Clusters Of Water Molecules Research Articles

Could the presence of sodium ion influence the accuracy and precision of the ligand-posing in the human A2A adenosine receptor orthosteric binding site using a molecular docking approach? Insights from Dockbench.

The allosteric modulation of G protein-coupled receptors (GPCRs) by sodium ions has received considerable attention as crystal structures of several receptors, in their inactive conformation, show a Na+ ion bound to specific residues which, in the human A2A adenosine receptor (hA2A AR), are Ser913.39, Trp2466.48, Asn2807.45, and Asn2847.49. A cluster of water molecules completes the coordination of the sodium ion in the putative allosteric site. It is absolutely consolidated that the progress made in the field of GPCRs structural determination has increased the adoption of docking-driven approaches for the identification or the optimization of novel potent and selective ligands. Despite the extensive use of docking protocols in virtual screening approaches, to date, almost any of these studies have been carried out without taking into account the presence of the sodium cation and its first solvation shell in the putative allosteric binding site. In this study, we have focused our attention on determining how the presence of sodium ion binding and additionally its first hydration sphere, in hA2AAR could influence the ligand positioning accuracy during molecular docking simulations for most of the available resting and activated hA2A AR crystal structures, using DockBench as a comparative benchmarking tool and implementing a new correlation coefficient (EM). This work provides indications on the evidence that the posing performance (accuracy and/or precision) of the docking protocols in reproducing the crystallographic poses of different hA2A AR antagonists is generally increased in the presence of the sodium cation and its first solvation shell, in agreement with experimental observations. Consequently, the inclusion of sodium ion and its first solvation shell should be considered in order to facilitate the selection of new potential ligands in all molecular docking-based virtual screening protocols that aim to find novel GPCRs antagonists and inverse agonists.

Steric effect of water molecule clusters on electrostatic interaction and electroosmotic transport in aqueous electrolytes: A mean-field approach

We theoretically study the size effect of water molecule clusters not only on electrostatic interaction between two charged surfaces in an aqueous electrolyte but also on electroosmotic transport in a nanofluidic channel. Applying a free energy based mean-field approach accounting for different sizes of ions and water molecule clusters, we derive a set of coupled equations to compute electrostatic and electroosmotic properties between charged surfaces. We verify that the smaller the size of a water cluster, the stronger the electroosmotic transport in nanofluidic channels. In addition, we find that an increase in size of a water cluster yields a decrease in electrostatic interaction strength between similar or oppositely charged planar surfaces.

A mixed valence copper coordination polymer with a new highly self-penetrated topology

Crystals of {[Cu5(oba)4(bpmp)3(H2O)2]·10H2O}n(1, oba = oxybisbenzoate, bpmp = bis(4-pyridylmethyl)piperazine) were prepared by hydrothermal methods. A single-crystal structure determination showed the presence of [Cu5(oba)4(H2O)2]n ribbons with {Cu2(OCO)4} paddlewheel dimers connected to isolated divalent copper atoms and isolated monovalent copper atoms. These ribbon motifs are pillared into the full complicated 3D coordination polymer net of 1 by long-spanning bpmp tethers. Compound 1 presents the unique example of a self-penetrated 3,4,4-connected (83)2(6.8.104)(64.8.10) topology. Decameric water molecule clusters entrained within the net play an important stabilization role.

Understanding the Role of Hydrophobic Terminal in the Hydrogen Bond Network of the Aqueous Mixture of 2,2,2-Trifluoroethanol: IR, Molecular Dynamics, Quantum Chemical as Well as Atoms in Molecules Studies

The aqueous mixture of 2,2,2-trifluoroethanol (TFE) is one of the important alcoholic solvents which has been extensively used for understanding the stability of proteins as well as several chemical reactions. In this paper, the deconvolution of the IR lines in the OH-stretching region has been applied to understand the local structure of water-water, alcohol-water, and alcohol-alcohol interactions in the water mixture of TFE and ethanol (ETH). Further, molecular dynamics simulations, quantum chemical calculations, and atoms in molecules analysis have been performed to encode the local structure information obtained from the experimental data. Addition of a small amount of alcohol in a pure aqueous medium enhances the aggregation of water molecules for the case of ETH, whereas the hydrogen bond between TFE and water is the dominant contributor for TFE. The -CF3 substitution changes the orientation and hydrogen-bonding site of water molecules from the hydrophilic OH terminal to the hydrophobic -CF3 terminal of TFE, which decreases the clustering of water molecules as well as enhances the hydrogen bonding between TFE and water. In the TFE-rich region of the water mixture of TFE, the fluorine of the TFE molecules interacts with each other through a weak fluorous interaction which reduces the hydrogen bonding between the -CF3 of TFE and water molecules. These findings about the hydrogen bond network of the water mixture of TFE induced by the hydrophobic -CF3 group provide a stepwise explanation of the unique hydrophobic properties of the trifluoromethyl group containing pharmaceutical molecules.

Insight into hydrogen bonds and characterization of interlayer spacing of hydrated graphene oxide.

The number of hydrogen bonds and detailed information on the interlayer spacing of graphene oxide (GO) confined water molecules were calculated through experiments and molecular dynamics simulations. Experiments play a crucial role in the modeling strategy and verification of the simulation results. The binding of GO and water molecules is essentially controlled by hydrogen bond networks involving functional groups and water molecules confined in the GO layers. With the increase in the water content, the clusters of water molecules are more evident. The water molecules bounding to GO layers are transformed to a free state, making the removal of water molecules from the system difficult at low water contents. The diffuse behaviors of the water molecules are more evident at high water contents. With an increase in the water content, the functional groups are surrounded by fewer water molecules, and the distance between the functional groups and water molecules increases. As a result, the water molecules adsorbed into the GO interlamination will enlarge the interlayer spacing. The interlayer spacing is also affected by the number of GO layers. These results were confirmed by the calculations of number of hydrogen bonds, water state, mean square displacement, radial distribution function, and interlayer spacing of hydrated GO. Graphical Abstract This work research the interaction between GO functional groups and confined water molecules. The state of water molecules and interlayer spacing of graphene oxide were proved to be related to the number of hydrogen bonds.

Fast Rotational Diffusion of Water Molecules in a 2D Hydrogen Bond Network at Cryogenic Temperatures.

Individual water molecules or small clusters of water molecules contained within microporous minerals present an extreme case of confinement where the local structure of hydrogen bond networks are dramatically altered from bulk water. In the zinc silicate hemimorphite, the water molecules form a two-dimensional hydrogen bond network with hydroxyl groups in the crystal framework. Here, we present a combined experimental and theoretical study of the structure and dynamics of water molecules within this network. The water molecules undergo a continuous phase transition in their orientational configuration analogous to a two-dimensional Ising model. The incoherent dynamic structure factor reveals two thermally activated relaxation processes, one on a subpicosecond timescale and another on a 10-100ps timescale, between 70 and 130K. The slow process is an in-plane reorientation of the water molecule involving the breaking of hydrogen bonds with a framework that, despite the low temperatures involved, is analogous to rotational diffusion of water molecules in the bulk liquid. The fast process is a localized motion of the water molecule with no apparent analogs among known bulk or confined phases of water.

Exploring the effect of oxygen-containing functional groups on the water-holding capacity of lignite.

Graphene oxide with different degrees of oxidation was prepared and selected as a model compound of lignite to study quantitatively, using both experiment and theoretical calculation methods, the effect on water-holding capacity of oxygen-containing functional groups. The experimental results showed that graphite can be oxidized, and forms epoxy groups most easily, followed by hydroxyl and carboxyl groups. The prepared graphene oxide forms a membrane-state as a single layer structure, with an irregular surface. The water-holding capacity of lignite increased with the content of oxygen-containing functional groups. The influence on the configuration of water molecule clusters and binding energy of water molecules of different oxygen-containing functional groups was calculated by density functional theory. The calculation results indicated that the configuration of water molecule clusters was totally changed by oxygen-containing functional groups. The order of binding energy produced by oxygen-containing functional groups and water molecules was as follows: carboxyl > edge phenol hydroxyl >epoxy group. Finally, it can be concluded that the potential to form more hydrogen bonds is the key factor influencing the interaction energy between model compounds and water molecules.

Surface Properties of Fluorite in Presence of Water: An Atomistic Investigation.

Density functional theory simulations, including a correction for dispersive interactions, were performed to investigate the adsorption of water on the main cleavage plane of the fluorite, namely, the (111) surface. In the case of a single molecule of water, we observe that the molecular form is preferred over the dissociated one, and absorbs on the surface with an energy of -55 kJ mol-1, including a significant contribution from the dispersion forces. Also, we show that the substitution of a fluorine atom by a hydroxyl group on the surface of fluorite is not energetically favorable. Then, the hydration of the surface in function of the coverage by water molecules was studied in a systematic way. It was shown that the geometries involving the formation of a cluster of water molecules on the surface, with half of the molecules adsorbed, are the most favorable. Finally, ab initio molecular dynamics conducted at 300 K confirms the trends observed at 0 K, albeit the adsorption energies are reduced by about 10 kJ mol-1. Also, we observe that once put in the interaction with a large number of water molecules, half of the calcium atoms at the surface are in close interaction with a water molecule, whereas the rest of the molecules are further away but present a relatively well-defined structure showing similarities with the one of water clusters.

Low-lying excited states by constrained DFT.

Exploiting the machinery of Constrained Density Functional Theory (CDFT), we propose a variational method for calculating low-lying excited states of molecular systems. We dub this method eXcited CDFT (XCDFT). Excited states are obtained by self-consistently constraining a user-defined population of electrons, Nc, in the virtual space of a reference set of occupied orbitals. By imposing this population to be Nc = 1.0, we computed the first excited state of 15 molecules from a test set. Our results show that XCDFT achieves an accuracy in the predicted excitation energy only slightly worse than linear-response time-dependent DFT (TDDFT), but without incurring into problems of variational collapse typical of the more commonly adopted ΔSCF method. In addition, we selected a few challenging processes to test the limits of applicability of XCDFT. We find that in contrast to TDDFT, XCDFT is capable of reproducing energy surfaces featuring conical intersections (azobenzene and H3) with correct topology and correct overall energetics also away from the intersection. Venturing to condensed-phase systems, XCDFT reproduces the TDDFT solvatochromic shift of benzaldehyde when it is embedded by a cluster of water molecules. Thus, we find XCDFT to be a competitive method among single-reference methods for computations of excited states in terms of time to solution, rate of convergence, and accuracy of the result.

The accuracy of ab initio calculations without ab initio calculations for charged systems: Kriging predictions of atomistic properties for ions in aqueous solutions.

Using the machine learning method kriging, we predict the energies of atoms in ion-water clusters, consisting of either Cl- or Na+ surrounded by a number of water molecules (i.e., without Na+Cl- interaction). These atomic energies are calculated following the topological energy partitioning method called Interacting Quantum Atoms (IQAs). Kriging predicts atomic properties (in this case IQA energies) by a model that has been trained over a small set of geometries with known property values. The results presented here are part of the development of an advanced type of force field, called FFLUX, which offers quantum mechanical information to molecular dynamics simulations without the limiting computational cost of ab initio calculations. The results reported for the prediction of the IQA components of the energy in the test set exhibit an accuracy of a few kJ/mol, corresponding to an average error of less than 5%, even when a large cluster of water molecules surrounding an ion is considered. Ions represent an important chemical system and this work shows that they can be correctly taken into account in the framework of the FFLUX force field.

Effect of Urea on Solvation Dynamics and Rotational Relaxation of Coumarin 480 in Aqueous Micelles of Cationic Gemini Surfactants with Different Spacer Groups.

The present work highlights the effect of urea on solvation dynamics and the rotational relaxation of Coumarin 480 (C-480) in the Stern layer of aqueous micelles of cationic gemini surfactants, 12-4(OH)n-12 (n = 0, 1, 2). UV–visible absorption, steady-state fluorescence and fluorescence anisotropy, time-resolved fluorescence and fluorescence anisotropy, and dynamic light scattering measurements have been carried out for this study. The formation of micelles becomes disfavored in the presence of urea at high concentration. Solvation dynamics is bimodal in nature with fast solvation as a major component. The average solvation time increases, reaches a maximum, and then decreases with increasing concentration of urea because the degree of counterion dissociation also follows the same order with the addition of urea in the micellar solution. With increased degree of counterion dissociation, the extent of clustering of water molecules is increased, resulting in slower solvation process. The −OH group present in the spacer group of gemini surfactant controls the rate of solvation by shielding the water molecules from the probe molecules forming hydrogen bond. The microviscosity of micelles is decreased with increasing concentration of urea, as a result of which the rotational relaxation process becomes faster. In the presence of the −OH group in the spacer group, the microviscosity of micelles is enhanced, resulting in longer rotational relaxation time. Rotational relaxation process is bimodal in nature with the major contribution from the fast component to the fluorescence depolarization. Slow rotational relaxation is mainly due to the lateral diffusion of C-480 molecules along the surface of the micelle. The tumbling motion of the micelle as a whole is much slower than the lateral diffusion of C-480. Wobbling motion of C-480 becomes faster with increasing concentration of urea as a result of decreased microviscosity of micelles. The alignment of C-480 molecules in micelles might change with changing microviscosity.

Structure and dynamics of the peptide strand KRFK from the thrombospondin TSP-1 in water.

Theoretical investigations of a solute in liquid water at normal temperature and pressure can be performed at different levels of theory. Static quantum calculations as well as classical and ab initio molecular dynamics are used to completely explore the conformational space for large solvated molecular systems. In the classical approach, it is essential to describe all of the interactions of the solute and the solvent in detail. Water molecules are very often described as rigid bodies when the most commonly used interaction potentials, such as the SPCE and the TIP4P models, are employed. Recently, a physical model based upon a cluster of rigid water molecules with a tetrahedral architecture (AB4) was proposed that describes liquid water as a mixture of both TIP4P and SPCE molecular species that occur in the proportions implied by the tetrahedral architecture (one central molecule versus four outer molecules; i.e., 20% TIP4P versus 80% SPCE molecules). In this work, theoretical spectroscopic data for a peptide strand were correlated with the structural properties of the peptide strand solvated in water, based on data calculated using different theoretical approaches and physical models. We focused on a particular peptide strand, KRFK (lysine-arginine-phenylalanine-lysine), found in the thrombospondin TSP-1, due to its interesting properties. As the activity and electronic structure of this system is strongly linked to its structure, we correlated its structure with charge-density maps obtained using different semi-empirical charge Qeq equations. The structural and thermodynamic properties obtained from classical simulations were correlated with ab initio molecular dynamics (AIMD) data. Structural changes in the peptide strand were rationalized in terms of the motions of atoms and groups of atoms. To achieve this, conformational changes were investigated using calculated infrared spectra for the peptide in the gas phase and in water solvent. The calculated AIMD infrared spectrum for the peptide was correlated with static quantum calculations of the molecular system based on a harmonic approach as well as the VDOS (vibrational density of states) spectra obtained using various classical solvent models (SPCE, TIP4P, and AB4) and charge maps.

Detectability of concentration‐dependent factors by application of PCA. An indicator curve for the determination of important principal components and a post‐correction for transformation of principal components to factors

AbstractA semi empirical model of light absorption for binary liquid mixtures, which includes linear, parabolic, and periodic terms of concentration‐dependent factors, has been developed and applied for investigating the revealability of the factors. Concentration‐dependent near infrared spectra of ethanol‐water mixtures and a two‐component model were decomposed by principal component analysis. Generated from the principal component analysis results and called the mean coefficient of determination, an indicator is introduced for separating the important or systematic principal components with deterministic information (factor PCs) from stochastic principal components originating from spectral noise (error PCs). Moreover, a post‐correction method is proposed to pull the concentration‐dependent factor effects out of the systematic principal components. The first PC of ethanol‐water NIR mixture spectra defines the contributions of clusters of both water and ethanol molecules in the solution to resultant absorbance signals. The second PC includes partial absorptions from ethanol‐water dimers and ethanol‐water‐ethanol trimers. The third PC is assumed to reflect concentration‐dependent restructuring of mixture structure.

Dielectric Jump and Negative Electrostriction in Metallosupramolecular Ionic Crystals

In natural ionic solids, cationic and anionic species are alternately arranged to minimize electrostatic energy. Aggregation of identical ionic species is commonly prohibited due to the repulsive, long-range nature of Coulombic interactions. Recently, we synthesized unique ionic solids, [AuI4CoIII2(dppe)2(d-pen)4]X2·nH2O (dppe = 1,2-bis(diphenylphosphino)ethane, d-pen = d-penicillaminate), in which complex cations are self-assembled into a cationic supramolecular octahedron, while monovalent or divalent inorganic anions are aggregated into an anomalous anionic cluster accommodating several water molecules. This quite unusual aggregation manner originates from various molecular-level non-Coulombic interactions such as hydrogen bonds and CH-π interactions; thus, this class of ionic solids is referred to as non-Coulombic ionic solids, abbreviated as NCISs. Herein, we report that the NCISs with a peculiar charge-separated (CS) structure in a cubic lattice show a negative, isotropic electrostriction phenomenon that has never been found in any ionic solids, as well as an anomalously large relaxer-like dielectric jump phenomenon reaching to an application level of ε′/ε0 ~ 105. The appearance of these phenomena was explained by the cooperative dynamics of inorganic anions and dipolar water molecules in the pliable anionic clusters that are surrounded by a rather robust cationic metallosupramolecular framework with a meso-scopic scale.

On the photocatalytic cycle of water splitting with small manganese oxides and the roles of water clusters as direct sources of oxygen molecules.

We theoretically studied the chemical principles behind the photodynamics of water splitting: 2H2O + 4hν + M → 4H+ + 4e- + O2 + M. To comprehend this simple looking but very complicated reaction, the mechanisms of at least three crucial phenomena, among others, need to be clarified, each of which is supposed to constitute the foundation of chemistry: (i) charge separation (4H+ + 4e-), (ii) the catalytic cycle for essentially the same reactions to be repeated by each of four photon absorptions with a catalyst M, and (iii) the generation of oxygen molecules of spin triplet. We have previously clarified the photodynamical mechanism of charge separation, which we refer to as coupled proton electron-wavepacket transfer (CPEWT), based on the theory of nonadiabatic electron wavepacket dynamics [K. Yamamoto and K. Takatsuka, ChemPhysChem, 2017, 18, 537]. CPEWT gives an idea of how charge separation can be materialized at each single photon absorption. Yet, this mechanism alone cannot address the above crucial items such as (ii) the catalytic cycle and (iii) O2 formation. In the studies of these fundamental processes, we constructed a possible minimal chemical system and perform semi-quantitative quantum chemical analyses, with which to attain insights about the possible mechanisms of photochemical water splitting. The present study has been inspired by the idea underlying the so-called Kok cycle, although we do not aim to simulate photosystem II in biological systems in nature. For instance, we assume here that a catalyst M (actually simple manganese oxides in this particular study) is pumped up to its excited states leading to charge separation by four-time photon absorption, each excitation of which triggers individual series of chemical reactions including the reorganization of the hydrogen-bonding network (cluster) of water molecules surrounding the photocatalytic center. It is shown that in the successive processes of restructuring of the relevant water cluster, the O[double bond, length as m-dash]O bond is formed and consequently an oxygen molecule of spin triplet can be isolated within a range of a given photon energy of about 3.0 eV.

Sub-nanosecond tryptophan radical deprotonation mediated by a protein-bound water cluster in class II DNA photolyases.

Class II DNA photolyases are flavoenzymes occurring in both prokaryotes and eukaryotes including higher plants and animals. Despite considerable structural deviations from the well-studied class I DNA photolyases, they share the main biological function, namely light-driven repair of the most common UV-induced lesions in DNA, the cyclobutane pyrimidine dimers (CPDs). For DNA repair activity, photolyases require the fully reduced flavin adenine dinucleotide cofactor, FADH-, which can be obtained from oxidized or semi-reduced FAD by a process called photoactivation. Using transient absorption spectroscopy, we have examined the initial electron and proton transfer reactions leading to photoactivation of the class II DNA photolyase from Methanosarcina mazei. Upon photoexcitation, FAD is reduced via a distinct (class II-specific) chain of three tryptophans, giving rise to an FAD˙- TrpH˙+ radical pair. The distal Trp388H˙+ deprotonates to Trp388˙ in 350 ps, i.e., by three orders of magnitude faster than TrpH˙+ in aqueous solution or in any previously studied photolyase. We identified a class II-specific cluster of protein-bound water molecules ideally positioned to serve as the primary proton acceptor. The high rate of Trp388H˙+ deprotonation counters futile radical pair recombination and ensures efficient photoactivation.

Mechanism of the formation of microphase separated water clusters in a water-mediated physical network of perfluoropolyether tetraol.

Perfluoropolyether tetraol (PFPE tetraol) possesses a hydrophobic perfluoropolyether chain in the backbone and two hydroxyl groups at each chain terminal, which facilitates the formation of hydrogen bonds with water molecules resulting in the formation an extended physical network. About 3 wt% water was required for the formation of the microphase separated physical network of PFPE tetraol. The mechanism responsible for the microphase separation of water clusters in the physical network was studied using a combination of techniques such as NMR spectroscopy, molecular dynamics (MD) simulations and DSC. MD simulation studies provided evidence for the formation of clusters in the PFPE tetraol physical network and the size of these clusters increased gradually with an increase in the extent of hydration. Both MD simulations and NMR spectroscopy studies revealed that these clusters position themselves away from the hydrophobic backbone or vice versa. The presence of intra- and inter-chain aggregation possibility among hydrophilic groups was evident. DSC results demonstrated the presence of tightly and loosely bound water molecules to the terminal hydroxyl groups of PFPE tetraol through hydrogen bonding. The data from all the three techniques established the formation of a physical network driven by hydrogen bonding between the hydrophilic end groups of PFPE tetraol and water molecules. The flexible nature of the PFPE tetraol backbone and its low solubility parameter favour clustering of water molecules at the terminal groups and result in the formation of a gel.

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 ...

The Influence of Clusters of Water Molecules in Natural Coesite on the Coesite-Quartz Phase Transition: Evidence from TEM and FTIR Investigation

The Influence of Clusters of Water Molecules in Natural Coesite on the Coesite-Quartz Phase Transition: Evidence from TEM and FTIR Investigation

Interfacial Mechanisms of Water Vapor Sorption into Cellulose Nanofibril Films as Revealed by Quantitative Models.

Humidity is an efficient instrument for facilitating changes in local architectures of two-dimensional surfaces assembled from nanoscaled biomaterials. Here, complementary surface-sensitive methods are used to collect explicit and precise experimental evidence on the water vapor sorption into (2,2,6,6-tetramethylpiperidin-1-yl)oxyl (TEMPO) oxidized cellulose nanofibril (CNF) thin film over the relative humidity (RH) range from 0 to 97%. Changes in thickness and mass of the film due to water vapor uptake are tracked using spectroscopic ellipsometry and quartz crystal microbalance with dissipation monitoring, respectively. Experimental data is evaluated by the quantitative Langmuir/Flory-Huggins/clustering model and the Brunauer-Emmett-Teller model. The isotherms coupled with the quantitative models unveil distinct regions of predominant sorption modes: specific sorption of water molecules below 10% RH, multilayer build-up between 10 to 75% RH, and clustering of water molecules above 75% RH. The study reveals the sorption mechanisms underlying the well-known water uptake behavior of TEMPO oxidized CNF directly at the gas-solid interface.