cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.15390655
title: modelforge curated dataset: QM9

description: Modelforge Curated QM9 Dataset:- Full dataset- Version: full_dataset_v1.1:

This provides a curated hdf5 file for a subset of the QM9 dataset to be used for testing purposes, designed to be compatible with modelforge, an infrastructure to implement and train NNPs.  This test dataset contains  133885 systems  with a single configuration for each unique molecule.

When applicable, the units of properties are provided in the datafile,  encoded as strings compatible with the openff-units package.  For more information about the structure of the data file, please see the following:



https://github.com/choderalab/modelforge/wiki/Dataset-and-curation#curation-module


Properties Included:     



atomic_numbers 

positions      



 "per_atom"

"nanometer"



partial_charges



"per_atom"

"elementary_charge"



polarizability 



"per_system"

"nanometer ** 3"



dipole_moment_per_system       



"per_system"

"elementary_charge * nanometer"



dipole_moment_scalar_per_system



"per_system"

"elementary_charge * nanometer"



energy_of_homo 



"per_system"

"kilojoule_per_mole"



lumo-homo_gap  



"per_system"

"kilojoule_per_mole"



zero_point_vibrational_energy  



"per_system"

"kilojoule_per_mole"



internal_energy_at_298.15K     



"per_system"

"kilojoule_per_mole"



internal_energy_at_0K  



"per_system"

"kilojoule_per_mole"



enthalpy_at_298.15K    



"per_system"

"kilojoule_per_mole"



free_energy_at_298.15K 



"per_system"

"kilojoule_per_mole"



heat_capacity_at_298.15K       



"per_system"

"kilojoule_per_mole / kelvin"



rotational_constants   



"per_system"

"gigahertz"



harmonic_vibrational_frequencies       



"per_system"

"1 / centimeter"



electronic_spatial_extent      



"per_system"

"nanometer ** 2"



smiles_gdb-17  



 "meta_data"

"meta_data"



inchi_corina    



"meta_data"



inchi_b3lyp    



"meta_data"



idx    



"meta_data"



tag    



"meta_data"




Original Source:

The QM9 dataset includes 133,885 organic molecules with up to nine total heavy atoms (C,O,N,or F; excluding H) original published by Ramakrishnan, et al. Properties in the QM9 dataset were calculated at the B3LYP/6-31G(2df,p) level of quantum chemistry.

Citations:

Original publication:



Ramakrishnan, R., Dral, P., Rupp, M. et al."Quantum chemistry structures and properties of 134 kilo molecules." Sci Data 1, 140022 (2014). https://doi.org/10.1038/sdata.2014.22


Source dataset, released with CCO 1.0 Universal license:



Ramakrishnan, Raghunathan; Dral, Pavlo; Rupp, Matthias; Anatole von Lilienfeld, O. (2014). Quantum chemistry structures and properties of 134 kilo molecules. figshare. Collection. https://doi.org/10.6084/m9.figshare.c.978904.v5
DOI: 10.15468/dl.fpgjfs
title: Occurrence Download

description: A dataset containing 23 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Exomalopsis pubescens Cresson, 1865"
 ]
}

 The dataset includes 23 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0026984-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14188395
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: 10.5281/zenodo.14188396
title: modelforge curated dataset: tmQM

description: Curated tmQM Dataset:

Full dataset, version "full_dataset_v0":

This provides a curated hdf5 file for the tmQM dataset (release 13Aug2024) designed to be compatible with modelforge, an infrastructure to implement and train NNPs.  This datafile includes 108541 unique molecules. Note, only a single configuration per unique molecule is provided. 

When applicable, the units of properties are provided in the datafile,  encoded as strings compatible with the openff-units package.  For more information about the structure of the data file, please see the following:



https://github.com/choderalab/modelforge/wiki/Dataset-and-curation#curation-module


This curated dataset was generated using the modelforge software at commit <add commit>:



Link to the source code at this commit: <add commit>

Link to the script file used to generate the dataset: <add commit>
DOI: 10.5281/zenodo.14188628
title: modelforge curated dataset: tmQM

description: Curated tmQM Dataset:

1000 conformer test set, version "nc_1000_v0":

This provides a curated hdf5 file for the tmQM dataset (release 13Aug2024) designed to be compatible with modelforge, an infrastructure to implement and train NNPs.  This datafile includes 108541 unique molecules. Note, only a single configuration per unique molecule is provided. 

When applicable, the units of properties are provided in the datafile,  encoded as strings compatible with the openff-units package.  For more information about the structure of the data file, please see the following:



https://github.com/choderalab/modelforge/wiki/Dataset-and-curation#curation-module


This curated dataset was generated using the modelforge software at commit <add commit>:



Link to the source code at this commit: <add commit>

Link to the script file used to generate the dataset: <add commit>
DOI: 10.5281/zenodo.14662046
title: modelforge curated dataset: tmQM

description: Curated tmQM Dataset:

Pd, Zn, Fe, Cu subset, version "subset_PdZnFeCu_v0":

This provides a curated hdf5 file for the tmQM dataset (release 13Aug2024) designed to be compatible with modelforge, an infrastructure to implement and train NNPs.  This datafile includes a subset of the original dataset (27685 unique molecules of the 108541 total), limited to those with metal centers of type Pd, Zn, Fe, or Cu. Note, only a single configuration per unique molecule is provided. 

When applicable, the units of properties are provided in the datafile,  encoded as strings compatible with the openff-units package.  For more information about the structure of the data file, please see the following:



https://github.com/choderalab/modelforge/wiki/Dataset-and-curation#curation-module
DOI: 10.5281/zenodo.14662151
title: modelforge curated dataset: tmQM

description: Curated tmQM Dataset:

Pd, Zn, Fe, Cu subset restricted to C, H, P, S, O, N, F, Cl, Br, version "subset_PdZnFeCu_CHPSONFClBr_v0":

This provides a curated hdf5 file for the tmQM dataset (release 13Aug2024) designed to be compatible with modelforge, an infrastructure to implement and train NNPs.  This datafile includes a subset of the original dataset (18515 unique molecules of the 108541 total), limited to those with metal centers of type Pd, Zn, Fe, or Cu and whose non-metal centers only sample from the following elements (C, H, P, S, O, N, F, Cl, Br). Note, only a single configuration per unique molecule is provided. 

 

Note, this has a bug where S is excluded and Se included.  Use v1 of this file.

When applicable, the units of properties are provided in the datafile,  encoded as strings compatible with the openff-units package.  For more information about the structure of the data file, please see the following:



https://github.com/choderalab/modelforge/wiki/Dataset-and-curation#curation-module
DOI: 10.5281/zenodo.14662309
title: modelforge curated dataset: tmQM

description: Curated tmQM Dataset:

Pd, Zn, Fe, Cu, Ni, Pt, Ir, Rh, Cr, Ag subset, version "subset_PdZnFeCuNiPtIrRhCrAg_v0":

This provides a curated hdf5 file for the tmQM dataset (release 13Aug2024) designed to be compatible with modelforge, an infrastructure to implement and train NNPs.  This datafile includes a subset of the original dataset (60637 unique molecules of the 108541 total), limited to those with metal centers of type Pd, Zn, Fe,  Cu, Ni, Pt, Ir, Rh, Cr, or Ag. Note, only a single configuration per unique molecule is provided. 

When applicable, the units of properties are provided in the datafile,  encoded as strings compatible with the openff-units package.  For more information about the structure of the data file, please see the following:



https://github.com/choderalab/modelforge/wiki/Dataset-and-curation#curation-module
DOI: 10.5281/zenodo.14662340
title: modelforge curated dataset: tmQM

description: Curated tmQM Dataset:

Pd, Zn, Fe, Cu, Ni, Pt, Ir, Rh, Cr, Ag subset restricted to C, H, P, S, O, N, F, Cl, Br, version "subset_PdZnFeCuNiPtIrRhCrAg_CHPSONFClBr_v0":

This provides a curated hdf5 file for the tmQM dataset (release 13Aug2024) designed to be compatible with modelforge, an infrastructure to implement and train NNPs.  This datafile includes a subset of the original dataset (60637 unique molecules of the 108541 total), limited to those with metal centers of type Pd, Zn, Fe,  Cu, Ni, Pt, Ir, Rh, Cr, or Ag and whose non-metal centers only sample from the following elements (C, H, P, S, O, N, F, Cl, Br).  Note, only a single configuration per unique molecule is provided. 

Note: this has a bug where S is exlcuded and Se included instead. Use, v1 of this.

When applicable, the units of properties are provided in the datafile,  encoded as strings compatible with the openff-units package.  For more information about the structure of the data file, please see the following:



https://github.com/choderalab/modelforge/wiki/Dataset-and-curation#curation-module
DOI: 10.5281/zenodo.14796762
title: modelforge curated dataset: tmQM

description: Curated tmQM Dataset:

Pd, Zn, Fe, Cu, Ni, Pt, Ir, Rh, Cr, Ag subset restricted to C, H, P, S, O, N, F, Cl, Br, version "subset_PdZnFeCuNiPtIrRhCrAg_CHPSONFClBr_v1":

This provides a curated hdf5 file for the tmQM dataset (release 13Aug2024) designed to be compatible with modelforge, an infrastructure to implement and train NNPs.  This datafile includes a subset of the original dataset (51258 unique molecules of the 108541 total), limited to those with metal centers of type Pd, Zn, Fe,  Cu, Ni, Pt, Ir, Rh, Cr, or Ag and whose non-metal centers only sample from the following elements (C, H, P, S, O, N, F, Cl, Br).  Note, only a single configuration per unique molecule is provided. 

Note: this fixes the bug in v0 where S was excluded and Se included.

When applicable, the units of properties are provided in the datafile,  encoded as strings compatible with the openff-units package.  For more information about the structure of the data file, please see the following:



https://github.com/choderalab/modelforge/wiki/Dataset-and-curation#curation-module
DOI: 10.5281/zenodo.14796780
title: modelforge curated dataset: tmQM

description: Curated tmQM Dataset:

Pd, Zn, Fe, Cu, subset restricted to C, H, P, S, O, N, F, Cl, Br, version "subset_PdZnFeCu_CHPSONFClBr_v1":

This provides a curated hdf5 file for the tmQM dataset (release 13Aug2024) designed to be compatible with modelforge, an infrastructure to implement and train NNPs.  This datafile includes a subset of the original dataset (23183 unique molecules of the 108541 total), limited to those with metal centers of type Pd, Zn, Fe,  Cu, and whose non-metal centers only sample from the following elements (C, H, P, S, O, N, F, Cl, Br).  Note, only a single configuration per unique molecule is provided. 

Note: this fixes the bug in v0 where S was excluded and Se included.

When applicable, the units of properties are provided in the datafile,  encoded as strings compatible with the openff-units package.  For more information about the structure of the data file, please see the following:



https://github.com/choderalab/modelforge/wiki/Dataset-and-curation#curation-module
DOI: 10.5281/zenodo.15331686
title: modelforge curated dataset: tmQM

description: Modelforge Curated tmQM Dataset: - full dataset- Version: full_dataset_v1.1

The 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 the tmQM dataset (release 13Aug2024) designed to be compatible with modelforge, an infrastructure to implement and train NNPs.  This dataset contains 108541 unique systems with 108541 total configurations (1 configuration per system). 

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.15331808
title: modelforge curated dataset: tmQM

description: Modelforge Curated tmQM Dataset: - 1000 conformer test set- Version: nc_1000_v1.1

The 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.15345127
title: modelforge curated dataset: tmQM

description: Modelforge Curated tmQM Dataset: - Dataset restricted to [Pd, Zn, Fe, and Cu] and [C, H, P, S, O, N, F, Cl, or Br]- Version: PdZnFe_CHPSONFClBr_v1.1





This dataset contains a subset of the tmQM dataset, with 23183 unique systems with 23183 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"