First-principles Molecular Dynamics Research Articles

Ion solvation free energy calculations based on first-principles molecular dynamics thermodynamic integration.

Numerous electrochemistry reactions require the precise calculation of the ion solvation energy. Despite the significant progress in the first-principles calculations for crystals and defect formation energies for solids, the liquid system free energy calculations still face many challenges. Ion solvation free energies can be calculated via different semiempirical ways, e.g., using implicit solvent models or cluster of explicit molecule models; however, systematically improving these models is difficult due to their lack of a solid theoretical base. A theoretically sound approach for calculating the free energy is to use thermodynamic integration. Nevertheless, owing to the difficulties of self-consistent convergence in first-principles calculations for unphysical atomic configurations, the computational alchemy approach has not been widely used for first-principles calculations. This study proposes a general approach to use first-principles computational alchemy for calculating the ion solvation energy. This approach is also applicable for other small molecules. The calculated ion solvation free energies for Li+, Na+, K+, Be2+, Mg2+, and Ca2+ are close to the experimental results, and the standard deviation due to molecular dynamics fluctuations is within 0.06eV.

First-principle molecular dynamics and in situ DRIFTS study the stability of the intermediates of CO2 hydrogenation to methanol on ZnZrOx solid solution catalyst

Among the many catalysts used for CO2 hydrogenation to methanol, ZnZrOx solid solution is a highly efficient catalyst. Although the reaction mechanism has been widely explored at 0 K using DFT, critical aspects such as the atomic structure of the solid solution and the stability of reaction intermediates during CO2 reduction at experimental temperatures remain unclear. This study employs first-principle molecular dynamics (MD) simulations, FTIR and DRIFTS characterization to address these important questions. During the MD simulation, oxygen vacancies are formed in the system and same as the doped Zn atoms. The formation of oxygen vacancies was further confirmed by the Transmission FTIR and in situ DRIFTS. Due to the creating of oxygen vacancies, the coordination of Zn and Zr in the bulk is reduced to five and seven, respectively. And on the surface, their coordination is reduced to three、four and six、seven, respectively. Subsequently, the hydrogenation of CO2 to methanol using the formate and CO* pathways was studied. In the formate pathway, all intermediates remained stable at 593 K. However, in the CO* pathway, we observe instability of key intermediates which also confirmed by transmission FTIR and in situ DRIFTS characterization.

The thermal equation of state of the magma Ocean

As the protolunar disk formed by the giant impact with the incoming asteroid Theia started to cool, the Earth condensed in its center as a molten planet. The outer layer, rich in lithophile oxides, formed the magma ocean, whose dynamical behavior heavily influenced the entire evolution of the early Earth. Here, we employ first-principles molecular dynamics simulations to characterize the magma ocean in its initial stage. We compute the compressibility and the viscosity of the molten pyrolite, which best approximates the bulk silicate Earth composition. With an extensive set of calculations, we span the entire relevant pressure-temperature range. We provide a detailed analysis of the athermal and thermal equations of state in various formulations. We obtain a linear temperature dependence for the bulk modulus using the 4th order Birch-Murnaghan equation of state. We show that the liquid silicate accommodates compression by the collapse of the second Si-O coordination sphere, whose corresponding coordination number passes from about 24 at the surface of the magma ocean to about 40 at its deepest point. We found that pyrolite melts have a very low viscosity, about one order of magnitude lower than that of molten basalt. We also propose a revised position of the critical point of the bulk silicate Earth, which lies around 6000 K and 1.1–1.2 kbars.

Study on the Structure and Transport Properties of Molten Salts of NaF–KF–AlF3 Electrolytes by First-Principles Molecular Dynamics Simulation

Study on the Structure and Transport Properties of Molten Salts of NaF–KF–AlF3 Electrolytes by First-Principles Molecular Dynamics Simulation

Structure and dynamical properties during the solidification of the liquid aluminum induced by cooling and compression

Abstract The structural transformation from a liquid to a crystalline solid is an important subject in condensed matter physics and materials science. In the present study, firstprinciples molecular dynamics calculations were performed to investigate the structure and properties of aluminum during the solidification which was induced by cooling and compression. During both the cooling and compression processes, it was found that the icosahedral short-range order was initially enhanced and then began to decay, the face-centered cubic short-range order eventually became dominant before it transformed to a crystalline solid.

Equation of state and thermodynamic properties of liquid Fe-O in the Earth’s outer core

Equation of state (EoS) plays a crucial role in the prediction of the composition of the outer core. Here, we calculated pressure (P)-volume (V)-temperature (T) data of liquid iron-oxygen alloys (Fe-X wt.% O, X = 0, 2.8, 6.1, and 9.9) under the outer core conditions (∼136–330 GPa, 4000–6000 K) by first-principles molecular dynamics simulations. We established an EoS for liquid Fe-O alloys with parameters including P, T, V, and O concentrations. Consequently, thermodynamic properties of liquid Fe-O alloys such as density (ρ), thermal expansion coefficient, isothermal and adiabatic bulk modulus, and sound velocity (VP) are calculated. To constrain the O content, we predicted the ρ-P and VP-P profiles along the geotherm and compared them with data from the Preliminary Reference Earth Model (PREM). We conclude that the adiabatic T profile as a function of depth affects the prediction of O content dramatically. With several anchored TICB, the composition of Fe-6.1 wt% O matches the PREM data with an acceptable range of error. But strictly speaking, the distribution in the outer core is probably uneven. In such case, we state that the O content in the outer core cannot be higher than approximately 6.1 wt%.

The Role of Grain Boundaries on Ion Migration and Charge Recombination in Halide Perovskites.

Grain boundaries (GBs) have a significant role in polycrystalline perovskite solar cells (PSCs). However, there is ongoing debate regarding the impact of GBs on the performance and long-term stability of PSCs. Employing the first-principles molecular dynamics for perovskites, the iodine vacancy defect migrations both in bulk and at GBs are investigated. i) The positive iodine vacancy (VI +) is found that have both lower formation energy (1.4eV) and activation energy (0.18eV) than those of neutral iodine vacancy (VI), statistically. It indicated the VI + acts as the dominant migrated iodine vacancy rather than VI; ii) the iodine vacancy at GBs has ≈0.48eV higher activation energy than those in bulk, which leads to the accumulation of iodine vacancy at GBs; iii) the presence of VI + result in a 3-fold increase in charge recombination ratio at GBs, compared to pristine PSCs. Based on quantum molecular dynamics statistical results, which are consistent with experimental measurements, insights into iodine vacancy migration both at GBs and in the bulk are gained. This understanding can be valuable for defects engineering related to ion migration, in order to improve the long-term stability and promote the performance of PSCs.

Gallium Trichloride Fluid: Dimer Dissociation Mechanism, Local Structure, and Atomic Dynamics.

Molten gallium trichloride emerges as a promising solvent for oxidative metal recycling. The use of supercritical fluid enhances the performance and kinetics of metal dissolution due to significantly lower viscosity in the reaction media. Additionally, the dual molecular nature of gallium trichloride, existing as edge-sharing ES-Ga2Cl6 dimers at low temperatures and high pressure, or flat trigonal GaCl3 monomers in the vicinity of the critical point and low pressures, creates the possibility to tailor the chemical geometry to a particular metallic species. Nevertheless, the mechanism of dimer dissociation, local structure, and atomic dynamics in supercritical gallium trichloride fluids are not known. Using first-principles molecular dynamics, validated by comparison with our high-energy X-ray diffraction results, we illustrate the elementary steps in dimer dissociation. These include the formation of intermediate corner-sharing CS-Ga2Cl6 dimers, the partial disproportionation of GaCl3 monomers at high temperatures and low pressures, changes in the local environment of molecular entities, and unusual atomic dynamics in supercritical fluids.

Enhancement of interfacial thermal conductance by introducing carbon vacancy at the Cu/diamond interface

Effective heat dissipation of semiconductor devices is crucial for their extended lifespan and operational stability, and the interface of semiconductors provides an effective window for thermal design and management. In this work, we have systematically investigated the effect of the carbon vacancy on the thermal conductivity of diamond and the interface thermal conductance (ITC) of Cu/diamond by using both first-principles calculation and molecular dynamics methods. Although the carbon vacancy leads to a decrease in the thermal conductivity of diamond, a marked increase in ITC from 37.98 MWm−2K−1 to about 177 MWm−2K−1 for diamond (1 1 1) plane and from 78.8 MWm−2K−1 to about 241 MWm−2K−1 for diamond (0 0 1) plane is observed between Cu and diamond with carbon vacancy. The increase of the ITC is mainly due to the anharmonic phonon scattering, revealed by the phonon density of states and phonon participation ratio.

Assessing the thermal conductivity of amorphous SiN by approach-to-equilibrium molecular dynamics.

First-principles molecular dynamics combined with the approach-to-equilibrium molecular dynamics methodology is employed to calculate the thermal conductivity of non-stoichiometric amorphous SiN. This is achieved by implementing thermal transients in five distinct models of different sizes along the direction of the heat transport. Such models have identical structural features and are representative of the same material, thereby allowing for a reliable analysis of thermal conductivity trends as a function of the relevant cell dimension. In line with the known physical law of heat propagation at short scale, the thermal conductivity increases in size with the direction of heat transport. The observed behavior is rationalized accounting for previous results on crystalline and amorphous materials, thus providing a unified description holding for a large class of materials and spanning a wide range of heat propagation lengths.

Lorenz number and transport properties of Fe: Implications to the thermal conductivity at Earth's core-mantle boundary

Abstract The electrical resistivity (ρ) and thermal conductivity (κ) of the Earth's core compositions are essential parameters for constraining the core's thermal state, the inner core age, and the evolutionary history of the geodynamo. However, controversies persist between experimental and computational results regarding the electronic transport properties (ρ and κ) of the Earth's core. Iron is the major element in the core, and its transport properties under high pressure and high temperature conditions are crucial for understanding the core's thermal state. We measured the ρ values of solid iron using the four-wire van der Pauw method at 300 K and pressures ranging from 3 to 26 GPa within a multi-anvil press. For comparison, we calculated the ρ and κ values of hexagonal close-packed (hcp) iron at conditions of 300-4100 K and 22-136 GPa using the first-principles molecular dynamics (FPMD) method. Our calculations generally align with prior studies, indicating that the electrical resistivity of solid hcp iron at Earth's core-mantle boundary (CMB) conditions is ~76-83 μΩ∙cm. The resistivity of hcp iron changes small as it melts from solid to liquid at pressures from 98 to 134 GPa. The impact of temperature and pressure on the Lorenz numbers of solid hcp iron are investigated according to our calculation results and previous studies. Under the CMB's pressure conditions, the κ of hcp iron initially decreases with increasing temperature and subsequently increases. The electron-electron scattering plays a dominant role at low temperatures and causes the decrease in κ. At high temperatures, the increase of electronic specific heat significantly increases the Lorentz number and κ. Overall, we estimate the κ of solid hcp iron at CMB's condition to be 114 ± 6 W/m/K, slightly lower than the room temperature value of 129 ± 9 W/m/K at the same pressure. Our model shows that a 0-525 km thickness of a thermally stratified layer may exist beneath the Earth's CMB depending on the core's heat flow and thermal conductivity.

Weakened Interfacial Hydrogen Bond Connectivity Drives Selective Photocatalytic Water Oxidation toward H2O2 at Water/Brookite-TiO2 Interface.

The formation of H2O2 through the two-electron photocatalytic water oxidation reaction (WOR) is significant but encounters the competition with the four-electron O2 evolution reaction. Recent studies showed a crystal-phase dependence in H2O2 selectivity, where high purity brookite TiO2 (b-TiO2) exhibits remarkable H2O2 selectivity in contrast to the common rutile phase TiO2 (r-TiO2). However, the origin of such a structure-induced selectivity preference remains elusive, primarily due to the complexities associated with the solid-liquid interface system and excited-state chemistry. Herein, we conducted a comprehensive investigation into the selectivity mechanism of WOR at the water/b-TiO2(210) and water/r-TiO2(110) interfaces, employing first-principles molecular dynamics simulations and microkinetic analyses. Intriguingly, our results reveal that the intrinsic catalytic ability of the b-TiO2(210) itself does not enhance H2O2 selectivity compared to r-TiO2(110). Instead, it is the weakened interfacial hydrogen bond connectivity, modulated by the herringbone-like local atomic structure of the b-TiO2(210) surface, that determines the selectivity. Specifically, this weakened H-bond connectivity (i.e., local low water density) at the interface, owing to the strong water adsorption and distinct adsorption orientation, can stabilize the OH• radical and inhibit its deprotonation, leading to an improved H2O2 selectivity. By contrast, the relatively strong interface H-bond connectivity established over r-TiO2(110) accelerates the deprotonation of OH•, with the OH• coverage being 3 orders of magnitude lower than at the water/b-TiO2(210) interface. This study quantitatively demonstrates that the local H-bond structure (water density) at the liquid/solid interface significantly influences photocatalytic selectivity, and this insight may offer a rational approach to enhance the H2O2 selectivity.

First-principles molecular dynamics simulations for the properties of boron-doped tetrahedral amorphous carbon

Based on first-principles molecular dynamics (FPMD) simulations combined with a liquid quenching method, we study the effects of boron doping at 0 %, 2 %, 4 %, 6 % on the properties of tetrahedral amorphous carbon (ta-C) with an initial density of 3.0 g/cm3. The results of bond structures and internal stress show the promotion of graphitization with increase in the concentration of boron doping. In addition, simulation of electronic states reveals that the Fermi level shifts to valence band and the intensity of density of electronic states near Fermi level increases with the boron concentration increasing. A covalent bond formation between carbon and boron atoms is also shown by analyzing projected densities of electronic states (PDOS) and electron density distribution. The results of electronic state and bond formation strongly indicate that the boron-doped ta-C is like a p-type semiconductor. The present simulation results provide useful information for deeper understanding on the physical properties of boron-doped ta-C.

Parameter-Free and Electron Counting Satisfied Material Representation for Machine Learning Potential Energy and Force Fields.

We proposed a parameter-free volume element representation that satisfies the electron counting model and obtains accurate machine learning potential energy and direct force fitting of randomly perturbed hexagonal BN. Our method preserves permutational, translational, and rotational invariance and can be extended to three-dimensional systems, verified by a system of bulk Si. As a result, we obtained 0.57 meV/atom potential energy root mean squared error (RMSE) and 59 meV/Å force RMSE for perturbed bulk BN systems and 0.43 meV/atom potential energy RMSE and 36 meV/Å force RMSE for perturbed Si systems. In addition, an unbiased perturbation-based data set construction scheme is introduced and a continuous population distribution is obtained with a training data set of 4500, which is about 1 order of magnitude smaller than standard methods based on first-principles molecular dynamics simulations and saves a large amount of computing resources. General validity of our model is verified by structure optimization, molecular dynamics simulations, and extrapolations.

Reactivity of Monoethanolamine at the Air-Water Interface and Implications for CO2 Capture.

The development of CO2-capture technologies is key to mitigating climate change due to anthropogenic greenhouse gas emissions. These cover a number of technologies designed to reduce the level of CO2 emitted into the atmosphere or to eliminate CO2 from ambient air. In this context, amine-based sorbents in aqueous solutions are broadly used in most advanced separation techniques currently implemented in industrial applications. It has been reported that the gas/liquid interface plays an important role in the early stages of the capture process, but how the interface influences the chemistry is still a matter of debate. With the help of first-principles molecular dynamics simulations, we show that monoethanolamine (MEA), a prototypical sorbent molecule, has a weak affinity for the air-water interface, where in addition it exhibits a lower nucleophilicity compared to bulk solution. The change in reactivity is due to the combination of structural and electronic factors, namely, the shift of the conformational equilibrium and the stabilization of the N-atom lone pair. Based on these results, strategies for improving the efficiency of alkanolamine sorbents are proposed.

Quantum Vibronic Effects on the Excitation Energies of the Nitrogen-Vacancy Center in Diamond.

We investigated the impact of quantum vibronic coupling on the electronic properties of solid-state spin defects using stochastic methods and first-principles molecular dynamics with a quantum thermostat. Focusing on the negatively charged nitrogen-vacancy center in diamond as an exemplary case, we found a significant dynamic Jahn-Teller splitting of the doubly degenerate single-particle levels within the diamond's band gap, even at 0 K, with a magnitude exceeding 180 meV. This pronounced splitting leads to substantial renormalizations of these levels and, subsequently, of the vertical excitation energies of the doubly degenerate singlet and triplet excited states. Our findings underscore the pressing need to incorporate quantum vibronic effects into first-principles calculations, particularly when comparing computed vertical excitation energies with experimental data. Our study also reveals the efficiency of stochastic thermal line sampling for studying phonon renormalizations of solid-state spin defects.

First principles molecular dynamics simulation and thermal decomposition kinetics study of CL-20.

2,4,6,8,10, 12-hexanitro-2,4,6,8,10, 12-hexazepane (CL-20) is a new energetic material with high performance and low sensitivity. In-depth study of the thermal decomposition mechanism of CL-20 is a necessary condition to improve its performance, ensure its safety, and optimize its application. On the basis of a large number of empirical force fields used in molecular dynamics simulation in the past, the machine learning augmented first-principles molecular dynamics method was used for the first time to simulate the thermal decomposition reaction of CL-20 at 2200 K, 2500 K, 2800 K, and 3000 K isothermal temperature. The main stable resulting compounds are N2, CO2, CO, H2O, andH2, where CO2 and H2O continue to decompose at higher temperatures. The initial decomposition pathways are denitration by N-N fracture, ring-opening by C-N bond fracture, and redox reaction involving NO2 and CL-20. After ring opening, two main compounds, fused tricyclic pyrazine and azadicyclic, were formed, which were decomposed continuously to form monocyclic pyrazine and pyrazole ring structures. The most common fragments formed during decomposition are those containing two, three, four, and six carbons. The formation rule and quantity of main small molecule intermediates and resulting stable products under different simulated temperatures were analyzed. Based on ab initio Bayesian active learning algorithm, efficient and accurate prediction of CL-20 is made using the dynamic machine learning function of Vienna Ab-Initio Simulation Package (VASP), which constructs the energy potential surface by learning a large number of data based on AIMD calculations. The result is a machine learning force field (MLFF). Then the molecular dynamics of CL-20 was simulated using the trained MLFF model. PAW pseudopotentials and generalized gradient approximation (GGA), namely, Perdew-Burke-Ernzerhof (PBE) functional, are used in the calculation. The plane wave truncation energy (ENCUT) is set to 550 eV, and using the Gaussian broadening, the thermal broadening size of the single-electron orbital is 0.05 eV. A van der Waals revision of the system with Grimme Version 3. The energy convergence accuracy (EDIFF) of electron self-consistent iteration is set to 1E-5 eV and 1E-6 eV, respectively. The two-step structure optimization is carried out using 1'1'1 k point grid and conjugate gradient method. The ENCUT was changed to 500 eV and EDIFF to 1E-5 eV, and NVT integration (ISIF = 2) of Langevin thermostat was used for machine learning force field training and AIMD simulation of the system.

Theoretical and experimental study of the mechanism for preparation of SiC nanowires by carbothermal reduction

High-quality SiC nanowires (NWs) were prepared at 1550 °C by carbothermal reduction of silica with carbon black under normal atmospheric pressure without a metallic catalyst. Linear and chain-beaded SiC NWs were synthesized in graphite and BN crucibles, respectively. The mass of the SiC NWs obtained from the BN crucible was greater than that obtained from the graphite crucible under the same conditions. Thermodynamic analyses and first-principles molecular dynamics simulations were performed to investigate the formation mechanism of the SiC NWs. Thermodynamic analysis revealed that in the carbothermal reduction reaction zone, SiO2 and C reacted to produce SiC particles, SiO, and CO. Subsequently, SiO reacted with CO during condensation, leading to the growth of SiC NWs. The first-principles molecular dynamics simulations indicate that the BN substrate has a greater affinity for gas-phase molecules than the graphite substrate, thereby creating optimal reaction sites for the reaction of SiO and CO molecules. This study provides a valuable reference for understanding the microscopic formation mechanisms and the large-scale production of SiC NWs.

Unravelling abnormal in-plane stretchability of two-dimensional metal-organic frameworks by machine learning potential molecular dynamics.

Two-dimensional (2D) metal-organic frameworks (MOFs) hold immense potential for various applications due to their distinctive intrinsic properties compared to their 3D analogues. Herein, we designed a highly stable NiF2(pyrazine)2 2D MOF in silico with a two-dimensional periodic wine-rack architecture. Extensive first-principles calculations and molecular dynamics (MD) simulations based on a newly developed machine learning potential (MLP) revealed that this 2D MOF exhibits huge in-plane Poisson's ratio anisotropy. This results in anomalous negative in-plane stretchability, as evidenced by an uncommon decrease in its in-plane area upon the application of uniaxial tensile strain, which makes this 2D MOF particularly attractive for flexible wearable electronics and ultra-thin sensor applications. We further demonstrated the unique capability of MLP to accurately predict the finite-temperature properties of MOFs on a large scale, exemplified by MLP-MD simulations with a dimension of 28.2 × 28.2 nm2, relevant to the length scale experimentally attainable for the fabrication of MOF films.

Molecular mechanism of elemental sulfur dissolution in H2S under stratal conditions.

Resulting from the solubility reduction of elemental sulfur during the development of high sulfur gas formations, sulfur deposition often occurs to reduce the gas production and threaten the safety of gas wells. Understanding the dissolution mechanism of elemental sulfur in natural gas is essential to reduce the risk caused by sulfur deposition. Because of the harsh conditions in the high-sulfur formations, it remains challenging to in situ characterize the dissolution-precipitation processes, making deficient the knowledge of sulfur dissolution mechanism. The dissolution of sulfur allotropes (SN, N = 2, 4, 6 and 8) in H2S, the main solvent of sulfur in natural gas, is studied in this work by means of first-principles calculations and molecular dynamics simulations. While S6 and S8 undergo physical interaction with H2S under the conditions corresponding to those at 1-6 km stratigraphic depths, S2 and S4 react with H2S and form stable polysulfides. Unravelling the mechanism would be helpful for understanding and controlling the sulfur deposition in high-sulfur gas development.