This example demonstrates how the chemnum package can be used to automatically number compounds in reaction schemes created with ChemDraw (saved as .eps files). While the chemstyle/chemscheme package can also be used, its author recommends the use of chemnum as it's deemed to be clearer.
Ideally, the ChemDraw-generated .eps files should contain "TMP1", "TMP2" etc as temporary markers, which will then be replaced with automatically incrementing compound counters using the \replacecmpd command. Switch the LaTeX engine to LaTeX+dvipdf from the project's Settings icon (the gear icon) so that the replacement actually takes place.
The Beilstein Journal of Nanotechnology is an international, peer-reviewed, Open Access journal published and financed by the Beilstein-Institut. The journal publishes original articles on all aspects of Nanoscience and Nanotechnology. It provides a broad coverage of both fundamental and applied research, including aspects of chemistry, physics and biology as well as materials science and engineering.
Beilstein-Institut for the Advancement of Chemical Sciences