{ "vercy": "1.0-draft", "publication": { "status": "research-draft", "adjudicationStatus": "unreviewed", "publishableCanonical": false, "generatedAt": "2026-09-12T11:29:35Z", "providers": [ "Codex" ], "breadth": "recalled by Codex without web access - no source was read", "missingProviders": [], "pass": 2, "cost": { "grok": { "seconds": 21.7, "error": "Reading additional input from stdin...\nOpenAI Codex v0.153.4\n--------\nworkdir: R:\\02_PROJECTS\\02_Meta_Models_Platforms\\Ver.cy\\current\\thing-registry-backlog\nmodel: gpt-6-astra\nprovider: openai\napproval: never\nsandbox: read-only\nreasoning effort: none\nreasoning summaries: none\nsession id: 01a09560-2516-71e1-af09-91dd3388f477\n--------\nuser\nDescribe what is already known about one registered thing. Answer as JSON only, no prose around it.\n\nThing: N-hydroxysuccinimide\nSense to describe: (none recorded)\nDomain code: PHY.MAT\nAlso known as: (none)\n\n\nContext for this batch of 1001 things:\n# Batch 044:", "usd": 0.0, "recall": true }, "codex": { "seconds": 73.8, "error": "Reading additional input from stdin...\nOpenAI Codex v0.153.4\n--------\nworkdir: R:\\02_PROJECTS\\02_Meta_Models_Platforms\\Ver.cy\\current\\thing-registry-backlog\nmodel: gpt-6-astra\nprovider: openai\napproval: never\nsandbox: read-only\nreasoning effort: none\nreasoning summaries: none\nsession id: 01a09560-251c-7513-ba8b-a1e95b3def7c\n--------\nuser\nYou are drafting a Vercy meta-model for one registered thing. Answer as JSON only, no prose around it.\n\nThing: N-hydroxysuccinimide\nRegistry id: vr.tr.n-hydroxysuccinimide\nPlane / domain: PHY / PHY.MAT\nRegistry definition: (none recorded)\nNames folded into thi" } }, "enrichment": { "pass": 3, "engine": "claude", "producedAt": "2026-10-06T12:00:00Z", "ingestedAt": "2026-10-06T08:53:40+00:00", "fields": [ "agent_conduct", "ethics", "failure_modes_and_hazards", "owners", "visual_identification" ] }, "gate": { "passed": true, "version": "1.0", "at": "2026-10-07T10:10:30+00:00", "evidence": [ "completeness 1.00", "sense: Wikidata description", "2 live sources", "review by codex: pass" ] } }, "metaModel": { "id": "THING-Q408833", "registryId": "vr.tr.n-hydroxysuccinimide", "name": "N-hydroxysuccinimide", "version": "0.1.0-research.1", "entryKind": "thing", "family": "Thing Registry", "domain": [ "PHY.MAT" ], "status": "research-draft" }, "canonicalUrl": "https://ver.cy/models/thing/q408833/", "model": { "registry_id": "vr.tr.n-hydroxysuccinimide", "name": "N-hydroxysuccinimide", "purpose": "Enable an agent to identify N-hydroxysuccinimide, assess the suitability of a particular sample, and judge its use as a reagent in carboxyl activation and amide coupling.", "definition": "N-hydroxysuccinimide is a cyclic N-hydroxyimide with molecular formula C4H5NO3, commonly used to form activated carboxylic acid esters that facilitate amide-bond formation with primary amines.", "scope_statement": "This model owns the identity, composition, physical state, quality, chemical capabilities, and handling constraints of N-hydroxysuccinimide under vr.tr.n-hydroxysuccinimide in PHY.MAT, including its presence in solutions and mixtures.", "in_scope": [ "Molecular identity and identifiers for free N-hydroxysuccinimide, abbreviated NHS", "Sample grade, assay, water content, impurities, and analytical evidence", "Physical form, dissolution, thermal behavior, and storage condition", "Participation in activation chemistry and relationships to NHS esters", "Substance-specific hazard evidence and suitability constraints" ], "out_of_scope": [ "Sulfo-NHS and other substituted succinimide reagents as independent substances", "Individual NHS esters, activated surfaces, and NHS-bearing crosslinkers", "Carbodiimides such as EDC and their independent substance properties", "Complete coupling protocols, manufacturing processes, and reaction optimization", "Biomolecule products, conjugate performance, and commercial kit composition" ], "distinguishing_features": [ "Match the substance against CAS 6066-82-6, formula C4H5NO3, and molar mass 115.09 g/mol; these identify free NHS rather than an unspecified NHS-containing reagent. [Manufacturer identity record](https://www.thermofisher.com/order/catalog/product/es/en/157270250)", "Require structural evidence for the N-hydroxy group on the succinimide framework; a label saying only succinimide does not establish NHS identity.", "Check for a sulfonate substituent: sulfo-NHS is a distinct related reagent and must not inherit this substance identity. [NHS and Sulfo-NHS guide](https://www.thermofisher.com/TFS-Assets/LSG/manuals/MAN0011309_NHS_SulfoNHS_UG.pdf)", "Distinguish free NHS from an NHS ester carrying an acyl group: the ester is the activated species used in subsequent amine coupling. [Manufacturer coupling guide](https://www.thermofisher.com/TFS-Assets/LSG/manuals/MAN0011309_NHS_SulfoNHS_UG.pdf)" ], "characteristics": [ { "name": "Chemical identity", "kind": "category", "unit_or_values": "Structure identifier; CAS 6066-82-6; formula C4H5NO3", "why_it_matters": "Prevents substitution of related compounds or activated derivatives for free NHS." }, { "name": "Registry and regulatory cross-references", "kind": "relation", "unit_or_values": "vr.tr.n-hydroxysuccinimide; verified PubChem and EC records with source dates", "why_it_matters": "Connects supplier and jurisdictional records to the same substance." }, { "name": "NHS assay", "kind": "measurement", "unit_or_values": "% with method and basis, such as mass fraction, dry basis, or chromatographic area", "why_it_matters": "Supports usable-quantity estimates without treating unlike purity measurements as equivalent." }, { "name": "Water and residual impurities", "kind": "measurement", "unit_or_values": "Water in % w/w or mg/kg; identified impurities in % or mg/kg; method and detection limit", "why_it_matters": "Helps judge compatibility with the intended activation chemistry." }, { "name": "Material grade", "kind": "category", "unit_or_values": "Supplier-declared grade and application-specific acceptance criteria", "why_it_matters": "A grade label alone does not establish fitness for a particular synthesis or conjugation." }, { "name": "Physical condition", "kind": "state", "unit_or_values": "Solid or dissolved; appearance; temperature; observed caking or contamination", "why_it_matters": "Records the actual sample condition relevant to sampling and preparation." }, { "name": "Solubility and prepared concentration", "kind": "measurement", "unit_or_values": "Solubility in g/L or mol/L with solvent and temperature; stock concentration in mol/L", "why_it_matters": "Determines whether a intended preparation is homogeneous and correctly dosed." }, { "name": "Thermal behavior", "kind": "measurement", "unit_or_values": "Melting interval in °C; decomposition observation; boiling data only with pressure and evidence", "why_it_matters": "Supports identity checks and avoids treating decomposition as ordinary boiling." }, { "name": "Chemical role", "kind": "relation", "unit_or_values": "Free reagent; participant in NHS ester formation; released NHS; residual free NHS", "why_it_matters": "Separates molecular identity from its role at a particular reaction stage." }, { "name": "Storage and solution history", "kind": "state", "unit_or_values": "Container condition; temperature history; opening date; solution solvent, pH, and age", "why_it_matters": "Supports reassessment against evidence applicable to free NHS and its particular preparation." }, { "name": "Hazard and exposure status", "kind": "category", "unit_or_values": "Dated jurisdiction-specific SDS classification; exposure-limit value and units, or explicitly unestablished", "why_it_matters": "Grounds handling decisions without inferring safety from missing information." } ], "affordances": [ "Resolve an NHS label to a verified chemical identity and reject mismatched derivatives.", "Assess a lot against assay, water, impurity, and application requirements.", "Calculate an assay-corrected reagent amount when the assay basis supports that calculation.", "Evaluate whether a proposed NHS solution is supported by solubility and stability evidence.", "Determine whether an activation workflow calls for free NHS, sulfo-NHS, or a preformed NHS ester.", "Select handling, storage, retesting, and disposal actions from applicable sample and hazard records." ], "agent_conduct": { "may": [ "Describe N-hydroxysuccinimide and its role in coupling reactions from chemical sources.", "Report hazard and storage information from safety data sheets." ], "must_not": [ "Advise handling it without the protective equipment its safety data sheet calls for.", "Advise mixing it with incompatible reagents outside a controlled laboratory.", "Help label or crosslink biological agents for harmful purposes." ], "requires_human": [ "Approving its use or disposal at a site." ] }, "ethics": { "considerations": [ "It is a routine lab reagent; its stakes are worker safety and honest reporting.", "Its use in labelling proteins supports research with dual-use potential." ], "affected_parties": [ "Laboratory workers", "Researchers relying on the chemistry" ] }, "owners": { "steward": "The laboratory or operator who holds it; chemical regulators register it.", "master_systems": [ "Chemical substance registries" ] }, "visual_identification": [ "A white crystalline powder supplied in sealed laboratory bottles.", "Identified by label and analysis." ], "failure_modes_and_hazards": [ "Can irritate the eyes, skin and airways.", "Absorbs moisture and degrades if poorly stored." ], "what_it_is_for": [ "N-hydroxysuccinimide is used in organic synthesis and bioconjugation work to support the formation of activated esters.", "These activated intermediates enable attachment of carboxyl-containing molecules to primary amines in peptide, protein and surface-modification applications.", "Laboratory records must distinguish the free reagent from its activated esters because they have different chemical roles and stability." ], "standards_and_regulation": [ "The Globally Harmonized System of Classification and Labelling of Chemicals issued by the United Nations provides the framework for communicating assessed hazards of N-hydroxysuccinimide." ] }, "sources": [ { "id": "wikidata", "title": "Wikidata item Q408833: N-hydroxysuccinimide", "url": "https://www.wikidata.org/wiki/Q408833", "url_status": "live", "what_it_supports": "identity and sense of the item", "checked_by": "wikidata-api" }, { "id": "wikipedia-en", "title": "Wikipedia: N-Hydroxysuccinimide", "url": "https://en.wikipedia.org/wiki/N-Hydroxysuccinimide", "url_status": "live", "what_it_supports": "general description of the item", "checked_by": "wikidata-api sitelink" } ], "structure": { "bundles": [ { "id": "nhs-identity-and-boundaries", "name": "NHS identity and boundaries", "description": "Establish which molecular substance the registry entry denotes.", "rationale": "The abbreviation NHS is also used when discussing activated esters, making identity errors consequential.", "layers": [ { "id": "molecular-identification", "name": "Molecular identification", "description": "Connect names and identifiers to verified molecular structure.", "findings": [ { "id": "free-nhs-identity", "name": "Free NHS identity", "description": "Recognition requires agreement between the chemical structure, substance identifiers, and the sample record.", "questions": [ { "text": "Does the assigned structure contain the N-hydroxy succinimide framework corresponding to free NHS?", "kind": "definition", "id": "free-nhs-identity-q01" }, { "text": "Which authoritative records establish the CAS, PubChem, and EC cross-references for this identity?", "kind": "provenance", "id": "free-nhs-identity-q02" } ] } ] }, { "id": "related-reagent-separation", "name": "Related reagent separation", "description": "Separate free NHS from related substances and functional groups.", "findings": [ { "id": "derivative-and-mixture-boundary", "name": "Derivative and mixture boundary", "description": "A derivative or mixture can reference NHS without being the free substance represented by this entry.", "questions": [ { "text": "Is the material free NHS, sulfo-NHS, succinimide, or an acylated NHS ester?", "kind": "boundary", "id": "derivative-and-mixture-boundary-q01" }, { "text": "Does the reported NHS quantity describe free molecules in a mixture or NHS ester groups attached to another molecule?", "kind": "measurement", "id": "derivative-and-mixture-boundary-q02" } ] } ] } ] }, { "id": "nhs-lot-quality", "name": "NHS lot quality", "description": "Describe the amount and condition of NHS actually available in a sample.", "rationale": "Nominal reagent mass and a supplier grade cannot substitute for lot-specific composition evidence.", "layers": [ { "id": "assay-and-traceability", "name": "Assay and traceability", "description": "Attach quality claims to the correct lot and analytical basis.", "findings": [ { "id": "interpretable-nhs-assay", "name": "Interpretable NHS assay", "description": "Purity must retain its measurement method and reporting basis before it informs reagent calculations.", "questions": [ { "text": "What NHS assay was measured for this lot, by which method, and on what reporting basis?", "kind": "measurement", "id": "interpretable-nhs-assay-q01" }, { "text": "Which certificate and identity test connect that assay to the container being used?", "kind": "provenance", "id": "interpretable-nhs-assay-q02" }, { "text": "Does the assay support mass correction when calculating moles of NHS?", "kind": "action", "id": "interpretable-nhs-assay-q03" } ] } ] }, { "id": "water-and-contaminants", "name": "Water and contaminants", "description": "Record non-NHS constituents that may affect preparation or reaction suitability.", "findings": [ { "id": "application-relevant-impurities", "name": "Application-relevant impurities", "description": "Water, residual solvents, and identified impurities require application-specific acceptance criteria.", "questions": [ { "text": "What water content and residual impurity levels were measured, with which detection limits?", "kind": "measurement", "id": "application-relevant-impurities-q01" }, { "text": "Which impurity limits are justified for the intended NHS activation or coupling application?", "kind": "action", "id": "application-relevant-impurities-q02" } ] } ] } ] }, { "id": "nhs-physical-state", "name": "NHS physical state", "description": "Capture physical properties under conditions relevant to identification and preparation.", "rationale": "An agent needs condition-specific evidence to distinguish an acceptable solid or solution from an unsuitable preparation.", "layers": [ { "id": "solid-and-thermal-evidence", "name": "Solid and thermal evidence", "description": "Relate observed sample appearance and thermal transitions to reference evidence.", "findings": [ { "id": "solid-condition-and-transitions", "name": "Solid condition and transitions", "description": "Appearance and thermal data support assessment but do not independently prove identity or purity.", "questions": [ { "text": "What physical form and appearance does this NHS sample exhibit at the recorded temperature?", "kind": "measurement", "id": "solid-condition-and-transitions-q01" }, { "text": "What melting interval is supported by a stated method, and is decomposition reported?", "kind": "measurement", "id": "solid-condition-and-transitions-q02" }, { "text": "Is any reported boiling value experimentally supported at a stated pressure?", "kind": "provenance", "id": "solid-condition-and-transitions-q03" } ] } ] }, { "id": "dissolution-and-stock-state", "name": "Dissolution and stock state", "description": "Describe NHS in a specified solvent system.", "findings": [ { "id": "verified-nhs-solution", "name": "Verified NHS solution", "description": "A stock preparation needs a supported concentration and an observed dissolution state.", "questions": [ { "text": "What NHS solubility is supported for the selected solvent composition and temperature?", "kind": "measurement", "id": "verified-nhs-solution-q01" }, { "text": "What is the prepared NHS concentration, and is undissolved material present?", "kind": "measurement", "id": "verified-nhs-solution-q02" }, { "text": "Does the solvent system meet the requirements of the linked activation workflow?", "kind": "action", "id": "verified-nhs-solution-q03" } ] } ] } ] }, { "id": "nhs-reactivity-and-role", "name": "NHS reactivity and role", "description": "Represent the chemical capabilities that make NHS useful without assigning derivative behavior to free NHS.", "rationale": "Correct use depends on distinguishing the activation reagent, the resulting ester, and the released NHS.", "layers": [ { "id": "carboxyl-activation-role", "name": "Carboxyl activation role", "description": "Connect free NHS to the activation chemistry in which it participates.", "findings": [ { "id": "activation-requirements", "name": "Activation requirements", "description": "NHS can participate with a carbodiimide in forming an NHS ester from a carboxyl-containing substrate. [Manufacturer guide](https://www.thermofisher.com/TFS-Assets/LSG/manuals/MAN0011309_NHS_SulfoNHS_UG.pdf)", "questions": [ { "text": "Which carboxyl-containing substrate and activating reagent define the intended role of this NHS sample?", "kind": "definition", "id": "activation-requirements-q01" }, { "text": "What evidence supports the required NHS amount and compatibility with the selected conditions?", "kind": "provenance", "id": "activation-requirements-q02" } ] } ] }, { "id": "ester-and-release-boundary", "name": "Ester and release boundary", "description": "Track the distinction between free NHS and the activated species.", "findings": [ { "id": "free-nhs-does-not-prove-coupling", "name": "Free NHS does not prove coupling", "description": "Both NHS ester hydrolysis and conjugation can release NHS, so NHS release alone does not establish productive conjugation. [Manufacturer reactivity note](https://tools.thermofisher.com/content/sfs/brochures/TR0003-NHS-reactivity-test.pdf)", "questions": [ { "text": "Does an observed signal quantify free NHS, intact NHS ester, or a combination of species?", "kind": "measurement", "id": "free-nhs-does-not-prove-coupling-q01" }, { "text": "What independent evidence distinguishes productive coupling from ester hydrolysis?", "kind": "measurement", "id": "free-nhs-does-not-prove-coupling-q02" }, { "text": "Which stability claims belong to the particular NHS ester rather than free NHS?", "kind": "boundary", "id": "free-nhs-does-not-prove-coupling-q03" } ] } ] } ] }, { "id": "nhs-preservation-and-handling", "name": "NHS preservation and handling", "description": "Determine whether the sample remains suitable and what handling evidence applies.", "rationale": "Instructions for free NHS must be grounded in its own records rather than copied from NHS ester products.", "layers": [ { "id": "storage-and-reassessment", "name": "Storage and reassessment", "description": "Connect storage history to supplier instructions and sample evidence.", "findings": [ { "id": "retained-nhs-suitability", "name": "Retained NHS suitability", "description": "Storage excursions and prepared-solution age trigger assessment against evidence for the actual material.", "questions": [ { "text": "What storage conditions and retest or expiry guidance apply to this NHS grade and lot?", "kind": "provenance", "id": "retained-nhs-suitability-q01" }, { "text": "What container, temperature, moisture-exposure, and solution-age history is recorded?", "kind": "measurement", "id": "retained-nhs-suitability-q02" }, { "text": "Which observations or analytical results require retesting or withholding the sample from use?", "kind": "action", "id": "retained-nhs-suitability-q03" } ] } ] }, { "id": "hazards-and-disposition", "name": "Hazards and disposition", "description": "Anchor handling and disposal decisions to applicable substance and mixture records.", "findings": [ { "id": "applicable-nhs-safety-evidence", "name": "Applicable NHS safety evidence", "description": "Hazard classification, exposure controls, and disposal requirements need dated evidence for the jurisdiction and material form.", "questions": [ { "text": "Which current SDS establishes the applicable NHS classifications and exposure controls?", "kind": "provenance", "id": "applicable-nhs-safety-evidence-q01" }, { "text": "Are substance-specific exposure limits established, absent from the consulted source, or still unverified?", "kind": "boundary", "id": "applicable-nhs-safety-evidence-q02" }, { "text": "What handling and waste route applies to this NHS solid or its particular solvent and reaction mixture?", "kind": "action", "id": "applicable-nhs-safety-evidence-q03" } ] } ] } ] }, { "id": "evidence-and-external-alignment", "name": "Evidence and external alignment", "description": "What the world already says about this thing, gathered so the model can be checked against it.", "rationale": "A model that cannot be lined up against existing standards, identifiers and practice cannot be adopted by anyone who already uses them.", "layers": [ { "id": "reported-evidence", "name": "Reported evidence", "description": "Findings from the breadth pass, kept separate from the structural claims.", "findings": [ { "id": "evidence-confidence-notes", "name": "Check these first", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ "This is a recall-based description; no sources were consulted.", "Verify the melting range against a reference and the purity of the specific material.", "Confirm current hazard classification, exposure guidance, and jurisdictional requirements from an applicable safety data sheet." ], "questions": [ { "id": "evidence-confidence-notes-q01", "text": "Which of these check these first hold for the sense of N-hydroxysuccinimide this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-identifiers", "name": "Identifiers and schemes", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ { "scheme": "CAS Registry Number", "value_or_pattern": "6066-82-6", "note": "Identifies N-hydroxysuccinimide." }, { "scheme": "Molecular formula", "value_or_pattern": "C4H5NO3", "note": "Describes elemental composition; does not uniquely identify molecular connectivity." }, { "scheme": "Common abbreviation", "value_or_pattern": "NHS", "note": "Context-dependent abbreviation used in coupling chemistry and bioconjugation." } ], "questions": [ { "id": "evidence-identifiers-q01", "text": "Which of these identifiers and schemes hold for the sense of N-hydroxysuccinimide this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-real-world-use", "name": "Real-world use", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ "Preparation of N-hydroxysuccinimide esters from carboxylic acids.", "Carbodiimide-mediated coupling of carboxyl groups to primary amines.", "Peptide synthesis through activated ester intermediates.", "Preparation of reagents for labeling proteins and other amine-bearing biomolecules." ], "questions": [ { "id": "evidence-real-world-use-q01", "text": "Which of these real-world use hold for the sense of N-hydroxysuccinimide this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-measurements", "name": "Typical measurements", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ { "quantity": "Molar mass", "typical_range": "115.09", "unit": "g/mol" }, { "quantity": "Melting point", "typical_range": "Approximately 95-98", "unit": "°C" } ], "questions": [ { "id": "evidence-measurements-q01", "text": "Which of these typical measurements hold for the sense of N-hydroxysuccinimide this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-failure-modes-and-hazards", "name": "Failure modes and hazards", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ "NHS activated esters can hydrolyze in aqueous solution, reducing coupling efficiency; this concerns the ester derivatives rather than free NHS.", "Amine-containing buffers can consume NHS ester reagents and compete with the intended coupling target.", "Coupling can modify multiple accessible amino groups, producing heterogeneous products when site selectivity is required.", "Dust and direct contact warrant laboratory exposure controls; specific hazard classifications should be checked against the supplied product's safety data sheet." ], "questions": [ { "id": "evidence-failure-modes-and-hazards-q01", "text": "Which of these failure modes and hazards hold for the sense of N-hydroxysuccinimide this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-neighbours", "name": "Neighbouring kinds and how to tell them apart", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ { "name": "Succinimide", "difference": "Succinimide has an N-H group where N-hydroxysuccinimide has an N-OH group." }, { "name": "Sulfo-N-hydroxysuccinimide", "difference": "Contains an additional sulfonate group that increases water solubility; it is a distinct reagent." }, { "name": "N-hydroxysuccinimide ester", "difference": "An NHS ester is an acylated derivative used as an activated carboxylic acid; free NHS is the parent reagent and leaving-group precursor." } ], "questions": [ { "id": "evidence-neighbours-q01", "text": "Which of these neighbouring kinds and how to tell them apart hold for the sense of N-hydroxysuccinimide this model covers, and on what evidence?", "kind": "provenance" } ] } ] } ] } ] }, "openQuestions": [ "Which PubChem CID and EC record should be adopted after direct verification against the free NHS structure?", "What experimentally supported melting, decomposition, and pressure-qualified boiling data should serve as reference values?", "What solvent-specific solubility and free-NHS solution stability data are available across relevant temperatures and pH values?", "Which assay methods, water limits, and impurity limits reliably predict suitability for different NHS coupling applications?", "What current jurisdiction-specific hazard classifications, exposure limits, and storage requirements apply to free NHS?" ], "statistics": { "bundles": 6, "layers": 11, "findings": 16, "questions": 32 } }