Molecular dynamics simulations are performed to study the temperature-dependent dynamics and structures of the hydration shells of elastin-like and collagen-like peptides. For both model peptides, it is consistently observed that, upon cooling, the mechanisms for water dynamics continuously change from small-step diffusive motion to large-step jump motion, the temperature dependence of water dynamics shows a weak crossover from fragile behavior to strong behavior, and the order of the hydrogen-bond network increases. The temperature of the weak crossover from fragile to strong behavior is found to coincide with the temperature at which maximum possible order of the hydrogen-bond network is reached so that the structure becomes temperature independent. In the strong regime, the temperature dependence of water translation and rotational dynamics is characterized by an activation energy of ca. E_a=0.43 eV, consistent with results from previous dielectric spectroscopy and nuclear magnetic resonance studies on protein hydration waters. At these temperatures, a distorted pi-flip motion about the twofold molecular symmetry axes, i.e., a water-specific beta process is an important aspect of water dynamics, at least at the water-peptide interfaces. In addition, it is shown that the hydration waters exhibit pronounced dynamical heterogeneities, which can be traced back to a strong slowdown of water motion in the immediate vicinity of peptide molecules due to formation of water-peptide hydrogen bonds.
At low temperatures proteins exist in a glassy state, a state which has no conformational flexibility and shows no biological functions. In a hydrated protein, at and above 220 K, this flexibility is restored and the protein is able to sample more conformational sub-states, thus becomes biologically functional. This 'dynamical' transition of protein is believed to be triggered by its strong coupling with the hydration water, which also shows a similar dynamic transition. Here we demonstrate experimentally that this sudden switch in dynamic behavior of the hydration water on lysozyme occurs pre…
We study the dynamics of hydration water/protein association in folded proteins, using lysozyme and myoglobin as examples. Extensive molecular dynamics simulations are performed to identify underlying mechanisms of the dynamical transition that corresponds to the onset of amplified atomic fluctuations in proteins. The number of water molecules within a cutoff distance of each residue scales linearly with protein depth index and is not affected by the local dynamics of the backbone. Keeping track of the water molecules within the cutoff sphere, we observe an effective residence time, scaling in…
2H NMR is used to study the mechanisms for the reorientation of protein hydration water. In the past, crossovers in temperature-dependent correlation times were reported at T_x1=225K (X1) and T_x2=200K (X2). We show that neither X1 nor X2 are related to a fragile-to-strong transition. Our results rule out an existence of X1. Also, they indicate that water performs thermally activated and distorted tetrahedral jumps at T<T_x2, implying that X2 originates in an onset of this motion, which may be related to a universal defect diffusion in materials with defined hydrogen-bond networks.
Water hydrating phospholipid membranes determine their stability and function, as well as their interaction with other molecules. In this article we study, using all-atom molecular dynamics simulations, the rotational and translational dynamical properties of water molecules confined in stacked phospholipid membranes at different levels of hydration, from poorly hydrated to a completely hydrated membrane. We find that both the translational and the reorientation dynamics of water are dramatically slowed down as the hydration is reduced. Analyzing in details the structure and dynamics of the hy…
Effects of presence of ions, at moderate to high concentrations, on dynamical properties of water molecules are investigated through classical molecular dynamics simulations using two well known non-polarizable water models. Simulations reveal that the presence of magnesium chloride (MgCl$_2$) induces perturbations in the hydrogen bond network of water leading to the formation of bulk-like domains with \textquoteleft defect sites\textquoteright~on boundaries of such domains: water molecules at such defect sites have less number of hydrogen bonds than those in bulk water. Reorientational autoco…
Molecular dynamics results on water confined in a silica pore in the low hydration regime are presented. Strong layering effects are found due to the hydrophilic character of the substrate. The local properties of water are studied as function of both temperature and hydration level. The interaction of the thin films of water with the silica atoms induces a strong distortion of the hydrogen bond network. The residence time of the water molecules is dependent on the distance from the surface. Its behavior shows a transition from a brownian to a non-brownian regime approaching the substrate in a…
In this manuscript, we present a general computational method for characterizing the molecular structure of liquid water interfaces as sampled from atomistic simulations. With this method, the interfacial structure is quantified based on the statistical analysis of the orientational configurations of interfacial water molecules. The method can be applied to generate position dependent maps of the hydration properties of heterogeneous surfaces. We present an application to the characterization of surface hydrophobicity, which we use to analyze simulations of a hydrated protein. We demonstrate t…
The formation of a spanning hydrogen-bonded network of hydration water is found to occur via a 2D percolation transition in various systems: smooth hydrophilic surfaces, the surface of a single protein molecule, protein powder and diluted peptide solution. The average number of water-water hydrogen bonds nH at the percolation threshold varies from 2.0 to 2.3, depending on temperature, system size and surface properties. Calculation of nH allows an easy estimation of the percolation threshold of hydration water in various systems, including biomolecules.
The ability of water to dissolve biomolecules is crucial for our life. It has been shown that protein has a profound effect on the behavior of water in its hydration shell, which in turn affects the structure and function of the protein. However, there is still no consensus on whether protein promotes or destroys the structural order of water in its hydration shell until today, because of the lack of proper structural descriptor incorporating hydrogen-bond (H-bond) information for water at the protein/water interface. Here we performed all-atom molecular dynamics simulations of lysozyme protei…
Water shapes and defines the properties of biological systems. Therefore, understanding the nature of the mutual interaction between water and biological systems is of primary importance for a proper assessment of biological activity and the development of new drugs and vaccines. A handy way to characterize the interactions between biological systems and water is to analyze their impact on water density and dynamics in the proximity of the interfaces. It is well established that water bulk density and dynamical properties are recovered at distances in the order of $\sim1$~nm from the surface o…
We investigate the 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 non-monotonic solute-size dependence, exhibiting extrema close to the well-known structural crossover length scale for hydrophobic hydration. Additionally, we find an apparently anomalous diffusion for water moving parallel to the surface of small solutes, which, however, can be explained by topology effects. The intimate…
The effects of static electric field on the dynamics of lysozyme and its hydration water have been investigated by means of incoherent quasi-elastic neutron scattering (QENS). Measurements were performed on lysozyme samples, hydrated respectively with heavy water (D2O) to capture the protein dynamics, and with light water (H2O), to probe the dynamics of the hydration shell, in the temperature range from 210 $<$ T $<$ 260 K. The hydration fraction in both cases was about $\sim$ 0.38 gram of water per gram of dry protein. The field strengths investigated were respectively 0 kV/mm and 2 kV/mm (2 …
In order to inquire the microscopic origin of observed multiple time scales in solvation dynamics we carry out several computer experiments. We perform atomistic molecular dynamics simulations on three protein-water systems namely, Lysozyme, Myoglobin and sweet protein Monellin. In these experiments we mutate the charges of the neighbouring amino acid side chains of certain natural probes (Tryptophan) and also freeze the side chain motions. In order to distinguish between different contributions, we decompose the total solvation energy response in terms of various components present in the sys…
Hydration or interfacial water present in biomolecules and inorganic solids have been shown to exhibit a dynamical transition upon supercooling. However, an understanding of the extent of the underlying surface hydrophilicity as well as the local distribution of hydrophilic/hydrophobic patches on the dynamical transition is unexplored. Here, we use molecular dynamics simulations with a TIP4P/2005 water model to study translational and rotational relaxation dynamics of interfacial water on graphene surfaces. The purpose of this study is to investigate the influence of both surface chemistry as …
Water activity and its relationship with interactions stabilising lamellar stacks of mixed lipid bilayers in their fluid state are investigated by means of osmotic pressure measurements coupled with small-angle x-ray scattering. The (electrically-neutral) bilayers are composed of a mixture in various proportions of lecithin, a zwitterionic phospholipid, and Simulsol, a non-ionic cosurfactant with an ethoxylated polar head. For highly dehydrated samples the osmotic pressure profile always exhibits the "classical" exponential decay as hydration increases but, depending on Simulsol to lecithin ra…
We present the frequency- and temperature-dependent dielectric properties of lysozyme solutions in a broad concentration regime, measured at subzero temperatures and compare the results with measurements above the freezing point of water and on hydrated lysozyme powder. Our experiments allow examining the dynamics of unfreezable hydration water in a broad temperature range including the so-called No Man's Land (160 - 235 K). The obtained results prove the bimodality of the hydration shell dynamics and are discussed in the context of the highly-debated fragile-to-strong transition of water.
Thin layers of water on biomolecular and other nanostructured surfaces can be supercooled to temperatures not accessible with bulk water. Chen et al. [PNAS 103, 9012 (2006)] suggested that anomalies near 220 K observed by quasi-elastic neutron scattering can be explained by a hidden critical point of bulk water. Based on more sensitive measurements of water on perdeuterated phycocyanin, using the new neutron backscattering spectrometer SPHERES, and an improved data analysis, we present results that show no sign of such a fragile-to-strong transition. The inflection of the elastic intensity at …
Since the pioneering works of Pethig, Grant and Wuthrich on protein hydration layer, many studies have been devoted to find out if there are any general and universal characteristic features that can distinguish water molecules inside the protein hydration layer from bulk. Given that the surface itself varies from protein to protein, and that each surface facing the water is heterogeneous, search for universal features has been elusive. Here, we perform atomistic molecular dynamics simulation in order to propose and demonstrate that such defining characteristics can emerge if we look not at av…
The low-frequency collective vibrational modes in proteins as well as the protein-water interface have been suggested as dominant factors controlling the efficiency of biochemical reactions and biological energy transport. It is thus crucial to uncover the mystery of hydration structure and dynamics as well as their coupling to collective motions of proteins in aqueous solutions. Here we report dielectric properties of aqueous bovine serum albumin protein solutions as a model system using an extremely sensitive dielectric spectrometer with frequencies spanning from megahertz to terahertz. The …
The density and orientational relaxation of bulk water can be separately studied by depolarized light scattering (DLS) and dielectric spectroscopy (DS), respectively. Here we ask the question of what are the leading collective modes responsible for polarization anisotropy relaxation (DLS) and dipole moment relaxation (DS) of solutions involving mostly hydrophobic solute-water interfaces. We study, by atomistic molecular dynamics simulations, the dynamics and structure of hydration water interfacing N-Acetyl-leucine-methylamide (NALMA) dipeptide. The DLS response of the solution is consistent w…
Studies of liquid water in its supercooled region have led to many insights into the structure and behavior of water. While bulk water freezes at its homogeneous nucleation temperature of approximately 235 K, for protein hydration water, the binding of water molecules to the protein avoids crystallization. Here we study the dynamics of the hydrogen bond (HB) network of a percolating layer of water molecules, comparing measurements of a hydrated globular protein with the results of a coarse-grained model that has been shown to successfully reproduce the properties of hydration water. With diele…
A water structure indicator suitable for generic contexts: two-liquid behavior at hydration and nanoconfinement conditions and a molecular approach to hydrophobicity and wetting
The mobility of water molecules confined in a silica pore is studied by computer simulation in the low hydration regime, where most of the molecules reside close to the hydrophilic substrate. A layer analysis of the single particle dynamics of these molecules shows an anomalous diffusion with a sublinear behaviour at long time. This behaviour is strictly connected to the long time decay of the residence time distribution analogously to water at contact with proteins.
The surface or contact potential at the water liquid-vapor interface is discussed in relation to determinations of absolute ion hydration free energies and distributions of ions near the interface. It is shown that, rather than the surface potential itself, the net electrostatic potential at the center of an uncharged solute can aid both in relating differences between tabulations of hydration free energies and in explaining differing classical and quantum surface potential estimates. Quantum mechanical results are consistent with conclusions from classical simulations that there is a net driv…
We present a probabilistic approach to water-water hydrogen bonding that allows one to obtain an analytic expression for the number of bonds per water molecule as a function of both its distance to a hydrophobic particle and hydrophobe radius. This approach can be used in the density functional theory (DFT) and computer simulations to examine particle size effects on the hydration of particles and on their solvent-mediated interaction. For example, it allows one to explicitly identify a water hydrogen bond contribution to the external potential whereto a water molecule is subjected near a hydr…
An understanding of density fluctuations in bulk water has made significant contributions to our understanding of the hydration and interactions of idealized, purely repulsive hydrophobic solutes. To similarly inform the hydration of realistic hydrophobic solutes that have dispersive interactions with water, here we characterize water density fluctuations in the presence of attractive fields that correspond to solute-water attractions. We find that when the attractive field acts only in the solute hydration shell, but not in the solute core, it does not significantly alter water density fluctu…
We examine five different popular rigid water models (SPC, SPCE, TIP3P, TIP4P and TIP5P) using MD simulations in order to investigate the hydrophobic hydration and interaction of apolar Lennard-Jones solutes as a function of temperature in the range between $275 {K}$ and $375 {K}$. For all investigated models and state points we calculate the excess chemical potential for the noble gases and Methane.All water models exhibit too small hydration entropies, but show a clear hierarchy. TIP3P shows poorest agreement with experiment whereas TIP5P is closest to the experimental data at lower temperat…
We determine the phase diagram of liquid supercooled water by extensive computer simulations using the TIP5P-E model [J. Chem. Phys. {\bf 120}, 6085 (2004)]. We find that the transformation of water into a low density liquid in the supercooled range strongly enhances the solubility of hydrophobic particles. The transformation of water into a tetrahedrally structured liquid is accompanied by a minimum in the hydration entropy and enthalpy. The corresponding change in sign of the solvation heat capacity indicates a loss of one characteristic signature of hydrophobic hydration. The observed behav…
2H NMR spin-lattice relaxation and line-shape analyses are performed to study the temperature-dependent dynamics of water in the hydration shells of myoglobin, elastin, and collagen.
For a wide range of modern soft functional materials the selective transport of sub-nanometer-sized molecules (`penetrants') through a stimuli-responsive polymeric membrane is key to the desired function. In this study, we investigate the diffusion properties of penetrants ranging from non-polar to polar molecules and ions in a matrix of collapsed Poly(N-isopropylacrylamide) (PNIPAM) polymers in water by means of extensive molecular dynamics simulations. We find that the water distributes heterogeneously in fractal-like cluster structures embedded in the nanometer-sized voids of the polymer ma…
Water and glycerol are well-known to facilitate the structural relaxation of amorphous protein matrices. However, several studies evidenced that they may also limit fast ($\sim$ pico-nanosecond, ps-ns) and small-amplitude ($\sim$ Å) motions of proteins, which govern their stability in freeze-dried sugar mixtures. To determine how they interact with proteins and sugars in glassy matrices and, thereby, modulate their fast dynamics, we performed molecular dynamics (MD) simulations of lysozyme/trehalose/glycerol (LTG) and trehalose/glycerol (TG) mixtures at low glycerol and water concentrations. U…
Using heterodyne-detected optical Kerr effect (HD-OKE) measurements, we investigate the vibrational dynamics and the structural relaxation of water nanoconfined in Vycor porous silica samples (pore size $\simeq~4~nm$ ) at different levels of hydration and temperatures. At low level of hydration, corresponding to two complete superficial water layers, no freezing occurs and water remains mobile at all the investigated temperatures with dynamic features similar, but not equal, to the bulk water. The fully hydrated sample shows formation of ice at about 248 K, this process does not involve all th…
We present a 2D lattice model of water to study the effects of ion hydration on the properties of water. We map the water molecules as lattice particles consisting of a single Oxygen at the center of a site and two Hydrogen atoms on each side. The internal state of the system, such as the dipole moment at a site, is defined with respect to the location of the Hydrogen atoms at the site depending on their role in Hydrogen bonds (H-bonds) being a donor or an acceptor. We study the influence of the charge and the radius of the ion on the insertion energy and on the H-bonds in the first and second…
In a previous work, we investigated a two-dimensional lattice-fluid model, displaying some waterlike thermodynamic anomalies. The model, defined on a triangular lattice, is now extended to aqueous solutions with apolar species. Water molecules are of the "Mercedes Benz" type, i.e., they possess a D3 (equilateral triangle) symmetry, with three equivalent bonding arms. Bond formation depends both on orientation and local density. The insertion of inert molecules displays typical signatures of hydrophobic hydration: large positive transfer free energy, large negative transfer entropy (at low temp…
Hydroxide ion transport and structure in aqueous media is fundamental to many chemical and biological processes. Research on hydroxide behavior has primarily focused on a single fully solvated hydroxide, either as an isolated cluster or in the bulk. This work presents the first computational study to consider a medium of low hydration levels where the hydroxide ion is microsolvated. Under such conditions, hydroxide ions are shown to be predominantly present as unique water-bridged double-hydroxide charged clusters, distinct from previously reported structures under hydrated conditions. Althoug…
The goal of this work is to propose a simple continuous model that captures the dielectric properties of water at the nanometric scale. We write an electrostatic energy as a functional of the polarisation field containing a term in $P^4$ and non-local Gaussian terms. Such an hamiltonian can reproduce two key properties of water: the saturation of the polarisation response of water in the presence of a strong electrostatic field and the nanometric dipolar correlations of the solvent molecules modifying the long range van der waals interaction. This model explores thus two fundamental aspects th…
Gigahertz-to-terahertz spectroscopy of macromolecules in aqueous environments provides an important approach for identifying their global and transient molecular structures, as well as directly assessing hydrogen-bonding. We report dielectric properties of zwitterionic dodecylphosphocholine (DPC) micelles in aqueous solutions over a wide frequency range, from 50 MHz to 1.12 THz. The dielectric relaxation spectra reveal different polarization mechanisms at the molecular level, reflecting the complexity of DPC micelle-water interactions. We have made a deconvolution of the spectra into different…
Eumelanin is a widespread biomacromolecule pigment in the biosphere and is intensively tested in numerous bioelectronics and energetic applications. Many of these applications depend on eumelanin's ability to conduct proton current at various levels of hydration. The origin of this behaviour is connected with a comproportionation reaction between oxidized and reduced monomer moieties and water. However, neither this reaction nor the formation of the aqueous proton species have ever been directly observed. Presented here is a hydration dependent FTIR spectroscopic study on eumelanin, which allo…
We have studied the ionic conductivity and the dipolar reorientational dynamics of aqueous solutions of a prototypical deep eutectic solvent (DES), ethaline, by using dielectric spectroscopy on a broad range of frequency (MHz-Hz) and for temperatures ranging from 128 to 283 K. The fraction of water in the DES was varied systematically to cover different regimes, starting from pure DES and its water-in-DES mixtures to the diluted electrolyte solutions. Depending on these parameters, different physical states were examined, including low viscosity liquid, supercooled viscous liquid, amorphous so…
We investigated the vibrational dynamics and the structural relaxation of water nanoconfined in porous silica samples with pore size of 4 nm at different levels of hydration and temperature. We used as spectroscopic technique the time-resolved optical Kerr effect, which enables to investigate the ultrafast water dynamics in a wide time (0.1-10 picosecond) or frequency (10-0.1 THz) window. At low levels of hydration, corresponding to two complete superficial water layers, no freezing occurs and the water remains mobile at all the investigated temperatures, while at the fully hydration we witnes…
The hydrophobic effect is the dominant force which drives a protein towards its native state, but its physics has not been thoroughly understood yet. We introduce an exactly solvable model of the solvation of non-polar molecules in water, which shows that the reduced number of allowed configurations of water molecules when the solute is present is enough to give rise to hydrophobic behaviour. We apply our model to a non-polar homopolymer in aqueous solution, obtaining a clear evidence of both ``cold'' and ``warm'' collapse transitions that recall those of proteins. Finally we show how the mode…
We investigate the co-nonsolvency of poly-N-isopropyl acrylamide (PNiPAM) in different water-alcohol mixtures and show that this phenomenon is due to two distinct solvation contributions governing the phase behavior of PNiPAM in the water-rich and alcohol-rich regime respectively. While hydrophobic hydration is the predominant contribution governing the phase behavior of PNiPAM in the water-rich regime, the mixing contributions governing the phase behavior of classical polymer solutions determine the phase behavior of PNiPAM in the alcohol-rich regime. This is evidenced by distinct scaling rel…
Graphene nanochannels are relevant for their possible applications, as in water purification, and for the challenge of understanding how they change the properties of confined liquids. Here, we use all-atom molecular dynamics simulations to investigate water confined in an open graphene slit-pore as a function of its width $w$, down to sub-nm scale. We find that the water translational and rotational dynamics exhibits an oscillatory dependence on $w$, due to water layering. The oscillations in dynamics correlate with those in hydration pressure, which can be negative (hydrophobic attraction), …
Small-angle neutron scattering (SANS) from cationic globular micellar solutions composed of sodium dodecyl sulfate (SDS) and in water was studied with contrast variation approach. Extensive computational studies have demonstrated that the distribution of invasive water is clearly an important feature for understanding the self-organization of SDS molecules and the stability of assemblies. However, in existing scattering studies the degree of hydration level was not examined explicitly. Here using the scheme of contrast variation, we establish a methodology of SANS to determine the intra-micell…
The authors use ab initio molecular dynamics and the density functional theory+U (DFT+U) method to compute the hydration environment of the manganese ion in manganese (II) and manganese (III) porphines (MnP) dispersed in liquid water. These are intended as simple models for more complex water soluble porphyrins, which have important physiological and electrochemical applications. The manganese ion in Mn(II)P exhibits significant out-of-porphine plane displacement and binds strongly to a single H2O molecule in liquid water. The Mn in Mn(III)P is on average coplanar with the porphine plane and f…
Ion hydration and interfacial water play crucial roles in numerous phenomena ranging from biological to industrial systems. Although biologically relevant (and mostly smaller) ions have been studied extensively in this context, very little experimental data exist about molecular scale behavior of heavy ions and their complexes at interfaces, especially under technologically significant conditions. It has recently been shown that PtCl62- complexes adsorb at positively charged interfaces in a two-step process that cannot fit into well-known empirical trends, such as Hofmeister series. Here, a co…
Molecular dynamics simulations of SPC/E water confined in a Silica pore are presented. The simulations have been performed at different hydration levels and temperatures to study the single-particle dynamics. Due to the confinement and to the presence of a hydrophilic surface, the dynamic behaviour of the liquid appears to be strongly dependent on the hydration level. On lowering temperature and/or hydration level the intermediate scattering function displays a double-step relaxation behaviour whose long time tail is strongly non-exponential. At higher hydrations two quite distinct subsets of …
Classification of interfacial water governed by water-polymer interactions in hydrated polymers: A molecular dynamics simulation study of ethylene-based and acrylate polymers
A hydrated 1,2-dimyristoyl-sn-glycero-3-phosphorylcholine (DMPC) lipid membrane is investigated using an all atom molecular dynamics simulation at 308K to find out the physical sources of universal slow relaxation of hydration layers. Continuously residing interface water (IW) hydrogen bonded to each other and concertedly to different moieties of lipid heads are identified. The non-gaussian parameter of all IW show a crossover from cage vibration to translational diffusion. A significant non-gaussianity is observed for the IW prevailing large length correlations in translational van Hove funct…
Enhanced dynamical fluctuations of RNAs, facilitated by a network of water molecules with strong interactions with RNA, are suspected to be critical in their ability to respond to a variety of cellular signals. Using atomically detailed molecular dynamics simulations at various temperatures of purine (adenine)- and preQ$_1$ sensing riboswitch aptamers, we show that water molecules in the vicinity of RNAs undergo complex dynamics depending on the local structures of the RNAs. The overall lifetimes of hydrogen bonds (HBs) of surface bound waters are more than at least 1-2 orders of magnitude lon…
Using molecular dynamics simulations, we investigate the relation between the dynamic transitions of biomolecules (lysozyme and DNA) and the dynamic and thermodynamic properties of hydration water. We find that the dynamic transition of the macromolecules, sometimes called a ``protein glass transition'', occurs at the temperature of dynamic crossover in the diffusivity of hydration water, and also coincides with the maxima of the isobaric specific heat $C_P$ and the temperature derivative of the orientational order parameter. We relate these findings to the hypothesis of a liquid-liquid critic…
An analysis of water clustering is used to study the quasi-2D percolation transition of water adsorbed at planar hydrophilic surfaces. Above the critical temperature of the layering transition (quasi-2D liquid-vapor phase transition of adsorbed molecules) a percolation transition occurs at some threshold surface coverage, which increases with increasing temperature. The location of the percolation line is consistent with the existence of a percolation transition at the critical point. The percolation threshold at a planar surface is weakly sensitive to the size of the system when its lateral d…
