Datasets:
Modalities:
Image
Size:
n<1K
Tags:
chemistry
ionic-liquids
thermodynamics
activity-coefficients
molecular-property-prediction
cosmo-rs
DOI:
License:
| license: cc-by-4.0 | |
| pretty_name: COSMOBridge — data, frozen predictions and DFT outputs | |
| size_categories: | |
| - n<1K | |
| tags: | |
| - chemistry | |
| - ionic-liquids | |
| - thermodynamics | |
| - activity-coefficients | |
| - molecular-property-prediction | |
| - cosmo-rs | |
| - dft | |
| # COSMOBridge — data, frozen predictions and DFT outputs | |
| Archive accompanying *"COSMOBridge: Bridging 2D Molecular Graphs and 3D Electrostatic | |
| Surfaces for Ionic Liquid Thermodynamic Property Prediction"* (submitted to the | |
| *Journal of Chemical Information and Modeling*). | |
| Source code: <https://github.com/taminulislam/COSMOBridge> (MIT licence). | |
| Archive DOI: [10.57967/hf/11424](https://doi.org/10.57967/hf/11424). | |
| This repository is the permanent record of the data, models and predictions behind the | |
| paper's tables and figures. | |
| > **The predictions in `predictions/` are deposited before the validation measurements | |
| > described in Section 5.3 of the paper are made.** Their purpose is to fix the model's | |
| > output so that those measurements score predictions made *ex ante*. Please do not | |
| > amend that directory after the measurements begin. | |
| ## Contents | |
| | Path | What it is | Used by | | |
| |---|---|---| | |
| | `dataset/` | the curated 28-ionic-liquid dataset, split by ionic-liquid identity into 19 train (152 rows) / 4 validation (32) / 5 test (39), plus `split_info.json` naming the ILs in each split | Table 1, §2.2, all training | | |
| | `predictions/candidates_110_frozen_ranking.csv` | the full 110-candidate virtual screen, per-seed means and standard deviations, in original units | Table 7, Figure 7 | | |
| | `predictions/test_set_predictions.npz` | held-out test-set predictions: 5 COSMOBridge seeds, the Chemprop baseline, the fusion path, and the targets | Tables 3 and 4, the bootstrap tests | | |
| | `predictions/top20_candidates.csv` | the 20 candidates carried forward to DFT | SI Table S2 | | |
| | `dft/nwchem_outputs/` | raw NWChem B3LYP/def2-SVP + COSMO outputs, 40 single points covering 16 unique ions | SI Table S2 | | |
| | `dft/nwchem_inputs/`, `dft/geometries/` | the inputs and GFN2-xTB geometries those runs used | reproduction | | |
| | `checkpoints/` | trained weights for the reported models | Table 3 | | |
| | `analysis/*.json` | outputs of the bootstrap and seed-matched baseline runs, as reported in the paper | §4.1, Table 3 | | |
| | `experimental/` | characterization report and figures for the two synthesized salts | §5.2, SI §S2 | | |
| ## Reproducing the analyses | |
| All code lives in the GitHub repository above; this archive holds only data and model | |
| weights. The scripts `scripts/revision/b5_chemprop_multiseed.py` (Chemprop over the five | |
| shared seeds, Table 3) and `scripts/revision/b6_cluster_bootstrap.py` (row-level and | |
| IL-level bootstrap, Section 4.1) read `dataset/` and `predictions/` from here and | |
| reproduce `analysis/b5_chemprop_multiseed.json` and `analysis/b6_cluster_bootstrap.json`. | |
| `analysis/c1_official_bootstrap.json` is the original row-level bootstrap that the paper | |
| reports alongside them. | |
| ## Notes on the data | |
| - **The 39 test rows are 8 temperatures of each of 5 ionic liquids and are not | |
| independent.** `b6_cluster_bootstrap.py` resamples at both levels; the IL-level | |
| interval is the conservative one. | |
| - **The DFT solvation energies are a null result.** They are the | |
| `(electrostatic) solvation energy` line of each NWChem COSMO block, reported as | |
| `E_sol - E_gas`, and they do **not** correlate with the screen's ranking | |
| (Spearman rho = -0.28, p = 0.23). Do not read them as support for the ranking. | |
| - **Activity coefficients are plain gamma, not ln gamma**, at `x1 = 0.5` and the stated | |
| temperature. The identity `G^E = RT(x1 ln g1 + x2 ln g2)` closes to within | |
| 0.09 kcal/mol on this footing. | |
| - The dataset grid is complete except for EMIMOAc at 323.15 K: 223 rows, not 224. | |
| - No data are withheld. | |
| ## Citation | |
| ```bibtex | |
| @article{cosmobridge2026, | |
| author = {Ahmed, Khaled and Islam, Taminul and Acquah, Alex and Achinivu-Ibagere, Ezinne C.}, | |
| title = {{COSMOBridge}: Bridging {2D} Molecular Graphs and {3D} Electrostatic | |
| Surfaces for Ionic Liquid Thermodynamic Property Prediction}, | |
| journal = {Journal of Chemical Information and Modeling}, | |
| year = {2026}, | |
| note = {Submitted} | |
| } | |
| ``` | |