Ab Initio Molecular Dynamics Calculations Research Articles

The effects of intercalated environmental gas molecules on carrier dynamics in WSe2/WS2 heterostructures.

Effective tuning of carrier dynamics in two-dimensional (2D) materials is significant for multi-scene device applications. Using first-principles and ab initio nonadiabatic molecular dynamics calculations, the kinetics of O2, H2O, and N2 intercalation into 2D WSe2/WS2 van der Waals heterostructures and its effect on carrier dynamics have been comprehensively explored. It is found that the O2 molecule prefers to dissociate into atomic O atoms spontaneously after intercalation of WSe2/WS2 heterostructures, whereas H2O and N2 molecules remain intact. O2 intercalation significantly speeds up the electron separation process, while H2O intercalation largely speeds up the hole separation process. The lifetime of excited carriers can be prolonged by O2 or H2O or N2 intercalations. These intriguing phenomena can be attributed to the effect of interlayer coupling, and the underlying physical mechanism for tuning the carrier dynamics is fully discussed. Our results provide useful guidance for the experimental design of 2D heterostructures for optoelectronic applications in photocatalysts and solar energy cells.

A First-principles investigation of the structural and electronic properties of Two-dimensional Hf2CSe2

In this work, we reported a 2D transition metal–carbon chalcogenide Hf2CSe2 monolayer. It consists of two popular families, transition metal chalcogenide (TMDCs) and transition metal carbide (MXenes). We have performed the first-principles calculations to investigate the structural or geometrical properties, phonon dispersion relation, electronic properties, and mechanical characteristics of the Hf2CSe2 nanosheet. The dynamical stability of Hf2CSe2 of the monolayer is demonstrated by obtained phonon dispersion relations. To examine thermodynamic stability, Ab-initio Molecular Dynamics (AIMD) calculation was also done, which confirms its thermodynamical stability. We determined that the Hf2CSe2monolayer are relatively robust nanosheet. The findings provide a valuable perspective on the fundamental physical properties of novel 2D Hf2CSe2monolayers.

Magneto-volume effect in Fe n Ti13–n clusters during thermal expansion

Ab initio molecular dynamics calculations have been carried out to search for the ground state structure of Fe n Ti13–n clusters and measure the thermal expansion of Fe n Ti13–n . The volume of Fe n Ti13–n clusters during thermal expansion is jointly determined by anharmonic interaction and magneto-volume effect. It has been found that Fe6Ti7, Fe9Ti4, Fe11Ti2, and Fe13 clusters can exhibit the remarkable magneto-volume effect with abnormal volume behaviors and magnetic moment behaviors during thermal expansion. A prerequisite for the magneto-volume effect of Fe n Ti13–n clusters during thermal expansion has been revealed and the magnitude of the magneto-volume is also approximately determined. Furthermore, the magneto-volume behaviors of Fe n Ti13–n clusters are qualitatively characterized by the energy contour map. Our results shed light on the mechanism of the magneto-volume effect in Fe n Ti13–n clusters during thermal expansion, which can guide the design of nanomaterials with zero expansion or even controllable expansion properties.

Activation of metal-free porous basal plane of biphenylene through defects engineering for hydrogen evolution reaction

The biggest challenge in the commercial application of electrochemical reduction of water through the hydrogen evolution reaction (HER) is hampered due to the scarcity of inexpensive and efficient catalysts. Herein, we propose a metal-free biphenylene nanosheet, a recently proposed two-dimensional (2D) carbon allotrope, as an excellent HER electrocatalyst. The dynamical and thermal stability of biphenylene nanosheet is validated through phonon dispersion and abinitio molecular dynamics (AIMD) calculations, respectively. At a low H coverage (1/54), the biphenylene nanosheet shows excellent catalytic activity with the Gibbs free energy (ΔGH∗) of 0.082 eV. The Bdoping and C-vacancy in biphenylene further improve ΔGH∗ to −0.016 eV and 0.005 eV, respectively. The interactions between the H atom and the nanosheet are explained through the relative position of the p-band center. Our study opens new possibilities to use non-metallic porous materials as highly efficient electrocatalysts for HER.

Augmented thermoelectric performance of LiCaX (X = As, Sb) Half Heusler compounds via carrier concentration optimization

The present study is focussed on the detailed physical insight into the structural, thermal, and dynamical properties of 8-valence electron Half Heusler (HH) compounds LiCaX (X = As, Sb) using Density functional theory. The thermal and dynamic stabilities of the compounds are assessed via ab-initio molecular dynamic simulations and phonon dispersion calculations, respectively. The Tran-Blaha modified Becke Johnson potential is used to accurately predict the band gap of investigated compounds. It is found that they are indirect band gap semiconductors with band gaps of 2.52 eV (LiCaAs) and 2.09 eV (LiCaSb). The transport parameters are obtained for p-type and n-type doping at temperatures ranging from 300 K to 800 K by solving the Boltzmann Transport equation. The deformation potential theory is employed to calculate the temperature dependent relaxation time for both compounds. The results of the various thermoelectric parameters obtained using actual values of time-dependent relaxation time are compared with that calculated under constant relaxation time approximation. The maximum power factor is 10.95 × 1011 (4.99 × 1011) Wm−1K−2s−1 for p-type (n-type) LiCaAs and 12.53 × 1011 (5.30 × 1011) Wm−1K−2s−1 for p-type (n-type) LiCaSb at optimized carrier concentration. The obtained low lattice thermal conductivities for LiCaSb (0.66 Wm−1K−1) and LiCaAs (0.88 Wm−1K−1) are explicated it in terms of different phonon modes. The Figure of Merit at 800 K for p-type (n-type) LiCaAs is as high as 0.90 (0.73) and 0.93 (0.84) for LiCaSb at optimum carrier concentration ∼1020 cm−3 (∼1019 cm−3), which has been experimentally realized in other 8-valence electron Li-based HH compounds. The good thermoelectric performance of p-type LiCaX in comparison to n-type suggests that p-type LiCaX alloys are viable candidates for high temperature energy harvesting applications.

Molecular Dynamics and Structural Studies of Zinc Chloroquine Complexes.

Chloroquine (CQ) is a first-choice drug against malaria and autoimmune diseases. It has been co-administered with zinc against SARS-CoV-2 and soon dismissed because of safety issues. The structural features of Zn-CQ complexes and the effect of CQ on zinc distribution in cells are poorly known. In this study, state-of-the-art computations combined with experiments were leveraged to solve the structural determinants of zinc-CQ interactions in solution and the solid state. NMR, ESI-MS, and X-ray absorption and diffraction methods were combined with ab initio molecular dynamics calculations to address the kinetic lability of this complex. Within the physiological pH range, CQ binds Zn2+ through the quinoline ring nitrogen, forming [Zn(CQH)Clx(H2O)3-x](3+)-x (x = 0, 1, 2, and 3) tetrahedral complexes. The Zn(CQH)Cl3 species is stable at neutral pH and at high chloride concentrations typical of the extracellular medium, but metal coordination is lost at a moderately low pH as in the lysosomal lumen. The pentacoordinate complex [Zn(CQH)(H2O)4]3+ may exist in the absence of chloride. This in vitro/in silico approach can be extended to other metal-targeting drugs and bioinorganic systems.

Corrugation-Induced Active Sites on Pristine Graphene for H2 Activation

Pristine graphene is widely considered to be chemically inert, but recent experimental studies have suggested that it can provide frustrated Lewis pairs (FLPs) for activating H2 under mild conditions. Using density functional theory (DFT) and ab initio molecular dynamics (AIMD) calculations, we explore in this work the possibility that corrugation in pristine graphene is responsible for the formation of FLPs and thus its observed catalytic activity. Our DFT results demonstrate that the ease of H2 activation is proportional to the degree of corrugation of graphene. For corrugated graphene, the two catalytic para-carbon sites show clear signs of transient Lewis acid/base properties along the reaction coordinate, a pre-requisite for FLPs. Furthermore, the two dissociating H atoms carry opposite charges, suggesting heterolytic activation of H2. This behavior is confirmed by AIMD simulations at room temperature, which show that fluctuations of the corrugated graphene lead to C sites with diverse distances and varying charges. These observations offer a plausible rationalization of the experimental observations and possible design principles for FLP catalysts using homogeneous two-dimensional materials.

Formation Mechanism of Odd- and Even-Numbered Hydrogen Cluster Cations Using the Direct Ab Initio Molecular Dynamics Approach.

The photoreaction of hydrogen clusters caused by cosmic-ray irradiations plays a crucial role in interstellar molecular clouds because the reaction of molecules takes place in these surrounding clusters. Previous gas-phase experiments introduced the reaction products after the ionization of the neutral hydrogen cluster. In the experiments, the odd-numbered hydrogen cluster cation, H+(H2)m, was the main product, while the even-numbered cluster cation, (H2)n+, was the minor product. However, the formation yield of (H2)n+ was significantly low. Despite many theoretical calculations and experiments, the formation mechanism of odd- and even-numbered cluster ions from ionized hydrogen clusters is still unclear. In this study, the direct ab initio molecular dynamics (AIMD) method was applied to the reaction of the hydrogen cluster cation (H2)n+ to understand the abovementioned formation mechanism. The trajectories of (H2)n+ following the vertical ionization of the neutral cluster were calculated. Direct AIMD calculations indicated that odd-numbered cluster cations, H3+(H2)n-2 + H (dissociation), were formed directly as the main product after the ionization of (H2)n. An even-numbered cluster, (H2)n+, was temporally formed when an H-shaped complex composed of three H2 molecules existed within a neutral cluster. However, it was rapidly dissociated to an odd-numbered cluster. Static ab initio calculations suggested that the odd-numbered cluster complex, H3+(H2)n-2-H, could be transferred to even-numbered ions via a transition state with a low energy barrier. The even-numbered cluster cation was formed stepwise from the odd-numbered cluster cation. The formation mechanism of odd- and even-numbered cluster cations is discussed based on these results.

Rational design of h‐AlC monolayer as anode material for Mg‐ion battery: A DFT study

AbstractIn the present work, we have analyzed the suitability of two‐dimensional (2D) h‐AlC as a high‐capacity anode material for Mg‐ion batteries (MIBs) by employing first principles‐based density functional theory (DFT). The structural parameters, electronic band structure, partial density of states (PDOS), theoretical storage capacity (TSC), diffusion energy barrier (DEB), open‐circuit voltage (OCV), and room temperature stability (from ab initio molecular dynamic (AIMD) simulations) are calculated and discussed. The band structure of h‐AlC monolayer remains metallic for all considered adsorption concentrations of Mg‐atoms which indicates its good electrical conductivity. A significant quantity of charge is transferred from Mg atom to h‐AlC during adsorption of the Mg atom due to its lower electronegativity compared with the Al and C atoms. The calculated TSC is 1221.75 mAh g−1 which is higher than many anode materials. For MIBs, calculated DEB and OCV are 1.21 and 0.73 V, respectively. However, transition from planar structure to buckled structure takes place during the adsorption of more than 9 Mg‐atoms over h‐AlC. The lattice change is negligible during adsorption of Mg atoms. The AIMD calculations revels that the 9 and 18 Mg atoms adsorbed h‐AlC is stable at T = 300 K. The aforementioned findings suggest that h‐AlC can be anode material for MIBs.

Reducing high-temperature dielectric loss of h-BN ceramics by orienting grains

The exponentially increasing dielectric loss with rising temperature is the biggest obstacle hindering the application of hexagonal boron nitride (h-BN) ceramics as radome materials. Herein, a novel strategy is proposed to reduce high-temperature dielectric loss of h-BN ceramics by orienting grains. The relationship between electrical conductivity and temperature of h-BN ceramics shows that conductance loss of intrinsic defect ions thermal-excited above 667 °C is main cause of dielectric loss. And ab initio molecular dynamics calculations indicate that thermal-excited defect ions show much higher self-diffusion coefficient along a/b-axis of layered h-BN than that along c-axis. Therefore, by orienting h-BN grains, high-temperature dielectric loss of bulk ceramics will be minimized due to the suppressed defect ions transport perpendicular to orientation direction. As validation, resulting h-BN ceramics with oriented grains shows low dielectric loss tangent of 6.1 × 10−3 at 1000 °C, which is 45.5% lower than that of typical h-BN ceramics with random grains.

Magnetic-translational sum rule and approximate models of the molecular Berry curvature.

The Berry connection and curvature are key components of electronic structure calculations for atoms and molecules in magnetic fields. They ensure the correct translational behavior of the effective nuclear Hamiltonian and the correct center-of-mass motion during molecular dynamics in these environments. In this work, we demonstrate how these properties of the Berry connection and curvature arise from the translational symmetry of the electronic wave function and how they are fully captured by a finite basis set of London orbitals but not by standard Gaussian basis sets. This is illustrated by a series of Hartree-Fock calculations on small molecules in different basis sets. Based on the resulting physical interpretation of the Berry curvature as the shielding of the nuclei by the electrons, we introduce and test a series of approximations using the Mulliken fragmentation scheme of the electron density. These approximations will be particularly useful in ab initio molecular dynamics calculations in a magnetic field since they reduce the computational cost, while recovering the correct physics and up to 95% of the exact Berry curvature.

Degenerate Lattice-Instability-Driven Amorphization under Compression in Metal Halide Perovskite CsPbI3.

Halide perovskites have been intensively investigated for photovoltaic applications because of their good optoelectronic properties and low cost. Various high-pressure experiments have shown that these materials generally undergo reversible phase transitions between different crystalline phases as well as between crystalline and amorphous phases under external pressure. Herein, using first-principles density functional theory (DFT) and ab initio molecular dynamics (AIMD) calculations, we investigate the origin of the pressure-induced amorphization in CsPbI3. We find that the amorphous-like structures obtained from AIMD calculations become more stable than the orthorhombic Pbnm phase above 6.66 GPa, in good agreement with the experimental value (4.44 GPa). We further find that an imaginary flat band appears in the phonon dispersion of the orthorhombic CsPbI3 phase across the Brillouin zone at 10 GPa, leading to degenerate lattice instabilities. These energetically degenerate phonon modes are related to PbI6 octahedral tilting modes and provide random local distortions, leading to amorphization.

Structure and Diffusive Properties of Water in Polymer Hydrogels.

To investigate the diffusive properties of water in hydrogels, ab initio molecular orbital and molecular dynamics calculations of poly-N,N-dimethylacrylamide-water systems were performed. The results show that the mean diffusion coefficient of water drastically decreases in the middle dehydration stage. In this stage, the mobilities of water are restrained because part of the water forms hydrogen bonds to bind polymer chains due to a glass transition. In addition to the three well-known types of water (i.e., bound, intermediate, and free water) around hydrophilic polymers in hydrogels, our results suggest that the intermediate water can be further classified into two types: first and second intermediate water. The bound and first intermediate water acts as a cross-linker between polymer chains, even if the polymer does not form intra- or intermolecular bonds itself. The diffusive properties of water might have important implications for the interpretation of properties of polymer hydrogels.

Viscosity of liquid gallium: Neural network potential molecular dynamics and experimental study

Gallium traditionally comprises a difficult object for theoretical description due to its complex short-range order structure. In this paper, deep learning potential for liquid gallium was developed, which allowed to significantly increase spatiotemporal scale of molecular dynamics (MD) simulation with preserving ab initio accuracy. Such increasing of performance of MD simulations allowed to calculate temperature dependence of viscosity value for liquid Ga, for which there is a considerable ambiguity in the available literature data, especially in low temperature range. Since direct ab initio viscosity calculations are not possible, as they do not allow enough statistical data to be collected, we combine several theoretical approaches: ab initio MD, for the implementation of which we used the VASP program code; the method of artificial neural networks (ANN) to obtain an effective interatomic interaction potential (ANN potential) using the DeePMD program; a classical MD method (LAMMPS program code); and the recently proposed viscosity calculation approach – time-decomposition method, which uses averaging over a large number of trajectories obtained by the MD. Ab initio MD calculations for liquid gallium were conducted in a temperature range from 303 to 1400 K (500 atoms were used in a supercell and 10,000 of 1 fs steps were performed for each temperature). The obtained data for the surface of potential energy and forces acting on atoms were used as a training set for constructing the ANN potential, whose high quality is confirmed by its almost ideal reproduction of ab initio structure at the level of pair correlations. In turn, the ab initio radial distribution functions are close to the results of other works. Self-diffusion coefficient, calculated via MD with developed deep learning potential, coincides well with the theoretical and experimental results of other authors. Temperature dependence of the viscosity was also computed via MD with developed potential using 10 independent trajectories (4000 atoms and 200,000 fs each) for every temperature point. Calculated viscosity data is in a good agreement with literature data at high temperatures, however at low temperatures some literature data agrees with our computational result, while the others – not. To check the results of our simulation, we experimentally measured viscosity from the melting point to 1270 K using an original setup based on oscillating cup method. Obtained experimental results are in excellent agreement with the results of our simulations. Thus, since both methods (experimental and computational) are modern and independent, presented at this work temperature dependence of viscosity is probably the most reliable at this moment.

Understanding the switching mechanism of oxygen-doped Sb phase-change material: Insights from first principles

The crystalline–amorphous–crystalline transition process of an oxygen-tuned Sb phase-change material has been obtained by employing ab initio molecular dynamic calculations. By analyzing the local atomic arrangement and the electron structure of the SbO system, the intrinsic mechanism is explored to comprehend the material function: (1) ultrafast crystallization and difficulty in creating a glassy state of a pure Sb material might be caused by the resonance bonding of linear arrangement Sb atoms in the rhombohedral phase; (2) the impurity oxygen atoms break the medium and long-range linear arrangement of the Sb network by steric effects and change the electronic structure of these Sb atoms bonded to oxygen atoms, i.e., the obvious increase in electron localization and the great decrease in state distribution around the Fermi surface due to the high electronegativity of oxygen. These factors set an effective barrier for crystallization and improve the amorphous stability and, thus, data retention. The present research and scheme provide important insights into the engineering and manipulation of a phase-change material through first-principles calculations toward non-volatile phase change memory.

Metal-modified s-C3N6 as a potential superior sensing medium for effective capture of toxic waste gases CO, H2S and SO2 in the iron and steel industry based on first-principles investigations

Theoretical studies on the adsorption of toxic gases CO, H2S and SO2 on pristine and Fe, Pt, Ti-modified s-C3N6 surfaces are carried out based on first-principles investigations. Compared with pristine s-C3N6 (−0.33 eV to −0.45 eV), Fe, Pt, Ti-modified s-C3N6 structures (−1.06 eV to −2.66 eV) have larger adsorption energies for the adsorption of toxic gases CO, H2S and SO2 on their surfaces. Larger adsorption energies could lead to more CO, H2S, and SO2 molecules adsorbed on the material, thereby increasing the sensitivity. CO, H2S and SO2 molecules can reduce the band gap by 27–100% and enhance the conductivity of s-C3N6-Fe/Ti. And s-C3N6-Fe exhibits metallic properties after adsorbing CO, but it exhibits semiconducting properties after adsorbing H2S and SO2. Ab initio molecular dynamics (AIMD) calculations reveal the thermal stability of s-C3N6-Fe for the adsorption of CO and SO2. The pristine and Fe, Pt, Ti-modified s-C3N6 may be superior adsorbents as promising sensing media for the toxic gases CO, H2S and SO2.

Metallic B2C3P Monolayer as Li-Ion Battery Materials: A First-Principles Study

The search for and design of high-performance electrode materials is always an important topic in rechargeable batteries. Using a global structure prediction method together with first-principles calculations, a free-standing two-dimensional B2C3P monolayer with honeycomb structure was identified. The stability of the B2C3P monolayer was confirmed by cohesive energy, phonon curves, and ab initio molecular dynamics calculations. Of note, the B2C3P monolayer was demonstrated to be metallic, which shows excellent performance for Li-ion batteries. For example, the B2C3P monolayer also exhibited a metallic characteristic after Li adsorption, therefore the ability to keep good electrical conductivity during battery operation. Furthermore, when a B2C3P monolayer is used as a lithium-ion battery anode, it shows an ultra-high theoretical capacity of 3024 mAh/g, and a comparatively low diffusion barrier of 0.33 eV. All calculated results showed that the B2C3P monolayer is an appealing anode material, and has great potential in energy storage devices.

Unexpected catalytic influence of atmospheric pollutants on the formation of environmentally persistent free radicals.

Environmentally persistent free radicals (EPFRs) have been recognized as harmful and persistent environmental pollutants. In polluted regions, many acidic and basic atmospheric pollutants, which are present at high concentrations, may influence the extent of the formation of EPFRs. In the present paper, density functional theory (DFT) and ab-initio molecular dynamics (AIMD) calculations were performed to investigate the formation mechanisms of EPFRs with the influence of the acidic pollutants sulfuric acid (SA), nitric acid (NA), organic acid (OA), and the basic pollutants, ammonia (A), dimethylamine (DMA) on α-Al2O3 (0001) surface. Results indicate that both acidic and basic pollutants can enhance the formation of EPFRs by acting as "bridge" or "semi-bridge" roles by proceeding via a barrierless process. Acidic pollutants enhance the formation of EPFRs by first transferring its hydrogen atom to the α-Al2O3 surface and subsequently reacting with phenol to form an EPFR. In contrast, basic pollutants enhance the formation of EPFRs by first abstracting a hydrogen atom from phenol to form a phenoxy EPFR and eventually interacting with the α-Al2O3 surface. These new mechanistic insights will inform in understanding the abundant EPFRs in polluted regions with high mass concentrations of acidic and basic pollutants.

Graph Theoretic Molecular Fragmentation for Multidimensional Potential Energy Surfaces Yield an Adaptive and General Transfer Machine Learning Protocol.

Over a series of publications we have introduced a graph-theoretic description for molecular fragmentation. Here, a system is divided into a set of nodes, or vertices, that are then connected through edges, faces, and higher-order simplexes to represent a collection of spatially overlapping and locally interacting subsystems. Each such subsystem is treated at two levels of electronic structure theory, and the result is used to construct many-body expansions that are then embedded within an ONIOM-scheme. These expansions converge rapidly with many-body order (or graphical rank) of subsystems and have been previously used for ab initio molecular dynamics (AIMD) calculations and for computing multidimensional potential energy surfaces. Specifically, in all these cases we have shown that CCSD and MP2 level AIMD trajectories and potential surfaces may be obtained at density functional theory cost. The approach has been demonstrated for gas-phase studies, for condensed phase electronic structure, and also for basis set extrapolation-based AIMD. Recently, this approach has also been used to derive new quantum-computing algorithms that enormously reduce the quantum circuit depth in a circuit-based computation of correlated electronic structure. In this publication, we introduce (a) a family of neural networks that act in parallel to represent, efficiently, the post-Hartree-Fock electronic structure energy contributions for all simplexes (fragments), and (b) a new k-means-based tessellation strategy to glean training data for high-dimensional molecular spaces and minimize the extent of training needed to construct this family of neural networks. The approach is particularly useful when coupled cluster accuracy is desired and when fragment sizes grow in order to capture nonlocal interactions accurately. The unique multidimensional k-means tessellation/clustering algorithm used to determine our training data for all fragments is shown to be extremely efficient and reduces the needed training to only 10% of data for all fragments to obtain accurate neural networks for each fragment. These fully connected dense neural networks are then used to extrapolate the potential energy surface for all molecular fragments, and these are then combined as per our graph-theoretic procedure to transfer the learning process to a full system energy for the entire AIMD trajectory at less than one-tenth the cost as compared to a regular fragmentation-based AIMD calculation.

N-based single and double transition metal V2N/CrVN monolayers as high capacity anode materials for Li-ion batteries

The electrochemical characteristics of N-based single and double transition metal V2N/CrVN monolayers were examined using density functional theory (DFT) approach. The ab-initio molecular dynamics (AIMD) calculations have demonstrated that both V2N and CrVN monolayers are thermally stable at 300 & 500 K. The multilayer adsorption of Li-ion on both lower and upper surfaces of V2N/CrVN leads to the specific capacity of 1040/1440 mAh g−1. Moreover, the energy diffusion barrier is found to be 0.034 and 0.030 eV for V2N and CrVN MXenes, respectively. This observation authenticates that the replacement of V-layer by Cr-atomic layer considerably reduces the energy barrier and boosts the cycling rate of the batteries. Also, the calculated average working voltage of V2N/CrVN monolayers comes out in the range of 0.20–0.54 V which implies their application as anode material in Li-ion batteries. Thus with the enhanced electrochemical properties, both monolayers offer alternative candidatures for anodes in futuristic Li-ion batteries.