Ab Initio Research Articles

State-of-the-RNArt: benchmarking current methods for RNA 3D structure prediction.

RNAs are essential molecules involved in numerous biological functions. Understanding RNA functions requires the knowledge of their 3D structures. Computational methods have been developed for over two decades to predict the 3D conformations from RNA sequences. These computational methods have been widely used and are usually categorised as either ab initio or template-based. The performances remain to be improved. Recently, the rise of deep learning has changed the sight of novel approaches. Deep learning methods are promising, but their adaptation to RNA 3D structure prediction remains difficult. In this paper, we give a brief review of the ab initio, template-based and novel deep learning approaches. We highlight the different available tools and provide a benchmark on nine methods using the RNA-Puzzles dataset. We provide an online dashboard that shows the predictions made by benchmarked methods, freely available on the EvryRNA platform: https://evryrna.ibisc.univ-evry.fr/evryrna/state_of_the_rnart/.

Adsorption of Glycine on TiO2 in Water from On-the-fly Free-Energy Calculations and In Situ Electrochemical Impedance Spectroscopy.

We report here an experimental-computational study of hydrated TiO2 anatase nanoparticles interacting with glycine, where we obtain quantitative agreement of the measured adsorption free energies. Ab initio simulations are performed within the tight binding and density functional theory in combination with enhanced free-energy sampling techniques, which exploit the thermodynamic integration of the unbiased mean forces collected on-the-fly along the molecular dynamics trajectories. The experiments adopt a new and efficient setup for electrochemical impedance spectroscopy measurements based on portable screen-printed gold electrodes, which allows fast and in situ signal assessment. The measured adsorption free energy is -30 kJ/mol (both from experiment and calculation), with preferential interaction of the charged NH3+ group which strongly adsorbs on the TiO2 bridging oxygens. This highlights the importance of the terminal amino groups in the adsorption mechanism of amino acids on hydrated metal oxides. The excellent agreement between computation and experiment for this amino acid opens the doors to the exploration of the interaction free energies for other moderately complex bionano systems.

Pressure effects on the structural, electronic, elastic, optical, and vibrational properties of YMg intermetallic compounds: a first-principles study

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.

Unlocking the Magnetic and Half-Metallic Properties of AMY2 (A = Cu, Ag; M = Sc, Ti, V, Cr, Mn, Fe; Y = S, Se) Compounds in Chalcopyrite Structure: An Ab Initio Study for Spintronics Applications

We present an investigation into the magnetism exhibited by AMY2 compounds characterized by a chalcopyrite structure, where A can be Cu or Ag, M can be Sc, Ti, V, Cr, Mn, or Fe, and Y can be either S or Se. By substituting M atoms at the Ga position of AGaY2 compounds, the magnetic properties were calculated using the full potential linearized augmented plane wave method under the generalized gradient approximation and local spin density approximation with the WIEN2K code. The obtained spin-polarized results confirmed the presence of ferromagnetic and half-metallic (HM) properties in AMY2 compounds (A = Cu, Ag; M = Ti, V, Cr, Mn; Y = S, Se), wherein the HM property is preserved through p-d hybridization of p states of Y (S, Se) atoms with d (t2g) states of M (M = Ti, V, Cr, Mn) atoms, and minimal contribution of −s states of A (A = Cu, Ag) atoms. The total magnetic moments for AMY2 compounds were calculated as 1.00, 2.00, 3.00, and 4.00 µB/f.u. for M = Ti, V, Cr, Mn, respectively. For AFeY2 compounds (A = Cu, Ag; Y = S, Se), electronic band structures for both up spin and down spin states were identical, suggesting antiferromagnetic behavior at equilibrium, while AScY2 compounds (A = Cu, Ag; Y = S, Se) exhibited nonmagnetic properties at equilibrium. Overall, the accurate HM properties of AMY2 materials suggest promising prospects for their utilization in spintronics and magnetic storage device applications.

Ab initio exploration of modified carbon nanotubes as potential corrosion inhibitors

In order to develop novel unexplored potential corrosion inhibitors, covalently modified single-walled carbon nanotubes (SWCNT) via benzoic (–PhCOOH) and aniline (–PhNH2) groups are being investigated as corrosion inhibitors for the first time. Utilizing a comprehensive approach, this study employed density functional theory (DFT), Monte Carlo (MC), and molecular dynamics simulations (MD) to assess the adsorption behavior of modified nanotubes as corrosion inhibitors on the Cu(111) surface within a simulated aqueous HCl corrosion medium. The results provided molecular information on the adsorption capability, geometry adsorption centers, and adsorption energies (Eads) of carbon nanotubes on the surface of Cu(111). The adsorption energy values unveiled robust interactions between SWCNT–PhCOOH and SWCNT–PhNH2 inhibitors and the Cu(111) surface, suggesting a highly effective corrosion protection mechanism. The calculated Eads values exhibited notable ranges, spanning from –260.82 to –308.18 kcal/mol for SWCNT–PhCOOH and –220.92 to –261.01 kcal/mol for SWCNT–PhNH2 with the maximum probability values, representing the most favorable adsorption scenarios, determined to be –292.96 and –229.39 kcal/mol, respectively. A key insight from Monte Carlo simulations underscored the inherent spontaneity of the adsorption process, corroborated by the consistently negative Eads values. These findings collectively underscore the substantial affinity of the inhibitors to the copper surface, contributing to a deeper comprehension of their corrosion inhibition capabilities.

Entanglement in photo-ionization process.

We report a study of the entanglement between the quantized photon field and an atom arising in the photo-ionization process. Our approach is based on an ab initio solution of the time-dependent Schrödinger equation (TDSE) describing the quantum evolution of a bipartite system consisting of the atom and the quantized electromagnetic field. Using the solution of the TDSE, we calculate the reduced photon density matrix, which we subsequently use to compute entanglement entropy. We explain some properties of the entanglement entropy and propose an approximate formula for the entanglement entropy based on the analysis of the density matrix and its eigenvalues. We present the results of a comparative study of the entanglement in the photo-ionization process for various ionization regimes, including the tunneling and the multiphoton ionization regimes.

Quantum Algorithm for Imaginary-Time Green's Functions.

Green's function methods lead to ab initio, systematically improvable simulations of molecules and materials while providing access to multiple experimentally observable properties such as the density of states and the spectral function. The calculation of the exact one-particle Green's function remains a significant challenge for classical computers and was attempted only on very small systems. Here, we present a hybrid quantum-classical algorithm to calculate the imaginary-time one-particle Green's function. The proposed algorithm combines the variational quantum eigensolver and the quantum subspace expansion methods to calculate Green's function in Lehmann's representation. We demonstrate the validity of this algorithm by simulating H2 and H4 on quantum simulators and on IBM's quantum devices.

Relativistic Quantum Chemical Investigation of Actinide Covalency Measured by Electron Paramagnetic Resonance Spectroscopy.

We investigate actinide covalency effects in two [AnCptt3] (An = Th, U) complexes recently studied with pulsed electron paramagnetic resonance spectroscopy, using the Hyperion package to obtain relativistic hyperfine coupling constants from relativistic multiconfigurational wave functions. 1H and 13C HYSCORE simulations using the computed parameters show excellent agreement with the experimental data, highlighting the accuracy of modern relativistic ab initio methods. The extent of covalency indicated from the calculations on [ThCptt3] is in agreement with the original report based on traditional spectral fitting methods, while the covalency in [UCptt3] is found to be previously overestimated. The latter is due to the paramagnetic spin-orbit effect that arises naturally in a relativistic theory of hyperfine coupling and yet was not accounted for in the original study, thus highlighting the necessity of relativistic approaches for the interpretation of magnetic resonance data pertaining to actinides.

Unraveling the Phosphorus Adsorption Mechanisms in Three-dimensional Reduced Graphene Oxide Materials.

To prevent eutrophication, controlling the phosphate concentration levels is one of the most important issues in surface water management. One of the most utilized methods is phosphate adsorption. However, its application faces a bottleneck due to the unclear understanding of adsorption and interaction mechanisms. The present work unlocks the phosphorus adsorption mechanisms in three-dimensional reduced graphene oxide with different reduction levels and pore sizes to remove phosphate from water using experiments and multiscale simulations. Experiments were performed to evaluate the influence of pH, ionic strength, and temperature on the adsorption. Molecular Dynamics and Ab Initio simulations evaluated the influence of the pore size and oxidation degrees of the materials. We show that the adsorption capacity of the materials increases with increasing pH and ionic strength and decreasing temperature. It is observed that the more oxidized the material and the less compact the structure, the better the adsorption. These results are theoretically explained in terms of the interaction of functional groups and the clustering of phosphate ions, which results in better adsorption in materials with larger pores. The underlying mechanisms for the 3D-reduced graphene oxide performance were confirmed by spectroscopy analysis. All the results show that 3D-reduced graphene oxide can sorb phosphate in different complex water remediation systems with characteristics that can be modulated by changing the material synthesis method.

Crystal orientation control of a-plane AlN films on r-plane sapphire fabricated by sputtering and high-temperature annealing

Face-to-face annealed and sputter-deposited aluminum nitride (FFA Sp-AlN) has potential in deep-ultraviolet light-emitting devices. Herein, the effects of the substrate off-cut angle (θsub) from an r-plane sapphire toward the c-axis projection direction and sputtering temperature (Tsp) on the crystallinity and surface morphology of a-plane AlN films are investigated. Increasing θsub in the minus-off direction, which occurs when the substrate surface approaches the sapphire c-plane, and lowering Tsp suppress the mixing of anomalous non-a-direction oriented domains. This reduced mixing enhances the surface flatness and crystallinity of a-plane FFA Sp-AlN. Moreover, the c-axis direction of the a-plane AlN film is inverted depending on the substrate off-cut angle. Ab initio calculations indicate that the interface stability between the r-plane sapphire substrate and the a-plane AlN film can explain the dependence of the crystallinity and c-axis orientation of FFA Sp-AlN on the surface off-cut of the r-plane sapphire.

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.

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 addresses 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 electrochemically 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 300h at 1mAcm-2. The full batteries matched with LiFePO4 exhibit high capacity (148mAhg-1), excellent rate performance (61mAhg-1 at 5C), 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.

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.

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.