AndreaBozzo/ceres-open-data-index huggingface dataset:
Operando tracking the interactions between CoOx and CeO₂ during oxygen evolution reaction

CeO₂ greatly enhances the electrocatalytic oxygen evolution reaction (OER) activity of CoOx, though the enhancement mechanism beyond this synergy is yet to be understood. Here, operando hard X-ray adsorption spectroscopy (hXAS) is applied to monitor the Co K edge and Ce L₃ edge in CoOx/CeO₂ to shed light on the evolution of the Co and Ce oxidation states during OER. In addition, ex situ soft XAS (sXAS) characterizations provide information on the irreversible surface-specific transformations of the Co L₃ edge as well as of the O K edge. Combining the operando and ex situ spectroscopic characterizations with comprehensive electrochemical analyses, we confirm CeO₂ is not the active center for the OER. However, coupling CeO₂ with CoOx introduces significant modifications in the Co and O species at the CoOx surface and alters the flat band potential (Efb), leading to more favorable Co oxidation state transformations during OER and possibly modifying the preferential reaction pathway. This work establishes the connections between electronic structures, Co oxidation state and the OER reaction mechanism for CoOx/CeO₂ composites electrodes.

Tags: ceo2, co-oxidation, co-redox, operando-xas, oxygen-evolution-reaction
Absolute energy levels of liquid water from many-body perturbation theory with effective vertex corrections

We demonstrate the importance of addressing the 𝚪 vertex and thus going beyond the GW approximation for achieving the energy levels of liquid water in many- body perturbation theory. In particular, we consider an effective vertex function in both the polarizability and the self-energy, which does not produce any computational overhead compared with the GW approximation. We yield the band gap, the ionization potential, and the electron affinity in good agreement with experiment and with a hybrid functional description. The achieved electronic structure and dielectric screening further lead to a good description of the optical absorption spectrum, as obtained through the solution of the Bethe–Salpeter equation. In particular, the experimental peak position of the exciton is accurately reproduced.

Tags: electronic-structure, gw, ionization-potential, many-body-perturbation-theory, vertex, water
Reaction-agnostic featurization of bidentate ligands for Bayesian ridge regression of enantioselectivity

Chiral ligands are important components in asymmetric homogeneous catalysis, but their synthesis and screening can be both time-consuming and resource-intensive. Data-driven approaches, in contrast to screening procedures based on intuition, have the potential to reduce the time and resources needed for reaction optimization by more rapidly identifying an ideal catalyst. These approaches, however, are often non-transferable and cannot be applied across different reactions. To overcome this drawback, we introduce a general featurization strategy for bidentate ligands that is coupled with an automated feature selection pipeline and Bayesian ridge regression to perform multivariate linear regression modeling. This approach, which is applicable to any reaction, incorporates electronic, steric, and topological features (rigidity/flexibility, branching, geometry, constitution) and is well-suited for early-stage ligand optimization. Using only a limited number of points per dataset, our workflow capably predicts the enantioselectivity of four metal-catalyzed asymmetric reactions. Uncertainty estimates provided by Bayesian ridge regression permit the use of Bayesian optimization to efficiently explore pools of prospective new ligands. Using this procedure, a new library of 312 chiral bidentate ligands was screened to identify promising ligand candidates for a challenging asymmetric oxy-alkynylation reaction.

Tags: bidentate-ligands, catalysis, epfl, homogenous-catalysis, ligands, nccr-catalysis
Do we really need machine learning interatomic potentials for modeling amorphous metal oxides?
Case study on amorphous alumina by recycling an existing ab-initio database.

In this study, we benchmarked various interatomic potentials and force fields in comparison to an ab initio dataset for bulk amorphous alumina. We investigated a comprehensive set of fixed-charge and variable-charge potentials tailored for alumina. We also train a machine learning interatomic potential, using the NequIP framework. Results highlight that the fixed-charge potential by Matsui provides an ideal blend of computational speed and alignment with ab initio findings for stoichiometric alumina. For non-stoichiometric variants, the variable charge potentials, especially ReaxFF, align remarkably well with DFT outcomes. The NequIP ML potential, while superior in some instances and adaptable, might not be the best fit for specific tasks.

Tags: machine-learning, marveldd1, molecular-dynamics
Hidden orders and (anti-)magnetoelectric effects in Cr₂O₃ and α-Fe₂O₃

We present ab initio calculations of hidden magnetoelectric multipolar order in Cr₂O₃ and its iron-based analogue, α-Fe₂O₃. We show the presence of hidden antiferroically-ordered magnetoelectric multipoles in both the prototypical magnetoelectric material Cr₂O₃, and centrosymmetric α-Fe₂O₃, which has the same crystal structure as Cr₂O₃, but a different magnetic dipolar ordering. In turn, we predict anti-magnetoelectric effects, in which local magnetic dipole moments are induced in opposite directions under the application of an external electric field, to create an additional antiferromagnetic ordering. We confirm the predicted induced moments using first-principles calculations. Our results demonstrate the existence of hidden magnetoelectric multipoles leading to local linear magnetoelectric responses even in centrosymmetric materials, where a net bulk linear magnetoelectric effect is forbidden by symmetry.  This archive contains input files and some output files necessary for creating all the data discussed in our paper with the title: Hidden orders and (anti-)Magnetoelectric Effects in Cr₂O₃ and α-Fe₂O₃.

Tags: erc, h2020, magnetoelectricity, multipoles
Solvation free energies from machine learning molecular dynamics

In this paper, we propose 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.
The record includes all molecular-dynamics trajectories, energies and forces used to obtain the solvation energies of alkaline and alkaline-earth ions in water, as reported in Table 2 of referenced paper.

Tags: machine-learning, molecular-dynamics, solvation
Machine learning of twin/matrix interfaces from local stress field

Twinning is an important deformation mode in plastically deformed hexagonal close-packed materials. The extremely high twin growth rates at the nanoscale make atomistic simulations an attractive method for investigating the role of individual twin/matrix interfaces such as twin boundaries and basal-prismatic interfaces in twin growth kinetics. Unfortunately, there is no single framework that allows researchers to differentiate such interfaces automatically, neither in experimental in-situ transmission electron microscopy analysis images nor in atomistic simulations. Moreover, the presence of alloying elements introduces substantial noise to local atomic environments, making it nearly impossible to identify which atoms belong to which interface. Here, with the help of advanced machine learning methods, we provide a proof-of-concept way of using the local stress field distribution as an indicator for the presence of interfaces and for determining their types. We apply such an analysis to the growth of twin embryos in Mg-10 at.% Al alloys under constant stress and constant strain conditions, corresponding to two extremes of high and low strain rates, respectively. We discover that the kinetics of such growth is driven by high-energy basal-prismatic interfaces, in line with our experimental observations for pure Mg. The data provided here allows for reproducing findings from our work.

Tags: machine-learning, magnesium-twinning, marveldd1, molecular-dynamics
Surface-symmetry-driven Dzyaloshinskii-Moriya interaction and canted ferrimagnetism in collinear magnetoelectric antiferromagnet Cr₂O₃

Antiferromagnets are normally thought of as materials with compensated magnetic sublattices. This adds to their technological advantages but complicates readout of the antiferromagnetic state. We demonstrate theoretically the existence of a Dzyaloshinskii-Moriya interaction (DMI) which is determined by the magnetic symmetry classes of Cr₂O₃ surfaces with an in-plane magnetic easy axis. The DMI explains a previously predicted out-of-plane magnetization at the nominally compensated surfaces of chromia, leading to a surface-localized canted ferrimagnetism. This is in agreement with magnetotransport measurements and with density functional theory predictions which further allow us to quantify the strength of DMI. The temperature dependence of the transversal resistance for these planes shows distinct behavior in comparison with that of the Cr₂O₃  plane, which we attribute to the influence of DMI. Our work provides a framework to analyze surface-driven phenomena in antiferromagnets, and motivates the use of nominally compensated chromia surfaces for antiferomagnetic spintronics and magnonics. Here, we provide the data for density functional theory and Monte Carlo calculations. Micromagnetic and experimental data for this joint experiment-theory collaboration are archived separately according to EU regulations.

Tags: density-functional-theory, dzyaloshinskii-moriya-interactions, magnetoelectrics, magnetotransport, micromagnetics, surface-magnetization
Understanding the role of Hubbard corrections in the rhombohedral phase of BaTiO₃

We present a first-principles study of the low-temperature rhombohedral phase of BaTiO₃ using Hubbard-corrected density-functional theory. By employing density-functional perturbation theory, we compute the onsite Hubbard U for Ti(3d) states and the intersite Hubbard V between Ti(3d) and O(2p) states. We show that applying the onsite Hubbard U correction alone to Ti(3d) states proves detrimental, as it suppresses the Ti(3d)-O(2p) hybridization and drives the system towards a cubic phase. Conversely, when both onsite U and intersite V are considered, the localized character of the Ti(3d) states is maintained, while also preserving the Ti(3d)-O(2p) hybridization, restoring the rhombohedral phase of BaTiO₃. The generalized PBEsol+U+V functional yields good agreement with experimental results for the band gap and dielectric constant, while the optimized geometry is slightly less accurate compared to PBEsol. Zone-center phonon frequencies and Raman spectra are found to be significantly influenced by the underlying geometry. PBEsol and PBEsol+U+V provide satisfactory agreement with the experimental Raman spectrum when the PBEsol geometry is used, while PBEsol+U Raman spectrum diverges strongly from experimental data highlighting the adverse impact of the U correction alone in BaTiO₃. Our findings underscore the promise of the extended Hubbard PBEsol+U+V functional with first-principles U and V for the investigation of other ferroelectric perovskites with mixed ionic-covalent interactions.

Tags: batio3, cscs, dftu, dftuv, marvelp4, phonons, raman-spectra
High-throughput dataset of impurity adsorption on common catalysts in biomass upgrading applications

An extensive dataset consisting of adsorption energies of pernicious impurities present in biomass upgrading processes on common catalysts and support materials has been generated. This work aims to inform catalyst and process development for the conversion of biomass-derived feedstocks to fuels and chemicals. A high-throughput workflow was developed to execute density functional theory calculations for a diverse set of atomic (Al, B, Ca, Cl, Fe, K, Mg, Mn, N, Na, P, S, Si, Zn) and molecular (COS, H₂S, HCl, HCN, K₂O, KCl, NH₃) species on 35 unique surfaces for transition-metal (Ag, Au, Co, Cu, Fe, Ir, Ni, Pd, Pt, Re, Rh, Ru) and metal-oxide (Al₂O₃, MgO, anatase-TiO₂, rutile-TiO₂, ZnO, ZrO₂) catalysts and supports. Approximately 3,000 unique adsorption geometries were obtained. The data record includes structure and calculation output files for each unique adsorbate geometry on each surface.

Tags: density-functional-theory, high-throughput, vasp
Synergistic effects in low-temperature CO oxidation on cerium oxide surfaces

The mechanisms underlying the reaction between carbon monoxide (CO) and activated dioxygen on metal oxide substrates to produce CO₂ remain poorly understood, particularly regarding the role of oxygen vacancies and the nature of the activated O₂ adsorbate. In this study, we present experimental findings from infrared reflection-absorption spectroscopy on a model system of bulk monocrystalline CeO₂(111). Contrary to expectations, exposing the reduced surface to dioxygen (O₂) at 80 K does not yield activated oxygen species, such as superoxo or peroxo. Notably, in the presence of adsorbed CO, an unexpected low-temperature oxidation reaction occurs, consuming CO while oxidizing the CeO₂ substrate. Since a direct reaction between impinging O₂ and adsorbed CO is unlikely at these low temperatures, a novel mechanism is proposed. Extensive spin-polarized density functional theory (DFT) calculations reveal that oxygen vacancies play a critical role in this low-temperature CO oxidation. Initially located in the subsurface region (Vss), these vacancies migrate to the surface (Vs) via a concerted interaction with coadsorbed CO and O₂, leading to O₂ activation and the formation of superoxo or peroxo species. Detailed analysis identifies key reaction intermediates and quantifies their adsorption energies and activation barriers. Our findings suggest that the peroxo-mediated pathway, with its lower activation barrier, is more favorable for CO oxidation at low temperatures compared to the carbonate pathway. This study provides valuable insights into the dynamic role of subsurface oxygen vacancies in the activation of gaseous O₂ and CO oxidation mechanisms on CeO₂.

Tags: ceria, co-oxidation, dft, peroxo-and-superoxo
Intermediate polaronic charge transport in organic crystals from a many-body first-principles approach

Predicting the electrical properties of organic molecular crystals (OMCs) is challenging due to their complex crystal structures and electron-phonon (e-ph) interactions. Charge transport in OMCs is conventionally categorized into two limiting regimes – band transport, characterized by weak e-ph interactions, and charge hopping due to localized polarons formed by strong e-ph interactions. However, between these two limiting cases there is a less well understood intermediate regime where polarons are present but transport does not occur via hopping. Here we show a many-body first-principles approach that can accurately predict the carrier mobility in OMCs in the intermediate regime and shed light on its microscopic origin. Our approach combines a finite-temperature cumulant method to describe strong e-ph interactions with Green-Kubo transport calculations. We apply this parameter-free framework to naphthalene crystal, demonstrating electron mobility predictions within a factor of 1.5–2 of experiment between 100–300 K. Our analysis reveals that electrons couple strongly with both inter- and intramolecular phonons in the intermediate regime, as evidenced by the formation of a broad polaron satellite peak in the electron spectral function and the failure of the Boltzmann transport equation (BTE). Our study advances quantitative modeling of charge transport in complex organic crystals. This dataset contains input and output files required to reproduce the BTE results presented in our work.

Tags: boltzmann-equation, carrier-mobility, charge-transport, electron-phonon-coupling, electron-phonon-scattering-rate, first-principles-calculations, molecular-crystal, naphthalene, organic-crystal, polaron
Engineering host-guest interactions in organic framework materials for drug delivery

Metal-organic frameworks (MOF) and covalent organic frameworks (COFs) are promising nanocarriers for targeted drug delivery. For their uptake and release, non-covalent interactions between the framework and the drugs play a fundamental role. However, an in-depth understanding of how different functional groups affect these interactions is still lacking. Using a multilevel approach combining molecular docking and density functional theory, we show in the publication associated with this data how computational modeling can be exploited to gain information on the interplay between functionalization and drug delivery features. We find that functional groups significantly impact the strength of the host-guest interactions. Moreover, the interaction strength qualitatively correlates with drug release data from experimental literature, providing a link between framework structure and release properties. The results of our study facilitate the customization of non-covalent interactions between MOFs/COFs and drugs and give direction on how to rationally design nanocarriers for sustaining the drug release in the body over longer times.
The data deposited on the Materials Cloud Archive contains the inputs and outputs of the molecular docking and DFT simulations.

Tags: covalent-organic-frameworks, dft, drug-delivery, metal-organic-frameworks
A general framework for active space embedding methods: applications in quantum computing

We developed a general framework for hybrid quantum-classical computing of molecular and periodic embedding calculations based on an orbital space separation of the fragment and environment degrees of freedom. We show its potential by presenting a specific implementation of periodic range-separated DFT coupled to a quantum circuit ansatz, whereby the variational quantum eigensolver and the quantum equation-of-motion approach are used to obtain the low-lying spectrum of the embedded fragment Hamiltonian.
Application of this scheme to study strongly correlated molecular systems and localized electronic states in materials is showcased through the accurate prediction of the optical properties for the neutral oxygen vacancy in magnesium oxide (MgO). Despite some discrepancies in absorption predictions, the method demonstrates competitive performance with state-of-the-art ab initio approaches, particularly evidenced by the accurate prediction of the photoluminescence emission peak.

Tags: cp2k, marvelqs, qiskit-nature, quantum-embedding, quantum-simulation
JuCLS database of core-level shifts from all-electron density functional theory simulations for chemical analysis of X-ray photoelectron spectra

We present the JuCLS (Jülich core-level shifts) database which collects first principles calculations of core-level binding energies and core-level shifts (also known as chemical shifts). The calculations for this database were performed with the FLEUR program [1], a feature-full, freely available, open source FLAPW (full-potential linearized augmented planewave) code, based on density-functional theory. The FLAPW-method is a very accurate all-electron method which within density functional theory is universally applicable to all atoms of the periodic table. All calculations are run with AiiDA through workflows within the AiiDA-FLEUR package (version 0.12.3) [2]. Our database collects predicted core-level shifts, binding energies for X-ray photoelectron spectroscopy (XPS) and as a side product formation energies. Core-level shifts are calculated within the initial state approximation and binding energies are extracted from core-hole simulations. The JuCLS v1.0 contains initial state core-level shifts and formation energies on 4435 of the 5058 stable binary metals from the Materials project database (MP) and calculations on 1271 elemental crystals from the Inorganic Crystal Structure Database (ICSD). This corresponds currently to over 130 000 unique core-level shifts and over 15 000 unique main line core-level shifts. The JuCLS database allows for the construction of theoretical X-ray photoelectron spectra containing a possible mixture of these materials. Furthermore, it allows for a direct chemical characterization of materials.

[1] https://flapw.de and www.judft.de
[2] https://github.com/JuDFTteam/aiida-fleur

Tags: ab-initio, aiida-fleur, binding-energies, chemical-shifts, core-level, core-level-shifts, density-functional-theory, esca, flapw, fleur, jucls, max, x-ray-photoelectron-spectroscopy, xps
High performance Wannier interpolation of Berry curvature and related quantities with WannierBerri code

The article presents a series of methods that boost the speed of Wannier interpolation by several orders of magnitude, as well as their implementation in the WannierBerri code. The present dataset contains input files, scripts, and the resulting data, which allow to reproduce the examples and figures published in the article. The current version of the code is also included.

Tags: anomalous-hall-effect, berry-curvature, erc, marveldd6, snsf, wannier-functions
Normal State of Nd_(1-x)Sr_xNiO2 from Self-Consistent GW+EDMFT

Superconductivity with a remarkably high Tc has recently been observed in hole-doped NdNiO2, a material that shares similarities with the high-Tc cuprates. This discovery promises new insights into the mechanism of unconventional superconductivity, but at the modeling level, there are fundamental issues that need to be resolved. While it is generally agreed that the low-energy properties of cuprates can, to a large extent, be captured by a single-band model, there has been a controversy in the recent literature about the importance of a multiband description of the nickelates. Here, we use a multisite extension of the recently developed GW+EDMFT method, which is free of adjustable parameters, to self-consistently compute the interaction parameters and electronic structure of hole-doped NdNiO2. This full ab initio simulation demonstrates the importance of a multiorbital description, even for the undoped compound, and it produces results for the resistivity and Hall conductance in qualitative agreement with experiment.

Tags: correlated-oxides, dynamical-mean-field-theory, erc, gwedmft, marveldd5
Hidden bulk and surface effects in the spin polarization of the nodal-line semimetal ZrSiTe

In the present record we provide the data obtained in ARPES experiments and input/output files of Quantum ESPRESSO calculations used in the publication entitled as this record. The experimental data consist of the Fermi surface at kz=π/c, the experimental band dispersion along the MΓM, XΓX and XMX, spin-resolved ARPES spectra, and spin-resolved ARPES spectra of surface states. The theoretical data consist in the bulk and slab calculations to support the experimental data.

Tags: arpes, epfl, hidden-polarization, marvel, snsf, spin-texture