Recently we reported a high-precision optical frequency measurement of the (v, L): (0, 2)rightarrow(8, 3) vibrational overtone transition in trapped deuterated molecular hydrogen (HD+) ions at 10 mK temperature. Achieving a resolution of 0.85 parts-per-billion (p.p.b.), we found the experimental value [ν0 = 383, 407, 177.38 (41) MHz] to be in agreement with the value from molecular theory [νth 383, 407, 177.150 (15) MHz] within 0.6 (1.1) p.p.b. (Biesheuvel et al. in Nat Commun 7:10385, 2016). This enabled an improved test of molecular theory (including QED), new constraints on the size of possible effects due to ‘new physics,’ and the first determination of the proton–electron mass ratio from a molecule. Here, we provide the details of the experimental procedure, spectral analysis, and the assessment of systematic frequency shifts. Our analysis focuses in particular on deviations of the HD+ velocity distribution from thermal (Gaussian) distributions under the influence of collisions with fast ions produced during (laser-induced) chemical reactions, as such deviations turn out to significantly shift the hyperfine-less vibrational frequency as inferred from the saturated and Doppler-broadened spectrum, which contains partly unresolved hyperfine structure.
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