The structure of H-bonded clusters in sub- and supercritical water

The structure of H-bonded complexes in sub- and supercritical water in regions close to and remote from the saturation curve was studied. The Car-Parrinello method was used to calculate water dipole moment distributions in 11 thermodynamic states. The dependence of the mean dipole moment of water molecules on the size of clusters and number of H-bonds was obtained.     

At nonzero temperatures, stacked structures of methylated nucleic acid base pairs and microhydrated nonmethylated nucleic acid base pairs are favored over planar hydrogen-bonded structures: a molecular dynamics simulations study

The dynamic structure of all ten possible nucleic acid (NA) base pairs and methylated NA base pairs hydrated by a small number of water molecules (from 1 to 16) was determined by using molecular dynamics simulations in the NVE microcanonical and NVT canonical ensembles with the Cornell force field (W. D. Cornell, P. Cieplak, C. I. Bayly, I. R. Gould, K. M. Merz, D. M. Ferguson, D. C. Spellmeyer, T. Fox, J. E. Caldwell, P. Kollman, J. Am. Chem. Soc. 1995, 117, 5179). The presence of one water molecule does not affect the structure of any hydrogen-bonded (H-bonded) nonmethylated base pair. An equal population of H-bonded and stacked structures of adenine...adenine, adenine...guanine and adenine... thymine pairs is reached if as few as two water molecules are present, while obtaining equal populations of these structures in the case of adenine...cytosine, cytosine...thymine, guanine... guanine and guanine...thymine required the presence of four water molecules, and in the case of guanine...cytosine, six. A comparable population of planar, H-bonded and stacked structures for cytosine...cytosine and thymine... thymine base pairs was only obtained if at least eight water molecules hydrated a pair. Methylation of bases changed the situation dramatically and stacked structures were favoured over H-bonded ones even in the absence of water molecules in most cases. Only in the case of methyl cytosine...methyl cytosine, methyl guanine...methyl guanine and methyl guanine...methyl cytosine pairs were two, two or six water molecules, respectively, needed in order to obtain a comparable population of planar, H-bonded and stacked structures. We believe that these results give clear evidence that the preferred stacked structure of NA base pairs in the microhydrated environment, and also apparently in a regular solvent, is due to the hydrophilic interaction of a small number of water molecules. In the case of methylated bases, it is also due to the fact that the hydrogen atoms most suitable for the formation of H-bonds have been replaced by a methyl group. A preferred stacked structure is, thus, not due to a hydrophobic interaction between a large bulk of water molecules and the base pair, as believed.     

Adsorbed monolayer of H-bonded water molecules with and without neutral polymer molecules: A statistical mechanical treatment accounting for local order

A statistical mechanical treatment of a monolayer consisting both of H-bonded solvent molecules adsorbed in an unspecified number of orientations and of polymeric molecules of a neutral solute is provided. The different size of solvent and solute molecules is accounted for using Flory—Huggins statistics, whereas local order within the monolayer is accounted for using the quasi-chemical approximation. The above treatment is applied to a hexagonal array of adsorbed water molecules oriented in such a way as to be in a condition to be singly or double H-bonded laterally in the monolayer; a further water orientation characterized by full alignment of the dipole moment in the direction away from the electrode and simulating chemisorbed water monomers is included in the molecular model treatment. An adsorption isotherm is derived upon generalizing the molecular model at hand so as to include the presence of polymeric neutral solute molecules adsorbed in a single orientation. The model accounts satisfactorily for a number of salient features of experimental capacity curves at metal—water interphases in the absence of adsorbed solute species, as well as for the adsorption behaviour of aliphatic compounds on mercury, provided that the doubly H-bonded water molecules are excluded from the molecular model. A justification for this exclusion, based on the existence of H-bonds between the first and second layer of water molecules, is provided.     

Structure and dynamics of hydrogen bonds in the interface of a C12E6 spherical micelle in water solution: a MD study at various temperatures

The temperature dehydration of a C(12)E(6) spherical micelle is characterized through the study of the structure and dynamics of the hydrogen bonds formed by water within the micellar interface. Water molecules in proximity of the hydrophilic fragment of the C(12)E(6) surfactants form strong H-bonds with the oxyethilene units E and with the polar alcoholic heads. The activation energies of such H-bonds fall in the range 2-3 Kcal mol(-1). On the exposed oil core, the number of water-water H-bonds decreases as an effect of dehydration. The dynamics of such bonds exhibits a slow relaxation with respect to the bulk, and two time scales can be discerned: the first one, tau approximately 3-6 ps, is typical of water-water H-bonds around small hydrophobic molecules, whereas the second one, tau approximately 40-80 ps, is probably due to the confining effect of the long hydrophilic fragments which reduces the probability of a water molecule to leave the hydration layer of the exposed oil core. Water molecules around the core form H-bond clusters whose size and distribution change with temperature. From a cluster analysis, the system appears to be below the percolation threshold, suggesting that the exposed oily surface is formed by disconnected patches of size around 1 nm(2), close to the estimate of the solvated hydrophobic patches on protein surfaces. The network connectivity is also considered for concentric hydration shells along the interface: it turns out that near the oil core, the cluster size is larger than elsewhere in the interface demonstrating a strong structural effect induced by the exposed hydrocarbon tails. Temperature affects the cluster size only in the innermost shell.     

Mechanism of OH radical hydration: a comparative computational study of liquid and supercritical solvent

Flexible models of the radical and water molecules including short-range interaction of hydrogen atoms have been employed in molecular dynamic simulation to understand mechanism of (●)OH hydration in aqueous systems of technological importance. A key role of H-bond connectivity patterns of water molecules has been identified. The behavior of (●)OH(aq) strongly depends on water density and correlates with topological changes in the hydrogen-bonded structure of water driven by thermodynamic conditions. Liquid and supercritical water above the critical density exhibit the radical localization in cavities existing in the solvent structure. A change of mechanism has been found at supercritical conditions below the critical density. Instead of cavity localization, we have identified accumulation of water molecules around (●)OH associated with the formation of a strong H-donor bond and diminution of non-homogeneity in the solvent structure. For all the systems investigated, the computed hydration number and the internal energy of hydration Δ(h)U showed approximately linear decrease with decreasing density of the solvent but a degree of radical-water hydrogen bonding exhibited non-monotonic dependence on density. The increase in the number of radical-water H-acceptor bonds is associated with diminution of extended nets of four-bonded water molecules in compressed solution at ~473 K. Up to 473 K, the isobaric heat of hydration in compressed liquid water remains constant and equal to -40 ± 1 kJ mol(-1).     

Theoretical IR spectra for water clusters (H2O)n (n = 6-22, 28, 30) and identification of spectral contributions from different H-bond conformations in gaseous and liquid water

The vibrational IR spectra in the O-H stretching region are computed for water clusters containing 6-22, 28, and 30 molecules using quantum-chemical calculations (B3LYP and an augmented basis set). For the cluster with 20 molecules, several different structures were studied. The vibrational spectrum was partitioned into contributions from different molecules according to their coordination properties. The frequency shifts depend on the number of donated/accepted H-bonds primarily of the two molecules participating in the H-bond, but also of the surrounding molecules H-bonding to these molecules. The frequencies of H-bonds between two molecules of the same coordination type are spread over a broad interval. The most downshifted hydrogen-bond vibrations are those donated by a single-donor 3-coordinated molecule where the H-bond is accepted by a single-acceptor molecule. The H-bonded neighbors influence the downshift, and their contribution can be rationalized in the same way as for the central dimer. Single donors/acceptors cause larger downshifts than 4-coordinated molecules, and the least downshift is obtained for double donors/acceptors. This result is at variance with the conception that experimental liquid water spectra may be divided into components for which larger downshifts imply higher H-bond coordination. A mean spectral contribution for each coordination type for the donor molecule was derived and fitted to the experimental liquid water IR spectrum, which enabled an estimation of the distribution of H-bond types and average number of H-bonds (3.0 +/- 0.2) in the liquid.     

Hydration of sulfonated polyimide membranes. II. Water uptake and hydration mechanisms of protonated homopolymer and block copolymers

The hydration of sulfonated polyimide membranes in their protonated form is probed by infrared spectrometry using a recently described method. The membranes considered are the homopolymer, made of identical sulfonated repeat units, and two block copolymers composed of these units plus similar ones with no sulfonic groups in two different proportions. The experiments consist of registering series of spectra of these membranes at various hygrometries of the surrounding atmosphere. The quantitative analysis of the evolution of these spectra allows one to measure precisely the water uptake and to define in terms of chemical reactions the various hydration mechanisms that are active at a definite value of the hygrometry. It shows how the dried homopolymer significantly differs from the two dried block copolymers: in the homopolymer, a good proportion of SO(3)H groups that represent 83% of sulfonate groups, cannot establish H-bonds on C=O groups that are in a relatively small number. As a consequence, all coexisting SO(3)(-) groups are H-bonded to single H(3)O(+) cations with no extra H(2)O molecules. In both dried block copolymers, each SO(3)H group (60% of the sulfonate groups) establishes H-bonds on C=O groups that are in a sufficiently great number. These H-bonds stabilize these SO(3)H groups, and coexisting SO(3)(-) groups are H-bonded to cations that are found in the form of H(5)O(2)(+) or H(7)O(3)(+) that contain several H(2)O molecules. When the hygrometry increases, these differences get less marked but can be precisely defined.     

Density and temperature effect on hydrogen-bonded clusters in water - MD simulation study

Molecular dynamics NVE simulations have been performed for five thermodynamic states of water including ambient, sub-and supercritical conditions. Clustering of molecules via hydrogen bonding interaction has been studied with respect to the increasing temperature and decreasing density to examine the relationship between the extent of hydrogen bonding and macroscopic properties. Calculations confirmed decrease of the average number of H-bonds per molecule and of cluster-size with increasing temperature and decreasing density. In the sub-and supercritical region studied, linear correlations between several physical quantities (density, viscosity, static dielectric constant) and the total engagement of molecules in clusters of size k > 4, P _k>4, have been found. In that region there was a linear relationship between P _k>4 and the average number of H-bonds per water molecule. The structural heterogeneity resulting from hydrogen bonding interactions in low-density supercritical water has been also discussed.      

Hydrogen-bonded clusters on the vapor/ethanol-aqueous-solution interface

The structure of the vapor/ethanol-aqueous-solution interface has been carefully investigated focusing on an intermolecular hydrogen bond (HB) and molecular clusters bound by HBs. This paper is a continuation of our previous molecular dynamics (MD) study (Langmuir 2005, 21, 10885), and all analysis was performed based on five independent adsorption-equilibrated configurations of a slab of ethanol solution at 298.15 K, where the ethanol mole fraction of the solution, chi(e), is 0.0052, 0.012, 0.024, 0.057, and 0.12, respectively. The geometrical definition of HB enabled the detection of the HB between ethanol-ethanol, ethanol-water, and water-water molecules. The variations of the density of HB and the coordination number of HB across the vapor/solution interface were analyzed. Analysis on the density of HB reveals that a monolayer of adsorbed ethanol can be classified into two parts where ethanol molecules prefer to form HBs with each other and ethanol molecules prefer to form HBs with water molecules. Despite chi(e), the coordination number of ethanol-ethanol HB monotonically increases toward the vapor region, while those of ethanol-water and water-water HBs monotonically decrease. In addition, the variation of the mean size of both ethanol one-component clusters and ethanol/water binary clusters across the interface were analyzed. The mean size of an ethanol one-component cluster and that of an ethanol/water binary cluster are expressed as a maximum at the interface. These behaviors are linked with the size distributions of both one-component and binary clusters. A relatively large system in this calculation also enables detailed discussion about the molar dependency of the bulk structural properties of an ethanol solution.     

Study of H-bond characteristics in sub- and supercritical methanol

Classical molecular dynamics simulations of various methanol phase lines near the saturation curve and the critical point have been performed to study the changes in H-bonded clusters structure at transition of methanol to supercritical state. Analysis of H-bonds statistics with combined distance-energy H-bond criterion showed that the correlations between topological characteristics of H-bonds and the mole fraction of H-bonded molecules have unique functional representation despite the phase path applied. In the present study, an attempt has been also made to evaluate the degree of hydrogen bonding by combining the DFT computations on classical MD configurations with the natural bond orbital analysis of the waves functions obtained.     

The dynamic behavior of ethanol and water mixtures inside an Au nanotube molecule filter

Molecular dynamics (MD) simulation was used to investigate the behavior of water and ethanol molecules, which were mixed with five water-ethanol weight fractions (100:0, 0:100, 25:75, 50:50, and 75:25) inside the Au nanotube. To investigate the nano-confinement effect on water and ethanol molecules, the data of both molecules were analyzed by the probability of the number H-bonds per water and ethanol molecule and radial density distribution. Our results reveal that the radial density distributions and the number of H-bonds are significantly influenced by the Au nanotube, and the molecules also display different behavior from those in the bulk environment. In addition, the interaction between water molecules and the Au nanotube is stronger than that between ethanol molecules and the Au nanotube, from the profile of radial density distribution. Finally, both the number of H-bonds per water and per ethanol will be affected by the weight fraction, because the H-bond not only forms between the same material, but also between different materials.     

Changes in water structure induced by the guanidinium cation and implications for protein denaturation

The effect of the guanidinium cation on the hydrogen bonding strength of water was analyzed using temperature-excursion Fourier transform infrared spectra of the OH stretching vibration in 5% H 2O/95% D 2O solutions containing a range of different guanidine-HCl and guanidine-HBr concentrations. Our findings indicate that the guanidinium cation causes the water H-bonds in solution to become more linear than those found in bulk water, and that it also inhibits the response of the H-bond network to increased temperature. Quantum chemical calculations also reveal that guanidinium affects both the charge distribution on water molecules directly H-bonded to it as well as the OH stretch frequency of H-bonds in which that water molecule is the donor. The implications of our findings to hydrophobic solvation and protein denaturation are discussed.     

Quantum-chemical predictions of the formation of H-bonds between the N-phenyl-N’-isopropyl-<Emphasis Type="Italic">p</Emphasis>-phenylenediamine and N,N’-diphenyl-<Emphasis Type="Italic">p</Emphasis>-phenylenediamine molecules

The frequencies and thermodynamic characteristics of the N-phenyl-N’-isopropyl-p-phenylenediamine and N,N’-diphenyl-p-phenylenediamine molecules and their H-bonded dimers were calculated quantum-chemically by the density functional theory method with the B3LYP functional. The dimers were shown to contain the NH...N, NH...π, and CH...π H-bonds.     

Ground state structures and excited state dynamics of pyrrole-water complexes: ab initio excited state molecular dynamics simulations

Structures of the ground state pyrrole-(H2O)n clusters are investigated using ab initio calculations. The charge-transfer driven femtosecond scale dynamics are studied with excited state ab initio molecular dynamics simulations employing the complete-active-space self-consistent-field method for pyrrole-(H2O)n clusters. Upon the excitation of these clusters, the charge density is located over the farthest water molecule which is repelled by the depleted pi-electron cloud of pyrrole ring, resulting in a highly polarized complex. For pyrrole-(H2O), the charge transfer is maximized (up to 0.34 a.u.) around approximately 100 fs and then oscillates. For pyrrole-(H2O)2, the initial charge transfer occurs through the space between the pyrrole and the pi H-bonded water molecule and then the charge transfer takes place from this water molecule to the sigma H-bonded water molecule. The total charge transfer from the pyrrole to the water molecules is maximized (up to 0.53 a.u.) around approximately 100 fs.     

Comparison of P···D (D = P,N) with other noncovalent bonds in molecular aggregates

All the minima on the potential energy surfaces of homotrimers and tetramers of PH(3) are identified and analyzed as to the source of their stability. The same is done with mixed trimers in which one PH(3) molecule is replaced by either NH(3) or PFH(2). The primary noncovalent attraction in all global minima is the BP···D (D = N,P) bond which is characterized by the transfer of charge from a lone pair of the donor D to a σ? B-P antibond of the partner molecule which is turned away from D, the same force earlier identified in the pertinent dimers. Examination of secondary minima reveals the presence of other weaker forces, some of which do not occur within the dimers. Examples of the latter include PH···P, NH···P, and PH···F H-bonds, and "reverse" H-bonds in which the source of the electron density is the smaller tail lobe of the donor lone pair. The global minima are cyclic structures in all cases, and exhibit some cooperativity, albeit to a small degree. The energy spacing of the oligomers is much smaller than that in the corresponding strongly H-bonded complexes such as the water trimer.     

Preferential formation of the different hydrogen bonds and their effects in tetrahydrofuran and tetrahydropyran microhydrated complexes

The role of cycloether-water (c-w) and water-water (w-w) hydrogen bonds (H-bonds) on the stability of the tetrahydrofuran THF/(H(2)O)(n) and the tetrahydropyran THP/(H(2)O)(n) complexes with n = 1-4 was investigated herein using the density functional and ab initio methods and the atoms in molecules theory. Geometry optimizations for these complexes were carried out with various possible initial guess structures. It was revealed that the major contributions of the mono and dihydrated complexes came from c-w H-bonds. A competition between c-w and w-w H-bonds contribution was observed for trihydrated complexes. For most of tetrahydrated complexes, the inter-water H-bonds provided the greatest contribution, whereas the c-w contributions were small but not negligible. It was confirmed that to produce a hydrophobic hydration of cycloethers, the C-H···O(w) H-bond should be associated with a network of H-bonds that connects both portions of the solute, through the formation of a bifunctional H-bond. A linear correlation is obtained for the sum of electron density at the bond critical points (ρ(b)) with the interaction energy (ΔE) and with the solute-solvent interaction energy (ΔE(s-w)) of the microhydrated complexes. In addition, a new way to estimate the energetic contribution as well as the preferential formation of the different H-bonds based completely on ρ(b) was found. Even more, it allows to differentiate the contribution from c-w interactions in both hydrophilic and hydrophobic contributions, it is therefore a useful tool for studying the hydration of large biomolecules. The analysis of the modifications in the atomic and group properties brought about by successive addition of H(2)O molecules allowed to pinpoint the atoms or molecular groups that undergo the greatest changes in electron population and energetic stabilization. It was identified that the remarkable stabilization of the water oxygen atoms is crucial for the stabilization of the complexes.     

Quantitative FTIR study of PHBV/bisphenol A blends

FTIR spectroscopy was used to verify the presence of intermolecular hydrogen bond (inter-H-bond) between poly(3-hydroxybutyrate co-3-hydroxyvalerate) (PHBV) and bisphenol A (BPA). By monitoring the spectral changes during PHBV crystallization and blends dissociation, the absorptivity ratio of CO bonds in crystalline and amorphous regions in PHBV and that of H-bonded and free CO in PHBV/BPA blends were experimentally determined as 1.40 and 1.68, respectively. Using curve-fitting program, the CO absorptions in spectra of blends were ascribed to three types of bonds: amorphous, crystalline and H-bonded CO. The crystallinity of PHBV and the fraction of H-bonded CO were calculated. These results indicated that the H-bond clearly suppressed the PHBV crystallization. Furthermore, the fraction of BPA molecules that simultaneously formed two hydrogen bonds (H-bonds) with CO was estimated. It revealed that there existed a H-bond network in PHBV/BPA blends. This network was compared with the covalent network by estimating the number of atoms between every two adjacent crosslink points in chain. Up to the high density of H-bond discussed in this paper, there was always a certain part in PHBV that crystallized due to the dynamic character of hydrogen bonds; however, the hydrogen bonds significantly reduced the crystallization rate of PHBV.     

Entropy convergence in the hydration thermodynamics of n-alcohols

Using experimental data from the literature, entropy convergence in the hydration thermodynamics of n-alcohols is shown to occur at about 125 degrees C. The phenomenon is reproduced in a more-than-qualitative manner by means of a theoretical approach that accounts for the entropy contributions associated with (a) creation of a cavity in water, (b) turning on solute-water van der Waals interactions, and (c) turning on the solute-water H-bonding potential. The density of water and the effective size of water molecules with their temperature dependence play the pivotal role for the occurrence of entropy convergence, together with the property of the alcohol hydroxyl group to form the same number of H-bonds with water molecules regardless of the length of the alkyl chain.     

Hydrogen-bonded networks in ethanol proton wires: IR spectra of (EtOH)qH+-Ln clusters (L = Ar/N2, q < or = 4, n < or = 5)

Isolated and microsolvated protonated ethanol clusters, (EtOH)qH+-Ln with L = Ar and N2, are characterized by infrared photodissociation (IRPD) spectroscopy in the 3 microm range and quantum chemical calculations. For comparison, also the spectrum of the protonated methanol dimer, (MeOH)2H+, is presented. The IRPD spectra carry the signature of H-bonded (EtOH)qH+ chain structures, in which the excess proton is either strongly localized on one or (nearly) equally shared between two EtOH molecules, corresponding to Eigen-type ion cores (EtOH2+ for q = 1, 3) or Zundel-type ion cores (EtOH-H+-HOEt for q = 2, 4), respectively. In contrast to neutral (EtOH)q clusters, no cyclic (EtOH)qH+ isomers are detected in the size range investigated (q < or = 4), indicative of the substantial impact of the excess proton on the properties of the H-bonded ethanol network. The acidity of the two terminal OH groups in the (EtOH)qH+ chains decreases with the length of the chain (q). Comparison between (ROH)qH+ with R = CH3 and C2H5 shows that the acidity of the terminal O-H groups increases with the length of the aliphatic rest (R). The most stable (EtOH)qH+-Ln clusters with n < or = 2 feature intermolecular H-bonds between the inert ligands and the two available terminal OH groups of the (EtOH)qH+ chain. Asymmetric microsolvation of (EtOH)qH+ with q = 2 and 4 promotes a switch from Zundel-type to Eigen-type cores, demonstrating that the fundamental structural motif of the (EtOH)qH+ proton wire sensitively depends on the environment. The strength of the H-bonds between L and (EtOH)qH+ is shown to provide a rather sensitive probe of the acidity of the terminal OH groups.     

The special features of H-bonding in supercritical water close to the saturation curve

A complex study of H-bonding in supercritical water in the region close to the saturation curve was performed at constant pressures of 30 and 50 MPa and a constant temperature of 673 K. The topological H-bond characteristics were calculated by the molecular dynamics method with the use of the TIP4P-HB potential. The calculations included the number of H-bonds per water molecule, the degree of H-bonding, and the distributions of molecules according to the number of H-bonds (fractions and the gradients of fractions of molecules with n H-bonds). Changes in these characteristics as the temperature, density, and pressure varied were studied.