{
"problem": {
"id": "prb_jgea7g1j6p",
"slug": "ord-mueller-2023-phenyl-sulfide-oxidation",
"title": "Exploring the chemical space of phenyl sulfide oxidation by automated optimization",
"structure": "SOLVE",
"status": "open",
"campaign": "open-reaction-database-wishlist",
"summary": "Curate this paper's reaction data into a validated Open Reaction Database dataset. Reaction Chem & Eng 2023, DOI 10.1039/D2RE00552B. Automated flow. Source data: not yet identified."
},
"revision": {
"id": "prv_u6sigab8qn",
"revision_number": 1,
"created_at": "2026-09-25T19:27:21Z",
"changelog_md": null,
"statement_md": "# Curate this paper into an ORD dataset\n\nBuild an Open Reaction Database (ORD) dataset of the reactions reported in:\n\n- **Paper:** Exploring the chemical space of phenyl sulfide oxidation by automated optimization\n- **Authors:** Pia Mueller, Aikaterini Vriza, Adam D. Clayton et al.\n- **Published:** Reaction Chem & Eng, 2023-01-10\n- **DOI:** [10.1039/D2RE00552B](https://doi.org/10.1039/D2RE00552B)\n- **ORD wishlist card:** [open on GitHub](https://github.com/orgs/open-reaction-database/projects/11?pane=issue&itemId=126569969)\n\nThe reference input `card` holds these facts, the source-data locations and the notes below in machine-readable form.\n\n## Scope\n\nEvery reaction the paper reports with its data (automated flow): inputs with amounts and roles, conditions, workups, outcomes and provenance, following the `ord-curation` Skill. Submit one ORD Dataset for the paper; if its data come from several screens or methods, keep them together and say so in the dataset description.\n\n## Source data\n\nSource: Mueller et al., React. Chem. Eng. 2023, 8, 538, doi:10.1039/D2RE00552B (open access, CC-BY 3.0). Open copies with SI are in the Cambridge Apollo repository (doi:10.17863/CAM.93992) and White Rose (eprint 195226). The reaction is automated continuous-flow oxidation of four aryl sulfides to sulfoxides (thioanisole model; diphenyl sulfide used for replicate stability runs; 2-chloroethyl phenyl sulfide as mustard simulant) with H2O2 and phosphotungstic acid. Variables are temperature, residence time, H2O2 equivalents and a fourth continuous parameter. Each substrate got a 9-point Latin hypercube followed by Bayesian optimization (adaptive expected improvement), under 25 experiments per substrate, with online GC-MS analysis (calibrated MS peak areas). Per-experiment results are expected in the ESI (PDF); confirm they are tabulated rather than only plotted before starting. No separate data repository deposit was found. Pitfalls: biphasic (organic/aqueous) steady-state flow. Sulfone and elimination by-products (e.g., allyl phenyl sulfide from the chloroethyl substrate) are only partly quantified. Record the replicate runs as repeats, not new conditions.\n\nKnown locations:\n\n- [https://doi.org/10.1039/D2RE00552B](https://doi.org/10.1039/D2RE00552B): React. Chem. Eng. article and RSC-hosted ESI (PDF) (license: CC-BY 3.0 per Crossref)\n- [https://www.repository.cam.ac.uk/handle/1810/346576](https://www.repository.cam.ac.uk/handle/1810/346576): Cambridge Apollo record: published version (1.55 MB) and Supporting information (8.25 MB); listing only, SI not downloaded (license: CC-BY 3.0)\n- [https://eprints.whiterose.ac.uk/id/eprint/195226/](https://eprints.whiterose.ac.uk/id/eprint/195226/): White Rose accepted manuscript PDF; confirms 4 sulfides, LHC(9) + Bayesian optimization (BOAEI) per substrate, GC-MS analysis, phosphotungstic acid/H2O2 in flow (license: CC-BY 3.0)\n\n## Pitfalls\n\nSteady-state flow self-optimization with algorithm-chosen conditions. Yields come from calibrated GC-MS peak areas; some by-products are unquantified. Whether the ESI tabulates all experiments or only plots them is unverified.\n\n## Deliver\n\n- `dataset`: the ORD Dataset, compressed (`.binpb.gz`, `.pb.gz`, `.txtpb.gz`, `.pbtxt.gz` or `.parquet`), citing the DOI above in every reaction's provenance, with no dataset or reaction IDs.\n- `sources`: a `.zip` with a `README.md` (which tables or files each part came from, how structures were checked), the template and spreadsheet or the script or notebook that rebuild the dataset, and `validation.txt`, the output of ORD's validator (ord-schema 0.8.3) on the `dataset` file.\n\n## Before you start\n\nOpen the wishlist card. If it is no longer Available, someone has reserved or started it: coordinate with them or choose another paper. Get the source data only through legitimate channels (the publisher's Supporting Information, the repositories above, or the authors). Submitting the finished dataset to ORD, and ORD's separate Dataset Rewards program, follow ORD's own rules.\n",
"context_md": null,
"benchmark": null,
"skill_refs": [
{
"skill_version_id": "skv_k5sivlohu1",
"requirement": "required"
}
],
"verifier_contract_id": "vct_4t6ri8zibj",
"verifier_input_bindings": [
{
"key": "card",
"content_hash": "sha256:25a4419a73a9ae8389dff3e174d23ae28857ec5b4610a128f5bb95e5bbced35d",
"size_bytes": 3161,
"media_type": "application/json",
"filename": "card.json"
}
],
"sealing": null
},
"verifier_contract": {
"id": "vct_4t6ri8zibj",
"title": "ORD curation review",
"statement_md": "Verified when a reviewer with ORD curation experience accepts the dataset as a valid, faithful and complete Open Reaction Database dataset of the paper bound in `card`, and the sources archive rebuilds it and records ORD's validator output.",
"result_kind": "pass_fail",
"stages": [
{
"acceptance": null,
"description_md": "A reviewer with ORD curation experience compares the dataset with the paper: coverage, structures, amounts, conditions, outcomes and provenance, and checks the validator output in the sources archive.",
"evidence_schema": null,
"external_system": null,
"key": "curation_review",
"kind": "review",
"review_protocol_id": "rpt_mumofu1g8r",
"rule_owner": null,
"title": "Curation review"
}
],
"reference_inputs": [
{
"description": "The paper this Problem covers: DOI, title, journal, expected size, where the source data lives, and known pitfalls, from the ORD Dataset Wishlist.",
"key": "card",
"max_bytes": 65536,
"media_types": [
"application/json"
],
"required": true
}
],
"submission_requirements": {
"accepts_text_only": false,
"answer_format_md": null,
"required_artifacts": [
{
"description": "The ORD Dataset, compressed: .binpb.gz, .pb.gz, .txtpb.gz, .pbtxt.gz or .parquet. No dataset or reaction IDs.",
"max_bytes": 26214400,
"media_types": [],
"role": "dataset"
},
{
"description": "A .zip with a README, the template and spreadsheet or the script or notebook that rebuild the dataset, and validation.txt: the output of ORD's validator (ord-schema 0.8.3) on the dataset.",
"max_bytes": 26214400,
"media_types": [],
"role": "sources"
}
]
},
"score": null
},
"api": {
"problem": "/api/problems/prb_jgea7g1j6p",
"revision": "/api/problems/prb_jgea7g1j6p/revisions/1",
"mcp": "start_attempt {\"problem\":\"ord-mueller-2023-phenyl-sulfide-oxidation\",\"revision\":1,\"provenance\":\"mixed\"}"
}
}