Effects of concentrated NaCl and KCl solutions on the behaviour of aqueous peptide bond environment: single-particle dynamics and H-bond structural relaxation

The effects of salt concentrations on the structure, dynamics and hydrogen bond structural relaxation properties of ～1.10 M aqueous N-methylacetamide (NMA) solution at 308 K are studied by classical molecular dynamics simulations. We have considered the concentration range of salts solution from 0.222 to 3.756 M to investigate the behaviour of aqueous environment of peptide bonds in the presence of concentrated NaCl and KCl solution. It is found that the addition of salt solution facilitates the structural breaking of aqueous NMA hydrogen bonds, as a result the number of hydrogen bonds per NMA molecule and their stability decreases. The water and NMA molecule shows slower translational and rotational dynamics with increasing salt concentrations due to additional ion atmospheric friction. Our result shows that the cation–O_NMA radial distribution function decreases whereas the Cl^?─H_NMA radial distribution function increases with ion concentration. On the other hand, the cation–O_water and Cl^?─H_water radial distribution function shows very negligible change with respect to ion concentration. We have also calculated NMA–water and water–water hydrogen bond structural relaxation times. It is observed that the hydrogen bond structural relaxation of O_NMA─H_water is comparatively slower than the H_NMA─O_water hydrogen bond, which can be attributed to higher number and greater stability of the former hydrogen bond than the latter. The change of the dynamical quantities observed here is more prominent in addition of NaCl rather than the KCl solution.     

Picosecond-time-scale fluctuations of proteins in glassy matrices: the role of viscosity

Through elastic neutron scattering we investigated the fast dynamics of lysozyme in hydrated powder form or embedded in glycerol-water and glucose-water matrices. We calculated the relaxational contribution to the mean square displacements of protein hydrogen atoms. We found that the inverse of this quantity is linearly proportional to the logarithm of the viscosity of the solvent glassy matrix. This relationship suggests a close connection between the picosecond-time-scale dynamics of protein side chains and the solvent structural relaxation.     

Effects of co-solutes on the hydrogen bonding structure and dynamics in aqueous N-methylacetamide solution: a molecular dynamics simulations study

The effects of trimethylamine-N-oxide (TMAO), urea and tetramethyl urea (TMU) on the hydrogen bonding structure and dynamics of aqueous solution of N-methylacetamide (NMA) are investigated by classical molecular dynamics simulations. The modification of the water's hydrogen bonding structure and interactions is calculated in presence of these co-solutes. It is observed that the number of four-hydrogen-bonded water molecules in the solution decreases significantly in the presence of TMAO rather than urea and TMU. The lifetime and structural relaxation time of water–water and NMA–water hydrogen bonds show a strong increase with the addition of TMAO and TMU in the solution, whereas the change is nominal in case of urea solution. It is also found that the translational and rotational dynamics of water and NMA slowdown with increasing the concentration of these osmolytes. The slower dynamics of water and NMA is more pronounced in case of TMAO and TMU solution, as these co-solutes strengthen the average hydrogen bond energies between water–water and NMA–water, whereas urea has a little effect on the hydrogen bonding structure and dynamics of aqueous NMA solution. The calculated self-diffusion coefficient values for water and these co-solutes are in similar pattern with experimental observations.     

Rotational dynamics of Di-tert-butyl-nitroxide in normal and supercooled water: an electron paramagnetic resonance study

In order to obtain dynamical information on the water solvent, which is characterized by a strong anomalous behavior in its structural and transport properties especially in the supercooled region, low concentration di-tert-butyl-nitroxide (DTBN) aqueous solutions were studied by Electron Paramagnetic Resonance spectroscopy in the temperature range from 28 down to ?17°C. The accurate spectra reconstruction, achieved by a multi-parameters Monte Carlo fitting algorithm, allowed us to reliably extract some relevant spectral parameters of the spin probe, which were connected to the probe dynamics in the framework of the motional narrowing magnetic relaxation theory. The observed trend with the temperature showed however a significant deviation from what expected from the magnetic relaxation model. This anomalous behavior is discussed in terms of the influence upon the probe motion of solvent-induced local fluctuating structures which, very likely, are connected to the water hydrogen bond network dynamics.     

Pressure effects on diffusion in liquid ammonia : A simulation study using a combination of isobaric-isothermal and microcanonical molecular dynamics

The effects of pressure on translational and rotational diffusion in liquid ammonia are investigated by means of molecular dynamics simulations. Calculations are done at two different temperatures and at many different pressures by using a two-part protocol involving molecular dynamics in isobaric-isothermal ensemble in the first part and in microcanonical ensemble in the second part. Our results are analyzed in terms of pressure-induced changes in structural properties such as packing and hydrogen bond properties. Also, the present results of liquid ammonia are compared with corresponding results for other hydrogen bonded liquids that were reported in recent years.      

Modulation of structure and dynamics of water under alternating electric field and the role of hydrogen bonding

Using Molecular Dynamics simulations, we investigate the effect of alternating (AC) electric field on static and dynamic properties of water. The central question we address is how hydrogen bonds respond to perpetual field-induced dipole reorientations. We assess structural perturbations of water network and changes of hydrogen bond dynamics in a range of alternating electric field strengths and frequencies using a non-polarisable water model, SPC/E, and two distinct polarisable models: SWM4-NDP and BK3. We confirm that AC field causes only moderate structural perturbations. Dynamic properties, including the rates of bond breaking, switching of hydrogen-bonding partners, and diffusion, accelerate with the strength of AC fields. All models reveal a nonmonotonic frequency dependence with fastest dynamics at frequencies around 200?GHz where the period of the field oscillation is commensurate with the average time it takes a typical proton to switch from one acceptor to another. Higher frequencies result in smaller amplitudes of angle oscillations and in reduced probability to complete the switch to another acceptor before the field reversal restores the original configuration. As frequency increases, these effects gradually weaken the influence of the field on the kinetics of hydrogen bonding and the associated rates of translational and rotational diffusion in water.     

Molecular Dynamics of Alkenylphenol Derivatives in Solution as Studied by NMR Spectroscopy

The formation of hydrogen bonds and molecular dynamics of alkenylphenol derivatives has been investigated in solution using nuclear magnetic resonance. The results confirm formation of an N···H, O···H-type intramolecular hydrogen bond. The spin–lattice relaxation times (T ₁) and activation energy of molecular dynamics have been investigated confirming the importance of relaxation times as a very sensitive tool for studying molecular mobility.     

Dynamical changes in hydration water accompanying lysozyme thermal denaturation

We study the dynamics of the first hydration shell of lysozyme to determine the role of hydration water that accompanies lysozyme thermal denaturation. We use nuclear magnetic resonance spectroscopy to investigate both the translational and rotational contributions. Data on proton self-diffusion and reorentational correlation time indicate that the kinetics of the lysozyme folding/unfolding process is controlled by the dynamics of the water molecules in the first hydration shell. When the hydration water dynamics change, because of the weakening of the hydrogen bond network, the three-dimensional structure of the lysozyme is lost and denaturation is triggered. Our data indicates that at temperatures above approximately 315 K, water behaves as a simple liquid and is no longer a good solvent.     

Hydrogen bond dynamics probed with ultrafast infrared heterodyne-detected multidimensional vibrational stimulated echoes

Hydrogen bond dynamics are explicated with exceptional detail using multidimensional infrared vibrational echo correlation spectroscopy with full phase information. Probing the hydroxyl stretch of methanol-OD oligomers in CCl4, the dynamics of the evolving hydrogen bonded network are measured with ultrashort (<50 fs) pulses. The data along with detailed model calculations demonstrate that vibrational relaxation leads to selective hydrogen bond breaking on the red side of the spectrum (strongest hydrogen bonds) and the production of singly hydrogen bonded photoproducts.     

A simulation study of vibrational relaxation of I− 3 in liquids

The temperature dependence of the vibrational relaxation of a flexible model of triiodide in a Lennard-Jones solvent (xenon) has been studied using equilibrium molecular dynamics simulations. The internal dynamics of the ion is calculated from a previously published semi-empirical valence bond model with a limited number of basis states. Vibrational decorrelation rates of the symmetric and antisymmetric stretching modes were found from the time correlation functions of the normal coordinate velocities and the vibrational energy relaxation rates from the time correlation functions of the kinetic energy in each mode. The vibrational dephasing rates and the energy relaxation rates decrease slowly as the temperature is lowered and do not show a discontinuity when the fluid solidifies, although the reorientational diffusion rates change rapidly at low temperatures. In order to interpret the results, perturbation theory expressions for the relaxation rates were evaluated for simulations of a rigid model of the ion and found to agree well with the direct observations. These showed that, unusually, both the solvent force and its derivative, the solvent potential curvature, contribute to the dephasing of the symmetric mode. The relevant fluctuation correlation times are very short, which may explain the insensitivity of the vibrational relaxation to the state of the solvent.     

Anion–water interactions of weakly hydrated anions: molecular dynamics simulations of aqueous NaBF4 and NaPF6

In aqueous ionic solutions, both the structure and the dynamics of water are altered dramatically with respect to the pure solvent. The emergence of novel experimental techniques makes these changes accessible to detailed investigations. At the same time, computational studies deliver unique possibilities for the interpretation of the experimental data at the molecular level. Here, using molecular dynamics simulations, we demonstrate how competing mechanisms can explain the seemingly contradictory statements about the structure and dynamics of ion-coordinated solvent in aqueous solutions of two interesting and technologically important electrolytes, NaBF₄ and NaPF₆. While the static structural data (i.e. radial, radial-angular and spatial distribution functions, as well as hydrogen bonding statistics) unequivocally point at very weak anion–water hydrogen bonding in both salts, dynamic analyses (in particular, orientational anisotropy decay and solvent residence times) reveal quite significant retardation of water rotation and mobility due to solute coordination. Additionally, rotational immobilisation of coordinated solvent molecules is clearly unrelated to the hydrogen bond strength between them, as demonstrated by the interatomic oxygen–oxygen distance distributions for coordinated and bulk water.     

Raman spectroscopy of alkali halide hydration: hydrogen bond relaxation and polarization

The solute–solvent interaction of salts has a striking impact on various biological and industrial processes but its mechanism remains yet mysterious despite intensive studies since 1888 when Franz Hofmeister established the salt series. A combination of confocal Raman spectroscopy and contact angle measurements has enabled us to resolve the hydrogen bond relaxation (O:H―O, HB) and the associated charge polarization dynamics at different molecular site because of alkali halides hydration. Results show consistently that salt hydration softens the O:H phonon but stiffens H―O phonon cooperatively. The extent of HB relaxation and polarization is proportional to the electronegativity difference and ionic radius, following the order of Hofmeister series: X (R/η) = I (2.2/2.5) > Br (1.96/2.8) > Cl (1.81/3.0) > F (1.33/4.0) ≈ 0 for anions, and Y(R/η) = Na (0.98/0.9) > K (1.33/0.8) > Rb (1.49/0.8) > Cs (1.65/0.8) for cations. Observations suggest that ions create each an electric field that aligns, stretches, and polarizes water molecules, which relaxes the O:H―O bond cooperatively, depresses the molecular dynamics, and enhances the hydration shell viscosity and the skin stress. Exercises also demonstrate that Raman spectroscopy performs as a powerful tool for probing the molecular‐site‐resolved HB network relaxation dynamics in terms of phonon stiffness, molecular fluctuation dynamics, and phonon abundance transition under external stimulus. Copyright © 2016 John Wiley & Sons, Ltd.     

Hydrogen-bond dynamics of interior and surface molecules in a water nanocluster: temperature and size effects

Molecular dynamics simulations are employed to investigate the effects of temperature and size on the hydrogen-bond dynamics of interior molecules and surface molecules in a water nanocluster. The flexible three-centred (F3C) water model is invoked in the simulations. To inspect the dynamics of the interior hydrogen bonds and the surface hydrogen bonds, a spherical water nanocluster is modelled and then divided into interior molecules and surface molecules according to the density profile of the water nanocluster. It is observed that at higher temperatures the average number of hydrogen bonds decreases and yields faster hydrogen-bond relaxation for both interior molecules and surface molecules of the water nanocluster. Furthermore, the surface molecules have a lower average number of hydrogen bonds than the interior molecules. The lifetime of the surface hydrogen bonds is slightly longer than that of the interior hydrogen bonds, whereas the hydrogen-bond structural relaxation time of the surface molecules is more obviously slower than that of the interior molecules. Regarding the size effect, a larger water nanocluster is seen to have a larger average number of hydrogen bonds and a longer hydrogen-bond structural relaxation time.     

Dynamics of hydroxyl deuterons and bonded water molecules in NaDY(0.8) zeolite as studied by means of deuteron NMR spectroscopy and relaxation

Deuteron spin–lattice relaxation and spectra were measured for NaDY (0.8) zeolite containing some heavy water. Two subsystems of deuterons with different mobility were disclosed at low temperatures with their respective relaxation rates differing by two orders of magnitude. Spectra exhibit different shapes related directly to a specific motional model. Hydroxyl deuterons perform incoherent tunneling along the hydrogen bond, then on increasing temperature jumps to excited states and over the barrier appear. Hydrogen bonded water molecules perform 180° rotational jumps about the twofold symmetry axis. Spectral amplitudes are consistent with the water content of 13 D₂O molecules per unit cell. Above about 240 K translational mobility becomes significant and finally water molecules diffuse across the free space of cages. Diversity in temperature dependence of hydroxyl deuteron dynamics may indicate location of adsorbed molecules.     

Evaluation of the thermodynamic parameters for association process of hydrogen bond complexes from the dielectric relaxation measurements.

A relation between the free energy for dipole relaxation process and that for the association process has been proposed. Using this relation, an equation has been defined for evaluating the association equilibrium constant from the dielectric relaxation measurements. These equations have been applied to study the association of dimethyl sulphoxide and p-tolyl sulphoxide with proton donors (phenol and O-cresol) in an inert solvent carbon-tetra-chloride in the temperature range 298–322K. The calculation of the association equilibrium constant and hence the thermodynamic parameters have shown the wide scope, the proposed relations can be put to in the study of the association process of hydrogen bond complexes.     

Reorientation dynamics in liquid alcohols from Raman spectroscopy

Polarized Raman spectroscopy has been employed to study the reorientational, or more specifically the translational relaxation dynamics, of alcohol molecules in pure liquids and aqueous solutions. It is found from the spectral width measurements that alcohol molecules in pure liquids have typically translational relaxation times on the order of picoseconds, following the order methanol < ethanol < i‐propanol < n‐propanol. Temperature‐dependent measurements show that hydrogen‐bonding (HB) and hydrophobic interactions control the translational motion. The hydrophobic interaction reduces the relaxation time more apparently in view of the  CH₃ group than the skeleton motion. For alcohol–water mixtures, the increase of water concentration generally slows down the relaxation process in a non‐monotonic behavior. However, the trend stops at a certain point and the motion of alcohol molecules becomes faster when the alcohol concentration further drops. Different mechanisms have been proposed to interpret these observations, which might be helpful to gain deeper insight into the HB networks of alcohols with water. Our study strongly illustrates that Raman spectroscopy can be applied to the study of fast translational motion of molecules in HB systems. Copyright © 2011 John Wiley & Sons, Ltd.     

Fluorescence characteristics of 5-aminoquinoline in acetonitrile: Water

Photophysical and spectral properties of 5-aminoquinoline (5-AQ) in acetonitrile: water binary mixture have been studied to understand the excited state relaxation processes occurring in the excited state. Fluorescence of 5-AQ has been found to be quite sensitive to the hydrogen bond donating ability of the solvent mixture and is quenched in the presence of water. Hydrogen bonding in the excited state appears to be responsible for the quenching.     

Dynamics and hydrogen bonding in liquid ethanol

Molecular dynamics simulations of liquid ethanol at three temperatures have been carried out. The hydrogen bonding states of ethanol molecules have been characterized by the number of hydrogen bonds in which the molecules participate. It is observed that the mean lifetimes of molecules in each hydrogen bonding state are markedly dependent on the temperature. Moreover, molecules with one hydrogen bond are more stable when they are donors than when they are acceptors. The dependence of the reorientational correlation functions on the hydrogen bonding state of molecules has been studied carefully. The decay of these functions is slower for molecules with higher numbers of hydrogen bonds and also becomes slower as temperature decreases. The relaxation for molecules with only one hydrogen bond is faster for those acting as proton donors than for those acting as proton acceptors. Finally, the results obtained by computer simulation are compared with those from recent measurements of the frequency-dependent dielectric permittivity of liquid ethanol.