## 2 Overview of the Experimental Setting  
A schematic representation of our experimental setup is shown in Figure 1. The ion source consists of a pulsed piezo valve, which injects a gas pulse into the vacuum system. In the current setup, a modified version of the design introduced by [29] is used. By actively controlling the discharge voltage and the gas flow into the vacuum chamber, a variety of ionic species can be created depending on the gas mixture used. Our benchmark system is the hydroxyl anion, which serves as our system of interest for the rest of this work. For the creation of hydroxyl anions, argon gas mixed with water vapor is used in the reservoir before the nozzle of the gas inlet. As the ions exit the source, they are guided via ion optics towards a Wiley-McLaren-based time-of-flight mass spectrometer, which is operated in a pulsed mode. Here, the ions are accelerated orthogonally with respect to their initial trajectory and are then separated in the time domain based on their mass-to-charge ratio. The ions are then focused through a pinhole into the next chamber where they are loaded into an octupole wire trap. The trap assembly is explained in detail in Section 3. A 3-dimensional (3D) model of the wire trap is illustrated in Figure 2a, and a qualitative representation of the potential during loading, trapping, and extraction of the ions is shown in Figure 2b. The mass selection of the ions is done by switching the entrance endcap of the trap between a high and low potential in order to load the desired species. As the ions approach the trap, the entrance endcap electrode is set to a lower potential. Once the ions enter the trap, the entrance endcap electrode is switched to a higher potential, thus confining the ions in the trap axially. In order to increase the trapping efficiency of the ions, a pulse of helium buffer gas is injected into the trap. This not only greatly enhances the number of ions trapped, but also ensures that the hot ions produced from the plasma discharge source are properly thermalized and lie in their vibrational ground state. This serves as the starting condition for the ion ensemble which can then be overlapped with a cloud of laser-cooled rubidium atoms. The implementation and characterization of the atom trapping setup is detailed in [30]. Additionally, a far-threshold laser beam can be shone onto the ions in order to characterize their spatial density distribution via photodetachment tomography [27]. Depending on the nature of the experiment, the ions can be confined in the trap for varying amounts of time. The interaction with laser-cooled atoms and/or a laser beam results in the change of the ions' energy distribution which is recorded by extracting the ions from the trap and measuring the spread in the TOF distribution. The ions are extracted by lowering the potential on the exit endcap electrode and exit shielding plate close to the detector. Furthermore, the entrance shielding plate is switched to a higher potential to facilitate an additional acceleration of the ions towards the ion detector. In our case, a microchannel plate (MCP) is used to detect the arrival time of the individual ions. It is imperative to note that the ion detector counts single ion events, and does not integrate the signal. This is critical for comparing the measured ion distributions to those obtained from the simulations. (An integrator would introduce an additional broadening of the detected distribution). The width  
Figure 1: Schematic representation of the Hybrid Atom–Ion Trap (HAI-trap). The ions are produced via a plasma discharge in a pulsed molecular beam and are then guided towards a Wiley–McLaren time-of-flight spectrometer, where the ions are separated according to their mass-to-charge ratio. The ion beam is then guided into the trap, and the entrance endcap is switched to mass-select the desired species.