Reorientation Time Research Articles

Solution dynamics of the natural bioactive molecule capsaicin: a relaxation study

Nuclear magnetic resonance spectroscopy is a straightforward technique for studying molecular dynamics that range in timescale from picosecond (motions faster than molecular reorientation) to those that occur in real-time. This approach is important to highlight the behavior of bioactive molecules in solution, and to acquire information about action mechanisms and potential pharmacological effects. Proton and carbon-13 spin–lattice relaxation experiments were performed to calculate the reorientational correlation time for protonated carbons. Capsaicin showed complex dynamical properties and the results revealed two regions with different dynamical properties: the aliphatic region with fast reorientation motions and the aromatic region with slow motions.

Simultaneous determination of deuteron quadrupole coupling constants and rotational correlation times: the model case of hydrogen bonded ionic liquids.

We show that deuteron quadrupole coupling constants (DQCCs), and reorientational correlation times of molecular bonds N-D that are involved in hydrogen bonding, can be determined from NMR T1 relaxation time experiments simultaneously. For this purpose, we used trialkylammonium-based protic ionic liquids (PILs) as model compounds. They exhibit high viscosities and wide liquid ranges that allow measurements far beyond the extreme narrowing region (ω0τc ≪ 1). The T1 minima already occur at temperatures significantly above room temperature. We obtain reasonable DQCCs for the liquid phase if anisotropic motion is considered. The DQCCs are very small due to attractive Coulomb interaction between the cation and anion, which is further enhanced by hydrogen bonding. The DQCCs strongly depend on the interaction strength of the anion but are independent of the alkyl chain length of the trialkyl ammonium cations pointing to the exclusive cation-anion interaction along the hydrogen bond.

Interparticle interactions and dynamics in BmimBF4 and LiBF4 solutions in propylene carbonate: MD simulation

Ionic liquids have gained immense popularity in recent decades due to a combination of unique properties. Despite the widespread use of ionic liquids mixtures with aprotic dipolar solvents in electrochemistry, it remains relevant to predict their macroscopic, primarily transport, properties based on the microscopic picture of the entire set of interparticle interactions in such systems. The method of molecular dynamics simulation (MDS) is one of the most powerful tools for solving problems of this kind. However, one of the unsolved problems of the classical MDS of ion-molecular systems is the correct accounting of polarization effects. Recently it was proposed to use a variation of the effective ion charges in solutions to solve this task. This paper presents the results of the MDS structural and dynamic properties of 1-butyl-3-methylimidazolium (BmimBF4) and lithium (LiBF4) tetrafluoroborates solutions in propylene carbonate (PC) at 298.15 K in NPT ensemble using GROMACS and MDNAES software packages. The possibility of reproducing the experimental dynamic properties (diffusion coefficients of cations and solvent, viscosity, and electrical conductivity) of binary systems based on mixtures of ionic liquids with PC in a wide concentration range was shown. Polarization effects were taken into account by reducing the partial charges of the ion atoms. The structure of the solvation shell of cations was studied within the framework of radial distribution functions, distribution of coordination numbers and the presence of hydrogen bonds between the organic cation and solvent molecules. The results point to stronger and more structured solvation shell of the Li+ cation compared to Bmim+, which is consistent with the conclusions about the mobility of these cations. The reorientation times of propylene carbonate molecules and their lifetimes in the framework of the first solvation shells of the cations are several times higher for the lithium cation.

Pulsed Optimal Spacecraft Orbit Reorientation by Means of Reactive Thrust Orthogonal to the Osculating Orbit. II

The first part of the article provides an overview of the work on the differential equations of the spacecraft (SC) orbit orientation and the problem of optimal reorientation of a spacecraft orbit in an inertial coordinate system by means of reactive acceleration orthogonal to the osculating plane of the spacecraft. The theory of solving the problem of the optimal reorientation of the orbit of the spacecraft using the quaternionic differential equation for the orientation of the orbital coordinate system in a non-linear continuous formulation (using limited (small) thrust) is presented. As a minimized quality functional, a combined functional is used equal to the weighted sum of the reorientation time and thrust impulse (characteristic speed) during the reorientation of the orbit of the spacecraft (special cases of this functional are the speed response case and the characteristic speed minimization separately).

Spectroscopic investigation of linear and branched tryptophan-containing peptides

Intrinsic fluorescence from amino acid tryptophan (Trp) is used extensively to monitor conformational dynamics and inter/intra-molecular interactions in proteins and related systems. Peptide systems with varied number of Trp residues are desirable model compounds for understanding fluorescence behaviour of Trp under different conditions. Investigations through model peptides will provide deep insight into photophysical properties of the Trp in a complex protein environment. In this work, three aspartic acid-based peptidic molecules possessing one, two and three Trp units are designed and synthesized for their detailed photophysical and fluorescence quenching investigations within polar-protic methanol, polar-aprotic acetonitrile, and apolar ethyl acetate. From various UV–vis absorbance and steady-state/time-resolved fluorescence measurements, relevant photophysical parameters, such as, absorbance and fluorescence emission maxima, molar absorptivity, fluorescence quantum yield, steady-state anisotropy, fluorescence lifetime, rotational reorientation time, and rates of radiative and non-radiative decays were estimated that reveal not only the solvent-dependent behavior of the compounds but also the presence of interactions between Trp-Trp units on the peptidic scaffold. Quenching of fluorescence of the three Trp-containing compounds by quenching agents, acrylamide (electron/charge acceptor during quenching) and triethylamine (electron/charge donor during quenching), in the three solvents is dynamic in nature. Quenching by acrylamide is found to be significantly more efficient than that by triethylamine. Stern-Volmer quenching constant and bimolecular quenching rate constant also exhibit solvent dependence. The differences in the quenching constants for the three compounds possessing one, two, and three Trp units not only further support the presence of interactions between Trp-Trp units but also imply differential accessibility of the quencher to the Trp moiety on the peptidic scaffold.

Importance of reorientational dynamics for the charge transport in ionic liquids

Most ionic liquids contain at least one rather complex ion species exhibiting a dipolar moment. In the present work, we provide a thorough evaluation of broadband dielectric spectra of 12 ionic liquids taking into account the often neglected reorientational dynamics of these ions. We confirm that this dynamics leads to a clear relaxational signature in the spectra, a fact that so far only was considered in few previous works. The obtained reorientational relaxation times are well consistent with earlier inelastic light-scattering and high-frequency dielectric investigations. Evaluating our dielectric spectra in terms of reorientational motions reveals a close coupling of the ion-rotation dynamics to the ionic charge transport in a broad temperature range from the low-viscosity liquid above room temperature deep into the high-viscosity supercooled state close to Tg. This coupling does not seem to be mediated by the viscosity but probably is of more direct nature, pointing to a revolving-door mechanism as also considered for plastic-crystalline ionic conductors. Our results show that the reorientational motion of the dipolar ions plays a significant and so far widely overlooked role for the ionic charge transport in ionic liquids.

Orientational Pair Correlations in a Dipolar Molecular Liquid: Time-Resolved Resonant and Nonresonant Pump-Probe Spectroscopies.

Orientational pair correlations (OPCs), when they are sufficiently strong in a liquid, contain information on the interplay between structure and dynamics that arise from intermolecular interactions. Consequently, the quantification of OPCs remains a subject of substantial interest in current experimental and theoretical works. In the case of benzonitrile, the importance of OPCs remains ambiguous, owing to the use of model-dependent analyses or reliance on a single spectroscopic technique. Here, IR polarization-selective pump-probe (PSPP) and optical heterodyne-detected optical Kerr effect (OHD-OKE) experiments were used to quantify OPCs in benzonitrile. These methods measure single molecule and collective orientational relaxation dynamics, respectively. A comparison of the orientational correlation function (PSPP) of the naturally abundant 13CN stretching mode and the polarizability anisotropy relaxation (OHD-OKE) of the liquid revealed that the collective reorientation time was a factor of 1.56 ± 0.08 slower than the single molecule reorientation time. The two types of measurements on dilute benzonitrile in carbon tetrachloride were the same within experimental error. These results support the proposition that OPCs exist and arise from the formation of parallel-aligned intermolecular structures in the neat liquid.

Rotation and translation dynamics of coumarin 153 in choline chloride-based deep eutectic solvents.

The equilibrium and dynamic solvation responses of coumarin 153 (C153) in a range of deep eutectic solvents (DESs) based on choline chloride with either urea (molar ratio 1:2, ChCl:U), glycerol (1:2, ChCl:G), ethylene glycol (1:2, ChCl:E), or malonic acid (1:1, ChCl:Mal) were investigated using both steady-state and time-resolved fluorescence emission spectroscopy at room temperature (298 K). From steady-state fluorescence data, "red-edge effects" were observed in all the DESs studied, attributed to spatial heterogeneity of the DES matrix. Time-resolved Stokes shifts were used to quantify dynamic solvation with the solvation response function in DES found to be a biexponential function of time, which were used to obtain average solvation times (⟨τ s ⟩) which are generally faster in DES than in ionic liquids of comparable viscosity. Average solvation times showed a partial correlation with viscosity between different DESs. The choline chloride-glycerol DES showed deviation from the viscosity trend observed in the other DES for both dynamic and steady-state results. Rotational reorientation times obtained from dynamic anisotropy (r(t)) measured for these DESs showed a partial correlation with viscosity between different DESs. Determination of the DES rotational coupling with C153 showed more "slip"-like behavior than the previously reported ionic liquids and dipolar solvents.

The activation energy for water reorientation differs between IR pump-probe and NMR measurements.

Molecular reorientation dynamics in liquid water are typically probed using either infrared (IR) pump-probe anisotropy experiments or the NMR spin-echo technique. While it is widely appreciated that the two yield different reorientation times based on the nature of the measurements, little attention has been paid to the implications for the corresponding activation energies. Here, the activation energies associated with reorientation of the OH bond vector in liquid water are calculated to high accuracy directly from simulations at a single temperature using a recently developed method [Z. A. Piskulich et al., J. Chem. Phys. 147, 134103 (2017)]. The results indicate that the reorientation times obtained from IR anisotropy and NMR measurements have different activation energies that, with improved accuracy, should be experimentally distinguishable. The origins of the differences in the two activation energies are examined in detail, including by a decomposition into the contributions to the activation energies due to the kinetic energy and the intermolecular interactions.

Temperature dependent dynamics in water-ethanol liquid mixtures

Temperature dependent hydrogen bond energetics and dynamical features, such as the diffusion coefficient and re-orientational times, have been determined for ethanol-water mixtures with 10, 20 and 30 mol% of ethanol. Concerning pairwise interaction energies between molecules, it is found that water-water interactions become stronger, while ethanol-ethanol ones become significantly weaker in the mixtures, than the corresponding values characteristic to the pure substances. Concerning the diffusion processes, for all concentrations the activation barrier of water and ethanol molecule become very similar to each other. Re-orientational motions of water and ethanol become slower as ethanol concentration is increasing. Characteristic re-orientational times of water in the mixtures are substantially longer than these values in the pure substance. On the other hand, this change for ethanol is only moderate. Re-orientational motions of water (especially the ones related to the H-bonded interaction) become very similar for those of ethanol in the mixtures.

Reorientation dynamics and structural interdependencies of actin, microtubules and intermediate filaments upon cyclic stretch application.

Any cell within a tissue is constantly confronted with a variety of mechanical stimuli. Sensing of these diverse stimuli plays an important role in cellular regulation. Besides shear stress, cells of the vascular endothelium are particularly exposed to a permanent cyclic straining originating from the interplay of outwards pushing blood pressure and inwards acting contraction by smooth musculature. Perpendicular alignment of cells as structural adaptation to this condition is a basic prerequisite in order to withstand deformation forces. Here, we combine live cell approaches with immunocytochemical analyses on single cell level to closely elucidate the mechanisms of cytoskeletal realignment to cyclic strain and consolidate orientation analyses of actin fibres, microtubules (MTs) and vimentin. We could show that strain-induced reorientation takes place for all cytoskeletal systems. However, all systems are characterized by their own, specific reorientation time course with actin filaments reorienting first followed by MTs and finally vimentin. Interestingly, in all cases, this reorientation was faster than cell body realignment which argues for an active adaptation mechanism for all cytoskeletal systems. Upon actin destabilization, already smallest alterations in actin kinetics massively hamper cell morphology under strain and therefore overall reorientation. Depolymerization of MTs just slightly influences actin reorientation velocity but strongly affects cell body reorientation.

How Does Solvation Layer Mobility Affect Protein Structural Dynamics?

Solvation is critical for protein structural dynamics. Spectroscopic studies have indicated relationships between protein and solvent dynamics, and rates of gas binding to heme proteins in aqueous solution were previously observed to depend inversely on solution viscosity. In this work, the solvent-compatible enzyme Candida antarctica lipase B, which functions in aqueous and organic solvents, was modeled using molecular dynamics simulations. Data was obtained for the enzyme in acetonitrile, cyclohexane, n-butanol, and tert-butanol, in addition to water. Protein dynamics and solvation shell dynamics are characterized regionally: for each α-helix, β-sheet, and loop or connector region. Correlations are seen between solvent mobility and protein flexibility. So, does local viscosity explain the relationship between protein structural dynamics and solvation layer dynamics? Halle and Davidovic presented a cogent analysis of data describing the global hydrodynamics of a protein (tumbling in solution) that fits a model in which the protein's interfacial viscosity is higher than that of bulk water's, due to retarded water dynamics in the hydration layer (measured in NMR τ2 reorientation times). Numerous experiments have shown coupling between protein and solvation layer dynamics in site-specific measurements. Our data provides spatially-resolved characterization of solvent shell dynamics, showing correlations between regional solvation layer dynamics and protein dynamics in both aqueous and organic solvents. Correlations between protein flexibility and inverse solvent viscosity (1/η) are considered across several protein regions and for a rather disparate collection of solvents. It is seen that the correlation is consistently higher when local solvent shell dynamics are considered, rather than bulk viscosity. Protein flexibility is seen to correlate best with either the local interfacial viscosity or the ratio of the mobility of an organic solvent in a regional solvation layer relative to hydration dynamics around the same region. Results provide insight into the function of aqueous proteins, while also suggesting a framework for interpreting and predicting enzyme structural dynamics in non-aqueous solvents, based on the mobility of solvents within the solvation layer. We suggest that Kramers' theory may be used in future work to model protein conformational transitions in different solvents by incorporating local viscosity effects.

Calculating the motion of highly confined, arbitrary-shaped particles in Hele\u2013Shaw channels

We combine theory and numerical calculations to accurately predict the motion of anisotropic particles in shallow microfluidic channels, in which the particles are strongly confined in the vertical direction. We formulate an effective quasi-two-dimensional description of the Stokes flow around the particle via the Brinkman equation, which can be solved in a time that is two orders of magnitude faster than the three-dimensional problem. The computational speedup enables us to calculate the full trajectories of particles in the channel. To validate our scheme, we study the motion of dumbbell-shaped particles that are produced in a microfluidic channel using ‘continuous-flow lithography’. Contrary to what was reported in earlier work (Uspal et al. in Nat Commun 4:2666, 2013), we find that the reorientation time of a dumbbell particle in an external flow exhibits a minimum as a function of its disk size ratio. This finding is in excellent agreement with new experiments, thus confirming the predictive power of our scheme.

Photophysics and rotational diffusion dynamics of large prolate non-polar laser dyes

The present work deals with experimental determination of steady state fluorescence anisotropies, fluorescence lifetimes and consequentially the rotational reorientation times of three large, nonpolar laser dyes that are modelled as prolate ellipsoids. Steady state and time resolved fluorescence spectroscopic measurements on Exalite 404 (E404), Exalite 417 (E417) and Exalite 428 (E428) dyes in series of alkane and alcohol solutions are discussed. All the three probes are observed to exhibit significantly shorter reorientation times in series of alcohols as compared to alkanes. The experimental results are explained in light of SED hydrodynamic and quasihydrodynamic theories. It is for the first time DKS theory is found to correctly predict the experimental results in alkanes with precision for all the three probes. Particularly in case of E417 DKS theory correlates exceptionally well with predictions of slip hydrodynamics. Interestingly, the largest probe (E428) being reported for the first time, exhibits slip behaviour in alkanes and alcohols; behaviour in higher alcohols as well as alkanes. This suggests the existence of nonhydrodynamic forces and speculates that the straightforward relation between the probe size and the nature of their behaviour may not be appropriate. Further, the nature and geometries of probes were fully explored and characterized using NBO and DFT studies employing Gaussian09 program. Optimized geometries, energy band gap and HOMO-LUMO levels were determined from DFT exchange-correlation function B3LYP with 6-311g basis set. Inter and intra hyper-conjugative interactions were estimated from NBO analysis. A very strong interactions between π(C19C21) → π⁎(C24C25), π(C1C6) → π⁎(C2C3) and π(C33C34) → π⁎(C28C30) with E(2) energies 21.44, 21.75 and 22.75 kcal/mol were observed for E404, E417 and E428, respectively. Electron occupancies and p-character were also determined for these molecules.

Aqueous solvation from the water perspective.

The response of water re-solvating a charge-transfer dye (deprotonated Coumarin 343) after photoexcitation has been measured by means of transient THz spectroscopy. Two steps of increasing THz absorption are observed, a first ∼10 ps step on the time scale of Debye relaxation of bulk water and a much slower step on a 3.9 ns time scale, the latter of which reflecting heating of the bulk solution upon electronic relaxation of the dye molecules from the S1 back into the S0 state. As an additional reference experiment, the hydroxyl vibration of water has been excited directly by a short IR pulse, establishing that the THz signal measures an elevated temperature within ∼1 ps. This result shows that the first step upon dye excitation (10 ps) is not limited by the response time of the THz signal; it rather reflects the reorientation of water molecules in the solvation layer. The apparent discrepancy between the relatively slow reorientation time and the general notion that water is among the fastest solvents with a solvation time in the sub-picosecond regime is discussed. Furthermore, non-equilibrium molecular dynamics simulations have been performed, revealing a close-to-quantitative agreement with experiment, which allows one to disentangle the contribution of heating to the overall THz response from that of water orientation.

Rotational and translational dynamics and their relation to hydrogen bond lifetimes in an ionic liquid by means of NMR relaxation time experiments and molecular dynamics simulation.

We report a concerted theoretical and experimental effort to determine the reorientational dynamics as well as hydrogen bond lifetimes for the doubly ionic hydrogen bond +OH⋯O- in the ionic liquid (2-hydroxyethyl)trimethylammonium bis(trifluoromethylsulfonyl)imide [Ch][NTf2] by using a combination of NMR relaxation time experiments, density functional theory (DFT) calculations, and molecular dynamics (MD) simulations. Due to fast proton exchange, the determination of rotational correlation times is challenging. For molecular liquids, 17O-enhanced proton relaxation time experiments have been used to determine the rotational correlation times for the OH vectors in water or alcohols. As an alternative to those expensive isotopic substitution experiments, we employed a recently introduced approach which is providing access to the rotational dynamics from a single NMR deuteron quadrupolar relaxation time experiment. Here, the deuteron quadrupole coupling constants (DQCCs) are obtained from a relation between the DQCC and the δ 1H proton chemical shifts determined from a set of DFT calculated clusters in combination with experimentally determined proton chemical shifts. The NMR-obtained rotational correlation times were compared to those obtained from MD simulations and then related to viscosities for testing the applicability of popular hydrodynamic models. In addition, hydrogen bond lifetimes were derived, using hydrogen bond population correlation functions computed from MD simulations. Here, two different time domains were observed: The short-time contributions to the hydrogen lifetimes and the reorientational correlation times have roughly the same size and are located in the picosecond range, whereas the long-time contributions decay with relaxation times in the nanosecond regime and are related to rather slow diffusion processes. The computed average hydrogen bond lifetime is dominated by the long-time process, highlighting the importance and longevity of hydrogen-bonded ion pairs in these ionic liquids.

Orientational dynamics in a room temperature ionic liquid: Are angular jumps predominant?

Reorientational dynamics of the constituent ions in a room temperature ionic liquid, 1-butyl-3-methylimidazolium hexafluorophosphate ([BMIM][PF6]), are explored via molecular dynamics simulations, and several features of orientation dynamics are summarized. The anion, [PF6]-, not only exhibits a higher propensity to orientation jumps than the cation, [BMIM]+ but also accesses a wider jump angle distribution and larger peak-angle. Jump and waiting time distributions for both the ions depict power-law dependences, suggesting temporally heterogeneous dynamics for the medium. This heterogeneity feature is further highlighted by the finding that the simulated first rank (ℓ = 1) and second rank (ℓ = 2) average reorientational correlation times reflect a severe break-down of Debye's ℓ(ℓ + 1) law for orientational diffusion in an isotropic homogeneous medium. Simulated average H-bond lifetime resides between the mean orientation jump and waiting times, while the structural H-bond relaxation suggests, as in normal liquids, a pronounced presence of translational motion of the partnering ions. Average simulated jump trajectories reveal a strong rotation-translation coupling and indicate relatively larger changes in spatial and angular arrangements for the anion during an orientation jump. In fact, a closer inspection of all these results points toward more heterogeneous dynamics for [PF6]- than [BMIM]+. This is a new observation and may simply be linked to the ion-size. However, such a generalization warrants further study.

Water, the special liquid

Some prominent special properties of liquid water are summarized and related to the characteristics of the water molecule. It is shown that the substance appears to be anomalous only when compared to hard-sphere models with molecular interactions restricted to excluded-volume effects. Besides the electric charge distribution and the balanced number of hydrogen bond donating and accepting sites, the strength of the hydrogen bonds and also of the covalent bonds are identified significant factors in making water so special. As another major feature the small size of the water molecule is emphasized. It is often neglected but is relevant in every respect. It contributes, for example, to the large permittivity of water which plays an important role in the solvent behavior of water. The paper also demonstrates that the smallness of the water molecule is a key property in the molecular mobility of the liquid. The single-dipole (molecular) reorientation time is deduced from the experimentally available relaxation time of the macroscopic dielectric polarization and is discussed in terms of the so-called wait-and-switch model of dielectric relaxation. By comparison of the waiting periods of the model with structure relaxation times from ultraviolet and X-ray Brillouin spectra, close coupling between the reorientational motions and translational motions, i.e. the hydrogen network fluctuations in water, is disclosed. This finding confirms the idea of the wait-and-switch model. In addition, the waiting period is seen to nicely follow Eyring behavior, indicating an activated switch (or jump) mechanism.

Dynamics of Deformation of a Nematic under Strong Crossed Electric and Magnetic Fields

A new mode of reorientation of the field of director $$\hat n$$ of a nematic liquid crystal (LC) encapsulated into a rectangular cell under strong crossed electric (E) and magnetic (B) fields has been proposed. Numerical calculations performed within the linear generalization of the classical Ericksen–Leslie theory show that transition periodic structures facilitating a decrease in the effective rotational viscosity of a nematic, formed by 4-n-pentyl-4'-cyanobiphenyl (5CB) molecules, may arise during reorientation of $$\hat n$$ at certain ratios of the moments and momenta per unit volume of the LC phase and when E ≫ Eth. The calculations conducted for 5CB also indicate that the periodic structures formed in a LC cell facilitate a decrease in reorientation time τon of the director field.

A quantitative correlation between polyethylene/graphene interfacial viscoelastic dissipation and deformation parameters: A molecular simulation study

In this study, the influence of applied tensile stretching rate and temperature on amorphous polyethylene/graphene (PE/G) and polyethylene/amino functionalized graphene (PE/aFG) interfaces were studied via molecular dynamics (MD) simulations. The simulations results indicated that the interfacial adhesion during stretching process was increased with increasing the stretching rate (V) while decreased with increasing the temperature (T). This behavior can be connected to changing the polymer chains friction arisen from inadequate reorientation time, which especially happened at the higher stretching rates and lower temperatures. Furthermore, the amino functionalization of G strengthened both the thermodynamic work of adhesion and interfacial viscoelastic energy dissipation function, φ (V, T), in the interface deformation process. In fact, relying the chains on aFG surface with stronger interfacial interactions also increased the required energy for the chains to disentangle and reorient on the surface. Moreover, the stretching rate dependency of the φ value well follows a power law at all the stretching temperatures. The effect of stretching rate and temperature on φ value was simultaneously investigated utilizing the time-temperature superposition principle. Master curves of the simulation data, φ (aTV), was obtained for PE/G and PE/aFG interfaces on which the horizontal (aT) and vertical shift factor (bT) were calculated using Williams-Landel-Ferry (WLF) equation and Bueche-Rouse theory, respectively.