The MoleculeSampleApp tries to use key combinations that do other things in OS X or otherwise don't seem to work even though there seems to be paths for those key combinations in the code.

For instance:
  Ctrl+RIGHT or Ctrl+LEFT displays the next full screen app to the right or left.
  Ctrl+UP or Ctrl+DOWN will show all windows at once or just a single window.
  Ctrl+Shift+UP and Ctrl+Shift+DOWN slowly animate showing all windows or restoring the desktop.
  Shift+UP|DOWN|LEFT|RIGHT does nothing.

Additionally:
  Shift+Z kind of zooms everything in on the molecule but there is no way to restore the original view.
  UP, DOWN, LEFT, RIGHT keys do nothing.

Adding some comments in the code might help explain what it is supposed to be doing.