PubChemQC-B3LYP/6-31G*//PM6 Dataset

Dataset Summary

The presented PubChemQC B3LYP/6-31G*//PM6 data set is composed of the electronic properties of 85,938,443 molecules, encompassing a broad spectrum of molecules from essential compounds to biomolecules with a molecular weight up to 1000. These molecules account for 94.0% of the original PubChem Compound catalog as of August 29, 2016. The electronic properties, including orbitals, orbital energies, total energies, dipole moments, and other pertinent properties, were computed by using the B3LYP/6-31G* and PM6 methods.

Dataset Structure

Data Instances

An example of a data instance is as follows:

{'cid': 1,
  'state': 'S0',
  'pubchem-inchi': 'InChI=1S/C9H17NO4/c1-7(11)14-8(5-9(12)13)6-10(2,3)4/h8H,5-6H2,1-4H3',
  'pubchem-charge': 0,
  'pubchem-version': '20160829',
  'name': '000000001.[email protected]',
  'coordinates': [
    4.543149670829423,
   -2.8411897941733857,
   -1.6418598810432616,
   ...,
   4.345629685137421
   ],
  'atomic-numbers': [
   6,
   6,
   8,
   ...,
   1
   ],
  'atom-count': 31,
  'heavy-atom-count': 14,
  'core-electrons': [
   0,
   0,
   0,
   ...,
   0
   ],
  'bond-order': [
   1,
   1,
   1,
   ...,
   1
   ],
  'connection-indices': [
   15,
   1,
   17,
   ...,
   30],
  'formula': 'C9H17NO4',
  'version': '1.0',
  'obabel-inchi': 'InChI=1S/C9H17NO4/c1-7(11)14-8(5-9(12)13)6-10(2,3)4/h8H,5-6H2,1-4H3/t8-/m0/s1',
  'pm6-obabel-canonical-smiles': '[O]C(=O)C[C@@H](C[N](C)(C)C)OC(=O)C',
  'charge': 0,
  'energy-beta-gap': 4.34837933099,
  'energy-beta-homo': -4.60960862747,
  'energy-beta-lumo': -0.2612292964799998,
  'energy-alpha-gap': 4.34837933099,
  'energy-alpha-homo': -4.60960862747,
  'energy-alpha-lumo': -0.2612292964799998,
  'total-energy': -19286.973573267132,
  'homos': [54],
  'orbital-energies': [
    [
      -522.303488065215,
      -521.209590386205,
      -518.042185166385,
      ...,
      127.37105114203999
    ]
  ],
  'mo-count': 244,
  'basis-count': 244,
  'multiplicity': 1,
  'molecular-mass': 203.23557999999983,
  'number-of-atoms': 31,
  'lowdin-partial-charges': [
   -0.459759,
   0.210106,
   -0.286001,
   ...,
   0.169819
   ],
  'mulliken-partial-charges': [
   -0.542286,
   0.622923,
   -0.486172,
   ...,
   0.185706
  ],
  'dipole-moment': 11.419443262233626,
  'pubchem-multiplicity': 1,
  'pubchem-obabel-canonical-smiles': '[O-]C(=O)CC(C[N+](C)(C)C)OC(=O)C',
  'pubchem-isomeric-smiles': 'CC(=O)OC(CC(=O)[O-])C[N+](C)(C)C',
  'pubchem-molecular-weight': 203.23558,
  'pubchem-molecular-formula': 'C9H17NO4'
}

Data Fields

Field	Description
cid	Pubchem Compound ID
state	Electronic state
pubchem-inchi	InChI extracted from PubChem Compound entry
pubchem-charge	Molecular charge extracted from PubChem Compound entry
pubchem-version	PubChem Compound database version
name	Name of the input file used for the B3LYP/6-31G*//PM6 calculation
coordinates	Cartesian coordinates of the molecular geometry optimized with PM6 method in Angstroem
atomic-numbers	An array of atomic numbers
atom-count	Number of atoms in the molecule
heavy-atom-count	Number of heavy atoms in the molecule
core-electrons	Number of core electrons in each atom's pseudopotentials
bond-order	Bond order
connection-indices	Connection indices between atoms
formula	Chemical formula
version	Version number
obabel-inchi	InChI of the structure generated by Open Babel
pm6-obabel-canonical-smiles	Canonical SMILES for the structure generated by Open Babel
charge	Molecular charge
energy-beta-gap	HOMO-LUMO energy gap for beta spin orbitals
energy-beta-homo	Energy of the highest-occupied molecular orbital (HOMO) of beta spin symmetry
energy-beta-lumo	Energy of the lowest-unoccupied molecular orbital (LUMO) of beta spin symmetry
energy-alpha-gap	HOMO-LUMO energy gap for alpha spin orbitals
energy-alpha-homo	Energy of the highest-occupied molecular orbital (HOMO) of alpha spin symmetry
energy-alpha-lumo	Energy of the lowest-unoccupied molecular orbital (LUMO) of alpha spin symmetry
total-energy	Total electronic energy of the molecule calculated at the B3LYP/6-31G* level of theory
homos	1D index array of the highest occupied molecular orbital (HOMO) with one (two) element(s) for the (un)restricted wavefunctions
orbital-energies	1D array of orbital energies in hartree with one (two) member(s) for the (un)restricted wavefunction
mo-count	Number of molecular orbitals
basis-count	Number of basis functions
multiplicity	Spin multiplicity
molecular-mass	Molecular mass
number-of-atoms	Number of atoms in the molecule
lowdin-partial-charges	Lowdin partial atomic charges
mulliken-partial-charges	Mulliken partial atomic charges
dipole-moment	Dipole moment
pubchem-multiplicity	Spin multiplicity of the molecule extracted from PubChem Compound
pubchem-obabel-canonical-smiles	Canonical SMILES of the molecule extracted from PubChem Compound generated by Open Babel
pubchem-isomeric-smiles	Isomeric SMILES of the molecule extracted from PubChem Compound calculated by the OpenEye's OEChem Toolkit
pubchem-molecular-weight	Molecular weight extracted from the PubChem Compound entry
pubchem-molecular-formula	Molecular formula extracted from the PubChem Compound entry

Data Splits and Configurations

The dataset has only one train split. The PubChemQC B3LYP/6-31G*//PM6 dataset has six configurations/subsets:

• b3lyp_pm6 (default)
• b3lyp_pm6_chon300nosalt
• b3lyp_pm6_chon500nosalt
• b3lyp_pm6_chnopsfcl300nosalt
• b3lyp_pm6_chnopsfcl500nosalt
• b3lyp_pm6_chnopsfclnakmgca500

How to Use the Dataset

Prerequisites

We recommend isolating your work in a virtualenv or conda environment. You can create a new conda environment, pubchemqc,

  conda create -n pubchemqc python=3.12

and activate it using the following command

  conda activate pubchemqc

Once the conda environment is activated, you can install the dependencies in it as shown below

  pip install huggingface_hub ijson

Accessing the Data

Once the required packages are installed, you can run the following code to access the data

  # import the modules
  from datasets import load_dataset

  # load the dataset with streaming
  hub_ds = load_dataset(path="molssiai-hub/pubchemqc-b3lyp",
                        name="b3lyp_pm6",
                        split="train",
                        streaming=True,
                        cache_dir="./tmp",
                        trust_remote_code=True)

  # fetch a batch of 32 samples from the dataset
  ds = list(hub_ds.take(32))

The argument name by default is set to b3lyp_pm6 which refers to the entire dataset. Other configurations (subsets), listed in Sec. Data Splits and Configurations, can also be selected.

The split must be set to train as it is the only split in our dataset. We recommend using streaming=True to avoid downloading the entire dataset on disk. The cache_dir allows us to store the Hugging Face datasets' and models' artifacts in a non-default directory (by default, it is set to ~/.cache/huggingface). As we are using a custom load script, the trust_remote_code argument should also be set to True.

Dataset Creation

Curation Rationale

The present version of PubChemQC B3LYP/6-31G*//PM6 dataset has been extracted from its original Postgresql database, transformed into a dictionary and stored in the .json format.

Source Data

The link to the original PubChemQC B3LYP/6-31G*//PM6 dataset repository can be found here

Initial Data Collection and Normalization

Other than the changes detailed in Sec. Curation Rationale, no data modification has been performed on the PubChemQC B3LYP/6-31G*//PM6 dataset.

Personal and Sensitive Information

The PubChemQC B3LYP/6-31G*//PM6 dataset does not involve any personal or sensitive information.

Considerations for Using the Data

Social Impact of Dataset

The PubChemQC B3LYP/6-31G*//PM6 dataset paves the way for applications in drug discovery and materials science, among others.

Additional Information

Dataset Curators

• Maho Nakata, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
• Toshiyuki Maeda, Software Technology and Artificial Intelligence Research Laboratory, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino, Chiba 275-0016, Japan

Licensing Information

Creative Commons Attribution 4.0 International License

Citation Information

@article{Nakata:2023:5734,
   author = {Maho Nakata and Toshiyuki Maeda},
   doi = {10.1021/ACS.JCIM.3C00899},
   issn = {1549960X},
   issue = {18},
   journal = {Journal of Chemical Information and Modeling},
   pages = {5734-5754},
   publisher = {American Chemical Society},
   title = {{PubChemQC B3LYP/6-31G*//PM6 Data Set: The Electronic Structures of 86 Million Molecules
   Using B3LYP/6-31G* Calculations}},
   volume = {63},
   url = {https://pubs.acs.org/doi/abs/10.1021/acs.jcim.3c00899},
   year = {2023},
}

Contributions

• Mohammad Mostafanejad, The Molecular Sciences Software Institute (MolSSI)