Title: Oxygen Vacancies in Niobium Pentoxide as a Source of Two-Level System Losses in Superconducting Niobium

Abstract: We identify a major source of quantum decoherence in three-dimensional superconducting radio-frequency (SRF) resonators and two-dimensional transmon qubits composed of oxidized niobium: oxygen vacancies in the niobium pentoxide which drive two-level system (TLS) losses. By probing the effect of sequential \textit{in situ} vacuum baking treatments on the RF performance of bulk Nb SRF resonators and on the oxide structure of a representative Nb sample using time-of-flight secondary ion mass spectrometry (ToF-SIMS), we find a non-monotonic evolution of cavity quality factor $Q_0$ which correlates with the interplay of Nb\textsubscript{2}O\textsubscript{5} vacancy generation and oxide thickness reduction. We localize this effect to the oxide itself and present the insignificant role of diffused interstitial oxygen in the underlying Nb by regrowing a new oxide \textit{via} wet oxidation which reveals a mitigation of aggravated TLS losses. We hypothesize that such vacancies in the pentoxide serve as magnetic impurities and are a source of TLS-driven RF loss.