{ "model": { "rank": 15355, "code": "thing-q911331", "model_id": "vr.tr.molecular-geometry", "name": "molecular geometry", "purpose": "Let an agent explain molecular geometry and its common shapes, relay VSEPR and related theories and experimental methods from chemistry references, describe coordination geometry, and distinguish molecular geometry from electron geometry, molecular structure in the connectivity sense and crystal structure.", "family": "Thing Registry", "category": "Cross-cutting context", "status": "research-draft", "kind": "thing", "plane": "XCT", "domain": "XCT.QLT", "industry": "", "version": "", "url": "/models/thing/q911331/", "tier": 2, "score": 34, "payload": { "layer": "wikidata", "aliases": [ "coordination geometry", "square planar molecular geometry", "trigonal planar molecular geometry", "trigonal pyramidal molecular geometry", "linear molecular geometry", "seesaw molecular geometry", "square pyramidal molecular geometry", "octahedral molecular geometry", "T-shaped molecular geometry", "tetrahedral molecular geometry", "pentagonal pyramidal molecular geometry", "trigonal bipyramidal molecular geometry", "pentagonal planar molecular geometry", "Capped square antiprismatic molecular geometry", "carbohydrate conformation", "macromolecular structure", "Capped octahedral molecular geometry", "Capped trigonal prismatic molecular geometry", "Dodecahedral molecular geometry", "Bicapped trigonal prismatic molecular geometry", "pentagonal bipyramidal molecular geometry", "bent molecular geometry", "Square antiprismatic molecular geometry", "Tricapped trigonal prismatic molecular geometry", "trigonal prismatic molecular geometry", "histone code", "solution structure" ], "aliasCount": 27, "merged": 27, "knownIn": 34, "facets": null, "markers": [], "lexicalClass": "", "senseRank": null, "alsoRegisteredAs": null, "source": { "dataset": "wikidata", "item": "Q911331", "url": "https://www.wikidata.org/wiki/Q911331", "license": "CC0 1.0" } }, "research": { "vercy": "1.0-draft", "publication": { "status": "research-draft", "adjudicationStatus": "unreviewed", "publishableCanonical": false, "generatedAt": "2026-09-13T05:57:32Z", "providers": [ "Claude" ], "breadth": "written by Claude from model knowledge without web access - no source was read, every claim is a lead to verify", "pass": 2, "wave": 3, "engine": "claude" }, "metaModel": { "id": "THING-Q911331", "registryId": "vr.tr.molecular-geometry", "name": "molecular geometry", "version": "0.2.0-wave.3", "entryKind": "thing", "family": "Thing Registry", "domain": [ "XCT.QLT" ], "status": "research-draft" }, "canonicalUrl": "https://ver.cy/models/thing/q911331/", "model": { "registry_id": "vr.tr.molecular-geometry", "name": "molecular geometry", "purpose": "Let an agent explain molecular geometry and its common shapes, relay VSEPR and related theories and experimental methods from chemistry references, describe coordination geometry, and distinguish molecular geometry from electron geometry, molecular structure in the connectivity sense and crystal structure.", "definition": "The three-dimensional arrangement of atoms in a molecule, including bond lengths, bond angles and torsion angles, which determines properties such as polarity, reactivity and biological activity, described by shapes such as linear, trigonal planar, bent, tetrahedral, trigonal pyramidal, seesaw, square planar and octahedral, predicted by VSEPR theory and hybridisation and, for metal complexes, described as coordination geometry; molecular geometry is determined experimentally by diffraction and spectroscopy.", "what_it_is_for": "Not applicable; a chemical concept.", "affordances": [ "explain shapes and theory", "relay methods", "describe coordination geometry", "distinguish related concepts" ], "distinguishing_features": [ "Bond angles and lengths", "Predicted by VSEPR", "Determines properties", "Measured by diffraction" ], "appearance": "Not a visible object; shapes shown in models.", "visual_identification": [ "Three-dimensional arrangement of atoms", "Linear, trigonal planar, trigonal pyramidal, tetrahedral, seesaw, square planar, octahedral; coordination geometry", "Electron geometry counts lone pairs; connectivity is the bonding pattern; crystal structure is the lattice" ], "physical_properties": [ { "quantity": "tetrahedral angle", "typical_range": "109.5", "unit": "degrees", "note": "" }, { "quantity": "water bond angle", "typical_range": "about 104.5", "unit": "degrees", "note": "" }, { "quantity": "common coordination numbers", "typical_range": "2 to 6 and higher", "unit": "range", "note": "" } ], "families_and_kinds": [ "linear geometry", "trigonal planar and bent geometries", "tetrahedral and trigonal pyramidal geometries", "trigonal bipyramidal, seesaw and T-shaped geometries", "octahedral, square pyramidal and square planar geometries", "coordination geometries of metal complexes" ], "related_models": [ { "relation": "is a kind of", "target": "shape", "why": "in registry terms" }, { "relation": "is predicted by", "target": "VSEPR theory", "why": "from electron pairs" }, { "relation": "is measured by", "target": "X-ray crystallography", "why": "and spectroscopy" }, { "relation": "includes", "target": "coordination geometry", "why": "for metal complexes" } ], "identifiers": [], "standards_and_regulation": [ "IUPAC definitions and nomenclature for geometry and stereochemistry", "No regulation" ], "failure_modes_and_hazards": [ "Confusing molecular and electron geometry", "Overreliance on VSEPR for transition metals", "Confusing shape names" ], "in_scope": [], "out_of_scope": [], "characteristics": [] }, "sources": [], "structure": { "bundles": [ { "id": "understand", "name": "Understand", "description": "What molecular geometry is.", "rationale": "Science.", "layers": [ { "id": "definition", "name": "Definition", "description": "Definition.", "findings": [ { "id": "definition-finding", "name": "Definition", "description": "Definition.", "questions": [ { "text": "What is molecular geometry, and how does it differ from electron geometry, connectivity and crystal structure?", "kind": "definition" }, { "text": "Is the question about molecular geometry, coordination geometry or crystal structure?", "kind": "boundary" } ] } ] }, { "id": "shapes", "name": "Shapes", "description": "Shapes.", "findings": [ { "id": "shapes-finding", "name": "Shapes", "description": "Shapes.", "questions": [ { "text": "What are the linear, trigonal planar, bent, tetrahedral, trigonal pyramidal, seesaw, square planar and octahedral shapes?", "kind": "definition" }, { "text": "Which entry fits the specific shape?", "kind": "action" } ] } ] } ] }, { "id": "predict", "name": "Predict", "description": "Theory.", "rationale": "Science.", "layers": [ { "id": "vsepr", "name": "VSEPR", "description": "VSEPR and hybridisation.", "findings": [ { "id": "vsepr-finding", "name": "VSEPR", "description": "VSEPR.", "questions": [ { "text": "How do VSEPR theory and hybridisation predict molecular shapes, and where do they fail?", "kind": "provenance" }, { "text": "Which references are standard?", "kind": "provenance" } ] } ] }, { "id": "computation", "name": "Computation", "description": "Computational methods.", "findings": [ { "id": "computation-finding", "name": "Computation", "description": "Computation.", "questions": [ { "text": "How do quantum chemical calculations determine geometry?", "kind": "provenance" }, { "text": "Which sources are cited?", "kind": "provenance" } ] } ] } ] }, { "id": "measure", "name": "Measure", "description": "Measurement.", "rationale": "Practice.", "layers": [ { "id": "methods", "name": "Methods", "description": "Experimental methods.", "findings": [ { "id": "methods-finding", "name": "Methods", "description": "Methods.", "questions": [ { "text": "How are geometries determined by X-ray, neutron and electron diffraction and by spectroscopy?", "kind": "provenance" }, { "text": "Which entry fits X-ray crystallography?", "kind": "action" } ] } ] }, { "id": "coordination", "name": "Coordination", "description": "Coordination geometry.", "findings": [ { "id": "coordination-finding", "name": "Coordination", "description": "Coordination.", "questions": [ { "text": "How are coordination geometries of metal complexes described and predicted?", "kind": "provenance" }, { "text": "Which entry fits coordination complex?", "kind": "action" } ] } ] } ] }, { "id": "context", "name": "Context", "description": "Importance and history.", "rationale": "Context.", "layers": [ { "id": "importance", "name": "Importance", "description": "Why it matters.", "findings": [ { "id": "importance-finding", "name": "Importance", "description": "Importance.", "questions": [ { "text": "How does geometry affect polarity, reactivity, drug binding and materials?", "kind": "provenance" }, { "text": "Which entry fits stereochemistry?", "kind": "action" } ] } ] }, { "id": "history", "name": "History", "description": "History.", "findings": [ { "id": "history-finding", "name": "History", "description": "History.", "questions": [ { "text": "How did van t Hoff, Le Bel, Werner and Gillespie develop the understanding of molecular shape?", "kind": "provenance" }, { "text": "Which entry fits the history of chemistry?", "kind": "action" } ] } ] } ] } ] }, "openQuestions": [ "Should VSEPR theory and coordination geometry be separate primary entries?", "How should chemistry references be linked?", "The registry entry has merged aliases naming specific shapes; should they be split off?" ], "statistics": { "bundles": 4, "layers": 8, "findings": 8, "questions": 16 } }, "draft": { "generator": "vr.draft.v3", "status": "draft-generated", "researched": false, "archetype": "abstract concept", "method": "Written from the archetype playbook - what this kind of thing needs beyond identity and provenance - and from the structure that recurred across 6,333 models already researched by two engines. Applied to this entry by rule. No source was read for this thing and no claim here is researched. This entry carries no facets of its own, so they were inferred from its domain - a guess about a whole domain applied to one thing.", "facetsInferred": true, "nextPass": "A researcher replaces this draft with a sourced specification. Treat every sentence below as a proposal to argue with.", "purpose": "Give an agent a durable, checkable way to recognise a molecular geometry, record what state it is in, and decide what may be done with it.", "whatItIs": "Let an agent explain molecular geometry and its common shapes, relay VSEPR and related theories and experimental methods from chemistry references, describe coordination geometry, and distinguish molecular geometry from electron geometry, molecular structure in the connectivity sense and crystal structure.", "characteristics": { "substance": "abstract", "origin": "conceptual", "agency": "inert" }, "whatYouCanDoWithIt": [ "observed and measured" ], "distinguishingFeatures": [ "Names folded into this entry, which a task may need to split apart again: coordination geometry, square planar molecular geometry, trigonal planar molecular geometry, trigonal pyramidal molecular geometry, linear molecular geometry, seesaw molecular geometry, square pyramidal molecular geometry, octahedral molecular geometry, T-shaped molecular geometry, tetrahedral molecular geometry, pentagonal pyramidal molecular geometry, trigonal bipyramidal molecular geometry.", "27 finer distinctions are held as aliases rather than separate entries, because telling them apart needs a task that asks for it.", "Described in 34 Wikipedia languages, which is a measure of how widely the thing is known, not of how important it is." ], "openQuestionsForResearch": [ "Which of the bundles below does a real task actually need, and which are ceremony?", "What does this thing have that the facets do not capture at all?", "Which neighbouring kind is most often confused with a molecular geometry, and on what evidence are they told apart?" ], "whatItIsMadeOf": "an abstraction with no physical instance", "physicalCharacter": [ "Does nothing on its own; everything it does, something else did to it.", "These come from the domain this entry sits in rather than from the entry itself, so treat them as a first guess about the whole domain applied to one thing." ], "whatCanBeDoneWithIt": [ "observe it, measure it, record its state" ], "howItIsRecognised": [ "Nothing to see. What is recognised is an instance of it, and which instances count is exactly what is argued about." ], "relatedModels": [ { "relation": "covers", "note": "Finer kinds folded into this entry because telling them apart needs a task that asks for it. Each is a model waiting to be split out when one does.", "targets": [ "coordination geometry", "square planar molecular geometry", "trigonal planar molecular geometry", "trigonal pyramidal molecular geometry", "linear molecular geometry", "seesaw molecular geometry", "square pyramidal molecular geometry", "octahedral molecular geometry", "T-shaped molecular geometry", "tetrahedral molecular geometry", "pentagonal pyramidal molecular geometry", "trigonal bipyramidal molecular geometry" ] } ], "standing": "Described in 34 Wikipedia languages, which measures how widely it is written about rather than how important or how common it is. 27 finer distinctions are held inside this entry as names rather than as separate models.", "structure": { "bundles": [ { "id": "identity-and-classification", "name": "Identity, naming and classification", "description": "How an agent tells one molecular geometry from another, and a molecular geometry from things that resemble it.", "rationale": "Recognition comes before every other claim. Without stable identity nothing else in the model can be trusted to be about the same thing twice.", "layers": [ { "id": "naming-and-identifiers", "name": "Names and identifiers", "description": "The names this thing goes by and the identifiers that survive translation and time.", "findings": [ { "id": "preferred-name-and-aliases", "name": "Preferred name, aliases and local names", "description": "Which name to use, which names mean the same thing, and which merely sound similar.", "questions": [ { "id": "preferred-name-and-aliases-q01", "text": "What identifies and describes the name of a molecular geometry, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "preferred-name-and-aliases-q02", "text": "Who or what asserted this about the name of a molecular geometry, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "preferred-name-and-aliases-q03", "text": "What may an agent decide or do once the name of a molecular geometry is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] }, { "id": "stable-identifiers", "name": "Stable identifiers and external keys", "description": "Identifiers that keep pointing at this kind of thing across systems and languages.", "questions": [ { "id": "stable-identifiers-q01", "text": "What identifies and describes an identifier for a molecular geometry, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "stable-identifiers-q02", "text": "Who or what asserted this about an identifier for a molecular geometry, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "stable-identifiers-q03", "text": "What may an agent decide or do once an identifier for a molecular geometry is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] }, { "id": "classification-and-granularity", "name": "Classification and granularity", "description": "Where a molecular geometry sits among kinds, and how finely a task needs to cut it.", "findings": [ { "id": "kind-and-parents", "name": "Kind, parents and neighbouring kinds", "description": "The classes this thing belongs to and the ones it is next to.", "questions": [ { "id": "kind-and-parents-q01", "text": "What identifies and describes the kind of a molecular geometry, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "kind-and-parents-q02", "text": "Who or what asserted this about the kind of a molecular geometry, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "kind-and-parents-q03", "text": "What may an agent decide or do once the kind of a molecular geometry is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] }, { "id": "distinguishing-features", "name": "Distinguishing features", "description": "What separates a molecular geometry from the things most often confused with it.", "questions": [ { "id": "distinguishing-features-q01", "text": "What identifies and describes what distinguishes a molecular geometry, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "distinguishing-features-q02", "text": "Who or what asserted this about what distinguishes a molecular geometry, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "distinguishing-features-q03", "text": "What may an agent decide or do once what distinguishes a molecular geometry is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] } ] }, { "id": "state-and-lifecycle", "name": "State and lifecycle", "description": "The states a molecular geometry passes through and the events that move it between them.", "rationale": "Most decisions about a thing depend on what state it is in now, which is a claim with a time on it, not a property.", "layers": [ { "id": "lifecycle-stages", "name": "Lifecycle stages", "description": "From coming into existence to ceasing to be one of these.", "findings": [ { "id": "stages-and-transitions", "name": "Stages and transitions", "description": "The stages worth naming and what moves a molecular geometry between them.", "questions": [ { "id": "stages-and-transitions-q01", "text": "What identifies and describes the lifecycle of a molecular geometry, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "stages-and-transitions-q02", "text": "Who or what asserted this about the lifecycle of a molecular geometry, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "stages-and-transitions-q03", "text": "What may an agent decide or do once the lifecycle of a molecular geometry is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] }, { "id": "observations-and-status", "name": "Observations and current status", "description": "What is observed about a molecular geometry, how often and by whom.", "findings": [ { "id": "observation-record", "name": "Observation record", "description": "How an observation of a molecular geometry is recorded so that it can be superseded rather than overwritten.", "questions": [ { "id": "observation-record-q01", "text": "What identifies and describes an observation of a molecular geometry, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "observation-record-q02", "text": "Who or what asserted this about an observation of a molecular geometry, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "observation-record-q03", "text": "What may an agent decide or do once an observation of a molecular geometry is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] } ] }, { "id": "definitions-in-contest", "name": "Definitions and who holds them", "description": "What molecular geometry is taken to mean, and by whom.", "rationale": "When a field disagrees about a concept, the disagreement is the content. A model that picks one definition silently destroys the information.", "layers": [ { "id": "competing-definitions", "name": "Competing definitions", "description": "The main readings and the traditions behind them.", "findings": [ { "id": "definition-map", "name": "Definitions and their holders", "description": "Each definition with the school or body that holds it.", "questions": [ { "id": "definition-map-q01", "text": "Which definitions of molecular geometry are in use, and which tradition or body holds each?", "kind": "definition" }, { "id": "definition-map-q02", "text": "What turns on the difference between them in practice?", "kind": "boundary" } ] } ] }, { "id": "operationalisation", "name": "Operationalisation", "description": "How it is measured or applied when it has to be.", "findings": [ { "id": "operational-record", "name": "Measures and proxies", "description": "Instruments and indicators used to stand in for it.", "questions": [ { "id": "operational-record-q01", "text": "How is molecular geometry operationalised or measured in practice, and by what instrument?", "kind": "measurement" }, { "id": "operational-record-q02", "text": "What does that operationalisation leave out, and when does that matter?", "kind": "boundary" } ] } ] } ] }, { "id": "instances-and-use", "name": "Instances, use and consequence", "description": "What counts as an instance of molecular geometry and what follows from calling something that.", "rationale": "Applying a concept is an act with consequences, so a model must say what the label licenses and what it does not.", "layers": [ { "id": "instances", "name": "What counts as an instance", "description": "Clear cases, borderline cases and non-cases.", "findings": [ { "id": "instance-tests", "name": "Tests for an instance", "description": "What would settle whether something falls under it.", "questions": [ { "id": "instance-tests-q01", "text": "What would settle whether something is an instance of molecular geometry?", "kind": "boundary" }, { "id": "instance-tests-q02", "text": "Which borderline cases are argued about, and on what grounds?", "kind": "definition" } ] } ] }, { "id": "consequence", "name": "Consequence of application", "description": "Rights, duties or decisions that follow from the label.", "findings": [ { "id": "consequence-record", "name": "What the label licenses", "description": "What an agent may do once something is classified this way.", "questions": [ { "id": "consequence-record-q01", "text": "What follows practically once something is treated as molecular geometry?", "kind": "action" }, { "id": "consequence-record-q02", "text": "What must an agent not infer from the label alone?", "kind": "action" } ] } ] } ] }, { "id": "provenance-and-evidence", "name": "Provenance, evidence and time", "description": "Where every claim about a molecular geometry came from and when it held.", "rationale": "A claim without a source and a time cannot be superseded, only overwritten, and an agent that overwrites loses the ability to explain itself.", "layers": [ { "id": "source-and-authority", "name": "Source and authority", "description": "Who said it, on what evidence, and how strongly.", "findings": [ { "id": "claim-provenance", "name": "Claim provenance and confidence", "description": "The authority behind each claim about a molecular geometry and how confident it is.", "questions": [ { "id": "claim-provenance-q01", "text": "What identifies and describes a claim about a molecular geometry, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "claim-provenance-q02", "text": "Who or what asserted this about a claim about a molecular geometry, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "claim-provenance-q03", "text": "What may an agent decide or do once a claim about a molecular geometry is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] }, { "id": "time-and-versions", "name": "Time, versions and supersession", "description": "When a claim was true, when it was learnt, and what replaced it.", "findings": [ { "id": "validity-and-supersession", "name": "Validity period and supersession", "description": "How an old claim about a molecular geometry is retired without being erased.", "questions": [ { "id": "validity-and-supersession-q01", "text": "What identifies and describes the validity of a claim about a molecular geometry, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "validity-and-supersession-q02", "text": "Who or what asserted this about the validity of a claim about a molecular geometry, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "validity-and-supersession-q03", "text": "What may an agent decide or do once the validity of a claim about a molecular geometry is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] } ] } ] }, "statistics": { "bundles": 5, "layers": 10, "findings": 12, "questions": 32 } } } }