Reactive Molecular Dynamics Simulations Research Articles

Unveiling the interaction regimes between atomic oxygen and amorphous carbon surface depending on incident energy

The chemical reactions between atomic oxygen (AO) and solid surface are particularly crucial for numerous fundamental fields. However, it is lack of clearly understanding the reaction mechanisms between AO and the solid surface because the complex interaction dynamics are extremely difficult to be measured experimentally and to be modelled theoretically. In this work, the reactive molecular dynamics simulations are conducted to fully reveal the interactive mechanisms of AO irradiation on the amorphous carbon surface. As the incident energy (E) increases, our simulations demonstrate three distinct interaction regimes: (I) surface oxidation without carbon removal, (II) surface oxidation accompanied by minor material removals, and (III) continuous material removal. The first critical energy (E1) of ∼3.5 eV as the boundary between regime I and II is related to the dissociative energy of C–C bonds. The second critical energy (E2) of ∼6.5 eV as the boundary between regime II and III corresponds to the largest repulsion energy that the oxidized surface could provide. We further establish a phenomenological model to quantitatively describe how the rebound ratio varies with incident energy and surfacial oxygen density, which not only fit all simulation data perfectly but also give a very precise prediction of E2 value.

Combustion characteristics and nitrogen conversion mechanism in ammonia/coal Co-firing process

The coupled combustion of coal with the carbon-free fuel NH3 is an effective technology for reducing CO2 emissions. Based on elemental analysis, proximate analysis, Fourier Transform infrared spectroscopy (FTIR), Carbon-13 Nuclear Magnetic Resonance (13C NMR), and X-ray photoelectron spectroscopy (XPS) characterizations, a coal macromolecular model was constructed. The combustion characteristics of coal/NH3 co-firing were investigated by reactive force field molecular dynamics simulations (ReaxFF MD). The transformation mechanism of elemental N was elucidated. The influence of temperature, oxygen concentration, and NH3 co-firing ratio (CR) on products was investigated. The results showed that during the non-isothermal combustion phase, the coal macromolecules decomposed more rapidly when the heating rate was low. In the isothermal phase, high temperatures promoted secondary reactions. The production of inorganic gases increased with increasing temperature. As the molar fraction of NH3 increased, the production of CO2 and CO was effectively reduced. There were three main pathways for NO formation. As NH3 decomposed to form NH2, NH2 was subsequently converted to NH, and NH reacted with O2 to form NO. The NH2 could also react with O radicals to form HNO, which was then converted to NO. Besides, both thermal NOx and prompt NOx were generated since the N2 was involved in the reaction. In addition, the production of NOx increased significantly at oxygen concentrations greater than 1.4.

Reactive molecular dynamics simulations of lithium-ion battery electrolyte degradation

The development of reliable computational methods for novel battery materials has become essential due to the recently intensified research efforts on more sustainable energy storage materials. Here, we use a recently developed framework allowing to consistently incorporate quantum-mechanical activation barriers to classical molecular dynamics simulations to study the reductive solvent decomposition and formation of the solid electrolyte interphase for a graphite/carbonate electrolyte interface. We focus on deriving condensed-phase effective rates based on the elementary gas-phase reduction and decomposition energy barriers. After a short initial transient limited by the elementary barriers, we observe that the effective rate shows a transition to a kinetically slow regime influenced by the changing coordination environment and the ionic fluxes between the bulk electrolyte and the interface. We also discuss the impact of the decomposition on the ionic mobility. Thus, our work shows how elementary first-principles properties can be mechanistically leveraged to provide fundamental insights into electrochemical stability of battery electrolytes.

The effect of H2 and NH3 on the pyrolysis of coal model compounds based on reactive molecular dynamics simulation

The co-combustion of coal and ammonia (NH3) has been receiving considerable attention due to its potential for mitigating CO2 emissions. Consequently, comprehending the pyrolysis mechanism of coal under the NH3 atmosphere is of paramount significance. Using pyrrole and pyridine, which are crucial model compounds of coal, the pyrolysis mechanisms within N2/H2/NH3 is systematacially investigated with the help of chemical reaction kinetics simulations (ReaxFF MD). The results revealed that pyrrole performs inferior structural stability compared to pyridine, resulting in accelerated and shorter pyrolysis, alongside a lower activation energy for the reaction. As a result, the pyrolysis process of pyrrole is more prone to C-C and C-N bond cleavage, ultimately producing more HCN. Moreover, this investigation revealed that both H2 and NH3 atmospheres promote the pyrolysis of pyrrole and pyridine, with the NH3 atmosphere having a more pronounced influence. The presence of an NH3/H2 atmosphere increased the production of HCN, lowered the activation energy required for the pyrolysis of pyrrole and pyridine, and aided in the cleavage of C-C and C-N bonds. Additionally, this study demonstrated the reaction network of pyrrole and pyridine in N2/H2/NH3 atmospheres, focusing on the observation that NH2 radicals, during the initial phases of the reaction, stimulate the production of low-carbon fragments and assist the fracture process of the model compounds. Furthermore, this study presents the reaction network of pyrrole and pyridine in N2/H2/NH3 atmospheres, with a particular focus on the NH3 atmosphere. The existence of NH3 in the atmosphere facilitates the formation of low-carbon fragments during the cleavage phase of the model compounds. This leads to the production of low-carbon intermediates and an increase in the generation of HCN during the subsequent condensation stage. These findings highlight the significant impact of the ammonia atmosphere on the pyrolysis of the model compounds. The outcomes of this study elucidate the fundamental principles of nitrogen-containing compound pyrolysis at the mechanistic level, providing critical insights for subsequent experimental and computational research.

Investigation of lubrication mechanism of phosphate ionic liquid by ReaxFF molecular dynamics simulations

The frictional characteristics of the interface between ionic liquid (IL) and metal can be significantly improved by the formation of a tribo-film, while the lubrication mechanism remains unclear. This study utilized reactive force field molecular dynamics (ReaxFF MD) simulation to investigate the tribological properties, interfacial tribochemical reactions, and formation mechanism of the tributyltetradecyl phosphonium di(2-ethylhexyl) phosphate ([P44414] [DEHP]) tribo-film. The findings indicate that the friction coefficients of ILs decrease as the normal pressure increases. The combination of normal pressure and shear force promotes the dissociation of ionic liquid chains and enhances the binding of free radicals to the end faces. The friction force is primarily influenced by the number of Fe-C bonds at the interface, which demonstrates a positive correlation with the normal pressure.

Effect of H2O on macroscopic flame behaviors and combustion reaction mechanism of 1,1-difluoroethane (R152a)

1,1-difluoroethane (R152a) is one of the most prospective low GWP refrigerants but may trigger fires and explosions once it leaks. Understanding the flame propagation process and combustion mechanisms at different relative humidity conditions is essential to use flammable refrigerants safely. In this study, a high-speed camera has recorded the flame propagation of R152a combustion near the flammability limit. Combining with macroscopic experimental phenomena, we revealed the effect of H2O on the microscopic mechanism of R152a combustion by using reactive force field molecular dynamics simulations with a reliable force field. The promotion effects of H2O on the oxidation of R152a were revealed from an atomistic perspective. The differences of oxidation intermediates and products in different environments were analyzed for the first time. The H2O/O2 environment was the most potent promoter of R152a decomposition, followed by the O2 and the pyrolysis environment. The O2/H2O environment reduced the apparent activation energy of R152a, significantly enhanced the consumption rate of R152a, and enriched the number of species. O2 reacts with H2O or H to form OH to accelerate the reaction process. The H2O could provide more OH active fragments for the reaction. Moreover, it promotes the formation of HF and H2, H2O+F→HF+OH, H2O+H→H2+HO. This study aims to provide a guiding theory for the safe application and disaster prevention of flammable refrigerants.

Molecular dynamics study of surface alkalization reaction in high calcium systems

Alkali-activated materials (AAMs) offer significant benefits in the field of civil engineering, thanks to their energy-efficient and environmentally-friendly properties, as well as their exceptional strength and durability. However, the fundamental chemical reaction underlying the use of AAMs has not yet been fully understood. The process of the silicate depolymerization of the supplementary gelling materials is determined by their nano characteristics, which have certain restrictions by using experimental techniques. In this study, we utilized reactive molecular dynamics (MD) simulations to elucidate the chemical events occurring during alkali-activation in different AAMs. The sodium hydroxide (NaOH) solution selectively dissolves the silicon chains, while the aluminum chains remain intact. Furthermore, the laminar structures of silicon and aluminum in metakaolin (MK) crystal are entirely disturbed. However, the disintegration of silicon chains is negligible, and the Slag minerals maintain their layered structure. Calcium ions are crucial in stabilizing the chemical process of alkali activation. Furthermore, this study evaluates the fluctuations in their activity. Gaining insight into the minute details of this reaction provides essential theoretical foundations for developing eco-friendly and high-performing alkali-activated concrete materials.

Coupling Process between Droplet and Iron Investigated by Reactive Molecular Dynamics Simulations.

The droplet-to-iron electrochemical reaction is common in nature and industrial production, and it causes damage to the economy, safety, and the environment. The electrochemical reaction of droplet-to-iron is a coupling process of wetting and corrosion. Presently, investigations into electrochemical reactions mainly focus on the corrosions caused by a solution, and wetting is rarely considered. However, for the droplet-to-iron electrochemical reaction, the mechanism of charge transfer in the process is still unclear. In this paper, a reactive molecular dynamics simulation model for the droplet-to-iron electrochemical reaction is developed for the first time. The electrochemical reaction of droplet-to-iron is studied, and the interaction between droplet wetting and corrosion on iron is investigated. The effects of temperature, electric field strength, and salt concentration on the electrochemical reaction are explored. Results show that droplet wetting on the iron surface and the formation of a single-molecular-layer ordered structure are prerequisites for corrosion. The hydroxyl radicals that penetrate the ordered structure acquire electrons from iron atoms on the substrate surface under the action of Coulomb forces and form iron-containing oxides with these iron atoms. The corrosion products and craters lead to a reduced droplet height, which promotes droplet wetting on iron and further intensifies the droplet-to-iron electrochemical reaction.

Spectroscopic and theoretical investigation of Brønsted acid sites in amorphous mixed Zr-Si oxide nanoparticles

Mixed Zr-Si oxide nanoparticles were investigated to disclose the relation between the Brønsted acidity of these materials and the atomic composition of the particles. To this aim, we combined experimental structural characterizations via X-ray absorption and Solid State Nuclear Magnetic Resonance spectroscopies with Reactive Molecular Dynamics simulations and Quantum Chemistry calculations. Despite the materials’ complexity, we identified the surface hydrogens responsible for the Brønsted acidity by estimating the adsorption energy of pyridine on several topologically distinct hydroxyl groups. Among the investigated sites, the hydrogens connected to the oxygen atoms bridging surface Zr and Si atoms (i.e., Zr-O(H)-Si) exhibited the most marked Brønsted acidity. The agreement of all the employed techniques demonstrates how the proposed concerted characterization effectively elucidates these complex amorphous materials’ structure/properties relationships. These new insights allowed us to develop a material with exceptionally high Brønsted acid character that outperformed benchmark silica-alumina and sulfonated zirconia in the dehydrogenation reaction of 1-octanol to produce olefins.

Neural network potential-based molecular investigation of pollutant formation of ammonia and ammonia-hydrogen combustion

This study developed neural network potentials (NNPs) specifically designed for ammonia and ammonia-hydrogen combustion systems for the first time. The NNPs were employed to perform reactive molecular dynamics (RMD) simulations, combining the precision of density functional theory (DFT) calculations with the efficiency of empirical force fields. NNP-based RMD simulations provide a more detailed and comprehensive understanding of chemical reaction mechanisms. The impacts of different equivalence ratios and hydrogen addition on ammonia combustion as well as NOX and N2O formation were analysed. The results indicate that both the addition of hydrogen and the reduction of equivalence ratios contribute to enhancing ammonia combustion. The primary reason is the enhancement of the oxidative environment within the system, leading to a significant increase in the frequency of reactions associated with oxidising radicals such as OH, O, and HO2. This is also the cause for the increased production of NO and NO2, because the formation of NO depends on the oxidation of NH and NH2, while NO2 is formed through the oxidation of NO. An interesting finding is that the addition of hydrogen decelerates the generation of N2O, while reducing the equivalence ratio promotes N2O production. This phenomenon is attributed to the additional H radicals generated during hydrogen decomposition, which hinders the binding between NH and NO, resulting in a reduction in the formation of the precursor HN2O required for N2O formation.

Managing Expectations and Imbalanced Training Data in Reactive Force Field Development: An Application to Water Adsorption on Alumina.

ReaxFF is a computationally efficient model for reactive molecular dynamics simulations that has been applied to a wide variety of chemical systems. When ReaxFF parameters are not yet available for a chemistry of interest, they must be (re)optimized, for which one defines a set of training data that the new ReaxFF parameters should reproduce. ReaxFF training sets typically contain diverse properties with different units, some of which are more abundant (by orders of magnitude) than others. To find the best parameters, one conventionally minimizes a weighted sum of squared errors over all of the data in the training set. One of the challenges in such numerical optimizations is to assign weights so that the optimized parameters represent a good compromise among all the requirements defined in the training set. This work introduces a new loss function, called Balanced Loss, and a workflow that replaces weight assignment with a more manageable procedure. The training data are divided into categories with corresponding "tolerances", i.e., acceptable root-mean-square errors for the categories, which define the expectations for the optimized ReaxFF parameters. Through the Log-Sum-Exp form of Balanced Loss, the parameter optimization is also a validation of one's expectations, providing meaningful feedback that can be used to reconfigure the tolerances if needed. The new methodology is demonstrated with a nontrivial parametrization of ReaxFF for water adsorption on alumina. This results in a new force field that reproduces both the rare and frequent properties of a validation set not used for training. We also demonstrate the robustness of the new force field with a molecular dynamics simulation of water desorption from a γ-Al2O3 slab model.

Inhibition mechanism of CHF3 on hydrogen–oxygen combustion: Insights from reactive force field molecular dynamics simulations

To mitigate the risks linked to hydrogen and oxygen (H2–O2) combustion through CHF3 additives, Reactive Force Field Molecular Dynamics (ReaxFF MD) simulations are performed in this study. The primary objective is to investigate the inhibition mechanism of CHF3 on H2–O2 combustion from 2000 K to 2800 K. The simulation results demonstrate that the reaction pathways of hydrogen combustion are changed under the extended second explosion limit, and the main radicals involved in elementary reactions transform from H, OH, and O to H, OH, and HO2. CHF3 predominantly engages in reactions with H radicals to impede the continuation of chain reactions by forming stable HF molecules. OH radicals react with modest amounts of secondary fluorides such as CHF2OH, CH2F, and so on, while HO2 radicals are combined with even fewer intermediates like CHF2O and CHFOH to prevent chain propagations. Moreover, comprehensive and novel reaction pathways are proposed for the inhibition of H2–O2 combustion by CHF3. The parameters of the reaction kinetics indicate that the ignition delay is advanced and the activation energy for the combustion process is increased under the influence of CHF3. This study is expected to provide practical guidance on the inhibition of H2–O2 combustion by CHF3.

Modeling the degradation of polypropylene and polystyrene under shock compression and mechanical cleaving using the ReaxFF force field

Polypropylene (PP) and polystyrene (PS) underwent a comprehensive investigation into their mechanical and chemical degradation through reactive molecular dynamics simulations. The simulations utilized the ReaxFF force field for CHO (carbon-hydrogen-oxygen) systems in the combustion branch. The study included equilibrium simulations to determine densities and melting temperatures, non-equilibrium simulations for stress-strain and Young moduli determination, mechanical cleaving to identify surface species resulting from material fragmentation, and shock compression simulations to elucidate chemical reactions activated by some external energy sources. The results indicate that material properties such as densities, phase transition temperatures, and Young moduli are accurately reproduced by the ReaxFF-CHO force field. The reactive dynamics analysis yielded crucial insights into the surface composition of fragmented polymers. Both polymers exhibited backbone breakage, leaving -CH2· and –CH·- radicals as terminals. PP demonstrated substantial fragmentation, while PS showed a tendency to develop crosslinks. A detailed analysis of chemical reactions resulting from increasing activation due to increasing value of compression pressure is presented and discussed.

Unveiling the interaction mechanisms of cold atmospheric plasma and amino acids by machine learning

AbstractPlasma medicine has attracted tremendous interest in a variety of medical conditions, ranging from wound healing to antimicrobial applications, even in cancer treatment, through the interactions of cold atmospheric plasma (CAP) and various biological tissues directly or indirectly. The underlying mechanisms of CAP treatment are still poorly understood although the oxidative effects of CAP with amino acids, peptides, and proteins have been explored experimentally. In this study, machine learning (ML) technology is introduced to efficiently unveil the interaction mechanisms of amino acids and reactive oxygen species (ROS) in seconds based on the data obtained from the reactive molecular dynamics (MD) simulations, which are performed to probe the interaction of five types of amino acids with various ROS on the timescale of hundreds of picoseconds but with the huge computational load of several days. The oxidative reactions typically start with H‐abstraction, and the details of the breaking and formation of chemical bonds are revealed; the modification types, such as nitrosylation, hydroxylation, and carbonylation, can be observed. The dose effects of ROS are also investigated by varying the number of ROS in the simulation box, indicating agreement with the experimental observation. To overcome the limits of timescales and the size of molecular systems in reactive MD simulations, a deep neural network (DNN) with five hidden layers is constructed according to the reaction data and employed to predict the type of oxidative modification and the probability of occurrence only in seconds as the dose of ROS varies. The well‐trained DNN can effectively and accurately predict the oxidative processes and productions, which greatly improves the computational efficiency by almost ten orders of magnitude compared with the reactive MD simulation. This study shows the great potential of ML technology to efficiently unveil the underpinning mechanisms in plasma medicine based on the data from reactive MD simulations or experimental measurements.

Accelerated carbonation of recycled concrete aggregate in semi-wet environments: A promising technique for CO2 utilization

The practical implementation of accelerated carbonation for recycled waste concrete is impeded by sluggish carbonation efficiency. In contrast to previous carbonation enhancement schemes using high-pressure gas and/or complex pre-/post-processing, this study introduces a novel semi-wet carbonation method that achieves high-efficiency carbonation of recycled concrete aggregates (RCA) in a practically simple way. A noteworthy carbonation degree of 10.6 % was achieved within 30 min at room temperature and ambient pressure, which enhanced the RCA by reducing the water absorption rate and porosity by 3.6 % and 20 % respectively. The formed CaCO3 is primarily in calcite form with poorer crystallinity and smaller grain size and the formed silica gel features a lower polymerization degree compared with those formed in wet carbonation. It is due to that the carbonation reactions for the semi-wet scenario happen at the spatially confined water film of the solid-liquid interface. Moreover, the addition of sodium bicarbonate significantly accelerated the semi-wet carbonation, which is due to the weak alkaline environment lowering the CO2 speciation free energy as revealed by reactive molecular dynamics simulations. The proposed semi-wet carbonation method provides a promising way of pushing industrial CO2 capture and utilization.

Co-pyrolysis behaviors of biomass and polymer plastics by using reactive molecular dynamics simulation

Co-pyrolysis of oxygen-rich biomass and hydrogen-rich plastic polymer is a promising approach for waste management, which has been investigated by using reactive molecular dynamics simulation (ReaxFF MD) in this work. The blend models containing multicomponent mixtures of polymer (polyethylene, polypropylene, polystyrene) and biomass (cellulose, hemicellulose and lignin) were constructed for the first time, which is close to the real utilization of waste materials. The simulation results show that the degree of positive synergistic effect between biomass and polymer increases with temperature, where the polymer promotes biomass pyrolysis and delays its recombination. Co-pyrolysis greatly affects the product yields through cross reactions of hydrogen and hydroxyl transfer, leading to more oxygen-containing bio-oils produced with the aid of polymers providing hydrogen. Produced from heavy tar at first and light char at late pyrolysis period, char precursors are generated more and faster in the co-pyrolysis system with more biomass because oxygen functional groups provide the initial cross-linking sites. As compared to pyrolysis of only binary components, the observed qualitative synergistic results in co-pyrolysis of biomass-polymer mixtures provide important insights into the detailed reactions for co-pyrolysis process, which can complement experimental observations to modulate the nature and yield of the desired bio-oils and bio-chars.

Temperature-dependent water corrosion mechanism of silicon carbide: Atomic insights from reactive molecular dynamics simulation

Temperature-dependent water corrosion mechanism of silicon carbide: Atomic insights from reactive molecular dynamics simulation

Mechanical behaviour and micro-mechanism of atomically precise edge graphene nanoribbons mechanical cutting guided by hydrogen atom adsorption

The preparation of graphene nanoribbons with atomically precise edges is a major challenge. In this paper, we proposed a mechanical cutting method for graphene nanoribbons guided by hydrogen atom adsorption and analysed the mechanical behaviour and microscopic cutting mechanism of graphene with hydrogen atom adsorption using reactive molecular dynamics simulations. The results showed that hydrogen atom adsorption weakened the mechanical properties and improved the cutting performance of graphene. Hydrogen atom adsorption showed a substantial guiding effect on graphene cutting, increasing the regular edge ratio from 12.21 % to 91.89 %, and graphene nanoribbons with atomically precise edges were prepared using this method. We determined that the cutting mechanism of graphene without hydrogen atom adsorption was a tensile-breaking mechanism. In contrast, graphene with hydrogen atom adsorption exhibited a shear-breaking mechanism. The cutting performance of the armchair-H graphene was lower than that of the zigzag-H graphene owing to the unique hexagonal distribution of carbon atoms. This study provides new insights into the cutting mechanism of graphene guided by hydrogen atom adsorption and establishes the method for preparing atomically precise edge graphene nanoribbons by mechanical cutting.

Corrosion behavior of droplet moving on metal copper surfaces: A reactive molecular dynamics simulation investigation

The corrosion behavior of moving droplet using reactive molecular dynamics simulation, especially the moving droplet induced is studied for the first time to the best of our knowledge. The effect of wetting on corrosion is mainly reflected in the ordered structure. The ordered structure, which promotes efficient interfacial charge transfer. Residues such as water molecules, aggressive ions and hydrogen ions fill copper surface defects. Moreover, the trace charge atoms on the metal surface and the anions in the ordered structure will form a built-in electric field by Coulomb interaction. Furthermore, there is a combination of “sliding” and “rolling” movement mechanisms.

Atomistic Insights into the Influence of High Concentration H2O2/H2O on Al Nanoparticles Combustion: ReaxFF Molecules Dynamics Simulation.

The combination of Al nanoparticles (ANPs) as fuel and H2O2 as oxidizer is a potential green space propellant. In this research, reactive force field molecular dynamics (ReaxFF-MD) simulations were used to study the influence of water addition on the combustion of Al/H2O2. The MD results showed that as the percentage of H2O increased from 0 to 30%, the number of Al-O bonds on the ANPs decreased, the number of Al-H bonds increased, and the adiabatic flame temperature of the system decreased from 4612 K to 4380 K. Since the Al-O bond is more stable, as the simulation proceeds, the number of Al-O bonds will be significantly higher than that of Al-H and Al-OH bonds, and the Al oxides (Al[O]x) will be transformed from low to high coordination. Subsequently, the combustion mechanism of the Al/H2O2/H2O system was elaborated from an atomic perspective. Both H2O2 and H2O were adsorbed and chemically activated on the surface of ANPs, resulting in molecular decomposition into free radicals, which were then captured by ANPs. H2 molecules could be released from the ANPs, while O2 could not be released through this pathway. Finally, it was found that the coverage of the oxide layer reduced the rate of H2O2 consumption and H2 production significantly, simultaneously preventing the deformation of the Al clusters' morphology.