chembricks/WB96MV-ORGANIC

Chembricks ωB97M-V Organic

Chembricks ωB97M-V Organic is a curated computational quantum-chemistry dataset containing 801,781 molecular structures. Each structure provides a gas-phase ωB97M-V single-point energy, HOMO and LUMO energies, an atom-resolved nuclear gradient, formal charge and spin, Cartesian coordinates, and traceable source provenance.

The DFT labels were evaluated on converged gas-phase GFN2-xTB geometries. They are protocol-defined computational reference values—not experimental measurements and not universal ground truth.

Dataset summary

Property	Value
Retained molecular identities	801,781
Retained conformers	801,781
Raw source records curated	805,046
Duplicate source occurrences merged	1,615
Hard-invalid source records rejected	1,650
Quarantined source occurrences	0
Retained records with an explicit connectivity flag	2,791
Formal charge −1 / 0 / +1	3,669 / 790,722 / 7,390
PySCF spin 2S = 0	801,781
Electronic-structure driver	RKS for every retained structure
Elements	H, B, C, N, O, F, Si, P, S, Cl, Br, I
Phase	Gas

The serialized format supports multiple conformers per molecular identity. In this release, the number of retained conformers equals the number of canonical identities, so each vacuum_conformers array contains one retained representative.

Intended uses

This dataset is suitable for research on:

• molecular energy and orbital-energy regression;
• atomistic energy/gradient and force-model development;
• representation learning on molecular geometries;
• uncertainty estimation and out-of-distribution detection;
• quantum-chemistry surrogate models; and
• analysis of SCF behavior across organic and main-group chemical space.

It is not intended to provide experimental observables, solvent-phase properties, reaction barriers, DFT-optimized stationary points, or thermochemical quantities.

Release scope

The release scope was fixed by a deterministic source-chunk rule:

Source campaign	Included chunk IDs	Source files	Raw records
Campaign 1	0–38	39	397,482
Campaign 2	0–81	82	407,564
Total		121	805,046

The chunk-prefix selection is reproducible, but it was not a randomized or distribution-preserving sample. Keep the supplied source references when constructing evaluations, and do not assume that records are independently and identically distributed solely because canonical identities are unique.

From SMILES to the stored DFT result

SMILES + formal charge
        │
        ▼
10 candidate 3D structures generated with g-xTB
        │
        ▼
gas-phase GFN2-xTB very-tight geometry optimization
        │
        ▼
identity, composition, convergence and geometry validation
        │
        ▼
gas-phase PySCF ωB97M-V single-point calculation
        │
        ▼
energy + HOMO/LUMO + nuclear gradient + xTB geometry
        │
        ▼
deduplication, conflict checks and robust outlier curation

The workflow starts from a molecular SMILES and explicit formal charge. g-xTB generates ten candidate three-dimensional structures. A selected candidate is optimized in the gas phase with GFN2-xTB using the very-tight convergence setting. PySCF then evaluates one ωB97M-V single point on that xTB geometry.

The DFT stage does not optimize the geometry (perform_opt: false) and does not request thermochemistry (thermo: false). The dataset therefore contains no DFT stationary geometries, Hessians, harmonic frequencies, zero-point energies, enthalpies, or finite-temperature Gibbs free energies. A nonzero stored gradient is expected because it is evaluated at an xTB-optimized rather than ωB97M-V-optimized geometry.

Quantum-chemistry protocol

Setting	Value
Functional	ωB97M-V (wb97m-v)
Functional class	Range-separated hybrid meta-GGA with VV10 nonlocal correlation
Program	PySCF 2.9.0
Phase	Gas; solvent: null
Geometry	Gas-phase GFN2-xTB very-tight optimization
DFT calculation	Single point only
Numerical grid	PySCF grid level 5 plus the VV10 nonlocal grid
Density fitting	RI-JK through PySCF density_fit()
Orbital basis/ECP scheme	qmcbasis: NWChem-format, commit-declared aug-cc-pVTZ orbital-basis and matching ccECP map for observed elements
Auxiliary basis	cc-pvdz-jkfit; iodine override def2-universal-jkfit
SCF level shift	0.5 Hartree
Maximum SCF cycles	250
Driver and spin	RKS; every retained entry has PySCF spin = Nα − Nβ = 2S = 0
Direct SCF	PySCF default behavior; no explicit screening tolerance was serialized
Coordinates	Å
Energies	Hartree (Eh)
Nuclear gradient	Hartree/bohr (Eh/a₀)

ωB97M-V includes exact Hartree–Fock exchange. RI-JK therefore fits both the Coulomb (J) and exchange (K) contributions rather than using a Coulomb-only J-fit.

CDS means cavitation–dispersion–solvent-structure correction. Because these calculations are gas phase and do not use SMD, solvent_energy and cds_correction are exactly zero for every retained structure.

Curation and quality control

The curation procedure canonicalized identity with RDKit and applied the following non-negotiable checks:

• converged GFN2-xTB geometry optimization and converged DFT SCF;
• finite SCF, solvent, CDS, HOMO, LUMO, coordinate, and gradient values;
• matching element composition, formal charge, electron-count parity, spin, and RKS driver;
• one coordinate and one gradient vector per atom, with three finite Cartesian components;
• HOMO <= LUMO and an SCF-cycle count between 1 and 250;
• the expected gas-phase ωB97M-V method, basis scheme, grid, level shift, and calculation mode;
• no severe atomic collisions; and
• robust median/MAD energy screens within canonical-identity and molecular-formula groups.

Within one canonical identity, symmetry-aware exact duplicates were identified after atom mapping and rigid alignment. Both the heavy-atom and all-atom RMSD had to be at most 10^-6 Å. Duplicate labels were required to agree within 10^-5 Hartree for SCF energy, solvent energy, CDS correction, HOMO, and LUMO; aligned gradient components were required to agree within 10^-6 Hartree/bohr. One deterministic representative was retained and redundant occurrences were attached to its provenance rather than emitted as extra training examples.

The released curation policy allows a composition-consistent geometry to differ in connectivity from its canonical SMILES. The diagnostic proximity graph uses 1.25 × the sum of RDKit covalent radii when checking expected SMILES bonds. The 2,791 retained structures for which an expected bond was not present carry:

"curation_flags": ["connectivity_mismatch_allowed_by_mild"]

These structures are intentionally visible rather than silently relabeled. Users can retain them, exclude them, or evaluate them as a separate slice. Geometry-derived identity inference was permitted when source SMILES was absent and uniquely resolvable, but no retained record in this release required it.

Curation accounting

Outcome	Count	Share of 805,046 raw records
Retained distinct representative	801,781	99.594%
Duplicate occurrence merged into provenance	1,615	0.201%
Quarantined	0	0.000%
Hard rejected	1,650	0.205%
Total	805,046	100.000%

The final artifact passed streaming standard-JSON parsing, non-finite-value checks, ID uniqueness checks, exact accounting closure, source-reference validation, geometry/gradient shape checks, method-profile validation, and a complete SHA-256 rehash.

Distributed file

File	Size	SHA-256
wb97m_v_organic_public_2026-08-16.json	3,266,960,267 bytes	e1abc9a68ca2a782d9bf0c9605325a9be67607c68e394f7b365df529599cffeb

The artifact is standard JSON, not JSON Lines. It uses an identity-grouped envelope rather than storing one independent object per line:

root
├── schema_version
├── metadata
├── source_files[]
└── molecules[]
    ├── molecular identity
    └── vacuum_conformers[]
        ├── geometry
        ├── log_data
        └── provenance and curation fields

JSON field reference

Top-level fields

Field	Type	Meaning
schema_version	string	Serialization schema version; currently 1.0.0.
metadata	object	Dataset identity, version, counts, curation settings, units, calculation protocol, and manifest fingerprints.
source_files	array of objects	Table of source-file provenance. source_ref.file_id values resolve against this table.
molecules	array of objects	The 801,781 retained canonical molecular identities.

metadata

Field	Meaning
dataset_name	Human-readable dataset name.
dataset_version	Version of the curated release.
description	Short description of the retained labels and structures.
counts	Exact molecules, conformers, and source_records counts.
state_mapping	Declares that vacuum_conformers stores validated gas-phase DFT states.
identity_policy	Canonical molecular-identity rule.
curation_policy	Duplicate, label-tolerance, identity-inference, and connectivity-policy settings.
units	Canonical units for coordinates, energies, gradients, and timing data.
calculation_protocols	Full protocol object referenced by each conformer's protocol_id.
source_manifest_logical_sha256	Logical fingerprint of the source manifest used for the build.
dependency_manifest_logical_sha256	Logical fingerprint of the curation implementation and runtime dependencies.
curation_config_logical_sha256	Logical fingerprint of the effective curation configuration.

source_files[]

Field	Type	Meaning
id	integer	Dataset-local file identifier used by conformer provenance.
relative_path	string	Stable logical source path; it is not a local machine path.
collection	string	Source campaign identifier.
protocol_id	string	Calculation protocol applied to records in the source file.
record_count	integer	Number of raw records in that source file.
size_bytes	integer	Raw source-file size in bytes.
sha256	string	SHA-256 digest of the raw source file.

molecules[]

Field	Type	Meaning
molecule_id	string	Deterministic ID of the form mol- plus 24 hexadecimal characters, derived from the canonical SMILES with a versioned SHA-256 namespace. It is a dataset ID, not an InChIKey.
canonical_smiles	string	RDKit canonical isomeric SMILES used as the molecular identity.
original_smiles	array of strings	Unique original SMILES carried by retained representative records grouped under this identity.
formal_charge	integer	Molecular formal charge; validated against both identity and log_data.charge.
vacuum_conformers	array of objects	Retained gas-phase conformer records. The schema supports multiple conformers; this release contains one per identity.

vacuum_conformers[]

Field	Type	Meaning
conformer_id	string	Deterministic ID of the form conf- plus 24 hexadecimal characters, derived from canonical identity and the normalized conformer payload.
geometry	object	Ordered atom symbols and Cartesian coordinates of the converged xTB geometry.
log_data	object	Normalized DFT labels, protocol fields, gradient, and optional runtime diagnostics.
source_occurrence_count	integer	Number of raw occurrences represented by this retained conformer. A value greater than one means redundant occurrences were merged.
source_ref	object	Provenance of the deterministic representative.
merged_source_refs	array of objects, optional	Provenance of redundant source occurrences merged into the representative. These are not extra training examples.
curation_flags	array of strings, optional	Explicit retained-policy flags. Absence means that no such flag applies.

geometry

Field	Type	Meaning
elements	array of strings, length N	Atomic symbols in the stored geometry atom order.
coordinates	array of [x, y, z], shape [N, 3]	Finite Cartesian coordinates aligned row-for-row with elements; unit is Å.
unit	string	Always angstrom.
method	string	xTB, indicating that the geometry came from the GFN2-xTB optimization.

geometry.elements[i], geometry.coordinates[i], and log_data.gradient[i] always refer to the same atom.

log_data

Field	Type	Unit	Meaning
converged	boolean	—	Always true for retained SCF calculations.
scf_energy	number	Hartree	Total gas-phase ωB97M-V SCF energy.
homo	number	Hartree	Highest occupied molecular-orbital energy.
lumo	number	Hartree	Lowest unoccupied molecular-orbital energy.
gradient	array of [gx, gy, gz], shape [N, 3]	Hartree/bohr	Nuclear derivative ∂E/∂R in geometry atom order. A force target is the negative gradient.
charge	integer	elementary charge	Total molecular charge; equals the enclosing formal_charge.
spin	integer	—	PySCF spin Nα − Nβ = 2S; every retained value is 0. This is not the multiplicity 2S + 1.
driver	string	—	SCF driver; always RKS in this release.
cycles	integer	—	Number of SCF cycles, from 1 through 250.
xc	string	—	Exchange-correlation functional identifier; wb97m-v.
basis	string	—	Basis/ECP scheme identifier; qmcbasis. Resolve details through the matching protocol object.
grid_level	integer	—	PySCF numerical grid level; 5.
level_shift	number	Hartree	SCF level shift; 0.5.
solvent	null	—	Always null; calculations are gas phase.
solvent_energy	number	Hartree	Always 0.0 in this gas-phase release.
cds_correction	number	Hartree	Always 0.0; CDS is the cavitation–dispersion–solvent-structure correction.
perform_opt	boolean	—	Always false; no DFT geometry optimization was performed.
thermo	boolean	—	Always false; no Hessian/frequency thermochemistry was requested.
protocol_id	string	—	Foreign key into metadata.calculation_protocols; here dev_crux_0153337.
time	number, optional	seconds	Reported total calculation timing diagnostic.
pyscf_time	number, optional	seconds	Reported PySCF-stage timing diagnostic.
memory_usage_mb	number, optional	MB	Reported memory-use diagnostic.
ncores	integer, optional	cores	Reported CPU-core count.

Runtime and resource fields are environment-dependent diagnostics, not molecular labels.

Provenance objects

source_ref and entries in optional merged_source_refs contain:

Field	Meaning
file_id	Foreign key into top-level source_files.
result_index	Zero-based record index inside that source file.
uuid	Original source UUID when supplied.
relative_path	Stable logical source path.
collection	Source campaign identifier.

For every conformer, source_occurrence_count is the representative occurrence plus the number of entries in merged_source_refs.

Memory-safe loading

The JSON file is approximately 3.27 GB, so avoid json.load() unless sufficient memory is available. The top-level molecules array can be streamed with ijson:

pip install huggingface_hub ijson

from huggingface_hub import hf_hub_download
import ijson

path = hf_hub_download(
    repo_id="chembricks/WB96MV-ORGANIC",
    filename="wb97m_v_organic_public_2026-08-16.json",
    repo_type="dataset",
)

with open(path, "rb") as handle:
    molecules = ijson.items(handle, "molecules.item")
    for molecule in molecules:
        conformer = molecule["vacuum_conformers"][0]
        elements = conformer["geometry"]["elements"]
        coordinates_angstrom = conformer["geometry"]["coordinates"]
        energy_hartree = conformer["log_data"]["scf_energy"]
        gradient_hartree_per_bohr = conformer["log_data"]["gradient"]
        # Train, transform, or yield the record here.

Recommended ML practice

• Split on molecule_id, canonical SMILES, or a molecular scaffold—not on provenance occurrences.
• Do not expand merged_source_refs into repeated examples; those objects document redundancy.
• Keep the coordinate, element, and gradient arrays in exactly the same atom order.
• If training forces, use force = -gradient and convert both energy and length units consistently.
• Preserve protocol_id, even though the release currently contains one protocol.
• Decide explicitly how to handle the 2,791 connectivity_mismatch_allowed_by_mild structures and report that decision.
• Do not compare raw total energies across different elemental compositions as though they were directly normalized molecular properties.
• Prefer scaffold-aware or source-aware evaluation when estimating chemical generalization.

Limitations

• These are computed labels and inherit the approximations of GFN2-xTB geometries, ωB97M-V, the basis/ECP scheme, RI-JK density fitting, and the numerical settings.
• The structures are not DFT stationary points; gradients generally do not vanish.
• The release contains closed-shell RKS calculations only and does not represent open-shell chemistry.
• It contains gas-phase values only. Solvation, condensed-phase effects, and finite-temperature thermochemistry are absent.
• Canonical SMILES is the identity key, but 2,791 retained geometries carry an explicit connectivity-change flag.
• The deterministic source-chunk selection is not equivalent to a random sample of chemical space.
• Timing and memory fields depend on the calculation environment and should not be treated as intrinsic molecular properties.

License

The dataset is released under the MIT License.

Citation

If you use the dataset, cite the Hugging Face repository and the ωB97M-V method paper:

@misc{chembricks_wb97mv_organic_2026,
  author       = {Chembricks},
  title        = {Chembricks ωB97M-V Organic},
  year         = {2026},
  howpublished = {Hugging Face dataset},
  url          = {https://huggingface.co/datasets/chembricks/WB96MV-ORGANIC},
  note         = {Version 2026-08-16-v1-mild}
}

• N. Mardirossian and M. Head-Gordon, “ωB97M-V: A combinatorially optimized, range-separated hybrid, meta-GGA density functional with VV10 nonlocal correlation,” Journal of Chemical Physics 144, 214110 (2016). DOI: 10.1063/1.4952647
• PySCF density-fitting documentation