Reaction mechanisms

A mechanism captures a multi-step reaction pathway with optional spectator ions.

Syntax

mechanism{
  label: reaction
  label: reaction
  spectator: ion1 ion2 ...
}

Each line is a key: value pair. Keys other than spectator are step labels (e.g. step1, step2).

Example: SN2 mechanism

Source Rendered

mechanism{ step1: OH- + CH3Br -> CH3OH + Br- spectator: Na+ }

$\mathrm{mechanism}\begin{array}{cc}\mathrm{step1}& \text{OH- + CH3Br -> CH3OH + Br-}\\ \mathrm{spectator}& \text{Na+}\end{array}$

Example: multi-step

Source Rendered

mechanism{ step1: A + B -> C step2: C -> D + E spectator: Na+ K+ }

$\mathrm{mechanism}\begin{array}{cc}\mathrm{step1}& \text{A + B -> C}\\ \mathrm{step2}& \text{C -> D + E}\\ \mathrm{spectator}& \text{Na+}\\ \mathrm{spectator}& \text{K+}\end{array}$

Validation (v0.18+)

Each entry must have a : separator. Malformed entries raise ParseError at parse time with the offending line number.

CML wire (v0.11+)

Emits as <reaction> with <mechanism> child:

<reaction>
  <mechanism title="mechanism{...}" convention="asciichem:text"/>
</reaction>

Future enhancement: structural <reactionStepList> with per-step reaction elements.