First-principles Molecular Dynamics Research Articles

Electrochemical Oxidation of UV Filters: A First-Principles Molecular Dynamics Study.

A theoretical model is proposed to study the oxidation mechanisms of the organic UV filters BP3 and BP4 during electrochemical water treatment utilizing Car-Parrinello molecular dynamics. Factors such as the amount of solvent to be included and how to design the system with the least possible intervention are discussed. The proposed model consist of the optimization of the geometries by density functional theory methods, the equilibration of the structure immersed in a water box, the inclusion of the reactive species, and the analysis of the reaction energies of each reaction pathway. The ab-initio molecular dynamics simulations lead to several products, and some trends can be identified, in accordance with the well-known reactivity rules of organic chemistry. The products proposed in this work are intermediates in longer oxidative pathways.

Enhanced Photosensitizer Wettability via Anchoring Competition of Violet Phosphorus Quantum Dots for Breakthroughs in Photodynamic Film Sterilization.

Wettability is important for photodynamic film sterilization since higher wettability enhances the capture of bacteria in contact with photosensitizers. Herein, a small number of violet phosphorus quantum dots (VPQDs) are anchored into hypericin bacterial cellulose films (VP/Hy-BC films) to improve wettability, reducing the water contact angle from 56.8° to 33.0°. This modification facilitated more effective interactions between the bacteria and photosensitizers, rapidly inactivating 7 log10 CFU/mL of Staphylococcus aureus within 60min. First-principles calculations and molecular dynamics simulations reveal that VPQDs, with their low spatial site resistance, reduced the intermolecular Hy self-aggregation force. This increased the solvent-accessible surface area of VP/Hy by ≈25.7%, thereby decreasing hydrophobic photosensitizer aggregation. Consequently, more active sites are exposed, remarkably improving the photoelectron transfer efficiency. VP/Hy-BC demonstrated exceptional efficacy in inhibiting bacterial proliferation; for instance, it extended beef shelf life by up to 10 days. The findings of this study will aid the development of health-conscious, eco-friendly, and efficient antimicrobial packaging films.

First-principles molecular dynamics of exciton-driven initial stage of plasma phase transition in warm dense molecular nitrogen.

Understanding the properties of molecular nitrogen N2 at extreme conditions is the fundamental problem for atomistic theory and the important benchmark for the capabilities of first-principles molecular dynamics (FPMD) methods. In this work, we focus on the connection between the dynamics of ions and electronic excitations in warm dense N2. The restricted open-shell Kohn-Sham method gives us the possibility to reach relevant time and length scales for FPMD modeling of an isolated exciton dynamics in warm dense N2. Wannier localization sheds light on the corresponding mechanisms of covalent bond network rearrangements that stand behind polymerization kinetics. FPMD results suggest a concept of energy transfer from the thermal energy of ions into the internal energy of polymeric structures that form in warm dense N2 at extreme conditions. Our findings agree with the thermobaric conditions for the onset of absorption in the optical spectroscopy study of Jiang et al. [Nat. Commun. 9, 2624 (2018)].

Predicting Collision-Induced-Dissociation Tandem Mass Spectra (CID-MS/MS) Using Ab Initio Molecular Dynamics.

Compound identification is at the center of metabolomics, usually by comparing experimental mass spectra against library spectra. However, most compounds are not commercially available to generate library spectra. Hence, for such compounds, MS/MS spectra need to be predicted. Machine learning and heuristic models have largely failed except for lipids. Here, quantum chemistry software can be used to predict mass spectra. However, quantum chemistry predictions for collision induced dissociation (CID) mass spectra in LC-MS/MS are rare. We present the CIDMD (Collision-Induced Dissociation via Molecular Dynamics) framework to model CID-based MS/MS spectra. It uses first-principles molecular dynamics (MD) to simulate the physical process of molecular collisions in CID tandem mass spectrometry. First, molecular ions are constructed at specific protonation sites. Using density functional theory, these protonated ions are targeted by argon collider gas atoms at user-specified velocities. Subsequent bond breakages are simulated over time for at least 1,000 fs. Each simulation is repeated multiple times from various collisional directions. Fragmentations are accumulated over those repeated collisions to generate CIDMD in silico mass spectra. Twelve small metabolites (<205 Da) were selected to test the accuracy of this framework in comparison to experimental MS/MS spectra. When testing different protomers, collider velocities, number of simulations, simulation time and impact factor b cutoffs, we yielded 261 predicted mass spectra. These in silico spectra resulted in entropy similarity scores of an average 624 ± 189 for all 261 spectra compared to their corresponding experimental spectra, which improved to 828 ± 77 when using optimal parameters of the most probable protomers for 12 molecules. With increasing molecular mass, higher velocities achieved better results. Similarly, different protomers showed large differences in fragmentation; hence, with increasing numbers of protomers and tautomers, the average CIDMD prediction accuracy decreased. Mechanistic details showed that specific fragment ions can be produced from different protomers via multiple fragmentation pathways. We propose that CIDMD is a suitable tool to predict mass spectra of small metabolites like produced by the gut microbiome.

Study on the Effect of Ce Doping Concentration on the Kinetics of Graphene Formation

The thermodynamic and kinetic processes of Ce-doped graphene were simulated by the method of first-principles molecular dynamics. The structural optimization and annealing, the kinetic properties of Ce-doped graphene composites were calculated by the classical mechanics Forcite module. The results show that with the increase of Ce doping concentration, the order of the radial distribution function in the system increases and presents a state of aggregation. According to the analysis of mean azimuth shift function, the mean square displacement (MSD) value of Ce doped graphene composite increases with the increase of doping concentration, and the corresponding diffusion coefficient also increases. The research of gyration radius and gyration evolution radius shows that with the increase of temperature and doping concentration, the gyration evolution radius of atoms becomes shorter and shorter, indicating that the interatomic force in the system is enhanced and the range of activity is shortened. Combined with the analysis of local cluster structure, it can be seen that the maximum cluster size and number of Ce doped graphene composites do not change significantly with the increase of doping concentration, indicating that Ce atom doping will improve the order in the system, increase the diffusion coefficient and enhance the interaction force between atoms. The paper aims to reduce the error between the theoretical properties and the actual properties, and provide a theoretical basis for the development of new materials with excellent properties.

Molecular Dynamics Simulation Model of Alkali Metal Reduction of Gaseous Halides and Reaction Mechanism Analysis.

The reaction of gaseous hydrogen halides with alkali metals provides a new pathway for producing hydrogen. The structure and reactivity of alkali metals are crucial for the reduction of gaseous halides. However, traditional gas-phase reaction models fail to provide insights into the dynamic processes occurring during alkali metal reactions. In this paper, based on the reaction between Hydrogen fluoride (HF) and alkali metal sodium (Na), we have established a metallic Na slab. HF molecules were randomly inserted above the surface of the Na slab, creating a reaction model for the reduction of HF by metallic Na. The reaction of HF on the Na surface was calculated using first-principles molecular dynamics. The configuration and reaction of the Na surface and HF molecules at different times were judged by analyzing the radial distribution function and mean squared displacement. Na atoms reacted with HF to produce intermediate NaFH, and then the F-H bond broke to form NaF and H. The F-H bond breaking of intermediate NaFH was the key step, and the kinetic parameters of this key step were calculated.

Molecular insights into the performance of promoters for carbon dioxide hydrate

Hydrate-based CO2 storage is a cost-effective and environmentally friendly approach to reduce carbon emission, and the addition of hydrate promoters has shown a promising avenue for enhancing CO2 hydrate formation. In this work, the promotion mechanism and promotion performance of five different hydrate promoters (denoted as DIOX, CP, THF, THP, and CH) were investigated and compared by first-principles calculations and molecular dynamics simulations. The results show that the hydrate promoters prefer to singly occupy 51264 cages of the sII hydrate, and CO2 molecules can singly occupy 512 cage or multiply occupy 51264 cages. The cohesive energy density indicates that the optimum CO2 storage capacity can reach up to ∼28 wt%. The stabilization effects of hydrate promoters on the hydrate stability should follow the order of CP > CH > DIOX > THF ≈ THP. The hydrate promoters can increase the water-water interactions, and the molecular diffusivity shows that the dynamic stability of the hydrates is THP ≈ CH > CP > DIOX > THF. Further, the hydrate promoters can accelerate the hydrate formation kinetics, which reduce the induction time and increase the nucleation and growth process.

Formation mechanism and luminescence properties of silicon carbide nanowires with core-shell structure

For the preparation of SiC nanowires (SiC NWs) by carbothermal reduction, it is of great significance to study the formation mechanism of sic nanowires for process optimization and the controllable preparation. Although first-principles molecular dynamics (FPMD) can simulate systems of hundreds of atoms on a picosecond time scale, the results of FPMD are still insufficient to elucidate the formation mechanism of core-shell SiC nanowires. To make up this deficiency, this article has conducted Deep Potential Molecular Dynamics (DPMD) simulation on nanoseconds timescales with near FPMD accuracy for systems containing thousands of atoms, the results more concretively show the formation process of core-shell SiC nanowires. DPMD simulation results show when CO molecules react with SiO molecules, CO molecules are wrapped by SiO molecules to form agglomerates, SiO molecules in the agglomerates that can come into contact with the wrapped CO molecules will react with wrapped CO molecules to form the SiC core, and SiO molecules that in the outer layer of the agglomerates will disproportionate into the amorphous SiO2 shell. Furthermore, the formation mechanism of SiC nanowires was validated in combination with thermodynamics and experimental methods. Thermodynamic results show that vacuum conditions are favorable for the formation of SiO and CO and lower the temperature of SiC preparation. Finally, the core-shell structure of SiC NWs with good luminescence properties were successfully prepared by carbothermal reduction method using carbon black and silicon dioxide as raw materials under the pressure of less than 5 kPa.

Breaking new ground in metal-ion battery anodes: First principles design of Dirac nodal line semimetallic carbon materials

With the rapid development of electronic devices, the demand for batteries has gradually increased, and existing batteries can no longer satisfy it. In this paper, a three-dimensional honeycomb carbon material is designed and termed pmma-C32. The mechanical stability, dynamic stability, thermal stability, and mechanical stability were investigated through first-principles molecular dynamics, phonon spectrum, and the Born-Huangkun criterion. The calculation results show that pmma-C32 not only has good thermodynamic stability, but also has static stability. Similar to graphene, pmma-C32 exhibits semi-metallic characteristics, featuring two Dirac node lines with high Fermi velocity, indicating a high capacity for electron transport. As a metal-ion battery material, pmma-C32 exhibits higher theoretical capacity(836.8, 732.2, and 418.4 mA h/g for Li, Na, and K), lower diffusion barrier (0.06–0.12 eV for Li, 0.10–0.11 eV for Na, and 0.05–0.06 eV for K), and lower open circuit voltage (0.34 V for Li, 0.37 V for Na, and 0.74 V for K). These remarkable properties endow semimetallic pmma-C32 as a promising anode material for metal-ion batteries, providing fast charge and discharge rates. This research not only broadens the family of three-dimensional carbon materials, but also greatly improves the performance for universal metal-ion battery anode materials through material structure design.

Design and Optimization of Iron-Based Superionic-Like Conductor Anode for High-Performance Lithium/Sodium-Ion Batteries.

Metal selenides have received extensive research attention as anode materials for batteries due to their high theoretical capacity. However, their significant volume expansion and slow ion migration rate result in poor cycling stability and suboptimal rate performance. To address these issues, the present work utilized multivalent iron ions to construct fast pathways similar to superionic conductors (Fe-SSC) and introduced corresponding selenium vacancies to enhance its performance. Based on first-principles calculations and molecular dynamics simulations, it is demonstrated that the addition of iron ions and the presence of selenium vacancies reduced the material's work function and adsorption energy, lowered migration barriers, and enhances the migration rate of Li+ and Na+. In Li-ion half batteries, this composite material exhibites reversible capacity of 1048.3 mAh g-1 at 0.1 A g-1 after 100 cycles and 483.6 mAh g-1 at 5.0 A g-1 after 1000 cycles. In Na-ion half batteries, it is 687.7 mAh g-1 at 0.1 A g-1 after 200 cycles and 325.9 mAh g-1 at 5.0 A g-1 after 1000 cycles. It is proven that materials based on Fe-SSC and selenium vacancies have great applications in both Li-ion batteries and Na-ion batteries.

Effects of transition metals (V, Cr, Mn, Fe and Ni) doping on magnetic properties of Co-based amorphous alloys

Amorphous alloys exhibit numerous interesting and abundant magnetic properties due to their disordered structural traits and have been extensively studied by researchers. In this work, the effects of a small amount of transition metals doping on the magnetic properties of Co80-xMxB20 (x = 0, 2, 4, 6, 8, 10; M = V, Cr, Mn, Fe, Ni) amorphous alloys were systematically investigated by utilizing first-principles molecular dynamics. The trend of the magnetic moment change in the simulated calculation conforms well to the experimental results. The doping of V atoms leads to the fastest rate of decrease in the magnetic moment of the surrounding Co atoms, and there is only an antiferromagnetic interaction between the V and Co atoms. When doped with Cr and Mn atoms, there is mutual competition between ferromagnetic and antiferromagnetic coupling in the amorphous alloy, Cr reduces the magnetic moment of the surrounding Co atoms, while the change in the magnetic moment of the Co atoms around Mn is small. The doping of Fe and Ni causes an increase in the magnetic moment of the surrounding Co atoms. The reason may be due to the charge transfer between atoms. The doping of Fe and Ni has a small effect on the average magnetic moment of the Co atoms in the amorphous alloy. The results provide necessary theoretical support for the development of the Co-based amorphous alloys with excellent magnetic characteristics.

A first-principles molecular dynamics study of molecular hydrogen diffusion in Fe-free olivine

Molecular hydrogen (H2) may be an important form of water in nominally anhydrous minerals in the Earth’s mantle and plays a critical role in mantle water cycle, but the transport properties of H2 remain unclear. Here, the diffusion of H2 in Fe-free olivine lattice is investigated at pressures of 1–13 GPa and temperatures of 1300–1900 K by first-principles molecular dynamics. The activation energy and activation volume for H2 diffusion in Fe-free olivine are determined to be 55 ± 8 kJ/mol and 3.6 ± 0.2 cm3/mol, respectively. H2 diffusion in Fe-free olivine is faster than H+ by 1–4 orders of magnitude and therefore it is more favorable for hydrogen transportation under upper mantle conditions. H2 can be carried to the mantle transition zone by subducting slabs without releasing to the surrounding mantle. The upper mantle may act as a lid, preventing the releasing of H2 produced in the deep mantle to the surface.

Corrosion inhibition of Ga-based thermal interface materials with Ni coating on Cu substrate

The gallium (Ga) base liquid metal (LM) with high thermal conductivity and deformability is applied widely in thermal management in electrical systems. However, Ga readily reacts with Cu to form intermetallic compounds (IMCs), which can cause failure in electronic devices. Herein, the thermal interface material (TIM) with Ga and diamond is prepared to analyze the reaction behavior of TIM and Cu/Ni-plated Cu under an aging test at 125 °C. The results show that Ga reacts with Cu substrate and forms CuGa2 bulk. Moreover, Ni coating can inhibit the corrosion of Ga and Cu. However, the as-volcano IMC structures were generated, also. The thermal resistance increased from 2.24 mm2·K·W−1 to 14.47 mm2·K·W−1 from initial time to 200 h. The interfacial corrosion behavior between TIM and Cu substrate is studied by first-principles molecular dynamics simulation. The diffusion coefficient in the z direction of Cu is 0.04 × 10−5 cm2/s. In a word, the work could provide the guidelines for the further design of high-performance corrosion resistance in the region where Ga was used for thermal management on electronic products.

Accelerated First-Principles Exploration of Structure and Reactivity in Graphene Oxide.

Graphene oxide (GO) materials are widely studied, and yet their atomic-scale structures remain to be fully understood. Here we show that the chemical and configurational space of GO can be rapidly explored by advanced machine-learning methods, combining on-the-fly acceleration for first-principles molecular dynamics with message-passing neural-network potentials. The first step allows for the rapid sampling of chemical structures with very little prior knowledge required; the second step affords state-of-the-art accuracy and predictive power. We apply the method to the thermal reduction of GO, which we describe in a realistic (ten-nanometre scale) structural model. Our simulations are consistent with recent experimental findings, including X-ray photoelectron spectroscopy (XPS), and help to rationalise them in atomistic and mechanistic detail. More generally, our work provides a platform for routine, accurate, and predictive simulations of diverse carbonaceous materials.

Reactant Discovery with an Ab Initio Nanoreactor: Exploration of Astrophysical N-Heterocycle Precursors and Formation Pathways.

The incorporation of nitrogen atoms into cyclic compounds is essential for terrestrial life; nitrogen-containing (N-)heterocycles make up DNA and RNA nucleobases, several amino acids, B vitamins, porphyrins, and other components of biomolecules. The discovery of these molecules on meteorites with non-terrestrial isotopic abundances supports the hypothesis of exogenous delivery of prebiotic material to early Earth; however, there has been no detection of these species in interstellar environments, indicating that there is a need for greater knowledge of their astrochemical formation and destruction pathways. Here, we present results of simulations of gas-phase pyrrole and pyridine formation from an ab initio nanoreactor, a first-principles molecular dynamics simulation method that accelerates reaction discovery by applying non-equilibrium forces that are agnostic to individual reaction coordinates. Using the nanoreactor in a retrosynthetic mode, starting with the N-heterocycle of interest and a radical leaving group, then considering the discovered reaction pathways in reverse, a rich landscape of N-heterocycle-forming reactivity can be found. Several of these reaction pathways, when mapped to their corresponding minimum energy paths, correspond to novel barrierless formation pathways for pyridine and pyrrole, starting from both detected and hypothesized astrochemical precursors. This study demonstrates how first-principles reaction discovery can build mechanistic knowledge in astrochemical environments as well as in early Earth models such as Titan's atmosphere where N-heterocycles have been tentatively detected.

First-principles study of non-linear thermal expansion in cadmium titanate by molecular dynamics incorporating nuclear quantum effects

First-principles molecular dynamics (FPMD) simulations were applied for analyzing structural evolutions around the paraelectric-ferroelectric phase transition temperature in the perovskite-type cadmium titanate, CdTiO3. Since the phase transition is reported to occur at the low temperature around 80 K, the quantum thermal bath (QTB) method was utilized in this study, which incorporates the nuclear quantum effects (NQEs). The structural evolutions in the QTB-FPMD simulations are in reasonable agreement with the experimental results, by contrast in the conventional FPMD simulations using the classical thermal bath (CTB-FPMD). Especially, the non-linear thermal expansion of lattice constants around the phase transition temperature was well reproduced in the QTB-FPMD with the NQEs. Thus, the NQEs are of importance in phase transitions at low temperatures, particularly below the room temperature, and the QTB is useful in that it incorporates the NQEs in MD simulations with low computational costs comparable to the conventional CTB.

Thermal performance of MgCl2–NaCl–KCl eutectic salt for the next generation concentrated solar power and correlation between structure and thermophysical properties: Insights from atomic and electronic levels

MgCl2–NaCl–KCl (MgNaK) eutectic salt has emerged as a highly promising candidate for concentrated solar power (CSP), with extensive research conducted in recent years. However, the thermal property data for the MgNaK eutectic salt are still very limited. Here, we present a novel and accurate many-body potential trained by machine learning (ML) for MgNaK eutectic salt (with mole fractions of 45.4 %, 33 %, and 21.6 % respectively), developed using energies and forces extracted from first-principles molecular dynamics calculations (FPMD). The performance of the potential is well tested. We conduct a detailed investigation on the temperature-dependent structural and corresponding thermal properties, analyzing them from both the atomic and electronic perspectives. The introduction of Na+ or K+ ions disrupts the net structure formed by corner-joint and edge-joint MgClx units, thereby affecting the transport properties. The calculated density (ρ) and constant pressure specific heat capacity (CP) exhibit agreement with experimental data within a margin of 2 %. We observe and discuss the typical λ of negative linear temperature correlation, which is similar to other molten alkali chloride salts. Finally, based on the simulated and experimental values, we provide reliable recommendations for the λ and viscosities (η) of MgNaK eutectic salt across its entire operating temperature range.

Estimation of antigorite wave velocities in subduction conditions based on first-principles thermoelasticity

The most abundant serpentine mineral in subduction settings, antigorite has one of the highest water storage capacities and is involved in seismicity. Seismic wave velocities of antigorite are important for detecting and quantifying serpentinization within the mantle wedge and the subducting oceanic plate. At present, the elastic properties of antigorite at high pressures and temperatures are unclear. In this study, we have investigated pressure-volume-temperature (P-V-T) data and thermodynamic properties of antigorite using first-principles molecular dynamics (FPMD) simulations. Using these simulations results, we computed the relevant thermoelastic parameters and estimated compressional and shear wave velocities (vP and vS) of antigorite in subduction conditions. A simplified velocity model of antigorite with its coexisting mantle anhydrous phases was introduced to help us understand the potential effect of serpentinization on the seismic velocity of mantle rocks. Combined with seismic observations, we re-evaluated some velocity anomalies within forearc mantle wedges and established reliable serpentinization budgets. These results can provide preliminary evaluations and reliable constraints on serpentinization and water content in mantle rocks, which has important implications for understanding global plate dynamics and the deep water cycle.

Molecular Simulation Insights into Chemical-Grafted EPDM for Improving Charge Traps, Moisture Resistance, and Pyrolysis Tolerance

This study explores and verifies the chemical modifications achieved by grafting 4-formylcyclohexyl heptanoate (FH) and 4-(2,5-dioxopyrrolidin-1-yl) cyclohexane-1-carbaldehyde (CC) onto ethylene propylene diene monomer (EPDM) elastomer, a prevalent dielectric material used for reinforced insulation in cable accessories. Employing a rigorous theoretical methodology combining first-principles calculations, molecular dynamics, and Monte Carlo molecular simulations, we elucidate the intricate effects of these chemical-graft modifications on the polymeric structure of EPDM to resist charge transport, moisture-aging, and thermal impact of partial discharge. Our investigation uncovers the emergence of both shallow and deep charge traps within the material, effectively mitigating electron avalanche breakdown. Additionally, we scrutinize the influence of two proposed organic species, acting as grafting agents, on several crucial properties of EPDM including water adsorption uptake, heat capacity, molecular thermal vibration, and polymer pyrolysis. These modifications substantially bolster EPDM’s resistance to high-temperature electrical breakdown and water thermodynamic adsorption, while also enhancing its thermal stability, rendering the proposed chemical-graft modifications an effective way and underling mechanisms for ameliorating electrical insulation performances of EPDM elastomer. Our findings highlight the significant potential of graft modification in molecular structures through comprehensive molecular simulations, offering valuable insights for advancing competent elastomeric polymers in cable accessory insulation.

The Hugoniot curve and sound velocity of forsterite to 1200 GPa

The comprehension of the composition and physical state of the deep interiors of large planets, as well as the impact events pertinent to planetary formation and evolution, necessitates an understanding of the properties of planetary materials under extreme conditions. Forsterite (Mg2SiO4), a significant geological mineral, has not been fully characterized in terms of its behavior under shock compression due to a lack of consensus among previous experiments and simulations aimed at determining its Hugoniot, as well as the absence of knowledge of sound velocity at high pressures, a critical parameter indicative of phase transformation and melting.In this study, we delineated the Hugoniot curve of the mineral forsterite up to immense pressures of 1200 GPa. For the first time, we successfully constrained its sound velocity along the Hugoniot curve up to 760 GPa by combining laser-driven shock experiments with first-principles molecular dynamics simulations. The measured Hugoniot data for forsterite corroborated previous findings and suggested the occurrence of incongruent melting during shock compression. Remarkably, along their respective Hugoniot curves, the sound velocity of forsterite was observed to fall between that of the minerals bridgmanite and periclase. The remarkable agreement between the experimental results and simulation data provides reliable sound velocity measurements on the forsterite Hugoniot, which is critical for comprehensively understanding the phase transition and melting behavior of forsterite under ultra-high pressures. This knowledge sheds invaluable light on the behavior of this significant geological mineral under extreme conditions akin to those found in the interiors of planets.