cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.24435/materialscloud:2019.0010/v2
title: Enhanced sampling of transition states

description: The free energy landscapes of several fundamental processes are characterized by high barriers separating long-lived metastable states. In order to explore these type of landscapes enhanced sampling methods are used. While many such methods are able to obtain sufficient sampling in order to draw the free energy, the transition states are often sparsely sampled. We propose an approach based on the Variationally Enhanced Sampling Method to enhance sampling in the transition region. To this effect, we introduce a dynamic target distribution which uses the derivative of the instantaneous free energy surface to locate the transition regions on the fly and modulate the probability of sampling different regions. Finally, we exemplify  the effectiveness of this approach in enriching the number of configurations in the transition state region in the cases of a chemical reaction and of a nucleation process.
DOI: 10.24435/materialscloud:4y-ak
title: A Standard Solid State Pseudopotentials (SSSP) library optimized for precision and efficiency

description: 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.
DOI: 10.24435/materialscloud:v6-zt
title: Enhanced sampling of transition states

description: The free energy landscapes of several fundamental processes are characterized by high barriers separating long-lived metastable states. In order to explore these type of landscapes enhanced sampling methods are used. While many such methods are able to obtain sufficient sampling in order to draw the free energy, the transition states are often sparsely sampled. We propose an approach based on the Variationally Enhanced Sampling Method to enhance sampling in the transition region. To this effect, we introduce a dynamic target distribution which uses the derivative of the instantaneous free energy surface to locate the transition regions on the fly and modulate the probability of sampling different regions. Finally, we exemplify  the effectiveness of this approach in enriching the number of configurations in the transition state region in the cases of a chemical reaction and of a nucleation process.
DOI: 10.24435/materialscloud:2018.0001/v2
title: A Standard Solid State Pseudopotentials (SSSP) library optimized for precision and efficiency (Version 1.0, data download)

description: 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.
DOI: 10.24435/materialscloud:2019.0002/v1
title: Coupled-Cluster Polarizabilities in the QM7b and a Showcase Database

description: 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.
DOI: 10.24435/materialscloud:2018.0007/v1
title: Mail-order metal-organic frameworks (MOFs): designing isoreticular MOF-5 analogues comprising commercially available organic molecules

description: 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.
DOI: 10.24435/materialscloud:r2-eq
title: Mail-order metal-organic frameworks (MOFs): designing isoreticular MOF-5 analogues comprising commercially available organic molecules

description: 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.
DOI: 10.24435/materialscloud:2018.0001/v3
title: A Standard Solid State Pseudopotentials (SSSP) library optimized for precision and efficiency (Version 1.1, data download)

description: 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.
DOI: 10.24435/materialscloud:2019.0002/v2
title: Coupled-Cluster Polarizabilities in the QM7b and a Showcase Database

description: 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.
DOI: 10.24435/materialscloud:y8-yw
title: A Standard Solid State Pseudopotentials (SSSP) library optimized for precision and efficiency

description: 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.
DOI: 10.24435/materialscloud:2019.0002/v3
title: Quantum Mechanical Static Dipole Polarizabilities in the QM7b and AlphaML Showcase Databases

description: 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.
DOI: 10.24435/materialscloud:3z-49
title: Quantum Mechanical Static Dipole Polarizabilities in the QM7b and AlphaML Showcase Databases

description: 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.
DOI: 10.24435/materialscloud:2019.0011/v1
title: TuTraST data for methane diffusion in IZA structures

description: 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.
DOI: 10.24435/materialscloud:45-h1
title: TuTraST data for methane diffusion in IZA structures

description: 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.
DOI: 10.24435/materialscloud:eg-28
title: A Standard Solid State Pseudopotentials (SSSP) library optimized for precision and efficiency

description: 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
DOI: 10.24435/materialscloud:f3-ym
title: A Standard Solid State Pseudopotentials (SSSP) library optimized for precision and efficiency

description: 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.
DOI: 10.24435/materialscloud:2020.0002/v1
title: Regioselective 3-O-Substitution of Unprotected Thiodigalactosides: Route to Specific Galectin Inhibitors

description: 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.
DOI: 10.24435/materialscloud:td-91
title: A Standard Solid State Pseudopotentials (SSSP) library optimized for precision and efficiency

description: 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.
DOI: 10.24435/materialscloud:2019.0077/v1
title: High-throughput computational screening for solid-state Li-ion conductors

description: 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.
DOI: 10.24435/materialscloud:2019.0067/v1
title: Simulating diffusion properties of solid-state electrolytes via a neural network potential:  Performance and training scheme

description: The recently published DeePMD model, based on a deep neural network architecture, brings the hope of solving the time-scale issue which often prevents the application of first principle molecular dynamics to physical systems. With this contribution we assess the performance of the DeePMD potential on a real-life application and model diffusion of ions in solid-state electrolytes. We consider as test cases the well known Li10GeP2S12, Li7La3Zr2O12 and Na3Zr2Si2PO12. We develop and test a training protocol suitable for the computation of diffusion coefficients, which is one of the key properties to be optimized for battery applications, and we find good agreement with previous computations. Our results show that the DeePMD model may be a successful component of a framework to identify novel solid-state electrolytes.
DOI: 10.24435/materialscloud:c3-58
title: Simulating diffusion properties of solid-state electrolytes via a neural network potential:  Performance and training scheme

description: The recently published DeePMD model, based on a deep neural network architecture, brings the hope of solving the time-scale issue which often prevents the application of first principle molecular dynamics to physical systems. With this contribution we assess the performance of the DeePMD potential on a real-life application and model diffusion of ions in solid-state electrolytes. We consider as test cases the well known Li10GeP2S12, Li7La3Zr2O12 and Na3Zr2Si2PO12. We develop and test a training protocol suitable for the computation of diffusion coefficients, which is one of the key properties to be optimized for battery applications, and we find good agreement with previous computations. Our results show that the DeePMD model may be a successful component of a framework to identify novel solid-state electrolytes.