First-principles Molecular Dynamics Research Articles

Accurate and Efficient Calculation of the Solution Enthalpy and Diffusivity of Solutes in Liquid Metals Using Machine Learning Potential.

Liquid metals (LMs) have various applications in energy systems, such as coolants in advanced nuclear reactors. In addition, room-temperature LMs are attracting attention as flexible components in robotics and electronics and as novel chemical reaction media to form low-dimensional materials. In many of these applications, the capabilities of LMs can be further enhanced if one can better understand and control the chemical reactivity of LMs, which is largely affected by the stability and mobility of solutes in LMs. Here, we propose an automated method using a machine learning moment tensor potential to efficiently calculate the solution enthalpy and diffusivity of solutes in LMs. From several test cases in liquid Na, we demonstrate that the method can achieve an accuracy comparable to that of a direct calculation using first-principles molecular dynamics, while significantly reducing the calculation cost to the order of 1/10 to 1/100. The method is expected to contribute to the advancement of LM chemistry and the development of new LMs.

Equilibrium boron isotope fractionation during serpentinization and applications in understanding subduction zone processes

Serpentinites entering subduction zones show selective enrichment in trace elements and are the most important carriers of B in this setting. The evolving B isotopic composition (δ11B) of serpentinite is used in studying water-mediated interactions between mantle and crust in subduction zones, but we lack a full understanding of the processes controlling B isotope fractionation during serpentinization that would allow this tracer to be better utilized. Boron isotope fractionation between lizardite/forsterite/diopside and aqueous fluids is investigated using quantum mechanics (density functional theory, DFT) and the first-principles molecular dynamics simulation (FPMD) here. The 11B enrichment sequence in minerals follows the order of forsterite > clinopyroxene (diopside) > white mica > phlogopite > lizardite. On the basis of boron configurations in aqueous fluid acquired from FPMD simulations based on DFT, the reduced isotopic partition function ratio (β-factor) of aqueous B(OH)3 and B(OH)4− are 1000lnβB(OH)3 = −20.1 + 37.07(1000/T) + 8.2(1000/T)2 and 1000lnβB(OH)4- = −13.94 + 24.43(1000/T) + 9.12(1000/T)2 at the P-T range of 0–500 MPa and 298–1000 K. This theoretical approach gives an equilibrium B isotope fractionation of Δ11Blizardite-fluid = 15.89–22.88(1000/T) - 0.19(1000/T)2 between lizardite and neutral serpentinization fluid in the temperature range from 298 to 673 K. By contrast, the boron isotope fractionation between minerals formed as the slab descends (e.g., forsterite, diopside) and fluid released from subducted crustal lithologies is limited, indicating that secondary olivine minerals may inherit the δ11B signatures of the dehydrated serpentinites. This study provides new insights into how B isotopes can constrain boron sources and pathways in subduction zones, and trace phases recycled into the deep mantle and their later recycling in ocean island basalts.

Partition model for trace elements between liquid metal and silicate melts involving the interfacial transition structure: An exploratory two-phase first-principles molecular dynamics study

Separation of trace elements has become a major obstacle for preparation of high-purity metal materials. Effective design of the separation medium depends on accurate partitioning prediction of the trace elements in the two phases. However, development of a separation prediction model is difficult because of the limitations of recognition of the interfacial transition structures of the trace elements. Here, a partition model for trace elements between metal and silicate melts involving an interfacial transition structure was developed by exploratory two-phase first-principles molecular dynamics simulation. The results showed that the distribution strongly depends on the local coordination structure in the cluster (LCSC) of the impurity element, which is the key for investigating the interfacial transition structure. A computational strategy for the trace-element distribution ratio is proposed to quantify the contribution of the trace element at the interface. The LCSC partition model was demonstrated for trace element boron removal from silicon for molten silicon and silicate melts. The LCSC model gave a better predicted value of the experimental value than the traditional activity model. The new model assists in explaining the transformation mechanism of B atoms at the silicate–silicon interface at the atomic scale. The LCSC partition model allows prediction of the trace element partitioning behavior solely from first-principles calculations.

Melting curve and transport properties of ammonia ice up to the deep mantle conditions of Uranus and Neptune

Motivated by the poor knowledge of the implication of planetary ice on the internal convection and anomalous magnetic field of ice giants, we perform extensive first-principles molecular dynamics simulation on ammonia ice to investigate its thermophysical behaviors at high temperature ($T$) and pressure ($P$) conditions relevant to the deep mantle of Neptune and Uranus. The melting curve, transport properties, and sound velocity of ammonia up to 350 GPa and 5500 K, spanning from fluid mixtures to a highly compressed superionic regime, are determined. A first-order phase transition of ammonia from the plastic state to the superionic state is observed explicitly, which is associated with the reduction of entropy. In contrast to previous predictions, the melting curve elucidates the existence of superionic ammonia in deep planetary interiors. Inspection of the reduction for transport properties and sound velocity along the isentrope of ice giants further evidences that superionic ammonia can sufficiently sustain the planetary dynamo mechanism and may contribute to the internal stratification which is responsible for the generation of the multipolar magnetic field. Finally, a comprehensive phase diagram of ammonia extended to a higher T-P regime is constructed, which provides a clear picture for studying the fundamental behavior and phase transition of ammonia in deep planets, and enhances our understanding of the interior structure and thermal convection of these planetary systems.

Evaluation of the local structure and electrochemical behavior in the LiCl-KCl-SmCl3 melt

This present work evaluates the local structure and electrochemical behavior of the LiCl-KCl-SmCl3 melt to facilitate the efficient reprocessing of spent nuclear fuel (SNF). At 723 K, the radial distribution function, coordination number, and structure factors were adopted to understand the local structure of LiCl-KCl and LiCl-KCl-SmCl3 based on first-principles molecular dynamics (FPMD) simulation. We found the SmCl3 slight effect on LiCl-KCl melts in short-range order and its influence on the distribution of Li-Li intermediate-range order. Moreover, the diffusion coefficient of Sm(III) 2.012 × 10-5 cm2/s in LiCl-KCl melts was determined by analyzing the mean square displacement. The electrochemical behavior of Sm(III) was conducted in the temperature range from 673 K to 823 K by a series of electrochemical methods. According to the theory of Matsuda and Ayabe, the Sm(III) + e- = Sm(II) is a quasi-reversible process. The diffusion coefficient of Sm(III) was measured by the chronoamperometry method, which verified the credibility of the FPMD simulation. Furthermore, this work explored the exchange current density of Sm(III)/Sm(II), whose value is between 0.826 × 10-3 and 2.383 × 10-3 A·cm−2, by the linear polarization.

The interface between long-period stacking-ordered (LPSO) structure and β' phase in Mg-Gd-Al alloys

The interface between LPSO and β' in the Mg-Gd-Al alloys is investigated by the high-angle annular dark-field scanning transmission electron microscope (HAADF-STEM) imaging and first-principles calculation. The formation energies of interface structures with different rare-earth-depleted layers (REDL) indicate that the interface structure with three-layer REDL is the most stable. The interfacial phase diagram with the chemical potential of Gd is obtained by the first-principles molecular dynamics analysis of interface energies, indicating that the β'/Mg interface layer in the three-REDL structure is the most stable, and the REDL is not only the Mg atomic layer, but also part of the LPSO phase. Moreover, it is also indirectly proved that the β'/Mg interface layer with three-layer REDL in Mg-Gd-Al alloys will form strong covalent and metallic bonds, and the bond energy is larger and more stable. Therefore, the characterization and calculations of the LPSO and β' interfaces provide a theoretical basis for future interface property analysis and interface design.

Influence of nuclear quantum effects on the electronic properties of amorphous carbon

We carry out quantum simulations to study the physical properties of diamond-like amorphous carbon by coupling first-principles molecular dynamics with a quantum thermostat, and we analyze multiple samples representative of different defective sites present in the disordered network. We show that quantum vibronic coupling is critical in determining the electronic properties of the system, in particular its electronic and mobility gaps, while it has a moderate influence on the structural properties. We find that despite localized electronic states near the Fermi level, the quantum nature of the nuclear motion leads to a renormalization of the electronic gap surprisingly similar to that found in crystalline diamond. We also discuss the notable influence of nuclear quantum effects on band-like and variable-hopping mechanisms contributing to electrical conduction. Our calculations indicate that methods often used to evaluate electron-phonon coupling in ordered solids are inaccurate to study the electronic and transport properties of amorphous semiconductors composed of light atoms.

Method to determine the electron–ion temperature relaxation rate from test particle distributions

A method to calculate the electron–ion energy exchange rate from the forces on and velocities of an ensemble of test particles is described. The essence of the method is that the energy exchange rate is related to the covariance between the distribution of velocities of test particles and the forces acting on them. The energy exchange rate is related to the electron–ion temperature relaxation rate in the limit of a low test particle speed. A proof of concept is conducted with first-principles molecular dynamics simulations.

Passivating Lead Halide Perovskites Using Pyridinium Salts with Superhalogen Atoms

Passivating lead halide perovskites using pyridinium salts has attracted enormous attention, but the excellent surface passivation of the halide perovskites has not been achieved by using only a pyridinium salt until now. Herein, passivating the (001) planes of the cubic CsPbI3, CH3NH3PbI3, and NH2CHNH2PbI3 perovskites using the pyridinium salts of C5NH6X (X = Cl, Br, I, PF6, ClO4, or BF4) is systematically studied by high-throughput first-principle calculations and ab initio molecular dynamics simulations. The results show that the excellent surface passivation of the three perovskites is achieved by the pyridinium salt of C5NH6BF4 (i.e., shallow level, negative formation energy, unchanged band-edge construction, and stable dynamics property are obtained for the three passivated perovskites), which strongly imply that their devices can show excellent performances, such as long-term stability, low ion migration, and high efficiency. However, the C5NH6ClO4 and C5NH6PF6 pyridinium salts are only profitable for passivating the (001) PbI2 plane of the three perovskites, and other C5NH6X pyridinium salts have adverse effects.

Sodium and Magnesium Ion Location at the Backbone and at the Nucleobase of RNA: Ab Initio Molecular Dynamics in Water Solution

The interactions between Na+ or Mg2+ ions with different parts of single-stranded RNA molecules, namely, the oxygen atoms from the phosphate groups or the guanine base, in water solution have been studied using first-principles molecular dynamics. Sodium ions were found to be much more mobile than Mg2+ ions and readily underwent transitions between a state directly bonded to RNA oxygen atoms and a completely solvated state. The inner solvation shell of Na+ ions fluctuated stochastically at a femtosecond timescale coordinating on average 5 oxygen atoms for bonded Na+ ions and 5.5 oxygen atoms for solvated Na+ ions. In contrast, the inner solvation shell of Mg2+ ions was stable in both RNA-bonded and completely solvated states. In both cases, Mg2+ ions coordinated 6 oxygen atoms from the inner solvation shell. Consistent with their stable solvation shells, Mg2+ ions were more effective than Na+ ions in stabilizing the RNA backbone conformation. The exclusion zones between the first and second solvation shells, solvation shell widths, and angles for binding to carbonyl oxygen of guanine for solvated Na+ or Mg2+ ions exhibited a number of quantitative differences when compared with RNA crystallographic data. The presented results support the distinct capacity of Mg2+ ions to support the RNA structure not only in the crystal phase but also in the dynamic water environment both on the side of the phosphate moiety and on the side of the nucleobase.

Finite Temperature Ultraviolet-Visible Dielectric Functions of Tantalum Pentoxide: A Combined Spectroscopic Ellipsometry and First-Principles Study

Tantalum pentoxide (Ta2O5) has demonstrated promising applications in gate dielectrics and microwave communication devices with its intrinsically high dielectric constant and low dielectric loss. Although there are numerous studies on the dielectric properties of Ta2O5, few studies have focused on the influence of external environmental changes (i.e., temperature and pressure) on the dielectric properties and the underlying physics is not fully understood. Herein, we synthesize Ta2O5 thin films using the magnetron sputtering method, measure the ultraviolet-visible dielectric function at temperatures varying from 300 to 873 K by spectroscopic ellipsometry (SE), and investigate the temperature influence on the dielectric function from first principles. SE experiments observe that temperature has a nontrivial influence on the ultraviolet-visible dielectric function, accompanying the consistently decreased amplitude and increased broadening width for the dominant absorption peak. First-principles calculations confirm that the dominant absorption peak originates from the aggregated energy states near the valence band maximum (VBM) and conduction band minimum (CBM), and the theoretically predicted dielectric functions demonstrate good agreement with the SE experiments. Moreover, by performing first-principles molecular dynamics simulations, the finite-temperature dielectric function is predicted and its change trend with increasing temperature agrees overall with the SE measurements. This work explores the physical origins of temperature influence on the ultraviolet-visible dielectric function of Ta2O5, aimed at promoting its applications in the field of micro-/nanoelectronics.

An effect of nitrogen incorporation on the structure and properties of amorphous SiC: First-principles molecular dynamics simulations

The structural, mechanical and electronic structure properties of amorphous silicon carbide and silicon carbonitride alloys were studied depending on chemical ordering, and nitrogen content, respectively, by using first-principles molecular dynamics simulations. The structure, chemical bonding, electronic structure, frequency-dependent dielectric functions, and mechanical properties (elastic moduli, Poisson ratio, bulk modulus to shear modulus ratio, ideal shear strength, Vickers hardness, Debye temperature and fracture toughness) were studied. It was established that an increase of nitrogen content in carbonitride alloys and a decrease of chemical ordering in carbide alloys cause the weakening of the Si–C network, strengthening of the C–C network, decrease in four-fold coordination and increase in three-fold coordination of Si and C atoms. All these factors lead to a deterioration of mechanical properties. The highly nitrided alloys are supposed to be wide-gap semiconductors with estimated mobility gaps in the range of 2.9–4.2 eV. The calculated data were used to elucidate available experimental results.

Green corrosion inhibitors for drilling operation: New derivatives of fatty acid-based inhibitors in drilling fluids for 1018 carbon steel in CO2-saturated KCl environments

Corrosion of the oilfield drilling equipment can considerably affect its drilling effectiveness, service life, and operation safety as well as the surrounding environment. In this study, inhibition effects of three eco-friendly fatty acid-based inhibitors, Polyethylene glycol-2 oleamide (PEG-2 oleamide), Glycerol myristate (GM) and Glycerol linoleate (GL), in emulsion-based drilling fluids against corrosion of carbon steel were investigated. The inhibitors were characterized by Fourier transform infrared (FT-IR) spectroscopy and CHNS–O analysis. Effects of the inhibitors on corrosion of the steel were evaluated by means of electrochemical measurements of open circuit potential (OCP) and potentiodynamic polarization as well as electrochemical impedance spectroscopy (EIS). Scanning electron microscopy (SEM), energy dispersive spectroscopy (EDS) and X-ray photoelectron spectrophotometer (XPS) were employed to study morphology and the chemical composition of surface layer adsorbed on the metal surface. The study demonstrates remarkable performance of the green inhibitors especially PEG-2 oleamide, which shows an inhibition efficiency of 99.7%. The high inhibition capability results from a formed protective layer that blocks corrosive ions to attack the steel surface. First-principles calculations and molecular dynamics simulation were performed, which reveal chemical bonding between the inhibitors and iron surface, and stronger intermolecular attraction in the adsorbed film of, e.g., PEG-2 oleamide, which renders the PEG-2 oleamide–induced film particularly durable.

Machine learning molecular dynamics simulations toward exploration of high-temperature properties of nuclear fuel materials: case study of thorium dioxide

Predicting materials properties of nuclear fuel compounds is a challenging task in materials science. Their thermodynamical behaviors around and above the operational temperature are essential for the design of nuclear reactors. However, they are not easy to measure, because the target temperature range is too high to perform various standard experiments safely and accurately. Moreover, theoretical methods such as first-principles calculations also suffer from the computational limitations in calculating thermodynamical properties due to their high calculation-costs and complicated electronic structures stemming from f-orbital occupations of valence electrons in actinide elements. Here, we demonstrate, for the first time, machine-learning molecular-dynamics to theoretically explore high-temperature thermodynamical properties of a nuclear fuel material, thorium dioxide. The target compound satisfies first-principles calculation accuracy because f-electron occupation coincidentally diminishes and the scheme meets sampling sufficiency because it works at the computational cost of classical molecular-dynamics levels. We prepare a set of training data using first-principles molecular dynamics with small number of atoms, which cannot directly evaluate thermodynamical properties but captures essential atomistic dynamics at the high temperature range. Then, we construct a machine-learning molecular-dynamics potential and carry out large-scale molecular-dynamics calculations. Consequently, we successfully access two kinds of thermodynamic phase transitions, namely the melting and the anomalous lambda transition induced by large diffusions of oxygen atoms. Furthermore, we quantitatively reproduce various experimental data in the best agreement manner by selecting a density functional scheme known as SCAN. Our results suggest that the present scale-up simulation-scheme using machine-learning techniques opens up a new pathway on theoretical studies of not only nuclear fuel compounds, but also a variety of similar materials that contain both heavy and light elements, like thorium dioxide.

Atomistic Insights into Structure and Dynamics of Neodymium(III) Complexation with a Bis-lactam Phenanthroline Ligand in the Organic Phase.

Rare-earth elements (REEs) such as neodymium are critical materials needed in many important technologies, and rigid neutral bis-lactam-1,10-phenanthroline (BLPhen) ligands show one of the highest extraction performance for complexing Nd(III) in REE uptake and separation processes. However, the local structure of the complexes formed between BLPhen and Nd(III) in a typical organic solvent such as dichloroethane (DCE) is unclear. Here, we perform first-principles molecular dynamics (FPMD) simulations to unveil the structure of complexes formed by BLPhen with Nd(NO3)3 in the DCE solvent. BLPhen can bind to Nd(III) in either 1:1 or 2:1 fashion. In the 1:1 complex, three nitrates bind to Nd(III) via the bidentate mode in the first solvation shell, leading to the formation of a neutral complex, [Nd(BLPhen)(NO3)3]0, in the organic phase. In contrast, there are two nitrates in the first solvation shell in the 2:1 complex, creating a charged complex, [Nd(BLPhen)2(NO3)2]+. The third nitrate was found to be far away from the metal center, migrating to the outer solvation shell. Our simulations show that the binding pocket formed by the two rigid BLPhen ligands allows ample space for two nitrates to bind to the Nd(III) center from opposite sides. Our findings of two nitrates in the first solvation shell of the 2:1 complex and the corresponding bond distances agree well with the available crystal structure. This study represents the first accurate FPMD modeling of the BLPhen–Nd(III) complexes in an explicit organic solvent and opens the door to more atomistic understanding of REE separations from first principles.

Tracing the Anharmonicity and Superionic Phase Transition of Hydrous FeO2H

The weak x-ray scattering of hydrogen (H) has brought major challenges to the characterization of superionic transitions in high-pressure ice, hydrides, and hydroxides. Combining first-principles molecular dynamics and simulated nuclear magnetic resonance (NMR) spectroscopy, we investigated the behavior of the hydroxyl bonding and structural transitions in the hydrous FeO2H between 300 and 2750 K and up to 130 GPa. Evidence show that an intermediate plastic state with regional H diffusion and anharmonic O-H vibration exists in between the ordinary solid and the superionic phase. The intermediate state features asymmetric hydrogen bonds and anharmonic vibrations, which are readily distinguished from the high-temperature superionic phase. Our work shows NMR is a more sensitive probe to detect H diffusion in superionic solids even in the extreme conditions of Earth’s deep interiors.

Atomic structure of amorphous SiN: Combining Car–Parrinello and Born–Oppenheimer first-principles molecular dynamics

First-principles molecular dynamics is employed to describe the atomic structure of amorphous SiN, a non-stoichiometric compound belonging to the SixNy family. To produce the amorphous state via the cooling of the liquid, both the Car–Parrinello and the Born–Oppenheimer approaches are exploited to obtain a system featuring sizeable atomic mobility. At high temperatures, due to the peculiar electronic structure of SiN, exhibiting gap closing effects, the Car–Parrinello methodology could not be followed since non-adiabatic effects involving the ionic and electronic degrees of freedom do occur. This shortcoming was surmounted by resorting to the Born–Oppenheimer approach allowing to achieve significant ionic diffusion at T= 2500 K. From this highly diffusive sample, an amorphous state at room temperature was obtained with a quenching rate of 10 K/ps. Four different models were created, differing by their sizes and the thermal cycles. We found that the subnetwork of atoms N has the same environment than in the stoichiometric material Si3N4 since N is mostly threefold coordinated with Si. Si atoms can also be found coordinated to four N atoms as in Si3N4, but a substantial fraction of them forms homopolar bonds with one, two, three and even four Si. Our results are not too dissimilar from former models available in the literature but they feature a higher statistical accuracy and refer more precisely to room temperature as the reference thermodynamical condition for the analysis of the structure in the amorphous state.

Experimental and theoretical studies on atomic structures of the interface states at SiO2/4H-SiC(0001) interface

We investigated the atomic structures of the interface states (gap states) at the SiO2/4H-SiC(0001) interface using hard x-ray photoelectron spectroscopy (HAXPES), operando hard x-ray photoelectron spectroscopy, extended x-ray absorption fine structure, and first principles molecular dynamics (FPMD) calculations. For the interface states, two types were observed: continuous interface states in the whole gap and interface states with discrete energy levels near the conduction band minimum (CBM). From HAXPES, we found that carbon clusters and carbon vacancies were formed at the SiO2/4H-SiC(0001) interface. FPMD calculations on the SiO2/4H-SiC(0001) interface showed that the interface states in the whole gap were attributed to the various atomic geometries of the CßSi3 species and the carbon clusters with various sizes and surrounding atoms. For the interface states with a discrete energy level near the CBM, we could not find their atomic structure using our current calculations. We calculated the carbon vacancies prepared on the side of an SiC substrate at the SiO2/4H-SiC(0001) interface, indicating the formation of a discrete energy level in the midgap. It is likely that carbon vacancies formed at the step of the interface may modulate the midgap energy level to energy below the CBM. Therefore, we propose that the interface states with discrete energy levels near the CBM could be attributed to the carbon vacancies formed on the steps at the SiO2/4H-SiC(0001) interface.

First-Principles Dynamics of Fluorine Adsorption on Clean and Monohydrogenated Si{001}.

The interaction of highly reactive species with solid surfaces can result in modes of adsorption quite distinct from the classic molecular and dissociative events that are usually thought to dominate. For instance, compelling experimental evidence suggests that adsorption of F2 at the Si{001} surface is often initiated by abstraction (and binding at the surface) of just one fluorine atom from the molecule; the second fluorine atom subsequently experiences either a separate atomic adsorption event or ejection from the surface altogether. Molecular dynamics simulations using empirical potentials support this concept but massively overestimate the prevalence of atomic ejection. In this work, we report first-principles molecular dynamics calculations that correctly show atomic ejection to be rare while providing insight into the details of abstractive adsorption. In addition, we also examine the case of F2 adsorption onto a monohydrogenated Si{001} surface, finding evidence for a different type of abstractive adsorption, in which a hydrogen atom may be removed from the surface to form a short-lived HFF intermediate. The latter rapidly decomposes to produce either HF or (via reaction with another surface hydrogen atom) H2.

Effect of liquidlike cations on electronic and defect properties of solid solutions of Cu2Te and Ag2Te

${\mathrm{Cu}}_{2}\mathrm{Te}$ was recently shown to be an excellent thermoelectric material with a figure of merit approaching 2. Ag alloying was found to be effective for tuning the electrical conductivity of ${\mathrm{Cu}}_{2}\mathrm{Te}$ toward high thermoelectric performance. The liquidlike behavior of cations is well-known to yield ultralow thermal conductivity in the cuprous chalcogenide materials. Here, we study the effect of the liquidlike behavior on the electronic and defect properties of the solid solutions ${\mathrm{Cu}}_{2\ensuremath{-}x}{\mathrm{Ag}}_{x}\mathrm{Te}$. Using first-principles molecular dynamics (MD) simulation, we found that the band-gap variation with increasing $x$ as obtained from MD ensemble averages is much slower than that from direct calculation using the high-symmetry ordered structures. The solid solutions within the whole range of $x$ exhibit significant band gaps. The liquidlike behavior also results in flattened top valence bands, which reduce the Seebeck coefficient and electrical conductivity. Regarding the defect properties, we found that the liquidlike behavior can fail the standard defect models employing the high-symmetry ordered structure. Again, MD simulation would be necessary for sampling the configuration space in defect calculations. However, converging the defect formation energy for the diffusive system would require much longer simulation time than converging the band gap. Our present results suggest that Ag alloying could slightly increase the formation energy of Cu vacancy.