Hydrogen-bonded Water Clusters Research Articles

Water binding and hygroscopicity in π-conjugated polyelectrolytes

The presence of water strongly influences structure, dynamics and properties of ion-containing soft matter. Yet, the hydration of such matter is not well understood. Here, we show through a large study of monovalent π-conjugated polyelectrolytes that their reversible hydration, up to several water molecules per ion pair, occurs chiefly at the interface between the ion clusters and the hydrophobic matrix without disrupting ion packing. This establishes the appropriate model to be surface hydration, not the often-assumed internal hydration of the ion clusters. Through detailed analysis of desorption energies and O–H vibrational frequencies, together with OPLS4 and DFT calculations, we have elucidated key binding motifs of the sorbed water. Type-I water, which desorbs below 50 °C, corresponds to hydrogen-bonded water clusters constituting secondary hydration. Type-II water, which typically desorbs over 50–150 °C, corresponds to water bound to the anion under the influence of a proximal cation, or to a cation‒anion pair, at the cluster surface. This constitutes primary hydration. Type-III water, which irreversibly desorbs beyond 150 °C, corresponds to water kinetically trapped between ions. Its amount varies strongly with processing and heat treatment. As a consequence, hygroscopicity—which is the water sorption capacity per ion pair—depends not only on the ions, but also their cluster morphology.

Effective-mode analysis of the dynamics of weakly bound molecular systems by an example of hydrogen-bonded water clusters

A method for the analysis of internal dynamics of nonlinear weakly bound polymolecular systems based on the effective-mode approach is proposed. The method enables one to estimate the number of the governing collective degrees of freedom of the system of interest at a preset accuracy under particular conditions and analyze the character of the modes depending on the activation energy of the system and the duration of its dynamic propagation, which provides qualitative and quantitative information about the coupling of diverse motions and the respective energy redistribution. The method is applied to the analysis of the dynamics of small water clusters stabilized by hydrogen bonds, which are unique spectacular examples of the systems with a pronounced coupling between the intramolecular and substantially delocalized intermolecular oscillations. The dynamic trajectories were generated in the adiabatic approximation at the Born-Oppenheimer level with the use of the quantum chemical description of selected clusters at the $\mathrm{MP}2/6\ensuremath{-}311++G(d,p)$ level. The initial conditions corresponded to different variants of the excitation of low-frequency normal modes, and the dynamic runs were carried out at a time step of 0.5 fs and the whole duration of 50 to 100 ps. Different prevailing characters of the cluster dynamics were identified depending on the molecular size, the total activation energy, and the mean potential-energy-increment to kinetic-energy-increment ratio, from an efficient accumulation of the excess kinetic energy on the effective modes of the cluster to the dissociation of the cluster into constituting fragments. The signs of the corresponding processes in the overlap matrices of the effective-mode vectors, kinetic-energy distribution over the modes, and the correlation between the number of the modes and the mean kinetic energy of the cluster are distinguished.

Study on the secondary structure and hydration effect of human serum albumin under acidic pH and ethanol perturbation with IR/NIR spectroscopy

Human serum albumin (HSA) is the most abundant protein in plasma and plays an essential physiological role in the human body. Ethanol precipitation is the most widely used way to obtain HSA, and pH and ethanol are crucial factors affecting the process. In this study, infrared (IR) spectroscopy and near-infrared (NIR) spectroscopy in combination with chemometrics were used to investigate the changes in the secondary structure and hydration of HSA at acidic pH (5.6–3.2) and isoelectric pH when ethanol concentration was varied from 0% to 40% as a perturbation. IR spectroscopy combined with the two-dimensional correlation spectroscopy (2DCOS) analysis for acid pH system proved that the secondary structure of HSA changed significantly when pH was around 4.5. What’s more, the IR spectroscopy and 2DCOS analysis showed different secondary structure forms under different ethanol concentrations at the isoelectric pH. For the hydration effect analysis, NIR spectroscopy combined with the McCabe–Fisher method and aquaphotomics showed that the free hydrogen-bonded water fluctuates dynamically, with ethanol at 0–20% enhancing the hydrogen-bonded water clusters, while weak hydrogen-bonded water clusters were formed when the ethanol concentration increased continuously from 20% to 30%. These measurements provide new insights into the structural changes and changes in the hydration behavior of HSA, revealing the dynamic process of protein purification, and providing a theoretical basis for the selection of HSA alcoholic precipitation process parameters, as well as for further studies of complex biological systems.

Research on the secondary structure and hydration water around human serum albumin induced by ethanol with infrared and near-infrared spectroscopy

Given the role of ethanol played in the precipitation of various proteins, it is of great significance for the refined purification of proteins to understand the mechanism of protein secondary structure and hydration effect under the ethanol perturbation. Infrared (IR) spectroscopy and near-infrared (NIR) spectroscopy combined with chemometrics and aquaphotomics were utilized to get a generalized picture of the second structure of human serum albumin (HSA) and the surrounding hydrogen bond network of water after perturbation with different concentrations of ethanol ranging from 0% to 45% (v/v). The two-dimensional correlation (2DCOS) and moving window two-dimensional correlation analysis (MW-2DCOS) of IR spectroscopy provide evidence that the native structure of HSA was stabilized by the formation of α-helical structure at a low concentration of ethanol. However, the formation of intermolecular β-sheet structure by increasing ethanol is an important reason for the aggregation and precipitation of HSA. The analysis of NIR spectroscopy with the McCabe-Fisher method and aquaphotomics showed that free hydrogen bonded water was dynamic and fluctuating, 0%-20% ethanol could enhance the hydrogen bonded water cluster while the increasement of ethanol from 20% to 45% would lead to the formation of weak hydrogen bonded water cluster. These measurements provide a novel perspective on the relationship between ethanol and HSA, which is useful for maintaining activity and improving purity during the purification of proteins or other biological macromolecules.

Ultrafast proton-coupled isomerization in the phototransformation of phytochrome

The biological function of phytochromes is triggered by an ultrafast photoisomerization of the tetrapyrrole chromophore biliverdin between two rings denoted C and D. The mechanism by which this process induces extended structural changes of the protein is unclear. Here we report ultrafast proton-coupled photoisomerization upon excitation of the parent state (Pfr) of bacteriophytochrome Agp2. Transient deprotonation of the chromophore’s pyrrole ring D or ring C into a hydrogen-bonded water cluster, revealed by a broad continuum infrared band, is triggered by electronic excitation, coherent oscillations and the sudden electric-field change in the excited state. Subsequently, a dominant fraction of the excited population relaxes back to the Pfr state, while ~35% follows the forward reaction to the photoproduct. A combination of quantum mechanics/molecular mechanics calculations and ultrafast visible and infrared spectroscopies demonstrates how proton-coupled dynamics in the excited state of Pfr leads to a restructured hydrogen-bond environment of early Lumi-F, which is interpreted as a trigger for downstream protein structural changes.

Percolation transitions of physically and hydrogen bonded clusters in supercritical water

Molecular Dynamics simulations were employed to locate the densities and pressures at which infinitely spanning networks form for both physically and hydrogen bonded water clusters along the 650, 700, 750 and 800 K supercritical isotherms. The SPC/E water model was used and the percolation thresholds were determined by examining the cluster size distributions. Average hydrogen bond numbers for the entire system are reported and are near the critical number of 1.55 expected at the hydrogen bonded percolation threshold. Percolating physical clusters appeared at lower densities than infinite hydrogen bonded networks. Physical and hydrogen bonded percolation thresholds were plotted on the P-ρ and P-T planes. Neither of the lines of percolation transitions match the extension of the vapor-liquid coexistence line into the supercritical region. Empirical relationships were obtained for each transition threshold as functions of temperature as well as density. Activation volumes of diffusion increase rapidly until they reach their maximum at the threshold densities where water molecules are connected via percolating network of hydrogen bonds.

Hydrogen bonding effects on the fluorescence properties of 4′-diethylamino-3-hydroxyflavone in water and water-acetone mixtures

The fluorescence properties of 4′-diethylamino-3-hydroxyflavone (FET), a dye probe sensitive to the polarity as well as the hydrogen bonding ability of its environment, have been studied in acetone-water mixtures by measuring spectra and decay curves over the whole composition range and analyzing the results on the basis of theoretical calculations. In acetone, like in most of organic solvents, the dye showed dual fluorescence, due to an excited state intramolecular proton transfer (ESIPT), in which a quasi-equilibrium between the two excited species, N* and T*, was reached. In acetone-water mixtures with lower molar fractions of water, where the water molecules are largely dispersed, only one type of hydrate could be detected, a complex with 1:1 composition, showing only N* emission, but with a high (0.45) fluorescence quantum yield. At higher water concentrations, the interaction of FET with the hydrogen-bonded water clusters resulted in fluorescence quenching. In neat water the fluorescence quantum yield fell to ~0.001. Theoretical calculations on a FET-acetone complex, a FET-water complex and a FET-water-acetone triple complex (the latter as model for the samples with low water concentrations) concluded that ESIPT was energetically favored in all the models, but the E(N*)-E(T*) energy difference for the water complexes was much lower. The kinetic barrier of ESIPT was found greatly higher in the FET-water complex than in the isolated solute. The intermolecular hydrogen bonds in the water complexes became significantly stronger following the excitation, stabilizing the N* form of the hydrated dye.

Dissociation Constants of Silanol Groups of Silic Acids: Quantum Chemical Estimations

Dissociation constants of silanol groups on the silica surface are calculated with the DFT quantum chemical method using B3LYP and M06 functionals. Structural features of silanol fragments and the presence of hydrogen-bonded water clusters are shown to have significant effects on pKa values of silanol groups. In particular, pKa values are shown to vary widely depending on the features of the system of hydrogen bonds.

Dissociation Mechanism of Water Molecules on the PuO2(110) Surface: An Ab Initio Molecular Dynamics Study

Reactions between water and plutonium oxide play a key role in determining the oxidation and corrosion rates of plutonium materials. We perform consecutive ab initio molecular dynamics simulations with the DFT + U approach, systematically studying the dissociation dynamics and mechanism of water molecule and small clusters on the PuO2(110) surface. The dissociation of water on the surface is found to be a two-step hydroxylation process for both monomer and clusters, but different dissociation mechanisms are revealed. Water monomer dissociation, as the consequence of the hybridizations between the molecular orbitals of water and the electronic state of the surface, needs to overcome a reaction energy barrier of 0.18 eV. In contrast, the dissociations of hydrogen-bonded small water clusters are exothermic by −0.42 eV with no transition energy barrier. Hydrogen-bonding interactions between water molecules facilitate the dissociation process and result in a more stable dissociation state with respect to that ...

Computational Study of the Forces Driving Aggregation of Ultrasmall Nanoparticles in Biological Fluids.

Nanoparticle (NP) aggregation can lead to prolonged retention in tissues or embolism, among other adverse effects. Successful use in biomedicine thus requires the capability to make NPs with limited aggregative potential. Rational design is presently a challenge due to incomplete knowledge of their interactions in biofluids. Recently, ultrasmall gold NPs passivated with endogenous antioxidant glutathione have shown promise for use in vivo. Computer simulations are here conducted to identify the forces underlying aggregation (or lack thereof) of these NPs in a cell culture. Electrostatic interactions are insufficient to induce association, but the van der Waals forces exerted by cations, anions, and net-neutral polar species can promote the formation of stable dimers. The entropic effects of depletion are negligible, but the combined effect of depletion and macromolecular crowding at physiological concentrations can stabilize aggregates containing just a few NPs. Interparticle interactions are controlled by modest changes in both the structure and dynamic of the interfacial liquid. The molecular origin of these effects and their dependence on NP size are described. The liquid is shown to be highly structured, with large and long-lived hydrogen-bonded water clusters developing often in the interparticle space; their potential role as transient, long-range proton wires connecting and enveloping neighboring NPs is discussed. The basis for a parsimonious theory of ultrasmall NPs in complex fluids is established.

Silanol-modified Calix[4]arene Conformers: Syntheses, Structures, and Properties

Organotetrasilanols 6a–6c based on calix[4]arene were synthesized from cone- and 1,3-alternate calix[4]arene tetrapropyl ether 3a and 3b following a modified literature method. X-ray analyses of the tetrasilanols revealed flattened cone- and 1,3-alternate conformational structures 6a, 6b and 6c respectively. Hydrogen-bonded water clusters are included in the crystal lattice and cavity of the cone tetrasilanols 6a and 6b. In solution, the binding structures of the cone tetrasilanols 6a and 6b for chloride ion are estimated by 1H NMR to be larger than that of 1,3-alternate 6c due to its circular hydrogen bonding.

Insights on Clusters Formation Mechanism by Time of Flight Mass Spectrometry. 1. The Case of Ethanol-Water Clusters.

In the present work, water clusters with the addition of an electrophilic molecule such as ethanol have been studied by time of flight mass spectrometry (TOFMS). Mass distributions of molecular clusters of ethanol, water, and ethanol-water mixed clusters were obtained by two different ionization methods: electron ionization (EI) and picosecond laser photo-ionization (PI) at a wavelength of 355 nm. It was shown that short pulse laser ionization increases the signal intensity and promotes the extension of the detected mass range of the clusters in comparison with EI. Much larger clusters were detected in our experiments with respect to the current literature. The autocorrelation function (AF) was introduced in the analysis of the composition of the water clusters in terms of fundamental periodicities for obtaining information on clusters formation mechanisms. Besides, it was found that ethanol molecules are capable of substitutional interaction with hydrogen-bonded water clusters in ethanol-water binary mixtures but the self-association of ethanol was the dominant process. Moreover, the increase of ethanol concentration promotes both the formation of hydrated ethanol clusters and the self-association of ethanol clusters in ethanol-water binary mixtures. The formation of water-rich clusters and subsequent metastable fragmentation were found to be the dominant processes determining the water-rich cluster distribution, irrespective of the ionization process, while the ionization process significantly affects the ethanol-rich cluster distribution.

Structural dynamics and thermostabilization of neurotensin receptor 1.

The neurotensin receptor NTSR1 binds the peptide agonist neurotensin (NTS) and signals preferentially via the Gq protein. Recently, Grisshammer and co-workers reported the crystal structure of a thermostable mutant NTSR1-GW5 with NTS bound. Understanding how the mutations thermostabilize the structure would allow efficient design of thermostable mutant GPCRs for protein purification, and subsequent biophysical studies. Using microsecond scale molecular dynamics simulations (4 μs) of the thermostable mutant NTSR1-GW5 and wild type NTSR1, we have elucidated the structural and energetic factors that affect the thermostability and dynamics of NTSR1. The thermostable mutant NTSR1-GW5 is found to be less flexible and less dynamic than the wild type NTSR1. The point mutations confer thermostability by improving the interhelical hydrogen bonds, hydrophobic packing, and receptor interactions with the lipid bilayer, especially in the intracellular regions. During MD, NTSR1-GW5 becomes more hydrated compared to wild type NTSR1, with tight hydrogen bonded water clusters within the transmembrane core of the receptor, thus providing evidence that water plays an important role in improving helical packing in the thermostable mutant. Our studies provide valuable insights into the stability and functioning of NTSR1 that will be useful in future design of thermostable mutants of other peptide GPCRs.

Hydrogen-bonded cyclic water clusters nucleated on an oxide surface.

We report the observation and molecular-scale scanning probe electronic structure (dI/dV) mapping of hydrogen-bonded cyclic water clusters nucleated on an oxide surface. The measurements are made on a new type of cyclic water cluster that is characterized by simultaneous and cooperative bonding interactions among molecules as well as with both metal and oxygen sites of an oxide surface. Density functional theory + U + D calculations confirm the stability of these clusters and are used to discuss other potential water-oxide bonding scenarios. The calculations show that the spatial distributions of electronic states in the system are similar in character to those of the lowest unoccupied molecular orbitals of hydrogen-bonded water molecules. On the partially oxidized Cu(111) investigated here, experiment and theory together suggest that Cu vacancies in the growing islands of cuprous oxide inhibit water adsorption in the centers of the islands (which have reached thermodynamic equilibrium). A stoichiometric, less stable cuprous oxide likely exists at island edges (the growth front) and selectively binds these water clusters.

Water confinement in faujasite cages: a deuteron NMR investigation in a wide temperature range. 1. Low temperature spectra.

Deuteron NMR spectra were measured for D2O confined in NaX, NaY, and DY faujasites with various D2O loadings at temperatures ranging from T = 70 K to T = 200 K with the aim to study the molecular mobility of confined water as a function of Si/Al ratio and loading. The recorded spectra were fitted with linear combinations of representative spectral components. At low loading, with the number of water molecules per unit cell close to the abundance of sodium cations, a component related to π-jumps of water deuterons about the 2-fold symmetry axis dominated. For loadings at levels 3 times and 5 times higher than the initial loading level, Pake dublets due to rigid water deuterons dominated the recorded spectra. A set of the quadrupole coupling constant values of localized water deuterons was derived from the analysis of the Pake dublets. Their values were attributed to deuteron positions corresponding to the locations at oxygen atoms in the faujasite framework and locations within hydrogen-bonded water clusters inside faujasite cages. The contributions of the different spectral components were observed to change with increasing temperature according to the Arrhenius law with a characteristic dynamic crossover point at T = 165 K. Below T = 165 K a spectral component was observed whose contribution changed with temperature, yielding the activation energy of about 2 kJ/mol, characteristic for jumps between inversion-related water positions in clusters.

Incomplete mixing versus clathrate-like structures: A molecular view on hydrophobicity in methanol–water mixtures

The underlying molecular mechanisms of macroscopic excess properties were studied by molecular dynamics simulations for different compositions of methanol-water mixtures. Structural data (nearest neighbor relationships, clustering analysis) and dynamic data (hydrogen bond lifetimes, rotational autocorrelation, translational diffusion) were evaluated. Nearest neighbor relationships provide quantitative evidence and a pictorial description of incomplete mixing at the molecular level as a source for mixture anomalies, while a comparative study of water surrounding methyl moieties versus water in the bulk-like environment provides evidence against the hydrophobicity model of clathrate-like hydration. Furthermore, the formation or breakdown of the system-wide hydrogen bonding network at a critical threshold of approximately equimolar mixture is perceived to separate the mixture system into two hydrogen bonding regimes: hydrogen-bonded water clusters embedded in methanol for mixtures with low water content and methanol molecules within a system-wide hydrogen-bonded water network for mixtures with high water content.

Redundant internal coordinates, compliance constants and non-bonded interactions – some new insights

A long standing problem in normal mode analysis is identifying the right internal coordinates given only the cartesian coordinates, the masses of the atoms and the cartesian force constants without using any other additional chemical information. A possible solution is suggested here as drawing the normal modes obtained from the mass weighted cartesian force constant matrix and identifying the correct bonds and angles from the normal mode pictures. If chosen properly, the internal coordinates will have minimum mixing in the normal mode representation. This can in principle lead to an automation algorithm. A complete basis of internal coordinates is defined as the minimum number of valence internal coordinates that describe all the normal modes as completely as possible. It was shown in the literature that the relaxed force constants could be used as a measure of bond order in all atom–atom distance coordinates. Some of the bonded and non-bonded atom pairs can have similar values of the relaxed force constants and hence to use the relaxed force constant as a measure of bond order we need to separate the bonded pairs from the non-bonded ones. This needs extra chemical information of which pairs are bonded. The new definition of complete basis of non-redundant valence internal coordinates helps to identify the bonded pairs effectively without extra information. The hydrogen bonded water clusters (H2O)n, n = 2–6, methane dimer and methane–water complex are used as examples to verify that the relaxed force constants of bonded pairs are indeed a measure of bond order. A new definition of a complete basis of valence internal coordinates and a way of choosing them from the normal mode pictures is provided. The meaning of redundancy in redundant internal coordinates is explored. This new definition helps to identify the bonded pairs for which the relaxed force constants are a measure of bond order. Hydrogen bonded clusters are used as examples.

Water clusters in mixed ionic complexes with metal dipicolinate anions

Formations of three different types of hydrogen-bonded water clusters in the interstices of mixed ionic complexes with metal dipicolinate anions are reported. In the complex [Co(phen)2(H2O)2][Zn(dpa)2]⋅7H2O (1) (where phen=1,10-phenanthroline, dpa=dipicolinate), both the cation and anion is hydrophilic in nature, exhibits an unusual 2D infinite cyclic water decamers (H2O)10 stabilized by four identical zinc dipicolinato complex anions. Modulating the cationic unit to a hydrophobic environment by replacing the aqua ligand with 2,2′-bipyridine ligand the water cluster can be modified. The complex [Ni(phen)2⋅bpy][Co(dpa)2]⋅8H2O (2) (where bpy=2,2′-bipyridine) has unprecedented discrete hydrogen bonded hexadecameric (H2O)16 water clusters encapsulated between eight anionic units. A rare wavelike infinite water chain (H2O)n is observed in complex [Co(phen)3][Mn(dpa)2]⋅12H2O (3), in this case the water chain fills the interstitial space created by packing of large hydrophilic anionic units and hydrophobic cationic units. The reported clusters are indefinitely stable in their respective complex at ambient temperature, but the water loss is irreversible when thermally decomposed.

Hidden Optimal Principle in Quantum Mechanics and Quantum Chemistry

Quantum Mechanic axio ms are the result of the microscopic cooperative equilibriu m among sym metric p layers (quantum object and human subject). On the other hand, we introduce Nash's equilibriu m in Hilbert space, which has two characteristics: it is a fixed point and it maximizes a utility function. Moreover, evolution and selfadjoint operators have interesting properties which allow us study steady state in Evolutionary Game Theory. Also, we present cooperative games in co mplex systems language.The concept of cooperation is important in game theory but is somewhat subtle. The term cooperate means to act together, with a common purpose. Incentive compatibility is equivalent synergy principle, which appears naturally (to add or multiply utilit ies, ec(34)). Finally, wein the relevant results not only proved the main theorems of Quantum Mechanics, Quantum Chemistry and its applications salt-water but also we resolved some main questions such us: Do hydrogen-bonded networks, in which tunneling plays an important role, exist?, Ho w cooperation and entropy affect water cluster equilibria?. Can salt (ClNa) p lay an Nobel role in photo-catalysis?. The answers are: tunnel effect it is possible in salt water but not in water, because ClNa, visib le light or electricity incentive produce catalysis or photo-catalysis. Also, If hydrogen-bonded networks and water cluster size increases complexity of an global equilibriu m, then tunnel effect appears as an local equilibriu m.

Structural changes in ethanol–water mixtures: Ultrasonics, Brillouin scattering and molecular dynamics studies

Mixing of two hydrogen-bonded liquids may lead to significant composition dependent changes of liquid microscopic structure, which in turn will be reflected by changes of the corresponding thermodynamic, thermophysical and spectroscopic properties. For the liquid system {xEtOHC2H5OH+(1−xEtOH)H2O} at ambient temperatures and pressures, we show that major structural rearrangements occur in the composition range of 0.15<xEtOH<0.20, where xEtOH denotes the ethanol mole fraction. Most interestingly, in this region, the excess enthalpy shows a minimum, the excess heat capacity at constant pressure shows a maximum, and both the ultrasonic speed and the hypersonic speed exhibit a maximum. In fact, molecular dynamics (MD) simulation results indicate the saturation of ethanol clustering in this low ethanol mole fraction region. The corresponding change of structural/vibrational dynamics is detected by Brillouin scattering, i.e. it is reflected by the observed sound dispersion in the composition region 0.15<xEtOH<0.65, where simulations show micro-segregated distributions of water and ethanol domains that form a bi-continuous mixture. At larger ethanol mole fractions, we found chain-like hydrogen-bonded water clusters.