OPOpenPithMake curiosity visibleChemistry lab / Reaction mechanisms

About this lab

An equation shows the start and the end; a mechanism shows what happens in between.

Each reaction is one table of atoms plus a few key structures. Atom numbers never change, so any atom can be followed to the end. Motion between key structures is interpolated; when a bond order changes, a dashed transition bond appears first. Curly arrows show where electrons go, not where atoms move: gold is an electron pair, a cyan fish-hook is one electron, purple is an electron transfer.

A check script verifies atoms, charge, bond lengths and valence in every frame, and the start and end structures must match the balanced equation.

Numbers you can check

Numbers you can check

  • Esterification: with ¹⁸O on ethanol the ester has M = 90 g/mol and water stays 18 g/mol; with ¹⁸O on the acid –OH the ester is 88 g/mol and water 20 g/mol.
  • Burning methane: break 4 C–H and 2 O=O, form 2 C=O and 4 O–H; average bond enthalpies give ΔH = -808 kJ/mol.
  • Hydrogen in chlorine: 436 + 242 - 2 × 431, ΔH = -184 kJ/mol.
  • Silver halide lattices: Ag⁺ to Cl⁻ is 2.775 Å in AgCl and 2.885 Å in AgBr.
  • SN2: in tert-butyl bromide three methyl groups block the back; the OH⁻ oxygen gets no closer than 3.41 Å to the central carbon, far more than the 1.43 Å C–O bond.

Model and sources

Model and sources

  • Geometry: bond lengths are typical experimental values (C–H 1.09, C–C 1.54, C=C 1.34, C–O 1.43, C=O 1.21, O–H 0.96 Å …); atoms are placed from existing bond directions with 109.5° (sp³) and 120° (sp²) angles, not typed in.
  • Bond enthalpies: an average table (C–H 413, O=O 495, C=O in CO₂ 799, O–H 463, H–Cl 431 kJ/mol …), used only when every species is neutral; solvation and ionic reactions are not estimated.
  • Teaching assumptions: burning and H₂–Cl₂ are shown as “break everything, then bond”, while real flames are radical chains; the organic esterification uses a four-centre sketch, the real path is the five-step mechanism; Br⁺ and CuO are simplified; animation time and distance are not real rates.
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