Ab Initio Research Articles

Molecular Dynamics Simulation of Complex Reactivity with the Rapid Approach for Proton Transport and Other Reactions (RAPTOR) Software Package.

Simulating chemically reactive phenomena such as proton transport on nanosecond to microsecond and beyond time scales is a challenging task. Ab initio methods are unable to currently access these time scales routinely, and traditional molecular dynamics methods feature fixed bonding arrangements that cannot account for changes in the system's bonding topology. The Multiscale Reactive Molecular Dynamics (MS-RMD) method, as implemented in the Rapid Approach for Proton Transport and Other Reactions (RAPTOR) software package for the LAMMPS molecular dynamics code, offers a method to routinely sample longer time scale reactive simulation data with statistical precision. RAPTOR may also be interfaced with enhanced sampling methods to drive simulations toward the analysis of reactive rare events, and a number of collective variables (CVs) have been developed to facilitate this. Key advances to this methodology, including GPU acceleration efforts and novel CVs to model water wire formation are reviewed, along with recent applications of the method which demonstrate its versatility and robustness.

Superconductivity properties of Pd-Heusler rare earth from ab initio and isotropic Eliashberg function

Ab initio was employed to investigate the structural, electronic, and superconducting properties of the Heusler alloys Pd2TmSn, Pd2YbSn, and Pd2LuSn. The results reveal that these alloys exhibit both structural and dynamic stability in a cubic face-centered lattice. The isotropic Eliashberg function was used to calculate the superconductor properties. The phonon–electron couplings fall within the range characteristic of medium-coupling superconductors. Analysis of the Fermi surfaces identifies the presence of necks connecting the first Brillouin zones, which facilitate electron pairing. The calculated superconducting critical temperatures using the Allen–Dynes equation are in agreement with previous experimental and theoretical findings.

Tracking the Dimensionality Transition from a Three Dimensional Single Crystal to a Two Dimensional Perovskite

AbstractThis work carefully studied the transition from 3D perovskite to 2D perovskite. Our system includes single crystals (SCs) of MAPbBr3, which were dipped in a solution of barrier molecules. Three monoammonium cations and one di‐ammonium cation were studied. Absorbance and cathodoluminescence were used to follow the formation of low‐dimensional perovskite on the SC surface. Quantitative nuclear magnetic resonance and scanning electron microscopy assist in quantitatively tracking the exchange process. We followed the barrier molecules′ concentration during the exchange process and their penetration depth into the 3D single crystal. The short aliphatic chain penetrates much farther into the crystal (ca. 450 μm) than the long aliphatic chain barrier molecule. In contrast, the process time is the opposite: the long aliphatic chain requires 5 days to achieve an equilibrium state compared with 15 days for the short aliphatic chain. Ab initio calculations indicate that the exchange process initiates due to the methylammonium vacancies on the surface, and the process is inhibited by the interactions between the −NH3 group and the PbBr2 planes. This work sheds light on the kinetics and thermodynamics of the transition from 3D to 2D perovskites, which is important for stabilizing the hybrid perovskites.

Ab Initio Design of Ni‐Rich Cathode Material with Assistance of Machine Learning for High Energy Lithium‐Ion Batteries

With the widespread use of lithium‐ion batteries in electric vehicles, energy storage, and mobile terminals, there is an urgent need to develop cathode materials with specific properties. However, existing material control synthesis routes based on repetitive experiments are often costly and inefficient, which is unsuitable for the broader application of novel materials. The development of machine learning and its combination with materials design offers a potential pathway for optimizing materials. Here, we present a design synthesis paradigm for developing high energy Ni‐rich cathodes with thermal/kinetic simulation and propose a coupled image‐morphology machine learning model. The paradigm can accurately predict the reaction conditions required for synthesizing cathode precursors with specific morphologies, helping to shorten the experimental duration and costs. After the model‐guided design synthesis, cathode materials with different morphological characteristics can be obtained, and the best shows a high discharge capacity of 206 mAh g−1 at 0.1C and 83% capacity retention after 200 cycles. This work provides guidance for designing cathode materials for lithium‐ion batteries, which may point the way to a fast and cost‐effective direction for controlling the morphology of all types of particles.

Anion-Dependent Strength Scale of Interactions in Ionic Liquids from X-ray Photoelectron Spectroscopy, Ab Initio Molecular Dynamics, and Density Functional Theory.

Using a combination of experiments and calculations, we have gained new insights into the nature of anion-cation interactions in ionic liquids (ILs). An X-ray photoelectron spectroscopy (XPS)-derived anion-dependent electrostatic interaction strength scale, determined using XPS core-level binding energies for IL cations, is presented here for 39 different anions, with at least 18 new anions included. Linear correlations of experimental XPS core-level binding energies for IL cations with (a) calculated core binding energies (ab initio molecular dynamics (AIMD) simulations were used to generate high-quality model IL structures followed by single-point density functional theory (DFT) to obtain calculated core binding energies), (b) experimental XPS core-level binding energies for IL anions, and (c) other anion-dependent interaction strength scales led to three main conclusions. First, the effect of different anions on the cation can be related to ground-state interactions. Second, the variations of anion-dependent interactions with the identity of the anion are best rationalized in terms of electrostatic interactions and not occupied valence state/unoccupied valence state interactions or polarizability-driven interactions. Therefore, the XPS-derived anion-dependent interaction strength scale can be explained using a simple electrostatic model based on electrostatic site potentials. Third, anion-probe interactions, irrespective of the identity of the probe, are primarily electrostatic, meaning that our electrostatic interaction strength scale captures some inherent, intrinsic property of anions independent of the probe used to measure the interaction strength scale.

Ab Initio Prediction of the Structural, Elastic and Thermodynamic Properties Under Hydrostatic Pressure of the Ternary Tetragonal Phosphides XRh2P2 (X = Ca, Ba) for Superconducting Application

Ab Initio Prediction of the Structural, Elastic and Thermodynamic Properties Under Hydrostatic Pressure of the Ternary Tetragonal Phosphides XRh2P2 (X = Ca, Ba) for Superconducting Application

Stable, while Still Active? A DFT Study of Cu, Ag, and Au Single Atoms at the C3N4/TiO2 Interface.

Hybrid DFT calculations are employed to compare the adsorption and stabilization of Cu, Ag, and Au atoms on graphitic C3N4 and on the heterojunction formed by g- C3N4 and TiO2. While Cu and Ag can be strongly chemisorbed in form of cations on g- C3N4, Au is only weakly physisorbed. On g- C3N4/TiO2, all coinage metal adatoms can be strongly chemisorbed, but, while Cu and Ag forms cations, Au form an Au- species. Ab Initio Molecular Dynamics simulations confirm that the metal adatoms on g-C3N4 are highly mobile at room temperature, while they remain confined in the interfacial spacing between C3N4 and TiO2 on the heterojunction, being both stably bound and reachable for the reactants in a catalytic cycle. Doping g-C3N4/TiO2 with metal single atoms permits thus to generate catalytic systems with tunable charge and chemical properties and improved stability with respect to bare C3N4. Moreover, the changes in the electronic structure of g-C3N4/TiO2 induced by the presence of the metal single atoms are beneficial also for photocatalytic applications.

Coherence mapping to identify the intermediates of multi-channel dissociative ionization

Identifying the short-lived intermediates and reaction mechanisms of multi-channel radical cation fragmentation processes remains a current and important challenge to understanding and predicting mass spectra. We find that coherent oscillations in the femtosecond time-dependent yields of several product ions following ultrafast strong-field ionization represent spectroscopic signatures that elucidate their mechanism of formation and identify the intermediate(s) they originate from. Experiments on endo-dicyclopentadiene show that vibrational frequencies from various intermediates are mapped onto their resulting products. Aided by ab initio methods, we identify the vibrational modes of both the cleaved and intact molecular ion intermediates. These results confirm stepwise and concerted fragmentation pathways of the dicyclopentadiene ion. This study highlights the power of tracking the femtosecond dynamics of all product ions simultaneously and sheds further light onto one of the fundamental reaction mechanisms in mass spectrometry, the retro-Diels Alder reaction.

Pressure Effects on the Structural, Electronic, Elastic, Optical, and Vibrational Properties of YMg Intermetallic Compounds:A First-Principles Study

Abstract The properties of YMg in B2 structure have been comprehensively analysed using the first-principles plane-wave pseudopotential method. Specifically, the structural, electronic, elastic, vibrational, and optical properties were investigated using the generalized gradient approximation (GGA) method in the context of density functional theory. The Vienna ab initio simulation package (VASP) was utilized for these calculations. The computed lattice parameter (3.803 Å) and bulk modulus (41.33 GPa) are consistent with the earlier data on ambient pressure. The electronic band structure and energy-dependent density of states reveal the metallic nature of the titled compounds. The Born stability requirements confirmed the mechanical stability. The analysis of Pugh's and Poisson's ratios and Cauchy's pressure reveals that YMg is ductile under the pressures in consideration. According to several anisotropy indices, the compound is noticeably anisotropic both in ambient and under pressure. Our investigation includes an analysis of several fundamental mechanical parameters of the material, including the bulk modulus, the pressure derivative of the Zener anisotropy factor, Poisson's ratio, isotropic shear modulus and Young's modulus with a particular focus on their dependence on pressure. We have determined that the elastic constants obtained remain mechanically stable, satisfying the Born Stability conditions even at high pressures of up to 60 GPa. To explore the dynamic stability of YMg, we analysed the material's phonon dispersion curves. The examined compound displays stability under dynamic conditions from 0 GPa to 30 GPa, as evidenced by its positive vibration frequencies. However, this stability is not sustained under higher pressure, as the compound becomes unstable after 30 GPa to 70 GPa. 
The electronic band structure and density of states diagrams demonstrate YMg's metallic properties. At atmospheric pressure (0 GPa), the total density of states (TDOS) near the Fermi level is approximately 1.63 states/eV, with pressure application reducing DOS. The dielectric function, refractive index, and energy loss spectra are examined within the 0–20 eV energy range. YMg exhibits its highest absorption between 4 and 11 eV. The peak optical conductivity is observed around 0.78 eV (equivalent to 1589.5409 nm), while the most significant energy loss occurs at 11.90 eV, roughly corresponding to 2.8 Hz in the ultraviolet spectrum. Moreover, we extensively analyzed the material's phonon thermodynamic and optical properties, providing insights into its behavior under various conditions. The outcomes acquired at zero pressure are generally coherent with the current theoretical values.

Uniform Tendency of Surface Dipoles Across Silicon Doping Levels and Types of H‐Terminated Surfaces

AbstractThe termination of surface‐dangling bonds on silicon through hydrogen atoms, also known as Si–H, can achieve chemical passivation and reduce surface states in the electronic bandgap, thus altering electronic properties. Through a comprehensive study of doping levels (1014–1020 cm−3) and types (n and p), a consistent surface dipole trend induced by Si–H termination is discovered. It is achieved by redistributing surface charges and establishing thermal equilibrium with the chemical bond. To resolve this, the surface work function, surface electron affinity, and the energy difference between the valence band and the Fermi level are measured by employing the Kelvin probe, X‐ray photoelectron spectroscopy, and photoelectron yield spectroscopy methods. These findings are further validated through ab initio simulations. This finding has immense implications not only for eliminating electronic defects at semiconductor interfaces, which is crucial in microelectronics but also for developing and engineering hybrid interfaces and heterojunctions with controlled electronic properties.

Ab initio dispersion potentials based on physics-based functional forms with machine learning.

In this study, we introduce SAPT10K, a comprehensive dataset comprising 9982 noncovalent interaction energies and their binding energy components (electrostatics, exchange, induction, and dispersion) for diverse intermolecular complexes of 944 unique dimers. These complexes cover significant portions of the intermolecular potential energy surface and were computed using higher-order symmetry-adapted perturbation theory, SAPT2+(3)(CCD), with a large aug-cc-pVTZ basis set. The dispersion energy values in SAPT10K serve as crucial inputs for refining the abinitio dispersion potentials based on Grimme's D3 and many-body dispersion (MBD) models. Additionally, Δ machine learning (ML) models based on newly developed intermolecular features, which are derived from intermolecular histograms of distances for element/substructure pairs to simultaneously account for local environments as well as long-range correlations, are also developed to address deficiencies of the D3/MBD models, including the inflexibility of their functional forms, the absence of MBD contributions in D3, and the standard Hirshfeld partitioning scheme used in MBD. The developed dispersion models can be applied to complexes involving a wide range of elements and charged monomers, surpassing other popular ML models, which are limited to systems with only neutral monomers and specific elements. The efficient D3-ML model, with Cartesian coordinates as the sole input, demonstrates promising results on a testing set comprising 6714 dimers, outperforming another popular ML model, component-based machine-learned intermolecular force field (CLIFF), by 1.5 times. These refined D3/MBD-ML models have the capability to replace the time-consuming dispersion components in symmetry-adapted perturbation theory-based calculations and can promptly illustrate the dispersion contribution in noncovalent complexes for supramolecular assembly and chemical reactions.

High-Performance Dendrite-Free Lithium Metal Anode Based on Metal-Organic Framework Glass.

The performance of lithium metal batteries is severely hampered by uncontrollable dendrite growth and volume change within the anode. This work tackles these obstacles by introducing a novel strategy: applying an isotropic and internal grain-boundary-free layer, specifically, a metal-organic framework (MOF) glass layer with nano-porosity onto the electrochemical plated lithium metal anode. Both ab initio and classical molecular dynamics simulations indicate that the MOF glass layer makes the lithium transport smooth and uniform via its internal monolithic and interfacial advantages. This MOF glass layer with the fast and more uniform lithium diffusion in the monolithic interior and its interface enables dendrite-free lithium plating and stripping through surface confinement effect and interfacial effect. When employed in symmetric batteries, the achieved Li metal anode can operate over 300 hours at 1mA cm-2. The full batteries matched with LiFePO4 exhibit high capacity (148 mAh g-1), excellent rate performance (61 mAh g-1 at 5 C), and outstanding cycling stability (with capacity retention of ∼90% after 1000 cycles). The full batteries matched with high-voltage LiCoO2 also show superior performances. Therefore, the strategy of utilizing a MOF glass layer enables the development of high-performance lithium metal anodes. This article is protected by copyright. All rights reserved.

Interatomic Potential For Carbon Based Quantum‐Technology Applications

AbstractTo optimize parameters for laser processing of quantum‐technology relevant materials, such as diamond, precise atomistic simulations of the light‐matter interaction on large scales (on the order of atoms) are essential. Classical empirical interatomic potentials are commonly employed for simulating such a large number of atoms, however they fail to accurately capture all relevant effects of light‐matter interaction. Conversely, ab initio methods like Density Functional Theory (DFT) can effectively incorporate quantum properties arising from photon excitations, but their applicability is limited to small systems containing at most approximately atoms. Consequently, bridging the gap between achieving DFT precision and handling millions of atoms necessitates the development of innovative classes of interatomic potentials. In this paper, the construction of a highly accurate interatomic potential for diamond is presented, derived from an extensive dataset of DFT calculations. The parameters of the interatomic potential depend on the electronic temperature (). The findings demonstrate that this newly developed interatomic potential can aptly describe the laser processing of diamond for nanophotonic applications, achieving accuracy comparable to ab initio methods for large systems.

Abstract PO4-28-07: SLC26A9 promotes triple-negative breast cancer progression by regulating lipid metabolism

Abstract Background: The disturbance of lipid metabolism in the microenvironment plays an important role in the occurrence and development of triple-negative breast cancer(TNBC). SLC26A9, a member of the SLC26A family of anion transporters, is involved in breast oncogenesis. However, the effect of SLC26A9 in triple-negative breast cancer on lipid metabolism in the tumor microenvironment remains unclear. Methods: Bioinformatics, tissue microarrays and TNBC cell lines were used to detect the expression of SLC26A9 and its clinical significance. By altering the expression of SLC26A9 gene in TNBC cells, the effects of SLC26A9 on the regulation of lipid metabolism, cell biological behavior and its related molecular mechanisms in the TNBC microenvironment were explored using adoptive staining techniques, flow cytometric analysis and animal models. Results: We found by tissue microarray (TNBC=105 cases, Nor=67 cases) that the expression of SLC26A9 was significantly up-regulated in BC compared to paracancerous tissues, where SLC26A9 expression was higher in TNBC, and the same results were obtained in BC cell lines. Secondly, we found that SCL26A9 was positively correlated with lipid metabolism status in TNBC microenvironment and possessed a close association with P53 mutation by analyzing GEO and TCGA databases. Therefore, we used two cell lines (MDA-MB-231, MDA-MB-468) in which SCL26A9 was highly expressed in TNBC cell lines. It was demonstrated by oil red O staining and lipid fluorescence staining that knockdown/silencing of SLC26A9 diminished the ability of MDA-MB-231 and MDA-MB-468 cells to uptake and utilize lipids, especially for metabolites such as neutral lipids: triglycerides, lipid droplets, and steroidal substances. Then we demonstrated by using fatty acid flow cytometric analysis that knockdown/silencing of SLC26A9 significantly reduced the utilization and production of fatty acids in MDA-MB-231 and MDA-MB-468 cells, which are the key metabolic indicators of cancer cells as well as important energy-providing substances for cancer progression. Therefore, we further verified functionally that cell proliferation, migration, invasion and anti-apoptosis were significantly inhibited in in vitro after knockdown/silencing of SLC26A9, and in vivo tumorigenesis was significantly inhibited in BALB/c nude mice in in vivo. In addition, the expression of markers of lipid metabolic activity (FASN, ACLY) was reduced after knockdown/silencing of SLC26A9 in MDA-MB-231 cells by Western Blot, and the reduced expression of FASN and ACLY mainly inhibited the ab initio synthesis, uptake and utilization of fatty acids in TNBC cells, which in turn regulated the proliferation and invasion of TNBC. Mechanistically, SLC26A9 silencing/knockdown inhibited the synthesis, uptake, and utilization of multiple metabolites of lipids in TNBC, which combined with the TCGA database results revealed the activation of the key signaling pathway, the JAK-STAT3 signaling pathway, to promote the progression of TNBC. Conclusion(s): SLC26A9 is involved in the disturbance of lipid metabolism in the TNBC microenvironment and regulates the progression of TNBC. The search for new SLC26A9 inhibitors is expected to provide a new direction for the treatment of TNBC, but the exact molecular mechanisms need to be further explored. SLC26A9 upregulation in TNBC leads to a poor prognosis by referencing lipid metabolism in the TNBC microenvironment Wench. SLC26A9 is involved in lipid metabolism disorders and cell biological functions in the TNBC microenvironment in vivo. SLC26A9 is involved in disordered lipid metabolism in the TNBC microenvironment. Citation Format: Yingming Zhou, Hu Wang, Zhengxing Zhou, Xuemei Liu, Biguang Tuo, Taolang Li. SLC26A9 promotes triple-negative breast cancer progression by regulating lipid metabolism [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO4-28-07.

Solvent Controlled Generation of Spin Active Polarons in Two-Dimensional Material under UV Light Irradiation.

Polarons belong to a class of extensively studied quasiparticles that have found applications spanning diverse fields, including charge transport, colossal magnetoresistance, thermoelectricity, (multi)ferroism, optoelectronics, and photovoltaics. It is notable, though, that their interaction with the local environment has been overlooked so far. We report an unexpected phenomenon of the solvent-induced generation of polaronic spin active states in a two-dimensional (2D) material fluorographene under UV light. Furthermore, we present compelling evidence of the solvent-specific nature of this phenomenon. The generation of spin-active states is robust in acetone, moderate in benzene, and absent in cyclohexane. Continuous wave X-band electron paramagnetic resonance (EPR) spectroscopy experiments revealed a massive increase in the EPR signal for fluorographene dispersed in acetone under UV-light irradiation, while the system did not show any significant signal under dark conditions and without the solvent. The patterns appeared due to the generation of transient magnetic photoexcited states of polaronic character, which encompassed the net 1/2 spin moment detectable by EPR. Advanced ab initio calculations disclosed that polarons are plausibly formed at radical sites in fluorographene which interact strongly with acetone molecules in their vicinity. Additionally, we present a comprehensive scenario for multiplication of polaronic spin active species, highlighting the pivotal role of the photoinduced charge transfer from the solvent to the electrophilic radical centers in fluorographene. We believe that the solvent-tunable polaron formation with the use of UV light and an easily accessible 2D nanomaterial opens up a wide range of future applications, ranging from molecular sensing to magneto-optical devices.

Thermoelectric properties and thermal transport in two-dimensional GaInSe3 and GaInTe3 monolayers: A first-principles study

We here report the electronic structure calculation of GaInSe3 and GaInTe3 monolayers with the P3m1 (no. 156) space group. The electronic structure and thermoelectric properties of the monolayers are calculated through the Vienna Ab initio Simulation Package and BoltzTraP2 codes. The dynamic and thermodynamic stabilities were verified by calculating their phonon spectra and simulating ab initio molecular dynamics. The monolayers were found to have a direct bandgap, with both PBE + SOC and HSE06 + SOC potentials. The lattice thermal conductivity of GaInTe3 monolayer calculated using Phono3py code shows ultra-low values due to enhanced phonon–phonon scattering. Combining electrical and thermal transport, the values have been evaluated. Importantly, the p-type GaInTe3 has excellent thermoelectric properties at 700 K, with a zT value of 2, indicating that the p-type GaInTe3 has potential application in the field of thermoelectricity.

High-Performance Schottky-Barrier Field-Effect Transistors Based on Two-Dimensional GaN with Ag or Au Contacts

The performance of two-dimensional (2D) monolayer GaN Schottky barrier field effect transistors (SBFETs) with four different metals (Ag, Au, Al, and Pt) as electrodes were studied by using ab initio simulations. The N-type Schottky contact is formed on Ag-GaN, Au-GaN, and Pt-GaN, characterized by electron Schottky barrier heights (SBH) of 0.6, 0.5, and 0.38 eV, respectively. Whereas, Al-GaN contact formed P-type Schottky contact with hole SBH of 1.42 eV. The 5.1 nm GaN SBFETs with four metal electrodes all could overcome the short-channel effect. Additionally, GaN SBFETs with Ag and Au electrodes have excellent performance, whose ON-currents are 1151.1 μA/μm and 1258.9 μA/μm, respectively. They could satisfy the demands of International Technology Roadmap for Semiconductors for high-performance transistor. Furthermore, research indicates that the device’s current increases with increasing temperature. Notably, under the constant bias and gate voltage, the current is unaffected by temperature variations between the left and right electrodes.

Time‐resolved photoelectron spectroscopy via trajectory surface hopping

AbstractTime‐resolved photoelectron spectroscopy is a powerful pump‐probe technique which can probe nonadiabatic dynamics in molecules. Interpretation of the experimental signals however requires input from theoretical simulations. Advances in electronic structure theory, nonadiabatic dynamics, and theory to calculate the ionization yields, have enabled accurate simulation of time‐resolved photoelectron spectra leading to successful applications of the technique. We review the basic theory and steps involved in calculating time‐resolved photoelectron spectra, and highlight successful applications.This article is categorized under: Electronic Structure Theory > Ab Initio Electronic Structure Methods Theoretical and Physical Chemistry > Spectroscopy

Reinterpreting Low Resistance in Sb–MoS2 Ohmic Contacts by Means of Ab Initio Transport Simulations

Reinterpreting Low Resistance in Sb–MoS₂ Ohmic Contacts by Means of Ab Initio Transport Simulations

Temperature study of deformation twinning behaviour in Nickel-base Superalloy 625

Deformation behaviour in the Nickel-base superalloy 625 has been studied by tensile testing at four temperatures: 295, 223, 173 and 77 K. The microstructure has been investigated using TEM, FIB-SEM, EBSD and ECCI techniques. Deformation in the alloy turns out to be a competitive course of events between at least two deformation mechanisms, namely dislocation slip and deformation twinning. Slip is the predominant deformation mechanism at higher temperatures. While at 77 K, deformation induced twinning gives an extra degree of freedom as one of the main deformation mechanisms, i.e., the material shows a twin induced plasticity, TWIP, behaviour. Ab initio calculations indicate that the influence of cryogenic/sub-zero temperatures on the stacking fault energy of this alloy can be limited and that the formation of deformation twins cannot be determined solely by the stacking fault energy. The results implies that it is the critical strain and strain hardening rate that influences the deformation twinning onset and twinning rate.