Datasets:

molssiai-hub
/

pubchemqc-b3lyp

	---
	license:
	- cc-by-4.0
	license_link: https://creativecommons.org/licenses/by/4.0
	tags:
	- homo-lumo-gaps
	- energy
	- dipole-moments
	- quantum-chemistry
	- pubchem
	- small-molecules
	annotations_creators:
	- crowdsourced
	pretty_name: pubchemqc-b3lyp
	size_categories:
	- 10K<n<100M
	source_datasets:
	- pubchem
	- pubchemqc-b3lyp
	task_categories:
	- tabular-regression
	- other
	task_ids:
	- tabular-single-column-regression
	viewer: false
	configs:
	- config_name: b3lyp_pm6
	data_files:
	- split: train
	path: "data/b3lyp_pm6/train/*.json"
	default: true
	- config_name: b3lyp_pm6_chon300nosalt
	data_files:
	- split: train
	path: "data/b3lyp_pm6_chon300nosalt/train/*.json"
	- config_name: b3lyp_pm6_chon500nosalt
	data_files:
	- split: train
	path: "data/b3lyp_pm6_chon500nosalt/train/*.json"
	- config_name: b3lyp_pm6_chnopsfcl300nosalt
	data_files:
	- split: train
	path: "data/b3lyp_pm6_chnopsfcl300nosalt/train/*.json"
	- config_name: b3lyp_pm6_chnopsfcl500nosalt
	data_files:
	- split: train
	path: "data/b3lyp_pm6_chnopsfcl500nosalt/train/*.json"
	- config_name: b3lyp_pm6_chnopsfclnakmgca500
	data_files:
	- split: train
	path: "data/b3lyp_pm6_chnopsfclnakmgca500/train/*.json"
	---

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

	## Table of Contents

	- [PubChemQC-B3LYP/6-31G\*//PM6 Dataset](#pubchemqc-b3lyp6-31gpm6-dataset)
	- [Table of Contents](#table-of-contents)
	- [Dataset Description](#dataset-description)
	- [Dataset Summary](#dataset-summary)
	- [Dataset Structure](#dataset-structure)
	- [Data Instances](#data-instances)
	- [Data Fields](#data-fields)
	- [Data Splits and Configurations](#data-splits-and-configurations)
	- [How to Use the Dataset](#how-to-use-the-dataset)
	- [Prerequisites](#prerequisites)
	- [Accessing the Data](#accessing-the-data)
	- [Dataset Creation](#dataset-creation)
	- [Curation Rationale](#curation-rationale)
	- [Source Data](#source-data)
	- [Initial Data Collection and Normalization](#initial-data-collection-and-normalization)
	- [Personal and Sensitive Information](#personal-and-sensitive-information)
	- [Considerations for Using the Data](#considerations-for-using-the-data)
	- [Social Impact of Dataset](#social-impact-of-dataset)
	- [Additional Information](#additional-information)
	- [Dataset Curators](#dataset-curators)
	- [Licensing Information](#licensing-information)
	- [Citation Information](#citation-information)
	- [Contributions](#contributions)

	## Dataset Description

	- Homepage: https://nakatamaho.riken.jp/pubchemqc.riken.jp/b3lyp_pm6_datasets.html
	- Repository: https://nakatamaho.riken.jp/pubchemqc.riken.jp/b3lyp_pm6_datasets.html
	- Paper: https://doi.org/10.1021/acs.jcim.3c00899
	- Point of Contact: [Maho Nakata](maho@riken.jp)
	- Point of Contact: [Mohammad Mostafanejad](smostafanejad@vt.edu)
	- Point of Contact: [MolSSI-AI Hub](hub@molssi.org)

	### 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:

	```json
	{'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.B3LYP@PM6.S0',
	'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`,

	```bash
	conda create -n pubchemqc python=3.12
	```

	and activate it using the following command

	```bash
	conda activate pubchemqc
	```

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

	```bash
	pip install huggingface_hub ijson
	```

	### Accessing the Data

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

	```python
	# 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](#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](https://huggingface.co/datasets/molssiai-hub/pubchemqc-b3lyp/blob/main/pubchemqc-b3lyp.py), 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](https://nakatamaho.riken.jp/pubchemqc.riken.jp/b3lyp_pm6_datasets.html)

	#### Initial Data Collection and Normalization

	Other than the changes detailed in Sec. [Curation Rationale](#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](https://creativecommons.org/licenses/by/4.0)

	### Citation Information

	```tex
	@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)