--- { "pretty_name": "ChemBricks Knowledge: Evidence-Linked Chemistry", "license": "mit", "language": [ "en" ], "task_categories": [ "question-answering", "text-generation" ], "tags": [ "chemistry", "computational-chemistry", "scientific-reasoning", "tool-use", "provenance", "synthetic", "text" ], "annotations_creators": [ "machine-generated" ], "language_creators": [ "machine-generated" ], "size_categories": [ "1K Why might caffeine favor one solvent over the other? Test a polarity-based explanation of its model-predicted logP against both solvation free energies and a competing structural explanation. In everyday language: **Why does the model say caffeine prefers water or octanol, and do its polarity and structure descriptors support that answer?** ### Scientific reasoning trace, abridged The following reading guide summarizes the recorded investigation. The expandable excerpt preserves the original tool calls, result values, and request IDs; the [complete original trace](examples/caffeine-trace.md) includes all steps, checks, interpretations, and follow-up questions. 1. **Define competing explanations.** The polarity-based hypothesis favors water. The competing structural explanation asks whether the methylated ring framework could favor octanol. State what observation would count against each explanation. 2. **Establish the input.** Canonicalize the caffeine structure and run the required safety screen so subsequent calculations refer to the same molecular representation. 3. **Measure the relevant evidence.** Record polarity and structural descriptors, then obtain the predicted logP and both solvent free energies from the primary solvation endpoint. Descriptors supply context for an explanation; their coexistence does not isolate a cause. 4. **Check the result through another route.** Obtain the screening-grade RDKit Crippen logP estimate. Use recorded calculator calls for the water-minus-octanol free-energy difference and the absolute difference between the logP predictions. 5. **Interpret within the tested scope.** The results favor water for this modeled molecular form. Review consistency between the observations, retain the limitations of the screening comparison, and propose an experimental partition measurement and a structural counterfactual to investigate the explanation further. This record retains **prediction_timing: unverified**. The original wording of its hypotheses is preserved, but their timing relative to computation is not independently established; read the hypothesis comparison as exploratory.
Read the recorded calculation and cross-check steps #### Step 6: Run the primary solvation and partition endpoint The authorized recovery probe asks one endpoint for both solvent free energies and the octanol-water partition prediction. The bare vacuum total energy is deliberately omitted. ```tool {"tool":"cmbx_solvation_logp_v2","args":{"smiles":"Cn1c(=O)c2c(ncn2C)n(C)c1=O"}} ``` ```result request_id=a3b1b491f9695d09-PRG {"job_id":"pred_c060f56099dc","status":"completed","smiles":"Cn1c(=O)c2c(ncn2C)n(C)c1=O","prediction":{"solvation_energy_water":{"Ha":-0.02153054236494381,"kcal/mol":-13.510619315719184},"solvation_energy_octanol":{"Ha":-0.02059061911148131,"kcal/mol":-12.920808569279254},"octanol_water_log_p":-0.4323343695216262},"trust_factor":55.75} ``` The primary endpoint returned all requested values. #### Step 7: Run the required screening-grade logP cross-route The legacy consensus field is a single RDKit Crippen estimate, not a multi-model consensus. ```tool {"tool":"logp_ensemble","args":{"smiles":"Cn1c(=O)c2c(ncn2C)n(C)c1=O"}} ``` ```result request_id=a3b1b4c29ecab605-PRG {"smiles":"Cn1c(=O)c2c(ncn2C)n(C)c1=O","logp_values":{"rdkit_crippen":-1.029},"consensus_logp":-1.029} ``` The screening-grade cross-route is available. #### Step 8: Calculate the signed solvent free-energy split The predeclared sign convention is water minus octanol. This arithmetic tests the solvent-preference direction without deriving logP from an assumed temperature. ```tool {"tool":"calculate","args":{"expression":"water - octanol","variables":{"water":-13.510619315719184,"octanol":-12.920808569279254}}} ``` ```result request_id=a3b1b509f8b21e28-PRG {"result":-0.5898107464399303,"expression":"water - octanol","variables_used":{"water":-13.510619315719184,"octanol":-12.920808569279254}} ``` The signed split has the polarity hypothesis's predicted direction. #### Step 9: Calculate the cross-route logP agreement band The absolute difference is an agreement measure between the primary model and the screening descriptor. ```tool {"tool":"calculate","args":{"expression":"abs(primary - screening)","variables":{"primary":-0.4323343695216262,"screening":-1.029}}} ``` ```result request_id=a3b1b52729acf980-PRG {"result":0.5966656304783737,"expression":"abs(primary - screening)","variables_used":{"primary":-0.4323343695216262,"screening":-1.029}} ``` The cross-route difference is within the configured tolerance.
### Recorded answer, excerpt These opening paragraphs are copied from the record, including the numerical evidence references: > For canonical caffeine, cmbx_solvation_logp_v2 predicts an octanol-water logP of -0.4323343695216262 with trust_factor 55.75 for a SMILES-generated geometry not reported by the endpoint, with water and octanol as the partition phases and temperature unspecified (request a3b1b491f9695d09-PRG). The same endpoint predicts a water solvation free energy of -13.510619315719184 kcal/mol and an octanol solvation free energy of -12.920808569279254 kcal/mol, each for the same unreported endpoint geometry and unspecified temperature and carrying the same trust_factor 55.75 (request a3b1b491f9695d09-PRG). > > The calculated water-minus-octanol solvation free-energy split is -0.5898107464399303 kcal/mol (request a3b1b509f8b21e28-PRG), while the primary logP is -0.4323343695216262 (request a3b1b491f9695d09-PRG). Both signs support the predeclared polarity-based direction: this model makes water solvation slightly more favorable for this molecular form. This is a model partition result, not a solubility measurement or a pH-dependent logD. > > The screening-grade single RDKit Crippen route gives logP -1.029 (request a3b1b4c29ecab605-PRG), compared with the primary value -0.4323343695216262 (request a3b1b491f9695d09-PRG); their absolute cross-route difference is 0.5966656304783737 log units (request a3b1b52729acf980-PRG). The comparison is within the configured tolerance. That difference is the on-record screening agreement band, explicitly not a calibrated experimental error estimate, and the primary endpoint returned no accuracy calibration beyond trust_factor 55.75 (request a3b1b491f9695d09-PRG). **What the example establishes:** a scoped computational prediction of water preference, with a screening cross-check and a traceable calculation. Its descriptor associations do not establish a causal solvent-interaction mechanism. The endpoint did not report its geometry or temperature, and the cross-route difference is not a calibrated experimental error bar. The [full trace](examples/caffeine-trace.md) retains the remaining answer, limitations, and proposed tests. ## Read a record Load this dataset from [Hugging Face](https://huggingface.co/datasets/chembricks/chemistry-knowledge): ```python from datasets import load_dataset records = load_dataset("chembricks/chemistry-knowledge", "records", split="corpus") print(records[0]["question"]) print(records[0]["answer"]) print(records[0]["limitations"]) ``` For a local copy, run from this dataset directory: ```python from datasets import load_dataset records = load_dataset( "json", data_files={"corpus": "data/records.jsonl"}, split="corpus", cache_dir=".cache/datasets", ) ``` The data also works with ordinary Python. See [examples/read_dataset.py](examples/read_dataset.py). ## Follow a claim to its evidence ```python import json from datasets import load_dataset claims = load_dataset("chembricks/chemistry-knowledge", "claims", split="corpus") evidence = load_dataset("chembricks/chemistry-knowledge", "evidence", split="corpus") item = claims[0] claim = json.loads(item["claim_json"]) reference = claim["evidence"][0] call = next( row for row in evidence if row["source_capture_id"] == item["source_capture_id"] and row["request_id"] == reference["request_id"] ) response = json.loads(call["response_json"]) print(item["statement"]) print(item["conditions_json"]) print(reference["path"]) print(response) ``` Columns ending in **_json** contain JSON strings so varying scientific structures load consistently in the dataset viewer. [DATA_DICTIONARY.md](DATA_DICTIONARY.md) describes the columns and JSON-path convention. ## How the data was created A question specifies molecules, methods, constraints and a budget. An isolated AI worker calls ChemBricks tools through a logging proxy and writes a scientific audit trail. Mechanical gates check schema, safety-screen completion, number provenance, methods, ranges, cross-checks and trust tags. Phase 1 uses an independent model referee and sampled replay checks. Accepted source records enter a hash-chained ledger. For this release, the original evidence hashes and mechanical checks were verified again offline. Applicable referee and replay evidence were checked. Arithmetic claims inherit the confidence limits of their source claims; a passed calculator result cannot upgrade an unresolved source. The default records subset requires every claim to qualify. This release includes 325 full records with a passing independent model referee and 164 with a matching recorded building-agent trace review. These counts overlap. Building-agent review is AI review, not an independent human annotation. Historical Phase 0 records retain their original gate states. The original question, answer, scientific trace, numerical claims and chemical responses are not scientifically rewritten during packaging. Local client metadata is removed from public request envelopes. [CURATION.md](CURATION.md) explains selection, privacy transformations and provenance. ## Coverage | Family | Question type | Complete records | |---|---|---:| | A1 | Facts and molecular properties | 54 | | A2 | Facts and molecular properties | 14 | | A3 | Facts and molecular properties | 157 | | B4 | Chemical series | 1 | | B6 | Chemical series | 1 | | C | Comparisons and counterfactuals | 82 | | C2 | Comparisons and counterfactuals | 1 | | E2 | Molecule design and discovery tasks | 1 | | E5 | Molecule design and discovery tasks | 35 | The complete-record subset covers 281 distinct canonical molecule strings in its recorded registries. This is a deliberately selected corpus of molecular properties, comparisons and design studies, not a representative sample of all chemical space. Paraphrases, related molecules and derived questions introduce substantial dependence. ## What verified means here Verified means **traceable to the recorded computation and checked under its declared policy**. It does not mean experimentally established truth. - Predictions retain their actual model, conditions, applicability and trust information. A high tool trust factor is not a calibrated experimental confidence probability. - Cross-route comparisons can support consistency without proving a mechanism or supplying an experimental error bar. - Interpretations are distinguished from measurements. A missing descriptor cannot establish a proposed causal explanation. - Some historical traces have unverified pre-call prediction timing. Their comparisons remain descriptive. The prediction_timing column preserves this distinction. - Low-trust and screening-grade results retain their tags. A passed claim can still have a limited domain of use. - Model-based designs are tested computational proposals. They do not establish synthesis, laboratory safety, availability, novelty, or broad chemical laws. - The underlying model-training datasets, model weights and full high-level simulation trajectories are not included. This release contains the recorded outputs and knowledge-building investigations. ## Potential application: LLM pretraining on scientific reasoning traces One potential application is **pretraining or continued pretraining of large language models on scientific reasoning traces**, alongside other training material. The goal would be to learn from the connection between a question, a proposed explanation, recorded calculations, checks, and an evidence-linked answer. A useful analogy is **coding traces with feedback from execution, compilers, type checks, and tests**. Here the traces concern scientific investigations, and the feedback comes from **physics-based or physics-informed calculations, empirical descriptors, provenance checks, and comparisons between computational routes**. | Coding-workflow analogy | Scientific investigation in this dataset | |---|---| | Task or specification | Chemical question and scoped hypothesis | | Code and execution trace | Tool calls, calculated observations, and scientific audit trail | | Compiler diagnostics, type checks, and tests | Evidence provenance, unit and method constraints, applicability checks, and required cross-route comparisons | | Checked program and output | Qualified claim, answer, and reusable context with its evidence | The analogy concerns learning from testable work and feedback. Scientific verification remains conditional on the models, methods, and conditions: approximate calculations and empirical descriptors can share errors, and consistency does not establish experimental truth. This release proposes a training use; it reports no LLM pretraining experiment or measured training benefit. ## Intended uses and evaluation limits Use the corpus to study evidence-grounded chemistry assistance, retrieve qualified computational context, inspect tool use, or develop scientific question-answering systems. Retain methods, uncertainty, limitations and provenance when constructing a downstream example. No frozen scaffold holdout exists in the source snapshot. Before training and evaluation, define and document one that keeps linked records, shared captures, generated candidates and scaffold-related molecules from leaking across partitions. The claims and evidence subsets are alternate views of the same source material, not independent datasets. ## Integrity and release files Run **python -B verify.py** with Python 3.11+ and jsonschema to verify file checksums, public schemas, the ledger commitment chain, preserved trace hashes, claim eligibility and evidence links. [manifest.json](manifest.json) records the exact source state, counts, code hashes and transformations. [SHA256SUMS](SHA256SUMS) covers the distributable files. The provenance directory retains source hashes and selection decisions. See [UPLOAD.md](UPLOAD.md) for publishing instructions. ## Creators, license and citation **Creator and publisher:** ChemBricks **Company:** [chembricks.ai](https://chembricks.ai) **AI platform:** [cmbx.ai](https://cmbx.ai) **License:** [MIT](LICENSE), copyright 2026 ChemBricks This release's curated data, documentation and figure are released under MIT at the dataset owner's direction. Historical source license labels are retained only in the provenance index. They describe the source records' earlier metadata. ```bibtex @misc{chembricks_knowledge_2026, author = {{ChemBricks}}, title = {ChemBricks Knowledge: Evidence-Linked Chemistry Questions and Claims}, year = {2026}, version = {2026-09-17.1}, url = {https://huggingface.co/datasets/chembricks/chemistry-knowledge} } ``` [CITATION.cff](CITATION.cff) provides machine-readable citation metadata. Include the Hub revision when citing a particular snapshot; no DOI or associated paper is claimed. Dataset layout follows the [Hugging Face dataset-card specification](https://huggingface.co/docs/hub/datasets-cards) and [data-file configuration](https://huggingface.co/docs/hub/datasets-data-files-configuration).