Adjacent Water Molecules Research Articles

Proton Coulomb Blockade Effect Involving Covalent Oxygen-Hydrogen Bond Switching.

Instead of the canonical Grotthuss mechanism, we show that a knock-on proton transport process is preferred between organic functional groups (e.g., -COOH and -OH) and adjacent water molecules in biological proton channel and synthetic nanopores through comprehensive quantum and classical molecular dynamics simulations. The knock-on process is accomplished by the switching of covalent O─H bonds of the functional group under externally applied electric fields. The proton transport through the synthetic nanopore exhibits nonlinear current-voltage characteristics, suggesting an unprecedented proton Coulomb blockade effect. These findings not only enhance the understanding of proton transport in nanoconfined systems but also pave the way for the design of a variety of proton-based nanofluidic devices.

Exploring the aqueous solubility and intermolecular interactions of diclofenac Diethylammonium: A molecular modeling study in solid state and solvation processes

Diclofenac, a widely used non-steroidal anti-inflammatory drug with analgesic, anti-inflammatory, and antipyretic properties, presents a challenge in oral administration due to its low aqueous solubility and subsequent low bioavailability. This issue, primarily attributed to the drug's high hydrophobicity, can lead to adverse side effects. To address this, our study delves into the aqueous solvation process of diclofenac through molecular modeling, employing both Carr-Parrinello molecular dynamics and Density Functional Theory. This combined approach enables a comprehensive investigation of the molecular interactions that influence solubility, encompassing non-polar interactions (van der Waals dispersion forces), dipole interactions, and hydrogen bonding. Our results highlight the formation of intermolecular interactions with water molecules through OH⋯Owater and CO⋯Hwater hydrogen bonds. Additionally, we observe intramolecular hydrogen bonds within diclofenac (NH⋯OH and NH⋯Cl) and weaker interactions involving CH⋯Cl. Notably, the protonation of diclofenac contributes to molecular rigidity, hindering hydrogen bonding with adjacent water molecules further. These insights offer a deeper understanding of the solubility challenges associated with diclofenac, paving the way for improved drug formulations that enhance bioavailability. The application of Carr-Parrinello molecular dynamics and density functional theory in this study highlights their valuable role in addressing complex drug solubility and design issues.

A moisture-absorbing cellulose nanofibril-based foam via ambient drying for high-performance dehumidification

Hygroscopic salt is often used as an important functional component of moisture-absorbing materials because of its excellent capability of capturing water from the air. However, hygroscopic salt cannot store large amounts of condensed water and has poor structural stability, as it dissolves easily in the condensate. The droplets leak from porous composites, resulting in hygroscopic salt consumption and poor water uptake. Herein, we aimed to develop a porous moisture-absorbing foam, which consists of a hydrophilic cellulose nanofibril (CNF)/4A molecular sieve network functionalized by hygroscopic lithium chloride (LiCl), using an ambient drying method. The hygroscopic LiCl considerably enhanced the moisture absorption of the porous foam, while strong hydrophilic CNFs captured the adjacent water molecules via hydrogen bonding and transported the condensed water to the inner part of the foam. The synergistic effect of LiCl and the CNF/4A molecular sieve network was critical for the air dehumidification performance, conferring the foam with excellent water uptake ability of 0.74 g/g within 8 h at 50 % relative humidity (RH). The liquefied water was confined completely in the porous foam during the moisture sorption process, thereby achieving good cyclic stability (10 cycles). Even when the volume was equivalent to 120 × of the volume of one foam, the RH was reduced by the foam from 55 to 58 % to 28–31 % (within 23 min) and then maintained stably up to 8 h. The foam possessed better dehumidification ability than desiccant wheel and silica gel, indicating that it may be used for air dehumidification and environmental humidity management.

Interplay of two low-barrier hydrogen bonds in long-distance proton-coupled electron transfer for water oxidation.

D1-Tyr161 (TyrZ) forms a low-barrier H-bond with D1-His190 and functions as a redox-active group in photosystem II. When oxidized to the radical form (TyrZ-O•), it accepts an electron from the oxygen-evolving Mn4CaO5 cluster, facilitating an increase in the oxidation state (Sn; n = 0-3). In this study, we investigated the mechanism of how TyrZ-O• drives proton-coupled electron transfer during the S2 to S3 transition using a quantum mechanical/molecular mechanical approach. In response to TyrZ-O• formation and subsequent loss of the low-barrier H-bond, the ligand water molecule at the Ca2+ site (W4) reorients away from TyrZ and donates an H-bond to D1-Glu189 at Mn4 of Mn4CaO5 together with an adjacent water molecule. The H-bond donation to the Mn4CaO5 cluster triggers the release of the proton from the lowest pKa site (W1 at Mn4) along the W1…D1-Asp61 low-barrier H-bond, leading to protonation of D1-Asp61. The interplay of the two low-barrier H-bonds, involving the Ca2+ interface and forming the extended Grotthuss-like network [TyrZ…D1-His190]-[Mn4CaO5]-[W1…D1-Asp61], rather than the direct electrostatic interaction, is likely a basis of the apparent long-distance interaction (11.4 Å) between TyrZ-O• formation and D1-Asp61 protonation.

NMR Analyses of Carbohydrate–Water and Water–Water Interactions in Water/DMSO Mixed Solvents, Highlighting Various Hydration Behaviors of Monosaccharides Glucose, Galactose and Mannose

Abstract Interaction with water molecules is a potential factor for regulating carbohydrate functions. We analyzed the influences of methyl α-glucoside, methyl α-galactoside and methyl α-mannoside on water in solution through NMR measurements. In order to compare the hydration behaviors according to the geometric characteristics of monosaccharides, proton exchanges between the carbohydrate and water and between water molecules were observed using H2O/D2O and dimethylsulfoxide mixed solvents to employ deuterium-induced isotope shifts. 13C NMR analyses focused on the carbohydrate hydroxy groups revealed that the carbohydrate–water proton exchange in the mannoside solution proceeded slower than in others. Meanwhile, the frequent proton exchange between waters in the mannoside solution was shown by NMR observations of water signals. Our NMR experimental results shed light on the variation of solvation environments of carbohydrates according to their geometric characteristics. Mannose presumably allows for unique orientations of the adjacent water molecules to induce the expansion of water networks efficiently.

Molecular and Supramolecular Structure of a New Luminescent Hybrid Compound: (C5N2H14)2[BiBr6]Br·H2O

The reaction of homopiperazine, C5N2H12, with BiBr3 in strong hydrobromic acid affords a new organic-inorganic hybrid (C5N2H14)2[BiBr6]Br·H2O. It crystallizes in the orthorhombic space group, Pbca, with unit cell dimensions of a = 15.0775 (2), b = 15.7569 (2), and c = 20.7881 (4) Å, and eight formula units per unit cell. The crystal structure features slightly distorted octahedral BiBr63− and monoatomic Br− anions in the inorganic substructure and C5N2H142+ dications and adjacent water molecules in the organic substructure. Various weak interactions that include (N)H···Br, (N)H···O, and (O)H···Br hydrogen bonds ensure the assembling of the structural moieties into a 3D supramolecular structure. (C5N2H14)2[BiBr6]Br·H2O shows two emission bands in the photoluminescence spectrum, a rather narrow deep-blue PL at 432 nm, and a broadband red PL centered at 650 nm. Their nature and relations to the crystal structure are discussed in this paper.

Molecular dynamics simulation of CO2 hydrate growth in salt water

To achieve the “carbon peaking and carbon neutrality goals”, carbon capture, utilization, and storage (CCUS) is a research hotspot. In our work, molecular dynamics simulation method is used to simulate the CO2 hydrate growth in NaCl aqueous solution with pure structure I CO2 hydrate as seed, at a temperature of 275 K, a pressure of 10 MPa, and a total simulation time of 5000 ns. It was found that not all water molecules participated in the formation of hydrate. The F3 and F4 order parameters and cage numbers proved the formation of structure I CO2 hydrate. According to independent gradient model based on Hirshfeld partition (IGMH) analysis, one water molecule could form four H-bonds with adjacent water molecules in a perfect hydrate; single Cl− could form multiple H-bonds with adjacent water molecules; but the specific water molecule which was near the Cl− might not form four H-bond with its adjacent water molecules, resulting in the inability to form a perfect hydrate and thus water molecules remain liquid; Na+ does not participate in the formation of hydrates. In addition, Na+ and Cl− always come in pairs, so we do believe that NaCl always act as hydrate inhibitor, regardless of its concentration. This is the mechanism how hydrate inhibitor works and plays a significant guiding role in developing highly effective hydrate inhibitors. From the perspective of binding energies of H-bonds, we believe that HOH···Cl− is stronger than HOH···OH2. The density of CO2 hydrate is higher than that of seawater, which could help CO2 hydrate sink spontaneously on the seabed.

Gas-liquid asynchronous cooling promoting gas hydrate formation with high energy efficiency and its promoting mechanism

Hydrate technology has a bright future in the development of high quality production and life for human being. However, the slow hydrate formation rate and low gas consumption are the biggest two obstacles to the commercial application of the technology. In this study, the macro experimental investigation, simulation calculation and microscopic analysis are combined to study the process of the hydrate formation and the effects of gas molecules at different cooling ways on the hydrate nucleation process from the perspective of the transformation of free-water to bound-water. Macroscopically, the difference of gas–liquid temperature makes the heat transfer process between gas and liquid at the interface more active, which is more conducive to the diffusion of gas to liquid; and microscopically, the transformation of free-water to bound-water and the distance between oxygen atoms dOO of adjacent water molecules in the hydrate nucleation are the two key factors affecting the rate of hydrate formation and gas consumption. The results of this study not only propose a more efficient hydrate formation way, but also provide direction for solving the key bottleneck of hydrate technology so that it possible for the hydrate technology from laboratory research to industrial application.

Atomistic insights into the performance of thermodynamic inhibitors in the nucleation of methane hydrate

Figure TOC Comparison of methane hydrate nucleation process (a) without or (b) with EG molecules. Critical nucleus size increase under the influence of Thermodynamic hydrate inhibitors. • Hydrophobic groups from the alcohols could approach the initial hydrate cages and destroy initial clusters. • The –OH groups were observed to form hydrogen bonds with the cage clusters and even initiate a new hydrate cage. • Alcohols can increase the critical nucleus size of gas hydrate. Thermodynamic inhibitors are intensively used in oil and gas pipelines to modify the formation conditions of gas hydrate, preventing the blockage of pipelines. However, their kinetic performance in hydrate nucleation is largely unclear. Herein, the molecular interactions of the small molecules of ethylene glycol and methanol with hydrate clusters were investigated. It was found that the hydrophobic groups from the glycols could approach the initial hydrate cages, thereby constricting the regional distribution of adjacent water molecules; thus, they functioned in the same way as the guest molecules that transiently helped to stabilize the water framework. However, these glycols would eventually dissolve into the solution to stay at the water/nanobubble interface; this would consequently destroy the initial cages upon losing the constraint from the surrounding hydrophobic molecules. In addition, the –OH groups were observed to form hydrogen bonds with the cage clusters and even initiate a new hydrate cage; however, they cannot stably reside there due to different atom coordination. Notably, these glycols can increase the critical nucleus size, which is considered the intrinsic mechanism of thermodynamic inhibition. Our results provide atomistic insights into the performance of glycols in the kinetic nucleation of gas hydrates and can help understand the interactions between guest and host molecules in the presence of hydrophobic and hydrophilic functional groups.

Demonstrating the Interfacial Polymer Thermal Transition from Coil-to-Globule to Coil-to-Stretch under Shear Flow Using SFG and MD Simulation.

Revealing interfacial shear-induced structural responsiveness has long been an important topic in that most fluids in nature and human life are in motion and cause interesting boundary phenomena. It is amazing how the polymer chain conformation or local structural features at a boundary change under the effective shear condition. In this study, microfluidic-assisted sum frequency generation (SFG) vibrational spectroscopy and all-atom molecular dynamics (MD) simulation are combined to reveal that the shear flow can effectively block the so-called thermal coil-to-globule transition of the poly(N-isopropylacrylamide) (PNIPAM) brushes on the solid substrate, and the normal coil-to-globule transition transfers to a coil-to-stretch one under shear flow with increasing ambient temperature. Such findings are attributed to the balance between the shear flow and the molecular interaction with respect to the polymer chains and adjacent water molecules, thus demonstrating the significant effect of the shear flow on the structural and dynamic behaviors of the polymer chains at the boundaries from the molecular level.

Isolation and Identification of Pseudo Seven-Coordinate Ru(III) Intermediate Completing the Catalytic Cycle of Ru-bda Type of Water Oxidation Catalysts

Isolation and Identification of Pseudo Seven-Coordinate Ru(III) Intermediate Completing the Catalytic Cycle of Ru-bda Type of Water Oxidation Catalysts

Unfolding of Dynamical Events in the Early Stage of Insulin Dimer Dissociation.

The dissociation of an insulin dimer is an important biochemical event that could also serve as a prototype of dissociations in similar biomolecular assemblies. We use a recently developed multidimensional free energy landscape for insulin dimer dissociation to unearth the microscopic and mechanistic aspects of the initial stages of the process that could hold the key to understanding the stability and the rate. The following sequence of events occurs in the initial stages: (i) The backbone hydrogen bonds break partially at the antiparallel β-sheet junction, (ii) the two α-helices (chain B) move away from each other while several residues (chain A) move closer, and (iii) a flow of adjacent water molecules occurs into the junction region. Interestingly, the intermonomeric center-to-center distance does not increase, but the number of native contacts exhibits a sharp decrease. Subsequent steps involve further disengagement of hydrophobic groups. This process is slow because of an entropic bottleneck created by the existence of the large configuration space available in the native state (NS), which is inhabited by low-frequency conformational fluctuations. We carry out a density-of-states analyses in the dimer NS to unearth distinctive features not present in the monomers. These low-frequency modes are also responsible for a large entropic stabilization of the NS. Hydrophobic disengagement in the early stage leads to the formation of a twisted intermediate state which itself is a metastable minimum (IS-1). The subsequent progress leads to another dimeric complex (IS-2), which is on the dissociative pathway and characterized by a further decrease in the native contacts. The dissociation process provides insights into the workings of a biomolecular assembly.

Ground-State Structures of Hydrated Calcium Ion Clusters From Comprehensive Genetic Algorithm Search.

We searched the lowest-energy structures of hydrated calcium ion clusters Ca2+(H2O)n (n = 10–18) in the whole potential energy surface by the comprehensive genetic algorithm (CGA). The lowest-energy structures of Ca2+(H2O)10–12 clusters show that Ca2+ is always surrounded by six H2O molecules in the first shell. The number of first-shell water molecules changes from six to eight at n = 12. In the range of n = 12–18, the number of first-shell water molecules fluctuates between seven and eight, meaning that the cluster could pack the water molecules in the outer shell even though the inner shell is not full. Meanwhile, the number of water molecules in the second shell and the total hydrogen bonds increase with an increase in the cluster size. The distance between Ca2+ and the adjacent water molecules increases, while the average adjacent O-O distance decreases as the cluster size increases, indicating that the interaction between Ca2+ and the adjacent water molecules becomes weaker and the interaction between water molecules becomes stronger. The interaction energy and natural bond orbital results show that the interaction between Ca2+ and the water molecules is mainly derived from the interaction between Ca2+ and the adjacent water molecules. The charge transfer from the lone pair electron orbital of adjacent oxygen atoms to the empty orbital of Ca2+ plays a leading role in the interaction between Ca2+ and water molecules.

Strong anisotropy in aqueous salt solutions revealed by terahertz-induced Kerr effect

Terahertz Kerr effect technology, as a novel tool, is expected to study the low-frequency molecular dynamics of liquids since it can directly distinguish the time-resolved anisotropy information on the sub-picosecond scale. Here, this technology is used to measure a variety of aqueous salt solutions and observe the effects of different anions and cations on the structure and dynamics of water network. The obtained bipolar anisotropic response increases under the influence of multiple ions, which is mainly due to the energy transfer between the permanent dipole moment rotation of water molecules and the restricted translational motion of adjacent water molecules with THz electric field excitation. The classic viscosity-related coefficient B is used to analyze the amplitude and characteristics of the obtained anisotropic response, which implies the relationship between the intermolecular hydrogen bond dynamics and the macroscopic thermodynamic properties in the ionic aqueous solution. This work provides a new perspective for observing the low-frequency molecular motion in aqueous salt solutions.

Two Distinct Oxygen-Radical Conformations in the X-ray Free Electron Laser Structures of Photosystem II

We report the existence of two distinct oxygen-radical-containing Mn4CaO5/6 conformations with short O···O bonds in the crystal structures of the oxygen-evolving enzyme photosystem II (PSII), obtained using an X-ray free electron laser (XFEL). A short O···O distance of <2.3 Å between the O4 site of the Mn4CaO5 complex and the adjacent water molecule (W539) in the proton-conducting O4-water chain was observed in the second flash-induced (2F) XFEL structure (2F-XFEL), which may correspond to S3. By use of a quantum mechanical/molecular mechanical approach, the OH• formation at W539 and the short O4···OW539 distance (<2.3 Å) were reproduced in S2 and S3 with reduced Mn1(III), which lacks the additional sixth water molecule O6. As the O•- formation at O6 and the short O5···O6 distance (1.9 Å) have been reported in another 2F-XFEL structure with reduced Mn4(III), two distinct oxygen-radical conformations exist in the 2F-XFEL crystals.

Ion-exchange mechanisms and interfacial reaction kinetics during aqueous corrosion of sodium silicate glasses

The ion-exchange and associated interfacial reaction mechanisms of silicate glasses are critical in elucidating their aqueous corrosion behaviors, surface modification and property changes, hence have potential impact on both science and technology. This work reports findings of the atomic and nanoscale details of the glass–water interfacial reactions revealed by applying reactive force field (ReaxFF) based molecular dynamics (MD) simulations, from which the key mechanisms of the ion exchange, as well as the kinetics of associated interfacial reactions, are elucidated. It was found that the Na+ and H+ ion exchange can happen between two oxygen ions on a single silicon oxygen tetrahedron or adjacent tetrahedra. In addition, the clustered reaction of two non-bridging oxygens mediated by an adjacent water molecule was also identified. The latter reaction might be the main mechanism of water transport after initial surface reactions that consume the non-bridging oxygen species on the surface. Water molecules thus can play two roles: as an intermediate during the proton transfer processes and as a terminator of the clustered reactions. Statistical analyses were performed to obtain reaction kinetics and the results show that silanol formation is a more favored process than the silanol re-formation within the first 3 ns of interfacial reactions. The results obtained thus shed lights on the complex ion-exchange mechanisms during glass hydration and enable more detailed understanding of the corrosion and glass–water interactions of silicate glasses.

5-Methoxyquinoline Photobasicity Is Mediated by Water Oxidation.

A mechanism explaining the photobasicity of 5-methoxyquinoline (5-MeOQ) is proposed on the basis of nonadiabatic molecular dynamics simulations using time-dependent hybrid density functional theory (TDDFT) and fewest switches surface hopping (SH) and analysis of existing ultrafast spectroscopy experiments. According to the TDDFT-SH simulations, the rate-determining step is hole transfer from photoexcited 5-MeOQ to adjacent water molecules within ∼5 ps followed by rapid electron-coupled proton transfer and deactivation to the ground state. This fast redox-catalyzed proton transfer mechanism is consistent with simple thermodynamic arguments, correlated wavefunction calculations, and recent isotope substitution time-resolved fluorescence experiments. Although energetically feasible, direct protonation of 5-MeOQ in the S1 state appears to be too slow to contribute significantly to 5-MeOQ photobasicity in aqueous solution.

Computational spectroscopy of trehalose, sucrose, maltose, and glucose: A comprehensive study of TDSS, NQR, NOE, and DRS.

The bioprotective nature of monosaccharides and disaccharides is often attributed to their ability to slow down the dynamics of adjacent water molecules. Indeed, solvation dynamics close to sugars is indisputably retarded compared to bulk water. However, further research is needed on the qualitative and quantitative differences between the water dynamics around different saccharides. Current studies on this topic disagree on whether the disaccharide trehalose retards water to a larger extent than other isomers. Based on molecular dynamics simulation of the time-dependent Stokes shift of a chromophore close to the saccharides trehalose, sucrose, maltose, and glucose, this study reports a slightly stronger retardation of trehalose compared to other sugars at room temperature and below. Calculation and analysis of the intermolecular nuclear Overhauser effect, nuclear quadrupole relaxation, dielectric relaxation spectroscopy, and first shell residence times at room temperature yield further insights into the hydration dynamics of different sugars and confirm that trehalose slows down water dynamics to a slightly larger extent than other sugars. Since the calculated observables span a wide range of timescales relevant to intermolecular nuclear motion, and correspond to different kinds of motions, this study allows for a comprehensive view on sugar hydration dynamics.

Molecular Dynamics Simulation of Surfactant Flooding Driven Oil-Detachment in Nano-Silica Channels.

Recovery of crude oil in rock nanopores plays an important role in the petroleum industry. In this work, we carried out molecular dynamics (MD) simulations to study the process of ionic surfactant solution driven oil-detachment in model silica (SiO2) nanochannels. Our MD simulation results revealed that the oil-detachment induced by the ionic surfactant flooding can be described by a three-stage process including the formation and delivery of surfactant micelles, the surfactant micelle disintegration-spread and migration on the oil-aggregate surface, and oil molecular aggregate deformation-to-detachment. A flooding from rear (FFR) phenomenon is revealed that the surfactant molecules tend to migrate to the rear bottom of the oil molecular aggregate caused by the water flow effect and hydration of polar head groups of surfactants, which facilitate the penetration of water molecules into the oil-rock interface, and the oil molecule detachment occurs at the rear bottom of the oil molecular aggregate. The present MD simulation results also indicate that the dodecyl benzenesulfonate (SDBS) has higher oil-driven efficiency than that of dodecyl trimethylammonium bromide (DTAB). The difference of oil displacement efficiency between the two surfactants is attributed to the hydration property of the polar head groups. Compared with the -N(CH3)3+ headgroup in DTAB, the bare O atom in the -SO3- group has a stronger H bond interaction with the surrounding water molecules. The stronger interaction between the headgroup of SDBS and the adjacent water molecule results in the surfactant migrating to the rear bottom of the oil molecules more quickly, thus accelerating the detachment of oil molecules.

Photoinduced hydrogen-transfer reactions in pyridine-water clusters: Insights from excited-state electronic-structure calculations

Recent experiments have shown that photoexcited pyridine can abstract a hydrogen atom from a water molecule in pyridine-water clusters containing at least four water molecules. To explain these findings, we explored the electron-driven proton-transfer reaction from water to pyridine in pyridine-(H2O)n, n = 1–4, complexes with ab initio methods. It is shown that the photoinduced electron/proton transfer reaction is energetically possible for all clusters. The calculations reveal that the hydrogen bond between pyridine and the adjacent water molecule is weakened (strengthened) in the 1nπ∗ (1ππ∗) excited state, which is unfavorable (favorable) for the H-atom transfer reaction. For pyridine-(H2O)n clusters with n = 1–3, the steepest descent path leads to a local minimum of 1nπ∗ character, while for the pyridine-(H2O)4 cluster, this path leads to a local minimum of 1ππ∗ character. The transition state calculations show the presence of this 1ππ∗ minimum substantially reduces the barrier height for the H-atom transfer reaction. These results provide a tentative explanation of the experimental observations.