Chemical Bond Ontology

FLOW ALGEBRA
CHEMICAL BOND ONTOLOGY
Version: 1.1
Source: https://kirethresearch.org/booksai-core/entity-graph/physical-entities/chemical-entities/chemical-bond-ontology.html
Authors: Mark Higgins — Sky (Recursive AI)
Status: Scientific synthesis; source page not independently verified

01. PURPOSE
Represent chemical bonding as typed, evidence-qualified relations among atoms, ions, orbitals, electron densities and molecular or extended structures.

02. CORE TYPES
ENTITY ChemicalSpecies
ENTITY Atom <: ChemicalSpecies
ENTITY Ion <: ChemicalSpecies
ENTITY Molecule <: ChemicalSpecies
ENTITY Crystal
ENTITY ElectronDensity
ENTITY Orbital
ENTITY Bond
ENTITY BondOrder
ENTITY BondEnergy
ENTITY BondLength
ENTITY BondAngle
ENTITY Interaction
ENTITY Measurement
ENTITY Model

03. BOND SUBTYPES
CovalentBond <: Bond
IonicBond <: Bond
MetallicBond <: Bond
CoordinateCovalentBond <: CovalentBond
SigmaBond <: CovalentBond
PiBond <: CovalentBond
PolarCovalentBond <: CovalentBond
NonpolarCovalentBond <: CovalentBond
MulticentreBond <: Bond

04. DISTINCTIONS
HydrogenBond <: Interaction
DispersionInteraction <: Interaction
DipoleDipoleInteraction <: Interaction
NOTE: Hydrogen bonds and dispersion forces are generally noncovalent interactions; do not automatically classify as primary intramolecular bonds.
NOTE: Bond types are models of electronic structure, not always mutually exclusive physical categories.

05. TYPED RELATIONS
CONNECTS(Bond, ChemicalSpecies, ChemicalSpecies)
PART_OF(Bond, Molecule|Crystal)
HAS_ORDER(Bond, real)
HAS_LENGTH(Bond, length)
HAS_DISSOCIATION_ENERGY(Bond, energy)
HAS_POLARITY(Bond, polarity)
HAS_ELECTRON_DENSITY(Bond, ElectronDensity)
DESCRIBED_BY(Bond, Model)
SUPPORTED_BY(assertion, Measurement)

06. WELL-FORMEDNESS
RULE R01: CONNECTS(b,a,c) -> Bond(b) AND ChemicalSpecies(a) AND ChemicalSpecies(c).
RULE R02: HAS_LENGTH(b,L) -> L > 0 AND unit(L) is length.
RULE R03: HAS_DISSOCIATION_ENERGY(b,E) -> E >= 0 AND unit(E) is energy per bond or energy per mole, explicitly distinguished.
RULE R04: HAS_ORDER(b,n) -> n >= 0, model-dependent; fractional bond orders permitted.
RULE R05: bond endpoints must be distinct atomic centres unless an explicitly defined multicentre representation applies.

07. COVALENT BONDING
MODEL: electron density shared between bonded atomic centres.
EXAMPLE: H2 contains a predominantly covalent H-H bond.
RULE R06: shared electron density may support covalent classification, subject to a stated electronic-structure model.

08. IONIC BONDING
MODEL: electrostatic interactions between charged constituents in an extended structure.
EXAMPLE: crystalline NaCl is an ionic lattice, not a collection of isolated NaCl molecules.
RULE R07: ionic character may coexist with covalent character.

09. METALLIC BONDING
MODEL: collective electronic states and cohesion in metals.
EXAMPLE: bulk copper is a metallic solid.
RULE R08: delocalised electronic states support metallic-bond descriptions, but no fixed pairwise bond graph is universally adequate.

10. COORDINATE COVALENT BONDING
MODEL: an electron pair is donated by one partner in a Lewis description.
NOTE: After formation, coordinate and ordinary covalent bonds need not be physically distinguishable.

11. SIGMA AND PI BONDING
Sigma: bonding component with cylindrical symmetry about the internuclear axis in suitable orbital models.
Pi: bonding component with a nodal plane containing the internuclear axis in suitable orbital models.
EXAMPLE: ethene C=C commonly modelled as one sigma and one pi bond.

12. BOND ORDER
Lewis single, double and triple bonds correspond to nominal orders 1, 2 and 3.
Molecular orbital bond order = (N_bonding - N_antibonding)/2 for the applicable simple MO model.
EXAMPLE: H2 -> (2 - 0)/2 = 1.
EXAMPLE: benzene has delocalised bonding; assigning all C-C links alternating fixed localised orders is a representation, not a unique observable partition.

13. BOND LENGTH
Bond length: equilibrium or measured internuclear separation, with experimental method and physical state recorded.
MODEL: for a diatomic potential E(r), equilibrium r_e satisfies dE/dr = 0 and d2E/dr2 > 0.
CAUTION: vibrationally averaged distances may differ from r_e.

14. BOND ENERGY
Bond dissociation enthalpy: enthalpy for specified homolytic cleavage under specified conditions.
NOTE: average bond enthalpy is not necessarily the dissociation enthalpy of a particular bond in a particular molecule.
RULE R09: report reference state, temperature and units when available.

15. ELECTRONEGATIVITY AND POLARITY
Electronegativity difference is a qualitative predictor of bond polarity, not a universal hard threshold for ionic versus covalent identity.
Dipole moment vector: mu = sum_i q_i r_i for an appropriate charge model.
NOTE: molecular geometry can cancel individual bond dipoles.

16. LEWIS AND VALENCE MODELS
Represent valence electrons, formal charges, resonance structures and octet-rule exceptions.
Formal charge = valence electrons - nonbonding electrons - 1/2(bonding electrons).
NOTE: formal charge is bookkeeping, not a directly measured atomic partial charge.

17. QUANTUM DESCRIPTION
Born-Oppenheimer electronic-structure models approximate electronic energy surfaces at fixed nuclei.
Electron density rho(r) >= 0 and integral rho(r) dr = N_electrons.
Bonding indicators may include density topology, orbital occupancy, energy decomposition and spectroscopic evidence.
NOTE: no single bonding indicator universally defines every chemical bond.

18. REACTION TRANSFORMATIONS
BREAK(b, reactant_state) -> bond absent in product graph.
FORM(b, product_state) -> bond present in product graph.
RULE R10: a graph edit is a representation of changed connectivity, not a complete reaction mechanism.
RULE R11: reaction bookkeeping must preserve total charge and each elemental atom count for a closed, balanced reaction description.

19. CONSERVATION
For balanced reactions: sum reactant atoms of element X = sum product atoms of element X.
For a closed system: total electric charge before = total electric charge after.
Energy conservation applies to system plus surroundings, not necessarily isolated bond energies alone.

20. STEREOCHEMISTRY
Bond topology alone is insufficient for stereochemical identity.
Capture bond angle, torsion, chirality and coordination geometry as separate typed properties.

21. CRYSTAL AND NETWORK STRUCTURES
Examples: diamond covalent network; NaCl ionic crystal; Cu metallic crystal.
NOTE: extended structures require periodic or lattice-aware graph semantics.

22. NONCOVALENT INTERACTIONS
Hydrogen bonds, van der Waals interactions and ion-dipole interactions influence structure and assembly.
RULE R12: annotate noncovalent interaction separately from covalent connectivity unless the ontology explicitly models a broader bond concept.

23. INFERENCE
IF covalent_model(b) AND shared_density(b) THEN classify_candidate(b,CovalentBond).
IF periodic_lattice(s) AND ionic_constituents(s) THEN classify_candidate(s,IonicSolid).
IF conjugated_system(s) THEN allow_delocalised_bond_order(s).
IF bond_length_observed(b,L) THEN attach provenance and uncertainty to L.
IMPORTANT: candidate classifications are not automatic experimental confirmations.

24. EXAMPLE: WATER
ENTITIES: O, H1, H2, H2O.
RELATIONS: CONNECTS(O-H1); CONNECTS(O-H2).
CLASSIFICATION: polar covalent O-H bonds.
GEOMETRY: bent molecular geometry.
INFERENCE: net molecular dipole is nonzero under standard conditions.

25. EXAMPLE: ETHENE
ENTITIES: C2H4, C1, C2.
RELATION: C1=C2 double bond in Lewis representation.
MODEL: one sigma and one pi bonding component.

26. EXAMPLE: SODIUM CHLORIDE
ENTITIES: Na+, Cl-, NaCl crystalline phase.
RELATION: extended electrostatic coordination in lattice.
VALIDATION: do not assert discrete molecular NaCl units for ordinary bulk crystal.

27. SEMANTIC EQUIVALENCE
ALIAS chemical bond ~ bonding interaction [context-dependent].
ALIAS dative bond ~ coordinate covalent bond [Lewis-model context].
NOT_EQUIVALENT bond energy != activation energy.
NOT_EQUIVALENT bond polarity != molecular polarity.
NOT_EQUIVALENT formal charge != partial atomic charge.

28. SEMANTIC DIFFERENCE
Differentiate chemical bonding, intermolecular association, lattice cohesion and transient collision.
Preserve model-dependent distinctions and avoid treating conventional bond lines as uniquely observable objects.

29. CONFIDENCE
CONFIDENCE_SCALE: 0.0..1.0.
CONFIDENCE(record) must reflect evidence quality, model applicability, measurement uncertainty and provenance.
NO fabricated numeric confidence values.

30. PROVENANCE
Each scientific assertion should include source identifier, measurement or calculation method, conditions, units, uncertainty, and verification date where available.
Unverified source-page wording must not be represented as extracted quotation.

31. VALIDATION
CHECK: all referenced entity IDs exist.
CHECK: each relation matches declared type signatures.
CHECK: physical dimensions are consistent.
CHECK: charge and elemental balances hold where applicable.
CHECK: experimental claims have provenance.
CHECK: theoretical model statements are marked as models.
CHECK: no false inference that all bonds are strictly pairwise or localised.

32. FLOW HASH
FLOW_HASH_ALGORITHM: SHA-256 over canonical UTF-8 normalised flow text, excluding mutable hash field.
FLOW_HASH_VALUE: NOT_COMPUTED.

33. UPDATE MODEL
UPDATE_MODEL: versioned revisions with change log, provenance retention and compatibility review.
ON_UPDATE: revalidate typed relations, units, examples and scientific status.

34. AI CONSUMPTION
AI_CONSUMPTION: typed semantic retrieval; entity linking; chemistry reasoning; knowledge-graph integration; provenance-aware inference.
GUARDRAIL: distinguish established chemistry from simplifying models and uncertain claims.

35. COMPLETENESS CHECK
SECTIONS_EXPECTED: 35
LAST_SECTION: COMPLETENESS CHECK
END_MARKER: END FLOW ALGEBRA — CHEMICAL BOND ONTOLOGY