Hydrophobic hydration of tert-butyl alcohol studied by Brillouin light and inelastic ultraviolet scattering

The longitudinal viscosity of diluted water-tert-butyl alcohol solutions in the 10 GHz frequency region has been measured by means of Brillouin light scattering and inelastic ultraviolet scattering. The main advantage of our hypersonic investigation compared to more traditional ultrasonic measurements is that in the gigahertz frequency range slow relaxation processes involving the alcohol dynamics are completely unrelaxed, so that the measured viscosity mainly originates from the hydrogen bond restructuring of water. In contrast with previous determinations, we estimate an activation energy which is independent from the alcohol mole fraction up to X = 0.1, and comparable to that of bulk water. A simple two-component model is used to describe the steep increase of viscosity with increasing alcohol mole fraction, and a retardation factor 1.7 ± 0.2 is found between the relaxation times of hydration and bulk water. These findings endorse a dynamic scenario where the slowing down of hydration water is mainly due to a reduction of configurational entropy and does not involve an arrested, icelike, dynamics.     

Absorption and velocity of ultrasonic waves in thiophene, o-, p-xylenes and their mixtures

The results of acoustic measurements of velocity and absorption in three pure liquids: thiophene, p-and m-xylenes and their mixtures are presented. The experiments for the mixtures of thiophene were carried out by Eggers' method at frequencies 0.3–5 MHz, and for pure liquids by the pulse method in the frequency range 10 MHz–10 GHz, all at 293.15 K except for thiophene (at 281 and 333 K).

The absorption in thiophene shows that all vibrational degrees of freedom take part in the observed relaxation, caused by the Kneser processes. This process can be described as a vibrational relaxation with one relaxation time. Absorption in the mixtures decreased when increasing the amount of xylenes, as predicted by theory of gases, thus suggesting that the absorption is probably due to the same phenomenon as in gases.     

Molecular dynamics simulation of the free surface of liquid formamide

Molecular dynamics simulations of liquid formamide (HCONH₂) were carried out using the GROMOS software. The formamide molecule is represented by all of its atoms with all internal degrees of freedom. In contrast to other simulations dealing with bulk properties, this study focuses on the interface liquid–vacuum for the first time. We show that the molecular plane is tilted out of the surface, exposing the HCO group to the vacuum. © 1997 John Wiley & Sons, Inc. Int J Quant Chem 63 : 1123–1131, 1997     

Considering vibrations in the thermodynamic functions of a solid adsorbate in slit-like pores

Problems that arise in refining calculations of the equilibrium thermodynamic functions of an adsorbate located near an adsorbent’s surface or inside slit-like pores when its collective vibrational motions are considered are discussed. A technique is proposed for calculating collective vibrations for a small number of vacancies in a defective heterogeneous adsorbate from changes in the number of degrees of freedom and the local frequencies in the frequency distribution function in an ideal bulk crystal.     

Hydration-induced far-infrared absorption increase in myoglobin

The interaction of proteins with an aqueous environment leads to a thin region of "biological water", the molecules of which have properties that differ from those of bulk water, in particular, reduced absorption of far-infrared radiation caused by protein-induced hindrance of the water rotational and vibrational degrees of freedom. New results at terahertz (THz) frequencies, however, show that absorption per protein molecule is increased by the presence of biological water. Absorption measurements were made of the heme protein myoglobin mixed with water from 3.6 to 98 wt % in the frequency range of 0.1-1.2 THz, using THz time-domain spectroscopy. Analysis shows greater THz absorption when compared to a non-interacting protein-water model. Including the suppressed absorption of biological water leads to a substantial hydration-dependent increase in absorption per protein molecule over a wide range of concentration and frequencies, meaning that water increases the protein's polarizability.     

Temperature dependence of density, thermal expansion coefficient and shear viscosity of supercooled glycerol as a reflection of its structure

The relationship of the microstructure of supercooled, highly viscous glycerol to the temperature dependence of its density, thermal expansion coefficient, and shear viscosity are discussed. The character of this temperature dependence at the transition from low viscosity state to the solid amorphous state (solidified state without nuclei) is described with help of function psi, which can be interpreted as the effective number of degrees of freedom responsible for the change of viscosity of glycerol over a broad range; these degrees of freedom are those related to the alpha-relaxation process. It is shown that the change in effective activation energy of the viscosity is completely determined by the parameter psi. The change in the shear viscosity of glycerol due to the influence of the solid-phase nuclei is considered. It is shown that the introduction of the parameter phi, equal to the specific volume occupied by the nuclei of the solid phase, together with psi provides a natural explanation of the temperature dependence of density and thermal expansion coefficients of glycerol in its liquid, solid amorphous, glassy, and crystal states. The peculiarities of the temperature dependence of phi(T) and psi(T) for glycerol and o-terphenyl are compared.     

A stereographic projection path integral study of the coupling between the orientation and the bending degrees of freedom of water

A Monte Carlo path integral method to study the coupling between the rotation and bending degrees of freedom for water is developed. It is demonstrated that soft internal degrees of freedom that are not stretching in nature can be mapped with stereographic projection coordinates. For water, the bending coordinate is orthogonal to the stereographic projection coordinates used to map its orientation. Methods are developed to compute the classical and quantum Jacobian terms so that the proper infinitely stiff spring constant limit is recovered in the classical limit, and so that the nonconstant nature of the Riemann Cartan curvature scalar is properly accounted in the quantum simulations. The theory is used to investigate the effects of the geometric coupling between the bending and the rotating degrees of freedom for the water monomer in an external field in the 250 to 500 K range. We detect no evidence of geometric coupling between the bending degree of freedom and the orientations.     

Brillouin scattering and hypersonic relaxation in amorphous polymers

Mechanical relaxation at hypersonic frequencies is measured using Brillouin spectroscopy for polyisobutylene, atactic polypropylene, polydimethyl siloxane, and polyvinyl acetate. The temperatures of maximum loss determined in the gigahertz range are compared to the published transitions maps for the above polymers. It is found that the hypersonic relaxation data fall on an extrapolation of the secondary main chain glass–rubber relaxation line above the region where the primary and secondary lines merge.     

Effects of classical nonlinear resonances in grazing diatom-surface collisions

Energy transfer between vibrational, rotational, and translational degrees of freedom of a molecule during a collision process is enhanced when the classical frequencies associated with the initial state are in the proximity of nonlinear resonance conditions. We present an analysis of the classical resonant effects in the collisions of light diatoms with periodic surfaces, and discuss the initial conditions in which these effects can be observed. In particular, we find that for grazing incidence and resonant initial values of the classical frequencies, corresponding to specific vibro-rotational molecular states and translational energies, an efficient energy transfer between the intramolecular vibro-rotational degrees of freedom and the translational degree of freedom along a symmetry direction on the surface can be found. This efficient energy transfer manifests itself in the emergence of specific peaks in the molecular diffraction patterns. The predictions of the resonance analysis are contrasted with the results of classical trajectory calculations obtained in a diatom-rigid surface collision model.     

State-resolved investigation of the photodesorption dynamics of NO from (NO)2 on Ag nanoparticles of various sizes in comparison with Ag(111)

The translational and internal state energy distributions of NO desorbed by laser light (2.3, 3.5, and 4.7 eV) from adsorbed (NO)(2) on Ag nanoparticles (NPs) (mean diameters, D = 4, 8, and 11 nm) have been investigated by the (1 + 1) resonance enhanced multiphoton ionization technique. For comparison, the same experiments have also been carried out on Ag(111). Detected NO molecules are hyperthermally fast and both rotationally and vibrationally hot, with temperatures well above the sample temperature. The translational and rotational excitations are positively correlated, while the vibrational excitation is decoupled from the other two degrees of freedom. Most of the energy content of the desorbing NO is contained in its translation. The translational and internal energy distributions of NO molecules photodesorbed by 2.3, 3.5, and in part also 4.7 eV light are approximately constant as a function of Ag NPs sizes, and they are the same on Ag(111). This suggests that for these excitations a common mechanism is operative on the bulk single crystal and on NPs, independent of the size regime. Notably, despite the strongly enhanced cross section seen on NP at 3.5 eV excitation energy in p-polarization, i.e., in resonance with the plasmon excitation, the mechanism is also unchanged. At 4.7 eV and for small particles, however, an additional desorption channel is observed which results in desorbates with higher energies in all degrees of freedom. The results are well compatible with our earlier measurements of size-dependent translational energy distributions. We suggest that the broadly constant mechanism over most of the investigated range runs via a transient negative ion state, while at high excitation energy and for small particles the transient state is suggested to be a positive ion.     

Dynamics of benzene molecules situated in metal-organic frameworks

In this paper, we investigate the gyroscopic motion of a benzene molecule C₆H₆, which comprises an inner carbon ring and an outer hydrogen ring, and is suspended rigidly inside a metal-organic framework. The metal-organic framework provides a sterically unhindered environment and an electronic barrier for the benzene molecule. We model such gyroscopic motion from the inter-molecular interactions between the benzene ring and the metal-organic framework by both the Columbic force and the van der Waals force. We also capture additional molecular interactions, for example due to sterical compensations arising from the carboxylate ligands between the benzene molecule and the framework, by incorporating an extra empirical energy into the total molecular energy. To obtain a continuous approximation to the total energy of such a complicated atomic system, we assume that the atoms of the metal-organic framework can be smeared over the surface of a cylinder, while those for the benzene molecule are smeared over the contour line of the molecule. We then approximate the pairwise molecular energy between the molecules by performing line and surface integrals. We firstly investigate the freely suspended benzene molecule inside the framework and find that our theoretical results admit a two-fold flipping, with the possible maximum rotational frequency reaching the terahertz regime, and gigahertz frequencies at room temperature. We also show that the electrostatic interaction and the thermal energy dominate the gyroscopic motion of the benzene molecule, and we deduce that the extra energy term could possibly reduce the rotational frequency of the rigidly suspended benzene molecule from gigahertz to megahertz frequencies at room temperature, and even lower frequencies might be obtained when the strength of these interactions increases.     

Influence of bond flexibility on the vapor-liquid phase equilibria of water

The authors performed Gibbs ensemble simulations on the vapor-liquid equilibrium of water to investigate the influence of incorporating intramolecular degrees of freedom in the simple point charge (SPC) water model. Results for vapor pressures, saturation densities, heats of vaporization, and the critical point for two different flexible models are compared with data for the corresponding rigid SPC and SPC/E models. They found that the introduction of internal vibrations, and also their parametrization, has an observable effect on the prediction of the vapor-liquid coexistence curve. The flexible SPC/Fw model, although optimized to describe bulk diffusion and dielectric constants at ambient conditions, gives the best prediction of saturation densities and the critical point of the examined models.     

Bayesian estimation of the internal structure of proteins from single-molecule measurements

In single-molecule protein experiments, the observable variables are restricted within a small fraction of the entire degrees of freedom. Therefore, to investigate the physical nature of proteins in detail, we always need to estimate the hidden internal structure referring only to the accessible degrees of freedom. We formulate this problem on the basis of Bayesian inference, which can be applied to various complex systems. In the ideal case, we find that in general the framework actually works. Although careful numerical studies confirm that our method outperforms the conventional method by up to two orders of magnitude, we find a striking phenomenon: a loss-of-precision transition occurs abruptly when the design of the observation system is inappropriate. The basic features of the proposed method are illustrated using a simple but nontrivial model.     

The role of reagent internal excitation in collision experiments

Variations in the rates of endoergic reactions due to different reagent excitations at the same total energy are of a limited (positive or negative) range and reflect a dynamical bias. Not so for bulk experiments, where all non-selected degrees of freedom have a thermal distribution.     

Elastic excitations in polycarbonate membranes

Brillouin light scattering was used to probe acoustic waves propagating with both longitudinal and transverse polarizations in the surface and the bulk of self‐supported particle track‐etched polycarbonate membranes with 15‐ and 80‐nm nanopores. The recorded scattering line shape at gigahertz frequencies reveals changes in the surface waves of the membranes which are more pronounced for the 80‐nm nanopores despite the low porosity (0.7 and 0.05%). Because the measured elastic constants (1.2 and 6.2 GPa) were found to compare very well with the values for thick polycarbonate film, modifications of the elasto‐optical coefficients and/or the transparency might be the reason for the different scattering line shapes. © 2004 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 42: 3311–3317, 2004     

Phonostat: thermostatting phonons in molecular dynamics simulations

Thermostat algorithms in a molecular dynamics simulation maintain an average temperature of a system by regulating the atomic velocities rather than the internal degrees of freedom. Herein, we present a "phonostat" algorithm that can regulate the total energy in a given internal degree of freedom. In this algorithm, the modal energies are computed at each time step using a mode-tracking scheme and then the system is driven by an external driving force of desired frequency and amplitude. The rate and amount of energy exchange between the phonostat and the system is controlled by two distinct damping parameters. Two different schemes for controlling the external driving force amplitude are also presented. In order to test our algorithm, the method is applied initially to a simple anharmonic oscillator for which the role of various phonostat parameters can be carefully tested. We then apply the phonostat to a more realistic (10,0) carbon nanotube system and show how such an approach can be used to regulate energy of highly anharmonic modes.     

Effect of high-viscosity interphases on drainage between hydrophilic surfaces

Drainage of water from the region between an advancing probe tip and a flat sample is reconsidered under the assumption that the tip and sample surfaces are both coated by a thin water "interphase" (of width approximately a few nanometers) whose viscosity is much higher than that of the bulk liquid. A formula derived by solving the Navier-Stokes equations allows one to extract an interphase viscosity of approximately 59 kPa x s (or approximately 6.6 x 10(7) times the viscosity of bulk water at 25 degrees C) from interfacial force microscope measurements with both tip and sample functionalized hydrophilic by OH-terminated tri(ethylene glycol) undecylthiol, self-assambled monolayers.     

Hydrogen in Palladium and Storage Properties of Related Nanomaterials: Size,Shape, Alloying,and Metal-Organic Framework Coating Effects

One of the key issues for an upcoming hydrogen energy-based society is to develop highly efficient hydrogen-storage materials. Among the many hydrogen-storage materials reported, transition-metal hydrides can reversibly absorb and desorb hydrogen, and have thus attracted much interest from fundamental science to applications. In particular, the Pd−H system is a simple and classical metal-hydrogen system, providing a platform suitable for a thorough understanding of ways of controlling the hydrogen-storage properties of materials. By contrast, metal nanoparticles have been recently studied for hydrogen storage because of their unique properties and the degrees of freedom which cannot be observed in bulk, i. e., the size, shape, alloying, and surface coating. In this review, we overview the effects of such degrees of freedom on the hydrogen-storage properties of Pd-related nanomaterials, based on the fundamental science of bulk Pd−H. We shall show that sufficiently understanding the nature of the interaction between hydrogen and host materials enables us to control the hydrogen-storage properties though the electronic-structure control of materials.