Stereochemistry

Stereochemistry

Since the October 2026 development version (to become 3.0) KinBot keeps stereoisomers apart. Every species has, besides its connectivity-based chemid, a stereochemical identity covering tetrahedral centres, double bonds (E/Z) and the axial chirality of substituted cumulenes (allenes and longer even cumulenes; odd cumulenes get terminal E/Z). The identity is read from the 3D geometry: no R/S labels are needed in the input. It is used for species and calculation names, for checking that an IRC leads back to the requested reactant, for telling reaction sites apart (homotopic, enantiotopic and diastereotopic sites give separate searches) and for the symmetry factors written to MESS.

Names

A species with fixed stereochemistry is named <chemid>-s<16 hex characters>; this suffix appears in the job names, in kinbot.db, in the PES directories and in the MESS output. Species without stereo elements keep the plain <chemid>. Diastereomers always get different names; enantiomers get different names too, which one depends on which enantiomer is in the input (see below). The full identity is stored in kinbot.db (rows named stereochemistry/<job>) and is checked before any saved result is reused.

Specifying the stereoisomer

• Coordinates (structure) define the stereoisomer exactly.
• SMILES with stereo marks (@, @@, /, \) are respected. For cumulene handedness no SMILES notation exists; use coordinates.
• SMILES without stereo marks: KinBot generates the 3D structure with RDKit using a fixed random seed, so the same SMILES gives the same stereoisomer and the same name every time (for a given RDKit version). The log reports which assignment was made. This selects one stereoisomer, it does not enumerate them; to study another one, give a stereo-SMILES or coordinates.

parameter	default	description
optical_population	"specified"	"specified": only the stereoisomer of the input is considered; its mirror image is excluded. "racemic": the input stereoisomer and its whole-molecule mirror image are both included (an RR input includes RR and SS, but not RS/SR). This restores the behaviour of earlier versions, which treated every chiral well as a racemate.
stereo_reference	None	Written by pes into the generated per-well inputs to preserve the requested configuration; not meant to be set by hand.
optical_factor_assumptions	{}	Expert option. Force the optical symmetry factor of a named state: {"<species or TS name>": {"multiplier": 1 or 2, "reason": "one line"}}, the name being <chemid>-s… for a well or the reaction name for a TS. Use when KinBot's geometric check cannot decide whether a mirror structure is covered.

Effect on the symmetry factors

MESS receives SymmetryFactor = sigma_ext / n_opt, with n_opt the number of optical isomers counted for the structure. Earlier versions gave every chiral well n_opt = 2. Now:

• a chiral well in specified mode has n_opt = 1 (factor 1.0 for sigma_ext = 1), in racemic mode n_opt = 2 (0.5);
• conformational mirrors of achiral molecules (e.g. a gauche ethanol) count as optical isomers when the mirror conformer is not already present in the model, so a single harmonic structure can get a factor 0.5 where older versions wrote 1.0; a hindered-rotor scan that covers both mirrors, or an MC-TST set that contains both, gets no extra factor.

Because the TS and the products are treated the same way, a rate coefficient does not simply change by a factor 2; check the SymmetryFactor comments in the MESS input when comparing with older results.

Reaction search

Different stereochemical pathways (e.g. attack from the two faces of a double bond, migration to diastereotopic hydrogens) are kept as separate reactions and separate TSs; MESS adds them with a Union. A product that changes its stereochemistry or connectivity during its first optimization is named after the optimized structure (see Output). Species belonging to disconnected networks, e.g. an R- and an S-reactant linked only through a common achiral product, get separate MESS inputs.

Limits

• Helical chirality is not identified. Atropisomers of biaryls are not separated: the ring–ring bond is an ordinary rotor, both twists belong to the same species.
• Unsupported coordination (e.g. square planar, trigonal bipyramidal) stops the run before any QC for the initial reactant, and omits the reaction with a warning for a discovered species.
• Calculations from earlier versions cannot be resumed with the new identities; start them in a fresh directory.