One puzzle concerning organic charge transfer salts (such as those based on the BEDT-TTF molecule) is how the Mott metal-insulator transition can be tuned with substituting hydrogen with deuterium. I find it particularly puzzling because the relevant hydrogen bonds are weak and so one does not expect significant isotope effects.
Similar concerns are relevant to cases of isotopic polymorphism [where the actual crystal structure changes] in molecular crystals such as pyridine.
I recently came across a nice example that I do understand.
Hydrogen-Bond-Dynamics-Based Switching of Conductivity and Magnetism: A Phase Transition Caused by Deuterium and Electron Transfer in a Hydrogen-Bonded Purely Organic Conductor Crystal
Akira Ueda, Shota Yamada, Takayuki Isono, Hiromichi Kamo, Akiko Nakao, Reiji Kumai, Hironori Nakao, Youichi Murakami, Kaoru Yamamoto, Yutaka Nishio, and Hatsumi Mori
The key to understanding how H/D substitution changes the electronic state is that there is a hydrogen bond between two of the organic molecules with an oxygen-oxygen distance of 2.45 A. As highlighted (and explained) in this paper, around this distance the geometric isotope effect is largest (the H bond length increases to almost 2.5 A), leading to a significant change in the energy barrier for proton transfer.
The figure below nicely shows, using DFT-based calculations and the measured crystal structures for both isotopes at two different temperatures, how the barrier changes, leading to a change in the charge state of the molecules.
The H and D isotopes are at the top and the bottom, respectively.