Instantaneous normal mode analysis of a series of model molten salts

A combination of analytical theory and molecular dynamics simulation was previously used to investigate how the dynamics of a fused salt are affected by the distributions of mass and charge in its component ions. These studies are now extended by using instantaneous normal mode analysis to explore how changes in ionic structure affect translational and rotational dynamics at different frequencies. The results indicate that the details of the charge distribution are important in coupling translational and rotational motion in ionic liquids. The observations are broadly consistent with the predictions of the charge lever moment formalism, and provide insight on the nature of dynamics in fused salts.     

Effects of water model and simulation box size on protein diffusional motions

We performed molecular dynamics simulations of ubiquitin with the distinct water models, TIP3P, SPC, SPC/E, and SPC/Fw, in different system sizes with different box shapes. The translational diffusion constants of pure water linearly depend on the effective box length, which is known as finite size effect, whereas the first and second rotational times of pure water are nearly constant. We then observed that both the overall translation and rotational motions of the protein are linearly correlated to the viscosity of pure water. As expected from the finite size effect in pure water, the translational diffusion of the protein is significantly affected by the system size, and rotational diffusion is nearly size-independent. After correction for the finite size effect, the SPC/E and SPC/Fw models reproduce both the translational and rotational motion of the protein relatively well. Thus, water models that reproduce the experimentally derived diffusional properties of pure water accurately are expected to also be suitable for simulating protein diffusion quantitatively.     

An investigation of water dynamics in binary mixtures of water and dimethyl sulfoxide

The motion of water molecules in mixtures of water and d6-dimethyl sulfoxide (DMSO) has been explored through molecular dynamics (MD) simulations using the SPC/E water model (J. Chem. Phys. 1987, 91, 6269) and the P2 DMSO model (J. Chem. Phys. 1993, 98, 8160). We evaluate the self-intermediate scattering functions, FS(Q,t), which are related by a Fourier transform to the incoherent structure factors, S(Q,omega), measured in quasielastic neutron scattering (QNS) experiments. We compare our results to recent QNS experiments on these mixtures reported by Bordallo et al. (J. Chem. Phys. 2004, 121, 12457). In addition to comparing the MD data to the experimental signals, which correspond to a convolution of S(Q,omega) with a resolution function, we examine the rotational and translational components of FS(Q,t) and investigate to what extent simulation results for the single-molecule dynamics follow the dynamical models that are used in the analysis of the experimental data. We find that the agreement between the experimental signal and the MD data is quite good and that the portion of FS(Q,t) due to translational dynamics is well represented by the jump-diffusion model. The model parameters and their composition dependence are in reasonable agreement with experiment, exhibiting similar trends in water mobility with composition. Specifically, we find that water motion is less hindered in water-rich and water-poor mixtures than it is near equimolar composition. We find that the extent of coupling between rotational and translational motion contributing to FS(Q,t) increases as the equimolar composition of the mixture is approached. Thus, the decoupling approximation, which is used to extract information on rotational relaxation from QNS spectra at higher momentum transfer (Q) values, becomes less accurate than that in water-rich or DMSO-rich mixtures. We also find that rotational relaxation deviates quite strongly from the isotropic rotational diffusion model. We explore this issue further by investigating the behavior of orientational time correlations for different unit vectors and corresponding to Legendre polynomials of orders 1-4. We find that the rotational time correlations of water molecules behave in a way that is more consistent with the extended jump rotation model recently proposed by Laage and Hynes (Science 2006, 311, 832).     

Specific heat of molecular crystals from atomic mean square displacements with the Einstein, Debye, and Nernst-Lindemann models

Analysis of atomic displacement parameters (ADPs) from multitemperature diffraction data provides mean-field molecular translation and libration frequencies. These quantities have been combined with molecular deformation frequencies calculated ab initio, e.g. by DFT methods, to calculate the specific heat Cv of molecular crystals of naphthalene, anthracene, and hexamethylenetetramine. If the difference Cp - Cv is represented by the Nernst-Lindemann relation, Cp curves from diffraction experiments and ab initio calculations agree well with those based on calorimetry. Agreement is better if the Debye rather than the Einstein model is chosen to represent the contribution of the translational vibrations. Compressibilities estimated from the differences Cp - Cv are 2-5 times higher than those obtained from compressibility measurements at 298 K and Grüneisen constants derived from the temperature dependence of ADPs.     

Characteristic behavior of short-term dynamics in reorientation for Gay-Berne particles near the nematic-isotropic phase transition temperature

A specific transition behavior was found in the tumbling motion near the nematic-isotropic phase boundary using molecular dynamics simulations of the Gay-Berne mesogenic model under isobaric conditions at a reduced pressure P* of 2.0. The relaxation time for the motion obtained from the second-rank orientational time correlation function and the rotational diffusion coefficient showed a clear jump at the nematic-isotropic phase transition temperature. Regardless of the temperature dependence of the relaxation time, the change in the rotational diffusion coefficient evaluated from the orientational order parameters and the relaxation time agreed qualitatively with that of real mesogens. The rotational viscosity coefficients gamma(1) and gamma(2) were obtained from the simulation data for the relaxation time for the short-term dynamics and for the rotational diffusion coefficients. gamma(1) was proportional to (2), where is the second-rank orientational parameter. Furthermore, the rotational behavior of the model was compared with that of the Debye approximation in the isotropic phase.     

Translational and rotational dynamics of colloidal rods by direct visualization with confocal microscopy

We report an experimental method to characterize the dynamics of colloidal rods by measuring their rotation and translation in three dimensions with confocal microscopy. The method relies on solvent viscosification to retard dynamics to time scales that are compatible with 3D confocal optical microscopy. Because the method yields a full three-dimensional characterization of rod displacement and orientation, it is applicable to situations in which complex, anisotropic dynamics emerge. Examples include behavior in liquid crystal phases with both orientational and positional order, suspensions subjected to applied fields such as shear flow or sedimentation, and the emerging area of anisotropic particle dynamics. We demonstrate the performance of the method by quantifying the Brownian motion of fluorescent poly(methyl methacrylate) rods (aspect ratio, L/D=3.1 and 7.0) grafted with poly(dimethylsiloxane) stabilizer. The rods are dispersed at dilute concentration in a solvent mixture of viscosity 2.0 Pa s. Rod translational and rotational diffusivities are extracted from the measured translational mean square displacement of the centroid positions and of the rod unit vector u(t), respectively. Rod orientational dynamics are characterized relative to both their azimuthal and polar angles. Probability distributions for the translation and rotation in the frame of rod are computed from the measurements. Experimental values obtained agree well with theory available for the dynamics of isolated rods.     

Time reversible and symplectic integrators for molecular dynamics simulations of rigid molecules

Molecular dynamics integrators are presented for translational and rotational motion of rigid molecules in microcanonical, canonical, and isothermal-isobaric ensembles. The integrators are all time reversible and are also, in some approaches, symplectic for the microcanonical ensembles. They are developed utilizing the quaternion representation on the basis of the Trotter factorization scheme using a Hamiltonian formalism. The structure is similar to that of the velocity Verlet algorithm. Comparison is made with standard integrators in terms of stability and it is found that a larger time step is stable with the new integrators. The canonical and isothermal-isobaric molecular dynamics simulations are defined by using a chain thermostat approach according to generalized Nosé-Hoover and Andersen methods.     

Rotational dynamics in supercooled water from nuclear spin relaxation and molecular simulations

Structural dynamics in liquid water slow down dramatically in the supercooled regime. To shed further light on the origin of this super-Arrhenius temperature dependence, we report high-precision (17)O and (2)H NMR relaxation data for H(2)O and D(2)O, respectively, down to 37 K below the equilibrium freezing point. With the aid of molecular dynamics (MD) simulations, we provide a detailed analysis of the rotational motions probed by the NMR experiments. The NMR-derived rotational correlation time τ(R) is the integral of a time correlation function (TCF) that, after a subpicosecond librational decay, can be described as a sum of two exponentials. Using a coarse-graining algorithm to map the MD trajectory on a continuous-time random walk (CTRW) in angular space, we show that the slowest TCF component can be attributed to large-angle molecular jumps. The mean jump angle is ～48° at all temperatures and the waiting time distribution is non-exponential, implying dynamical heterogeneity. We have previously used an analogous CTRW model to analyze quasielastic neutron scattering data from supercooled water. Although the translational and rotational waiting times are of similar magnitude, most translational jumps are not synchronized with a rotational jump of the same molecule. The rotational waiting time has a stronger temperature dependence than the translation one, consistent with the strong increase of the experimentally derived product τ(R)?D(T) at low temperatures. The present CTRW jump model is related to, but differs in essential ways from the extended jump model proposed by Laage and co-workers. Our analysis traces the super-Arrhenius temperature dependence of τ(R) to the rotational waiting time. We present arguments against interpreting this temperature dependence in terms of mode-coupling theory or in terms of mixture models of water structure.     

Rotational and translational dynamics of lysozyme in water-glycerol solution

In this paper, we report a study of the effect of solvent viscosity on both translational and rotational dynamics of a simple model protein: the egg white lysozyme. For this, we investigated the dynamical properties of lysozyme in mixtures water–glycerol by means of parallel measurements of photon correlation spectroscopy (PCS) and dielectric spectroscopy at radiofrequencies (DS). In the framework of the Debye–Stokes–Einstein theory, the translational and rotational coefficients allow an estimation of hydrodynamic radius of the protein. A decoupling between translational and rotational dynamics, observed as a different estimation of hydrodynamic radius, is reported in the literature for some systems. In order to ascertain if this effect is present also in our sample, we performed PCS and DS measurements on lysozyme–water–glycerol solutions. The content of glycerol was in the range of 0–70% w/w, with a solvent viscosity from 0.9 to about 10 cpoise, and the protein concentration was up to 20 mg ml⁻¹. The average sizes of lysozyme, obtained by the two methods, are remarkably different at high protein concentrations. However, the values of hydrodynamic radius extrapolated to infinite dilution are coincident and independent of glycerol. These results indicate that the diffusive behavior of lysozyme in the water–glycerol mixture is coherent with the Debye–Stokes–Einstein hydrodynamic model.     

On the Validity of Stokes–Einstein and Stokes–Einstein–Debye Relations in Ionic Liquids and Ionic‐Liquid Mixtures

Stokes–Einstein (SE) and Stokes–Einstein–Debye (SED) relations in the neat ionic liquid (IL) [C₂mim][NTf₂] and IL/chloroform mixtures are studied by means of molecular dynamics (MD) simulations. For this purpose, we simulate the translational diffusion coefficients of the cations and anions, the rotational correlation times of the C(2)? H bond in the cation C₂mim⁺, and the viscosities of the whole system. We find that the SE and SED relations are not valid for the pure ionic liquid, nor for IL/chloroform mixtures down to the miscibility gap (at 50 wt % IL). The deviations from both relations could be related to dynamical heterogeneities described by the non‐Gaussian parameter α(t). If α(t) is close to zero, at a concentration of 1 wt % IL in chloroform, both relations become valid. Then, the effective radii and volumes calculated from the SE and SED equations can be related to the structures found in the MD simulations, such as aggregates of ion pairs. Overall, similarities are observed between the dynamical properties of supercooled water and those of ionic liquids.     

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.     

Accelerated molecular dynamics simulation of the thermal desorption of n-alkanes from the basal plane of graphite

We utilize accelerated molecular dynamics to simulate alkane desorption from the basal plane of graphite. Eight different molecules, ranging from n-pentane to n-hexadecane, are studied in the low coverage limit. Acceleration of the molecular dynamics simulations is achieved using two different methods: temperature acceleration and a compensating potential scheme. We find that the activation energy for desorption increases with increasing chain length. The desorption prefactor increases with chain length for molecules ranging from pentane to decane. This increase subsides and the value of the preexponential factor fluctuates about an apparently constant value for decane, dodecane, tetradecane, and hexadecane. These trends are consistent with data obtained in experimental temperature-programed desorption (TPD) studies. We explain the dependence of the preexponential factor on alkane chain length by examining conformational changes within the alkane molecules. For the shorter molecules, torsional motion is not activated over experimental temperature ranges. These molecules can be treated as rigid rods and their partial loss in translational and rotational entropies upon adsorption increases as chain length increases, leading to an increasing preexponential factor. At their typical TPD peak temperatures, torsions are activated in the longer adsorbed chain molecules to a significant extent which increases with increasing chain length, increasing the entropy of the adsorbed molecule. This increase counteracts the decrease in entropy due to a loss of translation and rotation, leading to a virtually constant prefactor.     

Carbon nanotube motors driven by carbon nanotube

We propose a new type of carbon nanotube (CNT) motor composed of a single-wall CNT (SWCNT) and a double-wall CNT (DWCNT), that are in mechanical contact. The rotational motion of our CNT motor is controllable by the translational motion of the SWCNT along the axis of the DWCNT. From molecular dynamics simulations, we show how our CNT motor can be driven in a controlled manner.     

Structure and dynamics of water confined in silica nanopores

We report the results of molecular simulation of water in silica nanopores at full hydration and room temperature. The model systems are approximately cylindrical pores in amorphous silica, with diameters ranging from 20 to 40 ?. The filled pores are prepared using grand canonical Monte Carlo simulation and molecular dynamics simulation is used to calculate the water structure and dynamics. We found that water forms two distinct molecular layers at the interface and exhibits uniform, but somewhat lower than bulk liquid, density in the core region. The hydrogen bond density profile follows similar trends, with lower than bulk density in the core and enhancements at the interface, due to hydrogen bonds between water and surface non-bridging oxygens and OH groups. Our studies of water dynamics included translational mean squared displacements, orientational time correlations, survival probabilities in interfacial shells, and hydrogen bond population relaxation. We found that the radial-axial anisotropy in translational motion largely follows the predictions of a model of free diffusion in a cylinder. However, both translational and rotational water mobilities are strongly dependent on the proximity to the interface, with pronounced slowdown in layers near the interface. Within these layers, the effects of interface curvature are relatively modest, with only a small increase in mobility in going from the 20 to 40 ? diameter pore. Hydrogen bond population relaxation is nearly bulk-like in the core, but considerably slower in the interfacial region.     

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).     

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.     

Coupling of translational and rotational motion in chiral liquids in electromagnetic and circularly polarised electric fields

Non-equilibrium molecular dynamics simulations of R and S enantiomers of 1,1-chlorofluoroethane, both for pure liquids and racemic mixtures, have been performed at 298 K in the absence and presence of both electromagnetic (e/m) and circularly polarised electric (CP) fields of varying frequency (100-2200 GHz) and intensity (0.025-0.2 V ?(-1) (rms)). Significant non-thermal field effects were noted in the coupling of rotational and translational motion; for instance, in microwave and far-infrared (MW/IR) e/m fields, marked increases in rotational and translational diffusion vis-à-vis the zero-field case took place at 0.025-0.1 V ?(-1) (rms), with a reduction in translational diffusion vis-à-vis the zero-field case above 0.1 V ?(-1) (rms) above 100 GHz. This was due to enhanced direct coupling of rotational motion with the more intense e/m field at the ideal intrinsic rotational coupling frequency (approximately 700 GHz) leading to such rapidly oscillating rotational motion that extent of translational motion was effectively reduced. In the case of CP fields, rotational and translational diffusion was also enhanced for all intensities, particularly at approximately 700 GHz. For both MW/IR and CP fields, non-linear field effects were evident above around 0.1 V ?(-1) (rms) intensity, in terms of enhancements in translational and rotational motion. Simulation of 90-10 mol. % liquid mixtures of a Lennard-Jones solvent with R and S enantiomer-solutes in MW/IR and CP fields led to more limited promotion of rotational and translational diffusion, due primarily to increased frictional effects. For both e/m and CP fields, examination of the laboratory- and inertial-frame auto- and cross-correlation functions of velocity and angular velocity demonstrated the development of explicit coupling with the external fields at the applied frequencies, especially so in the more intense fields where nonlinear effects come into play. For racemic mixtures, elements of the laboratory- and inertial-frame velocity and angular velocity were found to couple with each other to a lesser extent.     

Rotational correlation and dynamic heterogeneity in a kinetically constrained lattice gas

We study the dynamical heterogeneity and glassy dynamics in a kinetically constrained lattice-gas model which has both translational and rotational degrees of freedom. We find that the rotational relaxation time tracks the structural relaxation time as density is increased whereas the translational diffusion constant exhibits a strong decoupling. We investigate distributions of exchange and persistence times for both the rotational and translational degrees of freedom and compare our results on the distributions of rotational exchange times to recent single molecule studies.     

Molecular dynamics simulation of the nematic liquid crystal phase in the presence of an intense magnetic field

The influence of an intense external field on the dynamics of the nematic liquid crystal phase is investigated using a molecular dynamics simulation for the Gay-Berne nematogen under isobaric-isothermal conditions. The molecular dynamics as a function of the second-rank orientational order parameter P<2> for a system consisting of a nematic liquid crystal in the presence of an intense magnetic field is compared with that of a similar system without the field. The translational motion of molecules is determined as a function of the translational diffusion coefficient tensor and the anisotropy and compared with the values predicted theoretically. The rotational dynamics of molecules is analyzed using the first- and the second-rank orientational time correlation functions. The translational diffusion coefficient parallel with respect to the director is constrained by the intense field, although the perpendicular one is decreased as the P<2> is increased, just as it is in the system without the field. However, no essential effect of the strong magnetic field is observed in the rotational molecular dynamics. Further, the rotational diffusion coefficient parallel with respect to the director obtained from the first-rank orientational time correlation function in the simulation is qualitatively in agreement with that in the real nematic liquid crystalline molecules. The P<2> dependence of the rotational diffusion coefficient for the system with the intense magnetic field shows a tendency similar to that for the system without the field.