折叠过程有关, 但在分子水平上, 还不清楚水分子的慢尺度动力学如何参与蛋白折叠过程. 以Trp-cage蛋白作为个案, 本文利用40条100 ns(总长4 μs)的全原子分子动力学轨迹,分析了蛋白折叠过程中蛋白表面水分子的停留行为,并探究影响蛋白表面水分子慢尺度行为的微观因素. 结果发现, 即使在蛋白折叠过程中蛋白拓扑结构变化很大, 残基之间也会形成稳定的局部暂态结构. 这些结构为水分子提供饱和、稳定的氢键, 通过与水分子之间的极性相互作用, 以及凹形的几何结构, 约束水分子长时停留, 我们称之为“停留中心”. 停留中心的形成是引起水分子慢尺度行为的重要因素. 另外, 停留中心的分布与蛋白折叠的进程有密切关系, 特别地, 在折叠轨迹中, 疏水核周围的残基组成了一个主要的停留中心. 研究结果不但有助于解释水分子慢尺度特征行为的来源, 还可以为实验中通过研究水分子在蛋白附近的慢尺度行为, 揭示蛋白折叠过程中的关键步骤提供一些启发.     

Anomalous mobility of molecules, structure of the guest sublattice, and transformation of tetra- to paranatrolite

The structure of the guest sublattice in the structural channels of natrolite zeolites oversaturated with water (also, at high pressures) is established. It was found from¹H NMR spectra that reduction of symmetry and sharply increased mobility of water molecules in paranatrolite and in the high- pressure phase of orthorhombic natrolite follow the same mechanism — half of positions in the structural channels are occupied by ordered water molecules. The other positions are vacant and may be involved in the mechanism of fast diffusion of water molecules. Translated fromZhumal Strukturnoi Khimii, Vol. 38, No. 4, pp. 676–685, July–August, 1997.     

A first principles simulation study of fluctuations of hydrogen bonds and vibrational frequencies of water at liquid-vapor interface

We present a theoretical study of the structure and dynamics of water-vapor interface by means of ab initio molecular dynamics simulations. The inhomogeneous density, hydrogen bond and orientational profiles, voids and vibrational frequency distributions are investigated. We have also studied various dynamical properties of the interface such as diffusion, orientational relaxation, hydrogen bond dynamics and vibrational frequency fluctuations. The diffusion and orientational relaxation of water molecules are found to be faster at the interface which can be correlated with the voids present in the system. The hydrogen bond dynamics, however, is found to be slightly slower at the interface than that in bulk water. The correlations of hydrogen bond relaxation with the dynamics of vibrational frequency fluctuations are also discussed.     

Water–Water and Water–Solute Interactions in Microsolvated Organic Complexes

A structural study of microsolvated clusters of β‐propiolactone (BPL) formed in a pulsed molecular jet expansion is presented. The rotational spectra of BPL–(H₂O)_n (n=1–5) adducts have been analyzed by broadband microwave spectroscopy. Unambiguous identification of the structures has been achieved using isotopic substitution and experimental measurements of the cluster dipole moment. The observed structures are discussed in terms of the different intermolecular interactions between water molecules and between water and BPL, which include n–π* interactions involving the lone pairs of electrons on water oxygen atoms and the antibonding orbital of the BPL carbonyl group. The changes induced in the structures of the water hydrogen‐bonding network by complexation to BPL indicate that water clusters adopt specific configurations to maximize their links to solute molecules.     

Solid–solvent molecular interactions observed in crystal structures of β-chitin complexes

Three β-chitin structures [anhydrous, di-hydrate, mono-ethylenediamine (EDA)] recently determined by synchrotron X-ray and neutron fiber diffraction were reviewed from the viewpoint of molecular interactions. Both water and EDA molecules interact with the chitin chains through multiple hydrogen bonds. When water complexes with chitin, the hydrogen bonding pattern rearranges with the replacement of an intrachain chitin hydrogen bond by a stronger hydrogen bond between chitin and water, with an associated reduction in the degrees of freedom; the water oxygen is a much stronger acceptor than the O5 ring atom. The behavior of hydrogen exchange by deuterium supports this interpretation. EDA-molecules change the conformation of hydroxymethyl group from gg to gt, accompanied by changes in hydrogen bonds due to the strong accepting ability of the EDA nitrogen atoms. Some important interactions are in common with experimental crystallographic results of cellulosic crystals and of molecular dynamics studies. These new insights into solid–solvent interactions are valuable in understanding molecular interactions in other polysaccharides-solvents system in solution or on surface.     

Ultrafast 2D IR anisotropy of water reveals reorientation during hydrogen-bond switching

Rearrangements of the hydrogen bond network of liquid water are believed to involve rapid and concerted hydrogen bond switching events, during which a hydrogen bond donor molecule undergoes large angle molecular reorientation as it exchanges hydrogen bonding partners. To test this picture of hydrogen bond dynamics, we have performed ultrafast 2D IR spectral anisotropy measurements on the OH stretching vibration of HOD in D(2)O to directly track the reorientation of water molecules as they change hydrogen bonding environments. Interpretation of the experimental data is assisted by modeling drawn from molecular dynamics simulations, and we quantify the degree of molecular rotation on changing local hydrogen bonding environment using restricted rotation models. From the inertial 2D anisotropy decay, we find that water molecules initiating from a strained configuration and relaxing to a stable configuration are characterized by a distribution of angles, with an average reorientation half-angle of 10°, implying an average reorientation for a full switch of ≥20°. These results provide evidence that water hydrogen bond network connectivity switches through concerted motions involving large angle molecular reorientation.     

Stability of nucleic acid base pairs in organic solvents: molecular dynamics, molecular dynamics/quenching, and correlated ab initio study

The dynamic structure and potential energy surface of adenine...thymine and guanine...cytosine base pairs and their methylated analogues interacting with a small number (from 1 to 16 molecules) of organic solvents (methanol, dimethylsulfoxide, and chloroform) were investigated by various theoretical approaches starting from simple empirical methods employing the Cornell et al. force field to highly accurate ab initio quantum chemical calculations (MP2 and particularly CCSD(T) methods). After the simple molecular dynamics simulation, the molecular dynamics in combination with quenching technique was also used. The molecular dynamics simulations presented here have confirmed previous experimental and theoretical results from the bulk solvents showing that, whereas in chloroform the base pairs create hydrogen-bonded structures, in methanol, stacked structures are preferred. While methanol (like water) can stabilize the stacked structures of the base pairs by a higher number of hydrogen bonds than is possible in hydrogen-bonded pairs, the chloroform molecule lacks such a property, and the hydrogen-bonded structures are preferred in this solvent. The large volume of the dimethylsulfoxide molecule is an obstacle for the creation of very stable hydrogen-bonded and stacked systems, and a preference for T-shaped structures, especially for complexes of methylated adenine...thymine base pairs, was observed. These results provide clear evidence that the preference of either the stacked or the hydrogen-bonded structures of the base pairs in the solvent is not determined only by bulk properties or the solvent polarity but rather by specific interactions of the base pair with a small number of the solvent molecules. These conclusions obtained at the empirical level were verified also by high-level ab initio correlated calculations.     

Local heterogeneous dynamics of water around lysozyme: a computer simulation study

Water present near the surface of a protein exhibits dynamic properties different from that of water in the pure bulk state. In this work, we have carried out atomistic molecular dynamics simulation of an aqueous solution of hen egg-white lysozyme. Attempts have been made to explore the correlation between the local heterogeneous mobility of water around the protein segments and the rigidity of the hydration layers with the microscopic dynamics of hydrogen bonds formed by water molecules with the protein residues. The kinetics of breaking and reformation of hydrogen bonds involving the surface water molecules have been calculated. It is found that the reformations of broken hydrogen bonds are more frequent for the hydration layers of those segments of the protein that are more rigid. The calculation of the low-frequency vibrational modes of hydration layer water molecules reveals that the protein influences the transverse and longitudinal degrees of freedom of water around it in a differential manner. These findings can be verified by appropriate experimental studies.     

Water superstructures within organic arrays; hydrogen-bonded water sheets, chains and clusters

A strategy for encouraging the formation of extended water arrays is presented, in which molecules that contain a 1,4-dihydroquinoxaline-2,3-dione core are used as supramolecular hosts for the accommodation of guest water molecules and arrays. These molecules were selected as they contain a hydrophilic oxalamide-based "terminus" that allows water molecules to hydrogen-bond to the host organic molecules as well as to each other. The host molecules also contain a hydrophobic "end" based upon an aromatic ring, which serves to encourage the formation of discrete water clusters in preference to three-dimensional networks, as the water molecules cannot form strong hydrogen bonds with this part of the molecule. A systematic study of several hydrated structures of four organic molecules based on 1,4-dihydroquinoxaline-2,3-dione (qd) is discussed. The organic molecules, qd, 6-methyl-1,4-dihydroquinoxaline-2,3-dione (mqd), 6,7-dimethyl-1,4-dihydroquinoxaline-2,3-dione (dmqd) and 1,4-dihydrobenzo[g]quinoxaline-2,3-dione (Phqd), act as supramolecular crystal hosts for the clusters of water, with zero-, one- and two-dimensional arrays of water being observed. The hydrogen bonding in the structures, both within the water clusters and between the clusters and organic molecules, is examined. In particular, the structure of dmqd6 H2O contains a two-dimensional water sheet composed of pentagonal and octagonal units. Phqd3 H2O forms a hydrophilic extended structure encouraging the formation of one-dimensional chains consisting entirely of water. Both qd2 H2O and dmqd2 H2O can be considered to form one-dimensional chains, but only by utilising bridging carbonyl groups of the oxalamide moieties to form the extended array; if only the water is considered, zero-dimensional water tetramers are observed. The remaining hydrated structures, [Na+dmqd-]dmqdH2O, dmqd1/3H2O and mqd1/2H2O, all contain discrete water molecules but do not form extended water structures.     

Ultrafast Vibrational Dynamics and Local Interactions of Hydrated DNA

Biochemical processes occur mainly in aqueous environments, where interactions with water molecules play a key role for both the structure and function of biomolecules. Deoxyribonucleic acid (DNA), the basic carrier of genetic information, is characterized by an equilibrium double helix structure which is held together by intermolecular hydrogen bonds between base pairs and hydrated by an environment of water molecules with fluctuating hydrogen bonds. Basic vibrational motions of hydrated DNA and the fastest changes in the DNA–water interactions and hydration geometries occur in less than 1 ps. These processes can be accessed by mapping the vibrational dynamics of DNA and water in a time‐resolved way by nonlinear ultrafast vibrational spectroscopy. Recent studies provide a detailed understanding of DNA vibrations and their dynamics, and give insight into nonequilibrium properties and structures of hydrated DNA.     

Molecular dynamics simulations of the hydration of poly(vinyl methyl ether):Hydrogen bonds and quasi-hydrogen bonds

Atomistic detailed hydration structures of poly(vinyl methyl ether)(PVME) have been investigated by molecular dynamics simulations under 300 K at various concentrations. Both radial distribution functions and the distance distributions between donors and acceptors in hydrogen bonds show that the hydrogen bonds between the polymer and water are shorter by 0.005 nm than those between water molecules. The Quasi-hydrogen bonds take only 7.2% of the van der Waals interaction pairs. It was found the hydrogen bonds are not evenly distributed along the polymer chain,and there still exists a significant amount(10%) of ether oxygen atoms that are not hydrogen bonded to water at a concentration as low as 3.3%. This shows that in polymer solutions close contacts occur not only between polymer chains but also between chain segments within the polymer,which leads to inefficient contacts between ether oxygen atoms and water molecules. Variation of the quasi-hydrogen bonds with the concentration is similar to that of hydrogen bonds,but the ratio of the repeat units forming quasi-hydrogen bonds to those forming hydrogen bonds approaches 0.2. A transition was found in the demixing enthalpy at around 30% measured by dynamic testing differential scanning calorimetry(DTDSC) for aqueous solutions of a mono-dispersed low molecular weight PVME,which can be related to the transition of the fractions of hydrogen bonds and quasi-hydrogen bonds at ～27%. The transition of the fractions of hydrogen bonds and quasi-hydrogen bonds at ～27% can be used to explain the demixing enthalpy transition at 30% at a molecular scale. In addition,at the concentration of 86%,each ether oxygen atom bonded with water is assigned 1.56 water molecules on average,and 'free' water molecules emerge at the concentration of around 54%.     

Molecular dynamics study of crystalline water ices

The behavior of structures of H₂O crystalline ices Ih, Ic, XI, VII, VIII, VI is studied in molecular dynamics experiment using the potential offered by Poltev and Malenkov. The behavior of the system consisting of one of the two identical interpenetrating, but without any common hydrogen bonds, water frameworks comprising the ice VI structure is also simulated. As a result of simulations, the ice VII structure has collapsed, whereas other systems proved to be stable. The reasons of instability of the ice VII and previously studied ice IV structures in molecular dynamics experiments are discussed. Based on the simulation results of the above-mentioned ices and previous simulation of ices II, III, IX, IV, and XII, the general regularities of dynamic properties of water molecules in crystalline water ices are formulated. Unreliability of results obtained by molecular dynamics in the investigation of self-organizing processes in aqueous systems is shown.