{ "model": { "rank": 5188, "code": "thing-q169324", "model_id": "vr.tr.hydrogen-bond", "name": "hydrogen bond", "purpose": "Let an agent explain hydrogen bonding and its importance, relay energies, geometry and the IUPAC definition from chemistry references, describe roles in water, biology and materials, and distinguish hydrogen bonds from covalent bonds and van der Waals forces.", "family": "Thing Registry", "category": "Activities and processes", "status": "research-draft", "kind": "thing", "plane": "ACT", "domain": "ACT.PRC", "industry": "", "version": "", "url": "/models/thing/q169324/", "tier": 2, "score": 69, "payload": { "layer": "wikidata", "aliases": [ "dihydrogen bond" ], "aliasCount": 1, "merged": 1, "knownIn": 69, "facets": null, "markers": [], "lexicalClass": "", "senseRank": null, "alsoRegisteredAs": null, "source": { "dataset": "wikidata", "item": "Q169324", "url": "https://www.wikidata.org/wiki/Q169324", "license": "CC0 1.0" } }, "research": { "vercy": "1.0-draft", "publication": { "status": "research-draft", "adjudicationStatus": "unreviewed", "publishableCanonical": false, "generatedAt": "2026-09-13T04:55:41Z", "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-Q169324", "registryId": "vr.tr.hydrogen-bond", "name": "hydrogen bond", "version": "0.2.0-wave.3", "entryKind": "thing", "family": "Thing Registry", "domain": [ "ACT.PRC" ], "status": "research-draft" }, "canonicalUrl": "https://ver.cy/models/thing/q169324/", "model": { "registry_id": "vr.tr.hydrogen-bond", "name": "hydrogen bond", "purpose": "Let an agent explain hydrogen bonding and its importance, relay energies, geometry and the IUPAC definition from chemistry references, describe roles in water, biology and materials, and distinguish hydrogen bonds from covalent bonds and van der Waals forces.", "definition": "An attractive interaction between a hydrogen atom bonded to an electronegative atom such as oxygen, nitrogen or fluorine and a nearby electronegative atom or electron-rich region, stronger than most intermolecular forces but weaker than covalent bonds, responsible for the properties of water, the structure of proteins and DNA, and the behaviour of many materials, with variants such as the dihydrogen bond between a protic hydrogen and a hydridic hydrogen; hydrogen bonds are characterised by their energy, geometry and spectroscopic signatures.", "what_it_is_for": "Not applicable; an interaction.", "affordances": [ "explain the interaction", "relay energies and geometry", "describe roles", "distinguish from other bonds" ], "distinguishing_features": [ "Directional", "Intermediate strength", "Donor and acceptor", "Ubiquitous in water and biology" ], "appearance": "Not a visible object; an interaction shown as dotted lines in structures.", "visual_identification": [ "Attraction between H on an electronegative atom and another electronegative atom", "Hydrogen bonds in water, proteins and DNA; dihydrogen bonds", "Covalent bonds share electrons; van der Waals forces are weaker and non-directional" ], "physical_properties": [ { "quantity": "typical energy", "typical_range": "about 4-40", "unit": "kJ/mol", "note": "" }, { "quantity": "O-H...O distance", "typical_range": "about 2.7-3.0", "unit": "angstrom", "note": "donor to acceptor" }, { "quantity": "water hydrogen bonds per molecule", "typical_range": "up to 4", "unit": "count", "note": "in ice" } ], "families_and_kinds": [ "conventional hydrogen bonds with O, N and F", "weak hydrogen bonds with C-H donors", "strong and symmetric hydrogen bonds", "dihydrogen bonds", "intramolecular and intermolecular hydrogen bonds" ], "related_models": [ { "relation": "is a kind of", "target": "chemical bond", "why": "in registry terms" }, { "relation": "is a kind of", "target": "dipole-dipole interaction", "why": "in registry terms" }, { "relation": "determines", "target": "water", "why": "properties" }, { "relation": "stabilises", "target": "DNA", "why": "base pairing" } ], "identifiers": [], "standards_and_regulation": [ "IUPAC 2011 definition of the hydrogen bond", "No regulation" ], "failure_modes_and_hazards": [ "Confusing hydrogen bonds with covalent bonds to hydrogen", "Overstating strength", "Ignoring weak and unconventional hydrogen bonds" ], "in_scope": [], "out_of_scope": [], "characteristics": [] }, "sources": [], "structure": { "bundles": [ { "id": "understand", "name": "Understand", "description": "What a hydrogen bond is.", "rationale": "Science.", "layers": [ { "id": "definition", "name": "Definition", "description": "Definition.", "findings": [ { "id": "definition-finding", "name": "Definition", "description": "Definition.", "questions": [ { "text": "What is a hydrogen bond, and how does the IUPAC definition describe it?", "kind": "definition" }, { "text": "Is the question about hydrogen bonds, covalent bonds to hydrogen or van der Waals forces?", "kind": "boundary" } ] } ] }, { "id": "kinds", "name": "Kinds", "description": "Kinds.", "findings": [ { "id": "kinds-finding", "name": "Kinds", "description": "Kinds.", "questions": [ { "text": "How do conventional, weak, strong and dihydrogen bonds differ?", "kind": "definition" }, { "text": "Which entry fits the specific kind?", "kind": "action" } ] } ] } ] }, { "id": "measure", "name": "Measure", "description": "Properties.", "rationale": "Science.", "layers": [ { "id": "energy", "name": "Energy", "description": "Energy and geometry.", "findings": [ { "id": "energy-finding", "name": "Energy", "description": "Energy.", "questions": [ { "text": "What energies, distances and angles characterise hydrogen bonds?", "kind": "measurement" }, { "text": "Which references are standard?", "kind": "provenance" } ] } ] }, { "id": "detection", "name": "Detection", "description": "Detection.", "findings": [ { "id": "detection-finding", "name": "Detection", "description": "Detection.", "questions": [ { "text": "How are hydrogen bonds detected by spectroscopy, crystallography and computation?", "kind": "provenance" }, { "text": "Which sources are cited?", "kind": "provenance" } ] } ] } ] }, { "id": "roles", "name": "Roles", "description": "Roles.", "rationale": "Application.", "layers": [ { "id": "water", "name": "Water", "description": "Water and materials.", "findings": [ { "id": "water-finding", "name": "Water", "description": "Water.", "questions": [ { "text": "How do hydrogen bonds explain the properties of water, ice and materials such as cellulose and nylon?", "kind": "provenance" }, { "text": "Which entry fits properties of water?", "kind": "action" } ] } ] }, { "id": "biology", "name": "Biology", "description": "Biology.", "findings": [ { "id": "biology-finding", "name": "Biology", "description": "Biology.", "questions": [ { "text": "How do hydrogen bonds shape proteins, DNA and drug binding?", "kind": "provenance" }, { "text": "Which entry fits protein structure?", "kind": "action" } ] } ] } ] }, { "id": "context", "name": "Context", "description": "History and research.", "rationale": "Context.", "layers": [ { "id": "history", "name": "History", "description": "History.", "findings": [ { "id": "history-finding", "name": "History", "description": "History.", "questions": [ { "text": "How was the hydrogen bond concept developed by Latimer, Rodebush and Pauling?", "kind": "provenance" }, { "text": "Which entry fits the history of chemistry?", "kind": "action" } ] } ] }, { "id": "research", "name": "Research", "description": "Research.", "findings": [ { "id": "research-finding", "name": "Research", "description": "Research.", "questions": [ { "text": "What current research explores unconventional hydrogen bonds and their role in catalysis?", "kind": "provenance" }, { "text": "Which entry fits supramolecular chemistry?", "kind": "action" } ] } ] } ] } ] }, "openQuestions": [ "Should dihydrogen bond be a separate entry?", "How should chemistry references be linked?", "How should biological roles be linked?" ], "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 hydrogen bond, record what state it is in, and decide what may be done with it.", "whatItIs": "Let an agent explain hydrogen bonding and its importance, relay energies, geometry and the IUPAC definition from chemistry references, describe roles in water, biology and materials, and distinguish hydrogen bonds from covalent bonds and van der Waals forces.", "characteristics": { "substance": "activity", "origin": "conceptual", "agency": "inert" }, "whatYouCanDoWithIt": [ "observed and measured" ], "distinguishingFeatures": [ "Names folded into this entry, which a task may need to split apart again: dihydrogen bond.", "1 finer distinctions are held as aliases rather than separate entries, because telling them apart needs a task that asks for it.", "Described in 69 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 hydrogen bond, and on what evidence are they told apart?" ], "whatItIsMadeOf": "something that happens over time", "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": [ "dihydrogen bond" ] } ], "standing": "Described in 69 Wikipedia languages, which measures how widely it is written about rather than how important or how common it is. 1 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 hydrogen bond from another, and a hydrogen bond 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 hydrogen bond, 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 hydrogen bond, 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 hydrogen bond 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 hydrogen bond, 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 hydrogen bond, 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 hydrogen bond 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 hydrogen bond 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 hydrogen bond, 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 hydrogen bond, 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 hydrogen bond 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 hydrogen bond from the things most often confused with it.", "questions": [ { "id": "distinguishing-features-q01", "text": "What identifies and describes what distinguishes a hydrogen bond, 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 hydrogen bond, 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 hydrogen bond 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 hydrogen bond 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 hydrogen bond between them.", "questions": [ { "id": "stages-and-transitions-q01", "text": "What identifies and describes the lifecycle of a hydrogen bond, 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 hydrogen bond, 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 hydrogen bond 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 hydrogen bond, how often and by whom.", "findings": [ { "id": "observation-record", "name": "Observation record", "description": "How an observation of a hydrogen bond 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 hydrogen bond, 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 hydrogen bond, 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 hydrogen bond is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] } ] }, { "id": "process-and-outcome", "name": "Process, inputs and outcome", "description": "How a hydrogen bond proceeds, what it needs and what it leaves behind.", "rationale": "An activity is known by its steps and its results, and both have to be recordable while it is still running.", "layers": [ { "id": "steps-and-sequence", "name": "Steps and sequence", "description": "The steps of a hydrogen bond, their order and what may run in parallel.", "findings": [ { "id": "steps-and-preconditions", "name": "Steps, preconditions and completion", "description": "What has to be true before each step of a hydrogen bond and what marks it done.", "questions": [ { "id": "steps-and-preconditions-q01", "text": "What identifies and describes a step of a hydrogen bond, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "steps-and-preconditions-q02", "text": "Who or what asserted this about a step of a hydrogen bond, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "steps-and-preconditions-q03", "text": "What may an agent decide or do once a step of a hydrogen bond is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] }, { "id": "inputs-and-results", "name": "Inputs, resources and results", "description": "What a hydrogen bond consumes and what it produces.", "findings": [ { "id": "inputs-and-outputs", "name": "Inputs, outputs and side effects", "description": "The resources a hydrogen bond takes and the results it leaves, wanted or not.", "questions": [ { "id": "inputs-and-outputs-q01", "text": "What identifies and describes the inputs and results of a hydrogen bond, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "inputs-and-outputs-q02", "text": "Who or what asserted this about the inputs and results of a hydrogen bond, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "inputs-and-outputs-q03", "text": "What may an agent decide or do once the inputs and results of a hydrogen bond 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 hydrogen bond 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 hydrogen bond 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 hydrogen bond 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 hydrogen bond 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 hydrogen bond?", "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 hydrogen bond?", "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 hydrogen bond 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 hydrogen bond and how confident it is.", "questions": [ { "id": "claim-provenance-q01", "text": "What identifies and describes a claim about a hydrogen bond, 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 hydrogen bond, 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 hydrogen bond 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 hydrogen bond is retired without being erased.", "questions": [ { "id": "validity-and-supersession-q01", "text": "What identifies and describes the validity of a claim about a hydrogen bond, 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 hydrogen bond, 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 hydrogen bond is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] } ] } ] }, "statistics": { "bundles": 6, "layers": 12, "findings": 14, "questions": 38 } } } }