Effect Of Water Molecules Research Articles

First principles molecular dynamics simulations of H2S dissociation on Fe (1 1 1) in aqueous environments

A wet H2S environment can cause significant mechanical failure and corrosion. In this study, we used first principles static and molecular dynamics calculations to investigate the behavior of water adsorption of Fe (111) at different temperatures, followed by the effect of water molecules on the dissociation of H2S on the Fe (111) surface. At room temperature, the structures of the water layer on the Fe (111) surface include the H-up and H-down mixed structures. H2S molecules exhibit stronger competitiveness in co-adsorption with water molecules. Moreover, because the interaction of H-S in H2S molecules can be weakened by hydrogen bonds with water and stronger Fe-H owing to water adsorption on the surface, the induced lower dissociation barriers can be sufficiently overcome at room temperature. Therefore, it can be concluded that conditions such as water adsorption layer and room temperature can promote the dissociation of H2S on Fe (111), which is helpful to understand the H2S corrosion process at the metal interface.

The homogeneous gas-phase formation mechanisms of PCPTs/PCDTs/PCDFs from the radical/radical cross-condensation of 2-CPR and 2-CTPR: a theoretical, mechanistic and kinetics study.

Polychlorinated phenoxathiins (PCPTs) are one group of dioxin-like compounds, which can be considered to be one-oxygen-substituted polychlorinated thianthrene (PCTA) compounds or one-sulfur-substituted polychlorinated dibenzo-p-dioxin (PCDD) compounds. Owing to their high toxicity and wide distribution, clarifying the formation and emission of PCPTs due to combustion and thermal processes can deepen our understanding of the dioxin formation mechanism and allow reduced-emission and dioxin-control strategies to be established. Chlorophenols (CPs) and chlorothiophenols (CTPs) are direct precursors in PCPT formation. In this paper, the homogeneous gas-phase formation mechanisms of PCPTs, as well as polychlorinated dibenzofurans (PCDFs) and polychlorinated dibenzothiophenes (PCDTs), from the cross-condensation of 2-chlorophenoxy radicals (2-CPRs) and 2-chlorothiophenoxy radicals (2-CTPRs) under thermal and combustion conditions were investigated theoretically using a density functional theory (DFT) method. The reaction priorities and effects of water molecules on the formation mechanisms were discussed. The rate constants of crucial elementary steps were calculated from 600–1200 K. The acute and chronic toxicities of the main products were predicted at three trophic levels. This study shows that routes starting with oxygen–carbon condensation are favored over those starting with sulfur–carbon condensation for PCPT formation, and routes ending with Cl loss can occur more easily than those ending with H loss. Water molecules have a negative catalytic effect on CH–S H-transfer steps but a positive catalytic effect on CH–O H-transfer steps.

Structural properties of a biotechnological capsule confined by a 3D‐cellulose acetate membrane

Small bioreactor platform (SBP) capsules are designed to implement selective bacterial cultures within aquatic media, mainly wastewaters, in a bioaugmentation process. Such capsules, coated with cellulose acetate (CA) membranes to form three‐dimensional (3D) structural barriers, are intended to provide a long‐term protected and confined environment for the introduced bacterial cultures. These state‐of‐the‐art 3D membranes allow the tailored design of the encapsulated bacteria and adjustment to several environmental properties, such as organics and nutrients, pressure, and the natural flora. Our study characterizes, for the first time, the mechanical and thermal properties of the SBPCA structural membrane and the effects of water molecules on these properties. High‐resolution scanning electron microscopy images of the CA membranes show mesh‐like porous structures, crucial for mass transport both inside and outside the capsule. Thermal gravimetric analysis shows a reduction of ~115°C in the thermal decomposition temperature of wet capsules compared to that of dry capsules. Mechanical testing shows that the modulus and maximum stress of wet samples are each decreased by an order of magnitude compared to those of dry samples at similar maximum strain. The permeability of the CA membrane to phenol, a model water organic pollutant, was found to be 3 × 10−8 cm2 s−1. It is concluded that water molecules soften CA structural membranes, yielding soft amorphous structures, which are needed for the optimized processing of the SBP capsule. The plasticizing effect is important in the membrane architecture formation and fiber elasticity when used in an aqueous environment.

The effect of water molecules on elastic and piezoelectric properties of diphenylalanine microtubes

The variation of elastic and electromechanical properties of microtubes of diphenylalanine dipeptide as a function of the degree of filing of nanochannels by water molecules is reported in this paper. Quantum chemical calculations reveal different contributions of water layers in the microtubes to Young's modulus and the effective piezoelectric coefficient. The application of diphenylalanine microtubes in micro-electromechanical systems is also discussed.

Computational mechanistic study of the unimolecular dissociation of ethyl hydroperoxide and its bimolecular reactions with atmospheric species

A detailed computational study of the atmospheric reaction of the simplest Criegee intermediate CH2OO with methane has been performed using the density functional theory (DFT) method and high-level calculations. Solvation models were utilized to address the effect of water molecules on prominent reaction steps and their associated energies. The structures of all proposed mechanisms were optimized using B3LYP functional with several basis sets: 6-31G(d), 6-31G (2df,p), 6-311++G(3df,3pd) and at M06-2X/6-31G(d) and APFD/6-31G(d) levels of theory. Furthermore, all structures were optimized at the B3LYP/6-311++G(3df,3pd) level of theory. The intrinsic reaction coordinate (IRC) analysis was performed for characterizing the transition states on the potential energy surfaces. Fifteen different mechanistic pathways were studied for the reaction of Criegee intermediate with methane. Both thermodynamic functions (ΔH and ΔG), and activation parameters (activation energies Ea, enthalpies of activation ΔHǂ, and Gibbs energies of activation ΔGǂ) were calculated for all pathways investigated. The individual mechanisms for pathways A1, A2, B1, and B2, comprise two key steps: (i) the formation of ethyl hydroperoxide (EHP) accompanying with the hydrogen transfer from the alkanes to the terminal oxygen atom of CIs, and (ii) a following unimolecular dissociation of EHP. Pathways from C1 → H1 involve the bimolecular reaction of EHP with different atmospheric species. The photochemical reaction of methane with EHP (pathway E1) was found to be the most plausible reaction mechanism, exhibiting an overall activation energy of 7 kJ mol−1, which was estimated in vacuum at the B3LYP/6-311++G(3df,3pd) level of theory. All of the reactions were found to be strongly exothermic, expect the case of the sulfur dioxide-involved pathway that is predicted to be endothermic. The solvent effect plays an important role in the reaction of EHP with ammonia (pathway F1). Compared with the gas phase reaction, the overall activation energy for the solution phase reaction is decreased by 162 and 140 kJ mol−1 according to calculations done with the SMD and PCM solvation models, respectively.

Theoretical investigation of epoxy detachment from C-S-H interface under aggressive environment

Reliable bonding between epoxy and concrete is necessary for FRP bonded concrete structures to ensure their durability. However, FRP bonded concrete structures are inevitably exposed to aqueous or saline environments, which would extremely threaten the interfacial bonding of structures. Here, the bonding properties of epoxy/hydrated calcium silicate (C-S-H) interface under aggressive environments is investigated by using molecular dynamics (MD) simulation. The configurational analysis reveals that the epoxy detaches gradually from the C-S-H surface under aqueous and saline conditions, indicating that the deterioration of the bonding between epoxy and C-S-H matrix. Simulation results show that the Caw-OC-S-H and Caw-Oepoxy connections are essential for good bonding of the epoxy/C-S-H interface. The H-bonds, formed between the epoxy and C-S-H matrix, are also not negligible for improving the interfacial bonding. In an aggressive environment, water molecules are adsorbed on the surface and become the main factor in the configurational changes. The Caw-OC-S-H, Caw-Oepoxy connection, and the H-bonds network will be weakened or destroyed under the effect of water molecules. This study could provide valuable information on the understanding the bonding degradation and configurational changes between epoxy and C-S-H matrix in different environments.

Effect of temperature, humidity and pressure on electric properties of the cells based on PTB7-Th, PC61BM and graphene composite

In this paper, fabrication and characterization of Cu/PTB7-Th (35 mass%)/PC $$_{61}$$ BM (35 mass%)/graphene (30 mass%)/Ag thin-film composite cells are given. First of all, Ag and Cu electrodes were deposited on flat glass substrate by vacuum evaporation with 130- $$\upmu $$ m inter-electrode gap. The PTB7-Th (35 mass%) composite and PC $$_{61}$$ BM (35 mass%) composite in chlorobenzene and graphene (30 mass%) were deposited on the inter-electrode gap by drop-casting technique, and film thickness of 8–12 $$\upmu $$ m was achieved. The dependence of forward and reverse bias resistance of the cells versus temperature in the range of 25–75 $${^{\circ }}$$ C, humidity in the range of 47–90 %RH and pressure in the range of 0–7.7 kN m $$^{-2}$$ was measured. The average temperature resistance coefficients were equal to (− 1.03)% $${^{\circ }}\hbox {C}^{-1}$$ and $$(-\,1.14)\%\ {^{\circ }}\hbox {C}^{-1}$$ for forward and reverse bias resistances, respectively. The reverse and forward bias resistances decreased 1.29 and 1.27 times due to $$\%\mathrm{RH}$$ , and due to pressure, it decreased by 9.0–9.2%. Impedance (Z) of the sample was also measured at different frequencies (100 Hz, 1 kHz, 10 kHz and 100 kHz) which decreased from 1.23 to 1.04 times. The obtained results are explained, firstly, by transfer of charges between donors and acceptors molecules and effect of water molecules on the PTB7-Th (35 mass%):PC $$_{61}$$ BM (35 mass%):graphene composite.

Effect of water absorption on the mechanical properties of bamboo/glass-reinforced polybenzoxazine hybrid composite

In this study, bamboo and glass fibers were successfully added into bisphenol A–aniline-based benzoxazine resin by hot pressing method. The effect of water absorption on the mechanical properties of the neat benzoxazine and its composites was studied. The composites prepared in this study has been proved to exhibit better water resistance than some conventional natural fiber/polymer composites due to good hydrophobicity of the benzoxazine matrix. From the mechanical tests, the tensile performance of both neat benzoxazine and the composites degraded seriously after prolonged immersion in water. However, neat benzoxazine and the composites maintained relatively higher residual flexural properties (residual mechanical properties refer to the ratio of strength and modulus of the saturated samples to that of the nonaged samples) after 20 days of water immersion. The effect of water molecules on the fracture surface morphologies of the composites was studied using a scanning electron microscope (SEM). The SEM images showed that the interfacial bonding between fibers and the matrix degraded seriously due to the attack of water.

Atomistic understanding of surface wear process of sodium silicate glass in dry versus humid environments

AbstractUnderstanding surface reactions of silicate glass under interfacial shear is critical as it can provide physical insights needed for rational design of more durable glasses. Here, we performed reactive molecular dynamics (MD) simulations with ReaxFF potentials to study the mechanochemical wear of sodium silicate glass rubbed with amorphous silica in the absence and presence of interfacial water molecules. The effect of water molecules on the shear‐induced chemical reaction at the sliding interface was investigated. The dependence of wear on the number of interfacial water molecules in ReaxFF‐MD simulations was in reasonable agreement with the experimental data. Confirming this, the ReaxFF‐MD simulation was used to find further details of atomistic reaction dynamics that cannot be obtained from experimental investigations only. The simulation showed that the severe wear in the dry condition is due to the formation of interfacial Sisubstrate–O–Sicounter_surface bond that convey the interfacial shear stress to the subsurface and the presence of interfacial water reduces the interfacial bridging bond formation. The leachable sodium ions facilitate surface reactions with water‐producing hydroxyl groups and their key role in the hydrolysis reaction is discussed.

Effects of Water Molecules on Metal Complexes of Hydroxyoxime and Carboxylic Acid Extractants

Effects of Water Molecules on Metal Complexes of Hydroxyoxime and Carboxylic Acid Extractants

Axial driving characteristics of water in rotating black phosphorus nanotubes

Since the advent of two-dimensional materials, the micro/nano technology has been greatly developed, and the design of micro/nano fluid devices has become an important research area. As a new two-dimensional material, the black phosphorus (BP) has attracted wide attention because of its excellent properties such as anisotropy, and it has been applied to many areas. In this paper, the axial motion properties of water molecules in the rotating black phosphorus nanotube (BPNT) are studied by the molecular dynamics method. The results show that water molecules in the rotating chiral BPNT can move along the axis, and the moving direction of water molecules is determined by the rotating direction of the nanotube. The velocity of water molecules and the resultant force of water molecules received from the nanotube in the axial direction increase with the angular velocity increasing. The friction coefficient and slip characteristics of the water-BP interface are calculated by using the Couette flow model, and it is clarified that the natural anisotropic microstructure on the surface of BP is the essential reason for the axial motion of water molecules in the rotating BPNT. Besides, we construct a model of filling water molecules between two BPNTs. It is found that the axial movement of water molecules between two nanotubes will be enhanced when the internal and external tube rotate simultaneously. The radius of the nanotubes will also affect the directional motion of the water molecules. Specifically, at the same angular velocity of BPNTs, with the increase of the radius, the axial motion velocity of water molecules in the BPNT will decrease, while the force received from the BPNT will increase. The axial motion of water molecules in the double-walled BPNT is little different from that in the single-walled BPNT, which proves that the number of layers has no significant influence on the driving effect of water molecules. The influence of temperature on the motion properties of water molecules depends on the coupling effect of pressure and temperature in the tube on the convection-solid interface friction coefficient. When the temperature is lower than the normal temperature, the axial velocity of water molecules and the force exerted by the BPNT will increase with the increase of temperature, and when the temperature reaches the normal temperature, it will become stable. The results will provide a theoretical basis for the study of the flow characteristics of the fluid in BPNTs and the application of the fluid drive devices based on BPNTs.

Improving protein–ligand binding prediction by considering the bridging water molecules in Autodock

Water plays a significant role in determining the protein–ligand binding modes, especially when water molecules are involved in mediating protein–ligand interactions, and these important water molecules are receiving more and more attention in recent years. Considering the effects of water molecules has gradually become a routine process for accurate description of the protein–ligand interactions. As a free docking program, Autodock has been most widely used in predicting the protein–ligand binding modes. However, whether the inclusion of water molecules in Autodock would improve its docking performance has not been systematically investigated. Here, we incorporate important bridging water molecules into Autodock program, and systematically investigate the effectiveness of these water molecules in protein–ligand docking. This approach was evaluated using 18 structurally diverse protein–ligand complexes, in which several water molecules bridge the protein–ligand interactions. Different treatment of water molecules were tested by using the fixed and rotatable water molecules, and a considerable improvement in successful docking simulations was found when including these water molecules. This study illustrates the necessity of inclusion of water molecules in Autodock docking, and emphasizes the importance of a proper treatment of water molecules in protein–ligand binding predictions.

Influence of water on HFO-1234yf oxidation pyrolysis via ReaxFF molecular dynamics simulation

ABSTRACTThe effect of water molecules on HFO-1234yf oxidation pyrolysis was investigated by ReaxFF-molecular dynamics simulation from 1900 to 4200 K. The initial pyrolysis of HFO-1234yf starts around 2500 K and the water molecules participate in chemical reactions at 2800 K when the reactants pyrolysis reached the highest reaction rate. The primary products including HF, COF2 and CO2 are observed at 2600, 2700 and 2900 K, respectively. The influence of water molecules on products is mainly reflected in the promotion activity on the conversion from COF2 to CO2 and the generation of HF molecules. Four formation pathways are observed and calculated to further elucidate the procedure of pyrolysis. The main conversion process from H2O to HF is the •F + H2O = HF+•OH reaction, and the paths from H2O to •OH radical and COF2 to •CFO radical which are promoted by •F and •H radical, respectively, have relatively low energy barriers of 10.44 and 40.29 kJ/mol, and both reaction processes released HF molecules.

Enhanced Quantum Yield of Nanographenes Incorporated in Supermicroporous Silicas and the Co-Adsorption Effect of Water Molecules

Abstract Nanographene with various molecular sizes was synthesized and incorporated into the size-controlled pores of super-microporous silica (SMPS). It was found that when the pore diameter of the SMPS matched the molecular size of the nanographene, the fluorescence quantum yield was greatly enhanced. Furthermore, co-adsorption of water molecules improved the quantum yield. This improvement is attributed to a suppression of the interaction between the nanographene and silica walls, which lowers the quantum yield. Since nanographene is insoluble in water, it becomes surrounded by water molecules, almost like in aqueous solution. Finally, highly fluorescent solid materials were obtained by incorporating nanographene into SMPS.

The effect of water molecules on the structure, dynamics, and mechanical properties of sodium aluminosilicate hydrate (NASH) gel: A molecular dynamics study

Sodium aluminosilicate hydrate (NASH) gel is the primary adhesive constituent in geopolymer. In the nanostructure of NASH gel, structural water has a great impact on the structure and mechanical properties of NASH. In this study, molecular dynamics simulation is utilized to investigate the effect of water on the structure, dynamics, and mechanical properties of NASH gel. The result shows that water molecules in NASH gel are physically and chemically bound to Si-Al framework by the formation of H-bond as well as Si-OH, Al-OH and Na-OH. These hydrolytic reactions result in the elongation of Al-O bond and the structural transformation from tetrahedral aluminum to pentahedral aluminum. The structural weakening caused by hydrolysis for aluminate skeleton leads to an increase in the mobility of aluminum and a decrease in the stability of Al-O bond. However, the sodium in NASH structure becomes stabilized as a result of the hydrolysis of aluminate skeleton and the formation of Na-OH. In contrast, silicate skeleton exhibits hydrophobic nature and not sensitive to water. Mechanically, hydrolytic reaction weakens the tensile performance of NASH gel by two mechanisms, which is promoting the de-polymerization of Si-Al framework during the tensile process, and preventing the re-polymerization of broken framework. Meanwhile, the de-polymerization of Si-Al framework can further promote hydrolytic reaction during the tensile testing.

Catalytic effect of a single water molecule on the OH + CH2NH reaction.

In recent work, there has been considerable speculation about the atmospheric reaction of methylenimine (CH2NH), because this compound is highly reactive, soluble in water, and sticky, thus posing severe experimental challenges. In this work, we have revisited the kinetics of the OH + CH2NH reaction assisted by a single water molecule. The potential energy surfaces (PESs) for the water-assisted OH + CH2NH reaction were calculated using the CCSD(T)//BH&HLYP/aug-cc-pVTZ levels of theory. The rate coefficients for the bimolecular reaction pathways CH2NHH2O + OH and CH2NH + H2OHO were computed using canonical variational transition state theory (CVT) with small curvature tunneling correction. The reaction without water has four elementary reaction pathways, depending on how the hydroxyl radical approaches CH2NH. In all cases, the reaction begins with the formation of a single pre-reactive complex before producing abstraction and addition products. When water is added, the products of the reaction do not change, and the reaction becomes quite complex, yielding four different pre-reactive complexes and eight reaction pathways. The calculated rate coefficient for the OH + CH2NH (water-free) reaction at 300 K is 1.7 × 10-11 cm3 molecule-1 s-1 and for OH + CH2NH (water-assisted), it is 5.1 × 10-14 cm3 molecule-1 s-1. This result is similar to the isoelectronic analogous reaction OH + CH2O (water-assisted). In general, the effective rate coefficients of the water-assisted reaction are 2∼3 orders of magnitude smaller than water-free. Our results show that the water-assisted OH + CH2NH reaction cannot accelerate the reaction because the dominated water-assisted process depends parametrically on water concentration. As a result, the overall reaction rate coefficients are smaller.

Effects of water molecules on material removal behavior in Vibration Assisted Nano Impact-machining by Loose Abrasives - A molecular dynamics simulation study

Vibration Assisted Nano Impact-machining by Loose Abrasives (VANILA) is a novel nanomachining process that performs target specific nano abrasive machining of hard and brittle materials. An atomic force microscope (AFM) is used as a platform in this process wherein, nano abrasives, injected in slurry between the workpiece and the vibrating AFM probe, impact the workpiece and cause nanoscale material removal. Liquid medium is required in this process to confine the abrasives within the machining zone. However, the presence of liquid medium could significantly influence the abrasive dynamics as well as the substrate deformation behavior during the VANILA process. This study focuses on understanding the effect of liquid medium on the material removal behavior during the VANILA process. A Molecular Dynamics Simulation (MDS) based study is conducted under different initial conditions with and without the presence of liquid medium (water). The results obtained from the study showed that while the water absorbs some energy from the abrasive grain, it also provides a lubricating layer to the grain preventing adhesion on the workpiece surface. Visualizations of the atomic configurations of the workpiece showed that the presence of water molecules could significantly affect the material dislocations during the impact process.

Different effects of water molecules on CO oxidation with different reaction mechanisms.

The effects of water molecules (promotion/prohibition) on CO oxidation remain debated. Herein, using density functional theory calculations, we demonstrate that water molecules can facilitate the CO + O/O2 oxidation process, but prohibit the CO + OH oxidation process, which is consistent with the experimental finding that water molecules have two distinct effects on CO oxidation. For the CO + O/O2 oxidation mechanisms, we find that the reactants were pushed towards each other due to the steric effect of the water molecules, which decreases the reaction barriers and promotes the CO + O/O2 oxidation process. For the CO + OH oxidation mechanisms, water molecules increase the stability of the COOH* intermeditae by H-bonds and van der Waals forces, which increase the barriers of the COOH* transformation process and the COOH*-tra dissociation process, and prohibit the CO + OH oxidation process. These results clarify the different effects of water molecules on CO oxidation and shed light on catalyst usage in the CO oxidation industry.

Deformation Simulation of Nylon 6 and the Effect of Water Molecule by using Molecular Dynamics Simulation

Deformation Simulation of Nylon 6 and the Effect of Water Molecule by using Molecular Dynamics Simulation

Unravelling the Chemical Influence of Water on the PMMA/Aluminum Oxide Hybrid Interface In Situ

Understanding the stability of chemical interactions at the polymer/metal oxide interface under humid conditions is vital to understand the long-term durability of hybrid systems. Therefore, the interface of ultrathin PMMA films on native aluminum oxide, deposited by reactive adsorption, was studied. The characterization of the interface of the coated substrates was performed using ambient pressure X-ray photoelectron spectroscopy (APXPS), Fourier transform infrared spectroscopy in the Kretschmann geometry (ATR-FTIR Kretschmann) and time-of-flight secondary ion mass spectrometry (ToF-SIMS). The formation of hydrogen bonds and carboxylate ionic bonds at the interface are observed. The formed ionic bond is stable up to 5 Torr water vapour pressure as shown by APXPS. However, when the coated samples are exposed to an excess of aqueous electrolyte, an increase in the amount of carboxylate bonds at the interface, as a result of hydrolysis of the methoxy group, is observed by ATR-FTIR Kretschmann. These observations, supported by ToF-SIMS spectra, lead to the proposal of an adsorption mechanism of PMMA on aluminum oxide, which shows the formation of methanol at the interface and the effect of water molecules on the different interfacial interactions.