Spatial hydration maps and dynamics of naphthalene in ambient and supercritical water

The hydration structures and dynamics of naphthalene in aqueous solution are examined using molecular-dynamics simulations. The simulations are performed at several state points along the coexistence curve of water up to the critical point, and above the critical point with the density fixed at 0.3 g/cm(3). Spatial maps of local atomic pair-density are presented which show a detailed picture of the hydration shell around a bicyclic aromatic structure. The self-diffusion coefficient of naphthalene is also calculated. It is shown that water molecules tend to form pi-type complexes with the two aromatic regions of naphthalene, where water acts as the H-bond donor. At ambient conditions, the hydration shell of naphthalene is comprised, on average, of about 39 water molecules. Within this shell, two water molecules can be identified as pi-coordinating, forming close to one H-bond to the aromatic rings. With increasing temperature, the hydration of naphthalene changes dramatically, leading to the disappearance of the pi-coordination near the critical point.     

Characterization of hydrated Na+(phenol) and K+(phenol) complexes using infrared spectroscopy

Hydrated alkali metal ion-phenol complexes were studied to model these species in aqueous solution for M=Na and K. IR predissociation spectroscopy in the O-H stretch region was used to analyze the structures of M+(Phenol)(H2O)n cluster ions, for n = 1-4. The onset of hydrogen bonding was observed to occur at n=4. Ab initio calculations were used to qualitatively explore the types of hydrogen-bonded structures of the M+(Phenol)(H2O)4 isomers. By combining the ab initio calculations and IR spectra, several different structures were identified for each metal ion. In contrast to benzene, detailed in a previous study of Na+(Benzene)n(H2O)m [J. Chem. Phys. 110, 8429 (1999)], phenol is able to bind directly to Na+ even in the presence of four waters. This is likely the result of the sigma-type interaction between the phenol oxygen and the ion. With K+, the dominant isomers are those in which the phenol O-H group is involved in a hydrogen bond with the water molecules, while with Na+, the dominant isomers are those in which the phenol O-H group is free and the water molecules are hydrogen-bonded to each other. Spectra and ab initio calculations for the M+(Phenol)Ar cluster ions for M=Na and K are reported to characterize the free phenol O-H stretch in the M+(Phenol) complex. While pi-type configurations were observed for binary M+(Phenol) complexes, sigma-type configurations appear to dominate the hydrated cluster ions.     

Effects of microhydration on the characteristics of cation–phenol complexes

The properties of complexes formed by phenol and K⁺, Na⁺, Li⁺ and Mg²⁺ in the presence of up to four water molecules have been studied by means of computational methods. The interaction becomes stronger as the size of the cation decreases, showing almost no preference between coordinating to the aromatic ring or to the hydroxyl oxygen. As water molecules are introduced, a variety of stable structures arise, where water molecules establish hydrogen bonds among themselves and with the hydroxyl group of phenol. For the most polarizing cations, the strong cation···water interaction gives most stable minima corresponding to arrangements with water molecules and phenol coordinated directly to the cation, with no significant hydrogen bonds among them. However, in Na⁺ complexes and especially in K⁺ ones, the interaction with the cation is weaker, so hydrogen bond formation starts to be competitive as more water molecules are included, the most stable minima corresponding to structures where not all water molecules or phenol are directly bound to the cation. This behavior is also reflected on the predicted vibrational spectra, which agree with those determined experimentally. Up to three water molecules, only for K⁺ and to a less extent Na⁺, stable minima are found showing red-shifted O–H stretching bands corresponding to water···water and water···phenol hydrogen bonds. With four water molecules, at least one water molecule is located in a second solvation shell, all cations exhibiting red-shifted bands.     

IR investigation of hydrogen bonds in weakly hydrated films of poly(vinyl alcohol)

A system of hydrogen bonds in weakly hydrated PVA films containing up to ≤8.5 wt % water is investigated via IR spectroscopy. It is shown that water molecules bind to only part of the hydroxyl groups of the polymer that are available for hydration and form the first hydrating layer. In a completely dehydrated film, practically every hydroxyl group of PVA forms hydrogen bonds with two other hydroxyl groups and serves as both a proton donor and a proton acceptor. In the hydrated film, one to three water molecules directly bind with one hydroxyl group of PVA.     

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.     

Studies of protein hydration in aqueous solution by high-resolution nuclear magnetic resonance spectroscopy

Individual hydration water molecules in aqueous protein solutions have been observed using experimental schemes for homonuclear two-dimensional and heteronuclear three-dimensional NMR experiments in H₂O solution, which do not require suppression of the solvent line by presaturation. In these experiments, the location of the hydration waters is determined from their nuclear Overhauser effects (NOE s) with individual hydrogen atoms of distinct amino acid residues. In the basic pancreatic trypsin inhibitor (BPTI ), four internal water molecules that had been reported in three different crystal forms were also found to be in the same locations in the solution structure, with lifetimes with respect to exchange of the water protons in excess of 0.3 ns. Additional NOE s with polypeptide protons located on the protein surface may involve either hydration water molecules or hydroxyl protons of amino acid side chains. Their total number is small compared to the number of NOE s expected from the hydration water molecules identified in the crystal structures of BPTI .     

Ultrafast hydration dynamics in the lipidic cubic phase: Discrete water structures in nanochannels

We report here our studies of hydration dynamics of confined water in aqueous nanochannels (approximately 50 A) of the lipidic cubic phase. By systematically anchoring the hydrocarbon tails of a series of tryptophan-alkyl ester probes into the lipid bilayer, we mapped out with femtosecond resolution the profile of water motions across the nanochannel. Three distinct time scales were observed, revealing discrete channel water structures. The interfacial water at the lipid surface is well-ordered, and the relaxation dynamics occurs in approximately 100-150 ps. These dynamically rigid water molecules are crucial for global structural stability of lipid bilayers and for stabilization of anchored biomolecules in membranes. The adjacent water layers near the lipid interface are hydrogen-bonded networks and the dynamical relaxation takes 10-15 ps. This quasi-bound water motion, similar to the typical protein surface hydration relaxation, facilitates conformation flexibility for biological recognition and function. The water near the channel center is bulklike, and the dynamics is ultrafast in less than 1 ps. These water molecules freely transport biomolecules near the channel center. The corresponding orientational relaxation at these three typical locations is well correlated with the hydration dynamics and local dynamic rigidity. These results reveal unique water structures and dynamical motions in nanoconfinements, which is critical to the understanding of nanoscopic biological activities and nanomaterial properties.     

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.     

Difference spatial distribution function analysis of aqueous solutions. IV. Hydration structure changes of ethylene glycol solutions throughout conformational change process from gGg' to tGg' conformers

Monte Carlo (MC) simulations were carried out for an infinitely dilute aqueous solution of two stable conformers (gGg' and tGg') and of three conformations between gGg' and tGg' conformers of ethylene glycol (EG) at 298K. Based on the spatial distribution function (SDF) goo(x,y,z), obtained from the MC simulation in the above conformations in liquid water, the high distribution of hydration water molecules could be divided into hydrogen acceptor (HA), hydrogen donor (HD), MIX (overlapped distribution of HA and HD), and hydrophobic hydration (HH) regions. The spatial orientations of hydrogen-bonded water molecules were found to be of a linear type with a triple-layer structure in the HA region and HA part (in the MIX region), and double-layer structures in the HD region and HD part (in the MIX region). In addition, it was apparent that the spatial orientations of these water molecules were of the linear type throughout the conformational change process from gGg' to tGg' conformers in liquid water. From the difference SDF (DSDF), deltagoo(x,y, z), between the SDFs of two conformations, we concluded that the distribution of hydration water molecules in the HA and HD parts of the MIX region are governed by the competition of internal hydrogen bonds between the hydrogen atom and two lone-pair electrons on the oxygen atom of an EG molecule.     

Raman study on conformational equilibria of fluoroacetone in aqueous solutions

The effects of water and heavy water on conformational equilibria of fluoroacetone have been investigated via Raman spectroscopy. Additional Raman bands have been observed in the C-F stretching and the C-C-C symmetric stretching regions for the aqueous solutions. Based on enthalpy and volume differences between the conformers, these bands are assigned to the syn conformer which has hydrogen bonds between the fluorine atom and water molecules (syn' conformer). The number of H2O molecules binding to the syn' conformer is estimated to be 2.4 from the concentration dependence of the spectrum. The enthalpy and the volume differences between the cis and syn conformers in the aqueous solutions show anomalous values in comparison with those in organic solvents. We discuss these thermodynamic behaviors from the viewpoint of the hydration structures of fluoroacetone.     

Structure and hydration of L-proline in aqueous solutions

The structure and hydration of L-proline in aqueous solution have been investigated using a combination of neutron diffraction with isotopic substitution, empirical potential structure refinement modeling, and small-angle neutron scattering at three concentrations, 1:10, 1:15, and 1:20 proline/water mole ratios. In each solution the carboxylate oxygen atoms from proline accept less than two hydrogen bonds from the surrounding water solvent and the amine hydrogen atoms donate less than one hydrogen bond to the surrounding water molecules. The solute-solute radial distribution functions indicate relatively weak interactions between proline molecules, and significant clustering or aggregation of proline is absent at all these concentrations. The spatial density distributions for the hydration of the COO- group in proline show a similar shape to that found previously in L-glutamic acid in aqueous solution but with a reduced coordination number.     

Hydration, swelling, interlayer structure, and hydrogen bonding in organolayered double hydroxides: insights from molecular dynamics simulation of citrate-intercalated hydrotalcite

Molecular dynamics (MD) simulation of the Mg/Al (3:1) layered double hydroxide (LDH), hydrotalcite (HT), containing citrate, C6H5O7(3-), as the charge balancing interlayer anion provides new molecular scale insight into the interlayer structure, hydrogen bonding, and energetics of the hydration and consequent swelling of LDH compounds containing organic and biomolecules. Citrate-HT exhibits affinity for water up to very high hydration levels, in contrast to the preferred low hydration states of most LDHs intercalated with small, inorganic anions. This result is consistent with the recent experimental observation of the delamination of lactate-HT. The high water affinity is rationalized in terms of the preference of citrate ion for hydrogen bonds (H-bonds) donated from water molecules rather than from the hydroxyl groups of the metal hydroxide layer and the need to develop an integrated interlayer H-bond network among the citrate ions, water, and -OH groups of the hydroxide layers. The changes in the orientation of citrate molecules with progressive hydration are also intimately related to its preference to accept hydrogen bonds from water.     

Secondary structure sensitivity of hydrogen bond lifetime dynamics in the protein hydration layer

The heterogeneous nature of a protein surface plays an essential role in its biological activity and molecular recognition, and this role is mediated at least partly through the surrounding water molecules. We have performed atomistic molecular dynamics simulations of an aqueous solution of HP-36 to investigate the correlation between the dynamics of the hydration layer water molecules and the lifetimes of protein-water hydrogen bonds. The nonexponential hydrogen bond lifetime correlation functions have been analyzed by using the formalism of Luzar and Chandler, which allowed identification of the quasi-bound states in the surface and quantification of the dynamic equilibrium between quasi-bound and free water molecules in terms of time-dependent rate of interconversion. It is noticed that, irrespective of the structural heterogeneity of different segments of the protein, namely the three alpha-helices, the positively charged amino acid residues form longer-lived hydrogen bonds with water. The overall relaxation behavior of protein-water hydrogen bonds is found to differ significantly among the three helices of the protein. Study of water number density fluctuation reveals that the hydration layer of helix-3 is much less rigid, which can be correlated with faster structural relaxation of the hydrogen bonds between its residues and water. This also agrees excellently with faster translational and rotational motions of water near helix-3, and hence the lower rigidity of its hydration layer. The lower rigidity of the helix-3 hydration layer also correlates well with the biological activity of the protein, as several of the active-site residues of HP-36 are located in helix-3.     

Hydroxyl radical in aqueous solution: Computer simulation

Molecular dynamics simulations of hydroxyl radical in water are carried out by use of a classical simple point charge extended (SPC/E) water model and a similar point charge model for hydroxyl radical. Structural and dynamical properties are studied along the coexistence curve of SPC/E water at 298, 373, 473, 573, and 633 K and above its critical point at 683, 733, 783, and 833 K with density fixed at 0.3 g/cm3. Dramatic changes in the diffusion dynamics of water and hydroxyl radical near the critical point are related to the reorganization of the three-dimensional structure of water around hydroxyl radical, as revealed by the study of the spatial distribution functions. This study helps us understand the kinetics of oxidation reactions in high-temperature water.     

Monolayer of aerosol-OT surfactants adsorbed at the air/water interface: an atomistic computer simulation study

An atomistic molecular dynamics (MD) simulation has been carried out to investigate the structural and dynamical properties of a monolayer of the anionic surfactant sodium bis(2-ethyl-1-hexyl) sulfosuccinate (aerosol-OT or AOT) adsorbed at the air/water interface. The simulation is performed at room temperature and at a surface coverage corresponding to that at its critical micelle concentration (78 A(2)/molecule). The estimated thickness of the adsorbed layer is in good agreement with neutron reflection data. The study shows that the surfactants exhibit diffusive motion in the plane of the interface. It is observed that the surfactant monolayer has a strong influence in restricting both the translational and reorientational motions of the water molecules close to the interface. A drastic difference in the dipolar reorientational motion of water molecules in the aqueous layer is observed with a small variation of the distance from the surfactant headgroups. It has been observed that the water molecules in the first hydration layer (region 1) form strong hydrogen bonds with surfactant headgoups. This results in the slower structural relaxation of water-water hydrogen bonds in the first hydration layer compared to that in the pure bulk water. Most interestingly, we notice that the water molecules present in the layer immediately after the first hydration layer form weaker hydrogen bonds and thus relax faster than even pure bulk water.     

Dynamics of protein and peptide hydration

Biological processes often involve the surfaces of proteins, where the structural and dynamic properties of the aqueous solvent are modified. Information about the dynamics of protein hydration can be obtained by measuring the magnetic relaxation dispersion (MRD) of the water (2)H and (17)O nuclei or by recording the nuclear Overhauser effect (NOE) between water and protein protons. Here, we use the MRD method to study the hydration of the cyclic peptide oxytocin and the globular protein BPTI in deeply supercooled solutions. The results provide a detailed characterization of water dynamics in the hydration layer at the surface of these biomolecules. More than 95% of the water molecules in contact with the biomolecular surface are found to be no more than two-fold motionally retarded as compared to bulk water. In contrast to small nonpolar molecules, the retardation factor for BPTI showed little or no temperature dependence, suggesting that the exposed nonpolar residues do not induce clathrate-like hydrophobic hydration structures. New NOE data for oxytocin and published NOE data for BPTI were analyzed, and a mutually consistent interpretation of MRD and NOE results was achieved with the aid of a new theory of intermolecular dipolar relaxation that accounts explicitly for the dynamic perturbation at the biomolecular surface. The analysis indicates that water-protein NOEs are dominated by long-range dipolar couplings to bulk water, unless the monitored protein proton is near a partly or fully buried hydration site where the water molecule has a long residence time.     

Phenol vs water molecule interacting with various molecules: Sigma-type, pi-type, and chi-type hydrogen bonds, interaction energies, and their energy components

The nature of interactions of phenol with various molecules (Y = HF, HCl, H2O, H2S, NH3, PH3, MeOH, MeSH) is investigated using ab initio calculations. The optimized geometrical parameters and spectra for the global energy minima of the complexes match the available experimental data. The contribution of attractive (electrostatic, inductive, dispersive) and repulsive (exchange) components to the binding energy is analyzed. HF favors sigma O-type H-bonding, while H2O, NH3, and MeOH favor sigma H-type H-bonding, where sigma O-/sigma H-type is the case when a H-bond forms between the phenolic O/H atom and its interacting molecule. On the other hand, HCl, H2S, and PH3 favor pi-type H-bonding, which are slightly favored over sigma O-, sigma H-, sigma H-type bonding, respectively. MeSH favors chi H-type bonding, which has characteristics of both pi and sigma H. The origin of these conformational preferences depending on the type of molecules is elucidated. Finally, phenol-Y complexes are compared with water-Y complexes. In the water-Y complexes where sigma O/sigma H-type involves the H-bond by the water O/H atom, HF and HCl favor sigma O-type, H2O involves both sigma O-/sigma H-type, and H2S, NH3, PH3, MeOH, and MeSH favor sigma H-type bonding. Except for HF, seven other species have larger binding energies with a phenol molecule than a water molecule.     

Effect of electrolyte additions and temperature on the structure self-organization of the water subsystem in water-supercritical Co<Subscript>2</Subscript>-NaCl ternary mixtures

The effect of electrolyte additions (6, 15, 23 wt % NaCl) and temperature (T 313–633 K, p 250 bar) on the structural state of the water subsystem in the water-rich phase of the water-supercritical CO₂-NaCl ternary system was studied by IR spectroscopy and the method of integral equations. With increasing salt concentration, the breaking effect of temperature on the structure of the water subsystem becomes weaker, and the fractions of H-bonded water n-mers are redistributed. In systems with a nonzero NaCl concentration, tetramers exist throughout the examined temperature range, and trimers become the main structural unit of the water subsystem at temperatures close to the critical point. The prevalent structural components of the system with 0 wt % NaCl near the critical point are dimers. The O?H bonds between water molecules and Cl?H bonds in the nearest surroundings of the anions make approximately equal contributions to the overall pattern of H bonds in the water subsystem.     

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.     

Assignment and NOE analysis of 2'-hydroxyl protons in RNA: implications for stabilization of RNA A-form duplexes

The ribose 2'-OH hydroxyl group distinguishes RNA from DNA. The 2'-OH hydroxyl protons are responsible for differences in conformation, hydration, and thermodynamic stability of RNA and DNA oligonucleotides. Additionally, the 2'-OH group plays a central role in RNA catalysis. This important group lies in the shallow groove of RNA, where it is involved in a network of hydrogen bonds with water molecules stabilizing RNA A-form duplexes. Structural and dynamical information on 2'-OH hydroxyl protons is essential to understand their respective roles. Here we report the 2'-OH hydroxyl proton assignments for a 30mer RNA, the HIV-2 transactivation region, in water using solution NMR techniques. We provide structural information on 2'-OH hydroxyl groups in the form of orientational preferences contradicting the paradigm that the 2'-OH hydroxyl typically points away from the ribose H1' proton.