The JME editor can be used to design molecular structures, so you
can ask questions such as "Please draw the structure of
2,3-dichloro-but-2-ene". In order to mark responses, they need to
be converted to a simple text format called SMILES (see
http://www.daylight.com/smiles/ for more information).

So, the student must design the molecule, using the JSME Javascript Applet.
The content of the student response is automatically saved when the
student change page in the quiz either by pressing on the "Next"
button, or using the quiz navigation panel. When quiz attempt is
submitted, this response is then marked in the same way as a
(case-sensitive) short-answer question.

You can use a similar process when designing the question. Using
the JME applet, design a molecule that is a possible (right or
wrong) answer and then press a button next to the answer boxes
to store the current design as a SMILES code.

JSME is a free and Open source molecule editor written in JavaScript.

See B. Bienfait and P. Ertl, JSME: a free molecule editor in JavaScript, J. Cheminformatics 5:24 (2013)