{ "vercy": "1.0-draft", "publication": { "status": "research-draft", "adjudicationStatus": "unreviewed", "publishableCanonical": false, "generatedAt": "2026-09-12T08:58:05Z", "providers": [ "Codex" ], "breadth": "recalled by Codex without web access - no source was read", "missingProviders": [], "pass": 2, "cost": { "grok": { "seconds": 19.2, "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: 01a094d5-8171-7f70-80ac-fd303b1b20db\n--------\nuser\nDescribe what is already known about one registered thing. Answer as JSON only, no prose around it.\n\nThing: cyclen\nSense to describe: (none recorded)\nDomain code: PHY.MAT\nAlso known as: (none)\n\n\nContext for this batch of 1001 things:\n# Batch 043: 1001 register", "usd": 0.0, "recall": true }, "codex": { "seconds": 70.6, "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: 01a094d5-817e-71e0-a4de-392ac3b19bb0\n--------\nuser\nYou are drafting a Vercy meta-model for one registered thing. Answer as JSON only, no prose around it.\n\nThing: cyclen\nRegistry id: vr.tr.cyclen\nPlane / domain: PHY / PHY.MAT\nRegistry definition: (none recorded)\nNames folded into this entry: (none)\n\n\nContext fo" } }, "enrichment": { "pass": 3, "engine": "claude", "producedAt": "2026-10-06T12:00:00Z", "ingestedAt": "2026-10-06T08:51:00+00:00", "fields": [ "agent_conduct", "ethics", "failure_modes_and_hazards", "owners", "standards_and_regulation", "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-Q416407", "registryId": "vr.tr.cyclen", "name": "cyclen", "version": "0.1.0-research.1", "entryKind": "thing", "family": "Thing Registry", "domain": [ "PHY.MAT" ], "status": "research-draft" }, "canonicalUrl": "https://ver.cy/models/thing/q416407/", "model": { "registry_id": "vr.tr.cyclen", "name": "cyclen", "purpose": "Enable an agent to identify cyclen, assess the chemical form and quality of a sample, and determine its suitability for coordination or derivatization work.", "definition": "Cyclen is 1,4,7,10-tetraazacyclododecane, a saturated twelve-membered macrocyclic amine with formula C8H20N4 whose four nitrogen atoms can coordinate metal ions.", "scope_statement": "This model owns vr.tr.cyclen in PHY / PHY.MAT: the parent macrocyclic tetraamine and the sample properties, speciation, and evidence needed to use it, with explicit boundaries to salts, derivatives, and metal complexes.", "in_scope": [ "Identity and connectivity of unsubstituted cyclen", "Free-base content, purity, water, and residual contaminants", "Physical state and condition-dependent material properties", "Protonation and availability of nitrogen donor sites", "Suitability for metal coordination and nitrogen functionalization", "Form-specific handling requirements and regulatory identifiers" ], "out_of_scope": [ "Independent substance identities of cyclen salts and hydrates", "Covalently substituted derivatives such as DOTA", "Metal-cyclen complexes as independently characterized substances", "Manufacturing routes and reaction procedures", "Commercial formulations containing cyclen", "Clinical performance of downstream contrast agents or radiopharmaceuticals" ], "distinguishing_features": [ "Cyclen has a saturated 12-membered ring with nitrogen at positions 1, 4, 7, and 10; its neutral parent formula is C8H20N4. [PubChem](https://pubchem.ncbi.nlm.nih.gov/compound/1_4_7_10-Tetraazacyclododecane)", "Identity matching should resolve to CAS 294-90-6 and PubChem CID 64963, supported by structural evidence rather than name similarity. [Fisher Scientific](https://www.fishersci.com/us/en/browse/cas/294-90-6)", "All four parent nitrogen sites are secondary amines without pendant substituents; covalent substitution must trigger a derivative boundary rather than a purity-grade change.", "A tetrahydrochloride label denotes a separate salt form with formula C8H24Cl4N4, not the neutral parent's formula or mass basis. [PubChem](https://pubchem.ncbi.nlm.nih.gov/compound/Cyclen-tetrahydrochloride)", "A trihydrate must be distinguished from anhydrous parent material when assigning formula and calculating cyclen content. [PubChem](https://pubchem.ncbi.nlm.nih.gov/compound/71345808)" ], "characteristics": [ { "name": "Parent connectivity", "kind": "category", "unit_or_values": "Saturated 12-membered ring; four NH sites separated by ethylene groups", "why_it_matters": "Distinguishes cyclen from different ring sizes, heteroatom patterns, and substituted macrocycles." }, { "name": "Chemical form", "kind": "category", "unit_or_values": "Free base; identified salt; hydrate or solvate; solution; unresolved", "why_it_matters": "Determines whether parent identifiers and dosing calculations apply directly." }, { "name": "Parent molar mass", "kind": "measurement", "unit_or_values": "172.27 g/mol for neutral C8H20N4", "why_it_matters": "Provides the parent conversion basis; salts and solvates require their own mass accounting. [Fisher Scientific](https://www.fishersci.com/us/en/browse/cas/294-90-6)" }, { "name": "Cyclen assay", "kind": "measurement", "unit_or_values": "Mass % or mol/kg; method and as-received or dry basis required", "why_it_matters": "Supports reliable reagent equivalents independently of nominal supplier grade." }, { "name": "Water and residual solvent", "kind": "measurement", "unit_or_values": "Mass %; identified solvent; analytical method", "why_it_matters": "Changes effective cyclen content and may affect subsequent chemistry." }, { "name": "Physical and thermal state", "kind": "state", "unit_or_values": "Observed phase at stated temperature; melting interval in °C; decomposition flag", "why_it_matters": "Allows comparison with a matching chemical form without treating a thermal event as sufficient proof of identity." }, { "name": "Solubility", "kind": "measurement", "unit_or_values": "g/L or mol/L with solvent, temperature, pH, and chemical form", "why_it_matters": "Supports preparation of usable solutions under specified conditions." }, { "name": "Protonation state", "kind": "state", "unit_or_values": "Species fractions or mean protonation; pH, solvent, temperature, and ionic strength", "why_it_matters": "Determines how many nitrogen lone pairs are available for coordination or reaction." }, { "name": "Metal contamination", "kind": "measurement", "unit_or_values": "Element-specific mg/kg or mol/mol cyclen, with detection limits", "why_it_matters": "Unintended metals can compromise controlled complex formation." }, { "name": "Coordination evidence", "kind": "relation", "unit_or_values": "Metal species, stoichiometry, linked complex identity, and condition-specific equilibrium or kinetic evidence", "why_it_matters": "Prevents transferring results between different metals or assuming that donor count proves complex stability." }, { "name": "Safety and regulatory evidence", "kind": "relation", "unit_or_values": "Applicable SDS, revision date, jurisdiction, chemical form, and verified inventory identifiers", "why_it_matters": "Anchors handling decisions to the material actually present." } ], "affordances": [ "Check structural and identifier evidence before accepting a sample as cyclen.", "Calculate available cyclen equivalents from assay and salt or solvate composition.", "Assess whether a specified solvent and pH support the intended preparation.", "Evaluate suitability for a named metal-coordination task using contamination and speciation evidence.", "Assess whether nitrogen sites are available for a proposed derivatization and link the resulting derivative separately.", "Select handling and storage controls from documentation applicable to the sample form." ], "agent_conduct": { "may": [ "Identify cyclen from analytical data and report the purity and form of a sample.", "Describe its use as a ligand and building block for metal complexes, citing sources." ], "must_not": [ "Handle or describe it as harmless when its safety data shows it is irritant or corrosive.", "Present a cyclen-based complex as safe for use in people without approved evidence.", "Release amine waste or metal complexes into drains.", "Confuse cyclen with its derivatives when reporting results." ], "requires_human": [ "Using cyclen or its complexes in any material intended for administration to people or animals.", "Disposing of metal complexes made from it." ] }, "ethics": { "considerations": [ "Derivatives of cyclen are used in medical imaging agents, so laboratory claims can reach patients.", "Waste containing metal complexes can persist in the environment." ], "affected_parties": [ "Laboratory workers", "Patients receiving derived agents", "Environment near disposal" ] }, "owners": { "steward": "The laboratory or supplier that holds the material.", "master_systems": [] }, "visual_identification": [ "A white to off-white crystalline solid that cannot be identified by appearance.", "Identity is settled by spectroscopy and melting point against a reference." ], "failure_modes_and_hazards": [ "Skin and eye irritation or burns from handling.", "Contamination of products with unreacted ligand or free metal." ], "standards_and_regulation": [ "Globally Harmonized System of Classification and Labelling of Chemicals (GHS), United Nations." ], "what_it_is_for": [ "Cyclen is encountered in coordination chemistry and synthetic laboratories as a macrocyclic ligand and chemical building block.", "Its derivatives are used to develop metal-binding systems for applications such as imaging research, sensing and radiochemistry, with performance depending on the attached groups and coordinated metal." ] }, "sources": [ { "id": "wikidata", "title": "Wikidata item Q416407: cyclen", "url": "https://www.wikidata.org/wiki/Q416407", "url_status": "live", "what_it_supports": "identity and sense of the item", "checked_by": "wikidata-api" }, { "id": "wikipedia-en", "title": "Wikipedia: Cyclen", "url": "https://en.wikipedia.org/wiki/Cyclen", "url_status": "live", "what_it_supports": "general description of the item", "checked_by": "wikidata-api sitelink" } ], "structure": { "bundles": [ { "id": "macrocycle-identity", "name": "Macrocycle identity", "description": "Establish the parent ring and separate it from related chemical entities.", "rationale": "Cyclen names and scaffold references can otherwise conceal salts, substituted ligands, or different macrocycles.", "layers": [ { "id": "ring-connectivity", "name": "Ring connectivity", "description": "Verify the defining nitrogen arrangement and unsubstituted parent structure.", "findings": [ { "id": "parent-structure-evidence", "name": "Parent structure evidence", "description": "Recognition requires evidence consistent with the 12-membered tetraamine ring.", "questions": [ { "text": "Does the assigned structure contain four NH sites at positions 1, 4, 7, and 10 with ethylene spacers?", "kind": "definition", "id": "parent-structure-evidence-q01" }, { "text": "Which analytical evidence distinguishes the sample from ring-size analogues or substituted cyclen?", "kind": "measurement", "id": "parent-structure-evidence-q02" } ] } ] }, { "id": "chemical-entity-boundaries", "name": "Chemical entity boundaries", "description": "Separate the parent reference identity from the supplied chemical form.", "findings": [ { "id": "form-aware-identification", "name": "Form-aware identification", "description": "A salt, hydrate, derivative, or complex requires explicit identity mapping.", "questions": [ { "text": "Do the supplier identifiers describe neutral cyclen or a separately identified salt, hydrate, derivative, or complex?", "kind": "boundary", "id": "form-aware-identification-q01" }, { "text": "Which source supports the mapping between the sample identity and vr.tr.cyclen?", "kind": "provenance", "id": "form-aware-identification-q02" } ] } ] } ] }, { "id": "usable-cyclen-content", "name": "Usable cyclen content", "description": "Determine how much parent ligand a sample actually supplies.", "rationale": "Nominal mass and chromatographic purity alone may not establish available ligand equivalents.", "layers": [ { "id": "assay-and-mass-basis", "name": "Assay and mass basis", "description": "Resolve assay, counterions, water, and solvent contributions.", "findings": [ { "id": "parent-equivalent-accounting", "name": "Parent-equivalent accounting", "description": "Cyclen equivalents must use a documented composition and assay basis.", "questions": [ { "text": "What is the cyclen assay, by which method, and on an as-received or dry basis?", "kind": "measurement", "id": "parent-equivalent-accounting-q01" }, { "text": "How must water, solvent, and any counterions be accounted for when converting sample mass to cyclen moles?", "kind": "action", "id": "parent-equivalent-accounting-q02" } ] } ] }, { "id": "interfering-impurities", "name": "Interfering impurities", "description": "Identify contaminants that affect coordination or nitrogen functionalization.", "findings": [ { "id": "task-relevant-contamination", "name": "Task-relevant contamination", "description": "Impurity acceptance depends on the intended ligand chemistry.", "questions": [ { "text": "What residual metals, other amines, or substituted macrocycles are detected, and with what detection limits?", "kind": "measurement", "id": "task-relevant-contamination-q01" }, { "text": "Which impurity limits are required by the intended complexation or derivatization task?", "kind": "action", "id": "task-relevant-contamination-q02" } ] } ] } ] }, { "id": "phase-and-protonation", "name": "Phase and protonation", "description": "Describe cyclen under the physical and solution conditions in which it will be used.", "rationale": "Physical availability and nitrogen protonation jointly constrain practical ligand behavior.", "layers": [ { "id": "physical-availability", "name": "Physical availability", "description": "Record phase, thermal behavior, and dissolution with their conditions.", "findings": [ { "id": "conditioned-material-properties", "name": "Conditioned material properties", "description": "Property values must refer to a specified form and measurement environment.", "questions": [ { "text": "What phase and melting interval are measured for the identified form, and is decomposition observed?", "kind": "measurement", "id": "conditioned-material-properties-q01" }, { "text": "What solubility is supported in the intended solvent at the specified temperature and pH?", "kind": "measurement", "id": "conditioned-material-properties-q02" } ] } ] }, { "id": "acid-base-speciation", "name": "Acid-base speciation", "description": "Resolve protonation without treating cyclen as a single-site base.", "findings": [ { "id": "nitrogen-protonation-evidence", "name": "Nitrogen protonation evidence", "description": "Stepwise protonation information is needed to interpret donor availability.", "questions": [ { "text": "Which stepwise protonation constants are supported, using what convention, solvent, temperature, and ionic strength?", "kind": "provenance", "id": "nitrogen-protonation-evidence-q01" }, { "text": "What protonation distribution follows at the intended pH, and how uncertain is that estimate?", "kind": "measurement", "id": "nitrogen-protonation-evidence-q02" } ] } ] } ] }, { "id": "nitrogen-site-use", "name": "Nitrogen site use", "description": "Assess cyclen as a coordination ligand and a functionalization starting material.", "rationale": "The four nitrogen sites define its practical chemical roles but do not guarantee a particular reaction outcome.", "layers": [ { "id": "metal-binding", "name": "Metal binding", "description": "Evaluate a specified metal interaction under explicit conditions.", "findings": [ { "id": "conditional-complexation", "name": "Conditional complexation", "description": "Binding claims require a named metal species and evidence for the resulting complex.", "questions": [ { "text": "For the intended metal and oxidation state, what stoichiometry and formation evidence are available under matching conditions?", "kind": "provenance", "id": "conditional-complexation-q01" }, { "text": "Do proton competition, competing ligands, or formation kinetics limit the proposed use?", "kind": "action", "id": "conditional-complexation-q02" } ] } ] }, { "id": "covalent-functionalization", "name": "Covalent functionalization", "description": "Track nitrogen substitution as conversion into a different substance.", "findings": [ { "id": "substitution-boundary", "name": "Substitution boundary", "description": "Functionalized products retain a cyclen scaffold but require separate identities.", "questions": [ { "text": "Are all four parent NH sites present, or does the material already contain protected or substituted nitrogen sites?", "kind": "measurement", "id": "substitution-boundary-q01" }, { "text": "Which separate derivative identity must be linked when the intended substitution changes the parent structure?", "kind": "boundary", "id": "substitution-boundary-q02" } ] } ] } ] }, { "id": "handling-and-release", "name": "Handling and release", "description": "Determine whether the identified cyclen sample can be handled and released for its intended task.", "rationale": "Safety documentation and acceptance criteria must match the actual form, concentration, and chemical use.", "layers": [ { "id": "form-specific-safety", "name": "Form-specific safety", "description": "Attach applicable hazard and regulatory evidence.", "findings": [ { "id": "documented-controls", "name": "Documented controls", "description": "Controls must follow verified documentation without importing classifications from related substances.", "questions": [ { "text": "Which current SDS and jurisdiction-specific classification apply to this exact form and concentration?", "kind": "provenance", "id": "documented-controls-q01" }, { "text": "What exposure controls, storage conditions, and incompatibilities does that evidence require?", "kind": "action", "id": "documented-controls-q02" } ] } ] }, { "id": "sample-fitness", "name": "Sample fitness", "description": "Connect sample history and analytical results to a specific intended use.", "findings": [ { "id": "release-or-retest", "name": "Release or retest", "description": "A sample is usable only against explicit task requirements and adequate evidence.", "questions": [ { "text": "Has storage or handling introduced uncertainty about water content, assay, or metal contamination?", "kind": "provenance", "id": "release-or-retest-q01" }, { "text": "Do the available results justify release for the named task, or which measurements are needed first?", "kind": "action", "id": "release-or-retest-q02" } ] } ] } ] }, { "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 description is recalled knowledge, not a researched source review.", "Verify melting point, purity, hydration state and storage requirements for the specific material.", "Check the current supplier safety data sheet for hazard classification; no GHS category, exposure limit or jurisdiction-specific regulatory status is asserted here." ], "questions": [ { "id": "evidence-confidence-notes-q01", "text": "Which of these check these first hold for the sense of cyclen 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": "294-90-6", "note": "Identifies cyclen as the free base; salts and derivatives have separate identities." }, { "scheme": "Systematic chemical nomenclature", "value_or_pattern": "1,4,7,10-tetraazacyclododecane", "note": "Specifies the twelve-membered saturated ring and its four nitrogen positions." } ], "questions": [ { "id": "evidence-identifiers-q01", "text": "Which of these identifiers and schemes hold for the sense of cyclen 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": [ "Macrocyclic ligand in coordination chemistry.", "Starting scaffold for synthesizing metal chelators, including DOTA.", "Research building block for metal complexes used in molecular recognition and catalysis." ], "questions": [ { "id": "evidence-real-world-use-q01", "text": "Which of these real-world use hold for the sense of cyclen 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 of the neutral free base", "typical_range": "172.27", "unit": "g/mol" } ], "questions": [ { "id": "evidence-measurements-q01", "text": "Which of these typical measurements hold for the sense of cyclen 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": [ "Protonation changes the availability of nitrogen donor sites, making metal binding dependent on pH.", "Competing metal ions can produce unintended complexes and affect chemical purity or experimental results." ], "questions": [ { "id": "evidence-failure-modes-and-hazards-q01", "text": "Which of these failure modes and hazards hold for the sense of cyclen 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": "Cyclam", "difference": "Cyclam has a fourteen-membered tetraamine ring; cyclen has a twelve-membered tetraamine ring." }, { "name": "DOTA", "difference": "DOTA bears four acetic acid substituents on the cyclen nitrogen atoms; unsubstituted cyclen has four secondary amine groups." }, { "name": "Cyclen salts", "difference": "Salts contain protonated cyclen and counterions, so their formula, molar mass and material properties differ from those of the neutral free base." } ], "questions": [ { "id": "evidence-neighbours-q01", "text": "Which of these neighbouring kinds and how to tell them apart hold for the sense of cyclen this model covers, and on what evidence?", "kind": "provenance" } ] } ] } ] } ] }, "openQuestions": [ "Which authoritative sources establish cyclen's EC number, applicable hazard classifications, and any substance-specific exposure limits in the intended jurisdiction?", "Which melting, boiling or decomposition, and solubility measurements are reliable for the anhydrous free base rather than a salt or hydrate?", "Which stepwise protonation constants and uncertainty estimates should be used for the intended solvent, temperature, and ionic strength?", "Which metal-specific equilibrium and kinetic measurements justify the intended coordination use?", "What assay, water, and trace-metal acceptance limits are necessary for the target application, and what storage evidence supports a retest interval?" ], "statistics": { "bundles": 6, "layers": 11, "findings": 16, "questions": 26 } }