Hydrogen Bond Network Of Water Research Articles

Unraveling the Influence of Osmolytes on Water Hydrogen-Bond Network: From Local Structure to Graph Theory Analysis.

Water structure in aqueous osmolyte solutions, deduced from the slight alteration in the water-water radial distribution function, the decrease in water-water hydrogen bonding, and tetrahedral ordering based only on the orientation of nearest water molecules derived from the molecular dynamics simulations, appears to have been perturbed. A careful analysis, however, reveals that the hydrogen bonding and the tetrahedral ordering around a water molecule in binary solutions remain intact as in neat water when the contribution of osmolyte-water interactions is appropriately incorporated. Furthermore, the distribution of the water binding energies and the water excess chemical potential of solvation in solutions are also pretty much the same as in neat water. Osmolytes are, therefore, well integrated into the hydrogen-bond network of water. Indeed, osmolytes tend to preferentially hydrogen bond with water molecules and their interaction energies are strongly correlated to their hydrogen-bonding capability. The graph network analysis, further, illustrates that osmolytes act as hubs in the percolated hydrogen-bond network of solutions. The degree of hydrogen bonding of osmolytes predominantly determines all of the network properties. Osmolytes like ethanol that form fewer hydrogen bonds than a water molecule disrupt the water hydrogen-bond network, while other osmolytes that form more hydrogen bonds effectively increase the connectivity among water molecules. Our observation of minimal variation in the local structure and the vitality of osmolyte-water hydrogen bonds on the solution network properties clearly imply that the direct interaction between protein and osmolytes is solely responsible for the protein stability. Further, the relevance of hydrogen bonds on solution properties suggests that the hydrogen-bonding interaction among protein, water, and osmolyte could be the key determinant of the protein conformation in solutions.

States of water in recast Nafion® films

The amount and states of water in a polymer electrolyte significantly affect the material's morphology as well as its mechanical and transport properties, and thus determine performance in many important applications such as fuel cells, electrolyzers, and other electrochemical energy conversion devices. In this study, recast H+-Nafion® films were characterized using attenuated total internal reflection FTIR (ATR-FTIR) spectroscopy before and after thermal annealing and subsequent rehydration. The states of water in the hydrated films were determined by analyzing the O–H stretching band of water using principle component analysis and multivariate curve resolution. It was found that annealing at a temperature above the glass transition temperature caused the water hydrogen-bonding networks in the water-ionic clusters to become restricted, suggesting that annealing forms a robust polymer matrix confining the water-ionic clusters. The evolution of film morphology with increasing thermal-annealing temperature was confirmed with small-angle X-ray scattering (SAXS) and CO2 diffusion measurements. Fuel cell performance tests using annealed and unannealed Nafion® in the cathode catalyst layer found improved stability when the cathode catalyst was annealed, indicating that thermal history is an important design parameter in electrochemical energy conversion device fabrication.

Local Mutations Can Serve as a Game Changer for Global Protein Solvent Interaction.

Although it is well-known that limited local mutations of enzymes, such as matrix metalloproteinases (MMPs), may change enzyme activity by orders of magnitude as well as its stability, the completely rational design of proteins is still challenging. These local changes alter the electrostatic potential and thus local electrostatic fields, which impacts the dynamics of water molecules close the protein surface. Here we show by a combined computational design, experimental, and molecular dynamics (MD) study that local mutations have not only a local but also a global effect on the solvent: In the specific case of the matrix metalloprotease MMP14, we found that the nature of local mutations, coupled with surface morphology, have the ability to influence large patches of the water hydrogen-bonding network at the protein surface, which is correlated with stability. The solvent contribution can be experimentally probed via terahertz (THz) spectroscopy, thus opening the door to the exciting perspective of rational protein design in which a systematic tuning of hydration water properties allows manipulation of protein stability and enzymatic activity.

A hierarchical clustering method of hydrogen bond networks in liquid water undergoing shear flow

Many properties of water, such as turbulent flow, are closely related to water clusters, whereas how water clusters form and transform in bulk water remains unclear. A hierarchical clustering method is introduced to search out water clusters in hydrogen bonded network based on modified Louvain algorithm of graph community. Hydrogen bonds, rings and fragments are considered as 1st-, 2nd-, and 3rd-level structures, respectively. The distribution, dynamics and structural characteristics of 4th- and 5th-level clusters undergoing non-shear- and shear-driven flow are also analyzed at various temperatures. At low temperatures, nearly 50% of water molecules are included in clusters. Over 60% of clusters remain unchanged between neighboring configurations. Obvious collective translational motion of clusters is observed. The topological difference for clusters is elucidated between the inner layer, which favors 6-membered rings, and the external surface layer, which contains more 5-membered rings. Temperature and shearing can not only accelerate the transformation or destruction of clusters at all levels but also change cluster structures. The assembly of large clusters can be used to discretize continuous liquid water to elucidate the properties of liquid water.

Unravelling hydrogen adsorption kinetics on Ir(111) electrode in acid solutions by impedance spectroscopy

The kinetics for hydrogen (H) adsorption on Ir(111) electrode has been studied in both HClO4 and H2SO4 solutions by impedance spectroscopy. In HClO4, the adsorption rate for H adsorption on Ir(111) increases from 1.74×10−8 mol·cm−2·s−1 to 3.47×10−7 mol·cm−2·s−1 with the decrease of the applied potential from 0.2 V to 0.1 V (vs. RHE), which is ca. one to two orders of magnitude slower than that on Pt(111) under otherwise identical condition. This is explained by the stronger binding of water to Ir(111), which needs a higher barrier to reorient during the under potential deposition of H from hydronium within the hydrogen bonded water network. In H2SO4, the adsorption potential is ca. 200 mV negatively shifted, accompanied by a decrease of adsorption rate by up to one order of magnitude, which is explained by the hindrance of the strongly adsorbed sulfate/bisulfate on Ir(111). Our results demonstrate that under electrochemical environment, H adsorption is strongly affected by the accompanying displacement and reorientation of water molecules that initially stay close to the electrode surface.

The Many-Body Expansion for Aqueous Systems Revisited: II. Alkali Metal and Halide Ion-Water Interactions.

We present a detailed study of the many-body expansion (MBE) for alkali metal and halide ion-water interactions and quantify the effect of these ions on the strength of the surrounding aqueous hydrogen bonding environment. Building on our previous work on neutral water clusters [J. P. Heindel and S. S. Xantheas, J. Chem. Theor. Comput. 16 (11), 6843-6855 (2020)], we carry out the MBE for the alkali metal and halide ion-water clusters, Z+/-(H2O)9, where Z = Li+, Na+, K+, Rb+, Cs+, F-, Cl-, Br-, and I- and compare them with the results for a pure water cluster with the same number of "bodies", viz., (H2O)10. The 2-B ion-water (I-W) interaction accounts for a larger percentage of the total cluster binding energy compared to a pure water cluster of the same size, with the total 3-B term being smaller and of opposite sign (repulsive), whereas higher order terms are essentially negligible. The same oscillating behavior around zero for the MBE terms higher than the 5-B with a basis set that was reported for water clusters is also observed for the ion-water clusters considered here, with the basis set superposition error (BSSE) corrections amending this as in the water cluster case. A remarkable, linear anticorrelation between the total 2-B (I-W), the total 2-B (W-W), and also the 3-B (W-W-W) interactions is found, quantifying the effect of the different ions in disrupting and altering (weakening) the neighboring hydrogen bonded water network: stronger (I-W) interactions result in weaker (W-W) interactions. Additional linear correlations across the two series of alkali metals and halide ions were found between the 3-B (I-W-W) and the 2-B (I-W) as well as between the 3-B (I-W-W) and the 3-B (W-W-W) interactions, suggesting the existence of previously unrealized underlying physics governing these 2-B intermolecular and 3-B collective interactions. Our results further suggest a universal behavior of the two different families of ions (alkali metals and halides) for both the correlations of the various components of the total binding energies and the estimate of the 2-B BSSE correction, which is reported to follow a common profile for ion-water and water-water interactions when cast in terms of reduced distances and energies of the respective dimers. We expect the current results that quantify the interplay between ion-water and water-water interactions in aqueous clusters to impact the development of classical, ab initio-based force fields for monatomic ion solvation, whereas the insights into the nature of the BSSE to be critical in future ab initio-based, many-body molecular dynamics studies.

Redefining the concept of hydration water near soft interfaces.

Water determines the properties of biological systems. Therefore, understanding the nature of the mutual interaction between water and biosystems is of primary importance for a proper assessment of any biological activity, e.g., the efficacy of new drugs or vaccines. A convenient way to characterize the interactions between biosystems and water is to analyze their impact on water density and dynamics in the proximity of the interfaces. It is commonly accepted that water bulk density and dynamical properties are recovered at distances of the order of 1 nm away from the surface of biological systems. This notion leads to the definition of hydration or biological water as the nanoscopic layer of water covering the surface of biosystems and to the expectation that all the effects of the water-interface interaction are limited to this thin region. Here, we review some of our latest contributions, showing that phospholipid membranes affect the water dynamics, structural properties, and hydrogen bond network at a distance that is more than twice as large as the commonly evoked ∼1nm thick layer and of the order of 2.4 nm. Furthermore, we unveil that at a shorter distance ∼0.5nm from the membrane, instead, there is an additional interface between lipid-bound and unbound water. Bound water has a structural role in the stability of the membrane. Our results imply that the concept of hydration water should be revised or extended and pave the way to a deeper understanding of the mutual interactions between water and biological systems.

Exploring the Proton-Transfer Mechanism in Hv1 by Multi-Scale Simulations

The Hv1 proton channel is expressed in a broad range of eukaryotic cells, where its chief physiological role is to mediate proton efflux. Hv1 is a potential target for the development of drugs to treat human pathologies, including breast cancer and ischemic stroke. Similar to other voltage sensor (VS) domain-containing proteins, Hv1 gating is controlled by changes in membrane potential. The H+ permeation pathway in Hv1 is formed by an hourglass-shaped hydrated VS central crevice, with several conserved hydrophobic residues forming a central bottleneck region. Although specific residues have been identified as potential sites for proton transfer by explicit side chain ionization, almost all neutralizations of ‘selectivity filter’ residues D112, R211, and other highly conserved ‘gating-charge’ or ‘counter-charge’ residues have so far failed to abolish H+ currents on Hv1. An alternative H+ transfer mechanism, in which VS-resident water molecules form a water wire, has not been ruled out. To investigate structural constraints on possible water wire formation in Hv1 we conducted classical molecular dynamics simulations followed by mixed quantum-mechanics/molecular-mechanics (QM/MM) simulations on a new, experimentally constrained activated-state Hv1 model structure. The calculations will allow us to focus on how dynamics in the bottleneck region that envelops a D112-R211 salt bridge impact water and side chain hydrogen bond network structures, possible water wire formation, and energetic barriers to proton migration.

Study and optimization of Diels-Alder reaction of piperine in aqueous ionic solutions using Gn.HCl as a catalyst

Study and optimization of Diels-Alder reaction of piperine in aqueous ionic solutions using Gn.HCl as a catalyst

Anion-water hydrogen bond vibration revealed by the terahertz Kerr effect.

The microscopic mechanism for ionic influence on the hydrogen bond network of water has not been fully understood. Here we employ the terahertz Kerr effect (TKE) technique to map the intermolecular hydrogen bond dynamics in a series of aqueous halide solutions at the sub-picosecond scale. Compared with pure water, the significantly enhanced bipolar TKE response associated with polarization anisotropy in an ionic aqueous solution is successfully captured. We decompose the measured TKE response into different molecular motion modes and demonstrate that the obviously increasing positive polarity response is mainly due to the anion-water hydrogen bond vibration mode with the resonant THz electric field excitation. Our measurement results provide an experimental basis for further insight into the effects of ions on the structure and dynamics of a hydrogen bond in water.

Relationship between hydrogen bond network dynamics of water and its terahertz spectrum

Water is the source of all life. The understanding of the terahertz absorption spectrum of water is the prerequisite for the application of terahertz technology to biomedicine. The choice of terahertz frequency is essential for achieving the biological effects of terahertz with high efficiency and low energy consumption. The complex hydrogen bond network of water possesses a broad terahertz absorption peak. Therefore, it is necessary to study the relation between the dynamics of the hydrogen bond network of water and its terahertz absorption spectrum. However, the research in this field is still lacking. Using molecular dynamics simulation methods, the terahertz absorption spectra of different water models at room temperature and pressure are studied in this work. Furthermore, taking the temperature as a variable, the dependence of the terahertz absorption spectrum of water on the strength of the hydrogen bond network is explored. It is found that rising temperature makes the terahertz absorption spectrum of the hydrogen bond network red-shift, indicating that the center frequency of the spectrum is strongly correlated with the strength of the hydrogen bond. Further studies show that there is a linear relationship between the hydrogen bond lifetime of water and the center frequency of vibration absorption peak of the hydrogen bond network. The underlying mechanism can be disclosed by imitating the hydrogen bonds in the hydrogen bond network as springs then using the spring oscillator model. These findings are conducive to understanding in depth the complex hydrogen bond network dynamics in water and promoting the study of terahertz biological effects.

Effects of molecular shape on alcohol aggregation and water hydrogen bond network behavior in butanol isomer solutions.

Despite butanol isomers such as n-butanol, sec-butanol, isobutanol and tert-butanol having the same chemical formula, their liquid-liquid phase diagrams are distinct. That is, tert-butanol is miscible in water at all concentrations, while the other three butanol isomers are partially miscible under ambient conditions. The molecular shape of tert-butanol is close to globular and differs from the other three butanol molecules with a relatively long carbon chain. By performing molecular dynamics simulations and graph theoretical analysis of the four water-butanol isomer mixtures at varying concentrations, we show how distinct butanol aggregates are formed which depend upon the molecular shape and affect the water H-bond network structure and phase diagram in the binary liquid. The three butanol isomers of n-butanol, sec-butanol and isobutanol at concentrated solutions form chain-like alcohol aggregates, but tert-butanol forms small aggregates due to the distinct packing behavior caused by its globular molecular shape. By employing the graph theoretical analysis such as the degree distribution and the eigenvalue spectrum from the adjacency matrix in the graphical representation of the alcohol H-bond network, we show that the tert-butanol aggregates have a different morphological structure from that of the other three butanol isomers in aqueous solution. The graph theoretically distinct butanol aggregates are categorized into two groups, water-compatible and water-incompatible, depending upon the interaction between the alcohol and water molecules. Based upon our observations, we propose that the water-incompatible networks of n-butanol, sec-butanol and isobutanol aggregates do not change the water structure significantly, forming two separate liquid phases that are alcohol-rich and water-rich. However, the water-compatible network of tert-butanol aggregates has a considerable interaction with the water molecules and causes significant disruption of the water H-bond network, forming a homogeneous solution. Understanding the alcohol aggregation behavior and water structure in butanol-water mixtures provides a critical clue in appreciating fundamental issues such as miscibility and phase separation in aqueous solution systems.

Molecular Clustering in Formaldehyde-Methanol-Water Mixtures Revealed by High-Intensity, High-q Small-Angle Neutron Scattering.

Methanol-Water (mw) mixtures, with or without a solute, display a nonideal thermodynamic behavior, typically attributed to the structure of the microphase. However, experimental observation of the microphase structures at the molecular length scale has been a challenge. We report the presence of molecular clusters in mw and formaldehyde-methanol-water (fmw) mixtures using small-angle neutron scattering (SANS) experiments and molecular dynamics (MD) simulations. Hydrophobic clusters of methanol in mw and formaldehyde-methanol in fmw mixtures were observed at low methanol compositions (xm ≤ 0.3). A three-dimensional hydrogen-bonded network of water with the solute is observed at xm = 0.5. Linear chains of methanol surrounding the formaldehyde and water molecules were observed at high methanol compositions (xm ≥ 0.7). The calculated size of the molecular clusters (r ≈ 0.5 nm, spherical) from the SANS data and their volume fraction closely matched the MD simulation results.

Unraveling the origin of interactions of hydroxychloroquine with the receptor-binding domain of SARS-CoV-2 in aqueous medium

Interactions of hydroxychloroquin (HCQ) with the receptor binding domain (RBD) of SARS-CoV-2 were studied from atomistic simulation and ONIOM techniques. The key-residues of RBD responsible for the human transmission are recognized to be blocked in a heterogeneous manner with the favorable formation of key-residue:HCQ (1:1) complex. Such heterogeneity in binding was identified to be governed by the differential life-time of the hydrogen bonded water network anchoring HCQ and the key-residues. The intermolecular proton transfer facilitates the most favorable Lys417:HCQ complexation. The study demonstrates that off-target bindings of HCQ need to be minimized to efficiently prevent the transmission of SARS-CoV-2.

Ion Solvation and Water Structure in an Aqueous Sodium Chloride Solution in the Gigapascal Pressure Range.

The structure of a 3 m (= mol/kg) NaCl aqueous solution at 1.3 and 1.7 GPa and 300 K, as well as at an ambient condition, is determined by synchrotron X-ray diffraction measurements combined with an empirical potential structure refinement (EPSR) modeling. When the solution is pressurized to the gigapascal pressure range, the ice-like hydrogen-bonded water network at 300 K/0.1 MPa is drastically perturbed to give rise to a simple, liquid-like water molecules arrangement retaining the hydrogen bonds. The coordination number of the chloride ion increases from around 6 at 0.1 MPa to about 16 at 1.7 GPa, accompanied by the extended solvation shells' evolution. On the other hand, the sodium ion's solvation structure does not change significantly with pressure and consists of 6-fold water molecules' coordination. We discuss a structure makers/breakers' concept for the ion solvation concerning the water structure in the gigapascal pressure range.

Three stages of hydrogen bonding network in DMF-water binary solution

Three stages of hydrogen bonding (HB) network in N, N-dimethylformamide (DMF)-water binary solution were investigated by Raman spectroscopy with different mixing ratios at room temperature and atmospheric pressure. The results show that the addition of DMF strengthens the HB network of water when the volume fraction of DMF (VDMF) is less than 0.4. However, the tetrahedral structure of water is destroyed when VDMF reaches 0.4, and water molecules and DMF molecules form two DMF-water complexes, namely DMF·3H2O and DMF·2H2O. While VDMF reaches 0.8, the DMF-water complex is transformed into DMF·H2O structure due to the instability of DMF·nH2O (n = 2, 3). In addition, the newly formed HB C=O···H-C, rather than the weak HB C-H···O, leads to the red shift of C–H stretching vibration mode.

Hydration Water Structure, Hydration Forces, and Mechanical Properties of Polysaccharide Films.

The interaction of polysaccharides with water has a critical impact on their biological function as well as their technological applications. We performed ellipsometry experiments at different relative humidities (RH) to measure the equilibrium swelling of ultrathin films of different polysaccharides: native and modified phytoglycogen (PG) nanoparticles, dextran, and hyaluronic acid. For RH > 70%, the swelling of hydrophilic polymers with increases in RH is described by hydration forces that are characterized by an exponential decay length λ. Our analysis of the high RH swelling regime allowed us to determine λ and the bulk modulus K of the films of different polysaccharides. We also probed the high RH swelling regime using attenuated total reflection infrared (ATR-IR) spectroscopy, which allowed us to determine the degree of hydrogen bonding of the hydration water within the polysaccharide films. Combining the ellipsometry and ATR-IR spectroscopy results, we find that increases in the order of the hydrogen bond network of the hydration water, as specified by the ATR-IR parameter Rnetwork, lead to linear increases in K and corresponding inverse changes in λ. These measurements help to elucidate the intimate relationships between the degree of ordering of hydration water, hydration forces, and the mechanical stiffness of polysaccharides. For phytoglycogen, the addition of chemical groups, both cationic and anionic, produced significant increases in its water holding capacity and mechanical properties, suggesting that chemical modification can be used to tune the properties of phytoglycogen for different applications.

Influence of Kosmotrope and Chaotrope Salts on Water Structural Relaxation.

The structural relaxation in water solutions of kosmotrope (structure maker) and chaotrope (structure breaker) salts, namely sodium chloride, potassium chloride, and cesium chloride, were studied through quasielastic neutron scattering measurements. We found that the collective dynamics relaxation time at the structure factor peak obtained using heavy water solutions shows a distinctively different behavior in the kosmotrope as opposed to the chaotrope solutions, increasing with the salt concentration in the former and decreasing in the latter. In both cases the trends are proportional to the concentration dependence of the relative viscosity of the solutions. These results indicate that kosmotropes and chaotropes influence the solution's viscosity by impacting in opposite ways the hydrogen bond network of water, strengthening it in one case and softening it in the other.

Atropisomeric Hydrogen Bonding Control for CO2 Binding and Enhancement of Electrocatalytic Reduction at Iron Porphyrins.

The manipulation of the second coordination sphere for improving the electrocatalytic CO2 reduction has led to breakthroughs with hydrogen bonding, local proton source, or electrostatic effects. We have developed two atropisomers of an iron porphyrin complex with two urea functions acting as multiple hydrogen-bonding tweezers to lock the metal-bound CO2 in a similar fashion found in the carbon monoxide dehydrogenase (CODH) enzyme. The αα topological isomer with the two urea groups on the same side of the porphyrin provides a stronger binding affinity to tether the incoming CO2 in comparison to the αβ disposition. However, the electrocatalytic activity of the αβ atropisomer outperforms its congener with one of the highest reported turnover frequencies at low overpotential. The strong H/D kinetic isotope effect (KIE) observed for the αα system indicates the existence of a tight water hydrogen-bonding network for proton delivery which is disrupted by addition of an acid source. The small H/D KIE for the αβ isomer and the enhanced electrocatalytic performance on addition of stronger acid indicate the free access of protons to the bound CO2 on the opposite side of the urea arm.

Mechanistic insights of evaporation-induced actuation in supramolecular crystals.

Water-responsive materials undergo reversible shape changes upon varying humidity levels. These mechanically robust yet flexible structures can exert substantial forces and hold promise as efficient actuators for energy harvesting, adaptive materials and soft robotics. Here we demonstrate that energy transfer during evaporation-induced actuation of nanoporous tripeptide crystals results from the strengthening of water hydrogen bonding that drives the contraction of the pores. The seamless integration of mobile and structurally bound water inside these pores with a supramolecular network that contains readily deformable aromatic domains translates dehydration-induced mechanical stresses through the crystal lattice, suggesting a general mechanism of efficient water-responsive actuation. The observed strengthening of water bonding complements the accepted understanding of capillary-force-induced reversible contraction for this class of materials. These minimalistic peptide crystals are much simpler in composition compared to natural water-responsive materials, and the insights provided here can be applied more generally for the design of high-energy molecular actuators.