Water In Hydration Shell Research Articles

Effect of the sulphur atom on geometry and spectra of the biomolecule 2-thiouracil and in the WC base pair 2-thiouridine-adenosine. Influence of water in the first hydration shell

The effect of the sulphur atom on 2-thiouracil (2TU) and 2-thiouridine molecules, as compared with uracil and uridine molecules, respectively, was carried out in several environments. The predicted IR spectrum of 2TU in the isolated state was compared with that obtained for uracil molecule and with those reported experimentally in matrix isolation. Its crystal unit cell in the solid state was simulated through a tetramer form using DFT methods for the first time. The calculated Raman spectrum was compared to the experimental ones in the solid state. A linear scaling procedure was used for this task. The first hydration shell was simulated by explicit number of water molecules surrounding 2TU up to 30 and was compared with that obtained in uracil molecule. Water molecules ‘distributed’ around 2TU was preferred over that ‘clustering’, because it can better reproduce the hydration and their effects on different parameters of the molecular structure of 2TU and uracil. The total atomic charges and several calculated thermodynamic parameters were discussed. The effect of the sulphur atom on the Watson-Crick (WC) and reverse WC base pair uridine-adenosine was estimated, and the CP corrected interaction energies were calculated. 2-thiouridine has a weaker WC pair than that with uridine, although its slight higher dipole moment (μ) facilitates the interaction with the water molecules. Several helical parameters were determined.

Solvent-Slaved Dynamic Processes Observed by Tryptophan Phosphorescence of Human Serum Albumin

Despite extensive experimental and computational efforts to understand the nature of the hierarchy of protein fluctuations and the modulating role of the protein hydration shell, a detailed microscopic description of the dynamics of the protein-solvent system has yet to be achieved. By using single tryptophan protein phosphorescence, we follow site-specific internal protein dynamics over a broad temperature range and demonstrate three independent dynamic processes. Process I is seen at temperatures below the bulk solvent Tg, has low activation energy, and is likely due to fast vibrations that may be enabled by water mobility on the protein surface. Process II is observed above 170 K, with activation energy typical of β relaxations in a glass; it has the same temperature dependence as fluctuations of hydration shell waters. Process III is observed at T > 200 K; it has super-Arrhenius temperature dependence and closely follows the primary relaxation of the bulk. The fluorescence of pyranine bound to the protein reports on the mobility of water in the hydration shell; it reveals a shift in emission spectra with increasing temperature, indicative of a changing H-bond network at the surface of the protein. These results support a model of solvent-slaved protein dynamics.

Computational smart polymer design based on elastin protein mutability.

Soluble elastin-like peptides (ELPs) can be engineered into a range of physical forms, from hydrogels and scaffolds to fibers and artificial tissues, finding numerous applications in medicine and engineering as "smart polymers". Elastin-like peptides are attractive candidates as a platform for novel biomaterial design because they exhibit a highly tunable response spectrum, with reversible phase transition capabilities. Here, we report the design of the first virtual library of elastin-like protein models using methods for enhanced sampling to study the effect of peptide chemistry, chain length, and salt concentration on the structural transitions of ELPs, exposing associated molecular mechanisms. We describe the behavior of the local molecular structure under increasing temperatures and the effect of peptide interactions with nearest hydration shell water molecules on peptide mobility and propensity to exhibit structural transitions. Shifts in the magnitude of structural transitions at the single-molecule scale are explained from the perspective of peptide-ion-water interactions in a library of four unique elastin-like peptide systems. Predictions of structural transitions are subsequently validated in experiment. This library is a valuable resource for recombinant protein design and synthesis as it elucidates mechanisms at the single-molecule level, paving a feedback path between simulation and experiment for smart material designs, with applications in biomedicine and diagnostic devices.

Communication: Stiffening of dilute alcohol and alkane mixtures with water.

We probe the anomalous compressibilities of dilute mixtures of alcohols and alkane gases in water using molecular simulations. The response to increasing solute concentration depends sensitively on temperature, with the compressibility decreasing upon solute addition at low temperatures and increasing at elevated temperatures. The thermodynamic origin of stiffening is directly tied to the solute's partial compressibility, which is negative at low temperatures and rises above water's compressibility with increasing temperature. Hydration shell waters concurrently tilt towards clathrate-like structures at low temperatures that fade with heating. Kirkwood-Buff theory traces the solute's partial compressibility to changes in the solute-water association volume upon heating and incongruous packing of waters at the boundary between the more structured hydration shell and bulk water.

Interactions of human serum albumin with doxorubicin in different media

Interactions of human serum albumin (10wt% H2O and 0.3wt% sodium caprylate) with doxorubicin hydrochloride (1wt%) were studied alone or with addition of HCl (3.6wt% HCl) using 1H NMR spectroscopy. A model of hydrated HSA/12DOX was calculated using PM7 method with COSMO showing large variations in the binding constant depending on structural features of DOX/HSA complexes. DOX molecules/ions displace bound water from narrow intramolecular voids in HSA that leads to diminution of freezing-melting point depression of strongly bound water (SBW). Structure of weakly bound water (WBW) depends much weaker on the presence of DOX than SBW because a major fraction of DOX is bound to adsorption sites of HSA. Addition of HCl results in strong changes in structure of macromolecules and organization of water in hydration shells of HSA (i.e., mainly SBW) and in the solution (i.e., WBW+non-bound bulk water).

Sensitivity of Protein Glass Transition to the Choice of Water Model.

The sensitivity of protein glass transition temperature and dynamics of Trp-cage miniprotein to the choice of water models have been investigated by performing molecular dynamics simulations at different temperatures between 130 and 300 K using mTIP3P, TIP4P, and TIP4P-Ew water models with the CHARMM22 force field. Analysis of the structure of the protein and the ordering of the hydration shell water molecules revealed correlated dynamic crossovers of the protein and its hydration water. It is demonstrated that the parametrization of different water models is robust enough to probe the onset temperatures for the two dynamic crossovers of the peptide: the first one around 150 K which is attributed to active methyl group rotations and the second one around 200-230 K specifically pertaining to glass transition of the protein. The behavior of the protein has been found to be qualitatively similar to the three water models employed, while the structural ordering and number of hydration shell waters vary significantly among the 3-site and 4-site water models. The changes in the probability density map of methyl hydrogens of the protein with temperature also show sensitivity to the choice of water model.

Molecular dynamics simulation of the hydration structure and hydrogen bonding behavior of phenol in aqueous solution

Molecular dynamics simulations are carried out to study the hydration structures and hydrogen bonding properties of phenol in aqueous solution with infinite dilution for several temperatures ranging from 273 to 363K. The hydration structures of phenol are characterized by radial distribution functions and orientational ordering. There appears structured local distribution of water around phenol within the distance of 8Å. Two hydration shells are defined to characterize the local structure. The orientation distribution of the water in the first hydration shell shows more ordered local structure than that in the second hydration shell. Increasing temperature leads to the disruption of the local structure. We mainly focus on the analysis of the hydrogen bonding interaction between phenol hydroxyl and water. The hydrogen bonds are identified based on the geometric criterion, which is defined according to analysis of radial distribution function and angle distribution. A definition of hydrogen bonding state f(m, n) is proposed to characterize the hydrogen bonding structure of phenol in aqueous solution. Phenol in the hydrogen bonding state f(m, n) means that the phenol hydroxyl forms m hydrogen bonds as donor and n hydrogen bonds as acceptor. At the different temperatures, the phenol hydroxyl prefers to stay in the hydrogen bonding state f(1, 1). It is shown that the hydrogen bonding state f(1, n) takes the dominant role. Thus phenol is proven to be a good hydrogen bond donor than acceptor. These findings help to further understand the hydration structure and hydrogen bonding behavior of phenol in aqueous solution.

Reaction Mechanism for Direct Proton Transfer from Carbonic Acid to a Strong Base in Aqueous Solution II: Solvent Coordinate-Dependent Reaction Path.

The protonation of methylamine base CH3NH2 by carbonic acid H2CO3 within a hydrogen (H)-bonded complex in aqueous solution was studied via Car-Parrinello dynamics in the preceding paper (Daschakraborty, S.; Kiefer, P. M.; Miller, Y.; Motro, Y.; Pines, D.; Pines, E.; Hynes, J. T. J. Phys. Chem. B 2016, DOI: 10.1021/acs.jpcb.5b12742). Here some important further details of the reaction path are presented, with specific emphasis on the water solvent's role. The overall reaction is barrierless and very rapid, on an ∼100 fs time scale, with the proton transfer (PT) event itself being very sudden (<10 fs). This transfer is preceded by the acid-base H-bond's compression, while the water solvent changes little until the actual PT occurrence; this results from the very strong driving force for the reaction, as indicated by the very favorable acid-protonated base ΔpKa difference. Further solvent rearrangement follows immediately the sudden PT's production of an incipient contact ion pair, stabilizing it by establishment of equilibrium solvation. The solvent water's short time scale ∼120 fs response to the incipient ion pair formation is primarily associated with librational modes and H-bond compression of water molecules around the carboxylate anion and the protonated base. This is consistent with this stabilization involving significant increase in H-bonding of hydration shell waters to the negatively charged carboxylate group oxygens' (especially the former H2CO3 donor oxygen) and the nitrogen of the positively charged protonated base's NH3(+).

The dielectric properties of LiOH aqueous solution under external electromagnetic fields by molecular dynamics simulation

Molecular dynamics simulation of LiOH aqueous solution has been performed both in the absence and presence of the external electromagnetic (E/M) fields (2.45GHz). The simulated dielectric constant results from the fluctuation method (69.3) and electric field method (70.12) are in quantitative agreement with the experiment result (64.5). The radial distribution function and coordination structure of Li+ and OH− ions of LiOH aqueous solution change significantly with the intensity of the external E/M fields in the range of 0 and 3×109V/m. At the high E/M fields (3×109V/m), the interactions of the Li+ and OH− ions with water in first hydration shell are weakening due to the acceleration rotational effect of ions driven by the external E/M fields. The rearrangement and interactions of water molecules around Li+ and OH− ions in hydration shell may be affected by the external E/M fields applied.

Hydrogen-bonding and vibrational coupling of water in a hydrophobic hydration shell as observed by Raman-MCR and isotopic dilution spectroscopy.

Hydrogen-bonding and intra/intermolecular vibrational coupling of water next to a hydrophobic molecule (tert-butyl alcohol, TBA) have been studied by Raman multivariate curve resolution (Raman-MCR) and isotopic dilution spectroscopy. Raman-MCR provides the vibrational spectrum of water pertinent to the hydration shell of TBA, which shows a distinct Raman band at around 3660 cm(-1) corresponding to the dangling OH in the hydration shell. The presence of positive charge on the hydrophobe decreases the propensity of dangling OH in the hydration shell, presumably due to unfavorable electrostatic interaction. Analysis of the dangling OH band with isotopic dilution reveals that the 'dangling OH' is intramolecularly coupled with the 'H-bonded OH' of the same water molecule. The hydration water spectrum in the H-bonded OH stretch region (3000-3600 cm(-1)) shows a depletion of weakly H-bonded water (∼3580 cm(-1)) and an increase of strongly H-bonded water (∼3250 cm(-1)), making the average H-bonding stronger in a hydrophobic hydration shell than that in bulk. This strongly H-bonded hydration water exhibits weaker intra- and intermolecular vibrational coupling than that of bulk water.

First-Principles Simulation Study of Vibrational Spectral Diffusion and Hydrogen Bond Fluctuations in Aqueous Solution of N-Methylacetamide.

We have presented a first-principles simulation study of the vibrational spectral diffusion and hydrogen bond dynamics in an aqueous solution of N-methylacetamide (NMA). We have studied the spectral diffusion of local OD stretch modes of deuterated water in the first hydration shells of the carbonyl (CO) and deuterated amide (ND) modes and their relations to the dynamics of hydrogen bonds formed by water with these groups. The frequency fluctuations of the amide I and amide A modes of the solute are also investigated. It is found that the vibrational spectral diffusion of water molecules in the first hydration shell of the carbonyl oxygen of NMA proceeds with three time scales: A short-time relaxation (∼100 fs) originating from the dynamics of NMA-water hydrogen bonds without breaking, a slower relaxation (∼3.3 ps) arising from the breaking dynamics of NMA(CO)-water hydrogen bonds, and another longer time constant (∼14 ps) coming from the escape dynamics of water from the first hydration shell of carbonyl oxygen. The current results show that the NMA(CO)-water hydrogen bonds have a longer lifetime than those between water molecules, although frequency calculations reveal a slightly higher stretch frequency of the water molecules in the first hydration shell of the carbonyl oxygen of NMA. An analysis of the vibrational spectral diffusion of solute modes is also presented in terms of the dynamics of solute-water hydrogen bonds. Effects of dispersion interactions on various calculated properties of the NMA-water system are also investigated in the present work.

Water in Hydration Shell of an Iodide Ion: Structure and Dynamics of Solute-Water Hydrogen Bonds and Vibrational Spectral Diffusion from First-Principles Simulations.

The dynamics of hydrogen bonds and vibrational spectral diffusion of water in the hydration shell of an iodide ion and in bulk have been investigated for aqueous iodide solutions of two different concentrations by using ab initio molecular dynamics simulations. The effects of dispersion interactions on the dynamics have also been investigated by using a dispersion corrected density functional. For the dilute solution containing a single iodide ion, three time scales are found for the spectral diffusion of solvation shell water: A short time scale of ∼150 fs, a slower time scale of ∼2-3 ps and a yet longer time scale of ∼14-16 ps. The long time scale of ∼14-16 ps is not noticed when calculations are done for all OD modes for both the dilute and concentrated solutions. It is found that a clear separation between the solvation shell and bulk water does not exist in terms of OD stretching frequencies for the concentrated solution. The dynamics of vibrational spectral diffusion is explained in terms of hydrogen bond dynamics, other dynamical modes such as orientational relaxation and molecular diffusion, and also structural aspects of water molecules in the solvation shells. The current results are compared with those of available experimental and other theoretical studies.

A Molecular Dynamics Study of the Effects of V2+ and V3+ on the Local Structure of Hydrated Nafion

Because Nafion is a commonly employed membrane in vanadium redox flow batteries, we have undertaken classical molecular dynamics simulations to understand the effects of absorbed V2+ and V3+ on the local structure of the ionomer. The simulations reveal that at low hydration the vanadium ions directly interact with the sulfonate groups forming contact ion pairs. As the water content is increased to nearly fully hydrated conditions (18 H2O/SO3–), the probability for direct interaction is significantly reduced because of solvation of the cations by the water molecules. Surprisingly, V3+ showed less affinity to the SO3– groups than did V2+, as demonstrated by fewer V3+ around the SO3– groups. This is attributed to the stronger attraction of the first hydration shell water molecules to V3+. Despite the inhomogeneity of the system, the population in the first hydration shell is similar to that observed in bulk water. The pair correlation function between the SO3– groups and the H3O+ cations is strongly affected...

Curvature dependence of hydrophobic hydration dynamics.

We investigate the solute curvature dependence of water dynamics in the vicinity of hydrophobic spherical solutes using molecular dynamics simulations. For both the lateral and perpendicular diffusivity, as well as for H-bond kinetics of water in the first hydration shell, we find a nonmonotonic solute-size dependence, exhibiting extrema close to the well-known structural crossover length scale for hydrophobic hydration. Additionally, we find an apparent anomalous diffusion for water moving parallel to the surface of small solutes, which, however, can be explained by topology effects. Our findings regarding the intimate connection between solute curvature and water dynamics has implications for our understanding of hydration dynamics at heterogeneous biomolecular surfaces.

Ab initio molecular dynamics studies of hydrogen bonded structure, molecular motion, and frequency fluctuations of water in the vicinity of azide ions.

First principles theoretical studies of vibrational spectral diffusion of the stretch modes of water and azide (N3(-)) ions are presented by means of ab initio molecular dynamics simulations for two different concentrations of the ions. The vibrational spectral diffusion of hydration shell water in a dilute solution containing a single azide ion is found to occur with three time scales while two time scales are found for the spectral diffusion in the solution of higher ion concentration. The frequency time correlation of the stretching vibration of azide ion is also found to have two time scales. The vibrational spectral diffusion of the stretching mode of azide ions in the concentrated solution is found to occur at a slightly faster rate while that of the water OD modes becomes slower with increase of ion concentration. The effects of dispersion interactions are also investigated by using a dispersion corrected density functional. The time constants of frequency correlations and dynamical spectral shifts are analyzed in terms of the relaxation of azide ion-water and water-water hydrogen bonds. The results of present theoretical calculations are compared with the available experimental and other theoretical results.

Water response to intense electric fields: A molecular dynamics study.

This paper investigated polarization properties of water molecules in close proximity to an ionic charge in the presence of external electric fields by using an approach based on simulations at the atomic level. We chose sodium and chloride ions in water as examples of dilute ionic solutions and used molecular dynamics simulations to systematically investigate the influence of an external static electric field on structural, dipolar, and polarization properties of water near charged ions. Results showed that a threshold electric field higher than 10(8) V/m is needed to affect water polarization and increase mean dipole moment of water molecules close to the ion. A similar threshold holds for water permittivity profiles, although a field 10× higher is needed to ensure that water permittivity is almost constant independently of the position close to the ion. Electric fields of such intensities can greatly enhance polarizability of water in hydration shells around ions.

Solvation Dynamics in Liquid Water. 1. Ultrafast Energy Fluxes.

Solvation dynamics in liquid water is addressed via nonequilibrium energy-transfer pathways activated after a neutral atomic solute acquires a unit charge, either positive or negative. It is shown that the well-known nonequilibrium frequency shift relaxation function can be expressed in a novel fashion in terms of energy fluxes, providing a clear-cut and quantitative account of the processes involved. Roughly half of the initial excess energy is transferred into hindered rotations of first hydration shell water molecules, i.e., librational motions, specifically those rotations around the lowest moment of inertia principal axis. After integration over all water solvent molecules, rotations account for roughly 80% of the energy transferred, while translations have a secondary role; transfer to intramolecular water stretch and bend vibrations is negligible. This picture is similar to that for relaxation of a single vibrationally or rotationally excited water molecule in neat liquid water, although solvation relaxation is more nonlocal. In addition, we find a remarkable independence of the main relaxation channels on the newly created charge's sign. Although the methodology is applied here to the simplest solute case, the approach is rather general, and it should be at least equally useful in more realistic and complex scenarios.

Vibrational probing of the hydrogen-bond structure and dynamics of water in aqueous NaPF6 solutions

The H-bond structures and dynamics of water in bulk and ionic hydration shells in aqueous NaPF6 solutions were measured at different NaPF6 concentrations.

Effects of dispersion interaction on vibrational spectral diffusion in aqueous NaBr solutions: An ab initio molecular dynamics study

Effects of dispersion interactions on the dynamics of water in bromide ion hydration shells have been studied by first principles simulations using a dispersion corrected density functional. The dynamics of vibrational spectral diffusion and its relations to hydrogen bond dynamics have been investigated for two different ion concentrations. It is found that the vibrational spectral diffusion of water molecules show faster dynamics with inclusion of dispersion interactions for both hydration shell and bulk water. The frequency calculations of hydration shell water reveal a weaker ion–water hydrogen bond than those between two water molecules. In the anionic hydration shell, the frequency of an OD bond is found to decrease with decrease of ion–water hydrogen bond distance. The hole dynamics calculations have been performed for further investigations of vibrational spectral diffusion of the two solutions. The current results are compared with those of recent experiments and other theoretical calculations.

Effects of ions on water structure: a low-field ¹H T₁ NMR relaxometry approach.

Aqueous salt solutions play an important role in nature because of their effects on environmental biogeochemical processes and on structural properties of biomolecules. Upon dissolution, salts split in ions that are solvated. Water in hydration shells is subjected to molecular motions that can be monitored by (1)H T1 NMR relaxometry. This technique allowed the evaluation of the nature of the interactions between water and ions via variable temperature experiments. Examination of relaxometry properties of aqueous solutions at variable salt concentrations allowed acknowledgement of the role played by ions in either structuring or destructuring water aggregates. A mathematical model has been applied on six environmentally relevant salts: NaCl, KCl, CaCl2, CaCO3, NaNO3, and NH4NO3. It was linear only for the concentration dependence of KCl-R1. This model accorded with the one reported in literature where it has been considered valid only for diluted solutions. However, in the present study, the range of linearity for KCl was extended up to the saturation point. The model was modified for NaCl, CaCl2, and CaCO3 by using it as an exponential form in order to account for the nonlinearity of the R1-versus-concentration curves. Nonlinearity was explained by the nonnegligible ion-ion interactions occurring as concentration was increased. Finally, further modification was needed to account for the asymmetric distribution of water around nitrate (in NaNO3 and NH4NO3) and ammonium (in NH4NO3). This study is preliminary to the comprehension of the diffusion mechanisms of ions in water solutions at the equilibrium condition with solid surfaces such as soils and biochar-amended soils.