AndreaBozzo/ceres-open-data-index huggingface dataset:
Efficient, interpretable graph neural network representation for angle-dependent properties and its application to optical spectroscopy

Graph neural networks are attractive for learning properties of atomic structures thanks to their intuitive graph encoding of atoms and bonds. However, conventional encoding does not include angular information, which is critical for describing atomic arrangements in disordered systems. In this work, we extend the recently proposed ALIGNN encoding, which incorporates bond angles, to also include dihedral angles (ALIGNN-d). This simple extension leads to a memory-efficient graph representation that captures the complete geometry of atomic structures. ALIGNN-d is applied to predict the infrared optical response of dynamically disordered Cu(II) aqua complexes, leveraging the intrinsic interpretability to elucidate the relative contributions of individual structural components. Bond and dihedral angles are found to be critical contributors to the fine structure of the absorption response, with distortions representing transitions between more common geometries exhibiting the strongest absorption intensity. Future directions for further development of ALIGNN-d are discussed.

Tags: aqua-complex, graph-neural-network, spectroscopy
Novel techniques for characterising graphene nanoplatelets using Raman spectroscopy and machine learning

A significant challenge for graphene nanoplatelet (GNP) suppliers is the meaningful characterisation of platelet morphology in an industrial environment. This challenge is further exacerbated to platelet surface chemistry when scalable functionalisation processes such as plasma treatment are used to modify the GNPs to improve the filler-matrix interphase in nanocomposites. The costly and complex suite of analytical equipment necessary for a complete material description makes quality control and process optimisation difficult. Raman spectroscopy is a facile and accessible characterisation technique with recent advancements unlocking fast mapping for rapid data collection. In this work we detail several big-data methodologies that extract full value out of Raman spectra so that GNP morphology and surface chemistry can be characterised. A unsupervised peak fitting and processing algorithm was used to extract crystallinity data rapidly and accurately and correlate it with laser-diffraction derived lateral size values for a commercial set of GNPs. Classical machine learning was used to find the most informative Raman features for classifying plasma functionalised GNPs. The initial material properties were found to affect which peak features are most useful for classification. In low-defect density and low specific surface area GNPs, the D peak FWHM is found the most useful, whereas the 2D/G ratio is most useful in the opposite case. Finally, a convolutional neural network was trained to discern between different GNP grades with 86% accuracy. This work demonstrates how computer vision could be deployed for rapid and accurate quality control on the factory floor.

Tags: experimental, graphene-nanoplatelets, machine-learning, raman
Numerical simulation of an electrochemical system and semi-analytical method

Electrochemical systems are often simulated by using numerical methods based on finite element solution of differential equations. We developed a method to decrease the needed computational resources, based on the analytical solution of a part of the system: the obtained analytical equations are applied as boundary conditions to the finite element calculation. The part of the system that is analytically solved is the region of the diffuse double layer. We provide two COMSOL models: i) a 1d fully numerical calculation and ii) the same simulation performed with the semi-analytical method. We also provide examples of the resulting impedances and frequency responses of various parameters.

Tags: diffuse-double-layer, electrochemical-system, finite-element-method, semi-analytical-solution
Anti-symmetric Compton scattering in LiNiPO4: Towards a direct probe of the magneto-electric multipole moment

We present a combined theoretical and experimental investigation of the anti-symmetric Compton profile in LiNiPO4 as a possible probe for magneto-electric toroidal moments. Understanding as well as detecting such magneto-electric multipoles is an active area of research in condensed matter physics. Our calculations, based on density functional theory, indicate an anti-symmetric Compton profile in the direction of the ty toroidal moment in momentum space, with the computed anti-symmetric profile around four orders of magnitude smaller than the total profile. The difference signal that we measure is consistent with the computed profile, but of the same order of magnitude as the statistical errors and systematic uncertainties of the experiment. Our results motivate further theoretical work to understand the factors that influence the size of the anti-symmetric Compton profile, and to identify materials exhibiting larger effects.

Tags: compton-scattering, density-functional-theory, erc, h2020, horizon-europe, linipo4, magneto-electric-toroidal-moment
Electronic decoupling and hole-doping of graphene nanoribbons on metal substrates by chloride intercalation

In this record we provide the data to support our recent finding on the intercalation of gold chloride underneath atomically precise graphene nanoribbons (GNRs). GNRs have a wide range of electronic properties that depend sensitively on their chemical structure. Several types of GNRs have been synthesized on metal surfaces through selective surface-catalyzed reactions. The resulting GNRs are adsorbed on the metal surface, which may lead to hybridization between the GNR orbitals and those of the substrate. This makes investigation of the intrinsic electronic properties of GNRs more difficult, and also rules out capacitive gating. In the manuscript where the data presented here is discussed, we demonstrate the formation of a dielectric gold chloride adlayer that can intercalate underneath GNRs on the Au(111) surface. The intercalated gold chloride adlayer electronically decouples the GNRs from the metal and leads to a substantial hole doping of the GNRs. Our results introduce an easily accessible tool in the in situ characterization of GNRs grown on Au(111) that allows for exploration of their electronic properties in a heavily hole-doped regime.

Tags: dft, electronic-properties, marvel, on-surface-synthesis, stm
Numerical simulation of an electrochemical system and semi-analytical method

Electrochemical systems are often simulated by using numerical methods based on finite element solution of differential equations. We developed a method to decrease the needed computational resources, based on the analytical solution of a part of the system: the obtained analytical equations are applied as boundary conditions to the finite element calculation. The part of the system that is analytically solved is the region of the diffuse double layer. We provide two COMSOL models: i) a 1d fully numerical calculation and ii) the same simulation performed with the semi-analytical method. For each model, we provide the .mph file (Comsol) and the .java file (Java+Comsol). We also provide examples of the resulting impedances and frequency responses of various parameters.

Tags: diffuse-double-layer, electrochemical-system, finite-element-method, semi-analytical-solution
Data-driven discovery of organic electronic materials enabled by hybrid top-down/bottom-up design

The high-throughput molecular exploration and screening of organic electronic materials often starts with either a 'top-down' mining of existing repositories, or the 'bottom-up' assembly of fragments based on predetermined rules and known synthetic templates. In both instances, the datasets used are often produced on a case-by-case basis, and require the high-quality computation of electronic properties and extensive user input: curation in the top-down approach, and the construction of a fragment library and introduction of rules for linking them in the bottom-up approach. Both approaches are time-consuming and require significant computational resources. Here, we generate a top-down set named FORMED consisting of 117K synthesized molecules containing their optimized structures, associated electronic and topological properties and chemical composition, and use these structures as a vast library of molecular building blocks for bottom-up fragment-based materials design. A tool is developed to automate the coupling of these building block units based on their available Csp2-H bonds, thus providing a fundamental link between the two philosophies of dataset construction. Statistical models are trained on this dataset and a subset of the resulting hybrid top-down/bottom-up compounds (selected dimers), which enable on-the-fly prediction of key ground state (frontier molecular orbital gaps) and excited state (S1 and T1 energies) properties from molecular geometries with high accuracy across all known p-block organic compound space.
With access to ab initio-quality optical properties in hand, it is possible to apply this bottom-up pipeline using existing compounds as molecular building blocks to any materials design campaign. To illustrate this, we construct and screen over a million molecular candidates (predicted dimers) for efficient intramolecular singlet fission, the leading candidates of which provide insight into the structural features that may promote this multiexciton-generating process.

Tags: crystal-structures, donor-acceptor-copolymers, optical-properties, organic-molecules, photophysical-properties
Interface polarization in heterovalent core/shell nanocrystals

The potential profile and the energy level offset of core/shell heterostructured nanocrystals (h-NCs) determine the photophysical properties and the charge transport characteristics of h-NC solids. However, limited material choices for heavy metal-free III-V/II-VI h-NCs pose challenges in comprehensive control of the potential profile. Herein, we present an approach to such control by steering dipole densities at the interface of III-V/II-VI h-NCs. The controllable heterovalency at the interface is responsible for interfacial dipole densities that result in the vacuum-level shift, providing an additional knob for the control of optical and electrical characteristics of h-NCs. The synthesis of h-NCs with atomic precision allows us to correlate interfacial dipole moments with the nanocrystals' photochemical stability and optoelectronic performance.

The description was referred to the abstract of the original paper. All numerical data of the main figures in the articles are included in this data repository.
In particular, each tab of the data file indicates each panel in the main figures.
Please refer to the main research article.

Tags: experimental, heterostructured-nanocrystal, interface-polarization
Electronic structure and magnetism of pristine and Fe-doped α-MnO₂ from density-functional theory with extended Hubbard functionals

We present a first-principles investigation of the structural, electronic, and magnetic properties of the pristine and Fe-doped α-MnO₂ using density-functional theory with extended Hubbard functionals. The onsite U and intersite V Hubbard parameters are determined from first principles and self-consistently using density-functional perturbation theory in the basis of Löwdin-orthogonalized atomic orbitals. Among the ferromagnetic and four types of antiferromagnetic (AFM) orderings for the pristine α-MnO₂ we find the C2-AFM spin configuration to be the most energetically favorable, in agreement with the experimentally observed AFM state. The computed lattice parameters, magnetic moments, and band gaps are overall in good agreement with the experimental ones when both the onsite and intersite Hubbard corrections are included. For the Fe-doped α-MnO₂ two types of doping are considered: Fe insertion in the 2 × 2 tunnels and partial substitution of Fe for Mn. The calculated formation energies show that Fe insertion is energetically favorable, in agreement with experiments. We find that both types of doping preserve the C2 AFM spin configuration of the host lattice. The oxidation state of Fe is found to be 2+ and 4+ in the case of the interstitial and substitutional doping, respectively, while the oxidation state of Mn is 4+ in both cases. This work opens a door for accurate studies of other Mn oxides and complex transition-metal compounds when the localization of 3d electrons occurs in the presence of strong covalent interactions with ligands.

Tags: band-gap, bond-angles, bond-length, crystal-structure, density-functional-theory, density-of-states, dftu, dftuv, fe-doped-mno2, formation-energy, hubbard-parameters, hubbard-projectors, interstitial-doping, magnetic-moment, mno2, orthogonalized-atomic-orbitals, oxidation-state, self-interactions, spin-configuration, substitutional-doping
A new dataset of 175k stable and metastable materials calculated with the PBEsol and SCAN functionals

In the past decade we have witnessed the appearance of large databases of calculated material properties. These are most often obtained with the Perdew-Burke-Ernzerhof (PBE) functional of density-functional theory, a well established and reliable technique that is by now the standard in materials science. However, there have been recent theoretical developments that allow for an increased accuracy in the calculations. Here, we present a dataset of calculations for 175k solid-state materials obtained with two improved functionals: PBE for solids (that yields consistently better geometries than the PBE) and SCAN (probably the best all-around functional at the moment). Our results provide an accurate overview of the landscape of stable (and nearly stable) materials, and as such can be used for more reliable predictions of novel compounds. They can also be used for training machine learning models, or even for the comparison and benchmark of PBE, PBE for solids, and SCAN.

Tags: density-functional-theory, high-throughput, pbe-for-solids, scan
Critical step in the HCl oxidation reaction over single-crystalline CeO2−x(111): Peroxo-induced site change of strongly adsorbed surface chlorine

The catalytic oxidation of HCl by molecular oxygen (Deacon process) over ceria allows the recovery of molecular chlorine from omnipresent HCl waste produced in various industrial processes. In previous density functional theory (DFT) model calculations by Amrute et al. [J. Catal. 2012, 286, 287–297.], it was proposed that the most critical reaction step in this process is the displacement of tightly bound chlorine at a vacant oxygen position on the CeO2(111) surface (Clvac) toward a less strongly bound cerium on-top (Cltop) position. This step is highly endothermic by more than 2 eV. On the basis of a dedicated model study, namely the re-oxidation of a chlorinated single crystalline Clvac-CeO2−x(111)-(√3 × √3)R30° surface structure, we provide in-situ synchrotron-based spectroscopic data (high-resolution core level spectroscopy (HRCLS) and X-ray adsorption near edge structure (XANES)) for this oxygen-induced de-chlorination process. Combined with theoretical evidence from DFT calculations, the Clvac → Cltop displacement reaction is predicted to be induced by an adsorbed peroxo species (O22-), making the displacement step concerted and exothermic by only 0.6 eV with an activation barrier of only 1.04 eV. The peroxo species is shown to be important for the re-oxidation of Clvac-CeO2−x(111) and is considered essential for understanding the function of ceria in oxidation catalysis.

Tags: deacon-process, displacement-of-strongly-adsorbed-chlorine, oxygen-induced-de-chlorination-process, peroxo-surface-species, reduced-ceria
Pivotal role of intersite Hubbard interactions in Fe-doped α-MnO₂

We present a first-principles investigation of the structural, electronic, and magnetic properties of the pristine and Fe-doped α-MnO₂ using density-functional theory with extended Hubbard functionals. The onsite U and intersite V Hubbard parameters are determined from first principles and self-consistently using density-functional perturbation theory in the basis of Löwdin-orthogonalized atomic orbitals. First, we analyze the pristine α-MnO₂ and show that the C2-AFM spin configuration is the most energetically favorable, in agreement with the experimentally observed antiferromagnetic state. For the Fe-doped α-MnO₂ two types of doping are considered: Fe insertion in the 2 × 2 tunnels and partial substitution of Fe for Mn. The calculated formation energies show that the experimentally observed Fe insertion is energetically favorable only when intersite Hubbard interactions are taken into account. Moreover, we find that both types of doping preserve the C2-AFM spin configuration of the host lattice only when Hubbard V corrections are included. The oxidation state of Fe is found to be +2 and +4 in the case of the interstitial and substitutional doping, respectively, while the oxidation state of Mn is +4 in both cases. This work opens a door for accurate studies of other Mn oxides and complex transition-metal compounds when the localization of 3d electrons occurs in the presence of strong covalent interactions with ligands.

Tags: band-gap, bond-angles, bond-length, crystal-structure, density-functional-theory, density-of-states, dftu, dftuv, fe-doped-mno2, hubbard-parameters, hubbard-projectors, interstitial-doping, magnetic-moment, mno2, orthogonalized-atomic-orbitals, oxidation-state, self-interactions, spin-configuration, substitutional-doping
The impact of valley profile on the mobility and Kerr rotation of transition metal dichalcogenides

The transport and optical properties of semiconducting transition metal dichalcogenides around room temperature are dictated by electron-phonon scattering mechanisms within a complex, spin-textured and multi-valley electronic landscape. The relative positions of the valleys are critical, yet they are sensitive to external parameters and very difficult to determine directly. We propose a first-principles model as a function of valley positions to calculate carrier mobility and Kerr rotation angles, and apply it to MoS₂, WS₂, MoSe₂, and WSe₂. The model brings valuable insights, as well as quantitative predictions of macroscopic properties for a wide range of carrier density. The doping-dependant mobility displays a characteristic peak, the height depending on the position of the valleys. In parallel, the Kerr rotation signal is enhanced when same spin-valleys are aligned, and quenched when opposite spin-valleys are populated. We provide guidelines to optimize and correlate these quantities with respect to experimental parameters, as well as the theoretical support for in situ characterization of the valley positions. 
The dataset contains the necessary data, a jupyter notebook, a supporting python library, and a small app with a simple user interface to reproduce the results.

Tags: 2d-materials, electron-phonon-coupling, kerr-angle, transport
BELLO: A post-processing tool for the local-order analysis of disordered systems

The characterization of the atomic structure of disordered systems, such as amorphous, glasses and (bio)molecule in solution, is a fundamental step for most theoretical investigations. The properties of short- and medium-range local order structures are responsible for the electronic, optical and transport properties of these systems. Here, we present the BELLO open source code, a post-processing script-tool created for the automatic analysis and extraction of structural characteristics of disordered and amorphous systems. BELLO is agnostic to the code that generated single configurations or trajectories, it provides an intuitive access through a graphical user interface (GUI), and it requires minimal computational resources. Its capabilities include the calculation of the order parameter , the folded structure identification, and statistical analysis tools such as atomic coordination number and pair/angle-distribution functions. The working principles of the code are described and tested on ab initio molecular dynamics trajectories of amorphous chalcogenides.

The code is also on the GitHub repository
https://github.com/behnood-dianat/BELLO

Tags: amorphous, disorder, intersect, molecular-dynamics, order, software
On-surface interchain coupling and skeletal rearrangement of indenofluorene polymers

On-surface synthesis serves as a powerful approach to construct π-conjugated carbon nanostructures that are not accessible by conventional wet chemistry. Nevertheless, this method has been limited by the types and numbers of available on-surface transformations. While the majority of successful cases exploit thermally triggered dehalogenative carbon–carbon coupling and cyclodehydrogenation, rearrangement of appropriate functional moieties has received limited research attention. In a recent work, we describe the unprecedented interchain coupling and thermally induced skeleton rearrangement  of (dihydro)indeno[2,1-b]fluorene (IF) polymers on an Au(111) surface under ultrahigh vacuum conditions, leading to different ladder polymers as well as fully fused graphene nanoribbon segments containing pentagonal and heptagonal rings. Au-coordinated nanoribbons are also observed. All structures are unambiguously characterized by high-resolution scanning probe microscopy. The results provide an avenue to fabricating a wider variety of π-conjugated polymers and carbon nanostructures comprising nonhexagonal rings as well as rarely explored organometallic nanoribbons. This record contains data of the calculations that support our results.

Tags: cscs, dft, indenofluorene, marvelp4, non-contact-atomic-force-microscopy, snsf, stm
Different ordering temperature of the Mn antisite sublattice in the intrinsic magnetic topological insulators of the MnBi₂Te₄ family

Magnetic topological insulators (TIs) promise a wealth of applications in spin-based technologies, relying on the novel quantum phenomena provided by their topological properties. Particularly promising is the (MnBi₂Te₄)(Bi₂Te₃)n layered family of established intrinsic magnetic TIs that can flexibly realize various magnetic orders and topological states. High tunability of this material platform is enabled by manganese–pnictogen intermixing, whose amounts and distribution patterns are controlled by synthetic conditions. Positive implication of the strong intermixing in MnSb₂Te₄ is the interlayer exchange coupling switching from antiferromagnetic to ferromagnetic, and the increasing magnetic critical temperature. On the other side, intermixing also implies atomic disorder which may be detrimental for applications. Here we employ nuclear magnetic resonance and muon spin spectroscopy, sensitive local probe techniques, to scrutinize the impact of the intermixing on the magnetic properties of (MnBi₂Te₄)(Bi₂Te₃)n and MnSb₂Te₄. Our measurements not only confirm the opposite alignment between the Mn magnetic moments on native sites and antisites in the ground state of MnSb₂Te₄, but for the first time directly show the same alignment in (MnBi₂Te₄)(Bi₂Te₃)n with n = 0, 1 and 2. Moreover, for all compounds, we find the static magnetic moment of the Mn antisite sublattice to disappear well below the intrinsic magnetic temperature, leaving a homogeneous magnetic structure undisturbed by the intermixing. Our findings provide microscopic understanding of the crucial role played by Mn–Bi intermixing in (MnBi₂Te₄)(Bi₂Te₃)n and offer pathways to optimizing the magnetic gap in its surface states. The data contained in this archive consists of both the µSR and NMR experimental data including DFT calculations for the muon and hyperfine coupling interactions, all required to reproduce the results and figures presented in this article.

Tags: cationic-intermixing, experimental, magnetic-topological-insulator