Paradigmatic molecular instances — H₂O, CO₂, NH₃, CH₄, benzene, glucose, CO, HCl, NaCl, methanol — each composed of the elemental atoms of Layer 2 via `composed_of` edges. Forms the compositional vocabulary for downstream biochemistry.
molecules
Water (H₂O)
Triatomic bent molecule (∠HOH ≈ 104.5°) with strong hydrogen bonding that drives its anomalous boiling point, density maximum at 4 °C, and…
Carbon dioxide (CO₂)
Linear non-polar triatomic with IR-active antisymmetric stretch — the principal greenhouse molecule in Earth's atmosphere and the end…
Ammonia (NH₃)
Pyramidal molecule with a lone pair on N; weak Brønsted base (pKa(NH₄⁺) ≈ 9.25). Industrial feedstock produced at ~200 Mt/yr via the…
Methane (CH₄)
Tetrahedral sp³-hybridised simplest alkane. Principal component of natural gas; potent greenhouse molecule (~28× CO₂ on a 100-yr GWP basis).
Benzene (C₆H₆)
Planar six-membered aromatic hydrocarbon with six delocalised π electrons (Hückel 4n+2 with n=1). Parent molecule of aromatic chemistry.
Glucose (C₆H₁₂O₆)
Six-carbon aldohexose sugar; pyranose ring form in aqueous solution. Primary metabolic fuel in most organisms; substrate of glycolysis.
Carbon monoxide (CO)
Diatomic with a formal triple bond (including a dative π-donation), highly toxic competitive ligand at haemoglobin Fe(II). Central…
Hydrogen chloride (HCl)
Polar diatomic; fully dissociated strong acid in water (pKa ≈ -7). Gaseous HCl and hydrochloric acid are stoichiometric workhorses of both…
Sodium chloride (NaCl)
Archetypal ionic compound; rock-salt cubic crystal structure with Na⁺ and Cl⁻ at alternating lattice sites. Osmotic backbone of seawater…
Methanol (CH₃OH)
Simplest alcohol; toxic to humans (ADH metabolism produces formaldehyde/formate). Feedstock for formaldehyde, acetic acid, and increasingly…
Ethanol (C₂H₅OH)
Two-carbon primary alcohol, molecular formula C₂H₅OH, molar mass 46.07 g/mol. Colourless, flammable liquid, miscible with water. Produced…
Sulfuric acid (H₂SO₄)
Diprotic strong mineral acid, molecular formula H₂SO₄, molar mass 98.08 g/mol. First dissociation is complete in water (pKₐ₁ ≈ −3); second…
Nitric acid (HNO₃)
Monoprotic strong mineral acid, molecular formula HNO₃, molar mass 63.01 g/mol. Complete dissociation in water (pKₐ ≈ −1.4). Strong…
Ozone (O₃)
Triatomic allotrope of oxygen, molecular formula O₃, molar mass 48.00 g/mol. Bent molecule (117°), with two resonance structures. Pale-blue…
Sodium hydroxide (NaOH)
Ionic strong base, formula NaOH, molar mass 40.00 g/mol. White solid; deliquescent. Complete dissociation in water (pOH → 0 at 1 M). Major…
Fullerenes and C₆₀
Truncated icosahedral C₆₀ (buckminsterfullerene); Kroto, Curl, Smalley 1985 Nobel; derivatives for photovoltaics, MRI contrast.
Carbon nanotubes (SWCNT/MWCNT)
Rolled graphene sheets; chirality (n,m) determines metallic/semi; ballistic conductance; aerospace composites.
Porphyrins & chlorins
Planar 18-π aromatic; heme (Fe-porphyrin), chlorophyll (Mg-chlorin), vitamin B12 (Co-corrin); photosynthesis, O₂ transport.
Phthalocyanines
Blue/green pigments; Co, Fe, Zn, Cu centers; electrocatalysts for CO₂ reduction; molecular semiconductors.
Calix[n]arenes & resorcinarenes
Cup-shaped macrocycles from phenols + CH₂O; host-guest chemistry; cation sensing via crown-like upper rim.
Cucurbit[n]urils
Glycoluril-based cucurbit[n]uril macrocycles; exceptional host-guest affinity (up to 10¹⁵ M⁻¹ for ferrocenes); drug delivery.
Rotaxanes & catenanes
Mechanically interlocked molecules; molecular shuttles, motors; Sauvage/Stoddart/Feringa 2016 Nobel.
Dendrimers & hyperbranched polymers
Globular polymers with generations; monodisperse; PAMAM, polyglycerol; nanoscale carriers, imaging agents.
Borane clusters (closo/nido/arachno)
Wade's rules classify polyhedral skeletons by skeletal electron pair count; dodecaborate ²⁻; drug candidates.
Artificial molecular machines
Rotary motors (Feringa overcrowded alkene), linear shuttles (Stoddart rotaxanes); unidirectional motion from photons/pH.
Ferrocene & metallocenes
Cp₂Fe sandwich compound (1951); aromatic Cp rings; Hafner-Kealy-Pauson-Wilkinson-Fischer; redox-active; 1973 Nobel.
Ionic liquids (RTILs)
Organic salts with mp<100°C (often RT); ImH⁺/PyH⁺ cations + [BF₄], [NTf₂]; green solvents, electrolytes, catalysis.
LCAO-MO theory: H_2 bonding / antibonding orbitals from [[alpha,beta],[beta,alpha]] (molecules)
Chemistry application of L1 schrodinger-equation and quantum-superposition. The LCAO-MO (linear combination of atomic orbitals - molecular…
Hueckel pi-MO eigenvalues of benzene: epsilon_k = alpha + 2 beta cos(2 pi k / 6) (molecules)
Chemistry application of L1 quantum-hilbert-space and angular-momentum-quantum. Hueckel's 1931 pi-electron theory replaces the full…