Water Molecules Research Articles

Toward a numerically efficient description of bulk-solvated anionic states.

We investigate the vertical electron attachment energy (VAE) of 1-methyl-4-nitroimidazole, a model radiosensitizer, employing quantum mechanics/molecular mechanics (QM/MM) and QM/polarized continuum (QM/PCM) solvation models. We considered the solvent-excluded surface (QM/PCM-SES) and Van der Waals (QM/PCM-VDW) cavities within the PCM framework, the electrostatic embedding QM/MM (EE-QM/MM) model, and the self-consistent sequential QM/MM polarizable electrostatic embedding (scPEE-S-QM/MM) model. Due to slow VAE convergence concerning the number of QM solvent molecules, full QM calculations prove inefficient. Ensemble averages in these calculations do not align with VAEs computed for the representative solute-solvent configuration. QM/MM and QM/PCM calculations show agreement with each other for sufficiently large QM regions, although the QM/PCM-VDW model exhibits artifacts linked to the cavity. QM/MM models demonstrate good agreement between ensemble averages and VAEs calculated with the representative configuration. Notably, the VAE computed with the scPEE-S-QM/MM model achieves faster convergence concerning the number of QM water molecules compared to the EE-QM/MM model, attributed to enhanced efficiency from MM charge polarization in the scPEE-S-QM/MM approach. This emphasizes the importance of QM/classical models with accurate solute-solvent and solvent-solvent mutual polarization for obtaining converged VAEs at a reasonable computational cost. The full-QM approach is very inefficient, while the microsolvation model is inaccurate. Computational savings in QM/MM models result from electrostatic embedding and the representative configuration, with the scPEE-S-QM/MM approach emerging as an efficient tool for describing bulk-solvated anions within the QM/MM framework. Its potential extends to improving transient anion state descriptions in biomolecules and radiosensitizers, especially given the frequent employment of microsolvation models.

PyDFT-QMMM: A modular, extensible software framework for DFT-based QM/MM molecular dynamics.

PyDFT-QMMM is a Python-based package for performing hybrid quantum mechanics/molecular mechanics (QM/MM) simulations at the density functional level of theory. The program is designed to treat short-range and long-range interactions through user-specified combinations of electrostatic and mechanical embedding procedures within periodic simulation domains, providing necessary interfaces to external quantum chemistry and molecular dynamics software. To enable direct embedding of long-range electrostatics in periodic systems, we have derived and implemented force terms for our previously described QM/MM/PME approach [Pederson and McDaniel, J. Chem. Phys. 156, 174105 (2022)]. Communication with external software packages Psi4 and OpenMM is facilitated through Python application programming interfaces (APIs). The core library contains basic utilities for running QM/MM molecular dynamics simulations, and plug-in entry-points are provided for users to implement custom energy/force calculation and integration routines, within an extensible architecture. The user interacts with PyDFT-QMMM primarily through its Python API, allowing for complex workflow development with Python scripting, for example, interfacing with PLUMED for free energy simulations. We provide benchmarks of forces and energy conservation for the QM/MM/PME and alternative QM/MM electrostatic embedding approaches. We further demonstrate a simple example use case for water solute in a water solvent system, for which radial distribution functions are computed from 100ps QM/MM simulations; in this example, we highlight how the solvation structure is sensitive to different basis-set choices due to under- or over-polarization of the QM water molecule's electron density.

Dynamics of an aqueous suspension of short hyaluronic acid chains near a DPPC bilayer.

The synergy between hyaluronic acid (HA) and lipid molecules plays a crucial role in synovial fluids, cell coatings, etc. Diseased cells in cancer and arthritis show changes in HA concentration and chain size, impacting the viscoelastic and mechanical properties of the cells. Although the solution behavior of HA is known in experiments, a molecular-level understanding of the role of HA in the dynamics at the interface of HA-water and the cellular boundary is lacking. Here, we perform atomistic molecular dynamics simulation of short HA chains in an explicit water solvent in the presence of a DPPC bilayer, relevant in pathological cases. We identify a stable interface between HA-water and the bilayer where the water molecules are in contact with the bilayer and the HA chains are located away without any direct contact. Both translation and rotation of the interfacial waters in contact with the lipid bilayer and translation of the HA chains exhibit subdiffusive behavior. The diffusive behavior sets in slightly away from the bilayer, where the diffusion coefficients of water and HA decrease monotonically with increase in HA concentration. On the contrary, the dependence on HA chain size is only marginal due to enhanced chain flexibility as their size increases.

Sodium alginate-based coaxial fibers synergistically integrate moisture actuation, length tracing, humidity sensing, and electric heating.

The development of wearable electronics has driven the need for smart fibers with advanced multifunctional synergy. In this paper, we present a design of a multifunctional coaxial fiber that is composed of a biopolymer-derived core and an MXene/silver nanowire (AgNW) sheath by wet spinning. The fiber synergistically integrates moisture actuation, length tracing, humidity sensing, and electric heating, making it highly promising for portable devices and protective systems. The biopolymer-derived core provides deformation for moisture-sensitive actuation, while the MXene/AgNW sheath with good conductivity enables the fiber to perform electric heating, humidity sensing, and self-sensing actuation. The coaxial fiber can be programmed to rapidly desorb water molecules to shrink to its original length by using the MXene/AgNW sheath as an electrical heater. We demonstrate proof-of-concept applications based on the multifunctional fibers for thermal physiotherapy and wound healing/monitoring. The sodium alginate@MXene-based coaxial fiber presents a promising solution for the next-generation of smart wearable electronics.

Under the Influence of Water: Molecular Recognition of Organic Hydrophilic Molecules in Water with a Prismarene Host Driven by Hydration Effects.

A water-soluble prism[5]arene host can form endo-cavity complexes with hydrophilic organic substances in water by displacing frustrated water molecules from its deep cavity. Water molecules structured at both rims of the prismarene host can mediate hydrogen bonding interactions with the guest. Water-mediated hydrogen bonding interactions were invoked here to elucidate the elevated binding affinities and selectivity of the prismarene host toward hydrophilic organic guests. We show that water at the interface of a host-guest complex can act as an extension of the host structure, facilitating the accommodation of neutral guests within the binding site. This study highlights the crucial role of water in facilitating supramolecular interactions between a deep-cavity prismarene host and organic hydrophilic guests in aqueous medium.

Mechanical release of homogenous proteins from supramolecular gels

A long-standing challenge is how to formulate proteins and vaccines to retain function during storage and transport and to remove the burdens of cold-chain management. Any solution must be practical to use, with the protein being released or applied using clinically relevant triggers. Advanced biologic therapies are distributed cold, using substantial energy, limiting equitable distribution in low-resource countries and placing responsibility on the user for correct storage and handling. Cold-chain management is the best solution at present for protein transport but requires substantial infrastructure and energy. For example, in research laboratories, a single freezer at −80 °C consumes as much energy per day as a small household1. Of biological (protein or cell) therapies and all vaccines, 75% require cold-chain management; the cost of cold-chain management in clinical trials has increased by about 20% since 2015, reflecting this complexity. Bespoke formulations and excipients are now required, with trehalose2, sucrose or polymers3 widely used, which stabilize proteins by replacing surface water molecules and thereby make denaturation thermodynamically less likely; this has enabled both freeze-dried proteins and frozen proteins. For example, the human papilloma virus vaccine requires aluminium salt adjuvants to function, but these render it unstable against freeze–thaw4, leading to a very complex and expensive supply chain. Other ideas involve ensilication5 and chemical modification of proteins6. In short, protein stabilization is a challenge with no universal solution7,8. Here we designed a stiff hydrogel that stabilizes proteins against thermal denaturation even at 50 °C, and that can, unlike present technologies, deliver pure, excipient-free protein by mechanically releasing it from a syringe. Macromolecules can be loaded at up to 10 wt% without affecting the mechanism of release. This unique stabilization and excipient-free release synergy offers a practical, scalable and versatile solution to enable the low-cost, cold-chain-free and equitable delivery of therapies worldwide.

Improving the Photoactivity of Porphyrin-Based Metal-Organic Frameworks via Constructing [Ce-O] Active Site and Vacancy.

Defect engineering of metal-organic frameworks (MOFs) is a versatile approach to tailoring their electronic structures and photocatalytic performance. Herein, Ce-based porphyrin MOFs (CMFs) featuring controlled structural defects were successfully prepared using a simple acid modulation strategy to drive the photocatalytic H2 generation. The [Ce-O] unit serves as the active site via a ligand-to-metal charge transfer process, which has been confirmed by in situ XPS analysis. Abundant exposed coordinatively unsaturated Ce-O centers are beneficial for the adsorption and activation of water molecules, which is an important factor for improving the photocatalytic performance of the synthesized defective MOFs. In addition, optical and electrochemical experiments indicate that CMFs with more oxygen vacancies possess higher charge separation efficiency. As a result, the optimized CMF(Zn)-200 sample afforded high stability and activity in the H2 generation (up to 1603.3 μmol·g-1·h-1 under cocatalyst-free conditions) and tetracycline hydrochloride removal efficiency (97%), which was 8.45 and 97 times higher than that of pure meso-tetra(4-carboxyphenyl)porphine. This study demonstrates that effective structural modulation and defect introduction can improve the activity and stability of PMOF-based photocatalysts.

The use of constrained methods to analyze the molecular reactivity and to define a new type of pseudo atoms

ContextConstrained methods in electronic structure methodologies add terms to the variational equations and generate solutions that represent distorted electronic distributions. In some cases, the new solutions can be used to study the chemical reactivity of parts of the molecule. Additionally, this contribution presents the use of population constraints to define pseudo atoms in a molecule. The effects of the pseudo atom on the molecular properties are analyzed. The pseudo atoms are used to simulate the inductive effect of the substituent in a group of carbonyl molecules and their effect on the stability of the complexes between these organic species and one molecule of water. A discussion on the assumptions involved in the present definition of pseudo atoms is also included.MethodThe constrained RHF computations are done in a modified Hartree-Fock code for Gaussian basis sets. The selected basis set is STO-6 G.

Evidence of a hydrated mineral enriched in water and ammonium molecules in the Chang’e-5 lunar sample

Evidence of a hydrated mineral enriched in water and ammonium molecules in the Chang’e-5 lunar sample

Calcium Binding Mechanism in TAT Rhodopsin.

TAT rhodopsin binds Ca2+ near the Schiff base region, which accompanies deprotonation of the Schiff base. This paper reports the Ca2+-free and Ca2+-bound structures of TAT rhodopsin by molecular dynamics (MD) simulation launched from AlphaFold structures. In the Ca2+-bound TAT rhodopsin, Ca2+ is directly coordinated by eight oxygen atoms, four oxygens of the side chains of E54 and D227, and four oxygens of water molecules. E54 is not involved in the hydrogen-bonding network of the Ca2+-free TAT rhodopsin, while flipping motion of E54 allows Ca2+ binding to TAT rhodopsin with deformation of helices observed by FTIR spectroscopy. The hydrogen-bonding network plays a crucial role in maintaining the Ca2+ binding, as mutations of E54, Y55, R79, Y200, E220, and D227 abolished the binding. Only T82V exhibited the Ca2+ binding like the wild type among the mutants in this study. The molecular mechanism of Ca2+ binding is discussed based on the present computational and experimental analysis.

Unraveling the Influence of Nafion Content on the Performance of Proton-Exchange Membrane Fuel Cells from the Perspective of Triple-Phase Boundary.

By combining molecular simulations and experimental measurements, the effect of the Nafion content on the performance of proton-exchange membrane fuel cells (PEMFCs) is explained from the perspective of the triple-phase boundary (TPB). The evaporation process of Nafion solvent is simulated on a triple-phase model to mimic the formation of the TPB, and the influence of the Nafion content on the TPB structure is investigated. When the Nafion content is 1.415 mg/m2, the coverages of Nafion on both Pt particles and the carbon carrier are saturated at 42.1% and 32.7%, respectively. With the increase of Nafion content, the amount of water molecules around Pt particles is increased, and the surrounding O2 content is decreased. The experimental PEMFC performance has confirmed such simulation results, which demonstrates a trend of enhancing first and then weakening with the increase of Nafion content and reaches a maximum with the Nafion content of 2.96 mg/m2. Therefore, the correlation between the structure of the TPB and the cell's efficiency has been established at a molecular level, enabling enhancements in the design of the TPB morphology and an increase in PEMFC efficiency.

A Study on Hydrogen Bonding and Energy Variation during Bubble Nucleation in Water on a Grooved Substrate by Molecular Dynamics Simulation.

In this paper, the bubble nucleation process of water was studied by molecular dynamics (MD) simulation. The nucleation mechanism of water on a grooved substrate was revealed from the perspective of hydrogen bond and energy change, and the effect of system pressure on nucleation was studied. The results show that the process of bubble nucleation of water molecules is essentially a process in which the thermal motion of water molecules gradually intensifies and the hydrogen bond continues to break with the increase in kinetic energy. As the hydrogen bond breaks, the kinetic energy of the water molecules is continuously converted to intermolecular potential energy. By analyzing the composition of the hydrogen bond energy, it is found that the electrostatic energy is much greater than the van der Waals energy, so the water nucleation process mainly overcomes the electrostatic force between molecules. With the gradual increase of pressure, although the kinetic energy distribution of molecules does not change significantly, it will cause the potential energy of water molecules to decrease significantly and then lead to the increase of the energy barrier that needs to be crossed for nucleation. Meanwhile, the rise of the nucleation barrier may result in the absence of obvious initial vapor nuclei inside the liquid so that the number of hydrogen bonds cannot be rapidly reduced, which is not conducive to boiling nucleation. The results of this study provide important implications for further understanding of the nucleate boiling process of water.

Binding of SARS-CoV-2 Nonstructural Protein 1 to 40S Ribosome Inhibits mRNA Translation.

Experimental evidence has established that SARS-CoV-2 NSP1 acts as a factor that restricts cellular gene expression and impedes mRNA translation within the ribosome's 40S subunit. However, the precise molecular mechanisms underlying this phenomenon have remained elusive. To elucidate this issue, we employed a combination of all-atom steered molecular dynamics and coarse-grained alchemical simulations to explore the binding affinity of mRNA to the 40S ribosome, both in the presence and absence of SARS-CoV-2 NSP1. Our investigations revealed that the binding of SARS-CoV-2 NSP1 to the 40S ribosome leads to a significant enhancement in the binding affinity of mRNA. This observation, which aligns with experimental findings, strongly suggests that SARS-CoV-2 NSP1 has the capability to inhibit mRNA translation. Furthermore, we identified electrostatic interactions between mRNA and the 40S ribosome as the primary driving force behind mRNA translation. Notably, water molecules were found to play a pivotal role in stabilizing the mRNA-40S ribosome complex, underscoring their significance in this process. We successfully pinpointed the specific SARS-CoV-2 NSP1 residues that play a critical role in triggering the translation arrest.

Microscopic Mechanism for Gradient Diffusion of Salt-Containing Droplets Induced by Electromagnetic Synergy: A Molecular Dynamics Study.

The electromagnetic synergy has been proven to be highly effective in separating oil-water emulsions. However, the dynamic impact mechanism of electromagnetic fields on the internal structure of salt droplets remains unclear. In this study, the molecular dynamics (MD) simulation was used to investigate the molecular diffusion of salt ions and water molecules, as well as the dynamic behavior of droplets under the combined influence of electromagnetic fields. The results indicate that ions accumulate in the electromagnetic synergistic field, causing the deformation amplitude of droplets to be smaller than that in a single electric field. The magnetic field affects the energy of the system, when the magnetic field strength is between 1 and 5T, the nonbonded energy significantly increases nonlinearly; when the magnetic field strength is greater than 5T, the total energy of the system significantly changes. In addition, the viscosity of the medium is significantly lower when the intensity of the magnetic and electric fields is controlled within a specific range, providing a new way to regulate the fluidity of fluids.

The Role of Phosphorus on Alkaline Hydrogen Oxidation Electrocatalysis for Ruthenium Phosphides.

Transition metal/p-block compounds are regarded as the most essential materials for electrochemical energy converting systems involving various electrocatalysis. Understanding the role of p-block element on the interaction of key intermediates and interfacial water molecule orientation at the polarized catalyst-electrolyte interface during the electrocatalysis is important for rational designing advanced p-block modified metal electrocatalysts. Herein, taking a sequence of ruthenium phosphides (including Ru2P, RuP and RuP2) as model catalysts, we establish a volcanic-relation between P-proportion and alkaline hydrogen oxidation reaction (HOR) activity. The dominant role of P for regulating hydroxyl binding energy is validated by active sites poisoning experiments, pH-dependent infection-point behavior, in situ surface enhanced absorption spectroscopy, and density functional theory calculations, in which P could tailor the d-band structure of Ru, optimize the hydroxyl adsorption sites across the Ru-P moieties, thereby leading to improved proportion of strongly hydrogen-bonded water and facilitated proton-coupled electron transfer process, which are responsible for the enhanced alkaline HOR performance.

The Role of Phosphorus on Alkaline Hydrogen Oxidation Electrocatalysis for Ruthenium Phosphides

Transition metal/p‐block compounds are regarded as the most essential materials for electrochemical energy converting systems involving various electrocatalysis. Understanding the role of p‐block element on the interaction of key intermediates and interfacial water molecule orientation at the polarized catalyst‐electrolyte interface during the electrocatalysis is important for rational designing advanced p‐block modified metal electrocatalysts. Herein, taking a sequence of ruthenium phosphides (including Ru2P, RuP and RuP2) as model catalysts, we establish a volcanic‐relation between P‐proportion and alkaline hydrogen oxidation reaction (HOR) activity. The dominant role of P for regulating hydroxyl binding energy is validated by active sites poisoning experiments, pH‐dependent infection‐point behavior, in situ surface enhanced absorption spectroscopy, and density functional theory calculations, in which P could tailor the d‐band structure of Ru, optimize the hydroxyl adsorption sites across the Ru‐P moieties, thereby leading to improved proportion of strongly hydrogen‐bonded water and facilitated proton‐coupled electron transfer process, which are responsible for the enhanced alkaline HOR performance.

Nonlinear composition dependence of hydrogen bond lifetime in water-DMSO binary mixtures: The role of hydrophobic interaction.

The lifetime of a hydrogen bond between water and dimethyl sulfoxide (DMSO) is found to be considerably longer than that between two water molecules in neat water. This is counter-intuitive because the charge on the oxygen in DMSO is considerably less than that in water. Additionally, the strength of the water-dimethyl sulfoxide (w-D) hydrogen bond is found to be strongly composition dependent; the lifetime of the hydrogen bond is ten times larger at 30% than at very low concentrations. Using computer simulations, we perform microscopic structural and dynamic analysis to find that these anomalies arise at least partly from an "action-at-a-distance" effect where the attraction between the hydrophobic methyl groups results in the self-aggregation of DMSO molecules that "cages" both the rotational and linear motions of the molecules involved. This is reflected in the observed strong correlation of the lifetime with the local coordination number of the associated methyl groups. The elongated w-D h-bond lifetime causes a slowdown of collective dynamics and affects the lifetime of the w-w h-bond. This nonlinear feedback mechanism explains the strong composition dependence of viscosity and is anticipated to play a dominant role in many self-assemblies. Furthermore, the w-D hydrogen bond breaking mechanism changes from low to high DMSO concentration, a phenomenon not anticipated a priori. We introduce a new order parameter-based free energy surface of the bond breaking pathway. A two-dimensional transition state rate theory calculation is performed for the lifetime of the w-D h-bond that is found to be semi-quantitatively accurate.

Unveiling the Structure of Metal–Nanodiamonds Bonds: Experiment and Theory

In this study, we conducted a theoretical simulation to compare the effects of various factors on the atomic and electronic structures and the magnetic properties of copper and gadolinium ions bonded to carboxylated species of (111) diamond surfaces. It was experimentally found that in the temperature range above 120 K, the magnetic moments of chelated Gd3+ and Cu2+ equal 6.73 and 0.981 Bohr magnetons, respectively. In the temperature range from 12 to 2 K, these magnetic moments sharply decrease to 6.38 and 0.88 Bohr magnetons. Specifically, we examined the effects of the number of covalent adatom–diamond substrate bridges, coordination of water molecules, and shallow carbon-inherited spins in the substrate on the physical properties of the metal center. Our simulation predicted that increasing the number of bonds between the chelated metal ion and substrate while decreasing the number of coordinating water molecules corresponded to a decrease in the magnetic moment of metal ions in a metal–diamond system. This is due to the redistribution of the electron charge density in an asymmetric metal–diamond system. By comparing our theoretical results with experimental data, we proposed configurations involving one and, in a minor number of cases, two surface –COO− groups and maximum coordination of water molecules as the most realistic options for Cu- and Gd-complexes.

Pervaporation Dehydration Mechanism and Performance of High-Aluminum ZSM-5 Zeolite Membranes for Organic Solvents

Membrane-based pervaporation (PV) for organic solvent dehydration is of great significance in the chemical and petrochemical industries. In this work, high-aluminum ZSM-5 zeolite membranes were synthesized by a fluoride-assisted secondary growth on α-alumina tubular supports using mordenite framework inverted (MFI) nanoseeds (~110 nm) and a template-free synthesis solution with a low Si/Al ratio of 10. Characterization by XRD, EDX, and SEM revealed that the prepared membrane was a pure-phase ZSM-5 zeolite membrane with a Si/Al ratio of 3.8 and a thickness of 2.8 µm. Subsequently, two categories of PV performance parameters (i.e., flux versus separation factor and permeance versus selectivity) were used to systematically examine the effects of operating conditions on the PV dehydration performance of different organic solvents (methanol, ethanol, n-propanol, and isopropanol), and their PV mechanisms were explored. Employing permeance and selectivity effectively disentangles the influence of operating conditions on PV performance, thereby elucidating the inherent contribution of membranes to separation performance. The results show that the mass transfer during PV dehydration of organic solvents was mainly dominated by the adsorption–diffusion mechanism. Furthermore, the diffusion of highly polar water and methanol molecules within membrane pores had a strong mutual slowing-down effect, resulting in significantly lower permeance than other binary systems. However, the mass transfer process for water/low-polar organic solvent (ethanol, n-propanol, and isopropanol) mixtures was mainly controlled by competitive adsorption caused by affinity differences. In addition, the high-aluminum ZSM-5 zeolite membrane exhibited superior PV dehydration performance for water/isopropanol mixtures.

In Situ Assembly of Metal‐Organic Coordination Polymer Layers Enables Highly Reversible Zn Anodes with a Long Cycle Life of over 6900 h

AbstractZn anodes in aqueous zinc‐ion batteries chronically suffer from pernicious side reactions and ineluctable dendrite growth, resulting in inadequate reversibility and suboptimal Coulombic efficiency (CE) and impeding commercialization. Herein, a multifunctional metal–organic coordination polymer layer (FAZ) is constructed on the zinc anode surface (FAZ@Zn) utilizing a simple self‐assembly strategy. The zincophilic FAZ interfacial layer with a high Zn2+ transfer number and low nucleation barrier effectively facilitates the de‐solvation process, supports the rapid transport of zinc ions, and contributes to the preferential growth of Zn (002) crystal planes, enabling dendrite‐free Zn deposition. Furthermore, the FAZ layer, as an interfacial pH regulating layer, effectively inhibits the direct contact between Zn and active water molecules, lowering the severity of side reactions. Consequently, the FAZ@Zn anode furnishes an eminent cycle stability over 6900 h, with a low polarization voltage at 1 mA cm−2 and 1 mA h cm−2 and a boosted CE of 99.88% over 4100 cycles. More encouragingly, when coupled with Na2V6O16·3H2O, the FAZ@Zn anode enables the full cell to deliver satisfactory rate performance and a 97% capacity retention over 1600 cycles. This work provides a simple strategy for the effective preparation of highly reversible zinc anodes for high‐performance aqueous zinc‐ion batteries.