README.md

---
license: cc-by-nc-4.0
language:
- en
pretty_name: THEMol
size_categories:
- 1B<n<10B
tags:
- chemistry
- molecular-dynamics
- density-functional-theory
- medicine
- electrolytes
configs:
- config_name: hessian
  data_files:
  - split: full
    path: "Hessian/hessian_dataset.csv"
- config_name: hessianrelax
  data_files:
  - split: full
    path: "HessianRelax/relax_dataset.csv"
- config_name: torsionscan
  data_files:
  - split: full
    path: "TorsionScan/torsion_dataset.csv"
- config_name: torsionscanrelax
  data_files:
  - split: full
    path: "TorsionScanRelax/torsion_relax_dataset.csv"
- config_name: mbis
  data_files:
  - split: full
    path: "MBIS/mbis_dataset.csv"
---

# 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](https://arxiv.org/abs/XXXX.XXXXX) and [GitHub repository](https://github.com/ByteDance-Seed/THEMol) 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](https://github.com/ByteDance-Seed/THEMol)
- **Paper** [https://arxiv.org/abs/XXXX.XXXXX](https://arxiv.org/abs/XXXX.XXXXX)
- **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)](https://creativecommons.org/licenses/by-nc/4.0/).

## Citation

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

```bibtex
@article{THEMol,
      title={THEMol: Torsion, Hessian, Energy of Molecules},
      author={Author1 and Author2},
      year={2026},
      eprint={XXXX.XXXXX},
      archivePrefix={arXiv},
      primaryClass={cs.XX}
}
```