Water inside a hydrophobic cavitand molecule

The structure and dynamics of water inside a water-soluble, bowl-shaped cavitand molecule with a hydrophobic interior are studied using molecular dynamics computer simulations. The simulations find that the number of inside water molecules is about 4.5, but it fluctuates from being completely empty to full on a time scale of tens of nanoseconds. The transition from empty to full is energetically favorable and entropically unfavorable. The water molecules inside have fewer hydrogen bonds than the bulk and in general weaker interactions; the lower energy results from the nearest-neighbor interactions with the cavitand atoms and the water molecules at the entrance of the cavitand, interactions that are lost upon dewetting. An analysis of translational and rotational motion suggests that the lower entropy of the inside water molecules is due to decreased translational entropy, which outweighs an increased orientational entropy. The cavitand molecule acts as a host binding hydrophobic guests, and dewetting can be induced by the presence of a hydrophobic guest molecule about 3 A above the entrance. At this position, the guest displaces the water molecules which stabilize the inside water molecules and the empty cavitand becomes more stable than the full.     

Structural and dynamic properties of water within the solvation layer around various conformations of the glycine-based polypeptide

Several conformations of the solvated glycine-based polypeptides were investigated using molecular dynamics simulations. Some properties of water in the neighboring space around these molecules were investigated. It was found that water forms a well-defined layer-the first solvation shell-around the peptide molecule, and thickness of this layer is independent of the peptide structure and is equal to approximately 0.28 nm. Within this layer, water molecules show marked orientations relative to a peptide surface. Using the two-particle contribution to entropy as a measure of structural ordering of water, we found that the first solvation shell contributes 95% or more to the total water ordering around the peptide molecule. In investigating the dynamic properties of water, diffusion coefficients and lifetime of the hydrogen bond, clear differences between solvation layer and the bulk water were observed. It was found that the translational diffusion coefficient, D(T), decreases by 30% or more compared to bulk water; also, the lifetime of the water-water hydrogen bond clearly increases. The rotational diffusion coefficient, however, decreases only slightly, no more than approximately 10%. These differences correspond to the slightly higher energy of the hydrogen bond, and to its slightly distorted geometry. Analyzing the translational dynamics of water in the vicinity of the peptide molecule, it was deduced that the structure of the first solvation shell becomes more rigid than the structure of the bulk water. Investigation of a "pure hydrophobic" form of the polypeptide shows that the structure and the properties of water within the solvation shell are predominantly determined by the hydrophobic effect. The specific interactions between water molecules and various charge groups of the peptide molecule modifies this effect only slightly.     

Quasi-elastic neutron scattering study of dimethyl-sulfoxide-water mixtures: probing molecular mobility in a nonideal solution

The translational and rotational motions of water and dimethyl sulfoxide, [DMSO, (CH(3))(2)SO] have been investigated using quasi-elastic neutron scattering. Water-DMSO mixtures at five DMSO mole fractions, chi(DMSO), ranging from 0 to 0.75, were measured. Hydrogen-deuterium substitution was used to extract independently the water proton dynamics (d-DMSO-H(2)O), the DMSO methyl proton dynamics (h-DMSO-D(2)O) and to obtain background corrections (d-DMSO-D(2)O). The translational diffusion of water slows down significantly compared to bulk water at all chi(DMSO)>0. The rotational time constant for water exhibits a maximum at chi(DMSO)=0.33 that corresponds to the observed maximum of the viscosity of the mixture. Data for DMSO can be analyzed in terms of a relatively slow tumbling of the molecule about its center-of-mass in conjunction with random translational diffusion. The rotational time constant for this motion exhibits some dependence on chi(DMSO), while the translational diffusion constant shows no clear variation for chi(DMSO)>0. The results presented reinforce the idea that due to the stronger associative nature of DMSO, DMSO-water aggregates are formed over the whole composition range, disturbing the tetrahedral natural arrangement of the water molecules. As a consequence adding DMSO to water causes a drastic slowing down of the dynamics of the water molecule, and vice versa.     

Energy controlled insertion of polar molecules in dense fluids

We present a method to search low energy configurations of polar molecules in the complex potential energy surfaces associated with dense fluids. The search is done in the configurational space of the translational and rotational degrees of freedom of the molecule, combining steepest-descent and Newton-Raphson steps which embed information on the average sizes of the potential energy wells obtained from prior inspection of the liquid structure. We perform a molecular dynamics simulation of a liquid water shell which demonstrates that the method enables fast and energy-controlled water molecule insertion in aqueous environments. The algorithm finds low energy configurations of incoming water molecules around three orders of magnitude faster than direct random insertion. This method represents an important step towards dynamic simulations of open systems and it may also prove useful for energy-biased ensemble average calculations of the chemical potential.     

Thermodynamics of water entry in hydrophobic channels of carbon nanotubes

Experiments and computer simulations demonstrate that water spontaneously fills the hydrophobic cavity of a carbon nanotube. To gain a quantitative thermodynamic understanding of this phenomenon, we use the recently developed two phase thermodynamics method to compute translational and rotational entropies of confined water molecules inside single-walled carbon nanotubes and show that the increase in energy of a water molecule inside the nanotube is compensated by the gain in its rotational entropy. The confined water is in equilibrium with the bulk water and the Helmholtz free energy per water molecule of confined water is the same as that in the bulk within the accuracy of the simulation results. A comparison of translational and rotational spectra of water molecules confined in carbon nanotubes with that of bulk water shows significant shifts in the positions of the spectral peaks that are directly related to the tube radius.     

Surface influence on the rotational and translational dynamics of molecules confined inside a mesoporous carbon xerogel

Low-field nuclear magnetic resonance techniques are employed to extract information about the effects introduced by the interaction with the surface on the rotational and translational dynamics of molecules confined inside a mesoporous carbon xerogel. The molecules under study were water, cyclohexane, and hexane. They were chosen due to their different interaction strength with the carbonaceous matrix. Frequency dependent longitudinal relaxation measurements, using the fast field cycling technique, allowed extraction of the fractal dimension of the carbon xerogel surface. It was observed that the measured value is influenced by the molecule affinity to the surface. Diffusion measurements, using the pulse field gradient technique, have revealed that the stronger interaction with the surface of cyclohexane and hexane molecules leads to an increased diffusive tortuosity, as compared with water.     

Entropy and dynamics of water in hydration layers of a bilayer

We compute the entropy and transport properties of water in the hydration layer of dipalmitoylphosphatidylcholine bilayer by using a recently developed theoretical scheme [two-phase thermodynamic model, termed as 2PT method; S.-T. Lin et al., J. Chem. Phys. 119, 11792 (2003)] based on the translational and rotational velocity autocorrelation functions and their power spectra. The weights of translational and rotational power spectra shift from higher to lower frequency as one goes from the bilayer interface to the bulk. Water molecules near the bilayer head groups have substantially lower entropy (48.36 J/mol/K) than water molecules in the intermediate region (51.36 J/mol/K), which have again lower entropy than the molecules (60.52 J/mol/K) in bulk. Thus, the entropic contribution to the free energy change (TΔS) of transferring an interface water molecule to the bulk is 3.65 kJ/mol and of transferring intermediate water to the bulk is 2.75 kJ/mol at 300 K, which is to be compared with 6.03 kJ/mol for melting of ice at 273 K. The translational diffusion of water in the vicinity of the head groups is found to be in a subdiffusive regime and the rotational diffusion constant increases going away from the interface. This behavior is supported by the slower reorientational relaxation of the dipole vector and OH bond vector of interfacial water. The ratio of reorientational relaxation time for Legendre polynomials of order 1 and 2 is approximately 2 for interface, intermediate, and bulk water, indicating the presence of jump dynamics in these water molecules.     

Structure and dynamics of N,N-diethyl-N-methylammonium triflate ionic liquid, neat and with water, from molecular dynamics simulations

We investigated by means of molecular dynamics simulations the properties (structure, thermodynamics, ion transport, and dynamics) of the protic ionic liquid N,N-diethyl-N-methylammonium triflate (dema:Tfl) and of selected aqueous mixtures of dema:Tfl. This ionic liquid, a good candidate for a water-free proton exchange membrane, is shown to exhibit high ion mobility and conductivity. The radial distribution functions reveal a significant long-range structural correlation. The ammonium cations [dema](+) are found to diffuse slightly faster than the triflate anions [Tfl](-), and both types of ions exhibit enhanced mobility at higher temperatures, leading to higher ionic conductivity. Analysis of the dynamics of ion pairing clearly points to the existence of long-lived contact ion pairs. We also examined the effects of water through characterization of properties of dema:Tfl-water mixtures. Water molecules replace counterions in the coordination shell of both ions, thus weakening their association. As water concentration increases, water molecules start to connect with each other and then form a large network that percolates through the system. Water influences ion dynamics in the mixtures. As the concentration of water increases, both translational and rotational motions of [dema](+) and [Tfl](-) are significantly enhanced. As a result, higher vehicular ionic conductivity is observed with increased hydration level.     

Dynamics of surface water in ZrO2 studied by quasielastic neutron scattering

A quasielastic neutron scattering experiment has revealed the dynamics of surface water in a high surface area zirconium oxide in the temperature range of 300-360 K. The characteristic times of the rotational (picoseconds) and translational (tens of picoseconds) components of diffusion motion are well separated. The rotational correlation time shows an Arrhenius-type behavior with an activation energy of 4.48 kJ/mol, which is lower compared to bulk water. The rotational diffusion at room temperature is slower by about a factor of 2 compared to bulk water, whereas the translational diffusion slows down by a factor of 40. In contrast to bulk water, the translational correlation time exhibits an Arrhenius-type temperature dependence with an activation energy of 11.38 kJ/mol. Comparison of different models for jump diffusion processes suggests that water molecules perform two-dimensional jumps at a well-defined, almost temperature-independent distance of 4.21-4.32 A. Such a large jump distance indicates a low molecular density of the layer of diffusing molecules. We argue that undissociated water molecules on an average form two hydrations layers on top of the surface layer of hydroxyl groups, and all the layers have similar molecular density. Quasielastic neutron scattering experiment assesses the dynamics of the outermost hydration layer, whereas slower motion of the water molecules in the inner hydration layer contributes to the elastic signal.     

Crystal structure and dynamics of Mg(ND3)6Cl2

The crystal structure and dynamics of Mg(ND(3))(6)Cl(2) have been investigated by powder neutron diffraction and molecular dynamics. The powder diffraction data can be well described by 4 partly occupied deuterium sites in a square arrangement around the N atoms, which is seemingly inconsistent with the 3-fold symmetry of the ND(3) molecule. Molecular dynamics show highly correlated rotational and translational motion of the ND(3) molecules which explains the apparent 4-fold symmetry of the deuterium arrangement. A more disordered structure model based on the molecular dynamics results gives a better fit to the experimental data and is in agreement with the 3-fold symmetry of ND(3).     

Hydrogen bond breaking mechanism and water reorientational dynamics in the hydration layer of lysozyme

The mechanism and the rate of hydrogen bond-breaking in the hydration layer surrounding an aqueous protein are important ingredients required to understand the various aspects of protein dynamics, its function, and stability. Here, we use computer simulation and a time correlation function technique to understand these aspects in the hydration layer of lysozyme. Water molecules in the layer are found to exhibit three distinct bond-breaking mechanisms. A large angle orientational jump of the donor water molecule is common among all of them. In the most common ( approximately 80%) bond-breaking event in the layer, the new acceptor water molecule comes from the first coordination shell (initially within 3.5 A of the donor), and the old acceptor water molecule remains within the first coordination shell, even after the bond-breaking. This is in contrast to that in bulk water, in which both of the acceptor molecules involve the second coordination shell. Additionally, the motion of the incoming and the outgoing acceptor molecules involved is not diffusive in the hydration layer, in contrast to their observed diffusive motion in the bulk. The difference in rotational dynamics between the bulk and the hydration layer water molecules is clearly manifested in the calculated time-dependent angular van Hove self-correlation function ( G(theta, t)) which has a pronounced two-peak structure in the layer, and this can be traced to the constrained translational motion in the layer. The longevity of the surrounding hydrogen bond network is found to be significantly enhanced near a hydrophilic residue.     

Hydrogen bonding and cooperativity in isolated and hydrated sugars: mannose, galactose, glucose, and lactose

The conformation of phenyl-substituted monosaccharides (mannose, galactose, and glucose) and their singly hydrated complexes has been investigated in the gas phase by means of a combination of mass selected, conformer specific ultraviolet and infrared double resonance hole burning spectroscopy experiments, and ab initio quantum chemistry calculations. In each case, the water molecule inserts into the carbohydrate at a position where it can replace a weak intramolecular interaction by two stronger intermolecular hydrogen bonds. The insertion can produce significant changes in the conformational preferences of the carbohydrates, and there is a clear preference for structures where cooperative effects enhance the stability of the monosaccharide conformers to which the water molecule chooses to bind. The conclusions drawn from the study of monosaccharide-water complexes are extended to the disaccharide lactose and discussed in the light of the underlying mechanisms that may be involved in the binding of carbohydrate assemblies to proteins and the involvement, or not, of key structural water molecules.     

Glasslike behavior in aqueous electrolyte solutions

When salts are added to water, generally the viscosity increases, suggesting that the ions increase the strength of the water's hydrogen-bond network. However, infrared pump-probe measurements on electrolyte solutions have found that ions have no influence on the rotational dynamics of water molecules, implying no enhancement or breakdown of the hydrogen-bond network. Here, we report optical Kerr effect and dielectric relaxation spectroscopic measurements, which have enabled us to separate the effects of rotational and transitional motions of the water molecules. These data show that electrolyte solutions behave like a supercooled liquid approaching a glass transition in which rotational and translational molecular motions are decoupled. It is now possible to understand previously conflicting viscosity data, nuclear magnetic resonance relaxation, and ultrafast infrared spectroscopy in a single unified picture.     

Orientational dynamics of water trapped between two nanoscopic hydrophobic solutes: A molecular dynamics simulation study

We investigate thoroughly the effect of confinement and solute topology on the orientational dynamics of water molecule in the interplate region between two nanoscopic hydrophobic paraffinlike plates. Results are obtained from molecular dynamics simulations of aqueous solutions of paraffinlike plates in the isothermal-isobaric ensemble. An analysis of survival time auto correlation function shows that the residence time of the water molecule in the confined region between two model nanoscopic hydrophobic plates depends on solute surface topology (intermolecular distance within the paraffinlike plate). As expected, the extent of confinement also changes the residence time of water molecules considerably. Orientational dynamics was analyzed along three different directions, viz., dipole moment, HH, and perpendicular to molecular plane vectors. It has been demonstrated that the rotational dynamics of the confined water does not follow the Debye rotational diffusion model, and surface topology of the solute plate and the extent of confinement have considerable effect on the rotational dynamics of the confined water molecules.     

Crystallization of the Lewis-Wahnström ortho-terphenyl model

Crystallization is observed during microsecond long molecular dynamics simulations of bent trimers, a molecular model proposed by Lewis and Wahnstro?m for ortho-terphenyl. In the crystal, the three spheres that make up the rigid molecule sit near sites of a body centered cubic lattice. The trimer bond angle is almost optimal for this structure. The crystal exhibits orientational disorder with the molecules aligned randomly along the three Cartesian axis, i.e., cubatic orientational order. The rotational and translational mobilities exhibit only modest decreases on crystallization, by factors of 10 and 3, respectively. The rotational relaxation does change from Debye-like in the liquid to large angle jumps in the crystal. We consider the origin of the superior glass forming ability of the trimer over the monatomic liquid.     

Long-range influence of carbohydrates on the solvation dynamics of water--answers from terahertz absorption measurements and molecular modeling simulations

We present new terahertz (THz) spectroscopic measurements of solvated sugars and compare the effect of two disaccharides (trehalose and lactose) and one monosaccharide (glucose) with respect to the solute-induced changes in the sub-picosecond network dynamics of the hydration water. We found that the solute affects the fast collective network motions of the solvent, even beyond the first solvation layer. For all three carbohydrates, we find an increase of 2-4% in the THz absorption coefficient of the hydration water in comparison to bulk water. Concentration-dependent changes in the THz absorption between 2.1 and 2.8 THz of the solute-water mixture were measured with a precision better than 1% and were used to deduce a dynamical hydration shell, which extends from the surface up to 5.7 +/- 0.4 and 6.5 +/- 0.9 A for the disaccharides lactose and trehalose, respectively, and 3.7 +/- 0.9 A for the glucose. This exceeds the values for the static hydration shell as determined, for example, by scattering, where the long-range structure was found to be not significantly affected by the solute beyond the first hydration shell. When comparing all three carbohydrates, we found that the solute-induced change in the THz absorption depends on the product of molar concentration of the solute and the number of hydrogen bonds between the carbohydrate and water molecules. We can conclude that the long-range influence on the sub-picosecond collective water network motions of the hydration water is directly correlated with the average number of hydrogen bonds between the molecule and adjacent water molecules for carbohydrates. This implies that monosaccharides have a smaller influence on the surrounding water molecules than disaccharides. This could explain the bioprotection mechanism of sugar-water mixtures, which has been found to be more effective for disaccharides than for monosaccharides.     

Solute rotational dynamics at the water liquid/vapor interface

The rotational dynamics of a number of diatomic molecules adsorbed at different locations at the interface between water and its own vapors are studied using classical molecular dynamics computer simulations. Both equilibrium orientational and energy correlations and nonequilibrium orientational and energy relaxation correlations are calculated. By varying the dipole moment of the molecule and its location, and by comparing the results with those in bulk water, the effects of dielectric and mechanical frictions on reorientation dynamics and on rotational energy relaxation can be studied. It is shown that for nonpolar and weekly polar solutes, the equilibrium orientational relaxation is much slower in the bulk than at the interface. As the solute becomes more polar, the rotation slows down and the surface and bulk dynamics become similar. The energy relaxation (both equilibrium and nonequilibrium) has the opposite trend with the solute dipole (larger dipoles relax faster), but here again the bulk and surface results converge as the solute dipole is increased. It is shown that these behaviors correlate with the peak value of the solvent-solute radial distribution function, which demonstrates the importance of the first hydration shell structure in determining the rotational dynamics and dependence of these dynamics on the solute dipole and location.     

1H NMR relaxation in glycerol solutions of nitroxide radicals: effects of translational and rotational dynamics

(1)H spin-lattice relaxation rates in glycerol solutions of selected nitroxide radicals at temperatures between 200 K and 400 K were measured at 15 MHz and 25 MHz. The frequency and temperature conditions were chosen in such a way that the relaxation rates go through their maximum values and are affected by neither the electron spin relaxation nor the electron-nitrogen nucleus hyperfine coupling, so that the focus could be put on the mechanisms of motion. By comparison with (1)H spin-lattice relaxation results for pure glycerol, it has been demonstrated that the inter-molecular electron spin-proton spin dipole-dipole interactions are affected not only by relative translational motion of the solvent and solute molecules, but also by their rotational dynamics as the interacting spins are displaced from the molecular centers; the eccentricity effects are usually not taken into account. The (1)H relaxation data have been decomposed into translational and rotational contributions and their relative importance as a function of frequency and temperature discussed in detail. It has been demonstrated that neglecting the rotational effects on the inter-molecular interactions leads to non-realistic conclusions regarding the translational dynamics of the paramagnetic molecules.     

Single particle and collective hydration dynamics for hydrophobic and hydrophilic peptides

We have conducted extensive molecular dynamics simulations to study the single particle and collective dynamics of water in solutions of N-acetyl-glycine-methylamide, a model hydrophilic protein backbone, and N-acetyl-leucine-methylamide, a model (amphiphilic) hydrophobic peptide, as a function of peptide concentration. Various analytical models commonly used in the analysis of incoherent quasielastic neutron scattering (QENS), are tested against the translational and rotational intermediate scattering function, the mean square displacement of the water molecule center of mass, and fits to the second-order rotational correlation function of water evaluated directly from the simulation data. We find that while the agreement between the model-free analysis and analytical QENS models is quantitatively poor, the qualitative feature of dynamical heterogeneity due to caging is captured well by all approaches. The center of mass collective and single particle intermediate scattering functions of water calculated for these peptide solutions show that the crossover from collective to single particle-dominated motions occurs at a higher value of Q for high concentration solutions relative to low concentration because of the greater restriction in movement of water molecules due to confinement. Finally, we have shown that at the same level of confinement of the two peptides, the aqueous amphiphilic amino acid solution shows the strongest deviation between single particle and collective dynamics relative to the hydrophilic amino acid, indicating that chemical heterogeneity induces even greater spatial heterogeneity in the water dynamics.