Reactive Molecular Dynamics Simulations Research Articles

Functionalized Amorphous Carbon Materials via Reactive Molecular Dynamics Simulations.

We derive a database of atomistic structural models of amorphous carbon materials endowed with exohedral functional groups. We start from phases previously derived using the DynReaxMas method for reactive molecular dynamics simulations, which exhibit atomistic and medium-length-scale features in excellent agreement with available experimental data. Given a generic input structure/phase, we develop postprocessing simulation algorithms mimicking experimental preparation protocols aimed at: (1) "curing" the phase to decrease the defect concentration; (2) automatically selecting the most reactive carbon atoms via interaction with a probe molecular species, and (3) stabilizing the phase by saturating the valence of carbon atoms with single-bond functional groups. Although we focus on oxygen-bearing functionalities, they can be replaced with other monovalent groups, such as -H, -COOH, -CHO, so that the protocol is quite general. We finally classify reactive sites in terms of their location within the structural framework and coordination environment (edges, tunnels, rings, aromatic carbons becoming aliphatic) and try to single out descriptors that correlate with tendency to functionalization.

Mechanistic Insights into the Dealumination of an H-ZSM-5 Zeolite Using Reactive Molecular Dynamics Simulations

Mechanistic Insights into the Dealumination of an H-ZSM-5 Zeolite Using Reactive Molecular Dynamics Simulations

Friction Mechanism of Sulfur-Containing Lubricant Additives Confined between Fe(100) Substrates.

Sulfur-containing lubricant additives can chemically react with metal surfaces under extreme conditions, such as high temperature and high pressure, forming protective films on the surfaces. However, the formation mechanisms and the friction-reducing and antiwear properties of these films remain unclear. In this study, we investigated the friction process of sulfur-containing additives confined between two iron surfaces using reactive molecular dynamics simulations. Our research revealed that in systems with a higher S/C ratio, an iron sulfide layer formed on the iron surfaces with Fe-S-Fe bridging bonds at the interface, resulting in relatively smaller friction and wear even under higher loads. However, in systems with lower S/C ratios, the presence of numerous interfacial Fe-Cn-Fe bridging bonds, caused by the hydrocarbon radicals released from the additives, led to the formation of thick amorphous shearing bands at the interface between the two substrates. In this case, the distributed sulfur atoms also exhibited some effect in reducing the shear resistance of the amorphous shearing bands due to the weak strength of S-Fe bonds compared to the strength of C-Fe bonds. These atomic-level insights help understand the antiwear characteristics of sulfur-containing lubricant additives confined between iron substrates.

Plasticity of Metal-Organic Framework Crystals: Thermally Activated Collapse of Nanopores.

Unrecoverable deformation or plasticity can be generated in crystalline metal-organic frameworks (MOFs) by compressive loading with different rates in various applications. Herein, plastic behaviors of MOF HKUST-1 crystals are investigated by a series of in situ strain-rate-dependent compression tests. The yield strength is found to significantly increase with increasing strain rate, following a logarithmic dependence. Our reactive molecular dynamics simulations illustrate that the yielding of crystalline HKUST-1 is induced by the irreversible collapse of its nanopores, which can be accelerated by thermal activation at finite temperatures. Based on this mechanism together with the reaction rate theory, we derive an analytical expression relating the yield strength of MOFs and strain rate, which fits experimental findings well. Overall, this work can expand our current understanding of MOF plasticity, which is of importance for the mechanical shaping and various applications of MOF crystals.

On the relationship between water adsorption and surface chemistry in soda-lime silicate glasses.

Understanding how the surface structure affects the bioactivity and degradation rate of the glass is one of the primary challenges in developing new bioactive materials. Here, classical and reactive molecular dynamics simulations are used to investigate the relationship between local surface chemistry and local adsorption energies of water on three soda-lime silicate glasses. The compositions of the glasses, (SiO2)(65-x)(CaO)35(Na2O)xwith x = 5, 10, and 15, were chosen for their bioactive properties. Analysis of the glass surface structure, compared to the bulk structure, showed that the surface is rich in modifiers and non-bridging oxygen atoms, which were correlated with local adsorption energies. The reactivity of the glasses is found to increase with higher Na2O content, attributed to elevated Na cations and undercoordinated species at the glass surfaces. The current work provides insights into the relationship between the surface structure, chemistry, and properties in these bioactive glasses and offers a step toward their rational design.

Reactive Molecular Dynamics Simulations of Micrometeoroid Bombardment for Space Weathering of Asteroid (162173) Ryugu

Remote sensing observations by Hayabusa2 and laboratory measurements have revealed that the phyllosilicates on asteroid (162173) Ryugu are dehydrated/dehydroxylated due to space weathering. Reactive molecular dynamics simulations were performed to evaluate the magnitude of the dehydroxylation of Mg-rich serpentine by micrometeoroid impacts. When micrometeoroids were not coupled with interplanetary magnetic fields, serpentine could be dehydroxylated by micrometeoroids as small as 2 nm in size. In particular, ∼200 O–H bonds dissociated when the meteoroids were derived from cometary activity (the impact velocity was ∼20 km s−1). When nano-sized dust particles were accelerated to ∼300 km s−1 by the magnetic fields of solar wind plasma, the number of dissociated O–H bonds increased by 1 order of magnitude. Consequently, even 1 nm-sized dust particles can contribute to the space weathering of Ryugu. In all cases, Si–OH, H2O, and free OH were generated from the hydroxyls initially connected to Mg, which could partially offset dehydration. Despite the limitations of our computational resources, which restricted the simulation timescale to 1 ps, reactive molecular dynamic simulations demonstrated that micrometeoroid bombardment could influence the space weathering of asteroids.

Interaction mechanism of cold atmospheric plasmas and fusion peptides of spike protein in SARS-CoV-2 revealed by reactive molecular dynamics simulation

Despite the conclusion of the COVID-19 pandemic, the coronavirus-killing ability of cold atmospheric plasma (CAP) remains impressive, and investigations into its underlying mechanisms are still ongoing. The fusion peptide (FP) is a crucial site of membrane fusion and toxicity exerted by the S-protein in severe acute respiratory syndrome CoV-2 (SARS-CoV-2). In this study, reactive molecular dynamics simulations were performed to investigate the interaction mechanisms of FP and reactive oxygen species (ROS). The simulation results show that the given ROS (O atoms and OH radicals as examples) can destroy hydrophobic residues, negatively charged acidic residues, and peptide bonds through structurally altering essential sites. Furthermore, the reaction typically initiates from the H-abstraction reaction, followed by various types of oxidative modifications such as dehydrogenation, hydroxylation, carbonylation, cyclogenesis, ring cleavage, and decarboxylation, which are consistent with the experimental findings made on peptides. Therefore, it can be predicted that the membrane fusion ability of FP and the toxicity of SARS-CoV-2 will be reduced, with CAP functioning as a bactericidal disinfectant. The dose effects were also investigated, providing experimental guidance for the optimization of CAP. In this study, the interaction processes of FP and CAP are explored by revealing the chemical pathways and final reaction products from the computational data, thus providing a fundamental understanding of the mechanisms for inactivating SARS-CoV-2 by CAP.

Experimental and numerical study of the decomposition, product spectrum, and sooting properties of adamantane fuels

This work combined experimental measurements with two theoretical approaches, reactive Molecular Dynamics (MD) simulations and Quantum Mechanics (QM) calculations, to investigate the combustion and sooting properties of three adamantane fuels, adamantane (AD), 1,3-dimethyl-adamantane (DMAD), and 1-ethyl-adamantane (EAD). These fuels were selected since the adamantane fuel family can potentially be used as sustainable aviation fuels and comparing these fuels would reveal the effects of side chain on their combustion and sooting properties. We determined the bond dissociation energies of the three test fuels using QM calculations and found that the functionalized side chains have the weakest bonds and their presence only slightly affects the bond strength in the AD multi-cyclic core. We performed pyrolysis simulations for all three fuels using ReaxFF-based MD simulations and found that DMAD and EAD have higher decomposition rates than AD and also generate more high-molecular-weight products. For all three fuels, these large products were observed to contribute significantly to hydrocarbon growth processes, which lead to large soot nucleating species and even soot-like structures. A higher yield of such soot nucleating compounds was found during the pyrolysis of DMAD and EAD than AD since the decomposition products of DMAD and EAD are more branched and those of AD have mostly straight chains. These theoretical analyses were supported by experimental measurements of yield-based sooting tendencies, which suggest that DMAD and EAD are sootier than AD and that all three fuels are sootier than standard alkane jet fuel surrogates but less sooty than jet fuel aromatic content.

Reactive molecular dynamics simulations of poly(vinyl alcohol) gasification in supercritical carbon dioxide

Supercritical fluid gasification technology, as an environmentally friendly technology, can convert organic components of plastic waste into fuels and chemical materials. Moreover, the utilization of CO2 as the gasification environment holds significant importance for reducing carbon emissions. To better comprehend the microscopic mechanism of plastic gasification in supercritical environment, this sthdy used the Reactive Force Field (ReaxFF) molecular dynamics method to study the gasification process of long-chain poly(vinyl alcohol) molecule in supercritical H2O/CO2 under different reaction conditions. The result illustrated that during the gasification process, poly(vinyl alcohol) initially depolymerized into multiple long carbon chain (C5+) molecular fragments. Subsequently, these fragments underwent cleavage into short carbon chains and various gaseous small molecules. In this reaction, O radicals generated by CO2 decomposition play a crucial role in promoting the cleavage of plastic C–C bonds. In addition, through the analysis of the products and chemical bonds, we found that increasing temperature and prolonging reaction time significantly enhance the gasification efficiency and hydrogen production of plastics. Conversely, exceedingly high pressure inhibits the gasification reaction.

The interface interaction and thermal sensitivity of nitrogen-rich energetic co-particles: A reactive molecular dynamics simulation study

Composite explosives are the ultimate used form of energetic materials in weapon systems and aerospace or deep-sea explorers. Among them, the energetic co-particles which combine high-energy crystals with low-sensitivity energetic crystals, is a excellent way to balance energy and safety for energetic materials. In this work, a kind of nitrogen-rich octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine(HMX) / 2,6-diamino-3,5-dinitropyrazine-1-oxide (LLM-105) co-particles were investigated using molecular modeling methods. Different ratios of HMX/LLM-105 co-particles were constructed by combining different high-energy HMX surfaces with low-sensitivity LLM-105 surfaces. Reactive molecular dynamics simulations (RMD) were carried out on the co-particle models to investigate the thermal sensitivity, as well as classical molecular dynamics simulations were performed to investigate the interfacial interactions. The results show that strong attractive forces including van der Waals and electrostatic interactions exist along the crystalline interfaces, and the thermal decomposition reactions were greatly influenced by the composition of the co-particles. Finally, recommended ratio of HMX/LLM-105, which has enough attractive interaction to enhance the interface, high energy as well as good thermal stability was selected. This research is of significance on the design of advanced insensitive energetic composites.

Thermal conversion studies of lignin pyrolysis and the catalytic effect of fe: A reactive molecular dynamics study

Lignin is one of the important components of biomass, and its pyrolysis process has been widely studied. The advantages of iron-based catalysts are their low cost, low environmental pollution, and the ability to extract and reuse from the system. However, research on the effect of metallic iron on lignin pyrolysis is limited. This study revealed the influence of iron on lignin pyrolysis process at the microscopic level through reactive molecular dynamics (ReaxFF MD) simulation, while considering the influence of different temperatures. It was found that increasing the temperature can increase the production of H2 and CO gases and improve the efficiency of lignin decomposition. In addition, the addition of catalyst iron can accelerate the decomposition of the benzene ring, making the lignin pyrolysis process deeper and more thorough, while increasing the production of H2 and CO. The activation energy of the system was calculated and it was found that the addition of catalyst iron can significantly reduce the activation energy of lignin pyrolysis, proving the excellent catalytic effect of the catalyst. The catalytic pyrolysis strategy provided in this study, using iron as a catalyst to catalyze the pyrolysis process of lignin, can effectively utilize biomass resources in industrial production.

Room-temperature solution processed silicon nanocluster: Theory prediction and experiment achievement

We have presented in this work that silicon nanoclusters (Si NCs) embedded in silicon nitride (▪) can be synthesized by vacuum ultra-violet irradiation of perhydropolysilazane (PHPS) at room temperature. The formation of Si NCs is first predicted by reactive molecular dynamics (ReaxFF-MD) simulations based on a self-developed Si/N/H force field. Then the existence of Si NCs is further verified by photoluminescence (PL) spectroscopy and Raman spectroscopy characterization. Additionally, the photochemical conversion mechanism of PHPS is examined. Moreover, it has been found based on Fourier transform infrared (FT-IR) measurements that ▪ samples prepared with an intermediate irradiation time are the most readily to be oxidized, which can be attributed to the high concentration of the active group -▪, being consistent with the reaction mechanism. We have demonstrated that ReaxFF-MD simulation can be a powerful complement to experimental investigations in revealing the conversion mechanism of polymer precursor to ceramics at the atomic level.

Insights into hydro thermal gasification process of microplastic polyethylene via reactive molecular dynamics simulations

Microplastics have become a pressing environmental issue due to their widespread presence in our ecosystems. Among various plastic components, polyethylene (PE) is a prevalent and persistent contaminant. Hydrothermal gasification (HTG), a promising technology for converting PE into syngas, holds great promise for mitigating the microplastic problem. In this study, we employ ReaxFF molecular dynamics simulations to investigate the HTG process of PE, shedding light on the intricate relationships between temperature, water content, carbon conversion efficiency, and product distributions. The results reveal that hydrothermal gasification of PE is a complex process involving multiple reaction pathways. Consistently with experimental findings, the calculations indicate that the gas phase exhibits a substantial hydrogen fraction, reaching up to 70%. Interestingly, our simulations reveal a dual role of water content in the HTG process. On one hand, water enhances hydrogen production by promoting the gas formation. On the other hand, it elevates the activation energy required for PE decomposition. Depending on the water content, the calculated activation energies range from 176 to 268 kJ/mol, which are significantly lower than those reported for thermal gasification (TG). This suggests that HTG may be a more efficient route for PE conversion. Furthermore, this study highlights the importance of optimizing both temperature and water content in HTG systems to achieve high yields of hydrogen-rich syngas. The results obtained from our ReaxFF MD simulations demonstrate the robustness of this computational methodology in elucidating complex chemical reactions under extreme conditions. Our findings offer critical insights into the design of advanced waste management strategies for microplastics and contribute to the development of sustainable practices for resource recovery. This work underscores the potential of HTG as a key technology for addressing the global challenge of plastic pollution.

Atomistic insights into role of urea additive in lithium nanoparticles formation

Recently, urea additive has been demonstrated to benefit the formation of cathode nanomaterials through spray flame synthesis with improved homogeneity in lithium atoms distribution. Nevertheless, its intrinsic mechanism has not been well understood. In this study, reactive molecular dynamic simulations are performed to gain atomistic insights into the pyrolysis and oxidation mechanisms of a lithium precursor droplet with or without urea additive. A series of comparisons involving the reaction kinetics and pathways of lithium clusters, along with the gas release, energy profiles and morphological characteristics of droplets, is conducted to elucidate the role of urea additive at 1500 K and 0.1 MPa. Urea additive is observed to exert a homogenising impact on the distribution of lithium atoms within the synthesized nanoparticles, as evidenced by the decreased number of large-sized lithium agglomerates and less concentrated lithium element. This can be ascribed to changed reaction pathways of lithium clusters due to urea additive, where the lithium clusters are prone to decompose into fine nanoparticles through initial bonding with urea atoms, followed by bond-breaking to generate gases. The increased amount of gas released from the decomposition of precursor with urea additive leads to a more violent droplet microexplosion, which in turn results in droplet breakup and thus fine droplets. As the ambient temperature is elevated, the presence of urea additive facilitates the formation of fine-sized nanoparticles with enhanced homogeneity of lithium atoms.

Multi-Scale Development and Integration of Granular Activated Carbon Electrodes in Multiphase Electrochemical Systems

Providing clean water remains a significant challenge in underserved areas that lack access to public water systems or are affected by extreme natural events like hurricanes. Electrochemical technologies show promise for developing affordable and effective water treatment systems due to their ability to efficiently oxidize contaminants. Particularly, the electrochemical synthesis of in-situ reagents, such as H2O2, systems can oxidize contaminants over the full range of pH with high oxidation potential, leaving only water and oxygen at the end of process, making it a safe and effective method for water treatment. This study is focused on integrating carbon-based electrodes into electrochemical water treatment systems emphasizing their scalability, cost effectiveness, and the efficient generation of reactive oxygen species (ROS). By employing multiscale computational approaches, we develop a comprehensive mechanistic understanding and optimization of ROS generation at the surface of granular activated carbon (GAC) electrodes. Using reactive molecular dynamics simulations, the thermodynamic and transport properties of water-based electrolyte (e.g., adsorption, viscosity, and diffusion) are investigated as a function of the GAC particle size and chemistry. The obtained results show that tuning the GAC particle structure at nanoscale can improve the local diffusion rates by three times. Subsequently, multiphase continuum simulations are used to integrate the GAC electrodes in full electrochemical systems through optimizing the dispersion and the solid-liquid-gas interactions in a reactive environment. The computational findings reveal that higher production of H2O2 and are observed at optimized electrode porosity values when the GAC electrodes are integrated at the system level. These observations are linked to the complex reactive solid-fluid interactions. Specifically, the electrochemical oxygen bubble splitting and coalescence are minimized by optimizing the electrode porosity, which improves the dispersion mass transfer processes by at least one order of magnitude. This leads to higher generation rates of ROS and enhanced degradation of water contaminants. These mechanistic observations will help in designing and scaling up carbon-based electrodes for developing efficient and cost-effective electrochemical water treatment reactors.

Unveiling the intricacies of steel corrosion induced by chloride: Insights from reactive molecular dynamics simulation

Corrosion of reinforcing steels induced by chloride has long been a focal point of research, yet the atomic behavior and mechanism is not fully understood. In present study, we developed a reactive force field (ReaxFF) incorporating the Fe/Cl system based on Density Functional Theory calculations to elucidate atomic-scale behavior and mechanism underlying chloride-induced corrosion of reinforcing steel. Results from ReaxFF simulations employing this force field indicate that the initiation of steel corrosion is catalytically induced by chloride present in the outer layer, and the electron transfer between atoms is identified as a critical factor in corrosion. Specifically, Fe atoms become positively charged, detaching from the matrix surface and dissolving into the solution to form iron chloride compounds with surface Cl, while oxygen atoms turn negatively charged, progressively infiltrating the matrix and combining with Fe to create intricate iron oxide compounds. Furthermore, the entire dynamic process of corrosion oxidation on the surface of the ferritic matrix and the formation of product species has been fully captured. This ongoing corrosion process leads to significant matrix loss from metal surface and a reduction in structural integrity.

Rational utilization of the size and electronic effect of inhibitors enabling high polishing rate with minimum corrosion in copper chemical mechanical polishing

Chemical mechanical polishing (CMP) relies on corrosion to remove excess materials, while also on corrosion inhibitors to ensure post-polished surface quality. The robust adsorption of inhibitors onto metal surfaces typically improves inhibition effectiveness but significantly reduces the polishing rate. In this study, we propose and validate a novel strategy that focuses on the utilization of large-sized physisorption-type inhibitors to address this inherent conflict. By incorporating disproportionated rosin (DR) as the inhibitor, the developed slurry facilely obtained a balance between polishing efficiency and quality for copper CMP. The inhibition mechanism of DR was elucidated through electrochemical characterization, adsorption isotherms, and reactive forcefield molecular dynamics (ReaxFF MD) simulations. The weak physisorption of the inhibitors facilitated their easy removal, resulting in minimal impact on the polishing rate. Additionally, the large-size structure of DR effectively hindered corrosive substances from reaching concave areas not under external force, thereby demonstrating superior inhibition efficacy. The adsorption mode of DR on copper was simultaneously determined through adsorption isotherms and ReaxFF MD simulations, marking the first instance of linking classic adsorption theory with MD simulations. The advantage of the ReaxFF MD simulations over classic MD simulations and density-functional-theory calculations for the metal-inhibitor adsorption systems was also discussed and demonstrated.

Study of ignition and combustion of aluminum/ethanol nanofluid based on reactive molecular dynamics simulation

Aluminum/ethanol nanofluid fuel offers high energy density, high combustion efficiency, and low pollutant emissions, making it highly promising for aerospace applications. In recent years, the fundamental combustion characteristics for aluminum/ethanol nanofluid fuel have been extensively studied. However, current experimental techniques are still difficult to reveal the micro-mechanisms ignition and combustion of aluminum/ethanol nanofluid fuel. Hence, the ignition and combustion mechanisms of aluminum/ethanol nanofluid fuel were investigated from a microscopic point of view through reactive molecular dynamics simulation. The simulation results show that the mechanisms of enhanced ethanol combustion by aluminum nanoparticles mainly consists of micro-explosion at high temperature and small particle size, chain reaction at low temperature and large particle size, melt-dispersion in the mild oxidation state and diffusive oxidation in the moderate and heavy oxidation states. In addition, the initial stage of the combustion of aluminum nanoparticles with core-shell structure in ethanol is mainly a non-homogeneous surface reaction. This work reveals the combustion characteristics and mechanisms of aluminum/ethanol nanofluid fuel from an atomic perspective, which is expected to provide insights for the exploration and application of ethanol-based nanofluid fuel in the future.

Atomic oxygen erosion mechanism of polyimide via reactive molecular dynamics simulation and density functional theory calculation

Atomic oxygen (AO) causes serious oxidative degradation on polymeric materials in the space environment, yet understanding its reaction mechanism is a challenging task. Herein, we primarily investigate the reaction sites and reaction paths of pure polyimide material to AO erosion and propose a modification strategy involving electron-withdrawing groups to enhance the material's resistance to AO with density functional theory (DFT) and reactive force field molecular dynamics (ReaxFF MD). DFT calculations reveal that AO erosion is an electrophilic reaction, which preferentially interacts on the benzene ring with pronounced electron density distribution on the third part of the polyimide molecule. ReaxFF MD simulations validate this finding and provide additional reaction pathways that are divided into the early-stage reactions and later secondary reactions. In the early stage, only small number of AOs take part in the reactions that include the formation of CO bonds and ring opening processes. These reactions are relatively slow and majorly determine the AO resistance of the material. In the subsequent stage, AO predominantly reacts with reactive species and radicals generated from earlier reactions, leading to fast degradation. With these findings, we propose a strategy to enhance the AO resistance by introducing electron-withdrawing functional groups in the polyimides. As exemplified, the polyimide with -CF3 group shows 21.1% lower erosion yield than unmodified polymer. The present study gives a deep insight for the mechanism of AO erosion on polyimide by exploring its reaction sites and provides valuable theoretical guidance for improving the material's resistance to erosion.

Simultaneous improvement in the elastic and fracture properties of graphene-epoxy nanocomposites–a computational perspective

The incorporation of stiff nano-additives (such as graphene) into a relatively soft polymer material (such as epoxy) usually leads to an improvement in elastic properties (i.e., Young's modulus) at the expense of fracture properties (i.e., tensile strength and toughness). Despite over a decade of research in polymer nanocomposites, we still lack a clear understanding of their structure-property relationships, which limits us from enhancing both elastic and fracture properties concurrently. Here, we performed large-scale reactive molecular dynamics simulations to study the deformation and fracture of model graphene/epoxy systems under uniaxial tension. A computationally efficient reactive force field was developed for graphene-epoxy system, allowing covalent bond formation, and breaking, which is crucial to model cross-linking in model epoxy as well as fracture. It was found the mechanical properties of the nanocomposite are very sensitive to the strength of the graphene-epoxy interface. As expected, elastic modulus increases with the interfacial strength. However, there appears to be an optimal interfacial strength to enhance the tensile strength and toughness. This is due to stress concentration occurring near the graphene edges at high interfacial strength, which leads to premature fracture. We show that by appropriately selecting an intermediate interface strength, one can simultaneously improve the ultimate tensile strength, toughness and the Young's modulus of the nanocomposite epoxy at ultra-low (∼0.2 % by weight) loading fraction of graphene additives. Our findings highlight the critical importance of properly engineered additive-matrix interfacial strength to develop high-performing polymer nanocomposites that are concurrently stiff, strong as well as tough.