User 25d107bd42
23-10-2014 13:33:57
Hi Marvin developers, there is a serious problem in MarvinSpace: Allene ist not planar.
We would like to use the combination MarvinSketch - MarvinSpace in basic education about the 3D structure of organic molecules. Starting MarvinSketch and then using the option "Open MarvinSpace" produces the marvelous combination: You see immediatly the structure drawn in MSketch in 3D in MSpace. There is even a short key for this option "Ctrl - Shift -M". For the following examples the MSpace option "Display - Draw Type - Ligand - Hydrogens" must be on.
Drawing a line - single bond now produces immediatly ethane with all hydrogens in staggered conformation. Super. Drawing a double line produces planar ethylene and a triple bond linear acetylene. All OK.
But now drawing two attached double bonds produces a planar allene structure which is wrong,
The orthogonal double bonds in allene are not conjugated. And adding now one bond produces methylallene having the correct orthogonal allene structure.
Using in MSketch the option "Calculation - Conformers" produces a correct allene with orthogonal double bonds. OK. But we want to use the fast immediately combination MSketch - MSpace. And for newcomers there is the question : "What's correct?" This means we cannot use MSpace educating basic structures.
Fluoroallene and other haloallenes have the wrong structure, too, but hyroxyallene or aminoallene have in MSpace the orthogonal double bonds. (Here the hydroxygroup is problematic but these will leaad to a new post).
This failure should be corrected as fast as possible. The correct algorithm is obviously present in the Marvin programs.
Best regards, Hans-Ulrich