Structure Of Liquid Water Research Articles

Preferential binding affinity of ions and their effect on structure and dynamics of water near antimicrobial peptide

Water containing dissolved salts is often found to play important roles in many chemical and biological processes. They affect the stability of the amino acids and proteins by altering the liquid water structure. The formation of a mixture of non-uniform density regions in liquid water; commonly known as Low-density water and High-density water is a well-known fact experimentally; which lends uniqueness to the ubiquitous water. The behavior of these different types of water at the interface and the bulk region of the biomolecules around the hydrophobic and hydrophilic residues under the influence of different alkali metal ions, such as LiCl, NaCl, and KCl is an important unexplored question in understanding of many biomolecular processes. To address this, we carried out MD simulation of antimicrobial peptide (PDB ID: 5Z32) for two different model potentials (CHARMM-SPC/E and AMBER-TIP4P) and performed the structural analysis of water in terms of the radial distribution function, number of hydrogen bonds, orientation, tetrahedral order parameter, voids analysis to analyze the related dynamical properties like preferential binding affinity, diffusion, hydrogen bond dynamics, entropy. The water molecules around the hydrophilic environment are found to be more disruptive containing more broken hydrogen bonds in comparison to the hydrophobic environment. It is also found that the water molecules present near the protein surface are of low density and that near the bulk is of high density. This leads to the higher self-diffusion coefficient of the water molecules and less hydrogen bond lifetime at the bulk. The maximum difference is found for the solutions containing high charge density, Lithium ions. Lithium ions have a strong preferential binding affinity towards protein surface resulting in strong solvation shells containing more tetrahedral-like water structure which has low diffusion, low entropy, and higher hydrogen bond lifetime. The diffusion of the water molecules, however, increases towards the higher solvation shells. Potassium on the other hand has less preference to live on protein surfaces resulting in similar diffusion values in the bulk and interface water molecules.

Rapid Freezing and Cryo CT Imaging of Liquid Water inside PEFCs

A cryo CT imaging to observe fixed three-dimensional liquid water structure of PEFC was developed. An operating at 40 °C cell temperature and 80 % gas relative humidity was instantaneously frozen, and the CT imaging was performed in low humidity and low temperature gas to prevent condensation from adhering to the MEA. The results of GDL visualization showed that the liquid water in the GDL was connected between the pores and formed a large structure. Moreover, it was found that, from the calculation of effective pore diameter, liquid water mainly accumulates in pores having 7

The influences of electric field intensity and driving force on the slip behaviour of water flow in a nanochannel.

In the present work, non-equilibrium molecular dynamics (MD) simulations are used to investigate the flow of liquid water between two metallic solid atomistic smooth walls. The present work focuses on the combined effect of external electric field and driving force on the slip behaviour and structure of liquid water at the solid-water interface. The upper wall of the set model is positively charged, and the lower wall of the model is negatively charged. The simulation results show that as the driving force increases, the slip length also increases. At a given driving force, no matter how the electric field intensity changes, there is almost no change in the slip length, so the slip length is independent of the electric field strength. In addition, the results found that there is a linear relationship between the slip length and the normalised main peak of the static structure factor under different driving forces.

On the centennials of the discoveries of the hydrogen bond and the structure of the water molecule: the short life and work of Eustace Jean Cuy (1897-1925).

The bent structure of the water molecule, and its hydrogen-bonding properties, arguably rank among the most impactful discoveries in the history of chemistry. Although the fact that the H-O-H angle must deviate from linearity was inferred early in the 20th century, notably from the existence of the electric dipole moment, it was not clear what that angle should be and why. One hundred years ago, a young PhD student at the University of California, Berkeley, Eustace J. Cuy, rationalized the V-shape structure of a water molecule using the Lewis theory of a chemical bond, i.e. a shared electron pair, and its tetrahedral stereochemistry. He was inspired, in part, by the proposal of a weak (hydrogen) bond in water by two colleagues at Berkeley, Wendell Latimer and Worth Rodebush, who published their classic paper a year earlier. Cuy went on to suggest that other molecules, notably H2S and NH3, have similar structures, and presciently predicted that this architecture has broader consequences for the structure of water as a liquid. This short, but brilliant paper has been completely forgotten, perhaps due to the tragic death of the author at the age of 28; the hydrogen-bond study is also rarely recognized. One of the most impactful publications on the structure of liquid water, a classic treatise published in 1933 by John Bernal and Ralph Fowler, does not mention either of the two pioneering papers. In this essay, the background for the two discoveries is described, including the brief history of Lewis's research on the nature of the chemical bond, and the history of the discovery of the hydrogen bond, which inspired Cuy to look at the structure of the water molecule. This is - to the best of the author's knowledge - the first biographical sketch of Eustace J. Cuy.

The Polarizable continuum potential model in the liquid state Calculations. Density functional computational analysis of the anharmonic vibrational spectrum of liquid water

A Density Functional calculation, using the Gaussian 03 W protocol with the B3LYP functional and the SCRF-Polarizable Continuum model (SCRF-PCM), has been performed on a pentameric unit, constituted by a central water molecule tetrahedrically coordinated to four other surrounding molecules by hydrogen bond (HB) interactions. The calculation has been aimed at reproducing vibrational distributions of the intra-molecular and intermolecular modes, which contribute at widening the stretching and bending OH bands in the liquid vibrational spectrum, and those at low frequencies, commonly considered intermolecular motions of O-H…O stretching and bending type, in the HB tetrahedral network of liquid water. The so called librational large distribution has been also nicely reproduced by this calculation. Energetic and geometrical considerations have been discussed for the equilibrium structure of this pentameric assembly, representing the basic unit presently used to simulate more space-extended structures of liquid water. These are constituted by different domains of ordered (open, or ice-like) and unordered (closed) patches of water clusters. Although the small cluster used in this calculation represents only an approximation to treat the real organization existing in the liquid water complex system, our results seems to reproduce quite well both the vibrational spectrum and the energetic and geometric situations for this very important liquid.

Distinguishing Weak and Strong Hydrogen Bonds in Liquid Water-A Potential of Mean Force-Based Approach.

The ability to form hydrogen bonds is one of the most important factors behind water's many anomalous properties. However, there is still no consensus on the hydrogen bond structure of liquid water, including the average number of hydrogen bonds in liquid water. We use molecular dynamics simulations of the polarizable iAMOEBA water model for investigating the hydrogen bond characteristics of liquid water over a wide range of temperatures and pressures. Geometric definitions of a hydrogen bond often use a rectangular region on the plane of hydrogen bond distances and angles. In this work, we find that an elliptical region is more appropriate for the identification of hydrogen bonds, based on statistically favorable molecular configurations. The two-dimensional potential of mean force (PMF) landscape along the hydrogen bond distance (O-H) and angle (O-H-O) is calculated for identifying the statistically favored molecular configurations, which is then used for defining hydrogen bond formation as well as the strength of a hydrogen bond. We further propose a new approach to characterize the hydrogen bonds as strong when the PMF is lower than -2 kT. Using this definition, a consistent explanation for the different average numbers of hydrogen bonds in water is obtained in agreement with the literature. Simulations are also performed with the rigid and nonpolarizable TIP4P/2005 water model. Both water models are qualitatively consistent in predicting the distribution of double-, single-, and non-donor configurations, in line with experimental data, while the iAMOEBA water model yields more quantitatively precise results, including a 10-15% double-donor fraction at 90 °C and 1 atm. The method is also demonstrated to be applicable to the recent, and more general, three-dimensional PMF-based definition of hydrogen bonds.

Assessing the Accuracy of the SCAN Functional for Water through a Many-Body Analysis of the Adiabatic Connection Formula.

We present a systematic analysis of the accuracy of a series of SCANα functionals for water, with varying fractions (α) of exact exchange, which are constructed through the adiabatic connection formula. Our results indicate that all SCANα functionals exhibit substantial errors in the representation of the water 2-body energies. Importantly, the inclusion of exact exchange is found to have opposite effects on the ability of the SCANα functionals to describe the interaction energies of water clusters with 2-dimensional and 3-dimensional hydrogen-bonding arrangements. These errors are found to directly affect the ability of the SCANα functionals to describe the structure of liquid water at ambient conditions, which is investigated using explicit many-body models (MB-SCANα) derived from the corresponding SCANα data. In particular, it is found that all MB-SCANα models predict a more compact first hydration shell, which results in a denser liquid with a more ice-like structure. These apparent opposite trends can be explained by the inability of the SCANα functionals to provide a balanced description of the water 2B and 3B energies at the fundamental level. The analyses presented in this study provide new insights that can guide future developments of improved exchange-correlation functionals for aqueous systems.

Hamiltonian based resonance-free approach for enabling very large time steps in multiple time-scale molecular dynamics

Extended phase-space isokinetic methods in their deterministic [Minary et al., Phys. Rev. Lett. 93, 150201 (2004)] and stochastic forms [Leimkuhler et al., Mol. Phys. 111, 3579 (2013)] have proved tremendously successful in allowing multiple time-scale molecular dynamics simulations to be performed with very large time steps. These methods work by coupling the physical degrees of freedom to a set of Nosé-Hoover chain or Nosé-Hoover Langevin thermostats via an isokinetic constraint, which has the effect of avoiding resonance artifacts that plague multiple time-step algorithms. In this paper, we introduce a new resonance-free approach that achieves the same gains in time step but without the imposition of isokinetic constraints or the introduction of extended phase-space variables. Rather, we modify the physical Hamiltonian that effects the same regulation of resonances achieved by the isokinetic constraints. In so doing, we show that sampling errors can be controlled and performance improvements are possible within a simpler Hamiltonian framework. The method is demonstrated in simulations of the structure of liquid water and, in conjunction with enhanced sampling, in generation of the Ramachandran free-energy surface of the solvated alanine dipeptide.

Relationship between Hydrogen-Bonding Motifs and the 1b1 Splitting in the X-ray Emission Spectrum of Liquid Water.

The split of the 1b1 peak observed in the X-ray emission (XE) spectrum of liquid water has been the focus of intense research. Although several hypotheses have been proposed to explain the origin of this split, a consensus has not yet been reached. Here, we introduce a novel theoretical/computation approach which, combining path-integral molecular dynamics simulations with the MB-pol model and time-dependent density functional theory calculations, predicts the 1b1 splitting in liquid water and not in crystalline ice, in agreement with the experimental observations. A systematic analysis of the underlying local structure of liquid water at ambient conditions indicates that several different hydrogen-bonding motifs contribute to the overall XE line shape in the energy range corresponding to emissions from the 1b1 orbitals. This suggests that it is not possible to unambiguously attribute the split of the 1b1 peak to only two specific structural arrangements of the underlying hydrogen-bonding network.

Liquid Water and Interfacial, Cubic, and Hexagonal Ice Classification through Eclipsed and Staggered Conformation Template Matching.

We propose a novel method based on template matching for the recognition of liquid water, cubic ice (ice Ic), hexagonal ice (ice Ih), clathrate hydrates, and different interfacial structures in atomistic and coarse-grained simulations of water and ice. The two template matrices represent staggered and eclipsed conformations, which are the building blocks of hexagonal and cubic ice and clathrate crystals. The algorithm is rotationally invariant and highly robust against imperfections in the ice structure, and its sensitivity for recognizing ice-like structures can be tuned for different applications. Unlike most other algorithms, it can discriminate between cubic, hexagonal, clathrate, mixed, and other interfacial ice types and is therefore well suited to study complex systems and heterogeneous ice nucleation.

Nuclear quantum effects: Their relevance in neutron diffraction studies of liquid water

Corrections for nuclear quantum effects (NQE) have been calculated for classical molecular dynamics (MD) simulation models of light (H2O), heavy (D2O) and ‘null’ [(H2O)0.64(D2O)0.36] water. New path integral molecular dynamics (PIMD) simulations have also been conducted for the same systems. NQEs have somewhat smaller influence on the O-D and D-D partial radial distribution functions of heavy water than on the O-H and H-H ones of light water. After correcting for NQEs the O-‘H’ bondlengths in light and heavy water have become different: the O-D ones are about 0.5% shorter than the O-H ones. Following NQE corrections, the total RDF of ‘null’ water does show hydrogen related features at the position of the intramolecular O-‘H’ peak. Based on a cross-check procedure involving the NQE-corrected total and partial radial distribution functions, it can be stated that concerning the structure of liquid water, the assumption that H and D are equal is valid to a very good approximation for intermolecular correlations. These findings are also supported by our path integral molecular dynamics simulations.

Could Chemical Reaction at the Molecular Level Show Distinction between Two Liquid-Water States? Study of the Excited-State Water-Catalyzed Proton Transfer Reaction Provides a Clue.

The two liquid-water states, which lead to some anomalies when temperature crosses over 50 ± 10 °C at the atmospheric pressure, have been continuously catching popular attention. In this study, using the excited-state proton transfer (ESPT) catalyzed by water molecules as a prototypical reaction, we demonstrate that the kinetics of ESPT indeed is influenced by the two liquid-water states. In the water-catalyzed ESPT of 3-cyano-7-azaindole (3CAI), a repetitive and comprehensive temperature-dependent study of ESPT in H2O from 0 to 90 °C shows anomalous behavior. The plot of the logarithm of ESPT rate constant as a function of inverse of absolute temperature deviates from a straight line. The convex-Arrhenius behavior manifests the activation free energy for water-assisted ESPT being dependent on temperature and hence the liquid water structure. To simplify the discussion, the plot is well fitted by using two straight lines that are crossed over in the vicinity of 40 °C. The free energy difference between water-solvated 3CAI and the 1:1 H2O:3CAI complex is deduced to be 2.29 ± 0.04 and 1.96 ± 0.04 kcal·mol-1 in the regions of 0-40 and 40-90 °C water, respectively, which also results in different frequency factors, i.e., the proton transfer/tunneling rates of (5.83 ± 0.36) × 1010 and (3.48 ± 0.27) × 1010 s-1, respectively. In a qualitative manner, the results are then rationalized by the different types of H-bonding configuration as proposed for two liquid-water phases, rendering experimental evidence to support the different water phases in ambient temperatures at 1 bar.

Long-Range Ordered Water Correlations between A–T/C–G Nucleotides

Summary The interactions between complementary base pairs are crucial to the helical duplex structure of DNA. Although base-base interactions have been widely reported, the study of long-range interactions in the base-pairing processes is still a major challenge in this field. Here, we first study the long-range interactions between the base pairs by atomic force microscopy-based single-molecule force spectroscopy (SMFS). The SMFS results of A–T/C–G imply that there are weak long-range interactions between them, which have a range of 15–25 nm. Raman spectroscopy results imply that these weak interactions can be attributed to multiplex hydrogen bond interaction of ordered water structure between A–T/C–G nucleotides. In addition, the theoretical calculations deduce that the ideal structure of these water molecules exhibits a specific helical structure. Our findings might open up a new understanding of biological assembly processes and provide helpful strategies for bio-nanotechnology.

Ultrafast hydrogen bond dynamics of liquid water revealed by terahertz-induced transient birefringence

The fundamental properties of water molecules, such as their molecular polarizability, have not yet been clarified. The hydrogen bond network is generally considered to play an important role in the thermodynamic properties of water. The terahertz (THz) Kerr effect technique, as a novel tool, is expected to be useful in exploring the low-frequency molecular dynamics of liquid water. Here, we use an intense and ultrabroadband THz pulse (peak electric field strength of 14.9 MV/cm, centre frequency of 3.9 THz, and bandwidth of 1–10 THz) to resonantly excite intermolecular modes of liquid water. Bipolar THz field-induced transient birefringence signals are observed in a free-flowing water film. We propose a hydrogen bond harmonic oscillator model associated with the dielectric susceptibility and combine it with the Lorentz dynamic equation to investigate the intermolecular structure and dynamics of liquid water. We mainly decompose the bipolar signals into a positive signal caused by hydrogen bond stretching vibration and a negative signal caused by hydrogen bond bending vibration, indicating that the polarizability perturbation of water presents competing contributions under bending and stretching conditions. A Kerr coefficient equation related to the intermolecular modes of water is established. The ultrafast intermolecular hydrogen bond dynamics of water revealed by an ultrabroadband THz pump pulse can provide further insights into the transient structure of liquid water corresponding to the pertinent modes.

Change of liquid water structure under the presence of phosphate anion during changing its kosmotropic character to chaotropic along its deprotonation route

Temperature dependence of OH-stretching bands of water and aqueous phosphoric acid solutions were compared to clarify how the presence of ions alters the hydrogen bonded structure of water. Investigations were performed by Raman measurements at different pH considering that the slightly chaotropic character of H2PO4− anion changes to kosmotropic in the cases of the HPO42− and PO43− anions. This property is determined by the number of OH groups (proton donors) versus the lone pairs of oxygen atoms (proton acceptors). The number of molecules assisted to form hydrogen bonds through their oxygen lone pairs decreases at elevated temperature and increased pH.

Towards Aqueous – Fluorous – Hydrogenous emulsions: Phase equilibria and liquid structure of (water + 1H,1H-Perfluorobutanol + 1-butanol) ternary mixture

The liquid-liquid equilibrium for the ternary mixture (1-Butanol + 1H,1H-Perfluorobutanol + Water) was determined at 298.6 K. The system displays a type 2 diagram (band-like) characterized by an immiscibility band resulting from the overlap of two regions of partial miscibility.The solubility of water in the binary mixtures of the two alcohols is very high, always above 0.34 mole fraction. The organic phase is thus a complex mixture of aqueous, fluorous and hydrogenous domains.Liquid densities were measured as a function of composition for (water + BuOH) and (water + HFB) binary mixtures and for the ternary mixtures along the organic saturation line. The excess volumes of the binary and ternary mixtures were calculated. The system displays remarkable volumetric effects: water dissolves in BuOH with volume contraction, in HFB with volume expansion and the excess volume of the ternary saturated organic mixtures is positive throughout most of the composition range.Atomistic molecular dynamics simulations were performed enabling a molecular level perception of the organization and interactions of the ternary system. The results accurately reproduce the experimental excess volumes data of the binary and ternary mixtures, fully validating the simulations. The simulation results reveal the existence of clusters of water molecules, coexisting with hydrogenated and fluorinated domains at concentrations near saturation.

Characterization of water structure in carbon nanotubes by various order parameters

Various order parameters have been suggested to characterize the local structure of liquid water in bulk. Characterization the local structure of water molecules in the confined systems by various order parameters is important but still unclear. In this work, a series of popular order parameters are used to analyze the local structure of water molecules in carbon nanotubes (CNTs) by molecular dynamics simulation. Based on the value of order parameters, the different structures of water molecules in CNTs and in bulk were discussed. The orientational tetrahedral order (q) and translational tetrahedral order (Sk) are much better than local structure index (LSI) to describe the local structure of water in CNTs. We also demonstrated that the local structure of water molecules in the CNT(40,40) is almost the same with that in bulk. The findings could give us a guideline to investigate the water molecules in confined system.

Structure, Dynamics, and Some Properties of Water

Development of ideas of liquid water structure since the end of the 19th century is briefly reviewed. According to the modern concepts based on experimental data and computer simulation, there is a three-dimensional hydrogen bond network in water. The structural and dynamic inhomogeneity of this network is analyzed in detail.

A Simplified Cluster Analysis of Electron Track Structure for Estimating Complex DNA Damage Yields.

Complex DNA damage, defined as at least two vicinal lesions within 10–20 base pairs (bp), induced after exposure to ionizing radiation, is recognized as fatal damage to human tissue. Due to the difficulty of directly measuring the aggregation of DNA damage at the nano-meter scale, many cluster analyses of inelastic interactions based on Monte Carlo simulation for radiation track structure in liquid water have been conducted to evaluate DNA damage. Meanwhile, the experimental technique to detect complex DNA damage has evolved in recent decades, so both approaches with simulation and experiment get used for investigating complex DNA damage. During this study, we propose a simplified cluster analysis of ionization and electronic excitation events within 10 bp based on track structure for estimating complex DNA damage yields for electron and X-ray irradiations. We then compare the computational results with the experimental complex DNA damage coupled with base damage (BD) measured by enzymatic cleavage and atomic force microscopy (AFM). The computational results agree well with experimental fractions of complex damage yields, i.e., single and double strand breaks (SSBs, DSBs) and complex BD, when the yield ratio of BD/SSB is assumed to be 1.3. Considering the comparison of complex DSB yields, i.e., DSB + BD and DSB + 2BD, between simulation and experimental data, we find that the aggregation degree of the events along electron tracks reflects the complexity of induced DNA damage, showing 43.5% of DSB induced after 70 kVp X-ray irradiation can be classified as a complex form coupled with BD. The present simulation enables us to quantify the type of complex damage which cannot be measured through in vitro experiments and helps us to interpret the experimental detection efficiency for complex BD measured by AFM. This simple model for estimating complex DNA damage yields contributes to the precise understanding of the DNA damage complexity induced after X-ray and electron irradiations.

Relaxation dynamics and power spectra of liquid water: a molecular dynamics simulation study

We present molecular dynamics simulations of liquid water at normal and supercooled conditions. Autocorrelation functions (ACFs) of several structural quantities and their fourier transforms are obtained and analysed. Structural correlations and relaxation times increase linearly with degree of supercooling. Power spectra of ACFs show increase in librational motion of liquid water with cooling. These modes intensify with supercooling because of structuring and ordering of water molecules. Overall, liquid water structure is homogenous over the temperatures and pressures studied and undergoes fluctuation–dissipation in its local-density variations [English and Tse, Phys. Rev. Lett. 106, 037801 (2011)].