gentle persons,

there several programs which offer, presumably in some aspect restricted, for drawing chemicla formula which run natetively on MacOSX. Beside some JAVA based software, you might want to take a look on xdrawchem. A binary installer, which does not need X11, is available here on versiontracker -> http://www.versiontracker.com/dyn/moreinfo/macosx/20542
To run it you have to install the native version of Trolltech's Qt 3 framework; a minimal installer is available here http://naranja.umh.es/~atg/QtMac334_Mini.zip. After installation of the framework you have XDrawChem running natetively under MacOSX without need of an X11-Server.