AndreaBozzo/ceres-open-data-index huggingface dataset:
High-throughput computational screening of nanoporous adsorbents for CO 2 capture from natural gas

With the growth of natural gas as an energy source, upgrading CO2-contaminated supplies has become increasingly important. Here we develop a single metric that captures how well an adsorbent performs the separation of CH4 and CO2, and we then use this metric to computationally screen tens of thousands of all-silica zeolites. We show that the most important predictors of separation performance are the CO2 heat of adsorption (Qst, CO2) and the CO2 saturation loading capacity. We find that a higher-performing material results when the absolute value of the CH4 heat of adsorption (Qst, CH4) is decreased independently of Qst, CO2, but a correlation that exists between Qst, CH4 and Qst, CO2 in all-silica zeolites leads to incongruity between the objectives of optimizing Qst, CO2 and minimizing Qst, CH4, rendering Qst, CH4 nonpredictive of separation performance. We also conduct a large-scale analysis of ideal adsorbed solution theory (IAST) by comparing results obtained using directly-generated mixture isotherms to those obtained using IAST; IAST appears adequate for the purposes of establishing performance trends and structure–property relationships in a high-throughput manner, but it must be tested for validity when analyzing individual adsorbents in detail since it can produce significant errors for materials in which there is site segregation of the adsorbate species.

Tags: 3d, database, dc, deliverable-capacities, gcmc, grand-canonical-monte-carlo, high-throughput, iza, methane-storage, nanoporous, porous-polymer-networks, three-dimensional, zeolites
A Standard Solid State Pseudopotentials (SSSP) library optimized for precision and efficiency

Despite the enormous success and popularity of density functional theory, systematic verification and validation studies are still very limited both in number and scope. Here, we propose a universal standard protocol to verify publicly available pseudopotential libraries, based on several independent criteria including verification against all-electron equations of state and plane-wave convergence tests for phonon frequencies, band structure, cohesive energy and pressure. Adopting these criteria we obtain two optimal pseudopotential sets, namely the Standard Solid State Pseudopotential (SSSP) efficiency and precision libraries, tailored for high-throughput materials screening and high-precision materials modelling. As of today, the SSSP precision library is the most accurate open-source pseudopotential library available. This archive entry contains the database of calculations (phonons, cohesive energy, equation of state, band structure, pressure, etc.) together with the provenance of all data and calculations as stored by AiiDA.

*** UPDATE April 2020 *** 
The zipped tarball archives and AiiDA export files had inconsistent internal formats and naming conventions, which made it difficult to work with them programmatically. In this update, the files are standardized according to the conventions that are detailed in the README.md file. Note that the actual content of pseudo potential files and the JSON metadata files has **not** changed, with the exception that the keys "cutoff" and "dual" in the JSON files have been replaced with "cutoff_wfc" and "cutoff_rho". Here the value of "cutoff_wfc" is equal to the old "cutoff", and "cutoff_rho" is equal to the product of the old "cutoff" and "dual". Besides that, the update concerns merely the renaming of certain files and the restructuring of archive formats.

*** UPDATE November 2020 *** 
The AiiDA export files contained in the sssp.tar archive have been modified and migrated to version format 0.9 in order to be imported in AiiDA 1.2.0 and later versions. The modifications are detailed in the README.md file in the sssp.tar archive.
The AiiDA export files contained in the sssp_bands.tar archive have been migrated to version format 0.9 as well.

Tags: calculations, chessboards, cohesive-energy, cscs, database, dft, efficiency, electronic-bands, electronic-properties, elemental-solids, high-throughput, library, marvel, max, phonons, prace, precision, pseudopotentials, sssp, standard, verification, vibrational-properties
Spin fluctuation induced Weyl semimetal state in the paramagnetic phase of EuCd2As2

This record mainly upload all the raw experimental data related to the manuscript. Fig1 include the transport data, magnetotransport data, AHE data, ESR data, uSR data. These data related to the conclusion that spin fluctuation established in the paramagnetic phase. Fig2 contains in-plane and out-of-plane 3D photoemission spectra, and high resolution cuts on top and side surface. Fig3 contains band electronic structure along high symmetry lines with spin along all kinds of typical directions. Fig4 contains 3-D in-plane and out-of-plane Fermi surfaces on the 101 cleavage, high resolution cuts, STM/STS data. The proved the observation of Weyl points.

Tags: arpes, magnetic-material, magnetic-weyl-semimetal, marveldd6, spin-fluctuation, topological-material
A Standard Solid State Pseudopotentials (SSSP) library optimized for precision and efficiency (Version 1.0, data download)

Despite the enormous success and popularity of density functional theory, systematic verification and validation studies are still very limited both in number and scope. Here, we propose a universal standard protocol to verify publicly available pseudopotential libraries, based on several independent criteria including verification against all-electron equations of state and plane-wave convergence tests for phonon frequencies, band structure, cohesive energy and pressure. Adopting these criteria we obtain two optimal pseudopotential sets, namely the Standard Solid State Pseudopotential (SSSP) efficiency and precision libraries, tailored for high-throughput materials screening and high-precision materials modelling. As of today, the SSSP precision library is the most accurate open-source pseudopotential library available. This archive entry contains the database of calculations (phonons, cohesive energy, equation of state, band structure, pressure, etc.) together with the provenance of all data and calculations as stored by AiiDA.

Tags: calculations, chessboards, cohesive-energy, database, dft, efficiency, electronic-bands, electronic-properties, elemental-solids, high-throughput, library, marvel, phonons, precision, pseudopotentials, sssp, standard, verification, vibrational-properties
Coupled-Cluster Polarizabilities in the QM7b and a Showcase Database

Dipole polarizabilities, computed using linear response coupled cluster theory and density functional theory (using d-aug-cc-pVDZ basis set), for 7211 molecules from the QM7b dataset of small molecules and for 52 molecules from a showcase dataset.

Tags: density-functional-theory, dipole-polarizability, linear-response-coupled-cluster
Mail-order metal-organic frameworks (MOFs): designing isoreticular MOF-5 analogues comprising commercially available organic molecules

Metal–organic frameworks (MOFs), a class of porous materials, are of particular interest in gas storage and separation applications due largely to their high internal surface areas and tunable structures. MOF-5 is perhaps the archetypal MOF; in particular, many isoreticular analogues of MOF-5 have been synthesized, comprising alternative dicarboxylic acid ligands. In this contribution we introduce a new set of hypothesized MOF-5 analogues, constructed from commercially available organic molecules. We describe our automated procedure for hypothetical MOF design, comprising selection of appropriate ligands, construction of 3D structure models, and structure relaxation methods. 116 MOF-5 analogues were designed and characterized in terms of geometric properties and simulated methane uptake at conditions relevant to vehicular storage applications. A strength of the presented approach is that all of the hypothesized MOFs are designed to be synthesizable utilizing ligands purchasable online.

Tags: 3d, database, dc, deliverable-capacities, gcmc, grand-canonical-monte-carlo, high-throughput, methane-storage, mof-5, nanoporous, three-dimensional
Mail-order metal-organic frameworks (MOFs): designing isoreticular MOF-5 analogues comprising commercially available organic molecules

Metal–organic frameworks (MOFs), a class of porous materials, are of particular interest in gas storage and separation applications due largely to their high internal surface areas and tunable structures. MOF-5 is perhaps the archetypal MOF; in particular, many isoreticular analogues of MOF-5 have been synthesized, comprising alternative dicarboxylic acid ligands. In this contribution we introduce a new set of hypothesized MOF-5 analogues, constructed from commercially available organic molecules. We describe our automated procedure for hypothetical MOF design, comprising selection of appropriate ligands, construction of 3D structure models, and structure relaxation methods. 116 MOF-5 analogues were designed and characterized in terms of geometric properties and simulated methane uptake at conditions relevant to vehicular storage applications. A strength of the presented approach is that all of the hypothesized MOFs are designed to be synthesizable utilizing ligands purchasable online.

Version 2 includes the structures in CIF format.

Tags: 3d, database, dc, deliverable-capacities, gcmc, grand-canonical-monte-carlo, high-throughput, methane-storage, mof-5, nanoporous, three-dimensional
A Standard Solid State Pseudopotentials (SSSP) library optimized for precision and efficiency (Version 1.1, data download)

Despite the enormous success and popularity of density functional theory, systematic verification and validation studies are still very limited both in number and scope. Here, we propose a universal standard protocol to verify publicly available pseudopotential libraries, based on several independent criteria including verification against all-electron equations of state and plane-wave convergence tests for phonon frequencies, band structure, cohesive energy and pressure. Adopting these criteria we obtain two optimal pseudopotential sets, namely the Standard Solid State Pseudopotential (SSSP) efficiency and precision libraries, tailored for high-throughput materials screening and high-precision materials modelling. As of today, the SSSP precision library is the most accurate open-source pseudopotential library available. This archive entry contains the database of calculations (phonons, cohesive energy, equation of state, band structure, pressure, etc.) together with the provenance of all data and calculations as stored by AiiDA.

Tags: calculations, chessboards, cohesive-energy, database, dft, efficiency, electronic-bands, electronic-properties, elemental-solids, high-throughput, library, marvel, phonons, precision, pseudopotentials, sssp, standard, verification, vibrational-properties
Mining the C-C Cross-Coupling Genome using Machine Learning

Applications of machine-learning (ML) techniques to the study of catalytic processes have begun to appear in the literature with increasing frequency. The computational speed up provided by ML allows the properties and energetics of thousands of prospective catalysts to be rapidly assessed. These results, once compiled into a database containing different properties, can be mined with the goal of establishing relationships between the intrinsic chemical properties of different catalysts and their overall catalytic performance. Previously, we applied ML models to predict the performance of 18,000 prospective catalysts for a Suzuki coupling reaction using molecular volcano plots. Here, we expand on our earlier work by examining a larger section of the C-C cross-coupling genome by using a dimensionality-reducing data-clustering algorithms (i.e., sketch-map) to, first, identify the compatibility of each catalyst with different C-C cross-coupling variants (e.g., Suzuki, Kumada, Negishi, Stille, and/or Hiyama) and, second, to uncover links between the chemical property of a catalyst and its catalytic activity. Our findings, based on the analysis of 18,000 catalysts, reveal strong correlations between a catalyst's HOMO energy and the suitability of its thermodynamic profile. These values can, subsequently, be tuned in order to maximize the thermodynamics of the catalytic cycle through the judicious choice of metal centers and the π-accepting/σ-donating nature of the flanking ligands. Overall, group 10 metals (Ni, Pd, Pt) are best coupled with the strong π-acceptor ligands and group 11 metals (Cu, Ag, Au) with weak π-acceptors, which maximize the thermodynamic drive of the catalytic cycle.

Tags: homogeneous-catalysis, machine-learning, sketch-map, transition-metal-complexes, volcano-plot
A Standard Solid State Pseudopotentials (SSSP) library optimized for precision and efficiency

Despite the enormous success and popularity of density functional theory, systematic verification and validation studies are still very limited both in number and scope. Here, we propose a universal standard protocol to verify publicly available pseudopotential libraries, based on several independent criteria including verification against all-electron equations of state and plane-wave convergence tests for phonon frequencies, band structure, cohesive energy and pressure. Adopting these criteria we obtain two optimal pseudopotential sets, namely the Standard Solid State Pseudopotential (SSSP) efficiency and precision libraries, tailored for high-throughput materials screening and high-precision materials modelling. As of today, the SSSP precision library is the most accurate open-source pseudopotential library available. This archive entry contains the database of calculations (phonons, cohesive energy, equation of state, band structure, pressure, etc.) together with the provenance of all data and calculations as stored by AiiDA.

*** UPDATE April 2020 *** 
The zipped tarball archives and AiiDA export files had inconsistent internal formats and naming conventions, which made it difficult to work with them programmatically. In this update, the files are standardized according to the conventions that are detailed in the README.md file. Note that the actual content of pseudo potential files and the JSON metadata files has **not** changed, with the exception that the keys "cutoff" and "dual" in the JSON files have been replaced with "cutoff_wfc" and "cutoff_rho". Here the value of "cutoff_wfc" is equal to the old "cutoff", and "cutoff_rho" is equal to the product of the old "cutoff" and "dual". Besides that, the update concerns merely the renaming of certain files and the restructuring of archive formats.

*** UPDATE November 2020 *** 
The AiiDA export files contained in the sssp.tar archive have been modified and migrated to version format 0.9 in order to be imported in AiiDA 1.2.0 and later versions. The modifications are detailed in the README.md file in the sssp.tar archive.
The AiiDA export files contained in the sssp_bands.tar archive have been migrated to version format 0.9 as well.

*** UPDATE April 2021 - Version 1.1.1 ***
The PBEsol pseudopotential files contained unescaped "&" characters. In this update, the files concerned have been fixed escaping the "&" characters contained in PP_INPUTFILE blocks.

Tags: calculations, chessboards, cohesive-energy, cscs, database, dft, efficiency, electronic-bands, electronic-properties, elemental-solids, high-throughput, library, marvel, max, phonons, prace, precision, pseudopotentials, sssp, standard, verification, vibrational-properties
Quantum Mechanical Static Dipole Polarizabilities in the QM7b and AlphaML Showcase Databases

Dipole polarizabilities (and other molecular properties) computed using linear response coupled cluster theory (LR-CCSD/d-aug-cc-pVDZ) and hybrid density functional theory (B3LYP/d-aug-cc-pVDZ, SCAN0/d-aug-cc-pVDZ, and B3LYP/d-aug-cc-pVTZ) for the 7,211 molecules in the QM7b database and the 52 molecules in the AlphaML showcase database.

Tags: density-functional-theory, dipole-polarizability, linear-response-coupled-cluster
TuTraST data for methane diffusion in IZA structures

Data for the case study of TuTraSt on methane diffusion in zeolites, using a standard kinetic Monte Carlo simulation based on the output of our grid analysis. We find that it is accurate, fast, and rigorous without limitations to the geometries of the diffusion tunnels or transition states.

Tags: diffusion, kinetic-monte-carlo, marvel, methane, transition-state-theory, tutrast, zeolite
A Standard Solid State Pseudopotentials (SSSP) library optimized for precision and efficiency

Despite the enormous success and popularity of density functional theory, systematic verification and validation studies are still very limited both in number and scope. Here, we propose a universal standard protocol to verify publicly available pseudopotential libraries, based on several independent criteria including verification against all-electron equations of state and plane-wave convergence tests for phonon frequencies, band structure, cohesive energy and pressure. Adopting these criteria we obtain two optimal pseudopotential sets, namely the Standard Solid State Pseudopotential (SSSP) efficiency and precision libraries, tailored for high-throughput materials screening and high-precision materials modelling. As of today, the SSSP precision library is the most accurate open-source pseudopotential library available. This archive entry contains the database of calculations (phonons, cohesive energy, equation of state, band structure, pressure, etc.) together with the provenance of all data and calculations as stored by AiiDA.

*** UPDATE April 2023 - Version 1.3.0 ***
The pseudopotentials of elements At, Fr, Ra are added from PSlibrary. The pseudopotential of actinides are added from dataset of https://www.uni-marburg.de/de/fb15/arbeitsgruppen/anorganische_chemie/ag-kraus/forschung/paw_datasets_for_the_actinoids

Tags: aiida, calculations, chessboards, cohesive-energy, cscs, database, dft, efficiency, electronic-bands, electronic-properties, elemental-solids, high-throughput, library, marvel, max, phonons, prace, precision, pseudopotentials, sssp, standard, verification, vibrational-properties
A Standard Solid State Pseudopotentials (SSSP) library optimized for precision and efficiency

Despite the enormous success and popularity of density functional theory, systematic verification and validation studies are still very limited both in number and scope. Here, we propose a universal standard protocol to verify publicly available pseudopotential libraries, based on several independent criteria including verification against all-electron equations of state and plane-wave convergence tests for phonon frequencies, band structure, cohesive energy and pressure. Adopting these criteria we obtain two optimal pseudopotential sets, namely the Standard Solid State Pseudopotential (SSSP) efficiency and precision libraries, tailored for high-throughput materials screening and high-precision materials modelling. As of today, the SSSP precision library is the most accurate open-source pseudopotential library available. This archive entry contains the database of calculations (phonons, cohesive energy, equation of state, band structure, pressure, etc.) together with the provenance of all data and calculations as stored by AiiDA.

*** Recent UPDATE April 2023 - Version 1.3.0 ***
The pseudopotentials of elements At, Fr, Ra are added from PSlibrary. The pseudopotential of actinides are added from dataset of https://www.uni-marburg.de/de/fb15/arbeitsgruppen/anorganische_chemie/ag-kraus/forschung/paw_datasets_for_the_actinoids

Please refer to the CHANGELOG.txt file within the archive to view a complete list of version changes.

Tags: aiida, calculations, chessboards, cohesive-energy, cscs, database, dft, efficiency, electronic-bands, electronic-properties, elemental-solids, high-throughput, library, marvel, max, phonons, prace, precision, pseudopotentials, sssp, standard, verification, vibrational-properties
Regioselective 3-O-Substitution of Unprotected Thiodigalactosides: Route to Specific 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
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.

Tags: big-map, computational-high-throughput-screening, first-principles-molecular-dynamics, li-ion-conductors, marvelinc1, solid-state-electrolytes
Optical imaging and spectroscopy of atomically precise armchair graphene nanoribbons

The record contains data that support the work where we report the optical imaging and absorption spectroscopy on atomically precise armchair graphene nanoribbons (GNRs) on insulating fused silica substrates. This is achieved by controlling light polarization on macroscopically aligned GNRs which greatly enhances the optical contrast of the submonolayer GNRs on the insulating substrates. We measure the linear absorption spectra of 7-armchair and 9-armchair GNRs in this study, and the experimental data agree qualitatively with ab inito calculation results. The polarization spectroscopy technique enables an unambiguous optical identification of GNRs and provides a rapid tool to characterize the transferred film over a large area.

Tags: absorption-spectroscopy, graphene-nanoribbons, marveldd3, optical-imaging, snsf