Modelforge Curated OpenFF PhAlkEthOH Dataset:
- 1000 configuration test set, final energy minimized configuration only
- Version: nc_1000_minimal_v1.1

This provides a curated hdf5 file for a subset of the OpenFF PhAlkEthOH dataset designed to be compatible with modelforge, an infrastructure to implement and train NNPs.  The This dataset contains 1000 unique records for 1000 total configurations.  This contains a single configuration corresponding to the final configuration in the optimization trajectory (i.e., the energy minimized configuration).

This excludes any configurations where the magnitude of any forces on the atoms are greater than 1 hartree/bohr.

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:

Source Dataset:

PhAlkEthOH: Phenyls, Alkanes, Ethers, and alcohols (OH) 

The PhAlkEthOH dataset contains a collection of optimization trajectories of linear and cyclic molecules containing phyl rings, small alkanes, ethers, and alcohols  containing  only elements carbon, oxygen and hydrogen.  For each unique molecule, configurations correspond to snapshots from the optimization trajectory.  All QM datapoints retrieved from The MolSSI qcarchive and were generated using B3LYP-D3BJ/DZVP level of theory, the default theory used for force field development by the Open Force Field Initiative.

Properties Included:

• atomic_numbers  
• positions       
  • "per_atom"
  • "nanometer"
• dispersion_correction_gradient  
  • "per_atom"
  • "kilojoule_per_mole / nanometer"
• dispersion_correction_force     
  • "per_atom"
  • "kilojoule_per_mole / nanometer"
• dft_total_gradient      
  • "per_atom"
  • "kilojoule_per_mole / nanometer"
• dft_total_force 
  • "per_atom"
  • "kilojoule_per_mole / nanometer"
• total_charge    
  • "per_system"
  • "elementary_charge"
• dispersion_correction_energy    
  • "per_system"
  • "kilojoule_per_mole"
• dft_total_energy        
  • "per_system"
  • "kilojoule_per_mole"
• scf_dipole      
  • "per_system"
  • "elementary_charge * nanometer"
• source  
  • "meta_data"
• molecular_formula       
  • "meta_data"
• canonical_isomeric_explicit_hydrogen_mapped_smiles      
  • "meta_data"

Citations:

Related manuscripts:

• Bannan CC, Mobley D. ChemPer: An Open Source Tool for Automatically Generating SMIRKS Patterns. ChemRxiv. 2019; doi:10.26434/chemrxiv.8304578.v1
• Wang Y, Fass J, Kaminow B, Herr JE, Rufa D, Zhang I, Pulido I, Henry M, Macdonald HE, Takaba K, Chodera JD. End-to-end differentiable construction of molecular mechanics force fields. Chemical Science. 2022;13(41):12016-33. doi:10.1039/d2sc02739a

Source dataset:

• Gokey, T,., "OpenFF Sandbox CHO PhAlkEthOH v1.0", 2020, https://github.com/openforcefield/qca-dataset-submission/tree/master/submissions/2020-09-18-OpenFF-Sandbox-CHO-PhAlkEthOH