Fig. 1: Single molecule tagging setup.

a, Ions are produced at room temperature and mass filtered before trapping. The competing mass 91 Da isomer benzylium (Bz⁺) is formed, along with Tr⁺, but only Tr⁺ is trapped due to the photodissociation of Bz⁺ by 422 nm laser light²⁹. Neon is pulsed into the trapping region during loading to dissipate the kinetic energy of incoming ions via collisions. After loading, a mechanical shutter is closed to separate the cold experimental region from the room temperature ionization region. b, Trap details are discussed in the Methods.⁸⁸Sr⁺ and Tr⁺ are co-trapped in a linear quadrupole trap with two endcap (EC) electrodes confining the ions along the trap axis. A 10:1 mixture of He:N₂ cooled to 13 K is pulsed into the trapping region, tagging the molecular ion with N₂. An a.c. voltage applied between the endcaps drives secular oscillation, which modulates the ⁸⁸Sr⁺ fluorescence. Lenses below the trap collect fluorescence light and image it onto a CCD camera and PMT. c, Two CCD images show ⁸⁸Sr⁺ and Tr⁺ flipping between two possible positions along the trap axis. Tr⁺ is dark to direct observation and is represented by a ball-and-stick model.