AndreaBozzo/ceres-open-data-index huggingface dataset:
Optimizing accuracy and efficacy in data-driven materials discovery for the solar production of hydrogen

The production of hydrogen fuels, via water splitting, is of practical relevance for meeting global energy needs and mitigating the environmental consequences of fossil-fuel-based transportation. Water photoelectrolysis has been proposed as a viable approach for generating hydrogen, provided that stable and inexpensive photocatalysts with conversion efficiencies over 10% can be discovered, synthesized at scale, and successfully deployed (Pinaud et al., Energy Environ. Sci., 2013, 6, 1983). While a number of first-principles studies have focused on the data-driven discovery of photocatalysts, in the absence of systematic experimental validation, the success rate of these predictions may be limited. We address this problem by developing a screening procedure with co-validation between experiment and theory to expedite the synthesis, characterization, and testing of the computationally predicted, most desirable materials. Starting with 70150 compounds in the Materials Project database, the proposed protocol yielded 71 candidate photocatalysts, 11 of which were synthesized as single-phase materials. Experiments confirmed hydrogen generation and favorable band alignment for 6 of the 11 compounds, with the most promising ones belonging to the families of alkali and alkaline-earth indates and orthoplumbates. This study shows the accuracy of a nonempirical, Hubbard-corrected density-functional theory method to predict band gaps and band offsets at a fraction of the computational cost of hybrid functionals, and outlines an effective strategy to identify photocatalysts for solar hydrogen generation.

Tags: density-functional-theory, dftu, h2020, high-throughput-screening, marvel, photocatalysis, snsf, water-splitting
Ab initio real-time quantum dynamics of charge carriers in momentum space

Application of the nonadiabatic molecular dynamics (NAMD) approach is severely limited to studying carrier dynamics in the momentum space, since a supercell is required to sample the phonon excitation and electron-phonon (e-ph) interaction at different momenta in a molecular dynamics simulation. Here, we develop an ab initio approach for the real-time quantum dynamics for charge carriers in the momentum space (NAMD_k) by directly introducing the e-ph coupling into the Hamiltonian based on the harmonic approximation. The NAMD_k approach maintains the quantum zero-point energy and proper phonon dispersion, and includes memory effects of phonon excitation. The application of NAMD_k to the hot carrier dynamics in graphene reveals the phonon-specific relaxation mechanism. An energy threshold of 0.2eV, defined by two optical phonon modes strongly coupled to the electrons, separates the hot electron relaxation into fast and slow regions with the lifetimes of pico- and nano-seconds, respectively. The NAMD_k approach provides a powerful tool to understand real-time carrier dynamics in the momentum space for different materials.

Tags: electron-phonon-coupling, first-principles, nonadiabatic-molecular-dynamics
Regioselective 3-O-Substitution of Unprotected Thiodigalactosides: Direct Route to Galectin Inhibitors

Regioselective derivatization of oligosaccharides is a challenging issue in carbohydrate chemistry. A commonly required series of (de)protection steps substantially lowers synthetic yields and increases time demands. We present here a regioselective one-step introduction of benzylic substituents at 3-hydroxy moieties of beta-D-galactopyranosyl-(1<->1)-thio-beta-D-galactopyranoside (TDG) employing tin butyl oxide in fair isolated yields. These glycomimetics act as inhibitors of galectins - human lectins, which are biomedically attractive targets for therapeutic inhibition. The affinity of prepared glycomimetics to recombinant galectin-1 and galectin-3 was studied in ELISA-type assay and their inhibitory potential was also demonstrated on the surface of a model HEK293 cell line. The results of biological experiments were correlated with data from molecular modelling with both galectins. The present work reveals a facile and elegant synthetic route for the preparation of glycomimetics that exhibit differing selectivity and affinity to various galectins depending on the choice of 3-O-substitution.
In order to rationalize structure-activity relationships of tested ligands we carried out a series of molecular dynamics simulations and quantum chemical calculations. We present input and output files for quantum chemical geometry optimizations and calculations of interactions energies. These calculations were carried out in Gaussian 09 package. These results can be visualized using Molden, Molekel or other programs.
Molecular dynamics simulations were carried out using Gromacs 5.1.3 package. Initial structures of production simulations and trajectories (without water) are presented. The results can be visualized by VMD or other structure visualization packages with a support for trajectory input.

Tags: galectin, glycobiology, molecular-dynamics-simulation
Second-harmonic generation tensors from high-throughput density-functional perturbation theory

Optical materials play a key role in enabling modern optoelectronic technologies in a wide variety of domains such as the medical or the energy sector. Among them, nonlinear optical crystals are of primary importance to achieve a broader range of electromagnetic waves in the devices. However, numerous and contradicting requirements significantly limit the discovery of new potential candidates, which, in turn, hinders the technological development. In the present work, the static nonlinear susceptibility and dielectric tensor are computed via density functional perturbation theory for a set of 579 inorganic semiconductors. The aim of this work is to provide a relevant dataset to foster the identification of promising nonlinear optical crystals in order to motivate their subsequent experimental investigation.

Tags: density-functional-perturbation-theory, first-principles, high-throughput, non-linear-optics, second-harmonic-generation
Multithermal-multibaric molecular simulations from a variational principle

We present a method for performing multithermal-multibaric molecular dynamics simulations that sample entire regions of the temperature-pressure (TP) phase diagram. The method uses a variational principle [Valsson and Parrinello, Phys. Rev. Lett. 113, 090601 (2014)] in order to construct a bias that leads to a uniform sampling in energy and volume. The intervals of temperature and pressure are taken as inputs and the relevant energy and volume regions are determined on the fly. In this way the method guarantees adequate statistics for the chosen TP region. We show that our multithermal-multibaric simulations can be used to calculate all static physical quantities for all temperatures and pressures in the targeted region of the TP plane. We illustrate our approach by studying the density anomaly of TIP4P/Ice water.

This record includes input and output files, and Jupyter Notebooks describing the analysis of the simulations and the creation of the figures for the paper.

Tags: density-anomaly, enhanced-sampling, multicanonical, multithermal-multibaric, wang-landau, water
Änderung des Jagdgesetzes

Schlussresultate der eidgenössischen Abstimmung "Änderung des Jagdgesetzes", 27. September 2020, Graubünden - Grischun - Grigioni, aufgeschlüsselt nach Gemeinden.

Tags: abstimmung, federal, national, nazionale, plaun-naziunal, votation, votazione, votaziun
High-throughput computational screening for solid-state Li-ion conductors

We present a computational screening of experimental structural repositories for fast Li-ion conductors, with the goal of finding new candidate materials for application as solid-state electrolytes in next-generation batteries. We start from ~1400 unique Li-containing materials, of which ~900 are insulators at the level of density-functional theory. For those, we calculate the diffusion coefficient in a highly automated fashion, using extensive molecular dynamics simulations on a potential energy surface (the recently published pinball model) fitted on first-principles forces. The ~130 most promising candidates are studied with full first-principles molecular dynamics, first at high temperature and then more extensively for the 78 most promising candidates. The results of the first-principles simulations of the candidate solid-state electrolytes found are discussed in detail.

Update April 2024:
Files are added that facilitate the Materials Cloud Archive OPTIMADE service to serve the structural data of this Archive entry via an OPTIMADE API. The molecular dynamics trajectories are served as individual structures per time-step.

Tags: big-map, computational-high-throughput-screening, first-principles-molecular-dynamics, li-ion-conductors, marvelinc1, solid-state-electrolytes
The solid-state Li-ion conductor Li7TaO6: A combined computational and experimental study

We study the oxo-hexametallate Li7TaO6 with first-principles and classical molecular dynamics simulations, obtaining a low activation barrier for diffusion of ∼0.29 eV and a high ionic conductivity of 5.7×10−4 S cm−1 at room temperature (300 K). We find evidence for a wide electrochemical stability window from both calculations and experiments, suggesting its viable use as a solid-state electrolyte in next-generation solid-state Li-ion batteries. To assess its applicability in an electrochemical energy storage system, we performed electrochemical impedance spectroscopy measurements on multicrystalline pellets, finding substantial ionic conductivity, if below the values predicted from simulation. We further elucidate the relationship between synthesis conditions and the observed ionic conductivity using X-ray diffraction, inductively coupled plasma optical emission spectrometry, and X-ray photoelectron spectroscopy, and study the effects of Zr and Mo doping.

Tags: big-map, density-functional-theory, electrochemical-stability, li-ion-batteries, marvelinc1, molecular-dynamics, polarizable-force-fields, solid-state-electrolyte
Pure Magnesium DFT calculations for interatomic potential fitting

This dataset provides DFT (density functional theory as implemented in VASP, Vienna Ab Initio Simulation Package) calculations for pure Magnesium. It was designed by Binglun Yin, Markus Stricker and William A. Curtin for fitting a neural network potential with Behler-Parrinello symmetry functions. Binglun Yin carried out the calculation.

Tags: decohesion, dft, elasticity, magnesium, marveldd2, metallurgy, stacking-faults, surfaces
Emergence of hidden phases of methylammonium lead-iodide (CH3NH3PbI) upon compression

We perform a thorough structural search with the minima hopping method (MHM) to explore low-energy structures of methylammonium lead iodide. By combining the MHM with a forcefield, we efficiently screen vast portions of the configurational space with large simulation cells containing up to 96 atoms. Our search reveals two structures of methylammonium iodide perovskite (MAPI) that are substantially lower in energy than the well-studied experimentally observed low-temperature orthorhombic phase. The data set containing approximately ~180,000 crystal structures is provided.

Tags: force-field-gulp, mapi-perovskites, minima-hopping-method, structure-prediction, vasp-scan--functional
Pure Magnesium DFT calculations for interatomic potential fitting

This dataset provides DFT (density functional theory as implemented in VASP, Vienna Ab Initio Simulation Package) calculations for pure Magnesium. It was designed by Binglun Yin, Markus Stricker and William A. Curtin for fitting a neural network potential with Behler-Parrinello symmetry functions. Binglun Yin carried out the calculation.

It corresponds to a dataset that is commonly used to fit interatomic potentials for mechanics applications and includes structure-energy relationships for structures used to calculate:
1. Bulk properties
2. Generalized stacking fault energies
3. Decohesion and relaxed surfaces
4. Dimer
5. Corner and rod geometries
6. Vacancy formation energy

Tags: decohesion, dft, elasticity, epfl, magnesium, marveldd2, metallurgy, snsf, stacking-faults, surfaces
Making the best of a bad situation: a multiscale approach to free energy calculation

Many enhanced sampling techniques rely on the identification of a number of collective variables that describe all the slow modes of the system. By constructing a bias potential in this reduced space one is then able to sample efficiently and reconstruct the free energy landscape. In methods like metadynamics, the quality of these collective variables plays a key role in convergence efficiency. Unfortunately in many systems of interest it is not possible to identify an optimal collective variable, and one must deal with the non-ideal situation of a system in which some slow modes are not accelerated. 
We propose a two-step approach in which, by taking into account the residual multiscale nature of the problem, one is able to significantly speed up convergence. To do so, we combine an exploratory metadynamics run with an optimization of the free energy difference between metastable states, based on the recently proposed variationally enhanced sampling method. This new method is well parallelizable and is especially suited for complex systems, because of its simplicity and clear underlying physical picture.

Tags: enhanced-sampling, free-energy, marveldd1, metadynamics
Stress-dependence of generalized stacking fault energies: a DFT study

Generalized stacking fault energy (GSFE) is a crucial material property for describing nanoscale plasticity in crystalline materials, such as dislocation dissociation, nucleation, and twinning. The dependence of the GSFE on applied stress normal to the stacking fault (SF) plane has been suggested to influence such phenomena. Here, the SF stress dependence is analyzed through (i) the generalized stacking fault potential energy (GSFE) and (ii) the generalized stacking fault enthalpy (GSFH). Our DFT calculations reveal that the GSFE is almost independent of the applied normal stress, which contradicts the long-standing wisdom and previous studies. We also reveal the inelastic inter-planar normal displacement associated with the SF. The coupling between the positive inelastic normal displacement and the applied normal stress decreases the GSFH.

Tags: erc, generalized-stacking-fault-energy, inelastic-displacement-of-stacking-fault, marveldd2, stacking-fault-stress-dependence
High-throughput screening of 2D materials identifies p-type monolayer WS2 as potential ultra-high mobility semiconductor

2D semiconductors are considered as a promising alternative to silicon for future electronics. This class of materials possesses different advantages including atomically sharp surfaces and the ability to scale channel thickness down to a single layer. However, they typically exhibit lower charge carrier mobility as well as higher contact resistance compared to 3D semiconductors, which deters the development of high-performance devices at scale. In this work, we searched for high-mobility 2D materials by combining high-throughput screening approach and advanced transport calculations based on the ab initio Boltzmann transport equation. Based on our calculations, we identified several promising candidates channel materials, and in particular monolayer WS₂ which exhibits a phonon-limited hole mobility in excess of 1300 cm²/Vs. Our work suggests that WS₂ can be ideal for channel of high-performance 2D transistors with Ohmic contacts and low defect density. This work has been published in [npj Comput. Mater. 10, 229 (2024)].

Tags: 2d-materials, ab-initio-boltzmann-transport-equation, high-throughput-computing
Nonempirical hybrid functionals for band gaps of inorganic metal-halide perovskites

Nonempirical hybrid functionals are investigated for band-gap predictions of inorganic metal-halide perovskites belonging to the class CsBX3 , with B = Ge, Sn, Pb and X = Cl, Br, I. We consider both global and range-separated hybrid functionals and determine the parameters through two different schemes. The first scheme is based on the static screening response of the material and thus yields dielectric-dependent hybrid functionals. The second scheme defines the hybrid functionals through the enforcement of Koopmans' condition for localized defect states. We also carry out quasiparticle self-consistent GW calculations with vertex corrections to establish state-of-the-art references. For the investigated class of materials, dielectric-dependent functionals and those fulfilling Koopmans' condition yield band gaps of comparable accuracy (∼0.2 eV), but the former only require calculations for the primitive unit cell and are less subject to the specifics of the material.

Tags: band-gaps, epfl, nonempirical-hybrid-functionals, perovskites, snsf
Design rules for interconnects based on graphene nanoribbon junctions

Graphene nanoribbons (GNRs) produced by means of bottom-up chemical self-assembly are considered promising candidates for the next-generation nanoelectronic devices. We address the electronic transport properties of angled two-terminal GNR junctions, which are inevitable in the interconnects in graphene-based integrated circuits. We construct a library of over 400000 distinct configurations of 60° and 120° junctions connecting armchair GNRs of different widths. Numerical calculations combining the tight-binding approximation and the Green's function formalism allow identifying numerous junctions with conductance close to the limit defined by the GNR leads. Further analysis reveals underlying structure-property relationships with crucial roles played by the bipartite symmetry of graphene lattice and the presence of resonant states localized at the junction. In particular, we discover and explain the phenomenon of binary conductance in 120° junctions connecting metallic GNR leads that guarantee maximum possible conductance. Overall, our study defines the guidelines for engineering GNR junctions with desired electrical properties.

Tags: electronic-transport, gnr, graphene, junctions, nanoribbon, snsf
Tailoring Bond Topologies in Open-Shell Graphene Nanostructures

The data contained in this record, raw data of images and input files to reproduce calculations, support our recent report for the on-surface synthesis and characterization of two ultralow-gap open-shell molecules, namely peri-tetracene, a benzenoid graphene fragment with zigzag edge topology, and dibenzo[a,m]dicyclohepta[bcde,nopq]rubicene, a nonbenzenoid nonalternant structural isomer of peri-tetracene with two embedded azulene units. Our results provide an understanding of the ramifications of altered bond topologies at the single-molecule scale, with the prospect of designing functionalities in carbon-based nanostructures via engineering of bond topology

Tags: atom-manipulation, density-functional-theory, marveldd3, nonalternant-polycyclic-aromatic-hydrocarbons, open-shell-polycyclic-aromatic-hydrocarbons, scanning-tunneling-microscopy, scanning-tunneling-spectroscopy
Volksinitiative «Für verantwortungsvolle Unternehmen – zum Schutz von Mensch und Umwelt»

Schlussresultate der eidgenössischen Abstimmung "Volksinitiative «Für verantwortungsvolle Unternehmen – zum Schutz von Mensch und Umwelt»", 29. November 2020, Graubünden - Grischun - Grigioni, aufgeschlüsselt nach Gemeinden.

Tags: abstimmung, federal, national, nazionale, plaun-naziunal, votation, votazione, votaziun
Volksinitiative «Für ein Verbot der Finanzierung von Kriegsmaterialproduzenten»

Schlussresultate der eidgenössischen Abstimmung "Volksinitiative «Für ein Verbot der Finanzierung von Kriegsmaterialproduzenten»", 29. November 2020, Graubünden - Grischun - Grigioni, aufgeschlüsselt nach Gemeinden.

Tags: abstimmung, federal, national, nazionale, plaun-naziunal, votation, votazione, votaziun
Determining interface structures in vertically aligned nanocomposite films

Vertically aligned nanocomposites (VANs) films have self-assembled pillar-matrix nanostructures. Owing to their large area-to-volume ratios,  interfaces in VAN films are expected to play key roles in inducing functional properties, but our understanding is hindered by limited knowledge about their structures. Motivated by the lack of definitive explanation for the experimentally-found enhanced ionic conductivity in Sm-doped-CeO2/SrTiO3 VAN films, we determine the structure at vertical interfaces using random structure searching and explore how it can affect ionic conduction. This record contains the candidate structures and provenance of the DFT validation calculations. Previously unknown interface structures are found, with lower energy than that of an optimized hand-built model. We find a strongly distorted oxygen sub-lattice which gives a complex landscape of vacancy energies. The cation lattice remains similar to the bulk phase but has a localized strain field. The excess energy of the interface is similar to that of high angle grain boundaries in SrTiO3.

Tags: density-functional-theory, solid-solid-interface, structure-prediction
Surface reconstructions and premelting of the (100) CaF2 surface

In this work, surface reconstructions on the (100) surface of CaF2 are comprehensively investigated. The configurations were explored by employing the Minima Hopping Method (MHM) coupled to a machine-learning interatomic potential, that is based on a charge equilibration scheme steered by a neural network (CENT). The combination of these powerful methods revealed about 80 different morphologies for the (100) surface with very similar surface formation energies differing by not more than 0.3 J m−2. To take into account the effect of temperature on the dynamics of this surface as well as to study the solid–liquid transformation, molecular dynamics simulations were carried out in the canonical (NVT) ensemble. By analyzing the atomic mean-square displacements (MSD) of the surface layer in the temperature range of 300–1200 K, it was found that in the surface region the F sublattice is less stable and more diffusive than the Ca sublattice. Based on these results we demonstrate that not only a bulk system, but also a surface can exhibit a sublattice premelting that leads to superionicity. Both the surface sublattice premelting and surface premelting occur at temperatures considerably lower than the bulk values. The complex behaviour of the (100) surface is contrasted with the simpler behavior of other low index crystallographic surfaces.

Tags: charge-equilibration-scheme, machine-learning, marvel, marveldd1, minima-hopping, snsf, surface-reconstructions
Data-Driven Collective Variables for Enhanced Sampling

Designing an appropriate set of collective variables is crucial to the success of several enhanced sampling methods. Here we focus on how to obtain such variables from information limited to the metastable states. We characterize these states by a large set of descriptors and employ neural networks to compress this information in a lower-dimensional space, using Fisher's linear discriminant as an objective function to maximize the discriminative power of the network. We test this method on alanine dipeptide, using the non-linearly separable dataset composed by atomic distances. We then study an intermolecular aldol reaction characterized by a concerted mechanism. The resulting variables are able to promote sampling by drawing non-linear paths in the physical space connecting the fluctuations between metastable basins. Lastly, we interpret the behavior of the neural network by studying its relation to the physical variables. Through the identification of its most relevant features, we are able to gain chemical insight into the process.

Tags: collective-variables, enhanced-sampling, erc, marveldd1, metadynamics, neural-networks, opes, plumed