Development of a ReaxFF reactive force field for glycine and application to solvent effect and tautomerization

Advancing DBD Plasma Chemistry: Insights into Reactive Nitrogen Species such as NO2, N2O5, and N2O Optimization and Species Reactivity through Experiments and MD Simulations

This study aims to fine-tune the plasma composition with a particular emphasis on reactive nitrogen species (RNS) including nitrogen dioxide (NO2), dinitrogen pentoxide (N2O5), and nitrous oxide (N2O), produced by a self-constructed cylindrical dielectric barrier discharge (CDBD). We demonstrated the effective manipulation of the plasma chemical profile by optimizing electrical properties, including the applied voltage and frequency, and by adjusting the nitrogen and oxygen ratios in the gas mixture. Additionally, quantification of these active species was achieved using Fourier transform infrared spectroscopy. The study further extends to exploring the aerosol polymerization of acrylamide (AM) into polyacrylamide (PAM), serving as a model reaction to evaluate the reactivity of different plasma-generated species, highlighting the significant role of NO2 in achieving high polymerization yields. Complementing our experimental data, molecular dynamics (MD) simulations, based on the ReaxFF reactive force field potential, explored the interactions between reactive oxygen species, specifically hydroxyl radicals (OH) and hydrogen peroxide (H2O2), with water molecules. Understanding these interactions, combined with the optimization of plasma chemistry, is crucial for enhancing the effectiveness of DBD plasma in environmental applications like air purification and water treatment.

Intramolecular and Water Mediated Tautomerism of Solvated Glycine

Understanding tautomerism and characterizing solvent effects on the dynamic processes pose significant challenges. Using enhanced-sampling molecular dynamics based on state-of-the-art deep learning potentials, we investigated the tautomeric equilibria of glycine in water. We observed that the tautomerism between neutral and zwitterionic glycine can occur through both intramolecular and intermolecular proton transfers. The latter proceeds involving a contact anionic-glycine-hydronium ion pair or separate cationic-glycine-hydroxide ion pair. These pathways with comparable barriers contribute almost equally to the reaction flux.

ReaxFF-Based Molecular Dynamics Study of the Mechanism of the Reaction of N2O4 with H2O

During long-term storage of the liquid propellant N2O4, it absorbs H2O to form the N2O4(H2O)n system, and this in turn generates HNO3, HNO2, and other substances in the storage tank because of corrosion, which seriously affects the performance of weaponry. In this work, we carried out computational simulations of N2O4 with different masses of water based on ReaxFF, analyzed the reaction intermediates and products, and investigated the mechanism of the reaction of N2O4 with H2O and of N2O4(H2O)n. The results show that the reaction product ω(HNO3+HNO2) undergoes a rapid growth in the early stage of the reaction and then tends toward dynamic equilibrium; the potential energy of the system decreases with the increase of ω(H2O), the reaction rate increases, and the rate of decomposition of HNO2 to form HNO3 increases. When ω(H2O) is 0.2 or 1.0%, the intermediate products are N2O4H2O or N2O4(H2O)2, respectively, and the reaction proceeds along two paths; when ω(H2O) ≥ 2.0%, N2O4(H2O)3 appears as the intermediate product, HNO3 and HNO2 are directly produced in one step, and a stable current loop can be formed within the whole system.

Conformational preference of dipeptide zwitterions in aqueous solvents

Proper description of solvent effects is challenging for theoretical methods, particularly if the solute is a zwitterion. Here, a series of theoretical procedures are used to determine the preferred solvated conformations of twelve hydrophobic dipeptides (Leu-Leu, Leu-Phe, Phe-Leu, Ile-Leu, Phe-Phe, Ala-Val, Val-Ala, Ala-Ile, Ile-Ala, Ile-Val, Val-Ile and Val-Val) in the zwitterionic state. First, the accuracy of density functional theory (DFT), combined with different implicit solvent models, for describing zwitterions in aqueous solvent is assessed by comparing the predicted against the experimental glycine tautomerization energy, i.e., the energetic difference between canonical and zwitterionic glycine in aqueous solvents. It is found that among the tested solvation schemes, the charge-asymmetric nonlocally determined local-electric solvation model (CANDLE) predicts an energetic difference in excellent agreement with the experimental value. Next, DFT-CANDLE is used to determine the most favorable solvated conformation for each of the investigated dipeptide zwitterions. The CANDLE-solvated structures are obtained by exploring the conformational space of each dipeptide zwitterion concatenating DFT calculations, in vacuum, with classical molecular dynamics simulations, in explicit solvents, and DFT calculations including explicit water molecules. It is found that the energetically most favorable conformations are similar to those of the dipeptide zwitterions in their respective crystal structures. Such structural agreement is indicative of the DFT-CANDLE accomplishment of the description of solvated zwitterions, and suggests that these biomolecules self-assemble as quasi-rigid objects.

Temperature driven transformations of glycine molecules embedded in interstellar ice

The formation of glycine amino acid on ice grains in space raises fundamental questions about glycine chemistry in interstellar media. In this work, we studied glycine conformational space and the related tautomerization mechanisms in water media by means of QM/MM molecular dynamics simulations of four glycine conformational isomers (cc, ct, tc, and tt). Interstellar low density amorphous (LDA) ice and T = 20 K were considered as representative for a cold interstellar ice environment, while temperatures of 250 and 450 K were included to model rapid local heating in the ice. In addition to the LDA environment, water clusters with 4, 17, and 27 H2O molecules were subjected to QM/MM dynamics simulations that allowed glycine tautomerization behaviour to be evaluated in water surface-like environments. The tautomerization processes were found to be strongly dependent on the number of water molecules and specific isomer structure. All the glycine isomers mostly preserve their canonical "neutral" conformations under interstellar conditions.

ReaxFF molecular dynamics of graphene oxide/NaCl aqueous solution interfaces

In this work, the interaction of NaCl aqueous solution with graphene (G), graphene oxide (GO), and graphite oxide (GTO) is studied using the ReaxFF module of Amsterdam Modeling Suite (AMS) software. We consider four models using the NaCl aqueous solution, containing a graphene sheet (G), a single sheet of GO with epoxide and hydroxyl groups on its surface, 4 layers of GO to model GTO, and a bulk NaCl solution as a reference. The structural and dynamical properties of G, GO, and GTO were quantified by analyzing the functional groups, radial distribution functions, density profiles and diffusivities of water and ions. Due to the reactive force field, the systems underwent spontaneous modification of surface functional groups during the first 750 ps after which the structure stabilizes (the energy stabilizes in less than 400 ps). Pristine graphene in contact with the NaCl solution formed hydroxyl groups on the edges, i.e., converted to partially reduced graphene oxide. The epoxy groups (Oe) on the initial GO were rather unstable, leading to a reduction of their number, however, there was an increase in the number of hydroxyl groups (Oh), mainly at the edges. The interactions of NaCl with the carbon-based sheets are rather weak, including GO and GTO which are decorated with numerous functional groups. Diffusion coefficients of water agree with the available data, but discrepancies in Na+ and Cl- diffusivity compared to other references underscore the need for further development in the dynamic parameters of the reactive force field used. In essence, our research provides specific data previously unreported, laying a foundation for advancing water desalination system design. The study's novelty lies in its realistic approach to graphene/graphene oxide modification, comprehensive characterization, and the application of the reactive force field to explore the graphene oxide-NaCl aqueous interface, contributing to the development of a practical membrane system for water desalination.

Close-Packed Ices in Nanopores

Water molecules in any of the ice polymorphs organize themselves into a perfect four-coordinated hydrogen-bond network at the expense of dense packing. Even at high pressures, there seems to be no way to reconcile the ice rules with the close packing. Here, we report several close-packed ice phases in carbon nanotubes obtained from molecular dynamics simulations of two different water models. Typically they are in plastic states at high temperatures and are transformed into the hydrogen-ordered ice, keeping their close-packed structures at lower temperatures. The close-packed structures of water molecules in carbon nanotubes are identified with those of spheres in a cylinder. We present design principles of hydrogen-ordered, close-packed structures of ice in nanotubes, which suggest many possible dense ice forms with or without nonzero polarization. In fact, some of the simulated ices are found to exhibit ferroelectric ordering upon cooling.

Conformational States of the CXCR4 Inhibitor Peptide EPI-X4-A Theoretical Analysis

EPI-X4, an endogenous peptide inhibitor, has exhibited potential as a blocker of CXCR4-a G protein-coupled receptor. This unique inhibitor demonstrates the ability to impede HIV-1 infection and halt CXCR4-dependent processes such as tumor cell migration and invagination. Despite its promising effects, a comprehensive understanding of the interaction between EPI-X4 and CXCR4 under natural conditions remains elusive due to experimental limitations. To bridge this knowledge gap, a simulation approach was undertaken. Approximately 150,000 secondary structures of EPI-X4 were subjected to simulations to identify thermodynamically stable candidates. This simulation process harnessed a self-developed reactive force field operating within the ReaxFF framework. The application of the Two-Phase Thermodynamic methodology to ReaxFF facilitated the derivation of crucial thermodynamic attributes of the EPI-X4 conformers. To deepen insights, an ab initio density functional theory calculation method was employed to assess the electrostatic potentials of the most relevant (i.e., stable) EPI-X4 structures. This analytical endeavor aimed to enhance comprehension of the inhibitor's structural characteristics. As a result of these investigations, predictions were made regarding how EPI-X4 interacts with CXCR4. Two pivotal requirements emerged. Firstly, the spatial conformation of EPI-X4 must align effectively with the CXCR4 receptor protein. Secondly, the functional groups present on the surface of the inhibitor's structure must complement the corresponding features of CXCR4 to induce attraction between the two entities. These predictive outcomes were based on a meticulous analysis of the conformers, conducted in a gaseous environment. Ultimately, this rigorous exploration yielded a suitable EPI-X4 structure that fulfills the spatial and functional prerequisites for interacting with CXCR4, thus potentially shedding light on new avenues for therapeutic development.

Advantages of Multidimensional Biasing in Accelerated Dynamics: Application to the Calculation of the Acid pKa for Acetic Acid

The use of accelerated sampling methods such as metadynamics has shown a significant advantage in calculations that involve infrequent events, which would otherwise require sampling a prohibitive number of configurations to determine the difference in free energies between two or more chemically distinct states such as in the calculation of acid dissociation constants Ka. In this case, the most common method is to bias the system via a single collective variable (CV) representing the coordination number of the proton donor group, which yields results in reasonable agreement with experiments. Here we study the deprotonation of acetic acid using the reactive force field ReaxFF and observe a significant dependence of Ka on the simulation box size when biasing only the coordination number CV, which is due to incomplete sampling of the deprotonated state for small simulation systems and inefficient sampling for larger ones. Incorporating a second CV representing the distance between the H3O+ cation and the acetate anion results in substantially more efficient sampling, both accelerating the dynamics and virtually eliminating the computational box size dependence.

Molecular Dynamic Simulation of Ni-Al Alloy-H2O Reactions Using the ReaxFF Reactive Force Field

Hydrogen as clean energy can effectively solve the problems of fossil energy shortage and environmental pollution. However, traditional methods of H₂ production are generally lacking in application value. The procedure for manufacturing H₂ by a reaction between active metals and H₂O has received wide attention due to its high efficiency. Profound insights into the mechanism and influencing factors of H₂ production from active metals are insufficient. The ReaxFF reaction force field module of the Amsterdam Modeling Suite (AMS) is applied in this paper to simulate the reaction of Ni-Al alloys with H₂O. It reveals the reaction route of H₂ production at the atomic level. The calculation results show that Al is the most critical active site. Moreover, the H₂ production capacity of the alloy varies with the crystal structure and atomic ratio. The H₂ production rate decreases due to the influence of the water solvation layer and surface coverage. Oxygen reduces the H₂ production capacity because oxygen reduces the active sites for H₂O adsorption by forming a stable oxide layer with Al.

ReaxFF-based nonadiabatic dynamics method for azobenzene derivatives

ReaxFF reactive force fields have been parameterized for the ground and first excited states of azobenzene and its derivatives. In addition, an extended set of ab initio reference data ensures wide applicability, including to azosystems in complex environments. Based on the optimized force fields, nonadiabatic surface hopping simulations produce photoisomerization quantum yields and decay times of azobenzene, both in the gas phase and in n-hexane solution, in reasonable agreement with higher level theory and experiment. The transferability to other azo-compounds is illustrated for different arylazopyrazoles as well as ethylene-bridged azobenzene. Moreover, it has been shown that the model can be easily extended to adsorbates on metal surfaces. The simulation of the ring-opening of cyclobutene triggered by the photoisomerization of azobenzene in a macrocycle highlights the advantages of a reactive force field model.

Reactive Molecular Dynamics Simulation of the Structural Damages of the B-DNA Induced by the Oxidation/Nitration of Guanine

Reactive molecular dynamics simulations (RMD) have been carried out to investigate structural alterations of the dodecamer double-strand B-DNA due to the oxidation/nitration modifications introduced to its guanine bases, including 8-oxoguanine, 8-nitroguanine, and 5-guanidino-4-nitroimidazole, considering two distribution patterns. These modifications may arise in the case of cancer treatment using oxidative/nitrosative reactive nitrogen species as anticancer agents. Results show that these mutations affect structural characteristics of the B-DNA dodecamer in the order 8-nitroguanine > 5-guanidino-4-nitroimidazole ≫ 8-oxoguanine. For instance, the base-pair per turn for these modified B-DNA are changed respectively to 9.79, 10.88 and 10.58 from 10.51 in the native defect-free B-DNA, which is compatible with the experimental value of 10.10. In addition, these mutations allow more water molecules to diffuse into the dodecamer structure and consequently increase the possibility of the penetration of reactive and nonreactive species toward constituting nucleic base-pairs. The largest variation of the B-DNA structure is observed for the mutated B-DNA with 8-nitroguanine modifications applied to its separated CG base-pairs along the dodecamer chain. The structural changes introduced by these nitro-/oxo-modified guanine bases can be considered as a critical step in the damage of the DNA structure and alterations of its function.

Degradation Mechanism of Micro-Nanobubble Technology for Organic Pollutants in Aqueous Solutions

Micro-nanobubbles (MNBs) technology has emerged as an effective means of sewage treatment, while the molecular mechanism for its pollutant degradation is still unknown. In this paper, the reactive molecular dynamics simulation technique is used to study the degradation mechanism of pollutants caused by shock-induced nanobubble collapse. We first demonstrate that the propagating shock wave can induce nanobubble collapse, and the collapsing nanobubble has the ability to focus mechanical energy via the converging motion of liquid in the interior of the bubble, leading to the formation of a high-speed jet with a much higher energy density. We also unveil the mechanical nature of long-chain pollutant degradation and the mechanism of free radical generation. Due to the impacting jet, the high-gradient flow has the ability to stretch the long-chain molecule and cause mechanical scission of the molecule in a homolytic manner. Finally, our simulation results reveal that adding ozone molecules to the collapsing bubble would introduce an additional dehydrogenation mechanism.

Molecular Dynamics Simulation of a Single Carbon Chain through an Asymmetric Double-Layer Graphene Nanopore for Prolonging the Translocation Time

In recent years, sensing technology based on nanopores has become one of the trustworthy options for characterization and even identification of a single biomolecule. In nanopore based DNA sequencing technology, the DNA strand in the electrolyte solution passes through the nanopore under an applied bias electric field. Commonly, the ionic current signals carrying the sequence information are difficult to detect effectively due to the fast translocation speed of the DNA strand, so that slowing down the translocation speed is expected to make the signals easier to distinguish and improve the sequencing accuracy. Modifying the nanopore structure is one of the effective methods. Through all-atom molecular dynamics simulations, we designed an asymmetric double-layer graphene nanopore structure to regulate the translocation speed of a single carbon chain. The structure consists of two nanopores with different sizes located on two layers. The simulation results indicate that the asymmetric nanopore structure will affect the chain's translocation speed and the ionic current value. When the single carbon chain passes from the smaller pore to the larger pore, the translocation time is significantly prolonged, which is about three times as long as the chain passing from the larger pore to the smaller pore. These results provide a new idea for designing more accurate and effective single-molecule solid-state nanopore sensors.

Competition of Hydrogen Bonds and Coordinate Bonds Induces a Reversible Crystal Transformation

Achieving reversible molecular crystal transformation between coordinate aggregates and hydrogen bonded assemblies has been a challenging task because coordinate bonds are generally much stronger than hydrogen bonds. Recently, we have reported the incorporation of silver ions into the cyanuric acid-melamine (CAM) network, resulting in the formation of a 1D coordination polymer (crystal 1) through forming the κ₁N-Ag-κ₂N coordination bonds. In this work, we find crystal 1 will undergo reversible transformation to hydrogen bonded coordinate units (crystal 2) through the breaking of coordinate chains and then the addition of CAM hydrogen bonding motifs into the framework. Crystal 2 presents a pseudohexagonal arrangement comprised of the κ₁N-Ag-κ₂N units connected by two sets of the triple hydrogen bonds, which extends two-dimensionally and stacks into a layer-structured crystal. Light was shed on the tautomerization of CA and M ligands associated with the crystal transformations using single crystal X-ray diffraction and infrared spectroscopy by analyzing the bond lengths and vibrations. We also highlight that photoluminescence can be a useful tool to probe the tautomer conversions of conjugated molecules. Furthermore, crystal 1 demonstrates high flexibility and can be bent over 180° and recover to its original shape after stress release. Crystal 2, on the contrary, is brittle and shows distinct mechanical anisotropy along different crystal orientations, as unveiled by nanoindentation measurements. The elastic modulus is well correlated with the chemical bonding strength along each orientation, and it is noteworthy that the contribution of the triple hydrogen bonds is comparable to that of the coordination bonds.

Plasma-induced destruction of Candida albicans cell wall components: A reactive molecular dynamics simulation

Cold atmospheric plasma (CAP) has attracted significant attention and has been widely used to inactivate pathogens based on its excellent effect; however, the mechanisms underlying the interactions between plasma-generated species and organisms have not yet been fully elucidated. In this paper, the interactions of reactive oxygen plasma species (O, OH and H₂O₂) with chitin polymer (the skeletal component of the Candida albicans cell wall) were investigated by means of reactive molecular dynamics simulations from a microscopic point of view. Our simulations show that O and OH species can break important structural bonds (e.g., N-H bonds, O-H bonds and C-H bonds) of chitin. This is followed by a cascade of bond cleavage and double bond formation events. This simulation study aimed to improve the understanding of the micromechanism of plasma-inactivated Candida albicans at the atomic level.

On the Mechanical Properties of Popgraphene-Based Nanotubes: a Reactive Molecular Dynamics Study

Carbon-based tubular materials have sparked a great interest in future electronics and optoelectronics device applications. In this work, we computationally studied the mechanical properties of nanotubes generated from popgraphene (PopNTs). Popgraphene is a 2D carbon allotrope composed of 5-8-5 rings. We carried out fully atomistic reactive (ReaxFF) molecular dynamics for PopNTs of different chiralities ( n , 0 and 0 , n ) and/or diameters and at different temperatures (from 300 up to 1200 K). Results showed that the tubes are thermally stable (at least up to 1200 K). All tubes presented stress/strain curves with a quasi-linear behavior followed by an abrupt drop of stress values. Interestingly, armchair-like PopNTs ( 0 , n ) can stand a higher strain load before fracturing when contrasted to the zigzag-like ones ( n , 0 ). Moreover, it was obtained that Young's modulus (Y_Mod ) (750-900 GPa) and ultimate strength (σ_US ) (120-150 GPa) values are similar to the ones reported for conventional armchair and zigzag carbon nanotubes. Y_Mod values obtained for PopNTs are not significantly temperature-dependent. While the σ_US values for the 0 , n showed a quasi-linear dependence with the temperature, the n , 0 exhibited no clear trends.

Atomistic Mechanisms of Thermal Transformation in a Zr-Metal Organic Framework, MIL-140C

To understand the mechanisms responsible for thermal decomposition of a Zr-MOF (MIL-140C), we perform atomistic-scale molecular dynamics (MD) simulations and discuss the simulation data in comparison with the TEM images obtained for the decomposed Zr-MOF. First, we introduce the ReaxFF parameters suitable for the Zr/C/H/O chemistry and then apply them to investigate the thermal stability and morphological changes in the MIL-140C during heating. Based on the performed simulations we propose an atomic mechanism for the collapse of the MIL-140C and the molecular pathways for carbon monoxide formation, the main product of the MIL-140C thermal degradation. We also determine that the oxidation state of the ZrO_x clusters, evolved due to the thermal degradation, approximates the tetragonal phase of ZrO₂. Both simulations and experiments show a distribution of very small ZrO_x clusters embedded in the disrupted organic sheet that could contribute to the unusual high catalytic activity of the decomposed MIL-140C.

Oxygen depletion in FLASH ultra-high-dose-rate radiotherapy: A molecular dynamics simulation

PURPOSE

We present a first-principles molecular dynamics (MD) simulation and expound upon a mechanism of oxygen depletion hypothesis to explain the mitigation of normal tissue injury observed in ultra-high-dose-rate (UHDR) FLASH radiotherapy.

METHODS

We simulated damage to a segment of DNA (also representing other biomolecules such as RNA and proteins) in a simulation box filled with H 2 O and O 2 molecules. Attoseconds physical interactions (ionizations, electronic, and vibrational excitations) were simulated by using the Monte Carlo track structure code Geant4-DNA. Immediately after ionization, ab initio Car-Parrinello molecular dynamics (CPMD) simulation was used to identify which H 2 O and O 2 molecules surrounding the DNA molecule were converted into reactive oxygen species (ROS). Subsequently, the femto- to nanosecond reactions of ROS were simulated by using MD with reactive force field (ReaxFF), to illustrate ROS merging into new types of non-reactive oxygen species (NROS) due to strong coupling among ROS. A coarse-grained model was constructed to describe the relevant collective phenomenon at the macroscopic level on ROS aggregation and formation of NROS agglomerates consistent with the underlying microscopic pathways obtained from MD simulations.

RESULTS

Time-dependent molecular simulations revealed the formation of metastable and transient spaghetti-like complexes among ROS generated at UHDR. At the higher ROS densities produced under UHDR, stranded chains (i.e., NROS) are produced, mediated through attractive electric polarity forces, hydrogen bonds, and magnetic dipole-dipole interactions among hydroxyl ( . OH ) radicals. NROS tend to be less mobile than cellular biomolecules as opposed to the isolated and sparsely dense ROS generated at conventional dose rates (CDR). We attribute this effect to the suppression of biomolecular damage induced per particle track. At a given oxygen level, as the dose rate increases, the size and number of NROS chains increase, and correspondingly the population of toxic ROS components decreases. Similarly, at a given high dose rate, as the oxygen level increases, so do the size and number of NROS chains until an optimum level of oxygen is reached. Beyond that level, the amount of oxygen present may be sufficient to saturate the production of NROS chains, thereby reversing the sparing effects of UHDRs.

CONCLUSIONS

We showed that oxygen depletion, hypothesized to lead to lower normal-tissue toxicity at FLASH dose rates, takes place within femto- to nanoseconds after irradiation. The mechanism is governed by the slow dynamics of chains of ROS complexes (NROS). Under physoxic (≈ 4-5% oxygen) conditions (i.e., in normal tissues), NROS are more abundant than in hypoxic conditions (e.g., <0.3% in parts of tumors), suggesting that biomolecular damage would be reduced in an environment with physoxic oxygen levels. Hence irradiation at UHDRs would be more effective for sparing physoxic normal tissues but not tumors containing regions of hypoxia. At much higher levels of oxygen (e.g., >10-15%), oxygen depletion by UHDRs may not be sufficient for tissue sparing.

Structure and phase behavior of high-density ice from molecular-dynamics simulations with the ReaxFF potential

We report a molecular dynamics simulation study of dense ice modeled by the reactive force field (ReaxFF) potential, focusing on the possibility of phase changes between crystalline and plastic phases as observed in earlier simulation studies with rigid water models. It is demonstrated that the present model system exhibits phase transitions, or crossovers, among ice VII and two plastic ices with face-centered cubic (fcc) and body-centered cubic (bcc) lattice structures. The phase diagram derived from the ReaxFF potential is different from those of the rigid water models in that the bcc plastic phase lies on the high-pressure side of ice VII and does the fcc plastic phase on the low-pressure side of ice VII. The phase boundary between the fcc and bcc plastic phases on the pressure, temperature plane extends to the high-temperature region from the triple point of ice VII, fcc plastic, and bcc plastic phases. Proton hopping, i.e., delocalization of a proton, along between two neighboring oxygen atoms in dense ice is observed for the ReaxFF potential but only at pressures and temperatures both much higher than those at which ice VII-plastic ice transitions are observed.

Reactive molecular dynamics simulation for isotope-exchange reactions in H/D systems: ReaxFFHD development

To investigate the chemical isotope-exchange reactions within a system composed of a mixture of hydrogen and deuterium (H/D) in the plasma media, the ReaxFF_HD potential was parameterized against an appropriate quantum mechanics (QM)-based training set. These QM data involve structures and energies related to bond dissociation, angle distortion, and an exchange reaction of the tri-atomic molecular ions, H₃ ⁺, D₃ ⁺, H₂D⁺, and D₂H⁺, produced in the hydrogen plasma. Using the ReaxFF_HD potential, a range of reactive molecular dynamics simulations were performed on different mixtures of H/D systems. Analysis of the reactions involved in the production of these tri-atomic molecular ions was carried out over 1 ns simulations. The results show that the ReaxFF_HD potential can properly model isotope-exchange reactions of tri-atomic molecular ions and that it also has a perfect transferability to reactions taking place in these systems. In our simulations, we observed some intermediate molecules (H₂, D₂, and HD) that undergo secondary reactions to form the tri-atomic molecular ions as the most likely products in the hydrogen plasma. Moreover, there remains a preference for D in the produced molecular ions, which is related to the lower zero-point energy of the D-enriched species, showing the isotope effects at the heart of the ReaxFF_HD potential.

Effect of an electric field during the deposition of silicon dioxide thin films by plasma enhanced atomic layer deposition: an experimental and computational study

The growth, chemical, structural, mechanical, and optical properties of oxide thin films deposited by plasma enhanced atomic layer deposition (PEALD) are strongly influenced by the average-bias voltage applied during the reaction step of surface functional groups with oxygen plasma species. Here, this effect is investigated thoroughly for SiO2 deposited in two different PEALD tools at average-bias voltages up to -300 V. Already at a very low average-bias voltage (< -10 V), the SiO2 films have significantly lower water content than films grown without biasing together with the formation of denser films having a higher refractive index and nearly stoichiometric composition. Substrate biasing during PEALD also enables control of mechanical stress. The experimental findings are supported by density functional theory and atomistic simulations. They demonstrate that the application of an electric field during the plasma step results in an increased energy transfer between energetic ions and the surface, directly influencing relevant surface reactions. Applying an electric field during the PEALD process leads to SiO2 thin films with significantly improved properties comparable to films grown by ion beam sputtering.

Tuning the Mechanical and Adhesion Properties of Carbon Nanotubes Using Aligned Cellulose Wrap (Cellulose Nanotube): A Molecular Dynamics Study

Improving the adhesion properties of carbon nanotubes (CNTs) at the molecular scale can significantly enhance dispersion of CNT fibers in polymer matrix and unleash the dormant extraordinary mechanical properties of CNTs in CNT-polymer nanocomposites. Inspired by the outstanding adhesion, dispersion, mechanical, and surface functionalization properties of crystalline nanocellulose (CNC), this paper studies the mechanical and adhesion properties of CNT wrapped by aligned cellulose chains around CNT using molecular dynamic simulations. The strength, elastic modulus, and toughness of CNT-cellulose fiber for different cellulose contents are obtained from tensile and compression tests. Additionally, the effect of adding cellulose on the surface energy, interfacial shear modulus, and strength is evaluated. The result shows that even adding a single layer cellulose wrap (≈55% content) significantly decreases the mechanical properties, however, it also dramatically enhances the adhesion energy, interfacial shear strength, and modulus. Adding more cellulose layers, subsequently, deceases and increases mechanical properties and adhesion properties, respectively. In addition, analysis of nanopapers of pristine CNT, pristine CNC, and CNT-wrapped cellulose reveals that CNT-wrapped cellulose nanopapers are strong, stiff, and tough, while for CNT and CNC either strength or toughness is compromised. This research shows that cellulose wraps provide CNT fibers with tunable mechanical properties and adhesion energy that could yield strong and tough materials due to the excellent mechanical properties of CNT and active surface and hydrogen bonding of cellulose.

Theoretical study on degradation mechanism of ornidazole on anatase TiO2(101) and (001) surfaces

The degradation mechanism of one new emerging pollutant ornidazole (ONZ) on TiO₂surface is explored using DFT calculations.

Experimental and theoretical elucidation of catalytic pathways in TiO2-initiated prebiotic polymerization

The tendency of glycine to form polymer chains on a rutile(110) surface under wet/dry conditions (dry-wet cycles at high temperature) is studied through a conjunction of surface sensitive experimental techniques and sequential periodic multilevel calculations that mimics the experimental procedures with models of decreasing complexity and increasing accuracy. X-ray photoemission spectroscopy (XPS) and thermal desorption spectroscopy (TDS) experimentally confirmed that the dry-wet cycles lead to Gly polymerization on the oxide support. This was supported by all the theoretical characterizations. First, classical reactive molecular dynamics (MD) simulations based on the ReaxFF approach were used to reproduce the adsorption of the experimental glycine solution droplets sprayed onto an oxide support and to identify the most probable arrangement of the molecules that triggered the polymerization mechanisms. Then, quantum chemistry density functional tight binding (DF-TB) MDs and static density functional theory (DFT) calculations were carried out to further explore favorable configurations and to evaluate the energy barriers of the most promising reaction pathways for the peptide bond-formation reactions. The results confirmed the fundamental role played by the substrate to thermodynamically and kinetically favor the process and disclosed its main function as an immobilizing agent: the molecules accommodated in the surface channels close to each other were the ones starting the key events of the dimerization process and the most favorable mechanism was the one where a water molecule acted as a proton exchange mediator in the condensation process.

Atomistic Simulations of Plasma-Enhanced Atomic Layer Deposition

Plasma-enhanced atomic layer deposition (PEALD) is a widely used, powerful layer-by-layer coating technology. Here, we present an atomistic simulation scheme for PEALD processes, combining the Monte Carlo deposition algorithm and structure relaxation using molecular dynamics. In contrast to previous implementations, our approach employs a real, atomistic model of the precursor. This allows us to account for steric hindrance and overlap restrictions at the surface corresponding to the real precursor deposition step. In addition, our scheme takes various process parameters into account, employing predefined probabilities for precursor products at each Monte Carlo deposition step. The new simulation protocol was applied to investigate PEALD synthesis of SiO₂ thin films using the bis-diethylaminosilane precursor. It revealed that increasing the probability for precursor binding to one surface oxygen atom favors amorphous layer growth, a large number of –OH impurities, and the formation of voids. In contrast, a higher probability for precursor binding to two surface oxygen atoms leads to dense SiO₂ film growth and a reduction of –OH impurities. Increasing the probability for the formation of doubly bonded precursor sites is therefore the key factor for the formation of dense SiO₂ PEALD thin films with reduced amounts of voids and –OH impurities.

Theoretical study of the adsorption characteristics and the environmental influence of ornidazole on the surface of photocatalyst TiO2

In this paper, density functional theory (DFT) was performed to study the adsorption properties of ornidazole on anatase TiO2(101) and (001) crystal facets under vacuum, neutral and acid-base conditions. We calculated the adsorption structure of ornidaozle on the anatase TiO2 surface, optimal adsorption sites, adsorption energy, density of states, electronic density and Milliken atomic charge under different conditions. The results show that when the N(3) atom on the imidazole ring is adsorbed on the Ti(5) atom, the largest adsorption energy and the most stable adsorption configuration could be achieved. According to the analysis of the adsorption configuration, we found that the stability of C(2)-N(3) bond showed a weakening trend. The adsorption wavelengths of the electronic transition between the valence band and conduction band of ornidazole on the TiO2 surface were in the visible light wavelengths range, showing that the TiO2 crystal plane can effectively make use of visible light under different conditions. We speculate the possibility of ornidazole degradation on the surface of TiO2 and found that the reactive site is the C-N bond on the imidazole ring. These discoveries explain the photocatalytic degradation of ornidazole by TiO2 and reveal the microscopic nature of catalytic degradation.

A complete depolymerization of scrap tire with supercritical water participation: A molecular dynamic simulation study

The growth of scrap tire (ST) has become an urgent environmental problem. In this work, the depolymerization process of ST in supercritical water (SCW) was studied with the ReaxFF molecular dynamic simulation. The depolymerization process and reaction pathway of ST in SCW were revealed. The simulation results indicated that the SCW molecules could promote the depolymerization of rubber into smaller molecules by releasing the OH radicals. After providing the OH radicals, the SCW molecules banded with the free H and turned into H₃O radicals which were the main resources to produce H₂. In the ST-SCW reaction system, more than 95% organic components in ST depolymerized into the valuable fuel (oil and fuel gas). The main compound in oil product was light oil with low viscosity. The gas products included the H₂, CO and C1-C4 gas. It was found that reaction temperature could dominate the component of final products from ST. In order to produce more oil, the optimal temperature to recycle ST with SCW participation was 647-659 K. This study demonstrates the feasibility of SCW in recovering the chemical products from ST, and provides a theoretical support for its further development.

Development of the ReaxFF Methodology for Electrolyte-Water Systems

A new ReaxFF reactive force field has been developed for water-electrolyte systems including cations Li⁺, Na⁺, K⁺, and Cs⁺ and anions F^-, Cl^-, and I^-. The reactive force field parameters have been trained against quantum mechanical (QM) calculations related to water binding energies, hydration energies and energies of proton transfer. The new force field has been validated by applying it to molecular dynamics (MD) simulations of the ionization of different electrolytes in water and comparison of the results with experimental observations and thermodynamics. Radial distribution functions (RDF) determined for most of the atom pairs (cation or anion with oxygen and hydrogen of water) show a good agreement with the RDF values obtained from DFT calculations. On the basis of the applied force field, the ReaxFF simulations have described the diffusion constants for water and electrolyte ions in alkali metal hydroxide and chloride salt solutions as a function of composition and electrolyte concentration. The obtained results open opportunities to advance ReaxFF methodology to a wide range of applications involving electrolyte ions and solutions.

Theoretical study of adsorption characteristics and the environmental influence for metronidazole on photocatalytic TiO2 anatase surfaces

The adsorption characteristics of metronidazole on anatase TiO₂(101) and (001) surfaces were studied by density functional theory (DFT). The adsorption structure of metronidazole on anatase TiO₂(101) and (001) surfaces has been optimized under vacuum, water, acidic, and alkaline conditions, respectively. The optimum adsorption site, adsorption energy, and electronic structure of the stable adsorption model were calculated. The adsorption characteristics of metronidazole on two different surfaces of TiO₂ were studied under acidic and alkaline conditions. Our calculated results found that the adsorption energy range is -0.95 ~ -3.11 eV on the TiO₂ (101) surface, and the adsorption energy range is -0.84 ~ -3.29 eV on the TiO₂ (001) surface. The adsorption wavelengths of electron transition between valence band and conduction band of metronidazole on the anatase TiO₂(101) surface is in the range of visible wavelength, indicating that the TiO₂(101) surface can effectively utilize visible light. However, the photocatalytic effect of the TiO₂(001) surface is greatly affected by the environment. The results reveal the adsorption characteristics and the environmental influence for metronidazole on photocatalytic anatase TiO₂ surfaces. Graphical abstract The adsorption characteristics of metronidazole on anatase TiO₂(101) and (001) crystal surfaces were studied by density functional theory (DFT).

Amino acid adsorption on anatase (101) surface at vacuum and aqueous solution: a density functional study

The adsorption of 20 amino acids (AAs) on the (101) surface of anatase titanium dioxide (TiO₂) has been investigated under the scheme of density functional theory. Through the analysis of adsorption geometries, amino group and side chains of AAs have been identified as the major side to adsorb on TiO₂, while the carboxyl group prefers to stay outside to avoid the repulsion between negatively charged oxygen from TiO₂ and AAs. On the surface, two-coordinated oxygen is the major site to stabilize AAs through O-H interactions. The above conclusion does not change when it is in the aqueous solution based on the calculations with AAs surrounded by explicit water molecules. The above knowledge is helpful in predicting how AAs and even peptides adsorb on inorganic materials. Graphical abstract The adsorption of 20 amino acids (AAs) on the (101) surface of anatase titanium dioxide (TiO₂) has been investigated under the scheme of density functional theory.

Explicit Solvation Matters: Performance of QM/MM Solvation Models in Nucleophilic Addition

Nucleophilic addition onto a carbonyl moiety is strongly affected by solvent, and correctly simulating this solvent effect is often beyond the capability of single-scale quantum mechanical (QM) models. This work explores multiscale approaches for the description of the reversible and highly solvent-sensitive nucleophilic N|···C=O bond formation in an Me₂N–(CH₂)₃–CH=O molecule. In the first stage of this work, we rigorously compare and test four recent quantum mechanical/molecular mechanical (QM/MM) explicit solvation models, employing a QM description of water molecules in spherical regions around both the oxygen and the nitrogen atom of the solute. The accuracy of the models is benchmarked against a reference QM simulation, focusing on properties of the solvated Me₂N–(CH₂)₃–CH=O molecule in its ring-closed form. In the second stage, we select one of the models (continuous adaptive QM/MM) and use it to obtain a reliable free energy profile for the N|···C bond formation reaction. We find that the dual-sphere approach allows the model to accurately account for solvent reorganization along the entire reaction path. In contrast, a simple microsolvation model cannot adapt to the changing conditions and provides an incorrect description of the reaction process.

Phase transitions of ordered ice in graphene nanocapillaries and carbon nanotubes

New phase diagrams for water confined in graphene nanocapillaries and single-walled carbon nanotubes (CNTs) are proposed, identifying ice structures, their melting points and revealing the presence of a solid-liquid critical point. For quasi-2D water in nanocapillaries, we show through molecular-dynamics simulations that AA stacking in multilayer quasi-2D ice arises from interlayer hydrogen-bonding and is stable up to three layers, thereby explaining recent experimental observations. Detailed structural and energetic analyses show that quasi-2D water can freeze discontinuously through a first-order phase transition or continuously with a critical point. The first-order transition line extends to a continuous transition line, defined by a sharp transition in diffusivity between solid-like and liquid-like regimes. For quasi-1D water, confined in CNTs, we observe the existence of a similar critical point at intermediate densities. In addition, an end point is identified on the continuous-transition line, above which the solid and liquid phases deform continuously. The solid-liquid phase transition temperatures in CNTs are shown to be substantially higher than 273 K, confirming recent Raman spectroscopy measurements. We observe ultrafast proton and hydroxyl transport in quasi-1D and -2D ice at 300 K, exceeding those of bulk water up to a factor of five, thereby providing possible applications to fuel-cells and electrolyzers.

Atomistic and continuum scale modeling of functionalized graphyne membranes for water desalination

Recent theoretical and experimental studies reported ultra-high water permeability and salt rejection in nanoporous single-layer graphene. However, creating and controlling the size and distribution of nanometer-scale pores pose significant challenges to application of these membranes for water desalination. Graphyne and hydrogenated graphyne have tremendous potential as ultra-permeable membranes for desalination and wastewater reclamation due to their uniform pore-distribution, atomic thickness and mechano-chemical stability. Using molecular dynamics (MD) simulations and upscale continuum analysis, the desalination performance of bare and hydrogenated α-graphyne and γ-{2,3,4}-graphyne membranes is evaluated as a function of pore size, pore geometry, chemical functionalization and applied pressure. MD simulations show that pores ranging from 20 to 50 Ų reject in excess of 90% of the ions for pressures up to 1 GPa. Water permeability is found to range up to 85 L cm^-2 day^-1 MPa^-1, which is up to three orders of magnitude larger than commercial seawater reverse osmosis (RO) membranes and up to ten times that of nanoporous graphene. Pore chemistry, functionalization and geometry are shown to play a critical role in modulating the water flux, and these observations are explained by water velocity, density, and energy barriers in the pores. The atomistic scale investigations are complemented by upscale continuum analysis to examine the performance of these membranes in application to cross-flow RO systems. This upscale analysis, however, shows that the significant increase in permeability, observed from MD simulations, does not fully translate to current RO systems due to transport limitations. Nevertheless, upscale calculations predict that the higher permeability of graphyne membranes would allow up to six times higher permeate recovery or up to 6% less energy consumption as compared to thin-film composite membranes at currently accessible operating conditions. Significantly higher energy savings and permeate recovery can be achieved if higher feed-flow rates can be realized.