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SquareHK/THEMol

THEMol: Torsion, Hessian, Energy of Molecules Dataset Summary THEMol is an open-source collection of quantum mechanical properties tailored for organic molecules. It provides large-scale density functional theory (DFT) data for exploring intramolecular potential energy surfaces, including optimized geometries, structural relaxation trajectories, torsion scans, constrained torsion relaxation trajectories, Hessian matrices, and MBIS-derived atomic properties. The… See the full description on the dataset page: https://huggingface.co/datasets/SquareHK/THEMol.

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THEMol: Torsion, Hessian, Energy of Molecules

Dataset Summary

THEMol is an open-source collection of quantum mechanical properties tailored for organic molecules. It provides large-scale density functional theory (DFT) data for exploring intramolecular potential energy surfaces, including optimized geometries, structural relaxation trajectories, torsion scans, constrained torsion relaxation trajectories, Hessian matrices, and MBIS-derived atomic properties.

The dataset contains five tailored subsets and over three billion DFT calculations for molecules with up to 50 non-hydrogen atoms. Its chemical space spans twelve essential elements and diverse molecular architectures relevant to drug discovery, electrolytes, ionic liquids, and broader molecular modeling applications.

See the paper and GitHub repository for more details. The GitHub repository provides data readers, validation utilities, and statistical scripts.

Dataset Details

Dataset Description

—Repository https://github.com/ByteDance-Seed/THEMol
—Paper https://arxiv.org/abs/2605.14973
—Data format CSV index files plus HDF5 data files.
—Computation scale more than three billion DFT calculations across five subsets.
—Molecular scope organic molecules with up to 50 non-hydrogen atoms.
—Element coverage H, C, N, O, S, F, Cl, Br, Si, B, P, and I.

Subsets

Subset	Level of Theory	Entries	Supplementary Metrics	Description
Hessian	B3LYP-D3(BJ)/DZVP	3,102,537	-	Optimized molecular geometries and corresponding Hessian matrices.
Hessian Relax	B3LYP-D3(BJ)/DZVP	4,811,722	281,123,880 relaxation steps	Complete structural relaxation trajectories for the Hessian subset.
TorsionScan	B3LYP-D3(BJ)/DZVP	4,192,791	2,436,985 molecules; 93,994,576 constraints	Comprehensive in-ring and non-ring torsional scans after constrained optimization.
TorsionScan Relax	B3LYP-D3(BJ)/DZVP	4,914,677	3,090,560 molecules; 110,235,160 constraints; 2,993,685,868 steps	Complete constrained structural relaxation trajectories for the TorsionScan subset.
MBIS	PBE0/def2-TZVPD, or DZVP for I atoms	3,082,151	-	Atomic properties and model parameters from Minimal Basis Iterative Stockholder (MBIS) partitioning.

Dataset Structure

The dataset is organized by subset. Each subset contains one CSV index file and HDF5 files referenced by the h5_file column.

text

/
├── Hessian/
│   ├── hessian_dataset.csv
│   └── *.h5
├── HessianRelax/
│   ├── relax_dataset.csv
│   └── *.h5
├── TorsionScan/
│   ├── torsion_dataset.csv
│   └── *.h5
├── TorsionScanRelax/
│   ├── torsion_relax_dataset.csv
│   └── *.h5
└── MBIS/
    ├── mbis_dataset.csv
    └── *.h5

Data Fields

All HDF5 files are keyed by uuid. The CSV index files contain the UUID, mapped SMILES strings, and the HDF5 file location needed to retrieve each molecular record.

Hessian

CSV columns: uuid, mapped_nonisomeric_smiles, mapped_isomeric_smiles, h5_file

HDF5 structure:

text

/<uuid>/
  mapped_nonisomeric_smiles  utf-8 string
  mapped_isomeric_smiles     utf-8 string
  atomic_numbers             (N, 1) int32
  coords                     (N, 3) float64
  hessian                    (3N, 3N) float64

Hessian Relax

CSV columns: uuid, mapped_nonisomeric_smiles, mapped_isomeric_smiles, num_steps, h5_file

HDF5 structure:

text

/<uuid>/
  mapped_nonisomeric_smiles  utf-8 string
  mapped_isomeric_smiles     utf-8 string
  atomic_numbers             (N, 1) int32
  step 0/
    energy                   scalar float64
    coords                   (N, 3) float64
    forces                   (N, 3) float64
  ...
  step k/
    energy                   scalar float64
    coords                   (N, 3) float64
    forces                   (N, 3) float64

TorsionScan

CSV columns: uuid, mapped_nonisomeric_smiles, mapped_isomeric_smiles, torsion_indices, h5_file, num_constraints

HDF5 structure:

text

/<uuid>/
  mapped_nonisomeric_smiles  utf-8 string
  mapped_isomeric_smiles     utf-8 string
  atomic_numbers             (N, 1) int32
  torsion_atom_indices       (4,) int32
  constraint 0/
    energy                   scalar float64
    coords                   (N, 3) float64
    forces                   (N, 3) float64
  constraint 1/
    ...

TorsionScan Relax

CSV columns: uuid, mapped_nonisomeric_smiles, mapped_isomeric_smiles, torsion_indices, h5_file, num_constraints, num_total_steps

HDF5 structure:

text

/<uuid>/
  mapped_nonisomeric_smiles  utf-8 string
  mapped_isomeric_smiles     utf-8 string
  atomic_numbers             (N, 1) int32
  torsion_atom_indices       (4,) int32
  constraint 0/
    energy                   (M,) float64
    coords                   (M, N, 3) float64
    forces                   (M, N, 3) float64
  constraint 1/
    ...

Here M is the number of steps.

MBIS

CSV columns: uuid, mapped_nonisomeric_smiles, mapped_isomeric_smiles, h5_file

HDF5 structure:

text

/<uuid>/
  mapped_nonisomeric_smiles  utf-8 string
  mapped_isomeric_smiles     utf-8 string
  atomic_numbers             (N, 1) int32
  coords                     (N, 3) float64
  mbis_info/
    atomic_volumes           (N, 1) float64
    atomic_charge            (N, 1) float64
    atomic_dipole            (N, 3) float64
    atomic_quadrupole        (N, 3, 3) float64
  parameters                 (M, 3) float64

Here M is the number of MBIS Slater functions.

For parameters, each row contains the 0-based parent atom index, the Slater-function charge population N_i, and the inverse width 1/sigma_i.

Units

Quantity	Unit
Coordinates	Å
Energy	kcal mol^-1
Force	kcal mol^-1 Å^-1
Hessian	kcal mol^-1 Å^-2
Charge	e
Dipole	e Å
Quadrupole	e Å^2
Volume	Å^3
1/sigma_i	Å^-1

Licenses

Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0).

Citation

If you use THEMol in your research or applications, please cite:

bibtex

@misc{THEMol,
      title={THEMol dataset: Torsion, Hessian, and Energy of Molecules}, 
      author={Jiashu Liang and Tianze Zheng and Yu Xia and Xingyuan Xu and Xu Han and Zhi Wang and Siyuan Liu and Ailun Wang and Yu Liu and Shiqian Tan and Dongfei Liu and Zhichen Pu and Yuanheng Wang and Qiming Sun and Xiaojie Wu and Wen Yan},
      year={2026},
      eprint={2605.14973},
      archivePrefix={arXiv},
      primaryClass={physics.chem-ph},
      url={https://arxiv.org/abs/2605.14973}, 
}