Effect of counterions on the structure and dynamics of water near a negatively charged surfactant: a theoretical vibrational sum frequency generation study.

Charged aqueous interfaces are of paramount importance in electrochemical, biological and environmental sciences. The properties of aqueous interfaces with ionic surfactants can be influenced by the presence of counterions. Earlier experiments involving vibrational sum frequency generation (VSFG) spectroscopy of aqueous interfaces with negatively charged sodium dodecyl sulfate (Na+DS- or SDS) surfactants revealed that the hydrogen bonding strength of the interfacial water molecules follows a certain order when salts of monovalent and divalent cations are added. It is known that cations do not directly participate in hydrogen bonding with water molecules, rather they only influence the hydrogen bonded network through their electrostatic fields. In the current work, we have simulated the aqueous interfacial systems of sodium dodecyl sulfate in the presence of chloride salts of mono and divalent countercations. The electronic polarization effects on the ions are considered at a mean-field level within the electronic continuum correction model. Our calculations of the VSFG spectra show a blue shift in the presence of added countercations whose origin is traced to different relative contributions of water molecules from the solvation shells of the surfactant headgroups and the remaining water molecules in the presence of countercations. Furthermore, the cations shield the electric fields of the surfactant headgroups, which in turn influences the contributions of water molecules to the total VSFG spectrum. This shielding effect becomes more significant when divalent countercations are present. The dynamics of water molecules is found to be slower at the interface in comparison to the bulk. The interfacial depth dependence of various dynamical quantities shows that the interface is structurally and dynamically more heterogeneous at the microscopic level.

All-atom simulations of the trimeric spike protein of SARS-CoV-2 in aqueous medium: Nature of interactions, conformational stability and free energy diagrams for conformational transition of the protein.

The spike protein of SARS-CoV-2 exists in two major conformational states, namely the 'open' and 'closed' states which are also known as the 'up' and 'down' states, respectively. In its open state, the receptor binding domain (RBD) of the protein is exposed for binding with ACE2, whereas the spike RBD is inaccessible to ACE2 in the closed state of the protein. In the current work, we have performed all-atom microsecond simulations of the full-length trimeric spike protein solvated in explicit aqueous medium with an average system size of ~0.7 million atoms to understand the molecular nature of intra- and inter-chain interactions, water-bridged interactions between different residues that contribute to the stability of the open and closed states of the protein, and also the free energy landscape for transition between the open and closed states of the protein. We have also examined the changes of such interactions that are associated with switching from one state to the other through both unbiased and biased simulations at all-atom level with total run length of 4 µs. Interestingly, after about 0.8 µs of unbiased molecular dynamics run of the spike system in the open state, we observed a gradual transition of the monomeric chain (B) from open to its partially closed or down state. Initially the residues at the interface of chain B RBD in the open state spike protein were at non-hydrogen-bonding distances from the residues of chain C RBD. However, the two RBDs gradually came closer and finally the residue S459 of the RBD of chain B made a hydrogen bond with F374 of chain C in the last 200 ns of the simulation along with formation of a few more hydrogen bonds involving other residues. Since no transition from closed to the open state of the protein is observed in the present 1 µs unbiased simulation of the closed state protein, the current study seems to suggest that the closed conformational state is preferred for the spike protein of SARS-CoV-2 in aqueous medium. Furthermore, calculations of the free energy surface of the conformational transition from open (up) to the closed (down) state using a biased simulation method reveal a free energy barrier of ~3.20 kcal/mol for the transition of RBD from open to the closed state, whereas the barrier for the reverse process is found to be significantly higher.

Vibrational Sum Frequency Generation Spectra of Water-Vapor Interfaces Covered by Alcohols: Effects of†Surface Coverage and Coupling between Oscillators.

The present study deals with the effects of varying coverage of water surface by alcohols on the vibrational sum frequency generation (VSFG) spectrum of interfacial water. We have considered two different alcohols: Tertiary butyl alcohol (TBA) whose alkyl part is fully branched and stearyl alcohol (STA) which has a long linear alkyl chain with larger hydrophobic surface area than that of TBA. With increase of the alcohol concentration, the hydrogen bonded OH stretch region of the VSFG spectrum is found to change following a regular trend for the STA-water system, whereas non-monotonic variation of the VSFG spectrum is observed for the TBA-water system which can be correlated with the presence of very different interactions of TBA molecules at different concentrations. On increasing the concentration of TBA, the hydrophobic groups get more tilted towards the water phase and significant hydrophobic interactions are introduced at higher concentrations. Whereas, for STA, there is a gradual increase in the hydrophilic interaction. Because of stacking interactions between the long chain alkyl groups, the hydrophobic parts stay outward from the water phase at higher concentrations and a regular change in the VSFG spectrum is observed. We have also presented a computationally efficient scheme to calculate the VSFG spectrum of interfacial systems for coupled oscillators which is expected to be beneficial for the treatment of coupling where the interfacial system size is inherently large.

A Multiple Proton Transfer Mechanism for the Charging Step of the Aminoacylation Reaction at the Active Site of Aspartyl tRNA Synthetase.

Aspartyl-tRNA synthetase catalyzes the attachment of aspartic acid to its cognate tRNA by the aminoacylation reaction during the initiation of the protein biosynthesis process. In the second step of the aminoacylation reaction, known as the charging step, the aspartate moiety is transferred from aspartyl-adenylate to the 3'-OH of A76 of tRNA through a proton transfer process. We have investigated different pathways for the charging step through three separate QM/MM simulations combined with the enhanced sampling method of well-sliced metadynamics and found out the most feasible pathway for the reaction at the active site of the enzyme. In the charging reaction, both the phosphate group and the ammonium group after deprotonation can potentially act as a base for proton transfer in the substrate-assisted mechanism. We have considered three possible mechanisms involving different pathways of proton transfer, and only one of them is determined to be enzymatically feasible. The free energy landscape along reaction coordinates where the phosphate group acts as the general base showed that, in the absence of water, the barrier height is 52.6 kcal/mol. The free energy barrier is reduced to 39.7 kcal/mol when the active site water molecules are also treated quantum mechanically, thus allowing a water mediated proton transfer. The charging reaction involving the ammonium group of the aspartyl adenylate is found to follow a path where first a proton from the ammonium group moves to a water in the vicinity forming a hydronium ion (H3O+) and NH2 group. The hydronium ion subsequently passes the proton to the Asp233 residue, thus minimizing the chance of back proton transfer from hydronium to the NH2 group. The neutral NH2 group subsequently takes the proton from the O3' of A76 with a free energy barrier of 10.7 kcal/mol. In the next step, the deprotonated O3' makes a nucleophilic attack to the carbonyl carbon forming a tetrahedral transition state with a free energy barrier of 24.8 kcal/mol. Thus, the present work shows that the charging step proceeds through a multiple proton transfer mechanism where the amino group formed after deprotonation acts as the base to capture a proton from O3' of A76 rather than the phosphate group. The current study also shows the important role played by Asp233 in the proton transfer process.

Effects of stearyl alcohol monolayer on the structure, dynamics and vibrational sum frequency generation spectroscopy of interfacial water.

The structure, dynamics and vibrational spectroscopy of a water surface covered by a monolayer of stearyl alcohol (STA) are investigated by means of molecular dynamics simulations and vibrational sum frequency generation (VSFG) spectral calculations. The STA molecules possess long linear alkyl chains without any branching and have a rather large hydrophobic surface area. The STA-water interface is found to be rather narrow with an ordered outward arrangement of the alcohol chains at the water surface. The water molecules in the interfacial region which contribute most to the observed VSFG spectrum are identified. It is shown that the observed red shift in the hydrogen bonded part of the VSFG spectrum can originate from partial cancellation of the spectral responses from up and down-oriented OH moieties of interfacial water which are hydrogen bonded, respectively, to alcohol and water molecules. The effects of intra and intermolecular coupling to the VSFG spectrum are also calculated for the STA-water interface considered here. On the dynamical side, a slowing down of the hydrogen bond and orientational relaxation is found for the interfacial water. It is found that the ordered arrangement of STA molecules at the surface holds the interfacial water molecules rather tightly and slows down the dynamics. The current results of the STA-water interface are also compared with those of the tertiary butyl alcohol (TBA)-water interface where the alcohol has a fully branched hydrophobic part of the lower surface area.

Transport of hydrated nitrate and nitrite ions through graphene nanopores in aqueous medium.

Nitrate ( NO 3 - ) and nitrite ( NO 2 - ) ions are naturally occurring inorganic ions that are part of the nitrogen cycle. High doses of these ions in drinking water impose a potential risk to public health. In this work, molecular dynamics simulations are carried out to study the passage of nitrate and nitrite ions from water through graphene nanosheets (GNS) with hydrogen-functionalized narrow pores in presence of an external electric field. The passage of ions through the pores is investigated through calculations of ion flux, and the results are analyzed through calculations of various structural and thermodynamic properties such as the density of ions and water, ion-water radial distribution functions, two-dimensional density distribution functions, and the potentials of mean force of the ions. Current simulations show that the nitrite ions can pass more in numbers than the nitrate ions in a given time through GNS hydrogen-functionalized pore of different geometry. It is found that the nitrite ions can permeate faster than the nitrate ions despite the former having higher hydration energy in the bulk. This can be explained in terms of the competition between the number density of the ions along the pore axis and the free energy barrier calculated from the potential of mean force. Also, an externally applied electric field is found to be important for faster permeation of the nitrite over the nitrate ions. The current study suggests that graphene nanosheets with carefully created pores can be effective in achieving selective passage of ions from aqueous solutions.

A QM/MM simulation study of transamination reaction at the active site of aspartate aminotransferase: Free energy landscape and proton transfer pathways.

Transaminase is a key enzyme for amino acid metabolism, which reversibly catalyzes the transamination reaction with the help of PLP (pyridoxal 5' -phosphate) as its cofactor. Here we have investigated the mechanism and free energy landscape of the transamination reaction involving the aspartate transaminase (AspTase) enzyme and aspartate-PLP (Asp-PLP) complex using QM/MM simulation and metadynamics methods. The reaction is found to follow a stepwise mechanism where the active site residue Lys258 acts as a base to shuttle a proton from α-carbon (CA) to imine carbon (C4A) of the PLP-Asp Schiff base. In the first step, the Lys258 abstracts the CA proton of the substrate leading to the formation of a carbanionic intermediate which is followed by the reprotonation of the Asp-PLP Schiff base at C4A atom by Lys258. It is found that the free energy barrier for the proton abstraction by Lys258 and that for the reprotonation are 17.85 and 3.57 kcal/mol, respectively. The carbanionic intermediate is 7.14 kcal/mol higher in energy than the reactant. Hence, the first step acts as the rate limiting step. The present calculations also show that the Lys258 residue undergoes a conformational change after the first step of transamination reaction and becomes proximal to C4A atom of the Asp-PLP Schiff base to favor the second step. The active site residues Tyr70* and Gly38 anchor the Lys258 in proper position and orientation during the first step of the reaction and stabilize the positive charge over Lys258 generated at the intermediate step.

Vibrational echo spectroscopy of aqueous sodium bromide solutions from first principles simulations.

A theoretical study of the time-dependent vibrational echo spectroscopy of sodium bromide solutions in deuterated water at two different concentrations of 0.5 and 5.0 M and at temperatures of 300 and 350 K is presented using the method of ab initio molecular dynamics simulations. The instantaneous fluctuations in frequencies of local OD stretch modes are calculated using time-series analysis of the simulated trajectories. The third-order polarization and intensities of three pulse photon-echo are calculated from ab initio simulations. The timescales of vibrational spectral diffusion are determined from the frequency time correlation functions (FTCF) and short-time slope of three pulse photon echo (S3PE) calculated within the second-order cumulant and Condon approximations. It is found that under ambient conditions, the rate of vibrational spectral diffusion becomes slower with increase in ionic concentration. Decay of S3PE calculated for different systems give timescales, which are in close agreement with those of FTCF and also with the results of experimental time-dependent vibrational spectroscopic experiments. © 2019 Wiley Periodicals, Inc.

Temperature dependence of the ultrafast vibrational echo spectroscopy of OD modes in liquid water from first principles simulations.

The rate of vibrational spectral diffusion of OD/OH stretch modes of water is known to be interconnected with the hydrogen bond rearrangement dynamics in aqueous media as found in several recent experiments and molecular simulations. In the present study, the temperature dependence of vibrational spectral diffusion of OD stretch modes in liquid water is investigated from first principles by using the method of ab initio molecular dynamics. Kinetic rates obtained from the frequency time correlation function (FTCF), the slope of the 3-pulse photon echo (S3PE) and local structure correlation functions are used in the Arrhenius equation to determine the energy barrier for hydrogen bond rearrangement in liquid water. The slope of the 3-pulse photon echo is determined within the cumulant and Condon approximations. Although the trend found at the low temperature is slightly non-Arrhenius, the barrier for hydrogen bond rearrangement is found to be around 4.2 kcal mol-1 from all the metrics considered here. It is in good agreement with the hydrogen bond energy determined from different experiments and theoretical studies. Based on the findings, a strong correlation between the vibrational spectral diffusion timescale and hydrogen bond dynamics is identified, which gets even more pronounced at low temperatures. Spatio-temporal correlations between frequency fluctuations and the local hydrogen bond network are also explored.

An ab initio molecular dynamics study of benzene in water at supercritical conditions: Structure, dynamics, and polarity of hydration shell water and the solute.

Anisotropic structure and dynamics of the hydration shell of a benzene solute in supercritical water are investigated by means of ab initio molecular dynamics simulations. The polarity and structural distortion of the benzene solute in supercritical water are also investigated in this study. Calculations are done at 673 K for three different densities of the solvent. The simulations are carried out using the Becke-Lee-Yang-Parr (BLYP) and also the Becke-Lee-Yang-Parr functional including dispersion corrections of Grimme (BYLP-D). The structural anisotropy is found to exist even at supercritical conditions as elucidated by the radial distribution functions of different conical regions and also by angular and spatial distribution functions. The benzene-water πH-bond and also the water-water hydrogen bonds are found to exist even at the supercritical temperature of 673 K. However, the numbers of these hydrogen bonds are reduced substantially with a decrease in water density. The water molecules in the axial region of benzene are found to be preferably oriented with one OH vector pointing toward the benzene ring, whereas the water molecules located in the equatorial region are found to orient their dipoles mostly parallel to the ring plane. The orientational distributions, however, are found to be rather broad at the supercritical temperature due to thermal fluctuations. Although the water molecules have faster dynamics at these supercritical conditions, a slight difference is observed in the dynamics of the solvation shell and bulk molecules. The conformational flexibility of the ring is found to be enhanced which causes an increase in polarity of the benzene solute in water under supercritical conditions.

Nature of hydration shells of a polyoxy-anion with a large cationic centre: The case of iodate ion in water.

The structural nature of the solvation shells of an iodate ion, which is known to be a polyoxy-anion with a large cationic centre, is investigated by means of Born-Oppenheimer molecular dynamics (BOMD) simulations using BLYP and the dispersion corrected BLYP-D3 functionals. The iodate ion is found to have two distinct solvation regions around the positively charged iodine (iodine solvation shell or ISS) and the negatively charged oxygens (oxygen solvation shell or OSS). We have looked at the spatial, orientational, and hydrogen bond distributions of water in the two solvation regions. It is found that the water orientational profile in the ISS is typical of a cation hydration shell. The hydrogen bonded structure of water in the OSS is found to be very similar to that of the bulk water structure. Thus, the iodate ion essentially behaves like a positively charged iodine ion in water as if there is no anionic part. This explains why the cationic character of the iodate ion was prominently seen in earlier studies. The arrangement of water molecules in the two solvation shells and in the intervening regions around the iodate ion is further resolved by looking at structural cross-correlations. The electronic properties of the solvation shells are also looked at by calculating the solute-solvent orbital overlap and dipole moments of the solute and solvation shell water. We have also performed BOMD simulations of iodate ion-water clusters at experimentally relevant conditions. The simulation results are found to be in agreement with experimental results. © 2018 Wiley Periodicals, Inc.

Free energy landscapes of prototropic tautomerism in pyridoxal 5'-phosphate schiff bases at the active site of an enzyme in aqueous medium.

We have performed hybrid quantum-classical metadynamics simulations and quantum chemical calculations to investigate the free energy landscapes of intramolecular proton transfer and associated tautomeric equilibrium in pyridoxal 5 '-phosphate (PLP) Schiff Bases, namely the internal and external aldimines, at the active site of serine hydroxymethyltransferase (SHMT) enzyme in aqueous medium. It is important to determine the relative stability of the two tautomers (ketoenamine and enolimine) of the PLP aldimines to study the catalytic activity of the concerned enzyme. Both the internal PLP aldimine (PLP-LYS) and the external PLP aldimine (PLP-SER) of SHMT are found to have a higher stability for the ketoenamine tautomer over the enolimine form. The higher stability of the ketoenamine tautomer can be attributed to the more number of favorable interactions of the ketoenamine form with its surroundings at the active site of the enzyme. The ketoenamine is found to be stabilized by about 2.5 kcal/mol in the PLP-LYS internal aldimine, while this stabilization is about 6.7 kcal/mol for the PLP-SER external aldimine at the active site of the enzyme compared to the corresponding enolimine forms. The interactions faced by the PLP aldimines at the active site pocket determine the relative dominance of the tautomers and could possibly alter the tautomeric shift in different PLP dependent enzymes. © 2018 Wiley Periodicals, Inc.

Dynamics of water in conical solvation shells around a benzene solute under different thermodynamic conditions.

Water molecules in different parts of the anisotropic hydration shell of an aromatic molecule experience different interactions. In the present study, we investigate the anisotropic dynamics of water molecules in different non-overlapping conical shells around a benzene solute at sub- and supercritical conditions by means of molecular dynamics simulations using both non-polarizable and polarizable models. In addition to the dynamical properties, the effects of polarizability on the hydration structure of benzene at varying thermodynamic conditions are also investigated in the current study. The presence of πH-bonding in the solvation shell is found to be an important factor that influences the anisotropic dynamics of the benzene hydration shell. The water molecules located axial to the benzene plane are found to be maximally influenced by the πH-bonding. The extent of πH-bonding is found to be somewhat reduced on inclusion of polarizability. The πH-bonded water molecules are found to reorient through large-amplitude angular jumps where the jump-angle amplitude increases at higher temperatures and lower densities. For both non-polarizable and polarizable models, it is found that the water molecules in the axial conical shells possess faster orientational and hydrogen bond dynamics compared to those in the equatorial plane. Water molecules in the axial conical shells are also found to diffuse at a faster rate than bulk molecules due to the relatively weaker benzene-water πH-bonding interactions in the axial region of the hydration shell. The residence dynamics of water molecules in different conical solvation shells around the solute is also investigated in the current study.

On the issue of closed versus open forms of gamma-aminobutyric acid (GABA) in water: Ab initio molecular dynamics and metadynamics studies.

Gamma-aminobutyric acid (GABA), a primary neurotransmitter, accomplishes its activities by binding to different receptor sites in different conformations. It is known to have two major conformers: the closed and open forms. Earlier studies on preferred conformation of GABA in water revealed differing results with some reporting the open form while others inferring the closed form to be more stable. We found the existence of many open forms and only one closed form of GABA in water through ab initio metadynamics simulation. Some of the open conformers are equally or more stable while others are less stable than the closed form. Free energy barriers reveal that different conformers are interconvertible at room temperature in typical experimental time scales. Ab initio molecular dynamics simulations are performed to further investigate the inter-conversion of various conformers of GABA in water and their dipole moments and also to make connections to experiments on the conformation of GABA in water.

Effects of dispersion interactions on the structure, polarity, and dynamics of liquid-vapor interface of an aqueous NaCl solution: Results of first principles simulations at room temperature.

The effects of dispersion interaction on the structure, polarity, and dynamics of liquid-vapor interface of a concentrated (5.3M) aqueous NaCl solution have been investigated through first-principles simulations. Among the structural properties, we have investigated the inhomogeneous density profiles of molecules, hydrogen bond distributions, and orientational profiles. On the dynamical side, we have calculated diffusion, orientational relaxation, hydrogen bond dynamics, and vibrational spectral diffusion of molecules. The polarity of water molecules across the interface is also calculated. Our simulation results are compared with those when no dispersion corrections are included. It is found that the inclusion of dispersion correction predicts an overall improvement of the structural properties of liquid water. The current study reveals a faster relaxation of hydrogen bonds, diffusion, and rotational motion for both interfacial and bulk molecules compared to the results when no such dispersion corrections are included. The dynamics of vibrational frequency fluctuations are also calculated which capture the relaxation of hydrogen bond fluctuations in the bulk and interfacial regions. Generally, the hydrogen bonds at the interfaces are found to have longer lifetimes due to reduced cooperative effects.

Orientational order and dynamics of interfacial water near a hexagonal boron-nitride sheet: An ab initio molecular dynamics study.

Structural and dynamical properties of interfacial water molecules near a hexagonal boron nitride sheet (h-BN) are investigated by means of Born-Oppenheimer molecular dynamics simulations. Orientational profiles in the interfacial regions reveal two distinct types of water molecules near the BN surface. Depending on the positions of the water molecules, on top of either N or B atoms, one type contains water molecules that are oriented with one OH bond pointing toward the N atoms and the other type contains water molecules that remain parallel to the BN sheet. Distinct hydrogen bonding and stabilization energies of these two types of water molecules are found from our calculations. In order to see the effects of dispersion interactions, simulations are performed with the BLYP (Becke-Lee-Yang-Parr) functional and also BLYP with Grimme's D3 corrections (BLYP-D3). An enhancement of water ordering near the surface is observed with the inclusion of dispersion corrections. Further analysis of the diffusion coefficients, rotational time correlation functions, and hydrogen bond dynamics shows that water molecules near the h-BN sheet move faster compared to bulk water molecules both translationally and rotationally. The water molecules in the first layer are found to show substantial lateral diffusion. The escape dynamics of water from the solvation layer at the BN surface is also looked at in the current study. We have also investigated some of the electronic properties of interfacial water such as the charge density and dipole moment. It is found that the water molecules at the surface of the BN sheet have a lower dipole moment than bulk molecules.

Preferential solvation, ion pairing, and dynamics of concentrated aqueous solutions of divalent metal nitrate salts.

We have investigated the characteristics of preferential solvation of ions, structure of solvation shells, ion pairing, and dynamics of aqueous solutions of divalent alkaline-earth metal nitrate salts at varying concentration by means of molecular dynamics simulations. Hydration shell structures and the extent of preferential solvation of the metal and nitrate ions in the solutions are investigated through calculations of radial distribution functions, tetrahedral ordering, and also spatial distribution functions. The Mg2+ ions are found to form solvent separated ion-pairs while the Ca2+ and Sr2+ ions form contact ion pairs with the nitrate ions. These findings are further corroborated by excess coordination numbers calculated through Kirkwood-Buff G factors for different ion-ion and ion-water pairs. The ion-pairing propensity is found to be in the order of Mg(NO3)2 < Ca(NO3)2 < Sr(NO3)2, and it follows the trend given by experimental activity coefficients. It is found that proper modeling of these solutions requires the inclusion of electronic polarization of the ions which is achieved in the current study through electronic continuum correction force fields. A detailed analysis of the effects of ion-pairs on the structure and dynamics of water around the hydrated ions is done through classification of water into different subspecies based on their locations around the cations or anions only or bridged between them. We have looked at the diffusion coefficients, relaxation of orientational correlation functions, and also the residence times of different subspecies of water to explore the dynamics of water in different structural environments in the solutions. The current results show that the water molecules are incorporated into fairly well-structured hydration shells of the ions, thus decreasing the single-particle diffusivities and increasing the orientational relaxation times of water with an increase in salt concentration. The different structural motifs also lead to the presence of substantial dynamical heterogeneity in these solutions of strongly interacting ions. The current study helps us to understand the molecular details of hydration structure, ion pairing, and dynamics of water in the solvation shells and also of ion diffusion in aqueous solutions of divalent metal nitrate salts.

Anisotropic structure and dynamics of the solvation shell of a benzene solute in liquid water from ab initio molecular dynamics simulations.

The anisotropic structure and dynamics of the hydration shell of a benzene solute in liquid water have been investigated by means of ab initio molecular dynamics simulations using the BLYP (Becke-Lee-Yang-Parr) and dispersion corrected BLYP-D functionals. The main focus has been to look at the influence of π-hydrogen-bonding and hydrophobic interactions on the distance and angle resolved various structural and dynamic properties of solvation shell. The structure of hydration shell water molecules around benzene is found to be highly anisotropic as revealed by the radial distribution functions of different conical regions and joint radial/angular distribution functions. The benzene-water dimer potential energy curves are calculated for a variety of orientations of water along the axial and equatorial directions for both BLYP and BLYP-D functionals. The simulation results of the hydration shell structure of benzene, particularly the axial and equatorial benzene-water RDFs are discussed based on the differences in the benzene-water potential energies for different orientations and functionals. The inter-particle distance/angle correlations show an enhanced water structure in the solvation shell of benzene compared to that between the solvation shell and bulk and also between the bulk molecules. On average, a single πH-bond is found to be formed between water and benzene in the 45° axial conical region of the solvation shell. The πH-bonded water molecules are found to have faster translational dynamics and also found to follow a fast jump mechanism of reorientation to change their hydrogen bonded partners. The presence of π-hydrogen-bonded water makes the overall dynamics of the axial region faster than that of the equatorial region where the water molecules are hydrophobically solvated and hydrogen bonded to other water molecules.

Wetting and dewetting of narrow hydrophobic channels by orthogonal electric fields: Structure, free energy, and dynamics for different water models.

Wetting and dewetting of a (6,6) carbon nanotube in presence of an orthogonal electric field of varying strengths are studied by means of molecular dynamics simulations using seven different models of water. We have looked at filling of the channel, occupancy and structure of water inside it, associated free energy profiles, and also dynamical properties like the time scales of collective dipole flipping and residence dynamics. For the current systems where the entire simulation box is under the electric field, the nanotube is found to undergo electrodrying, i.e., transition from filled to empty states on increase of the electric field. The free energy calculations show that the empty state is the most stable one at higher electric field as it raptures the hydrogen bond environment inside the carbon nanotube by reorienting water molecules to its direction leading to a depletion of water molecules inside the channel. We investigated the collective flipping of water dipoles inside the channel and found that it follows a fast stepwise mechanism. On the dynamical side, the dipole flipping is found to occur at a faster rate with increase of the electric field. Also, the rate of water flow is found to decrease dramatically as the field strength is increased. The residence time of water molecules inside the channel is also found to decrease with increasing electric field. Although the effects of electric field on different water models are found to be qualitatively similar, the quantitative details can be different for different models. In particular, the dynamics of water molecules inside the channel can vary significantly for different water models. However, the general behavior of wetting and dewetting transitions, enhanced dipole flips, and shorter residence times on application of an orthogonal electric field hold true for all water models considered in the current work.

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.