Ion-molecule Reactions Research Articles

Exploring the Role of Ion–Molecule Reactions on Interstellar Icy Grain Surfaces

Exploring the Role of Ion–Molecule Reactions on Interstellar Icy Grain Surfaces

Empirical Approach to Quantifying Sensitivity in Different Chemical Ionization Techniques for Organonitrates and Nitroaromatics Constrained by Ion-Molecule Reaction and Transmission Efficiency.

Accurate identification and quantification of nitro-containing species are of great significance to understanding their chemical behaviors in the atmosphere. By optimizing the operational conditions of the H3O+ and NO+ ionization modes in a proton-transfer-reaction time-of-flight mass spectrometer (PTR-TOF-MS) and evaluating the performance of an iodide chemical ionization mass spectrometer (I- CIMS), this study leveraged the individual advantages of each ionization mode to effectively detect a diverse array of nitroaromatics and organonitrates (ONs). The H3O+ ionization mode largely fulfilled the criteria for real-time monitoring of gas-phase alkyl-, aryl-, and hydroxy-nitrates, and nitrophenols, albeit its reduced sensitivity toward ONs due to extensive fragmentation. In contrast, the NO+ mode demonstrated enhanced sensitivity for ONs with less fragmentation than the H3O+ mode. The I- CIMS featured distinguished sensitivity toward oxidized compounds containing polar functional groups, particularly increasing with the incorporation of hydroxyl, carboxyl, or nitrate groups. Further, we developed a calibration-based semiquantitative framework to enhance the accuracy of sensitivity estimation, constrained by ion-molecule reaction, transmission efficiency, along with possible decomposition of ion-clusters, with uncertainties ranging from 21% to 41% for H3O+ and 21-43% for NO+. Given considerable discrepancies (up to 1 order of magnitude) between measured and predicted sensitivity in I- CIMS using previously reported log-linear fitting, a declustering voltage (dV50)-based categorization approach was introduced, leading to a 5-fold improvement in measurement accuracy and an overall uncertainty of I- CIMS in quantifying nitro-containing species varying from 27% to 60%.

Evaluation of a reduced-pressure chemical ion reactor utilizing adduct ionization for the detection of gaseous organic and inorganic species

Abstract. Volatile organic compounds (VOCs) and volatile inorganic compounds (VICs) provide critical information across many scientific fields including atmospheric chemistry and soil and biological processes. Chemical ionization (CI) mass spectrometry has become a powerful tool for tracking these chemically complex and temporally variable compounds in a variety of laboratory and field environments. It is particularly powerful with time-of-flight mass spectrometers, which can measure hundreds of compounds in a fraction of a second and have enabled entirely new branches of VOC and/or VIC research in atmospheric and biological chemistry. To accurately describe each step of these chemical, physical, and biological processes, measurements across the entire range of gaseous products is crucial. Recently, chemically comprehensive gas-phase measurements have been performed using many CI mass spectrometers deployed in parallel, each utilizing a different ionization method to cover a broad range of compounds. Here we introduce the recently developed Vocus AIM (adduct ionization mechanism) ion–molecule reactor (IMR), which samples trace vapors in air and ionizes them via chemical ionization at medium pressures. The Vocus AIM supports the use of many different reagent ions of positive and negative polarity and is largely independent of changes in the sample humidity. Within the present study, we present the performance and explore the capabilities of the Vocus AIM using various chemical ionization schemes, including chloride (Cl−), bromide (Br−), iodide (I−), nitrate (NO3-), benzene cations (C6H6+), acetone dimers ((C3H6O)2H+), and ammonium (NH4+) reagent ions, primarily in laboratory and flow tube experiments. We report the technical characteristics and operational principles, and compare its performance in terms of time response, humidity dependence, and sensitivity to that of previous chemical ionization approaches. This work demonstrates the benefits of the Vocus AIM reactor, which provides a versatile platform to characterize VOCs and VICs in real time at trace concentrations.

B-166 Differentiation of Aziridine Functionality from Related Functional Groups in Protonated Analytes by Using Selective Ion-Molecule Reactions

Abstract Background The development of better methods for the rapid and reliable identification of unknown compounds in mixtures is urgently needed in drug development. Aziridines, in particular, are used for drug synthesis but are potentially mutagenic and carcinogenic compounds. However, the detection and identification of these compounds pose challenges for many analytical methods, such as Nuclear Magnetic Resonance (NMR) spectroscopy, Fourier-transform infrared spectroscopy (FT-IR), and X-ray crystallography. These techniques are time-consuming and often require large quantities of highly pure compounds. Methods Therefore, this study demonstrates that selective gas-phase ion-molecule reactions of protonated analytes with neutral tris(dimethylamino)borane (TDMAB), followed by diagnostic collision-activated dissociation (CAD), can be used to differentiate aziridines from structurally related compounds in a modified linear quadrupole ion trap (LQIT) mass spectrometer. The experiments were performed using an atmospheric pressure chemical ionization (APCI) source in positive ion detection mode. TDMAB was purchased from Sigma-Aldrich and used without purification. It was introduced into the ion trap (2 mtorr of helium buffer gas) via an external reagent mixing manifold through a syringe pump at a flow rate of 10 μL h-1 and diluted with helium before entering the ion trap through a variable leak valve. All analytes were prepared at a concentration of 1 mM in methanol. The protonated analytes were transferred into the ion trap, isolated, and allowed to react with TDMAB (MS2 experiments). Results Product ions formed upon reactions of the analyte ions with TDMAB were subjected to a collision-activated dissociation (CAD) experiment (MS3 experiments). CAD on product ions produced diagnostic fragment ions with 25- and 43 m/z-units lower m/z values than the adduct - DMA product ions. Quantum chemical calculations were employed using the Gaussian 16 program calculated at the M06-2X/6-311++G(d,p) level of theory to provide theoretical foundation and to explore the underlying mechanisms of the observed gas-phase reactions. None of the tested structurally related analytes produced a similar fragmentation pattern Conclusions The innovative approach presented in this study offers a promising avenue for enhancing efficiency and accuracy in drug development. The successful differentiation of aziridine is an alternative method in overcoming the limitation of traditional techniques. The findings from the research contributes to the advancement of analytical techniques, addressing critical issues in identifying impurities in drug products. The versatility of the methods extends beyond drug developments, making it applicable in various other fields such as in molecular diagnostics, metabolism and laboratory medicines.

Making OzID go FFASTer: Combining stable-isotope tagging with ozone-induced dissociation to uncover changes in fatty acid unsaturation within neurosecretory cells

Despite lipids providing a major contribution to the mass of the brain, at the molecular level, the brain lipidome remains incompletely described and the functions of many of the species identified to date are unknown. Recently, unusual unsaturated fatty acids –with carbon-carbon double bonds in positions not predicted by canonical lipid metabolism– were identified in the mouse brain. The extent to which these unusual lipids contribute to neurochemical processes presents a significant gap in knowledge that is challenging to close due to technological impediments to the detection and tracing of such novel fatty acids. Here we deploy state-of-the-art mass spectrometric methods coupled with diagnostic ion-molecule reactions in the form of ozone-induced dissociation to enable detection and relative quantification of unsaturated fatty acids in an in vitro brain model based on the PC12 cell line. This approach revealed the presence of abundant populations of non-canonical fatty acids, including FA 16:1n-10,cis (sapienic acid) and FA 18:1n-10,cis (dihomosapienic acid), in extracts from PC-12 cell lines. Neither of these fatty acids have previously been reported in neurons or neurosecretory-like cells, with both demonstrated to increase between 2 and 4-fold in relative abundance upon active stimulation.

David Smith. 26 November 1935—15 February 2023

David Smith was an exceptional chemical physicist who greatly contributed to the field of molecular science by inventing novel techniques and instruments to study gas-phase reactions of electrons and ions. These reactions are important for understanding the atmospheres and interstellar media. One of his inventions was the flowing afterglow Langmuir probe apparatus, which was used to collect data on electron attachment and electron–ion recombination. Another technique he developed was the selected ion flow tube (SIFT), which helped to understand thousands of ion–molecule reactions. This innovative technique has become the foundation of a new analytical method called SIFT-MS, which is currently used in various industries such as semiconductors and pharmaceuticals, as well as in biological and medical research.

Pursuing drug laboratories: Analysis of drug precursors with High Kinetic Energy Ion Mobility Spectrometry

High Kinetic Energy Ion Mobility Spectrometry (HiKE-IMS) is a technique for rapid and reliable detection of trace compounds down to ppbV-levels within one second. Compared to classical IMS operating at ambient pressure and providing the ion mobility at low electric fields, HiKE-IMS can also provide the analyte-specific field dependence of the ion mobility and a fragmentation pattern at high reduced electric field strengths. The additional information about the analyte obtained by varying the reduced electric field strength can contribute to reliable detection. Furthermore, the reduced number of ion-molecule reactions at the low operating pressure of 10 – 40 mbar and the shorter reaction times reduce the impact of competing ion-molecule reactions that can cause false negatives. In this work, we employ HiKE-IMS for the analysis of phenyl-2-propanone (P2P) and other precursor chemicals used for synthesis of methamphetamine and amphetamine. The results show that the precursor chemicals exhibit different behavior in HiKE-IMS. Some precursors form a single significant ion species, while others readily form a fragmentation pattern. Nevertheless, all drug precursors can be distinguished from each other, from the reactant ions and from interfering compounds. In particular, the field-dependent ion mobility as an additional separation dimension aids identification, potentially reducing the number of false positive alarms in field applications. Furthermore, the analysis of a seized illicit P2P sample shows that even low levels of P2P can be detected despite the complex background present in the headspace of real samples.

Laser Printer Printed Ion Sources for Ambient Ionization Mass Spectrometric Analysis of Volatiles and Semivolatiles.

In this study, we demonstrated a facile method to fabricate ion sources using a laser printer for ambient ionization mass spectrometry (MS). Toner spots printed by a printer can readily facilitate ionizing volatile and semivolatile compounds derived from solid or liquid samples for MS analysis. The experimental arrangement involved positioning the toner-printed paper near the inlet of a mass spectrometer, which was subjected to a high electric potential (e.g., -6 kV). Volatile or semivolatile compounds deriving from the sample positioned below the metal inlet of the mass spectrometer were promptly ionized upon activating the mass spectrometer. No direct electrical connection or voltage application was required on the paper substrate. An electric field was established between the toner spot on the paper and the inlet applied with a high voltage to induce the dielectric breakdown of the surrounding air and water molecules. Consequently, ionic species, including electrons and cationic radicals, were generated. Subsequent ion-molecule reactions facilitated the production of protons for ionizing analytes present in the gas phase proximal to the inlet of the mass spectrometer. Deprotonated analytes were detected in the resultant mass spectra when employing the method in negative ion mode. This methodology presents a straightforward approach for analyzing analytes in the gas phase under ambient conditions utilizing an exceptionally uncomplicated experimental setup. In addition, the developed method can be used to detect trace 2,4-dinitrophenol, an explosive, with a limit of detection as low as ∼30 pg.

Noncovalent Interactions Steer the Formation of Polycyclic Aromatic Hydrocarbons.

Aromatic molecules play an important role in the chemistry of astronomical environments such as the cold interstellar medium (ISM) and (exo)planetary atmospheres. The observed abundances of (polycyclic) aromatic hydrocarbons such as benzonitrile and cyanonaphthalenes are, however, highly underestimated by astrochemical models. This demonstrates the need for more experimentally verified reaction pathways. The low-temperature ion-molecule reaction of benzonitrile•+ with acetylene is studied here using a multifaceted approach involving kinetics and spectroscopic probing of the reaction products. A fast radiative association reaction via an in situ experimentally observed prereactive complex shows the importance of noncovalent interactions in steering the pathway during cold ion-molecule reactions. Product structures of subsequent reactions are unambiguously identified using infrared action spectroscopy and reveal the formation of nitrogen-containing, linked bicyclic structures such as phenylpyridine•+ and benzo-N-pentalene+ structures. The results, contradicting earlier assumptions on the product structure, demonstrate the importance of spectroscopic probing of reaction products and emphasize the possible formation of linked bicyclic molecules and benzo-N-pentalene+ structures in astronomical environments.

Experimental Reactivity of (MoO3)NO- (N = 1-21) Cluster Anions with C1-C4 Alkanes: A Simple Model to Predict the Reactivity with Methane.

Metal oxide clusters with atomic oxygen radical anions are important model systems to study the mechanisms of activating and transforming very stable alkane molecules under ambient conditions. It is extremely challenging to characterize the activation and conversion of methane, the most stable alkane molecule, by metal oxide cluster anions due to the low reactivity of the anionic species. In this study, using a ship-lock type reactor that could be run at relatively high pressure conditions to provide a high number of collisions in ion-molecule reactions, the rate constants of the reactions between (MoO3)NO- (N = 1-21) cluster anions and the light alkanes (C1-C4) were measured under thermal collision conditions. The relationships among the reaction rates of different alkanes were obtained to establish a model to predict the low rate constants with methane from the high rate constants with C2-C4 alkanes. The model was tested by using available experimental results in literature. This study provides a new method to estimate the relatively low reactivity of atomic oxygen radical anions with methane on metal oxide clusters.

Inverse Isotope Kinetic Effect of the Charge Transfer Reactions of Ar+ with H2O and D2O.

Hydrogen isotopic effect, as the key to revealing the origin of Earth's water, arises from the H/D mass difference and quantum dynamics at the transition state of reaction. The ion-molecule charge-exchange reaction between water (H2O/D2O) and argon ion (Ar+) proceeds spontaneously and promptly, where there is no transition-state or intermediate complex. In this energetically resonant process, we find an inverse kinetic isotope effect (KIE) leading to the higher charge transfer rate for D2O, by the velocity map imaging measurements of H2O+/D2O+ products. Using the average dipole orientation capture model, we estimate the orientation angles of C2v axis of H2O/D2O relative to the Ar+ approaching direction and attribute to the difference of stereodynamics. According to the long-distance Landau-Zener charge transfer model, this inverse KIE could be also attributed to the density-of-state difference of molecular bending motion between H2O+ and D2O+ around the resonant charge transfer.

A new photoionization-induced substitution reaction chemical ionization time-of-flight mass spectrometry for highly sensitive detection of trace exhaled ethylene

Highly sensitive and rapid detection of ethylene, the smallest alkene of great significance in human physiological metabolism remains a great challenge. In this study, we developed a new photoionization-induced substitution reaction chemical ionization time-of-flight mass spectrometry (PSCI-TOFMS) for trace exhaled ethylene detection. An intriguing ionization phenomenon involving a substitution reaction between the CH2Br2+ reactant ion and ethylene molecule was discovered and studied for the first time. The formation of readily identifiable [CH2Br·C2H4]+ product ion greatly enhanced the ionization efficiency of ethylene, which led to approximately 800-fold improvement of signal intensity over that in single photon ionization mode. The CH2Br2+ reactant ion intensity and ion-molecule reaction time were optimized, and a Nafion tube was employed to eliminate the influence of humidity on the ionization of ethylene. Consequently, a limit of detection (LOD) as low as 0.1 ppbv for ethylene was attained within 30 s at 100 % relative humidity. The application of PSCI-TOFMS on the rapid detection of trace amounts of exhaled ethylene from healthy smoker and non-smoker volunteers demonstrated the satisfactory performance and potential of this system for trace ethylene measurement in clinical diagnosis, atmospheric measurement, and process monitoring.

Low-Cost Alternative for Online Analysis of Volatile Organic Compounds.

The use of online mass spectrometry for detecting volatile organic compounds (VOCs) has proven to be a powerful technique, allowing for real-time analysis of many chemical and biochemical processes. Unfortunately, online mass spectrometry has had limited application due to high instrument costs and limited availability. Here, we detail the design, construction, and performance characteristics of a custom ion-molecule reactor retrofitted to a commonly used single quadrupole mass spectrometer to operate as an online chemical ionization mass spectrometer (CIMS). This low-cost modified CIMS is capable of limits of detection below 10 parts per trillion for select VOCs including dimethyl sulfide, dimethylamine, and trimethylamine.

Proton Transfer Processes in 2-Butenenitrile Dimer Cation Studied by Mass-Selective Infrared Spectroscopy.

2-Butenenitrile (2-Bu) is a recently discovered crucial interstellar molecule. Herein, an abnormal NH band was observed in the infrared spectrum of the 2-Bu dimer cation, suggestive of a proton transfer reaction within the cluster. Through a comprehensive theoretical analysis of the IR spectrum of (2-Bu)2+, we discovered not only the formation of a new C-N bond through the attachment of one 2-Bu to another but also the occurrence of a proton transfer reaction in the cluster. This proton was identified as originating from the methyl group of the attaching 2-Bu in the cluster based on the analysis of IR spectra of (2-Bu)+ and [2-Bu-acrylonitrile (AN)]+. Furthermore, the detailed reaction process of this ion-molecule reaction is examined with theoretical calculation. This finding contributes significantly to our deeper understanding of ion-molecule reactions in the gas phase and the formation of nitrogen-containing prebiotic molecules in the interstellar medium.

Gas-phase ion mobility of protonated aldehydes in helium measured using a selected ion flow-drift tube.

In soft chemical ionization mass spectrometry, analyte ions are produced via ion-molecule reactions in the reactor. When an electric field E is imposed, the ion drift velocity vd determines the reaction time and the effective ion temperature. Agreement between experimental ion mobilities and theoretical predictions confirms the accuracy of the ion residence time measurement procedure. A selected ion flow-drift tube (SIFDT), an instrument with a chemical ionization source, was used to produce protonated aldehydes and selectively inject them into the resistive glass drift tube filled with He. Arrival-time distributions of ions were obtained using the Hadamard modulation. Reduced ion mobilities were then obtained at a pressure of 2hPa in the E/N range of 5-15 Td. Theoretical ion mobility values were calculated using two methods: hard-sphere approximation and trajectory modelling. The measured mobilities of three saturated and three unsaturated protonated aldehydes do not show substantial variation across the studied E/N range. Effective temperatures calculated using the Wannier formula from measured gas temperatures ranged from 300 to 315 K. Experimentally obtained values of the near-zero- E/N-reduced ion mobilities agree with both methods of calculations typically within ±3% standard deviation (maximum ±5%). The experimental SIFDT values of reduced mobilities in He of protonated aldehyde molecules generated from a chemical ionization source are in close agreement with two different theoretical methods based on the density functional theory calculations of ion geometries and partial atomic charges. Besides its fundamental importance, the ion mobility results validate the correct operation of the drift tube reactor and the ion residence time measurement procedure. Diffusion losses can also be determined from these results.

Ion Velocity Map Imaging Study of the Reactive Collisions between Carbon Dioxide and Helium Ion.

The reactive collision between He+ and CO2 plays an important role in substance evolutions of the planetary CO2-rich atmosphere. Using a three-dimensional ion velocity map imaging technique, we investigate the low-energy ion-molecule reactions He+ + CO2 → He + CO2+/He + CO+ + O/He + CO + O+. The velocity images of the products CO+ and O+ of dissociative charge-exchange reactions are distinctly different from those of charge-exchange product CO2+. The remarkable features of stereodynamics are observed in the dissociative charge-exchange reaction and are attributed to the spatial alignment of the initially random target CO2 during the He+ approach. Branching ratios of different channels of dissociative charge exchange are further obtained with the Doppler kinematics model, indicating a high preference for the energy-resonant channel.

Gas-phase formation of fullerene/9-hydroxyfluorene cluster cations

ABSTRACT In interstellar environment, fullerene species readily react with large molecules (e.g. polycyclic aromatic hydrocarbons, PAHs and their derivatives) in the gas phase, which may be the formation route of carbon dust grains in space. In this work, the gas-phase ion–molecule collision reaction between fullerene cations (${\rm C}_{n}\, ^+$, n = 32, 34,…, 60) and functionalized PAH molecules (9-hydroxyfluorene, C13H10O) are investigated both experimentally and theoretically. The experimental results show that fullerene/9-hydroxyfluorene cluster cations are efficiently formed, leading to a series of large fullerene/9-hydroxyfluorene cluster cations (e.g. [(C13H10O)C60]+, [(C13H10O)3C58]+, and [(C26H18O)(C13H10O)2C48]+). The binding energies and optimized structures of typical fullerene/9-hydroxyfluorene cluster cations were calculated. The bonding ability plays a decisive role in the cluster formation processes. The reaction surfaces, modes, and combination reaction sites can result in different binding energies, which represent the relative chemical reactivity. Therefore, the geometry and composition of fullerene/9-hydroxyfluorene cluster cations are complicated. In addition, there is an enhanced chemical reactivity for smaller fullerene cations, which is mainly attributed to the newly formed deformed carbon rings (e.g. 7 C-ring). As part of the co-evolution network of interstellar fullerene chemistry, our results suggest that ion–molecule collision reactions contribute to the formation of various fullerene/9-hydroxyfluorene cluster cations in the interstellar medium, providing insights into different chemical reactivity caused by oxygenated functional groups (e.g. hydroxyl, OH, or ether, C-O-C) on the cluster formations.

Response of protonated, adduct, and fragmented ions in Vocus proton-transfer-reaction time-of-flight mass spectrometer (PTR-ToF-MS)

Abstract. Volatile organic compounds (VOCs) affect secondary pollutant formation via active chemistry. Proton-transfer-reaction mass spectrometry (PTR-MS) is one of the most important techniques to study the highly variable spatial and temporal characteristics of VOCs. The response of protonated, adduct, and fragmented ions in PTR-MS in changing instrument settings and varying relative humidity (RH) requires rigorous characterization. Herein, we present dedicatedly designed laboratory experiments conducted to investigate the response of these ions for 21 VOCs, including 12 oxygenated VOCs and 2 nitriles, using the recently developed Vocus PTR-MS. Our results show that the focusing ion–molecule reactor (FIMR) axial voltage increases sensitivity by 3 to 4 orders of magnitude but does not significantly change the fractions of protonated ions. Reducing the FIMR pressure, however, substantially increases fragmentation. Applying a high radio frequency (RF) amplitude radially to the FIMR can enhance sensitivity by 1 to 2 orders of magnitude without affecting the protonated ion fractions. The change in big segmented quadrupole (BSQ) amplitude mainly affects sensitivity and protonated ion fraction by modifying ion transmission. The relationship between sensitivity and proton-transfer reaction rate constant is complicated by the influences from both ion transmission and protonated ion fraction. The protonated ions of most VOCs studied (19 out of 21) show less than 15 % variations in sensitivity as RH increases from ∼ 5% to ∼ 85 %, except for some long-chain aldehydes which show a positive RH variation of up to 30 %. Our results suggest that the Vocus PTR-MS can reliably quantify the majority of VOCs under ambient conditions with varying RH. However, caution is advised for small oxygenates such as formaldehyde and methanol due to their low sensitivity and for long-chain aldehydes due to their slight RH dependence and fragmentation.

Gas-phase hydrogenation of large, astronomically relevant PAH cations

ABSTRACT To investigate the gas-phase hydrogenation processes of large, astronomically relevant cationic polycyclic aromatic hydrocarbon (PAH) molecules under the interstellar environments, the ion–molecule collision reaction between six PAH cations and H-atoms is studied. The experimental results show that the hydrogenated PAH cations are efficiently formed, and no even–odd hydrogenated mass patterns are observed in the hydrogenation processes. The structure of newly formed hydrogenated PAH cations and the bonding energy for the hydrogenation reaction pathways are investigated with quantum theoretical calculations. The exothermic energy for each reaction pathway is relatively high, and the competition between hydrogenation and dehydrogenation is confirmed. From the theoretical calculation, the bonding ability plays an important role in the gas-phase hydrogenation processes. The factors that affect the hydrogenation chemical reactivity are discussed, including the effect of carbon skeleton structure, the side-edged structure, the molecular size, the five- and six-membered C-ring structure, the bay region structure, and the neighbouring hydrogenation. The infrared spectra of hydrogenated PAH cations are also calculated. These results we obtain once again validate the complexity of hydrogenated PAH molecules, and provide the direction for the simulations and observations under the co-evolution interstellar chemistry network. We infer that if we do not consider other chemical evolution processes (e.g. photoevolution), then the hydrogenation states and forms of PAH compounds are intricate and complex in the interstellar medium.

Spatial and Temporal Detection of Ions Ejected from Coulomb Crystals.

Coulomb crystals have proven to be powerful and versatile tools for the study of ion-molecule reactions under cold and controlled conditions. Reactions in Coulomb crystals are typically monitored through a combination of in situ fluorescence imaging of the laser-cooled ions and destructive time-of-flight mass spectrometry measurements of the ejected ions. However, neither of these techniques is able to provide direct structural information on the positions of nonfluorescing "dark" ions within the crystal. In this work, structural information is obtained using a phosphor screen and a microchannel plate detector in conjunction with a Timepix3 camera. The Timepix3 camera simultaneously records the spatial and temporal distribution of all ions that strike the phosphor screen detector following crystal ejection at a selected reaction time. A direct comparison can be made between the observed Timepix3 ion distributions and the distributions established from SIMION simulations of the ion trajectories through the apparatus and onto the detector. Quantitative agreement is found between the measured Timepix3 signal and the properties of Coulomb crystals assigned using fluorescence imaging─independently confirming that the positions and numbers of nonfluorescing ions within Coulomb crystals can be accurately determined using molecular dynamics simulations. It is anticipated that the combination of high-resolution spatial and temporal data will facilitate new measurements of the ion properties within Coulomb crystals.