cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.15345149
title: modelforge curated dataset: tmQM

description: Modelforge Curated tmQM Dataset: - Dataset restricted to [Pd, Zn, Fe, Cu, Ni, Pt, Ir, Rh, Cr, or Ag] and [C, H, P, S, O, N, F, Cl, or Br]- Version: PdZnFeCuNiPtIrRhCrAg_CHPSONFClBr_v1.1





This dataset contains a subset of the tmQM dataset, with 51258 unique systems with 51258 total configurations (1 configuration per system). This dataset is limited to systems that contain transition metals Pd, Zn, Fe, or Cu, and also only contain elements C, H, P, S, O, N, F, Cl, or Br.



The full  tmQM dataset contains the geometries and properties of 108,541 mononuclear complexes extracted from the Cambridge Structural Database, including Werner, bioinorganic, and organometallic complexes based on a large variety of organic ligands and 30 transition metals (the 3d, 4d, and 5d from groups 3 to 12). All complexes are closed-shell, with a formal charge in the range {+1, 0, −1}e. 

 

This provides a curated hdf5 file for a subset of the tmQM dataset (release 13Aug2024) designed to be compatible with modelforge, an infrastructure to implement and train NNPs.  This dataset contains 1000 unique systems with 1000 total configurations (1 configuration per system), designed to be used for testing. 

The original tmQM repository (https://github.com/uiocompcat/tmQM) was forked and a release made that corresponds to the data committed on 13 August 2024 (https://github.com/chrisiacovella/tmQM/releases/tag/2024Aug13).

When applicable, the units of properties are provided in the datafile,  encoded as strings compatible with the openff-units package. 

This dataset is compatible with modelforge hdf5 schema 2.

Original Citation:

David Balcells and Bastian Bjerkem Skjelstad,tmQM Dataset—Quantum Geometries and Properties of 86k Transition Metal ComplexesJournal of Chemical Information and Modeling 2020 60 (12), 6135-6146DOI: 10.1021/acs.jcim.0c01041

Properties Included:      



atomic_numbers  

positions       



"per_atom"

"nanometer"



partial_charges 



"per_atom"

"elementary_charge"



total_charge    



"per_system"

"elementary_charge"



spin_multiplicities     



"per_system"

"dimensionless"



electronic_energy       



"per_system"

"kilojoule_per_mole"



dispersion_energy       



"per_system"

"kilojoule_per_mole"



total_energy    



"per_system"

"kilojoule_per_mole"



dipole_moment_magnitude 



"per_system"

"elementary_charge * nanometer"



dipole_moment_computed  



"per_system"

"elementary_charge * nanometer"



dipole_moment_computed_scaled   



"per_system"

"elementary_charge * nanometer"



energy_of_lumo  



"per_system"

"kilojoule_per_mole"



energy_of_homo  



"per_system"

"kilojoule_per_mole"



homo_lumo_gap   



"per_system"

"kilojoule_per_mole"



stoichiometry  



"meta_data"



metal_n_ligands



 "meta_data"



metal_center_charge     



"meta_data"
DOI: 10.5281/zenodo.15345571
title: modelforge curated dataset: tmQM

description: Modelforge Curated tmQM Dataset: - Dataset restricted to [Pd, Zn, Fe, or Cu] and [C, H, P, S, O, N, F, Cl, or Br]- Version: PdZnFeCu_CHPSONFClBr_nc_1000_v1.1





This dataset contains a subset of the tmQM dataset, with 1000 unique systems with 1000 total configurations (1 configuration per system). This dataset is limited to systems that contain transition metals Pd, Zn, Fe, or Cu, and also only contain elements C, H, P, S, O, N, F, Cl, or Br.



The full  tmQM dataset contains the geometries and properties of 108,541 mononuclear complexes extracted from the Cambridge Structural Database, including Werner, bioinorganic, and organometallic complexes based on a large variety of organic ligands and 30 transition metals (the 3d, 4d, and 5d from groups 3 to 12). All complexes are closed-shell, with a formal charge in the range {+1, 0, −1}e. 

 

This provides a curated hdf5 file for a subset of the tmQM dataset (release 13Aug2024) designed to be compatible with modelforge, an infrastructure to implement and train NNPs.  This dataset contains 1000 unique systems with 1000 total configurations (1 configuration per system), designed to be used for testing. 

The original tmQM repository (https://github.com/uiocompcat/tmQM) was forked and a release made that corresponds to the data committed on 13 August 2024 (https://github.com/chrisiacovella/tmQM/releases/tag/2024Aug13).

When applicable, the units of properties are provided in the datafile,  encoded as strings compatible with the openff-units package. 

This dataset is compatible with modelforge hdf5 schema 2.

Original Citation:

David Balcells and Bastian Bjerkem Skjelstad,tmQM Dataset—Quantum Geometries and Properties of 86k Transition Metal ComplexesJournal of Chemical Information and Modeling 2020 60 (12), 6135-6146DOI: 10.1021/acs.jcim.0c01041

Properties Included:      



atomic_numbers  

positions       



"per_atom"

"nanometer"



partial_charges 



"per_atom"

"elementary_charge"



total_charge    



"per_system"

"elementary_charge"



spin_multiplicities     



"per_system"

"dimensionless"



electronic_energy       



"per_system"

"kilojoule_per_mole"



dispersion_energy       



"per_system"

"kilojoule_per_mole"



total_energy    



"per_system"

"kilojoule_per_mole"



dipole_moment_magnitude 



"per_system"

"elementary_charge * nanometer"



dipole_moment_computed  



"per_system"

"elementary_charge * nanometer"



dipole_moment_computed_scaled   



"per_system"

"elementary_charge * nanometer"



energy_of_lumo  



"per_system"

"kilojoule_per_mole"



energy_of_homo  



"per_system"

"kilojoule_per_mole"



homo_lumo_gap   



"per_system"

"kilojoule_per_mole"



stoichiometry  



"meta_data"



metal_n_ligands



 "meta_data"



metal_center_charge     



"meta_data"
DOI: 10.15468/dl.f6qs5m
title: Occurrence Download

description: A dataset containing 32 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Gastrotheca pacchamama Duellman, 1987"
 ]
}

 The dataset includes 32 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0026986-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.15264766
title: modelforge curated dataset: Fe (II) dataset

description: Modelforge Curated Fe (II) Dataset- 1000 conformer test set- Version: nc_1000_v1.1

This provides a modelforge curated hdf5 file for the Fe (II) dataset.  This dataset contains 102 unique systems with a total of 1000 configurations (max of 10 configurations per system). The full dataset contains systems with elements: H, C, N, O, P, S, Cl, and Fe.

This dataset is compatible with modelforge hdf5 schema 2.

The full Fe(II) dataset includes 28834 total configurations Fe(II) organometallic complexes.Specifically, this includes 15568 HS geometries and 13266 LS geometries. These complexes originate from the Cambridge Structural Database (CSD) as curated by Nandy, et al. (Journal of Physical Chemistry Letters (2023), 14 (25), 10.1021/acs.jpclett.3c01214), and were filtered into “computation-ready” complexes, (those where both oxidation states and charges are already specified without hydrogen atoms missing in the structures), following the procedure outlined by Arunachalam, et al. (Journal of Chemical Physics (2022), 157 (18), 10.1063/5.0125700)The original Fe (II) dataset is available from github:https://github.com/Neon8988/Iron_NNPsThe modelforge  dataset was curated from a forked release (no modifications made to the dataset, forked/released to ensure provenance). https://github.com/chrisiacovella/Iron_NNPs/releases/tag/2024Jan16

Citation to the original dataset:Modeling Fe(II) Complexes Using Neural NetworksHongni Jin and Kenneth M. Merz Jr.Journal of Chemical Theory and Computation 2024 20 (6), 2551-2558DOI: 10.1021/acs.jctc.4c00063

 

Properties  included in the dataset:   



atomic_numbers  

positions       



 "per_atom"

  "nanometer"



forces  



 "per_atom"

  "kilojoule_per_mole / nanometer"



energies        



  "per_system"

   "kilojoule_per_mole"



total_charge    



  "per_system"

  "elementary_charge"



spin_multiplicities     



  "per_system"



mol_id  "meta_data"
DOI: 10.15468/dl.s383yq
title: Occurrence Download

description: A dataset containing 11277 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "StateProvince is one of (Nevada, CALIFORNIA USA., CAlifornia, California, CaliforniA, NevADA)",
 "TaxonKey is Salix lasiolepis Benth."
 ]
}

 The dataset includes 11277 records from 104 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0026988-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.15264720
title: modelforge curated dataset: Fe (II) dataset

description: Modelforge Curated Fe (II) Dataset- 1000 conformer test set- Version: nc_1000_v1.1

This provides a modelforge curated hdf5 file for the Fe (II) dataset.  This dataset contains 102 unique systems with a total of 1000 configurations (max of 10 configurations per system). The full dataset contains systems with elements: H, C, N, O, P, S, Cl, and Fe.

This dataset is compatible with modelforge hdf5 schema 2.

The full Fe(II) dataset includes 28834 total configurations Fe(II) organometallic complexes.Specifically, this includes 15568 HS geometries and 13266 LS geometries. These complexes originate from the Cambridge Structural Database (CSD) as curated by Nandy, et al. (Journal of Physical Chemistry Letters (2023), 14 (25), 10.1021/acs.jpclett.3c01214), and were filtered into “computation-ready” complexes, (those where both oxidation states and charges are already specified without hydrogen atoms missing in the structures), following the procedure outlined by Arunachalam, et al. (Journal of Chemical Physics (2022), 157 (18), 10.1063/5.0125700)The original Fe (II) dataset is available from github:https://github.com/Neon8988/Iron_NNPsThe modelforge  dataset was curated from a forked release (no modifications made to the dataset, forked/released to ensure provenance). https://github.com/chrisiacovella/Iron_NNPs/releases/tag/2024Jan16

Citation to the original dataset:Modeling Fe(II) Complexes Using Neural NetworksHongni Jin and Kenneth M. Merz Jr.Journal of Chemical Theory and Computation 2024 20 (6), 2551-2558DOI: 10.1021/acs.jctc.4c00063

 

Properties  included in the dataset:   



atomic_numbers  

positions       



 "per_atom"

  "nanometer"



forces  



 "per_atom"

  "kilojoule_per_mole / nanometer"



energies        



  "per_system"

   "kilojoule_per_mole"



total_charge    



  "per_system"

  "elementary_charge"



spin_multiplicities     



  "per_system"



mol_id  "meta_data"
DOI: 10.5281/zenodo.15264721
title: modelforge curated dataset: Fe (II) dataset

description: Modelforge Curated Fe (II) Dataset-full dataset-Version: full_dataset_v1.1

This provides a modelforge curated hdf5 file for the Fe (II) dataset.  This dataset contains 384 unique systems with a total of 28,834 configurations (note, the original publication states 383 unique systems).  The dataset contains systems with elements: H, C, N, O, P, S, Cl, and Fe.

This is compatible with modelforge hdf5 scheme 2. 

The Fe(II) dataset includes 28834 total configurations Fe(II) organometallic complexes.Specifically, this includes 15568 HS geometries and 13266 LS geometries. These complexes originate from the Cambridge Structural Database (CSD) as curated by Nandy, et al. (Journal of Physical Chemistry Letters (2023), 14 (25), 10.1021/acs.jpclett.3c01214), and were filtered into “computation-ready” complexes, (those where both oxidation states and charges are already specified without hydrogen atoms missing in the structures), following the procedure outlined by Arunachalam, et al. (Journal of Chemical Physics (2022), 157 (18), 10.1063/5.0125700)The original Fe (II) dataset is available from github:https://github.com/Neon8988/Iron_NNPsThe modelforge  dataset was curated from a forked release (no modifications made to the dataset, forked/released to ensure provenance). https://github.com/chrisiacovella/Iron_NNPs/releases/tag/2024Jan16

Citation to the original dataset:

Modeling Fe(II) Complexes Using Neural NetworksHongni Jin and Kenneth M. Merz Jr.Journal of Chemical Theory and Computation 2024 20 (6), 2551-2558DOI: 10.1021/acs.jctc.4c00063

 

Properties  included in the dataset:   



atomic_numbers  

positions       



 "per_atom"

  "nanometer"



forces  



 "per_atom"

  "kilojoule_per_mole / nanometer"



energies        



  "per_system"

   "kilojoule_per_mole"



total_charge    



  "per_system"

  "elementary_charge"



spin_multiplicities     



  "per_system"



mol_id  "meta_data"
DOI: 10.34740/kaggle/dsv/11787827
title: DisProtBenchmark
DOI: 10.15468/dl.dmaphs
title: Occurrence Download

description: A dataset containing 3985 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Oxypogon stuebelii A.B.Meyer, 1884"
 ]
}

 The dataset includes 3985 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0026990-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.r94qms
title: Occurrence Download

description: A dataset containing 470 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is one of (University of South Florida Herbarium (USF), University of North Carolina at Chapel Hill Herbarium: Vascular Plants, Louisiana State University, Shirley C. Tucker Herbarium - Vascular Plants, University of Georgia Herbarium)",
 "TaxonKey is Drosera capillaris Poir."
 ]
}

 The dataset includes 470 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0026991-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fhc9u9
title: Occurrence Download

description: A dataset containing 2138 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Achatina fulica Bowdich, 1822"
 ]
}

 The dataset includes 2138 records from 114 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0026989-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5519/qd.bzarcp6p
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (14 records)
DOI: 10.15468/dl.uxwb83
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Gastrotheca pachachacae Catenazzi & von May, 2011"
 ]
}

 The dataset includes 2 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0026992-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mhnner
title: Occurrence Download

description: A dataset containing 792841 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "TaxonKey is Setophaga townsendi (J.K.Townsend, 1837)",
 "Year is greater than or equal to 1950",
 {
 "or" : [
 "GadmGid is USA",
 "GadmGid is CAN",
 "GadmGid is MEX"
 ]
 }
 ]
}

 The dataset includes 792841 records from 91 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0026983-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.nnjhwz
title: Occurrence Download

description: A dataset containing 60 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Ambrosia artemisiifolia L.",
 "Country is Portugal",
 "Year is greater than or equal to 1500"
 ]
}

 The dataset includes 60 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0026993-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.e88ycn
title: Occurrence Download

description: A dataset containing 3470133 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Plantae)",
 "Country is New Zealand",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 0"
 ]
}

 The dataset includes 3470133 records from 395 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0026981-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14920177
title: tmQM-xtb dataset

description: This provides an hdf5 file for the tmQM-xtb dataset.  This dataset was generated starting from the tmQM dataset (release 13Aug2024, https://github.com/uiocompcat/tmQM) containing 108541 unique molecules; each molecule was evaluated using gfn2-xtb, and then a short MD simulation performed to provide additional configurations of the molecules. 



The tblite package was used to evaluate the energetic of the system using the gfn2-xtb formalism.

MD simulations were performed using the Atomic Simulation Environment (ASE), using the Langevin integrator 

Simulations were performed at 100K with a 1 fs timestep and 0.01 1/fs friction damping factor.  

In all trajectories, the first configuration corresponds to the energy minimized configuration reported in the original tmQM dataset.

100 steps were taken between snapshots,  with 10 total snapshots per molecule

During MD sampling, gfn2-xtb accuracy was set to 2; all reported properties were calculated at accuracy level 1. 


Scripts used to perform the sampling can be found https://github.com/chrisiacovella/xtb_config_gen

Note, this dataset correpsonds to the raw output of the gfn2-xtb based calculations. No validation or exclusions have been made and thus not all configurations will necessarily be stable or realistic.
DOI: 10.5281/zenodo.15015031
title: modelforge curated dataset: tmQM-xtb

description: Curated tmQM-xtb Dataset: T=100K dataset restricted to Pd, Zn, Fe, Cu, Ni, Pt, Ir, Rh, Cr, Ag

This dataset contains 51160 unique systems with 460330 total configurations.  This dataset is limited to systems that contain transition metals Pd, Zn, Fe,  Cu, Ni, Pt, Ir, Rh, Cr, or Ag and also only contain elements C, H, P, S, O, N, F, Cl, or Br. 

Potentially problematic configurations (i.e., unstable or those with underlying structural changes) were removed. Briefly, bond inference was performed on the initial configuration using RDKit and a configuration was excluded if any of those bond distances changed by more than 0.1  angstroms compared to the initial, energy minimized state. 

NOTE: This dataset may include configurations that do not fully satisfy the cutoff criteria due to a bug in the application of the filtering. Please use the updated version.

This dataset was generated starting from the tmQM dataset (release 13Aug2024, https://github.com/uiocompcat/tmQM) containing 108541 unique molecules; each molecule was evaluated using gfn2-xtb, and then a short MD simulation performed to provide additional configurations of the molecules. 



The tblite package was used to evaluate the energetic of the system using the gfn2-xtb formalism.

MD simulations were performed using the Atomic Simulation Environment (ASE), using the Langevin integrator 

Simulations were performed at 100K with a 1 fs timestep and 0.01 1/fs friction damping factor.  

In all trajectories, the first configuration corresponds to the energy minimized configuration reported in the original tmQM dataset.

100 steps were taken between snapshots,  with 10 total snapshots per molecule

During MD sampling, gfn2-xtb accuracy was set to 2; all reported properties were calculated at accuracy level 1. 


Scripts used to perform the sampling can be found https://github.com/chrisiacovella/xtb_config_gen



Properties included: 



atomic_numbers  

positions  



"per_atom"

"nanometer"



forces



"per_atom"

 "kilojoule_per_mole / nanometer"



partial_charges 



"per_atom"

"elementary_charge"



energies  



"per_system"

"kilojoule_per_mole"



dipole_moment_per_system  



"per_system"

 "elementary_charge * nanometer"



total_charge  



 "per_system"

"elementary_charge"



spin_multiplicities 



"per_system"

"dimensionless"



stoichiometry 



"meta_data"
DOI: 10.5281/zenodo.15015505
title: modelforge curated dataset: tmQM-xtb

description: Curated tmQM-xtb Dataset: T=100K dataset restricted to Pd, Zn, Fe, Cu, 1000 configuration test set

This dataset contains 112 unique systems with 1000 total configurations.  This dataset is limited to systems that contain transition metals Pd, Zn, Fe,  or Cu, and also only contain elements C, H, P, S, O, N, F, Cl, or Br. 

Potentially problematic configurations (i.e., unstable or those with underlying structural changes) were removed. Briefly, bond inference was performed on the initial configuration using RDKit and a configuration was excluded if any of those bond distances changed by more than 0.1  angstroms compared to the initial, energy minimized state. 

NOTE: This dataset may include configurations that do not fully satisfy the cutoff criteria due to a bug in the application of the filtering. Please use the updated version.

This dataset was generated starting from the tmQM dataset (release 13Aug2024, https://github.com/uiocompcat/tmQM) containing 108541 unique molecules; each molecule was evaluated using gfn2-xtb, and then a short MD simulation performed to provide additional configurations of the molecules. 



The tblite package was used to evaluate the energetic of the system using the gfn2-xtb formalism.

MD simulations were performed using the Atomic Simulation Environment (ASE), using the Langevin integrator 

Simulations were performed at 100K with a 1 fs timestep and 0.01 1/fs friction damping factor.  

In all trajectories, the first configuration corresponds to the energy minimized configuration reported in the original tmQM dataset.

100 steps were taken between snapshots,  with 10 total snapshots per molecule

During MD sampling, gfn2-xtb accuracy was set to 2; all reported properties were calculated at accuracy level 1. 


Scripts used to perform the sampling can be found https://github.com/chrisiacovella/xtb_config_gen



Properties included: 



atomic_numbers  

positions  



"per_atom"

"nanometer"



forces



"per_atom"

 "kilojoule_per_mole / nanometer"



partial_charges 



"per_atom"

"elementary_charge"



energies  



"per_system"

"kilojoule_per_mole"



dipole_moment_per_system  



"per_system"

 "elementary_charge * nanometer"



total_charge  



 "per_system"

"elementary_charge"



spin_multiplicities 



"per_system"

"dimensionless"



stoichiometry 



"meta_data"