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Research draft

molecule

vr.tr.molecule · PHY.MAT

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

Thing Registry Physical world and living systems

Research draft, second pass

A second pass drafted this model: the structure a model of this thing needs, and what is known about it in the world. The line under this one says how the second half was obtained - researched against sources, or recalled without web access, in which case nothing here was read anywhere and every claim is a lead to verify. Unreviewed either way.

written by Claude from model knowledge without web access - no source was read, every claim is a lead to verify

Researched by: Claude

Purpose and description

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

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.

What it is for: Understanding chemistry, materials and biology.

It can be identify molecules by formula and name; describe structure and bonding; look up properties in databases; represent molecules in software.

Distinguishing features

Bonded group of atoms

Neutral overall

Defined composition

Property of a substance

What it looks like

Invisible to the eye; shown as formulas, models and computer structures.

How it is recognised

Molecular formulas and structures

Identifiers such as InChI and SMILES

Ions and ionic lattices are related but different

Related models

is a kind of - category

molecular entity

is made of - components

atom

is held by - bonding

chemical bond

is identified by - identifiers

InChI and CAS number

In practice

Families and kinds

diatomic molecules

small organic molecules

macromolecules and polymers

biomolecules

molecular ions (related)

Identifiers

InChI IUPAC identifier structure

CAS Registry Number numeric substance

Standards and regulation

IUPAC nomenclature

REACH substance registration

Failure modes and hazards

Confusing molecules and ions

Ambiguous names

Also called

monomer moleculedinuclear copperhelium dimernitrogen monofluoridemercury polycationmTOR inhibitors(¹⁶O₂)dioxygen(¹⁷O₂)dioxygen(¹⁴N₂)dinitrogenditritium(¹⁵N₂)dinitrogenmotor proteinFlagellar hook-basal body complex protein FliEFlagellar motor switch FliN/Type III secretion HrcQbFlagellar M-ring protein FliFFlagellar motor switch protein FliGFlagellar motor switch protein FliMFlagellar assembly protein FliHFlagellar L-ring proteinUnconventional myosin-IXapentamergene productcyclopropatrienedihydrogen chalcogenidecyclic trinitrogenspasminMyosin S1 fragment, N-terminalFlagellar FliJ, proteobacteriamyosinactinMyosin, N-terminal, SH3-like, protein familyClass I myosin tail homology domain, protein familyMyosin tail, protein familyMyosin head, motor domain, protein familyframeshift mutantcarbon monosulfidecell pumptriatomic moleculediatomic moleculehomonuclear triatomic molecule

+32

Where this came from

wikidata · CC0 1.0

Source repository Registry entry point

Also registered as vr.tr.molecule

Drafted structure

Bundle to layer to finding to question, as the second pass will find it: 4 bundles · 8 layers · 8 findings · 16 questions.

Identity Which molecule.

Identifiers disambiguate.

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.

Structure explains behaviour.

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.

Data need sources.

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.

Clear models help.

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

What the second pass must settle

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