cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.15021819
title: modelforge curated dataset: tmQM-xtb

description: Curated tmQM-xtb Dataset: T=100K dataset restricted to Pd, Zn, Fe, Cu without MD sampling



This dataset contains 23134 unique systems with 23134 total configurations (1 configuration per system). Each configuration corresponds to the geometry distributed as part of the original tmQM dataset, with no MD sampling applied. 

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.   This dataset was generated starting from the tmQM dataset; 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). 


 



The tblite package was used to evaluate the energetic of the system using the gfn2-xtb formalism, using the calculator as part of the Atomic Simulation Environment (ASE), 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.15226639
title: modelforge curated dataset: tmQM-xtb

description: Curated tmQM-xtb Dataset: - T=300K dataset restricted to [Pd, Zn, Fe, Cu, Ni, Pt, Ir, Rh, Cr, and Ag] - Version: v1.1_PdZnFeCuNiPtIrRhCrAg_T300K

This dataset contains 51252 unique systems with 1118541 total configurations (~30 per system), with MD sampling performed at T=300K.  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 0.15  angstroms compared to the initial, energy minimized state. 

This dataset was generated starting from the tmQM dataset; 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).

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 300K 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 30 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.15227086
title: modelforge curated dataset: tmQM-xtb

description: Curated tmQM-xtb Dataset: - T=200K dataset restricted to [Pd, Zn, Fe, and Cu] max of 10 configs per system- Version: v1.1_PdZnFeCu_ncr10_T200K

This dataset contains 23175  unique systems with 230,030 total configurations (maximum of 10 per system), sampled at T=200K.  While 30 configurations were generated per system during sampling, this dataset limits this to be a maximum of 10 configurations per system, to allow for more direct comparison with T=100K data.

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 0.15  angstroms compared to the initial, energy minimized state. 

This dataset was generated starting from the tmQM dataset; 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).

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 200K 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 30 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.15015000
title: modelforge curated dataset: tmQM-xtb

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

This dataset contains 23134 unique systems with 208141 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"
DOI: 10.5281/zenodo.15059379
title: modelforge curated dataset: tmQM-xtb

description: Curated tmQM-xtb Dataset: - T=100K dataset restricted to [ Pd, Zn, Fe, and  Cu] 1000 configuration test set - version: v1.1_PdZnFeCu_ntc1000_T100K



This dataset contains 103 unique systems with 1000 total configurations (max of 10 configurations per system), where MD sampling was performed at T=100K.

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 0.15 angstroms compared to the initial, energy minimized state.

This dataset was generated starting from the tmQM dataset; 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).

Each system in the tmQM database was evaluated using gfn2-xtb, and then a short MD simulation performed to provide additional configurations of the systems. 




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 gfn2-xtb 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.15059433
title: modelforge curated dataset: tmQM-xtb

description: Curated tmQM-xtb Dataset: - T=100K dataset restricted to [Pd, Zn, Fe, and Cu] - Version: v1.1_PdZnFeCu_T100K

This dataset contains 23134 unique systems with 225068 total configurations, where MD sampling was performed at T=100K.  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 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 0.15 angstroms compared to the initial, energy minimized state. 

This dataset was generated starting from the tmQM dataset; 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).

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.15059465
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, and Ag]- Version: v1.1_PdZnFeCuNiPtIrRhCrAg_T100K

This dataset contains 51160 unique systems with 499087 total configurations, with MD sampling at T=100K.  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 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 0.15  angstroms compared to the initial, energy minimized state. 

This dataset was generated starting from the tmQM dataset; 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).

Eeach 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.15226046
title: modelforge curated dataset: tmQM-xtb

description: Curated tmQM-xtb Dataset: - T=200K dataset restricted to [Pd, Zn, Fe, Cu, Ni, Pt, Ir, Rh, Cr, and Ag]- Version: v1.1_PdZnFeCuNiPtIrRhCrAg_T200K

This dataset contains 51249 unique systems with 1317625 total configurations (~30 per system), sampled at T=200K.  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 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 0.15  angstroms compared to the initial, energy minimized state. 

This dataset was generated starting from the tmQM dataset; 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).

Tach 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 200K 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 30 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.15227023
title: modelforge curated dataset: tmQM-xtb

description: Curated tmQM-xtb Dataset: - T=200K dataset restricted to [Pd, Zn, Fe, and Cu]- Version: v1.1_PdZnFeCu_T200K

This dataset contains 23175  unique systems with  584,935 total configurations (~30 per system), with MD sampling at T=200K. 

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 0.15  angstroms compared to the initial, energy minimized state. 

This dataset was generated starting from the tmQM dataset; 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).

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 200K 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 30 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.15227144
title: modelforge curated dataset: tmQM-xtb

description: Curated tmQM-xtb Dataset: - T=300K dataset restricted to [Pd, Zn, Fe, and Cu]- Version: v1.1_PdZnFeCu_T300K

This dataset contains  23177  unique systems with  490,861 total configurations, sampled at T=300K. 

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 0.15  angstroms compared to the initial, energy minimized state. 

This dataset was generated starting from the tmQM dataset; 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).

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 300K 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 30 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"