Residence Time Of Water Molecules Research Articles

Insights into dynamic properties of water in lipidic cubic phases by 2D nuclear Overhauser effect (NOE) NMR spectroscopy

Two-dimensional NOE (nuclear Overhauser effect) NMR spectroscopy was employed to investigate the dynamic properties of water within lyotropic bicontinuous lipidic cubic phases (LCPs) formed by monoolein (MO). Experiments observed categorically different effective residence times of water molecules: (i) in proximity to the glycerol moiety of MO, and (ii) adjacent to the hydrophobic chain towards the hydrocarbon tail of MO, as evidenced by the opposite signs of intermolecular NOE cross peaks between protons of water and those of MO in 2D 1H–1H NOESY spectra. Spectroscopic data delineating the different effective residence times of water molecules within both the gyroid (QIIG) and diamond (QIID) phase groups corresponding to hydration levels of 35 and 40 wt%, respectively, are presented. Additionally, an increase in effective residence time of water molecules in proximity to the glycerol moiety of MO in LCPs was observed upon storage at ambient temperature and in the presence of an additive lipid, cholesterol. Atom-specific NOE build-up curves for protons of water and those of MO are also given. The results presented herein provide new insight into the physicochemical properties and behaviour of water in LCPs, and demonstrate an additional avenue for experimental study of water–lipid interactions and hydration dynamics in model membranes and nanomaterials using 2D NOE NMR spectroscopy.

The effect of Si/Al ratio on local and nanoscale water diffusion in H-ZSM-5: A quasielastic neutron scattering and molecular dynamics simulation study

The dynamics of water confined in H-ZSM-5 (protonated form of the Zeolite Socony Mobil – 5) has been studied using quasielastic neutron scattering (QENS) and classical molecular dynamics simulations (MD). QENS measurements probed water confined in ZSM-5 samples with Si/Al ratios of 15, 40 and 140 at 2.8 wt% loadings. In the lower silica samples, fitting of the elastic incoherent structure factor (EISF) showed that water diffusion was confined to a sphere (with radii ranging from 3.4 to 4.3 Å), suggesting the mobile water was located within the MFI (framework type of H-ZSM-5) channel intersections, giving localised diffusion coefficients in the range of ∼0.9–1.8 × 10−9 m2s−1. In the high silica zeolite, the diffusion was observed to be far less confined and more long range in nature, with diffusion coefficients significantly higher than in the lower silica systems (∼1.8–4.8 × 10−9 m2s−1). MD simulations further investigated the effect of the Si/Al ratio on water diffusivity at 2.8 wt% loading (9 molecules/unit cell (UC)) in H-ZSM-5 with Si/Al ratio = 15, 47, 95 and fully siliceous. The Si/Al ratio had a significant effect on the MD calculated nanoscale diffusivity of water, reducing the self-diffusion coefficient by a factor of 2 from a fully siliceous system to that with Si/Al = 15, due to the strong coordination and increased residence time of water molecules at the Brønsted acid sites which range from ∼5 ps to ∼2 ps in the Si/Al = 15 and Si/Al = 95 systems respectively. QENS observables, both the EISF and quasielastic line broadenings, were reproduced from the MD trajectories upon sampling the experimental timescale giving both qualitative and quantitative agreement with the QENS experiments. Fitting of the MD calculated EISF showed that the experimentally observed diffusion confined to a sphere of radii ranging from 3.5 to 6.8 Å was also present in our simulations, with diffusion coefficients calculated to within a factor of 0.5 of experiment.

Folding Dynamics of 3,4,3-LI(1,2-HOPO) in Its Free and Bound State with U4+ Implicated by MD Simulations

The octadentate hydroxypyridonate ligand 3,4,3-LI(1,2-HOPO) (t-HOPO) shows strong binding affinity with actinide cations and is considered as a promising decorporation agent used to eliminate in vivo actinides, while its dynamics in its unbound and bound states in the condensed phase remain unclear. In this work, by means of MD simulations, the folding dynamics of intact t-HOPO in its neutral (t-HOPO0) and in its deprotonated state (t-HOPO4-) were studied. The results indicated that the deprotonation of t-HOPO in the aqueous phase significantly narrowed the accessible conformational space under the simulated conditions, and it was prepared in a conformation that could conveniently clamp the cations. The simulation of UIV-t-HOPO showed that the tetravalent uranium ion was deca-coordinated with eight ligating O atoms from the t-HOPO4- ligand, and two from aqua ligands. The strong electrostatic interaction between the U4+ ion and t-HOPO4- further diminished the flexibility of t-HOPO4- and confined it in a limited conformational space. The strong interaction between the U4+ ion and t-HOPO4- was also implicated in the shortened residence time of water molecules.

Irregular structure of the hydrated Ag+ in aqueous solution and its Dynamics: An insight from perturbation theory hybrid forces molecular dynamics simulation

The structural and dynamical properties of hydrated Ag+ in a water solution were investigated theoretically using hybrid forces molecular dynamics simulation. The quantum mechanical region was treated using the resolution of identity MP2 (RI-MP2) level of a theory enabling the description of the properties of the hydration shell accurately.In contrast to the previously reported linear configuration, the first hydration shell had an irregular shape, with an average coordination number of 5.5. The Ag+–O distance in the first hydration shell was 2.59 Å. The mean residence time of water molecules in the first hydration shell was 0.89 ps, indicating that Ag+ acted as a structure-breaking agent.

Preparation and MRI performance of a composite contrast agent based on palygorskite pores and channels binding effect to prolong the residence time of water molecules on gadolinium ions.

Herein, gadolinium tannate was simply and conveniently coated on the surface of palygorskite by in situ reaction of a coordination polymer formed between tannic acid and Gd3+. The palygorskite–tannate gadolinium–polyvinyl alcohol integrated composite (PAL@Gd@PVA) is successfully prepared after the introduction of polyvinyl alcohol onto the palygorskite–tannate gadolinium. The structure is characterized by Fourier transform infrared spectroscopy, thermogravimetric analysis, X-ray diffraction spectroscopy, X-ray photoelectron spectroscopy, and transmission electron microscopy analysis. The results show that TA-Gd and PVA are successfully loaded on the surface of palygorskite, and the rod crystal structure of palygorskite in the composite remains intact. Palygorskite fibres constitute the framework of the composite and play a key role in supporting and crosslinking the composite. The prepared compounds showed negligible cytotoxicity and low haemolysis rate, showing good biocompatibility. In vitro MRI results showed that the longitudinal and transverse relaxation rates of the composite are 59.56 and 340.81 mm−1 s−1, respectively.

How polar hydroxyl groups affect surface hydrophobicity on model talc surfaces

Based on molecular dynamics simulations, we have studied the wetting behaviors of water on the talc-like surface with different surface polarity by modifying the charge distribution of surface hydroxyl (–OH) groups. With the change of the charge of the hydrogen atom (denoted as δ q ) in –OH group, the contact angle decreases from 91° to 50° and then remains constant. On the surfaces with the larger charge of hydrogen atoms (δ q ≥ 0.2 e), a water droplet is formed above a water monolayer, which is exactly contacted on the surface. Each water molecule in the monolayer forms one hydrogen bond (H bond) with surface –OH groups, without participating in any H bond with the water molecules within the monolayer or with the water molecules above the monolayer. The polarity of the –OH group also has a great influence on the dynamic behaviors of the interface water, such as residence time, hydrogen bond lifetime and self-diffusion coefficient. The diffusion of water molecules in the water monolayer near the highly polar surface is greatly suppressed, and the residence time of water molecules in the water monolayer even exceeds 12 ns.

Structure and stretching dynamics of water molecules around an amphiphilic amide from FPMD simulations: A case study of N,N-dimethylformamide

N,N-Dimethylformamide (DMF) is a unique tertiary amphiphilic amide, where the presence of a hydrophilic aldehyde group favors hydrogen bond acceptance, but two hydrophobic methyl substituents inhibit interaction with water molecules. As a result, the water molecules encounter two different environments in the vicinity of DMF molecule: around the hydrophobic nitrogen site; and near the hydrophilic carbonyl oxygen. We employ first principles molecular dynamics methods to simulate an aqueous solution of DMF using PBE functional with Grimme's D3 dispersion correction at 330 K. Investigations on the liquid structure to understand inter-atomic interactions in amides attract much attention. We calculated various structural and dynamical properties along with vibrational stretching frequency of water molecules to understand heterogeneously affected water molecules by an amphiphilic amide molecule. In solvated DMF, the first peak minimum of the N-OW and OC-OW radial distribution functions (‘w’ subscript denotes atoms of water) are located at 5.72 and 3.16 Å, respectively. These distance cutoffs decide the boundary of the solvation shell. At OC-HW distance 2.45 Å, the deep peak minimum indicates stable OC … HW hydrogen bond. Previous Monte Carlo simulations reported the presence of hydrogen bonds between the oxygen site of DMF and hydrogen of water. The time-series wavelet method was used to compute the time-dependent frequencies of the hydroxyl groups of water. The average frequency of the OH modes inside the CO solvation shell (~3364 cm−1) in DMF is higher than bulk (~3337 cm−1), and the trend matches with an aqueous solution of acetone. In nitrogen hydration shell, the intense band resembles the bulk frequency distribution, and a narrow distinctive peak at the high-frequency side (range ~3650–3750 cm−1) represents the non‑hydrogen bonded or dangling OH groups. Raman spectroscopy in hydrophobic TBA and air/water interface displayed dangling OH stretch peak at ~3660 cm−1 and ~3710 cm−1, respectively. Our calculation of the frequency distribution, frequency-frequency correlation function, and hydrogen bond dynamics show the water molecules at bulk behave as in pure water. Inside the solvation shell of aminic nitrogen, non‑hydrogen bonded OH modes with a dangling lifetime ~0.38 ps dominates over the water-water hydrogen bonds. The time-dependent decay of the frequency correlation inside CO solvation shell has three decay components, a rapid decay, then, an intermediate component (~1.52 ps) corresponding to the lifetime of the carbonyl-water hydrogen bond, and the longer timescale ~11.97 ps representing the residence time of water molecules in the vicinity of carbonyl oxygen. We find that the carbonyl-water hydrogen bond (OC … HW) is stronger than the water-water hydrogen bond. The methyl substituents on the nitrogen of DMF impose weak hydrophobic interaction, and the hydrophilic carbonyl oxygen forms a strong hydrogen bond with the neighboring water resulting in localized dynamics.

Molecular insights into the microstructure of ethanol/water binary mixtures confined within typical 2D nanoslits: The role of the adsorbed layers induced by different solid surfaces

With the emergence of membrane separation and heterogeneous catalysis applications that are associated with confined ethanol/water binary mixture in the pores of two-dimensional (2D) nanomaterials, understanding their confined microstructures is the first step for further relevant applications. In this work, molecular dynamics was performed to investigate the microstructure of ethanol/water binary mixture of 5% mole fraction confined within the four typical 2-nm width 2D-nanoslits (i.e. hBN, GO-0.2, GO-0.4 and Ti3C2(OH)2). Results demonstrated that different chemical properties of solid surfaces can induce distinctive microstructures of mixed fluid within the interfacial contact (adsorbed) layer and thus can result in different mobility of water molecules within the subcontact layer. The residence times of water molecules in the subcontact layer were found in the sequence of Ti3C2(OH)2 > hBN > GO-0.4 > GO-0.2, whereas their sequence of diffusion coefficient within the x-z plane was Ti3C2(OH)2 > hBN > GO-0.2 > GO-0.4. Detailed hydrogen bond (HB) microstructure analysis showed that a high average number of HBs (between fluid molecules of the interfacial contact layer and water molecules of the subcontact layer) induced by solid surfaces could facilitate water molecules to reside in the subcontact layer. Moreover, the small average number of HBs between the water molecules themselves in the subcontact layer could lead to high in-plane diffusion coefficients.

Origin of Slow Solvation Dynamics in DNA: DAPI in Minor Groove of Dickerson-Drew DNA.

The measurement and understanding of collective solvation dynamics in DNA have vital biological implications, as protein and ligand binding to DNA can be directly controlled by complex electrostatic interactions of anionic DNA and surrounding dipolar water, and ions. Time-resolved fluorescence Stokes shift (TRFSS) experiments revealed anomalously slow solvation dynamics in DNA much beyond 100 ps that follow either power-law or slow multiexponential decay over several nanoseconds. The origin of such dispersed dynamics remains difficult to understand. Here we compare results of TRFSS experiments to molecular dynamics (MD) simulations of well-known 4',6-diamidino-2-phenylindole (DAPI)/Dickerson-Drew DNA complex over five decades of time from 100 fs to 10 ns to understand the origin of such dispersed dynamics. We show that the solvation time-correlation function (TCF) calculated from 200 ns simulation trajectory (total 800 ns) captures most features of slow dynamics as measured in TRFSS experiments. Decomposition of TCF into individual components unravels that slow dynamics originating from dynamically coupled DNA-water motion, although contribution from coupled water-Na+ motion is non-negligible. The analysis of residence time of water molecules around the probe (DAPI) reveals broad distribution from ∼6 ps to ∼3.5 ns: Several (49 nos.) water molecules show residences time greater than 500 ps, of which at least 14 water molecules show residence times of more than 1 ns in the first solvation shell of DAPI. Most of these slow water molecules are found to occupy two hydration sites in the minor groove near DAPI binding site. The residence time of Na+, however, is found to vary within ∼17-120 ps. Remarkably, we find that freezing the DNA fluctuations in simulation eliminates slower dynamics beyond ∼100 ps, where water and Na+ dynamics become faster, although strong anticorrelation exists between them. These results indicate that primary origin of slow dynamics lies within the slow fluctuations of DNA parts that couple with nearby slow water and ions to control the dispersed collective solvation dynamics in DNA minor groove.

Microwave heating and non-thermal effects of sodium chloride aqueous solution

ABSTRACTThe dielectric thermal and non-thermal properties of sodium chloride aqueous solution under the microwave region have been estimated. The dielectric properties, hydrogen bonding, transport properties, energy distribution and local structure have been evaluated by classical molecular dynamics method. In the process of microwave energy distribution, the direct coupling of rotational motion, vibration and redirection is revealed. Microwave energy is converted into kinetic energy and interaction energy between two molecules. A mechanism for exploring the effects of microwaves on the non-thermal effects of brine systems over a longer simulation time and a wider microwave range is proposed. The increase in field intensity is usually accompanied by local damage to the water structure near the hydrated ions. More specifically, above the field threshold, the residence time of water molecules near the ions significantly decreases.HighlightsMicrowave energy is transferred to the kinetic energy and the energy between the molecules.The increase in field intensity is usually accompanied by local damage to the water structure near the hydrated ions.The larger electric field strength amplifies the effect of frequency.The residence time of water molecules near the ions significantly decreases.

Confined Dynamics of Water in Transmembrane Pore of TRPV1 Ion Channel.

Solvation effects play a key role in chemical and biological processes. The microscopic properties of water near molecular surfaces are radically different from those in the bulk. Furthermore, the behavior of water in confined volumes of a nanometer scale, including transmembrane pores of ion channels, is especially nontrivial. Knowledge at the molecular level of structural and dynamic parameters of water in such systems is necessary to understand the mechanisms of ion channels functioning. In this work, the results of molecular dynamics (MD) simulations of water in the pore and selectivity filter domains of TRPV1 (Transient Receptor Potential Vanilloid type 1) membrane channel are considered. These domains represent nanoscale volumes with strongly amphiphilic walls, where physical behavior of water radically differs from that of free hydration (e.g., at protein interfaces) or in the bulk. Inside the pore and filter domains, water reveals a very heterogeneous spatial distribution and unusual dynamics: It forms compact areas localized near polar groups of particular residues. Residence time of water molecules in such areas is at least 1.5 to 3 times larger than that observed for similar groups at the protein surface. Presumably, these water “blobs” play an important role in the functional activity of TRPV1. In particular, they take part in hydration of the hydrophobic TRPV1 pore by localizing up to six waters near the so-called “lower gate” of the channel and reducing by this way the free energy barrier for ion and water transport. Although the channel is formed by four identical protein subunits, which are symmetrically packed in the initial experimental 3D structure, in the course of MD simulations, hydration of the same amino acid residues of individual subunits may differ significantly. This greatly affects the microscopic picture of the distribution of water in the channel and, potentially, the mechanism of its functioning. Therefore, reconstruction of the full picture of TRPV1 channel solvation requires thorough atomistic simulations and analysis. It is important that the naturally occurring porous volumes, like ion-conducting protein domains, reveal much more sophisticated and fine-tuned regulation of solvation than, e.g., artificially designed carbon nanotubes.

Characterization of hydration water in supercooled water-trehalose solutions: The role of the hydrogen bonds network.

The structural and dynamical properties of hydration water in aqueous solutions of trehalose are studied with molecular dynamics simulation. We simulate the systems in the supercooled region to investigate how the interaction with the trehalose molecules modifies the hydrogen bond network, the structural relaxation, and the diffusion properties of hydration water. The analysis is performed by considering the radial distribution functions, the residence time of water molecules in the hydration shell, the two body excess entropy, and the hydrogen bond water-water and water-trehalose correlations of the hydration water. The study of the two body excess entropy shows the presence of a fragile to strong crossover in supercooled hydration water also found in the relaxation time of the water-water hydrogen bond correlation function, and this is in agreement with predictions of the mode coupling theory and of previous studies of the oxygen-oxygen density correlators [A. Iorio et al., J. Mol. Liq. 282, 617 (2019); Sci. China: Phys., Mech. Astron. 62, 107011 (2019)]. The water-trehalose hydrogen bond correlation function instead evidences a strong to strong crossover in the relaxation time, and this crossover is related to a trehalose dynamical transition. This signals the role that the strong interplay between the soluted molecules and the surrounding solvent has in determining the dynamical transition common to both components of the system that happens upon cooling and that is similar to the well known protein dynamical transition. We connect our results with the cryoprotecting role of trehalose molecules.

Propane-Water Mixtures Confined within Cylindrical Silica Nanopores: Structural and Dynamical Properties Probed by Molecular Dynamics.

Despite the multiple length and time scales over which fluid-mineral interactions occur, interfacial phenomena control the exchange of matter and impact the nature of multiphase flow, as well as the reactivity of C–O–H fluids in geologic systems. In general, the properties of confined fluids, and their influence on porous geologic phenomena are much less well understood compared to those of bulk fluids. We used equilibrium molecular dynamics simulations to study fluid systems composed of propane and water, at different compositions, confined within cylindrical pores of diameter ∼16 Å carved out of amorphous silica. The simulations are conducted within a single cylindrical pore. In the simulated system all the dangling silicon and oxygen atoms were saturated with hydroxyl groups and hydrogen atoms, respectively, yielding a total surface density of 3.8 −OH/nm2. Simulations were performed at 300 K, at different bulk propane pressures, and varying the composition of the system. The structure of the confined fluids was quantified in terms of the molecular distribution of the various molecules within the pore as well as their orientation. This allowed us to quantify the hydrogen bond network and to observe the segregation of propane near the pore center. Transport properties were quantified in terms of the mean square displacement in the direction parallel to the pore axis, which allows us to extract self-diffusion coefficients. The diffusivity of propane in the cylindrical pore was found to depend on pressure, as well as on the amount of water present. It was found that the propane self-diffusion coefficient decreases with increasing water loading because of the formation of water bridges across the silica pores, at sufficiently high water content, which hinder propane transport. The rotational diffusion, the lifespan of hydrogen bonds, and the residence time of water molecules at contact with the silica substrate were quantified from the simulated trajectories using the appropriate autocorrelation functions. The simulations contribute to a better understanding of the molecular phenomena relevant to the behavior of fluids in the subsurface.

Ultrafast Vibrational Spectroscopy of Aqueous Solution of Methylamine from First Principles MD Simulations

AbstractWe performed Car‐Parrinello molecular dynamics (CPMD) simulations of deuterated aqueous solution of methylamine (MA) to investigate the structure, dynamics and time dependent vibrational spectra of water molecules in the first solvation shell. Our results show that the hydrogen bond of DOD…ND2 is the dominant interaction between ND2 and D2O as compared to the D2O…D2N. The hydrogen bond involving DOD…ND2 has longer lifetime (2.6 ps) than both D2O…D2N (1.1 ps) and water‐water hydrogen bonds. The residence time of water molecule inside the first solvation shell of ND2 is 5.72 ps. The vibrational spectral diffusion of water molecules in the first hydration shell of the amine nitrogen of methylamine proceeds with three time scales. A short‐time relaxation originates from dynamics of amine‐water hydrogen bonds without breaking (90 fs), and a slower relaxation (∼1.8 ps) is due to the breaking of amine‐water hydrogen bonds. Another longer time constant (∼7 ps) is due to the escape dynamics of water molecules from the first hydration shell of the amine group.

Functionalized single walled carbon nanotubes as template for water storage device

Single walled carbon nanotubes, endohedrally functionalized with a protonated/unprotonated carboxylic acid group, are examined as potential templates for water storage using classical molecular dynamics simulation studies. Following a spontaneous entry of water molecules into the core of model functionalized carbon nanotubes (FCNTs), a large fraction of water molecules are found to be trapped inside FCNTs of lengths 50 and 100Å. Only water molecules near the two open ends of the nanotube are exchanged with the bulk solvent. The residence times of water molecules inside FCNTs are investigated by varying the length of the tube, the length of suspended functional group and the protonation state of the carboxylic acid group. Favorable energetic interactions between the functional group and water, assisted by a substantial gain in rotational entropy, are found to compensate for the entropy loss resulting from restricted translational diffusion of trapped water molecules.

Water exchange rates and mechanisms in tetrahedral [Be(H2O)4]2+ and [Li(H2O)4]+ complexes using DFT methods and cluster‐continuum models

AbstractThe water exchange reactions in aquated Li+ and Be2+ ions were investigated with density functional theory calculations performed using the [Li(H2O)4]+·14H2O and [Be(H2O)4]2+·8H2O systems and a cluster‐continuum approach. A range of commonly used functionals predict water exchange rates several orders of magnitude lower than the experimental ones. This effect is attributed to the overstabilization of coordination number four by these functionals with respect to the five‐coordinated transition states responsible for the associative (A) or associative interchange (Ia) water exchange mechanisms. However, the M06 and M062X functionals provide results in good agreement with the experimental data: M062X/TZVP calculations yield a concerted Ia mechanism for the water exchange in [Be(H2O)4]2+·8H2O that gives an average residence time of water molecules in the first coordination sphere of 260 μs. For [Li(H2O)4]+·14H2O the water exchange reaction is predicted to follow an A mechanism with a residence time of inner‐sphere water molecules of 25 ps.

Lutetium(iii) aqua ion: On the dynamical structure of the heaviest lanthanoid hydration complex.

The structure and dynamics of the lutetium(iii) ion in aqueous solution have been investigated by means of a polarizable force field molecular dynamics (MD). An 8-fold square antiprism (SAP) geometry has been found to be the dominant configuration of the lutetium(iii) aqua ion. Nevertheless, a low percentage of 9-fold complexes arranged in a tricapped trigonal prism (TTP) geometry has been also detected. Dynamic properties have been explored by carrying out six independent MD simulations for each of four different temperatures: 277 K, 298 K, 423 K, 632 K. The mean residence time of water molecules in the first hydration shell at room temperature has been found to increase as compared to the central elements of the lanthanoid series in agreement with previous experimental findings. Water exchange kinetic rate constants at each temperature and activation parameters of the process have been determined from the MD simulations. The obtained structural and dynamical results suggest that the water exchange process for the lutetium(iii) aqua ion proceeds with an associative mechanism, in which the SAP hydration complex undergoes temporary structural changes passing through a 9-fold TTP intermediate. Such results are consistent with the water exchange mechanism proposed for heavy lanthanoid atoms.

Water Dynamics and Ion Interaction at Channel Entrance of Aquaporin 1

The aquaporins (AQPs) are transmembrane water channels which exclusively transport water molecules across the plasma membranes corresponding to the osmotic gradients. At the inner part of the pore, single-file water permeation obeys a non-Poisson process attributed to 1/f fluctuations of amino acids [1]. Recently, using finite-element calculations it is suggested that the characteristic hourglass shape of AQPs may optimize the water transportation though the AQPs [2]. The cone-shaped vestibules with suitable opening angle can make an increase of water permeability. However, molecular details of the interaction of water and ion molecules with the amino acids at the cone-shaped vestibules remain unclear. Here we use all-atom molecular dynamics simulations for a system of AQP1/lipid membrane to investigate dynamics of water and ion molecules at the con-shaped vestibules of the AQP1. Analyzing the residence time of water and ion molecules at the surface of the AQP1, we found that residence time of water molecules at the con-shaped vestibules is long, which cases the water retardation at the entrance and increase the reorientation time of water molecules. Moreover, we analyze the interaction of ions at the conical entrance.[1] E. Yamamoto et al., Phys. Rev. E 89, 022718 (2014).[2] S. Gravelle et al., Proc. Natl. Acad. Sci. USA 110, 16367 (2013).

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.

Local Structure and Dynamics of Hydration Water in Intrinsically Disordered Proteins.

Hydration water around protein surface plays a key role in structure, folding and dynamics of proteins. Intrinsically disordered proteins lack secondary and/or tertiary structure in their native state. Thus, characterizing the local structure and dynamics of hydration water around disordered proteins is challenging for both experimentalists and theoreticians. The local structure, orientation and dynamics of hydration water in the vicinity of intrinsically disordered proteins is investigated through molecular dynamics simulations. The analysis of the hydration capacity reveals that the disordered proteins have much larger binding capacity for hydration water than globular proteins. The surface and radial distribution of water molecules around the disordered proteins depict a similar trend. The local structure of the hydration water evaluated in terms of the tetrahedral order parameter, shows a higher order among the water molecules surrounding disordered proteins/regions. The residence time of water molecules clearly exhibits slow dynamics of hydration water around the surface of disordered proteins/regions as compared to globular proteins. The orientation of water molecules is found to be distinctly different for ordered and disordered proteins/regions. This analysis provides a better insight into the structure and dynamics of hydration water around disordered proteins.