ChemDoodle v1.4.0 is still under development, but I would like to introduce some of the new features that are being implemented. The first of many is the introduction of functions to specify and force the stereochemistry of various centers. In the next few weeks we will be posting some more stories about some of the other new features before the tentative release of ChemDoodle v1.4.0 in late (very late) November.
UPDATE: ChemDoodle v1.4.0 was released on 12/19/08.
The stereochemistry of chiral centers and double bonds can now be determined by selecting the Stereochemistry functions located in the new Structure menu. Shortcuts to these functions are also found in the right-click menu. The designated configurations will add an Identifier object to the Doodle Sheet (Identifiers are new objects introduced in ChemDoodle v1.4.0 that are both logically and spatially associated with another object). Several naming conventions can be used. The first is for chiral centers utilizing Cahn-Ingold-Prelog (CIP) priority rules for designating rectus (R) and sinister (S) enantiomers. The following image shows the output for a handful of sample molecules.
The second two are for specifying the orientations around double bonds. You may use CIP priority rules for designating entgegen (E) or zusammen (Z) configurations or you may also want to use the less robust cis/trans conventions for designating olefin enantiomers. The E/Z system will work for any double bond presented, while the cis/trans conventions will be ambiguous for some (ChemDoodle does not designate -cis or -trans in these cases). The following two images show the differences between these two functions.
In addition to determining the configurations of these isomers, you may also use newly implemented functions to force them into one or the other. For chiral centers, this involves interchanging the protruding and recessed bonds. You may also select an ambiguous chiral center (with all single bonds) and force one of the two configurations on it. For double bonds, this involves flipping both substituents on one atom’s side of the double bond through the double bond axis. These functions are accessible in the right-click menu.
ChemDoodle v1.4.0 will have new functions for determining and setting stereochemical configurations. We will be adding more naming conventions, such as the D/L system, as time goes on.