Argon and water

Computer simulation of liquid argon and water has shown that the structural inhomogeneity pattern visualized by coloring their instantaneous structures according to the volumes of the Voronoi polyhedra is the same for both liquids. The dynamics of argon atoms in the cavity of a clathrate hydrate and in liquid water is considered. The argon atoms included in the network of hydrogen bonds in liquid water are involved in concerted motion. As a result of this concerted motion, the distance between two argon atoms can fluctuate around some value for a fairly long time. The environment of argon atoms in a liquid aqueous solution differs significantly from their environment in clathrate hydrates.     

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%.     

Description of collective effects in computer models of water

The dynamics of a system containing 3456 water molecules in a cubic cell with periodic boundary conditions at 297 K was simulated. The time dependence of distances between oxygen atoms was examined for many pairs of molecules. These distances often oscillate around a certain average value over long periods of time (10 ps and longer). These average values can be about 2.8 Å (hydrogen bond) or much larger, up to 12–13 Å and more. This suggests that big groups of molecules are involved in a concerted motion. Lists of hydrogen bonds in 50 configurations divided by an interval of about 1 ps are compared. The average lifetime of a hydrogen bond is about 7 ps. The network of hydrogen bonds is colored according to their lifetimes for one of the configurations. The bonds that live longer than 7 ps form an infinite cluster. The bonds that live longer than 8 ps join to form a great number of finite clusters including several hundreds of nodes (molecules). These clusters contain few closed cycles. Even the bonds that live longer than 20 ps are united into clusters each containing two or three nodes (molecules). The self-diffusion coefficient for molecules involved in long-lived bonds is likely to be slightly smaller than that for molecules which do not participate in these bonds.     

Theoretical and experimental study of montmorillonite intercalated with tetramethylammonium cation

Structural and vibrational features of Na-montmorillonite and montmorillonite intercalated with tetramethylammonium cation (TMA⁺) were characterized theoretically and experimentally. Theoretical study was performed using density functional theory with inclusion of dispersion corrections. The analysis of the hydrogen bonds in the calculated models has shown that the Na⁺ cations coordinated by six water molecules (Na-M model) are bound to montmorillonite layers by moderate hydrogen bonds between water molecules and basal oxygen atoms of the tetrahedral sheets. Hydrated Na⁺ cations are stabilized by relatively strong hydrogen bonds among water molecules. In the intercalate model, the TMA⁺ cation is fixed in the interlayer space by weak hydrogen bonds between the methyl groups and basal oxygen atoms of montmorillonite layers. The calculated vibrational spectra are in a good agreement with the measured infrared spectra. The detailed analysis of the simulated vibrational spectra allowed unambiguous identification of corresponding bands in the measured spectra and their assignment to the particular vibrational modes. For example, calculations clearly distinguished between AlMgOH and AlAlOH stretching vibrations and also between the coupled vibrations of the methyl groups of the TMA⁺ cations.     

Monte Carlo Simulation of the Local Ordering of Water Molecules. II. Spatial Correlations and Hydrogen Bonds

The Monte Carlo method is used to calculate spatial distribution functions of oxygen and hydrogen atoms within a large-size water model (33666 SPC/E water molecules) under atmospheric pressure at room temperature. The work focuses on structural interpretation of local densities of water at the distances of about 3–5 Å from its molecules. The distribution of the distances between water molecules connected by chains of two or more hydrogen bonds indicates that the molecules between the first and second peaks of the radial distribution function (RDF) are mainly second and, to a lesser extent, third neighbors along the chain of bonds.     

Hydrogen Bonding between Metal‐Ion Complexes and Noncoordinated Water: Electrostatic Potentials and Interaction Energies

The hydrogen bonding of noncoordinated water molecules to each other and to water molecules that are coordinated to metal‐ion complexes has been investigated by means of a search of the Cambridge Structural Database (CSD) and through quantum chemical calculations. Tetrahedral and octahedral complexes that were both charged and neutral were studied. A general conclusion is that hydrogen bonds between noncoordinated water and coordinated water are much stronger than those between noncoordinated waters, whereas hydrogen bonds of water molecule in tetrahedral complexes are stronger than in octahedral complexes. We examined the possibility of correlating the computed interaction energies with the most positive electrostatic potentials on the interacting hydrogen atoms prior to interaction and obtained very good correlation. This study illustrates the fact that electrostatic potentials computed for ground‐state molecules, prior to interaction, can provide considerable insight into the interactions.     

A first principles molecular dynamics study of lithium atom solvation in binary liquid mixture of water and ammonia: structural, electronic, and dynamical properties

The preferential solvation of solutes in mixed solvent systems is an interesting phenomenon that plays important roles in solubility and kinetics. In the present study, solvation of a lithium atom in aqueous ammonia solution has been investigated from first principles molecular dynamics simulations. Solvation of alkali metal atoms, like lithium, in aqueous and ammonia media is particularly interesting because the alkali metal atoms release their valence electrons in these media so as to produce solvated electrons and metal counterions. In the present work, first principles simulations are performed employing the Car-Parrinello molecular dynamics method. Spontaneous ionization of the Li atom is found to occur in the mixed solvent system. From the radial distribution functions, it is found that the Li(+) ion is preferentially solvated by water and the coordination number is mostly four in its first solvation shell and exchange of water molecules between the first and second solvation shells is essentially negligible in the time scale of our simulations. The Li(+) ion and the unbound electron are well separated and screened by the polar solvent molecules. Also the unbound electron is primarily captured by the hydrogens of water molecules. The diffusion rates of Li(+) ion and water molecules in its first solvation shell are found to be rather slow. In the bulk phase, the diffusion of water is found to be slower than that of ammonia molecules because of strong ammonia-water hydrogen bonds that participate in solvating ammonia molecules in the mixture. The ratio of first and second rank orientational correlation functions deviate from 3, which suggests a deviation from the ideal Debye-type orientational diffusion. It is found that the hydrogen bond lifetimes of ammonia-ammonia pairs is very short. However, ammonia-water H-bonds are found to be quite strong when ammonia acts as an acceptor and these hydrogen bonds are found to live longer than even water-water hydrogen bonds.     

Exploring DNA groove water dynamics through hydrogen bond lifetime and orientational relaxation

Dynamics of water molecules in the grooves of DNA are of great interest both for practical (functionality of DNA) and fundamental (as examples of confined systems) interest. Here the authors employ atomistic molecular dynamics simulations to understand varying water dynamics at the minor and the major grooves of a 38 base-pair long DNA duplex in water. In order to understand and quantify the diversity in the nature of hydrogen bond due to many hydrogen bond donors and acceptors present in the four bases, they have undertaken study of hydrogen bond lifetime (HBLT) correlation functions of all the specific hydrogen bonds between the base atoms and water molecules. They find that the HBLT correlation functions are in general multiexponential, with the average lifetime depending significantly on the specificity and may thus be biologically relevant. The average hydrogen bond lifetime is longer in the minor groove than that in the major groove by almost a factor of 2. Analysis further shows that water hydrogen bonds with phosphate oxygen have substantially shorter lifetimes than those with the groove atoms. They also compute two different orientational time correlation functions (OTCFs) of the water molecules present at the major and the minor grooves and attempt to correlate OTCF with HBLT correlation function. The OTCFs in the minor groove exhibit three time scales, with the time constant of the slowest component one to two orders of magnitude longer than what is observed for bulk water. A slow component is also present for the major groove water but with shorter time constant. Interestingly, correlation between reformations allowed HBLT correlation function [C(HB)(t)] and the OTCF markedly deviates from each other in the grooves, indicating enhanced rigidity of water molecules in the grooves.     

环双(对-蒽基-对草快)的分子识别与谱学性质

环双(对-蒽基-对草快)是一种新型的缺电子大环仿生主体, 分子识别是其最重要的应用之一. 考察主体对一系列客体分子如水、氨、醇及杂环等的识别能力, 用密度泛函理论(DFT)中的B3LYP/3-21G基组对主客体复合物的结构进行优化. 在B3LYP/6-31G(d)水平上进行单点能计算, 校正后得到复合物的结合能. 用B3LYP/3-21G方法计算13C和3He化学位移. 结果表明, 主体对客体分子的识别主要靠客体上的杂原子与主体上的氢原子之间的氢键进行. 复合物的稳定化能受氢键的数目和距离影响. 氢键的形成导致部分复合物LUMO与HOMO能隙增大, 同时导致与氢键相连的C—H键上C原子的化学位移向低场移动. 复合物的芳香性与其结合能的大小及结合方式有关. 主体的芳香性因其与客体之间的弱相互作用而提高, 但太强的相互作用及客体在主体空腔内都将影响主体的环电流, 从而削弱其芳香性.     

Tetraaquabis(pyridine)metal(II) saccharinate tetrahydrate, [M(H2O)4(py)2](sac)2·4H2O; M = Co,Ni. Crystal structure determination

The crystal structure determination of the title compounds showed that they are isomorphous, revealing the general formula [M(H₂O)₄(py)₂](sac)₂·4H₂O. Their structures are built up of [M(H₂O)₄(py)₂]²⁺ cations, saccharinato anions and non-coordinated water molecules. The metal atom lies on the inversion center and is octahedrally coordinated by four water oxygens and two pyridine nitrogen atoms. The crystal structure packing is achieved through the hydrogen bonds of O_w⋯O_w, O_w⋯O and O_w⋯N type. Coordinated water molecules are hydrogen bonded to non-coordinated ones at the same time participating in hydrogen bonding with carbonyl oxygen and nitrogen atom from the saccharinato anions. Non-coordinated water molecules participate in hydrogen bonding with the oxygen atoms belonging to the saccharinato CO and SO₂ groups. The hydrogen bond network between the oxygen atoms belonging to the SO₂ group of the saccharinato anions and one of the non-coordinated water molecules (OW3) constructs the centrosymmetric cavity in the structure.     

Infrared spectroscopy of acetone-water liquid mixtures. II. Molecular model

In aqueous acetone solutions, the strong bathochromic shifts observed on the OH and CO stretch infrared (IR) bands are due to hydrogen bonds between these groups. These shifts were evaluated by factor analysis (FA) that separated the band components from which five water and five acetone principal factors were retrieved [J. Chem. Phys. 119, 5632 (2003)]. However, these factors were abstract making them difficult to interpret. To render them real an organization model of molecules is here developed whose abundances are compared to the experimental ones. The model considers that the molecules are randomly organized limited by the hydrogen bond network formed between the water hydrogen atoms and the acetone or water oxygen atoms, indifferently. Because the oxygen of water has two covalent hydrogen atoms which are hydrogen-bonded and may receive up to two hydrogen atoms from neighbor molecules hydrogen-bonded to it, three types of water molecules are found: OH2, OH3, and OH4 (covalent and hydrogen bonds). In the OH stretch region these molecules generate three absorption regimes composed of nu3, nu1, and their satellites. The strength of the H-bond given increases with the number of H-bonds accepted by the oxygen atom of the water H-bond donor, producing nine water situations. Since FA cannot separate those species that evolve concomitantly the nine water situations are regrouped into five factors, the abundance of which compared exactly to that retrieved by FA. From the factors' real spectra the OH stretch absorption are simulated to, respectively, give for the nu3 and nu1 components the mean values for OH2, 3608, 3508; OH3, 3473, 3282 and OH4, 3391, 3223 cm(-1). The mean separations from the gas-phase position which are respectively about 150, 330, and 400 cm(-1) are related to the vacancy of the oxygen electron doublets: two, one, and zero, respectively. No acetone hydrate that sequesters water molecules is formed. Similarly, acetone produces ten species, two of which evolve concomitantly. Spectral similarities further reduce these to five principal IR factors, the abundance of which compared adequately to the experimental results obtained from FA. The band assignment of the five-acetone spectra is given.     

Electronic basis of the comparable hydrogen bond properties of small H2CO/(H2O)n and H2NO/(H2O)n systems (n = 1, 2)

The electronic and structural properties of dihydronitroxide/water clusters are investigated and compared to the properties of formaldehyde/water clusters. Exploring the stationary points of their potential energy surfaces (structurally, vibrationally, and energetically) and characterizing their hydrogen bonds (by both atoms in molecules and natural bond orbitals methods) clearly reveal the strong similarity between these two kind of molecular systems. The main difference involves the nature of the hydrogen bond taking place between the X-H bond and the oxygen atom of a water molecule. All the properties of the hydrogen bonds occurring in both kind of clusters can be easily interpreted in terms of competition between intermolecular and intramolecular hyperconjugative interactions.     

Two polymorphs of bis(2‐carbamoylguanidinium) fluorophosphonate dihydrate

Two polymorphs of bis(2‐carbamoylguanidinium) fluorophosphonate dihydrate, 2C₂H₇N₄O⁺·FO₃P²⁻·2H₂O, are presented. Polymorph (I), crystallizing in the space group Pnma, is slightly less densely packed than polymorph (II), which crystallizes in Pbca. In (I), the fluorophosphonate anion is situated on a crystallographic mirror plane and the O atom of the water molecule is disordered over two positions, in contrast with its H atoms. The hydrogen‐bond patterns in both polymorphs share similar features. There are O—H...O and N—H...O hydrogen bonds in both structures. The water molecules donate their H atoms to the O atoms of the fluorophosphonates exclusively. The water molecules and the fluorophosphonates participate in the formation of R⁴₄(10) graph‐set motifs. These motifs extend along the a axis in each structure. The water molecules are also acceptors of either one [in (I) and (II)] or two [in (II)] N—H...O hydrogen bonds. The water molecules are significant building elements in the formation of a three‐dimensional hydrogen‐bond network in both structures. Despite these similarities, there are substantial differences between the hydrogen‐bond networks of (I) and (II). The N—H...O and O—H...O hydrogen bonds in (I) are stronger and weaker, respectively, than those in (II). Moreover, in (I), the shortest N—H...O hydrogen bonds are shorter than the shortest O—H...O hydrogen bonds, which is an unusual feature. The properties of the hydrogen‐bond network in (II) can be related to an unusually long P—O bond length for an unhydrogenated fluorophosphonate anion that is present in this structure. In both structures, the N—H...F interactions are far weaker than the N—H...O hydrogen bonds. It follows from the structure analysis that (II) seems to be thermodynamically more stable than (I).     

Argon–water system at low temperatures

The molecular dynamics method is used to simulate argon solutions in water and a thin water film–argon system at low temperatures. The correlation in motions of two closely spaced argon atoms is of another nature than the correlation of two neon atoms in a neon solid solution in ice II. The structure of hydrate shells of argon atoms contains five-membered rings composed of water molecules. The solubility of argon in a water film at low temperatures is noticeably higher than at room temperature. If a water film is first cooled to the glassy state and then argon atoms are added to it, then approximately as many argon atoms are absorbed on the film surface as they are present in a cooled film in equilibrium with the argon atmosphere. Argon atoms migrate from one pit to another on the rough surface of a solid water film.     

Structural studies on the hydration of L-glutamic acid in solution

A combination of neutron diffraction augmented with isotopic substitution and computer modeling using empirical potential structure refinement has been used to extract detailed structural information for L-glutamic acid dissolved in 2 M NaOH solution. This work shows that the tetrahedral hydrogen bonding network in water is severely disrupted by the addition of glutamic acid and NaOH, with the number of water-water hydrogen bonds being reduced from 1.8 bonds per water molecule in pure water to 1.4 bonds per water molecule in the present solution. In the glutamic acid molecule, each carboxylate oxygen atom forms an average of three hydrogen bonds with the surrounding water solvent with one of these hydrogens being shared between the two oxygen atoms on each carboxylate group, while each amine hydrogen forms a single hydrogen bond with the surrounding water solvent. Additionally, the average conformation of the glutamic acid molecules in these solutions is extracted.     

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.     

A novel 1:2 cucurbit[8]uril inclusion complex with N-phenylpiperazine hydrochloride

A new 1:2 inclusion complex of cucurbit[8]uril (CB[8]) and protonated N-phenylpiperazine was synthesized and characterized by ¹H NMR and X-ray crystallography. The crystal structure showed that the phenyl rings of the two equivalents of guest encapsulated in the cavity of CB[8] are parallel to one another with a mean plane separation of 3.899 Å. In contrast, the piperazinyl phenyl ammonium moieties slightly protrude from the ureidyl carbonyl lined portals in order to accommodate the ion–dipole interaction between host and guest which provides a substantial driving force for the assembly. The oxygen atoms of the carbonyl groups form hydrogen bonds with the hydrogen atoms in both bridging methylene groups of CB[8] and water molecules. There are also hydrogen bonds formed among CB[8], water, and the protonated piperazinyl rings. These hydrogen bonds are formed between the ureidyl C=O groups and hydrogens in methylenes of piperazinyl rings; through hydrogen bonding N⁺–H···O(H)–H···O=C. The protonated piperazinyl rings connect the carbonyl groups with the bridging water molecules.     

Structure of bilirubin and its anion according to quantum chemical calculations and molecular dynamics simulation

Quantum chemical calculations of the structural characteristics of the bilirubin molecule and its anion are performed. Intramolecular hydrogen bonds are studied using NBO analysis. It is shown that hydrogen bonds in the bilirubin molecule are nonequivalent, and the bond formed by the keto oxygen of the pyrrole ring and the hydrogen of the carboxyl group belonging to the propionate residue is energetically more favorable. Structural characteristics of the molecular and ion forms of bilirubin in aqueous solution are studied by molecular dynamics simulation. It is found that intermolecular hydrogen bonds with water molecules are formed due to oxygen atoms of the carboxyl group and the keto group of bilirubin, and the probability of their formation by anions is much higher than that for molecules.     

Behavior of water molecules near monolayer-protected clusters with different terminal segments of ligand

Molecular dynamics simulations are performed to investigate the behavior of water molecules near gold monolayer protected clusters (MPCs) with two different types of surfactant, HS(CH(2))(5)(OCH(2)CH(2))(2)COOH (type1) and HS(CH(2))(11)COOH (type2). The effects of the different moieties of the two ligands on the local structure of the water molecules are quantified by means of the reduced density profiles of oxygen and hydrogen atoms, and the hydrogen bond statistics. The adsorption characteristics of water molecules are evaluated by means of their residence time near the MPCs. The results show that the hydrophilic oligo (ethylene glycol) segment increases the number of water molecules, which penetrate the protective layer of MPC. As a result, the inter-water hydrogen bond network in the protective layer of type1 MPC is stronger than that in the protective layer of the type2 MPC. It is shown that the presence of interfacial hydrogen bonds increases the adsorption of water molecules near the MPCs and therefore constrains the motion of MPCs. As a result, the residence time of the water molecules adjacent to the type1 MPC is longer than that of the molecules adjacent to the type2 MPC.     

Charge‐transfer‐to‐solvent absorption spectra of I−(H2O)3–5 at a finite temperature via simulation

Ground‐state equilibrium Born–Oppenheimer molecular dynamics on I^?(H₂O)_3–5 clusters at ～200 K are performed to sample configurations for calculating the charge‐transfer‐to‐solvent (CTTS) absorption spectra for these clusters. When there are more water molecules in clusters, the calculated CTTS spectra are found to become more intense with the absorption maxima shifting to higher energies, which is in agreement with experimental results. In addition, compared with the findings for optimized structures, the absorption energies of the iodide 5p orbitals are red‐shifted at ～200 K because, on average, the distances between the iodide and the dangling hydrogen atoms are increased at finite temperatures which weakens the interactions between the iodide and water molecules in the clusters. Moreover, the number of ionic hydrogen bonds in the clusters are also reduced. However, it is found that all dangling hydrogen atoms must be considered to obtain a good correlation between the CTTS excitation energy and the average distance between the iodide and the dangling hydrogen atoms, which indicates the existence of the strong interactions of the CTTS electron with all of the dangling hydrogen atoms.