Isotopic, hydrogen-to-deuterium substitution has been an invaluable tool in the characterization of small molecules and biological nanostructures. The natural variability of most inorganic nanomaterials has hindered the use of isotopic substitution to gaining meaningful insights of their structure. The ideal helical wrapping of flavin mononucleotide (FMN) around (8,6)-SWNTs (single-walled carbon nanotubes) is presently utilized to probe isotopic-dependent intermolecular interactions. The facile proton-to-deuterium exchange of the imide group of FMN, enabled us to alter the intermolecular stability of the helix depending on the surrounding solvent (i.e. H2O vs. D2O). Our studies show that FMN-dispersed (8,6)-SWNTs exhibit greater stability in D2O as opposed to H2O. The higher complex stability in D2O was verified based on: (i) FMN helix replacement with SDBS (sodium dodecylbenzenesulfate); as well as (ii) thermal-, and (iii) pH-induced helix dissociation. This is in agreement with the previously observed stronger amide H-bonding of proteins in D2O, and to the best of our knowledge, it demonstrates the architectural fidelity of FMN-wrapped SWNTs, which is expected to further enhance the assembly repertoire of carbon nanotubes.