Reorientation Time Research Articles

Reorientation of Isomeric Butanols: The Multiple Effects of Steric Bulk Arrangement on Hydrogen-Bond Dynamics.

Molecular dynamics simulations are used to investigate OH reorientation in the four isomeric butanols in their bulk liquid state to examine the influence of the arrangement of the steric bulk on the alcohol reorientational and hydrogen-bond (H-bond) dynamics. The results are interpreted within the extended jump model in which the OH reorientation is decomposed into contributions due to "jumps" between H-bond partners and "frame" reorientation of the intact H-bonded pair. Reorientation is fastest in iso-butanol and slowest in tert-butanol, while sec- and n-butanol have similar reorientation times. This latter result is a fortuitous cancellation between the jump and frame reorientation in the two alcohols. The extended jump model is shown to provide a quantitative description of the OH reorientation times. A detailed analysis of the jump times shows that a combination of entropic, enthalpic, and dynamical factors, including transition state recrossing effects, all play a role. A simple model based on the liquid structure is proposed to estimate the energetic and entropic contributions to the jump time. This represents the groundwork for a predictive model of OH reorientation in alcohols, but additional studies are required to better understand the frame reorientation and transition state recrossing effects.

Rotational Diffusion of a New Large Non Polar Dye Molecule in Alkanes.

Rotational reorientation times of a newly synthesized 2,5-bis(phenylethynyl)1,4-bis(dodecyloxy) benzene (DDPE) are experimentally determined in series of n-alkanes by employing steady state and time resolved fluorescence depolarization technique with a view to understand rotational dynamics of large non-polar solute molecule in non-polar solvents and few general solvents of different sizes and varying viscosity. It is observed that rotational reorientation times vary linearly as function of viscosity. The hydrodynamic stick condition describes the experimental results at low viscosities while the results tend to deviate significantly from it at higher viscosities. This is attributed to the possibility of long chains in solvents hosting a variety of chain defects (end-gauche, double-gauche, all-trans, kink, etc.) thereby reducing the effective length of the molecule, leading to a slightly reduced friction. The experimental results are compared with the predictions of Stokes-Einstein-Debye (SED) hydrodynamic theory as well as the quasi-hydrodynamic theories of Gierer-Wirtz (GW) and Dote-Kivelson-Shwartz (DKS). The predictions from these theories underestimate τr in the solvents employed in the study.

Composition dependence of thermodynamic, dynamic and dielectric properties of water–methanol model mixtures. Molecular dynamics simulation results with the OPLS-AA model for methanol

We have studied thermodynamic and dynamic properties, as well as the dielectric constant, of water–methanol model mixtures in the entire range of composition, by using constant pressure molecular dynamics simulations at room temperature and ambient pressure. The SPC-E and TIP4P-Ew water models are explored in combination with the OPLS-AA (all atom) model of methanol. Changes of the average number of hydrogen bonds between particles of different species and of the fractions of differently bonded molecules are put in correspondence with the evolution of excess mixing properties, of self-diffusion coefficients, reorientational relaxation times and power spectra. We were looking for the existence of correlations between properties of a different kind, in order to find reasons of satisfactory or dissatisfactory performance of the models applied. It seems that any improvement of the description of water–methanol mixtures requires a more sophisticated, carefully parametrized model for methanol and possibly, certain deviations in the combination rules.

Rotational Diffusion of Charged and Nondipolar Solutes in Ionic Liquid-Organic Solvent Mixtures: Evidence for Stronger Specific Solute-Solvent Interactions in Presence of Organic Solvent.

Rotational diffusion of a charged solute, rhodamine 110 (R110), and a nondipolar solute, 2,5-dimethyl-1,4-dioxo-3,6-diphenylpyrrolo[3,4-c]pyrrole (DMDPP), has been investigated in ionic liquids, 1-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide ([BMIM][Tf2N]) and 1-butyl-3-methylimidazolium tris(pentafluoroethyl)trifluorophosphate ([BMIM][FAP]), with 0.8 mole fraction of dibenzyl ether (DBE). This study has been undertaken to find out how specific interactions between the solute and the ionic liquid are affected upon dilution with a nondipolar solvent. It has been observed that at a given viscosity (η) and temperature (T), the reorientation times of R110 increase by 40-60% in the ionic liquid-organic solvent mixtures compared to ones in the corresponding neat ionic liquids. In the case of DMDPP, the influence of DBE is less pronounced, and its reorientation times increase by 25-50% at a given η/T. The addition of DBE weakens the numerous interactions prevailing between the cations and the anions of the ionic liquids, which results in stronger specific interactions between the solutes and the constituent ions, consequently leading to slower rotation of the solutes.

Methylammonium Rotational Dynamics in Lead Halide Perovskite by Classical Molecular Dynamics: The Role of Temperature

An interatomic model potential for molecular dynamics is derived from first-principles and used to study the molecular rotations and relaxation times in methylammonium lead halide, here considered the prototypical example of a hybrid crystal with a strong reorientational dynamics. Within the limits of a simple ionic scheme, the potential is able to catch the main qualitative features of the material at zero and finite temperature and opens the way to the development of classical potentials for hybrid perovskites. In agreement with experiments and previous theoretical findings, the molecule trajectories exhibit a transition from a dynamics dominated by high symmetry directions at low temperature to a fast dynamics at room temperature in which the molecule can reorient quasi-randomly. By computing the angular time correlation function we discuss the reorientational time as a function of temperature in comparison with existing literature, providing a simple model and a clear attribution of the relaxation times in terms of their temperature dependence. This work clarifies the temperature dependence of the relaxation times and the interpretation of the experimental data in terms of the different mechanisms contributing to the molecule dynamics.

Raman band shape analysis of cyanate-anion ionic liquids

Raman band shape analysis of the C≡N stretching mode was carried out for ionic liquids based on [SCN]−, [N(CN)2]−, [C(CN)3]−, and [B(CN)4]−, with a common cation, 1-ethyl-3-methylimidazolium, [C2C1im]+. Vibrational and reorientational time correlation functions were obtained by Fourier transforming isotropic and anisotropic Raman spectra. Comparison is provided between results for [C2C1im][SCN] and literature data available for molten alkali thiocyanates. Vibrational dephasing of the ωCN mode in [C2C1im][SCN] belongs to the regime of inhomogeneous broadening as it is determined by the distribution of vibrational frequencies, <Δω2>. Vibrational dephasing in [N(CN)2]−, [C(CN)3]−, and [B(CN)4]−, depends on both the <Δω2> and the correlation time of frequency fluctuation. Decay rates of reorientational time correlation functions within the range of 1.0ps do not correlate with the viscosity of these ionic liquids. Molecular dynamics simulations of these ionic liquids provide support to the experimental finding that the reorientational time correlation function of [SCN]− decays faster than the other anions. The Raman band shape analysis suggests that the short-time dynamics of these ionic liquids is structure-limited because of steric hindrance.

Size‐Dependent Ligand Layer Dynamics in Semiconductor Nanocrystals Probed by Anisotropy Measurements

Colloidal semiconductor nanocrystals (NC) have reached a high level of synthetic control allowing the tuning of their properties, and their use in various applications. However, the surface of NCs and in particular their size-dependent capping organic ligand behavior, which play an important role in the NC synthesis, dispersibility, and optoelectronic properties, is still not well understood. We study the size-dependent properties of the ligand shell on the surface of NCs, by embedding surface bound dyes as a probe within the ligand shell. The reorientation times for these dyes show a linear dependence on the NC surface curvature indicating size-dependent change in viscosity, which is related to a change in the density of the ligand layer because of the geometry of the surface, a unique feature of NCs. Understanding the properties of the ligand shell will allow rational design of the surface to achieve the desired properties, providing an additional important knob for tuning their functionality.

Size‐Dependent Ligand Layer Dynamics in Semiconductor Nanocrystals Probed by Anisotropy Measurements

AbstractColloidal semiconductor nanocrystals (NC) have reached a high level of synthetic control allowing the tuning of their properties, and their use in various applications. However, the surface of NCs and in particular their size‐dependent capping organic ligand behavior, which play an important role in the NC synthesis, dispersibility, and optoelectronic properties, is still not well understood. We study the size‐dependent properties of the ligand shell on the surface of NCs, by embedding surface bound dyes as a probe within the ligand shell. The reorientation times for these dyes show a linear dependence on the NC surface curvature indicating size‐dependent change in viscosity, which is related to a change in the density of the ligand layer because of the geometry of the surface, a unique feature of NCs. Understanding the properties of the ligand shell will allow rational design of the surface to achieve the desired properties, providing an additional important knob for tuning their functionality.

Does addition of an electrolyte influence the rotational diffusion of nondipolar solutes in a protic ionic liquid?

Rotational diffusion of two structurally similar nondipolar solutes, 2,5-dimethyl-1,4-dioxo-3,6-diphenylpyrrolo[3,4-c]pyrrole (DMDPP) and 1,4-dioxo-3,6-diphenylpyrrolo[3,4-c]pyrrole (DPP), has been examined in ethylammonium nitrate-lithium nitrate (EAN-LiNO3) mixtures to understand the influence of added electrolyte on the local environment experienced by the solute molecules. The measured reorientation times of both DMDPP and DPP in EAN-LiNO3 mixtures fall within the broad limits set by the hydrodynamic slip and stick boundary conditions. The hydrogen bond accepting DMDPP and the hydrogen bond donating DPP experience specific interactions with the cation and anion of the ionic liquid, respectively. Addition of LiNO3 (0.1 and 0.2 mole fraction) to EAN induces only viscosity related effects on the rotational diffusion of the two nondipolar solutes. These observations suggest that the local environment experienced by DMDPP and DPP in EAN is not altered upon the addition of LiNO3. Our results are consistent with the structural details available in the literature for EAN-LiNO3 mixtures.

Femtosecond mid-infrared study of the dynamics of water molecules in water-acetone and water-dimethyl sulfoxide mixtures.

We study the vibrational relaxation dynamics and the reorientation dynamics of HDO molecules in binary water-dimethyl sulfoxide (DMSO) and water-acetone mixtures with polarization-resolved femtosecond mid-infrared spectroscopy. For low solute concentrations we observe a slowing down of the reorientation of part of the water molecules that hydrate the hydrophobic methyl groups of DMSO and acetone. For water-DMSO mixtures the fraction of slowed-down water molecules rises much steeper with solute concentration than for water-acetone mixtures, showing that acetone molecules show significant aggregation already at low concentrations. At high solute concentrations, the vibrational and reorientation dynamics of both water-DMSO and water-acetone mixtures show a clear distinction between the dynamics of water molecules donating hydrogen bonds to other water molecules and the dynamics of water donating a hydrogen bond to the S═O/C═O group of the solute. For water-DMSO mixtures both types of water molecules show a very slow reorientation. The water molecules forming hydrogen bonds to the S═O group reorient with a time constant that decreases from 46 ± 14 ps at XDMSO = 0.33 to 13 ± 2 ps at XDMSO = 0.95. The water molecules forming hydrogen bonds to the C═O group of acetone show a much faster reorientation with a time constant that decreases from 6.1 ± 0.2 ps at Xacet = 0.3 to 2.96 ± 0.05 ps at Xacet = 0.9. The large difference in reorientation time constant of the solute-bound water for DMSO and acetone can be explained from the fact that the hydrogen bond between water and the S═O group of DMSO is much stronger than the hydrogen bond between water and the C═O group of acetone. We attribute the strongly different behavior of water in DMSO-rich and acetone-rich mixtures to their difference in molecular shape.

Dielectric relaxation of hydration water in the Dickerson–Drew duplex solution probed by THz spectroscopy

The contribution of water to DNA conformational change, DNA–protein interactions, and DNA–ligand recognition has been underlined. Here, we investigate the relaxation process of water around the Dickerson–Drew B-DNA duplex using terahertz spectroscopy. By controlling the DNA concentration, the relaxation time for water reorientation and the width of the DNA hydration layer are determined. We found that a layer of weakly bound hydration water, with a relaxation time of 11.6ps, extends 7.6Å from the tight-binding water layer. This result demonstrates that a shell of hydration water, with reorientation time on the order of tens of picoseconds, exists beyond the structurally integrated water usually observed around DNA.

Boundary condition effects on the dynamic and electric properties of hydration layers.

Water solvation has a central role in several biochemical processes ranging from protein folding to biomolecular recognition and enzyme catalysis. Because of its importance, the structure and dynamics of hydration layers around biological macromolecules have been the targets of a great number of experimental and computational studies. In the present contribution, we have investigated the effects of periodic boundary conditions (PBCs), as used in conjunction with molecular dynamics (MD) simulations, on the dynamic and electric properties of water layers. In particular, we have systematically performed MD simulations of neat water and biomolecules in aqueous solutions by imposing a different external dielectric constant, a generally overlooked parameter in PBC simulations. The effect of the system size has also been addressed. Overall, our results consistently indicate that the dipole moment properties of water layers, and specifically the dipole moment fluctuations and the reorientational correlation functions, can be sensitive to the choice of the external boundary conditions, whereas other molecular properties, such as the self-diffusion coefficient and the reorientational relaxation times, are not affected. We think that our investigation may help to assess appropriate simulation conditions for modeling the aqueous environment of relevant biochemical systems and processes.

Post-electroconvulsive therapy recovery and reorientation time with methohexital and ketamine: a randomized, longitudinal, crossover design trial.

Methohexital, a barbiturate anesthetic commonly used for electroconvulsive therapy (ECT), possesses dose-dependent anticonvulsant properties, and its use can interfere with effective seizure therapy in patients with high seizure thresholds. Ketamine, an N-methyl-d-aspartate antagonist with epileptogenic properties not broadly used for ECT inductions, is a commonly used induction agent for general anesthesia. Recent studies suggest that the use of ketamine is effective in allowing successful ECT treatment in patients with high seizure thresholds without an increase in adverse effects. In this preliminary study, we directly compared the recovery and reorientation times of subjects receiving ketamine and methohexital for ECTs. Twenty patients were randomized in a crossover design to receive methohexital and ketamine for ECT inductions in alternating fashion in 6 trials. Primary outcome measures were recovery time (voluntary movement, respiratory effort, blood pressure, consciousness, and O2 saturation) and reorientation time. Secondary outcome measures were individual recovery variables, adverse effect occurrence, and seizure duration. Overall recovery time was not significantly different between the 2 treatment arms (F(1, 17) = 0.72; P = 0.41). Reorientation time was faster in the methohexital arm (F(1, 17) = 9.23; P = 0.007). Ketamine inductions resulted in higher number of adverse effects, higher subject dropout rates, and a longer reorientation time with respect to methohexital inductions. No significant difference in postanesthesia recovery time was found between the ketamine and methohexital arms. Intolerability to ketamine affected a significant proportion of subjects and suggests that ketamine should remain as an alternative or adjunctive agent for patients with high seizure thresholds.

Model-free estimation of the effective correlation time for C-H bond reorientation in amphiphilic bilayers: (1)H-(13)C solid-state NMR and MD simulations.

Molecular dynamics (MD) simulations give atomically detailed information on structure and dynamics in amphiphilic bilayer systems on timescales up to about 1 μs. The reorientational dynamics of the C-H bonds is conventionally verified by measurements of (13)C or (2)H nuclear magnetic resonance (NMR) longitudinal relaxation rates R1, which are more sensitive to motional processes with correlation times close to the inverse Larmor frequency, typically around 1-10 ns on standard NMR instrumentation, and are thus less sensitive to the 10-1000 ns timescale motion that can be observed in the MD simulations. We propose an experimental procedure for atomically resolved model-free estimation of the C-H bond effective reorientational correlation time τe, which includes contributions from the entire range of all-atom MD timescales and that can be calculated directly from the MD trajectories. The approach is based on measurements of (13)C R1 and R1ρ relaxation rates, as well as (1)H-(13)C dipolar couplings, and is applicable to anisotropic liquid crystalline lipid or surfactant systems using a conventional solid-state NMR spectrometer and samples with natural isotopic composition. The procedure is demonstrated on a fully hydrated lamellar phase of 1-palmitoyl-2-oleoyl-phosphatidylcholine, yielding values of τe from 0.1 ns for the methyl groups in the choline moiety and at the end of the acyl chains to 3 ns for the g1 methylene group of the glycerol backbone. MD simulations performed with a widely used united-atom force-field reproduce the τe-profile of the major part of the acyl chains but underestimate the dynamics of the glycerol backbone and adjacent molecular segments. The measurement of experimental τe-profiles can be used to study subtle effects on C-H bond reorientational motions in anisotropic liquid crystals, as well as to validate the C-H bond reorientation dynamics predicted in MD simulations of amphiphilic bilayers such as lipid membranes.

Effect of low viscous nondipolar solvent on the rotational diffusion of structurally similar nondipolar solutes in an ionic liquid.

Fluorescence anisotropies of two structurally similar nondipolar solutes, 2,5-dimethyl-1,4-dioxo-3,6-diphenylpyrrolo[3,4-c]pyrrole (DMDPP) and 1,4-dioxo-3,6-diphenylpyrrolo[3,4-c]pyrrole (DPP), have been measured in 1-methyl-3-octylimidazolium hexafluorophosphate-dibenzyl ether ([MOIM][PF6]-DBE) mixtures to understand how the addition of a low viscous nondipolar solvent influences solute rotation. The data when analyzed with Stokes-Einstein-Debye hydrodynamic theory reveals that the measured reorientation times of DMDPP are closer to the predictions of slip boundary condition, whereas those of DPP follow stick hydrodynamics. This outcome arises due to specific interactions between DPP and the solvent medium. Nevertheless, the important result of this study is that the rotational diffusion of DMDPP becomes gradually slower with an increase in the mole fraction of DBE (xDBE) for a given viscosity and temperature. In contrast, such a trend is not noticed for the hydrogen-bond donating solute DPP. Instead, two sets of reorientation times have been obtained, one corresponding to xDBE = 0.0-0.2 and the other xDBE = 0.4-1.0. The results for DMDPP have been rationalized on the basis of the organized structure of [MOIM][PF6], which attains homogeneity at the microscopic level with an increase in xDBE. In case of DPP, however, the propensity of the solute to be in the neighborhood of DBE, as a consequence of its stronger hydrogen bond accepting ability compared to the ionic liquid, appears to be the reason for the observed behavior.

Phase Behavior, Diffusion, Structural Characteristics, and pH of Aqueous Hydrophobic Ionic Liquid Confined Media: Insights into Microviscosity and Microporsity in the [C4C4im][NTf2] + Water System

We present our studies on the physicochemical properties of water confined in Dibutylimidazolium bis(trifluoromethanesulfonylimide) ([C4C4im][NTf2]) reverse micelles through the NMR relaxation measurements that provide us an understanding of microviscosity and pH in the confined condition. We present experimental results on phase behavior, diffusion, structural characteristics and pH in aqueous ionic liquid-confined media. The ternary phase diagram was constructed by the cloud point measurements and the microheterogeneous regions were detected by the measurement of bulk viscosity and diffusion coefficients of K4[Fe(CN)6] inside the homogeneous microemulsion systems through the cyclic voltammetric (CV) measurements. The size of the microemulsion systems was characterized by the dynamic light scattering (DLS) method. The (1)H NMR spectra of homogeneous microemulsion systems were taken which indicates the presence of bound and free water molecules inside the microemulsion system. The NMR spin-lattice relaxation time (T1) of water molecules in its homogeneous microemulsion systems were measured and the reorientational correlation time (τc) of water molecules obtained from it indicates that the fluidity of homogeneous confined media decreases with the decrease in the composition of water. Microviscosity of the aqueous confined media was calculated from the measured T1 relaxation time values by applying the Debye-Stokes equation and correlated with the bulk viscosity of the samples. It was observed that both the microviscosity and bulk viscosity show inverse relationship. The fraction of bound and free water molecules were calculated from the measured T1 values. NMR spin-spin relaxation time (T2) of water molecules in its homogeneous microemulsion systems were measured with the varying pH of the aqueous core. A change in the T2 relaxation time of the water proton was observed proposing an exchange of proton between the H2O and -OH group of the TX-100 molecules. Finally, methyl orange (MO) was used as a UV-vis spectrophotometric molecular probe and the measured λmax values of the probe were used for the detection of micropolarity of the homogeneous aqueous confined media and was found to be increase with the increase in the size of the confined media.

Hydrogen bond dynamics in primary alcohols: a femtosecond infrared study.

Hydrogen-bonded liquids are excellent solvents, in part due to the highly dynamic character of the directional interaction associated with the hydrogen bond. Here we study the vibrational and reorientational dynamics of deuterated hydroxyl groups in various primary alcohols using polarization-resolved femtosecond infrared spectroscopy. We show that the relaxation of the OD stretch vibration is similar for ethanol and its higher homologues (∼0.9 ps), while it is appreciably faster for methanol (∼0.75 ps). The fast relaxation for methanol is attributed to strong coupling of the OD stretch vibration to the overtone of the CH3 rocking mode. Subsequent to excited state relaxation, the dissipation of the excess energy leads to structural relaxation of the alcohol liquid structure. We show that this relaxation of the H-bonded network depends on the alkyl chain length. We find that the anisotropy of the excitation decays by both thermal diffusion from excited OD groups to nonexcited molecules and reorientational motion. The reorientation is described well by a model employing two relaxation times that increase linearly with increasing alcohol size. The short reorientation time is assigned to the partial reorientation of molecules within the alcohol cluster, while the long reorientation times can be attributed to breaking and reforming of hydrogen bonds.

Ion hydration and associated defects in hydrogen bond network of water: observation of reorientationally slow water molecules beyond first hydration shell in aqueous solutions of MgCl2.

Effects of the presence of ions, at moderate to high concentrations, on dynamical properties of water molecules are investigated through classical molecular dynamics simulations using two well-known nonpolarizable water models. Simulations reveal that the presence of magnesium chloride (MgCl(2)) induces perturbations in the hydrogen bond network of water leading to the formation of bulklike domains with ''defect sites'' on boundaries of such domains: water molecules at such defect sites have less number of hydrogen bonds than those in bulk water. Reorientational autocorrelation functions for dipole vectors of such defect water molecules are computed at different concentrations of ions and compared with system of pure water. Earlier experimental and simulation studies indicate significant differences in reorientational dynamics for water molecules in the first hydration shell of many dissolved ions. Results of this study suggest that defect water molecules, which are beyond the first hydration shells of ions, also experience significant slowing of reorientation times as a function of concentration in the case of MgCl(2). However, addition of cesium chloride (CsCl) to water does not perturb the hydrogen bond network of water significantly even at higher concentrations. This difference in behavior between MgCl(2) and CsCl is consistent with the well-known Hofmeister series.

Kinematically optimal spacecraft attitude control

The problem of optimal control of a spacecraft reorientation from an arbitrary initial position into a prescribed final angular position is studied. The reorientation time is minimized. The case when the velocity parameters are limited is investigated. On the basis of necessary optimality conditions in the form of Pontryagin's maximum principle and using quaternion variables for the control problems of the spacecraft motion, an analytical solution of the stated problem is obtained. The kinematic problem of spacecraft reorientation is solved completely. Formal equations are derived and computational expressions for constructing the optimal control program are obtained. For the symmetric form of constraints on the angular velocity vector, the optimal reorientation problem is solved analytically (the result is obtained in terms of elementary functions). Results of the mathematical simulation of the spacecraft motion under the optimal control are presented that demonstrate the practical usefulness of the proposed algorithm for the spacecraft attitude control.

Gyrotaxis in uniform vorticity

AbstractAnalysis of bioconvection in dilute suspensions of bottom-heavy but randomly swimming micro-organisms is commonly based on a model introduced in 1990. This couples the Navier–Stokes equations, the cell conservation equation and the Fokker–Planck equation (FPE) for the probability density function for a cell’s swimming direction$\boldsymbol{p}$, which balances rotational diffusion against viscous and gravitational torques. The results have shown qualitative agreement with observation, but the model has not been subjected to direct quantitative testing in a controlled experiment. Here, we consider a simple configuration in which the suspension is contained in a circular cylinder of radius$R$, which rotates at angular velocity${\rm\Omega}$about a horizontal axis. We solve the FPE and calculate the cells’ mean swimming velocity, which proves to be horizontal when$B{\rm\Omega}\gg 1$, where$B$is the gyrotactic reorientation time scale. Then we compute the cell concentration distribution, which is non-uniform only in a thin boundary layer near the cylinder wall when${\it\beta}^{2}={\rm\Omega}R^{2}/D\gg 1$, where$D$is the cells’ translational diffusivity. The fact that cells are denser than water means that this concentration distribution drives a perturbation to the underlying solid-body rotational flow which can be calculated analytically. The predictions of the theory are evaluated in terms of a proposed experimental realisation of the configuration, using suspensions of the algaChlamydomonas nivalisorChlamydomonas reinhardtiior the algal colonyVolvox.