User 25d107bd42
23-06-2011 18:05:02
Hi,
using MarvinSketch Clean 3D with Hydrogenize leads to an unacceptable structure for phenol. As can be seen in the attached image, the hydrogen of the hydroxy group is orthogonal to the phenyl ring. So, the hydroxy-group cannot be in pi-conjugation with the pi-system of the phenyl ring. A DFT RB3LYP/6-31G(d,p) calculation leads to a totally planar molecule. And experimetal results show, the hydroxy group influences the phenyl-ring as a pi-conjugated donor.
As I remember, there was the same situation for amino-groups attached to a phenyl ring. MarvinSketch version 5.2 calculated amino groups in wrong orthogonal geometries, too. (There is a documentation in the Mifegyne calculation https://www.chemaxon.com/forum/ftopic4210.html ). But this failure has been fixed.
There is the possibility to use the "workaround" shown in the attached image.
Clean 3D with Hydrogenize is a super highlight of the Marvin software. So this hydroxy group failure should be fixed, too.
BTW: MarvinSpace now shows the aromatic rings !!!
Best regards, Hans-Ulrich