ReaxFF-based Molecular Dynamics Research Articles

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.

ReaxFF molecular dynamics simulation of single-crystalline silicon plasma polishing and subsurface damage removal

Recently, plasma etching has become one of the most promising polishing methods due to its low cost and environmental friendliness. In this study, the mechanism and parametric influence of plasma etching were investigated using ReaxFF-based molecular dynamics (RBMD) simulation, allowing the characterization of the process of F atom etching of monocrystalline silicon and the removal of subsurface defects from an atomic perspective. We simulated the process of F-atom etching and the mechanism of F-atom removal of the subsurface damage of single-crystalline silicon. The simulation results indicate that SiF4 generated by monocrystalline silicon under the action of F atoms gradually generated SiF5- groups and detached from the substrate as the reaction time increases. Simultaneously, under the action of F atoms, Si atoms gradually filled the subsurface defects, achieving damage removal. In addition, the incident angle can be increased in the plasma polishing process to reduce the thickness of the amorphous deformation layer and improve the surface quality.

A ReaxFF-based molecular dynamics study of the destruction of PFAS due to ultrasound

This work uses a computational approach to provide a mechanistic explanation for the experimentally observed destruction of per- and polyfluoroalkyl substances (PFAS) in water due to ultrasound. The PFAS compounds have caused a strong public and regulatory response due to their ubiquitous presence in the environment and toxicity to humans. In this research, ReaxFF -based Molecular Dynamics simulation under several temperatures ranging from 373 K to 5,000 K and different environments such as water vapor, O2, N2, and air were performed to understand the mechanism of PFAS destruction. The simulation results showed greater than 98% PFAS degradation was observed within 8 ns under a temperature of 5,000 K in a water vapor phase, replicating the observed micro/nano bubbles implosion and PFAS destruction during the application of ultrasound. Additionally, the manuscript discusses the reaction pathways and how PFAS degradation evolves providing a mechanistic basis for the destruction of PFAS in water due to ultrasound. The simulation showed that small chain molecules C1 and C2 fluoro-radical products are the most dominant species over the simulated period and are the impediment to an efficient degradation of PFAS. Furthermore, this research confirms the empirical findings observations that the mineralization of PFAS molecules occurs without the generation of byproducts. These findings highlight the potential of virtual experiments in complementing laboratory experiments and theoretical projections to enhance the understanding of PFAS mineralization during the application of ultrasound.

A molecular investigation on the mechanism of co-pyrolysis of ammonia and biodiesel surrogates

As renewable energy sources with great potential to reduce carbon footprints and pollutant emissions, ammonia and biodiesel both have garnered substantial research interest. This study aimed to investigate the detailed mechanism of co-pyrolysis of ammonia and biodiesel surrogates, including the pyrolysis of different biodiesel surrogates, the effect of biodiesel decomposition on ammonia reactions, nitric oxide (NO) generation during the ammonia-biodiesel reaction process, and the effect of ammonia on soot formation during biodiesel pyrolysis. Using ReaxFF-based molecular dynamics simulations, the results revealed that the presence of ester groups in biodiesel lowers the activation energy of the reaction compared to alkanes. Meanwhile, biodiesel structures with shorter chain lengths, isomerisation, and carbon-carbon double bond effectively lower the activation energy. Time evolutions of the main pyrolysis products of methyl butanoate (MB), ethyl propionate (EP), and methyl crotonate (MC), as well as their detailed decomposition pathways, were produced. The coexistence of biodiesel and ammonia can promote the decomposition of ammonia, with MC containing carbon-carbon double bonds providing the most abundant free radical environment for ammonia decomposition. High temperature promotes the occurrence of the reaction, with MC, MB, and EP producing NO in the order of MC > MB > EP. Ammonia addition reduces soot production in the pyrolysis of different biodiesel surrogates, with MC exhibiting the most significant effect. The roles of oxygen-containing and nitrogen-containing species in soot suppression and their synergistic impact were identified at the atomic-scale. The insights into the detailed reaction mechanism of the co-pyrolysis of ammonia and biodiesel obtained in this study can be used to guide the development of ammonia-biodiesel co-firing technology.

Theoretical Investigation of W(CO)6 and CO Selenization Process

Detailed atomic-level insight into the mechanism of W(CO)6 and CO selenization is essential for the fabrication of cheap and environmentally benign transition metal chalcogenides such as MoS2 and WSe2. Earlier discussions in literature have focused mainly on the CO methanation by sulfur and its derivatives but H2Se mediated CO methanation at the atomic level is yet to be explored. First-principles calculations and ReaxFF-based molecular dynamics simulations are conducted here to explore the relative stabilities of intermediates formed during the gas-phase interactions of W(CO)6 and H2Se, determined associated reaction energies and kinetic barriers. The methanation of CO, which is released from the organometal, by H2Se is further investigated. The results indicate that the chain reactions of W(CO)6 and H2Se lead to the formation of a thermodynamically stable end product of W(SeH)2Se2. Depending on the temperature, W(HSe)2Se2 is expected to go through a last uphill reaction by releasing H2Se into the environment and evolving into a WSe3 molecule. Additionally, the dehydrogenation of organometallic molecules is thermodynamically feasible but kinetically controlled, requiring a significant activation energy. When all CO groups are released from the W atom, the H2 release from W-compund becomes nearly barrierless. Since CO radical groups are dominant byproducts formed during the MOCVD chain reactions but in a chalcogen rich environment, this work also shed light into the CO selenization during the growth of transition metal diselenides (e.g., WSe2, MoSe2, CrSe2) and discusses the formation of potential products such as CSe2, CH4, H2Se, CO, H2O, Se2.

A ReaxFF-based molecular dynamics study of the pyrolysis mechanism of hexamethyldisiloxane

Hexamethyldisiloxane (MM) is one of the commonly used working fluids of organic Rankine cycle at medium and high temperatures, but there is a risk of decomposition of organic working fluids in high temperature environment. In this study, the pyrolysis mechanism of MM is analyzed by using ReaxFF force field and density functional theory (DFT). During the simulation process, three initial reaction routes were observed. By calculating the reaction energy barriers, it is found that the fracture of C-Si bond is the main initial reaction of pyrolysis. In the MM pyrolysis process, small molecule gases such as CH4, C2H6 and H2, linear siloxane represented by C8H24O2Si3（MDM）are the main thermal decomposition products. Free radical attacking reaction and free radical binding reaction are the main formation mechanism of methane. The intermediate condensation reaction is the formation mechanism of MDM. Most of the chain reactions are exothermic reactions, which can provide the energy for the system and further promote the decomposition of MM.

Atomistic insights into the protection failure of the graphene coating under the hyperthermal impacts of reactive oxygen species: ReaxFF-based molecular dynamics simulations

ReaxFF-based molecular dynamics was used to demonstrate the limited coating effect of pristine graphene in protecting a typical Ni(111) substrate against hyperthermal oxygen species. Under 10-eV O2 and O3 molecules, graphene remained intact, and served as a protective coating by preventing the diffusion of molecules towards underlying Ni(111). By increasing the initial energy of incident species to 20 and 30 eV, graphene failed to provide efficient protection, offering protection degrees of 53.16 and 40.87% against O2, and 55.12 and 47.78% against O3. As opposed to O2 and O3, 10-eV O exposure led to a low protection degree of 58.95%, decreasing to 21.98%, and switching to 6.20% anti-protection when the initial energy increased to 20 and 30 eV. Through the detailed analysis of simulated trajectories, a three-stage oxidation process was proposed, elucidating the mechanism for these low protection degrees. On the basis of the proposed mechanism, the graphene’s coating effect is limited by the formation and growth of defects on graphene, enabling atomic diffusion across the graphene-Ni(111) interface, and leading to NiO formation over the damaged regions of graphene. The structural analysis then confirmed graphene’s transformation from a crystalline to a highly disordered carbon phase decorated by an amorphous NiO phase.

Anomalous strain effect on the thermal conductivity of low-buckled two-dimensional silicene.

The thermal conductivity of two-dimensional materials, such as graphene, typically decreases when tensile strain is applied, which softens their phonon modes. Here, we report an anomalous strain effect on the thermal conductivity of monolayer silicene, a representative low-buckled two-dimensional (LB-2D) material. ReaxFF-based molecular dynamics simulations are performed to show that biaxially stretched monolayer silicene exhibits a remarkable increase in thermal conductivity, by as much as 10 times the freestanding value, with increasing applied strain in the range of [0, 0.1], which is attributed to increased contributions from long-wavelength phonons. A further increase in strain in the range of [0.11, 0.18] results in a plateau of the thermal conductivity in an oscillatory manner, governed by a unique dynamic bonding behavior under extreme loading. This anomalous effect reveals new physical insights into the thermal properties of LB-2D materials and may provide some guidelines for designing heat management and energy conversion devices based on such materials.

ReaxFF-based molecular dynamics study of bio-derived polycyclic alkanes as potential alternative jet fuels

This work investigates the initial stages of the pyrolysis of HtH-1 (C18H32; 2,2,7,7,8a,8b-hexamethyl-dodecahydrobiphenylene) and HtH-2 (C18H34; 1,1′,3,3,3′,3′-hexamethyl-1,1′-bi(cyclohexane)), which are bio-derived polycyclic alkanes and potential jet fuels, using ReaxFF force field based molecular dynamics (MD) simulations. Global Arrhenius parameters, such as activation energies and pre-exponential factors, are calculated and used to analyze the overall decomposition kinetics of the fuels. HtH-1 decomposes faster than HtH-2 at the same temperature and density conditions, and they have a faster decomposition rate compared to some existing jet-fuels, such as JP-10. A systematic reaction analysis framework developed in this work is applied to determine a temperature-dependent decomposition mechanism. At lower temperature, the central C–C bond connecting the two cyclohexane rings is dominantly broken in both HtH-1 and HtH-2. However, C-CH3 bond breaking becomes dominant with increasing temperature due to the large increase in entropy during this reaction. Major products from HtH-1 are C5H8 and C4H8, and those from HtH-2 are C4H8 and C2H4. The major products predict that HtH-1 has a higher sooting tendency than HtH-2, which is consistent with measurements. The impact of HtH-2 on the pyrolysis of HtH-1 is also investigated in their binary mixtures. HtH-1 and HtH-2 decompose by unimolecular reactions, and they rarely interact with each other during the pyrolysis of the mixtures. This work demonstrates that ReaxFF can be used to investigate pyrolysis and combustion chemistry of existing or future fuels and to contribute to the development of their chemical kinetic models without any a priori input and chemical intuition.

Thermal decomposition mechanism of some hydrocarbons by ReaxFF-based molecular dynamics and density functional theory study

In order to investigate the decomposition mechanism of hydrocarbons, pyrolysis processes of 11 typical hydrocarbons (isobutane, isopentane, isohexane, n-butane, n-pentane, n-hexane, cyclobutane, cyclopentane, cyclohexane, benzene and toluene) are performed by using ReaxFF MD and DFT method. The results show that the initial pyrolysis reactions of these hydrocarbons can be divided into two types: homolytic cleavage of C–H bond and C–C bond. The bond dissociation energies of C–H bonds are higher than that of C–C bonds in these hydrocarbons except for toluene. The thermal decomposition rates of branched-chain hydrocarbons are faster than that of straight-chain hydrocarbons. The thermal decomposition rates of chain hydrocarbons gradually increase with the increases of C atom number. The main product molecules of hydrocarbon pyrolysis are H2, CH4, C2H2 and C2H4. The apparent activation energies of 4 hydrocarbons (n-pentane, isohexane, neopentane and cyclopentane) pyrolysis are calculated by the kinetic analysis. In further reactions, CH3, C2H5 and H radicals are collided with hydrocarbons to undergo H-abstraction reactions. The energy barriers of H-abstraction reactions are calculated by DFT.

ReaxFF-based molecular dynamics simulation of DNA molecules destruction in cancer cells by plasma ROS

Medical applications of plasma have been a hot topic of research recently. Studies have shown that cold atmospheric pressure plasma (CAP) plays a beneficial role in cancer treatments and can selectively kill cancer cells. Some reactive oxygen species (ROS) in plasma react with cancer cells, altering the cellular structure and inducing apoptosis. Currently, however, it is difficult to determine the microscopic mechanism of the reaction between plasma and cancer cells. In this work, a reactive force field was used to model the deoxyribonucleic acid (DNA) damage caused by three ROS (O, OH, and H2O2) at the atomic level. The simulation showed that the ROS of CAP reacted with the DNA of cancer cells, breaking important chemical bonds in DNA molecules and damaging the genes of cancer cells. Therefore, the reaction between ROS and DNA molecules affects gene transcription, replication, and reproduction of cancer cells and inhibits their unlimited proliferation. O atoms, OH radicals, and H2O2 can damage DNA molecules at different structural positions, causing major irreversible damage to the molecular structure of the DNA.

ReaxFF-based molecular dynamics simulation of the initial pyrolysis mechanism of lignite

In this paper, a series of ReaxFF molecular dynamics (ReaxFF-MD) simulations were employed to explore the characteristics of pyrolysis products, transformation behavior of major elements, and thermal decomposition mechanism of lignite. The results suggest that the pyrolysis of lignite mainly undergoes decomposition of macromolecular structure and breakage of bridge bonds at lower temperatures. At relatively high temperatures, further cracking of tar fragments and condensation of aromatic structures occur. The relationship between the main pyrolysis gases and the structural characteristics of lignite has been studied. The results show that the formation of H2O, CO2, and C2H4 is associated with the typical structure of lignite i.e., hydroxyl groups, carboxyl groups, and methylene carbon, respectively. Unlike bituminous coal and subbituminous coal, light tar is the main component of pyrolysis tar, which is due to large amounts of monocyclic and bicyclic structures in lignite. The pyrolysis mechanism of lignite was further analyzed through element migration behavior, and the simulation results are consistent with the above reaction mechanism. This work provides in-depth insight into the initial reaction mechanism of lignite pyrolysis and may be useful for the industrialization of lignite clean utilization.

Predicting the preferred morphology of hexagonal boron nitride domain structure on nickel from ReaxFF-based molecular dynamics simulations.

An understanding of the nucleation and growth of hexagonal boron nitride (hBN) on nickel substrates is essential to its development as a functional material. In particular, fundamental insights into the formation of the hexagonal lattices with alternating boron (B) and nitrogen (N) atoms could be exploited to control hBN lattice morphologies for targeted applications. In this study, the preferred shapes and edge configurations of atomically smooth hBN on Ni(111) were investigated using molecular dynamics (MD) simulations, along with reactive force field (ReaxFF) developed to represent the Ni/B/N system and the lattice-building B-N bond formation. The obtained hBN lattices, from different B : N feed ratios, are able to confirm that hBN domain geometries can indeed be tuned by varying thermodynamic parameters (i.e., chemical potentials of N and B) - a finding that has only been predicted using quantum mechanical theories. Here, we also showed that the nitrogen fed to the system plays a more crucial role in dictating the size of hBN lattices. With an increase of the relative N content, the simulated hBN domain shapes also transition from equilateral triangles to hexagons, again, consistent with the anticipation based on Density Functional Theory (DFT) calculations. Hence, a plausible approach to acquire a desired hBN nanostructure depends on careful control over the synthesis conditions, which now can benefit from reliable molecular simulations.

Study of mechanisms for electric field effects on ethanol oxidation via reactive force field molecular dynamics

Molecular dynamics simulations based on reactive force fields (ReaxFF) were conducted to study the effects of an external electric field with varying electric field strengths on ethanol oxidation reactions. Time evolutions of the reactants and intermediate species indicate that imposition of the electric field has modified the reaction pathways in addition to changing the reaction rate in a non-linear way. Intermediates of ethanol oxidation reactions with and without the electric field are identified and quantified. For the first time, reaction pathways of ethanol oxidation with and without an imposed electric field are scrutinized at the atomic scales. The reaction pathways without the electric field are consistent with previous experimental and numerical studies, which validate the present approach. Reaction pathways under varying electric field strengths, on the other hand, show some common pathways but also unique pathways associated with different strengths of the imposed electric field. The ReaxFF-based molecular dynamics method provides new insight into mechanisms for the effects of an electric field with varying electric field strengths on ethanol oxidation reactions. The present research demonstrates that ReaxFF-based reactive molecular dynamics is a valuable tool for detailed study of reaction mechanisms of hydrocarbon or oxygenated fuels, which complements commonly used experimental and computational techniques.

A ReaxFF-based molecular dynamics study of the oxidation decomposition mechanism of HFO-1336mzz(Z)

The oxidation decomposition mechanism of HFO-1336mzz(Z) were studied by ReaxFF simulations. The initial oxidation dissociation reactions of HFO-1336mzz(Z) can be divided into two types: thermal decomposition of HFO-1336mzz(Z) and the collision of O2 with HFO-1336mzz(Z). Most of the latter reactions are more likely to occur than the former ones. By comparing the energy barriers of initiation pathways, the pathway 2 and pathway 3 which involve the collision of CC bonds with O2 molecules are main reaction pathways and the energy barriers of these reactions are 153.3 and 135.3 kJ mol−1, respectively. HF, COF2 and CO2 are main products and the formation pathways of these products are observed from ReaxFF MD simulations. The main small radicals CF3, F, O, COF and COF3 play an important role in the oxidation decomposition of HFO-1336mzz(Z) because they can promote the decomposition of molecules and radicals and the formation of main products.

ReaxFF molecular dynamics simulation of intermolecular structure formation in acetic acid-water mixtures at elevated temperatures and pressures.

The intermolecular structure formation in liquid and supercritical acetic acid-water mixtures was investigated using ReaxFF-based molecular dynamics simulations. The microscopic structures of acetic acid-water mixtures with different acetic acid mole fractions (1.0 ≥ xHAc ≥ 0.2) at ambient and critical conditions were examined. The potential energy surface associated with the dissociation of acetic acid molecules was calculated using a metadynamics procedure to optimize the dissociation energy of ReaxFF potential. At ambient conditions, depending on the acetic acid concentration, either acetic acid clusters or water clusters are dominant in the liquid mixture. When acetic acid is dominant (0.4 ≤ xHAc), cyclic dimers and chain structures between acetic acid molecules are present in the mixture. Both structures disappear at increased water content of the mixture. It was found by simulations that the acetic acid molecules released from these dimer and chain structures tend to stay in a dipole-dipole interaction. These structural changes are in agreement with the experimental results. When switched to critical conditions, the long-range interactions (e.g., second or fourth neighbor) disappear and the water-water and acetic acid-acetic acid structural formations become disordered. The simulated radial distribution function for water-water interactions is in agreement with experimental and computational studies. The first neighbor interactions between acetic acid and water molecules are preserved at relatively lower temperatures of the critical region. As higher temperatures are reached in the critical region, these interactions were observed to weaken. These simulations indicate that ReaxFF molecular dynamics simulations are an appropriate tool for studying supercritical water/organic acid mixtures.

A ReaxFF-based molecular dynamics study of the mechanisms of interactions between reactive oxygen plasma species and the Candida albicans cell wall

Atmospheric pressure non-equilibrium plasmas have attracted significant attention and have been widely used to inactivate pathogens, yet the mechanisms underlying the interactions between plasma-generated species and bio-organisms have not been elucidated clearly. In this paper, reactive molecular dynamics simulations are employed to investigate the mechanisms of interactions between reactive oxygen plasma species (O, OH, and O2) and β-1,6-glucan (a model for the C. albicans cell wall) from a microscopic point of view. Our simulations show that O and OH species can break structurally important C-C and C-O bonds, while O2 molecules exhibit only weak, non-bonded interactions with β-1,6-glucan. Hydrogen abstraction from hydroxyl or CH groups occurs first in all bond cleavage mechanisms. This is followed by a cascade of bond cleavage and double bond formation events. These lead to the destruction of the fungal cell wall. O and OH have similar effects related to their bond cleavage mechanisms. Our simulation results provide fundamental insights into the mechanisms underlying the interactions between reactive oxygen plasma species and the fungal cell wall of C. albicans at the atomic level.

Liquid Adsorption of Organic Compounds on Hematite α-Fe2O3 Using ReaxFF.

ReaxFF-based molecular dynamics simulations are used in this work to study the effect of the polarity of adsorbed molecules in the liquid phase on the structure and polarization of hematite (α-Fe2O3). We compared the adsorption of organic molecules with different polarities on a rigid hematite surface and on a flexible and polarizable surface. We show that the displacements of surface atoms and surface polarization in a flexible hematite model are proportional to the adsorbed molecule's polarity. The increase in electrostatic interactions resulting from charge transfer in the outermost solid atoms in a flexible hematite model results in better-defined adsorbed layers that are less ordered than those obtained assuming a rigid solid. These results suggest that care must be taken when parametrizing empirical transferable force fields because the calculated charges on a solid slab in vacuum may not be representative of a real system, especially when the solid is in contact with a polar liquid.

A ReaxFF-based molecular dynamics study of the pyrolysis mechanism of HFO-1336mzz(Z)

A series of ReaxFF molecular dynamics simulations are performed to investigate the pyrolysis mechanisms of HFO-1336mzz(Z). Five initiation reaction pathways are observed in the process of pyrolysis. By comparing the activation energy of the reactions, the ground state CF3CH=CHCF3 exciting into the triplet state CF3CH-CHCF3 is the main initial reaction pathway with the activation energy of 238.553 kJ mol−1. HF and C2F2 are the dominant products and other final products including CF4, CHF3 and C2F4 are detected in the process of pyrolysis as well. The intra-molecular elimination (1, 2-elimination), radical attacking mechanism and radical combination reaction are three formation mechanisms of HF. The formation mechanism of C2F2 is slightly different from HF, including fluorine transfer reaction, radical combination reaction and defluorination. By the kinetic analysis of HFO-1336mzz(Z) pyrolysis, the pre-exponential factor and activation energy are obtained from ReaxFF simulations.

High-temperature decomposition of the cellulose molecule: a stochastic molecular dynamics study

The kinetics and products of cellulose pyrolysis can be studied using large-scale molecular dynamics simulations at high temperatures, where the reaction rates are high enough to make the simulation times practical. We carried out molecular dynamics simulations employing the ReaxFF reactive force field to study the initial step of the thermal decomposition process. We gathered statistics of simulated reactive events at temperatures ranging from 1400 to 2200 K, considering cellulose molecules with different molecular weights and initial conformations. Our simulations suggest that, in gas-phase conditions at these high temperatures, the decomposition occurs primarily through random cleavage of the β(1 → 4)-glycosidic bonds, for which we obtained an activation energy of (171 ± 2) kJ mol−1 and a frequency factor of left( {1.07 pm 0.12} right) times 10^{15} s−1. We did not observe dependency of the kinetic parameters on the molecular weight or initial conformation. Some of the decomposition reactions involved the release of low-molecular-weight products. Excluding radicals, the most commonly observed species were glycolaldehyde, water, formaldehyde and formic acid. Many of our observations are supported by the existing experimental and theoretical knowledge. We did not, however, observe the formation of levoglucosan, which is the dominant product in conventional pyrolysis experiments at much lower temperatures. This is understandable, since the high temperatures can force the dominance of radical reactions over pericyclic reactions. Nevertheless, our results support further use of ReaxFF-based molecular dynamics simulations in the study of cellulose pyrolysis.