Been playing this awesome game for a couple days... This was really fun and I improved my score from 32 to 27 to 26.
There are only very limited ways to rotate this huge molecule, so a couple of the tiles ware forced to be covered. Thus, you need to overlap the output molecules with as many of those tiles as possible. I think it's really hard to anything without two arms and two debonders but I'm ready to be proven wrong. Arm 2 somehow does not collide with the molecule but the tile would've counted for area anyways, so I get an arm for free. In the last couple days I also managed to improve my cycle count by 1454 (don't ask me how I had this many cycles in the first place). Uneducated guess for min area is... 25?