First-principles Molecular Dynamics Simulations Research Articles

Solvation Free Energies from Machine Learning Molecular Dynamics.

The present work proposes an extension to the approach of [Xi, C; et al. J. Chem. Theory Comput. 2022, 18, 6878] to calculate ion solvation free energies from first-principles (FP) molecular dynamics (MD) simulations of a hybrid solvation model. The approach is first re-expressed within the quasi-chemical theory of solvation. Then, to allow for longer simulation times than the original first-principles molecular dynamics approach and thus improve the convergence of statistical averages at a fraction of the original computational cost, a machine-learned (ML) energy function is trained on FP energies and forces and used in the MD simulations. The ML workflow and MD simulation times (≈200 ps) are adjusted to converge the predicted solvation energies within a chemical accuracy of 0.04 eV. The extension is successfully benchmarked on the same set of alkaline and alkaline-earth ions.

ZIF-8 Vibrational Spectra: Peak Assignments and Defect Signals.

Zeolitic imidazolate framework (ZIF-8) is a promising material for gas separation applications. It also serves as a prototype for numerous ZIFs, including amorphous ones, with a broader range of possible applications, including sensors, catalysis, and lithography. It consists of zinc coordinated with 2-methylimidazolate (2mIm) and has been synthesized with methods ranging from liquid-phase to solvent-free synthesis, which aim to control its crystal size and shape, film thickness and microstructure, and incorporation into nanocomposites. Depending on the synthesis method and postsynthesis treatments, ZIF-8 materials may deviate from the nominal defect-free ZIF-8 crystal structure due to defects like missing 2mIm, missing zinc, and physically adsorbed 2mIm trapped in the ZIF-8 pores, which may alter its performance and stability. Infrared (IR) spectroscopy has been used to assess the presence of defects in ZIF-8 and related materials. However, conflicting interpretations by various authors persist in the literature. Here, we systematically investigate ZIF-8 vibrational spectra by combining experimental IR spectroscopy and first-principles molecular dynamics simulations, focusing on assigning peaks and elucidating the spectroscopic signals of putative defects present in the ZIF-8 material. We attempt to resolve conflicting assignments from the literature and to provide a comprehensive understanding of the vibrational spectra of ZIF-8 and its defect-induced variations, aiming toward more precise quality control and design of ZIF-8-based materials for emerging applications.

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

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%.

Stress-Relief Engineering in a N-Doped C-Modified Hierarchical Nanoporous Si Anode with a Microcurved Pore Wall Structure for Enhanced Lithium Storage.

The commercialization of alloy-type anodes has been hindered by rapid capacity degradation due to volume fluctuations. To address this issue, stress-relief engineering is proposed for Si anodes that combines hierarchical nanoporous structures and modified layers, inspired by the phenomenon in which structures with continuous changes in curvature can reduce stress concentration. The N-doped C-modified hierarchical nanoporous Si anode with a microcurved pore wall (N-C@m-HNP Si) is prepared from inexpensive Mg-55Si alloys using a simple chemical etching and heat treatment process. When used as the anode for lithium-ion batteries, the N-C@m-HNP Si anode exhibits initial charge/discharge specific capacities of 1092.93 and 2636.32 mAh g-1 at 0.1 C (1 C = 3579 mA g-1), respectively, and a stable reversible specific capacity of 1071.84 mAh g-1 after 200 cycles. The synergy of the hierarchical porous structure with a microcurved pore wall and the N-doped C-modified layer effectively improves the electrochemical performance of N-C@m-HNP Si, and the effectiveness of stress-relief engineering is quantitatively analyzed through the theory of elastic bending of thin plates. Moreover, the formation process of Li15Si4 crystals, which causes substantial mechanical stress, is investigated using first-principles molecular dynamic simulations to reveal their tendency to occur at different scales. The results demonstrate that the hierarchical nanoporous structure helps to inhibit the transformation of amorphous LixSi into metastable Li15Si4 crystals during lithiation.

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.

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.

Theoretical study of the structural and thermodynamic properties of U-He compounds under high pressure.

Uranium is considered as a very important nuclear energy material because of the huge amount of energy it releases. As the main product of the spontaneous decay of uranium, it is difficult for helium to react with uranium because of its chemical inertness. Therefore, bubbles will be formed inside uranium, which could greatly reduce the performance of uranium or cause safety problems. Additionally, nuclear materials are usually operated in an environment of high-temperature and high-pressure, so it is necessary to figure out the exact state of helium inside uranium under extreme conditions. Here, we explored the structural stability of the U-He system under high pressure and high temperature by using density functional theory calculations. Two metastable phases are found between 50 and 400 GPa: U4He with space group Fmmm and U6He with space group P1̄. Both are metallic and adopt layered structures. Electron localization function calculation combined with charge density difference analysis indicates that there are covalent bonds between U and U atoms in both Fmmm-U4He and P1̄-U6He. Regarding the elastic modulus of α-U, the addition of helium has certain influence on the mechanical properties of uranium. Besides, first-principles molecular dynamics simulations were carried out to study the dynamical behavior of Fmmm-U4He and P1̄-U6He at high-temperature. It was found that Fmmm-U4He and P1̄-U6He undergo one-dimensional superionic phase transitions at 150 GPa. Our study revealed the exotic structure of U-He compounds beyond the formation of bubbles under high-pressure and high-temperature, which might be relevant to the performance and safety issues of nuclear materials under extreme conditions.

First-principles molecular dynamics study on the behaviors of Cs in a mixed system of liquid metal and LiCl-KCl molten salt.

The structure and dynamic properties of Cs in the mixed system of LiCl-KCl molten salt and a liquid metal (Bi and Pb) electrode are investigated through first-principles molecular dynamics simulation. It is found that the dynamic properties of different ions in molten salt could be significantly affected when the liquid metal electrode is coupled and this influence varies with the type of liquid metal applied. The microstructures of the mixed systems of molten salt and liquid metal electrode: MS-Cs-Bi, MS-CsCl-Bi, MS-Cs-Pb, and MS-CsCl-Pb, are also investigated by the bond angle distribution function, Voronoi tessellation analysis, five-fold symmetry parameter, and bond-orientational order parameter. The comparison study of the microstructures of the mixed systems when different liquid metal electrodes are applied provides information on the liquid metal electrode selection when conducting electrolysis. The present study represents the first demonstration of the study of a mixed system of salt and liquid electrode for practical applications and would be greatly beneficial to the development of pyroprocessing of spent nuclear fuel.

Fast access of the lattice thermal conductivity and phonon quasiparticle spectra of Mo2TiC2T2 (T = -O and -F) and Janus Mo2TiC2OF MXenes from machine learning potentials.

The presence of strong anharmonic effects in surface functionalized MXenes greatly challenges the use of harmonic lattice dynamics calculations to predict their phonon spectra and lattice thermal conductivity at finite temperatures. Herein, we demonstrate the workflow for training and validating machine learning potentials in terms of moment tensor potential (MTP) for MXenes including Mo2TiC2, Mo2TiC2O2, Mo2TiC2F2 and Janus-Mo2TiC2OF monolayers. Then, the MTPs of MXenes are successfully combined with the harmonic lattice dynamics calculations to obtain the temperature renormalized phonon spectra, three-phonon scattering rates, phonon relaxation times and lattice thermal conductivity at finite temperatures. Furthermore, combining MTPs with classic molecular dynamics simulations at finite temperatures directly enables the calculation of phonon quasi-particle spectral energy density with a full inclusion of all anharmonic effects in MXenes. Our current results indicate that anharmonic effects are found to be relatively weak in Mo2TiC2 and Mo2TiC2O2 monolayers, whereas the phonon quasi-particle spectral energy densities largely resemble those of harmonic or renormalized lattice dynamics calculations. Significant broadening of spectral energy density at finite temperature is predicted for Mo2TiC2F2 and Janus-Mo2TiC2OF monolayers, implying strong anharmonic effects in those MXenes. Our work paves a new way for fast and reliable calculation of the phonon scattering process and lattice thermal conductivity of MXenes within MTPs trained from first-principles molecular dynamics simulations in the future.

Improved ion adsorption capacities and diffusion dynamics in surface anchored MoS2⊥Mo4/3B2 and MoS2⊥Mo4/3B2O2 heterostructures as anodes for alkaline metal-ion batteries.

First-principles calculations were performed to analyze the atomic structures and electrochemical energy storage properties of novel MoS2⊥boridene heterostructures by anchoring MoS2 nanoflakes on Mo4/3B2 and Mo4/3B2O2 monolayers. Both thermodynamic and thermal stabilities of each heterostructure were thoroughly evaluated from the obtained binding energies and through first-principles molecular dynamics simulations at room temperature, confirming the high formability of the heterostructures. The electrochemical properties of MoS2⊥Mo4/3B2 and MoS2⊥Mo4/3B2O2 heterostructures were investigated for their potential use as anodes for alkaline metal ion batteries (Li+, Na+ and K+). It was revealed that Li+ and Na+ can form multiple stable full adsorption layers on both heterostructures, while K+ forms only a single full adsorption layer. The presence of a negative electron cloud (NEC) contributes to the stabilization of a multi-layer adsorption mechanism. For all investigated alkaline metal ions, the predicted ion diffusion dynamics are relatively sluggish for the adsorbates in the first full adsorption layer on MoS2⊥boridene heterostructures due the relatively large migration energies (>0.50 eV), compared to those of second or third full adsorption layers (<0.30 eV). MoS2⊥Mo4/3B2O2 exhibited higher onset and mean open circuit voltages as anodes for alkaline metal-ion batteries than MoS2⊥Mo4/3B2 hybrids because of enhanced interactions between the adsorbate and the Mo4/3B2O2 monolayer with the presence of O-terminations. Tailoring the size and horizontal spacing between two neighboring MoS2 nano-flakes in heterostructures led to high theoretical capacities for LIBs (531 mA h g-1), SIBs (300 mA h g-1) and PIBs (131 mA h g-1) in the current study.

A promising high temperature 2D thermoelectric material: novel single-layer ZrHfS4.

Based on the first-principles calculation and Boltzmann transport theory, we report the discovery of a promising candidate for high-performance two-dimensional (2D) thermoelectric material: the single-layer (1L) ZrHfS4. Through the first-principles molecular dynamics simulation and phonon calculation, 1L-ZrHfS4 is predicted to be thermodynamically stable even at high temperatures. In addition, the lattice thermal conductivity of 1L-ZrHfS4 is calculated to be 10.2 W m-1 K-1, which is smaller than that of 2D transition-metal dichalcogenides, such as MoS2 and WS2. Notably, considering not only all the transport coefficients but also the relaxation time for both acoustic and optical phonon scattering, the maximum figure of merit (ZT) of 1L-ZrHfS4 at 1200 K can achieve 1.92 at moderate n-type doping. These findings suggest 1L-ZrHfS4 as a potential material for efficient thermoelectric energy conversion, particularly in applications requiring high temperature operation.

Developing semi-empirical water model for efficiently simulating temperature-dependent chemisorption of CO2 in amine solvents.

Classical molecular dynamics (MD) simulations without bond forming/breaking cannot be used to model chemical reactions (CRs) among small molecules. Although the first-principle MD simulation can adequately describe CRs with explicit water molecules, such simulation is normally too costly for most researchers to afford. Generally, water molecules in a solvent can exert hydrophobic forces on reacting molecules, which yields a so-called caging effect that cannot be ignored when constructing a free energy landscape for reacting molecules. Many recently developed semi-empirical methods (such as DFTB, PM6 and xTB) are highly efficient for modeling CRs, however none of them can be directly used to model bulk water properly. Here, we developed a modified xTB approach that enables the simulation of CRs in explicit water. Using the chemisorption of CO2 by amines in water as an example application, we demonstrate that our approach yielded results comparable with the first-principle ones, while only using a limited computing resource. Potentially, our proposed semi-empirical water model can be utilized for the computational study of any CR in water.

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.

Mixture of hydrogen and methane under planetary interior conditions.

We employ first-principles molecular dynamics simulations to provide equation-of-state data, pair distribution functions (PDFs), diffusion coefficients, and band gaps of a mixture of hydrogen and methane under planetary interior conditions as relevant for Uranus, Neptune, and similar icy exoplanets. We test the linear mixing approximation, which is fulfilled within a few percent for the chosen P-T conditions. Evaluation of the PDFs reveals that methane molecules dissociate into carbon clusters and free hydrogen atoms at temperatures greater than 3000 K. At high temperatures, the clusters are found to be short-lived. Furthermore, we calculate the electrical conductivity from which we derive the non-metal-to-metal transition region of the mixture. We also calculate the electrical conductivity along the P-T profile of Uranus [N. Nettelmann et al., Planet. Space Sci., 2013, 77, 143-151] and observe the transition of the mixture from a molecular to an atomic fluid as a function of the radius of the planet. The density and temperature ranges chosen in our study can be achieved using dynamic shock compression experiments and seek to aid such future experiments. Our work also provides a relevant data set for a better understanding of the interior, evolution, luminosity, and magnetic field of the ice giants in our solar system and beyond.