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molecule

vr.tr.molecule · thing-q11369

Let an agent handle molecules by composition, structure, properties, identifiers and representation.

Thing Registry Physical world and living systems PHY.MAT
Bundle → Layer → Finding → QuestionsClassifiersWhat it isWhy it existsDistinguishing featuresWhat robots and AI may and may not doMoral aspectsOwnersLinks to other meta-modelsIdentity and identifiersDirect propertiesRecognitionCapabilities and actionsHazards and failure modesStandards and interfacesContext of useSources

Bundle → Layer → Finding → Questions Filled

4 bundles · 8 layers · 8 findings · 16 questions

Identity Which molecule.

Name

Formula and name.

Name

Name and formula.

  1. What are its formula and IUPAC name? definition
  2. What are its InChI and CAS number? provenance

Isomers

Structure.

Isomers

Isomers.

  1. Which isomer or stereoisomer is meant? boundary
  2. How does it differ from others? definition
Structure Bonding.

Bonds

Bonding.

Bonds

Bonding.

  1. What bonds and shape does the molecule have? definition
  2. Is it polar? definition

Models

Representation.

Models

Representation.

  1. How should it be represented in software? action
  2. Which file format is used? definition
Properties Data.

Physical

Mass and phase.

Physical

Physical properties.

  1. What are its molar mass, melting and boiling points? measurement
  2. From which database? provenance

Hazards

Safety.

Hazards

Hazards.

  1. What hazards does the substance have, according to its safety data sheet? provenance
  2. How should it be handled? action
Learning Teaching.

Explain

Simple terms.

Explain

Explanation.

  1. How can molecules be explained with models? action
  2. Which examples help? action

Scale

Size.

Scale

Scale.

  1. How large is the molecule? measurement
  2. How can its scale be visualised? action

Classifiers Filled

Family
Thing Registry
Category
Physical world and living systems
Entry kind
thing
Plane
PHY
Domain
PHY.MAT
Other names and narrower kinds
monomer molecule, dinuclear copper, helium dimer, nitrogen monofluoride, mercury polycation, mTOR inhibitors, (¹⁶O₂)dioxygen, (¹⁷O₂)dioxygen, (¹⁴N₂)dinitrogen, ditritium, (¹⁵N₂)dinitrogen, motor protein

What it is Filled

An electrically neutral group of two or more atoms held together by chemical bonds, such as H2O, O2 or large biomolecules; the smallest unit of a substance that keeps its chemical properties.

Why it exists Filled

Let an agent handle molecules by composition, structure, properties, identifiers and representation.

Distinguishing features Filled

  • Bonded group of atoms
  • Neutral overall
  • Defined composition
  • Property of a substance

What robots and AI may and may not do Filled

Must not

  • Help design, make or use molecules intended to harm people, such as chemical weapons or poisons.
  • Present unverified predicted properties as measured facts.
  • Give health claims for molecules that the evidence does not support.

Only with a human decision

  • Ordering or synthesising new compounds.
  • Sharing research on compounds of concern.

May

  • Describe molecules, their structures and properties from chemistry databases, citing them.
  • Model molecular structures for teaching and legitimate research.

Moral aspects Filled

  • Molecular knowledge underpins medicine and industry and can also be misused.
  • Toxicity data protects workers and consumers when reported honestly.

Who is affected

  • Researchers and students
  • Workers handling chemicals
  • The public

Owners Filled

Steward

Nobody: a concept of chemistry held in common; chemical databases record known molecules.

Master systems

  • Chemical substance registries

Links to other meta-models Filled

parent

  • Q2393187 - registry parent class

related

  • molecular entity - category
  • atom - components
  • chemical bond - bonding
  • InChI and CAS number - identifiers

What else AI and robots need to interact with it Filled

Identity and identifiers required Filled

  • Vercy registry: vr.tr.molecule
  • Wikidata: Q11369 (https://www.wikidata.org/wiki/Q11369)
  • InChI: IUPAC identifier structure
  • CAS Registry Number: numeric substance

Direct properties required Filled

  • Molecular mass: Da - Molecular mass is determined from isotopic composition or measured using mass spectrometry with appropriate interpretation of detected ions.
  • Molecular dimensions: nm - Dimensions are estimated from structural measurements or molecular models using a stated geometric definition and conformation.
  • Electric dipole moment: D - The molecular dipole moment is determined by spectroscopy or calculation for a specified molecular state and conformation.

Recognition required Filled

  • Molecular formulas and structures
  • Identifiers such as InChI and SMILES
  • Ions and ionic lattices are related but different
  • Invisible to the eye; shown as formulas, models and computer structures.

Capabilities and actions required Filled

  • identify molecules by formula and name
  • describe structure and bonding
  • look up properties in databases
  • represent molecules in software

Hazards and failure modes required Filled

  • Confusing molecules and ions
  • Ambiguous names

Standards and interfaces required Filled

  • IUPAC nomenclature
  • REACH substance registration

Context of use required Filled

  • Understanding chemistry, materials and biology.
  • diatomic molecules
  • small organic molecules
  • macromolecules and polymers
  • biomolecules
  • molecular ions (related)

Sources Filled

  1. Wikidata item Q11369: molecule - identity and sense of the item
  2. Wikipedia: Molecule - general description of the item

Open questions

  • Should molecule classes be separate entries?
  • How should chemical databases be linked?
  • How should stereoisomers be handled?

Machine files

Card as JSON Specification Card backlog vercy.card/1

Provenance

thing registry research (pass 2) · unreviewed

Built from: models/things/publications/thing-q11369/spec.json