AndreaBozzo/ceres-open-data-index huggingface dataset:
How robust is the reversible steric shielding strategy for photoswitchable organocatalysts?

A highly appealing strategy to modulate a catalyst's activity and/or selectivity in a dynamic and non-invasive way is to incorporate a photoresponsive unit into a catalytically competent molecule. However, the description of the photoinduced conformational or structural changes that alter the catalyst's intrinsic reactivity is often reduced to a handful of intuitive static representations, which can struggle to capture the complexity of flexible organocatalysts. Here, we show how a comprehensive exploration of the free energy landscape of N-alkylated azobenzene-tethered piperidine catalysts is essential to unravel the conformational characteristics of each configurational state and explain the experimentally observed reactivity trends. Mapping the catalysts' conformational space highlights the existence of false ON or OFF states that lower their switching ability. Our findings expose the challenges associated with the realisation of reversible steric shielding for the photocontrol of Brønsted basicity of piperidine photoswitchable organocatalysts.

Tags: epfl, erc, photoswitchable-organocatalysis, reversible-steric-shielding, snsf, statistical-sampling
Landau levels as a probe for band topology in graphene moiré superlattices

We propose Landau levels as a probe for the topological character of electronic bands in two-dimensional moiré superlattices. We consider two configurations of twisted double bilayer graphene (TDBG) that have very similar band structures, but show different valley Chern numbers of the flat bands. These differences between the AB-AB and AB-BA configurations of TDBG clearly manifest as different Landau level sequences in the Hofstadter butterfly spectra calculated using the tight-binding model. The Landau level sequences are explained from the point of view of the distribution of orbital magnetization in momentum space that is governed by the rotational C2 and time-reversal T symmetries. Our results can be readily extended to other twisted graphene multilayers and h-BN/graphene heterostructures thus establishing the Hofstadter butterfly spectra as a powerful tool for detecting the nontrivial valley band topology.

Tags: band-topology, landau-level, marveldd6, moire-superlattice, twisted-double-bilayer-graphene
Multicellularity of delicate topological insulators

Being Wannierizable is not the end of the story for topological insulators. We introduce a family of topological insulators that would be considered trivial in the paradigm set by the tenfold way, topological quantum chemistry, and the method of symmetry-based indicators. Despite having a symmetric, exponentially localized Wannier representation, each Wannier function cannot be completely localized to a single primitive unit cell in the bulk. Such multicellular topology is shown to be neither stable nor fragile, but delicate; i.e., the topology can be nullified by adding trivial bands to either valence or conduction band.

Tags: delicate-topology, erc, h2020, hopf-insulator, marveldd6, multicellular-wannier-functions, returning-thouless-pump, snsf, topological-insulators
Shape-controlled pathways in the hydrogen production from ethanol steam reforming over ceria nanoparticles

The ethanol surface reaction over CeO₂ nanooctahedra (NO) and nanocubes (NC), which mainly expose (111) and (100) surfaces, respectively, was studied by means of infrared spectroscopy (TPSR-IR), mass spectrometry (TPSR-MS) and density functional theory (DFT) calculations. TPSR-MS results show that the production of H₂ is 2.4 times higher on CeO₂ -NC than on -NO, which is rationalized starting from the different types of adsorbed ethoxy species controlled by the shape of the ceria particles. Over the CeO₂(111) surface, monodentate type I and II ethoxy species with the alkyl chain perpendicular or parallel to the surface, respectively, were identified. Whereas on the CeO₂(100) surface, bidentate and monodentate type III ethoxy species on the checkerboard O-terminated and on a pyramid of the reconstructed (100) surface, respectively, are found. The more labile surface ethoxy species on each ceria nanoshape, which are the monodentate type I or III ethoxy on CeO₂ -NO and -NC, respectively, react on the surface to give acetate species that decomposes to CO₂ and CH₄, while H₂ is formed via the recombination of hydroxyl species. In addition, the more stable monodentate type II and bidentate ethoxy species on CeO₂ -NO and -NC, respectively, give an ethylenedioxy intermediate the binding of which is facet dependent. On the (111) facet, the less strongly bound ethylenedioxy desorbs as ethylene, whereas on the (100) facet, the more strongly bound intermediate also produces CO₂ and H₂ via formate species. Thus, on the (100) facet an additional pathway towards H₂ formation is found. ESR activity measurements show an enhanced H₂ production on the nanocubes.

Tags: ceria-nanostructures, ethanol-decomposition, ethylenedioxy-species, facet-dependent-activity, green-hydrogen
Wigner formulation of thermal transport in solids

Two different heat-transport mechanisms are discussed in solids: in crystals, heat carriers propagate and scatter like particles, as described by Peierls' formulation of Boltzmann transport equation for phonon wavepackets; in glasses, instead, carriers behave wave-like, diffusing via a Zener-like tunneling between quasi-degenerate vibrational eigenstates, as described by the Allen-Feldman equation. Recently, it has been shown that these two conduction mechanisms emerge as limiting cases from a unified transport equation, which describes on an equal footing solids ranging from crystals to glasses; moreover, in materials with intermediate characteristics the two conduction mechanisms coexist, and it is crucial to account for both. Here, we discuss the theoretical foundations of such transport equation as is derived from the Wigner phase-space formulation of quantum mechanics, elucidating how the interplay between disorder, anharmonicity, and the quantum Bose-Einstein statistics of atomic vibrations determines thermal conductivity. This Wigner formulation argues for a preferential phase convention for the dynamical matrix in the reciprocal Bloch representation and related off-diagonal velocity operator's elements; such convention is the only one yielding a conductivity which is invariant with respect to the non-unique choice of the crystal's unit cell and is size-consistent. We rationalize the conditions determining the crossover from particle-like to wave-like heat conduction, showing that phonons below the Ioffe-Regel limit (i.e. with a mean free path shorter than the interatomic spacing) contribute to heat transport due to their wave-like capability to interfere and tunnel. Finally, we show that the present approach overcomes the failures of the Peierls-Boltzmann formulation for materials with ultralow or glass-like thermal conductivity, with case studies of materials for thermal barrier coatings and thermoelectric energy conversion. 

Here, we release the crystal structures, interatomic force constants, and computational parameters needed to reproduce the results discussed in the article "Wigner formulation of thermal transport in solids" (arXiv preprint, 2021) by M. Simoncelli, N. Marzari, and F. Mauri.

Tags: anharmonicity, phonons, thermal-conductivity, wigner-heat-transport-equation
E(3)-equivariant graph neural networks for data-efficient and accurate interatomic potentials

This work presents Neural Equivariant Interatomic Potentials (NequIP), an E(3)-equivariant neural network approach for learning interatomic potentials from ab-initio calculations for molecular dynamics simulations. While most contemporary symmetry-aware models use invariant convolutions and only act on scalars, NequIP employs E(3)-equivariant convolutions for interactions of geometric tensors, resulting in a more information-rich and faithful representation of atomic environments. The method achieves state-of-the-art accuracy on a challenging and diverse set of molecules and materials while exhibiting remarkable data efficiency. NequIP outperforms existing models with up to three orders of magnitude fewer training data, challenging the widely held belief that deep neural networks require massive training sets. The high data efficiency of the method allows for the construction of accurate potentials using high-order quantum chemical level of theory as reference and enables high-fidelity molecular dynamics simulations over long time scales.

Tags: density-functional-theory, machine-learning, molecular-dynamics
Ab initio simulation of structure and properties in Ni-based superalloys Haynes282 and Inconel740

The electronic structure, interatomic bonding, and mechanical properties of two supercell models of Ni-based super alloys are calculated by using ab initio density functional theory methods. The alloys are in the face centered cubic lattice having 864 atoms and eleven elements: Haynes282 (Ni₄₄₄Cr₂₀₂Co₇₉Al₅₆Ti₂₅Mo₂₅Fe₁₂Mn₃Si₅C₁₂B) and Inconel740 (Ni₃₇₃Cr₂₄₆Co₁₅₃Al₃₃Ti₂₁Nb₆MoFe₆
Mn₃Si₁₇C₅). These multi-component alloys have very complex electronic structure, bonding and partial charge distributions depending on the composition and strength of local bonding environment. We employ the novel concept of total bond order density (TBOD) and its partial components (PBOD) to ascertain the internal cohesion that controls the intricate balance between the propensity of metallic bonding between Ni, Cr and Co, and the strong bonds with C and Al. We find Inconel740 has slightly stronger mechanical properties than Haynes282. Comparison with more conventional high entropy alloys with equal components are discussed.

Tags: effective-charge, haynes282, inconel740
Discovery of Ĉ₂ rotation anomaly in topological crystalline insulator SrPb

Topological crystalline insulators (TCIs) are insulating electronic states with nontrivial topology protected by crystalline symmetries. Recently, theory has proposed new classes of TCIs protected by rotation symmetries Ĉ_n, which have surface rotation anomaly evading the fermion doubling theorem, i.e., n instead of 2n Dirac cones on the surface preserving the rotation symmetry. Here, we report the first realization of the Ĉ_2 rotation anomaly in a binary compound SrPb. Our first-principles calculations reveal two massless Dirac fermions protected by the combination of time-reversal symmetry T̂ and Ĉ_2y on the (010) surface. Using angle-resolved photoemission spectroscopy, we identify two Dirac surface states inside the bulk band gap of SrPb, confirming the Ĉ_2 rotation anomaly in the new classes of TCIs. The findings enrich the classification of topological phases, which pave the way for exploring exotic behavior of the new classes of TCIs.

Tags: electronic-structure, marveldd6, snsf, topological-materials
Equivariant representations for molecular Hamiltonians

The application of machine learning to the modeling of materials and molecules has proven to be extremely successful in accelerating the understanding, design, and characterization of materials. A major factor in this success has been the development of representations of atomic structures that reflect physics-based symmetries of the underlying interactions. Most of the descriptions of atomic properties or even global observables rely on decompositions into atomic contributions that are subsequently learnt in an atom-centered framework. However, many quantities associated with quantum mechanical calculations, such as the single-particle Hamiltonian matrices written in an atomic-orbital basis, are associated with multiple atom-centers. 
Following the introduction of equivariant N-center structural descriptors, in the reference below, that generalize the very successful atom-centered density correlation features to the problem of learning properties indexed by N atoms, we present benchmarks showing how the construction can be applied to efficiently learn the matrix elements of the (effective) single-particle Hamiltonian in an atom-centered orbital basis. 
In this record, we include the dataset comprising the Fock and overlap matrices in the def2-SVP of 1000 distorted water molecules, up to 4500 ethanol structures, and a subset of QM7-CHNO molecules. We also provide scripts to generate the two-center representations and fit linear and sparse kernel models for the Hamiltonians.

Tags: epfl, equivariant-representations, erc, h2020, hamiltonian-learning, machine-learning-hamiltonians, marvel, n-center-representations
Recursive quality optimization of a smart forming tool under use of perception based hybrid datasets for training of a deep neural network

In industrial metal forming processes, the generation of datasets for inline and optical quality assessment is expensive and time-consuming. Within the research project SimKI, conventional metal forming plants were digitalized under use of perception-based sensors in combination with a completely redesigned forming tool. The integration of optical quality observation methods connected with a retrofitting approach of the press tool provides the opportunity to generate an information-feedback loop that predicts part defects prior to their occurrence. The SimKI-method additionally combines conventional statistical measurement methods with AI-based defect detection algorithms that are trained by a) generic datasets of a finite-element simulation, b) real component images of a 3D imaging device, and c) a combination of both. The generated datasets are used to accelerate the training of a DNN-based algorithm in order to identify the position and deviation from the agreed quality. The high degree of innovation is based on obtaining real-time component quality information under use of AI-based optical quality assessment, which in turn provides information to the control algorithm of the smart forming tool.

Tags: artificial-intelligence, defect-detection, gocator
Theory of spontaneous grain boundary roughening in high entropy alloys

High Entropy Alloys (HEAs) are a new broad class of near-random solid solution alloys that can possess some impressive mechanical and physical properties including high stability against grain growth (i.e. low grain boundary (GB) mobility). Here, it is shown that an initially flat GB in an HEA can become spontaneously rough, driven by natural local compositional fluctuations. Roughening lowers the total GB energy and thus can inhibit migration. A parameter-free theoretical framework is developed to demonstrate the energetics and size scales of the roughening in terms of solute/GB interaction energies and GB disconnection energies. Above a critical level of solute/GB interactions, a planar GB is predicted to roughen down to the scale of the GB periodic unit. A similar theory for 1D GBs (minimum periodic length in one direction) is also developed since such geometries are common in atomistic simulations. Specific predictions are made for the symmetric tilt boundaries Σ17 [100] (530) and Σ5 [100] (310) in a model CoCuFeNi alloy and atomistic simulations demonstrate roughening consistent with the theory. Analysis of the stresses needed to drive migration shows how migration can be inhibited or enhanced, rationalizing variations in mobility of GBs in HEAs.

Tags: grain-boundaries, high-entropy-alloys, pinning, spontaneous-roughening
On-surface polyarylene synthesis by cycloaromatization of isopropyl substituents

In this record we provide the data to support our recent finding on surface catalyzed cycloaromatization. Immobilization of organic building blocks on metal surfaces and their coupling via thermally induced C-C bond formations are developing as an important addition to the toolbox of organic and polymer synthesis. Additional advantages of this technique are the in situ monitoring of the reaction by scanning probe methods and the accessibility of insoluble and reactive carbon nanostructures. The diversity of conceivable products, however, sensitively depends on the number of available on-surface reactions. In the manuscript where the results are discussed, we introduce an unprecedented example, the intermolecular oxidative coupling of isopropyl substituents of arenes. With a new phenylene ring being formed, this [3+3] dimerization can be regarded as a formal cycloaromatization. The synthetic value of this novel reaction is proven by the synthesis of polyarylenes and co-polyarylenes, which we demonstrate by synthesizing poly(2,7-pyrenylene-1,4-phenylene). Scanning tunneling microscopy and non-contact atomic force microscopy studies complemented by density functional theory calculations are employed to obtain mechanistic insights into the title reaction.

Tags: ab-initio, catalysis, marveldd3, on-surface-synthesis, snsf
Many-body screening effects in liquid water

The screening arising from many-body excitations is a crucial quantity for describing ab-sorption and inelastic X-ray scattering (IXS) of materials. Similarly, the electron screening plays a critical role in state-of-the-art approaches for determining the fundamental band gap. However, ab initio studies of the screening in liquid water have remained limited. Here, we use a combined analysis based on the Bethe-Salpeter equation and time-dependent density functional theory. We first show that absorption spectra at near-edge energies are insufficient to assess the accuracy by which the screening is described. Next, when the energy range under scrutiny is extended, we instead find that the IXS spectra are highly sensitive and allow for the selection of the optimal theoretical scheme. This leads to good agreement with experiment over a large range of transferred energies and momenta, and enables establishing the elusive fundamental band gap of liquid water at 9.3 eV.

Tags: dft, epfl, mbpt, snsf, water
Vibrational frequencies of CO bound to all three low-index cerium oxide surfaces: a consistent theoretical description of vacancy-induced changes using density functional theory

The facet-dependent adsorption of CO on oxidized and reduced CeO₂ single crystal surfaces is reviewed, with emphasis on the effect of CO coverage and the ability of state-of-the-art quantum-mechanical methods to provide reliable energies and an accurate description of the IR vibrational frequency of CO. Comparison with detailed, high-resolution experimental IRRAS data performed on single crystal samples allows the assignment of the different CO vibrational bands observed on all three low-index ceria surfaces. Good agreement is achieved with the hybrid DFT approach with the HSE06 functional and with saturation coverage. It is shown that CO is very sensitive to the structure of cerium oxide surfaces and to the presence of oxygen vacancies. The combined theoretical-experimental approach offers new opportunities for a better characterization of ceria nanoparticles and for unraveling changes occurring during reactions involving CO at higher pressures.

Tags: ceo2111-110-100, co-vibrational-frequency, dft-hse06-and-pbe, oxidized-and-reduced-ceria
Photochemical anisotropy and direction-dependent optical absorption properties in semiconductors

Photochemical reactions on semiconductors are anisotropic, since they occur with different rates on surfaces of different orientation. Understanding the origin of this anisotropy is crucial to engineering more efficient photocatalysts. In this work, we use hybrid density functional theory (DFT) to identify the surfaces associated with the largest number of photo-generated carriers in different semiconductors. For each material we create a spherical heat map of the probability of optical transitions at different wave vectors. These maps allow to identify the directions associated with the majority of the photo-generated carriers and can thus be used to make predictions about the most reactive surfaces for photochemical applications. Results indicate that it is generally possible to correlate the heat maps with the anisotropy of the bands observed in conventional band-structure plots, as previously suggested. However, we also demonstrate that conventional bands-structure plots do not always provide all the informations and that taking into account the contribution of all possible transitions weighted by their transition dipole moments is crucial to obtain a complete picture.

Tags: anisotropy, cscs, dft, hybrid-functionals, marveldd5, optical-properties, photocatalysis, photochemistry, semiconductors, snsf
Temperature- and vacancy-concentration-dependence of heat transport in Li₃ClO from multi-method numerical simulations

Despite governing heat management in any realistic device, the microscopic mechanisms of heat transport in all-solid-state electrolytes are poorly known: existing calculations, all based on simplistic semi-empirical models, are unreliable for superionic conductors and largely overestimate their thermal conductivity. In this work, we deploy a combination of state-of-the-art methods to calculate the thermal conductivity of a prototypical Li-ion conductor, the Li₃ClO antiperovskite. By leveraging ab initio, machine learning, and forcefield descriptions of interatomic forces, we are able to reveal the massive role of anharmonic interactions and diffusive defects on the thermal conductivity and its temperature dependence, and to eventually embed their effects into a simple rationale which is likely applicable to a wide class of ionic conductors.
In this record, we provide data and scripts to generate the plots supporting our findings. We also provide the machine learning model and the dataset to train it.

Tags: batteries, heat-transport, max, snsf, solid-state-electrolytes, superionics
Maximum volume simplex method for automatic selection and classification of atomic environments and environment descriptor compression

Fingerprint distances, which measure the similarity of atomic environments, are commonly calculated from atomic environment fingerprint vectors. In this work, we present the simplex method that can perform the inverse operation, i.e., calculating fingerprint vectors from fingerprint distances. The fingerprint vectors found in this way point to the corners of a simplex. For a large dataset of fingerprints, we can find a particular largest simplex, whose dimension gives the effective dimension of the fingerprint vector space. We show that the corners of this simplex correspond to landmark environments that can be used in a fully automatic way to analyze structures. In this way, we can, for instance, detect atoms in grain boundaries or on edges of carbon flakes without any human input about the expected environment. By projecting fingerprints on the largest simplex, we can also obtain fingerprint vectors that are considerably shorter than the original ones but whose information content is not significantly reduced.

Tags: atomic-environment-selection, atomic-fingerprints, classification-of-atomic-environments, dimensionality-reduction, largest-volume-simplex, machine-learning, overlap-matrix-fingerprint, quantum-non-local-effects
ML-ready Curie temperatures and descriptors extracted from the JuHemd database

The uploaded archive provides a ML-ready data set extracted from the juHemd database (see references) augmented with supplemental data for atomic descriptors. Descriptors provided in this data set include structural, magnetic, atomic quantities as well as derived (summed) quantities. In total, 118 possible descriptors are included of which 12 are DFT generated. For each simulation type (LDA/GGA) there is also a data set cleaned from DFT data available. 

After data cleaning and preprocessing we extracted 387 LDA calculated magnetic Heusler structures as well as 408 GGA structures which have a full structural and magnetic data set. As we only aim at magnetic compounds, we chose to filter out compounds from the original JuHemd which have at least 0.1 Bohr magneton as total absolute magnetic moment. For each data file there is an existing descriptor file naming all the descriptors included in the data set.

Tags: critical-temperature, curie-temperature, density-functional-theory, electronic-structure, heusler-alloy, judft, kkr, machine-learning, magnetic, magnetic-phase-transition, magnetic-structure, max, monte-carlo