Release 2.2.1
EZ nomenclature support has been implemented. Now in addition to the RS stereochemistry designations for atoms with chirality, attachment ordering around double bonds will be designated according to EZ nomenclature conventions. Similar to RS stereochemistry, the EZ nomenclature may be turned on and off, depending on the user's preferences. In off mode, any stereochemistry resulting from double bonds will not be named and enantiomers will not be considered separate molecules. Reactions will not target molecules with specific EZ stereochemistry. In on mode, double bonds that generate EZ stereochemistry WILL result in separate molecules, and these separate molecules will be targeted when considering reactions.
For this iteration, chiral stereochemistry generated by an addition reaction to an alkene will ONLY result in one enantiomer to be considered in the pathway generator. This generally results in S stereocenters, but that is not guaranteed, as a counter-example can likely be found. Nevertheless, for demonstration this can be seen by the generator successfully finding a pathway between (2E)-but-2-ene and (2S,3S)-2,3-dichlorobutane yet unsuccessfully finding a pathway between (2E)-but-2-ene and (2S,3R)-2,3-dichlorobutane. Furthermore, for this iteration, when a double bond is generated as a result of a reaction in the pathway generator and the double bond has alkyl segments protruding from both sides, ONLY the trans formation result will be considered. That is, (2S)-butan-2-ol to (2E)-but-2-ene will be successful, but (2S)-butan-2-ol to (2Z)-but-2-ene will not.
On a related note, the toggle stereochemistry button (previously toggle chirality) in the workspace will now be applied globally. When it is set to "hide stereochemistry" ALL molecules in the workspace will ignore stereochemistry (both RS and EZ) and vice versa. When the stereochemistry mode is off, the reaction butan-2-ol to but-2-ene will have a pathway found.
Finally this particular reaction previously caused an error when run in hide stereochemistry mode. This has been fixed.
Standards - IUPAC nomenclature will be followed. Cahn Ingold Prelog priority rules are followed for assigning E/Z designation of arrangements around double bonds. No further drawing changes were applied. As a note, trans isomerism (generally E, but not always) will not be considered for cyclical skeletons of length less than 10 for torsional strain reasons. As such, we will not consider any EZ stereochemistry for double bonds in a cyclical alkene of length less than 10.
Controls - Stereochemistry support mode may be toggled on and off by clicking on the hide/show stereochemistry button. This will control all aspects of stereochemistry support: nomenclature, molecule display, and reaction pathways. Stereochemistry for a specific stereocenter may be toggled by clicking on the stereocenter. In the case of a chiral stereocenter, toggling will alter the arrangements of the first 2 child attachments. This will result in a toggle of R -> S stereochemistry and vice versa. In the case of clicking on one of the Carbon atoms of a double bond, the arrangements of the attachments NOT involved in the double bond will be altered. This will result in a toggle of the E/Z nomenclature associated with that double bond.
Future considerations - I am interested in coming up with an alternative way to toggle stereochemistry, similar to having different methods to toggle bond size. Also, ALL products of stereochemistry generating reactions will be considered in the pathway generator. That is, the addition of Cl2 to but-2-ene will result in (2S,3S)-2,3-dichlorobutane, (2R,3R)-2,3-dichlorobutane, and (2S,3R)-2,3-dichlorobutane. (Not (2R,3S)-2,3-dichlorobutane as that is a meso isomer of (2S,3R)-2,3-dichlorobutane).
