# iSELECTION: An Instrument to Study the Kinetics of Isomer-Selected Gas-Phase Ion-Molecule Reactions

Corentin Rossi, Anne P Rasmussen, Bérenger Gans, Juraj Jašík, Jan Žabka, Marc Albaret, Hugo Bauduin, Christophe Charrière, Jean-philippe Dugal, Jérôme Guigand, et al.

► To cite this version:

Corentin Rossi, Anne P Rasmussen, Bérenger Gans, Juraj Jašík, Jan Žabka, et al., iSELECTION: An Instrument to Study the Kinetics of Isomer-Selected Gas-Phase Ion-Molecule Reactions. Chemistry–Methods, In press, 10.1002/cmtd.202500013. [https://hal.science/hal-05120315v1](https://hal.science/hal-05120315v1)

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# iSELECTION: An Instrument to Study the Kinetics of Isomer-Selected Gas-Phase Ion-Molecule Reactions

Corentin Rossi, Anne P. Rasmussen, Bérenger Gans, Juraj Jašík, Jan Žabka, Marc Albaret, Hugo Bauduin, Christophe Charrière, Jean-Philippe Dugal, Jérôme Guigand, Catherine Le Bris, and Ugo Jacovella*

Distinguishing the chemical reactivity of isomers is a fundamental challenge in chemistry, particularly in cluster chemistry, where the number of possible structures increases dramatically with cluster size. This study presents a novel approach for measuring the kinetics of ion-molecule reactions of laser-ablated species in an isomer-specific fashion. This is achieved by combining drift-tube ion mobility with mass spectrometry, enabling shape selection prior to investigating the chemical reactivity of species of interest. First, the capability of obtaining reaction rate coefficients

by studying the nucleophilic addition reactions of small monocyclic carbon rings ($C_{11}^+$, $C_{15}^+$, and $C_{17}^+$) with pyridine, comparing the results with previously reported values is validated. Then the ability to determine isomer-specific reaction rate coefficients using the $C_{40}^+$ cluster, where multiple isomers coexist is demonstrated. This highlights the potential of our new instrument for accurately characterizing isomer-specific reactivities in complex chemical systems.

## 1. Introduction

Chemical reactivity is inherently linked to molecular structure. Since different isomers of the same species can exhibit distinct reactivities, unraveling their chemical behavior can be a complicated task. Cluster chemistry serves as a prime example of a field where this issue is particularly critical. As cluster size grows, the number of possible coexisting stable isomers increases dramatically, making the chemical analysis challenging. In the context of this study, the selected example is carbon cluster cations, whose chemistry plays a key role in combustion processes such as soot formation[1] and in interstellar environments.[2]

Gas-phase ion mobility measurements have unambiguously revealed that $C_n^+$ clusters adopt different structural forms

depending on their mass range: linear isomers for $n = 3–10$, monocyclic for $n \ge 7$, bicyclic for $n \ge 21$, and fullerene for $n \ge 30$. [3] Interestingly, the coexistence of linear and ring structures for carbon clusters from $C_7^+$ to $C_{10}^+$ was initially inferred from gas-phase reactivity studies. These studies revealed that linear clusters react rapidly with $H_2$, $D_2$, $O_2$, and hydrocarbons, while cyclic clusters exhibit little to no reactivity with these neutral species.[4–6] These findings explain why two particular size ranges were investigated: between $C_{10}^+$ and $C_{20}^+$, where exclusively monocyclic structures are formed[7–10] and above $C_{50}^+$, where fullerenes predominantly emerge.[11–13] This highlights that, for cationic carbon clusters, investigating the intermediate size range will inevitably require experimental setups capable of isolating specific isomers prior to studying their reactivity. Such an approach is essential to disentangle the chemical properties of individual isomers.

A first method, proposed by McElvany,[4] relies on a MS3 approach (three consecutive mass isolation steps), which takes advantage of the difference in reactivity between the linear and cyclic isomers of $C_7^+$ toward $D_2$, to study the reaction between $c - C_7^+$ and acetylene. The parent ions are first mass-selected and introduced into a Fourier transform mass spectrometer cell with a mixture of $C_2H_2$ and $D_2$ with an excess of $D_2$. A second mass selection stage is used to isolate the nonreactive cyclic population. Finally, products of the reaction between the selected ions and acetylene are mass-analyzed. However, this technique is not suitable as a universal method, as it requires a reactant with sufficiently different reactivity toward each coexisting isomer.

A more direct technique relies on combining ion mobility-separation with reactivity measurements, which allows selection based on collision cross section (CCS). This approach was first used by Von Helden on the reaction of clusters containing 3–15 carbon atoms with $O_2$ and NO.[3] Their rate coefficients are determined by adding the reacting gas inside the drift cell.

C. Rossi, A. P. Rasmussen, B. Gans, M. Albaret, H. Bauduin, C. Charrière,

J.-P. Dugal, J. Guigand, C. Le Bris, U. Jacovella

Institut des Sciences Moléculaires d'Orsay

CNRS

Université Paris-Saclay

91405 Orsay, France

E-mail: ugo.jacovella@cnrs.fr

A. P. Rasmussen

Department of Physics and Astronomy

Aarhus University

Ny Munkegade 120, Aarhus C 8000, Denmark

J. Jašík, J. Žabka

J. Heyrovský Institute of Physical Chemistry

Czech Academy of Sciences

Prague 18223, Czech Republic

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Supporting information for this article is available on the WWW under https://doi.org/10.1002/cmtd.202500013

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© 2025 The Author(s). Chemistry - Methods published by Chemistry Europe and Wiley-VCH GmbH. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
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Using a comparable approach, Misaizu et al. have shown in their study that they could disentangle the chemistry of the linear and cyclic structures of clusters containing 4–9 carbon atoms with D₂.[¹⁴] However, this method gives imperfect control over the drift time and, ultimately, the ion-mobility selection, as the reactivity occurs along the length of the drift region.

Outside the framework of cluster chemistry, Shiels et al. used field asymmetric ion mobility separation (FAIMS) to achieve such purpose by probing individually the reactivity of the two protomers of diazanaphthalene with ethylene.[¹⁵] This overcame the problem as ions are separated prior to the reactivity measurement. However, the FAIMS technique has an inherent limitation, as its inability to obtain direct CCS measurements, which hinders the straightforward identification of many unknown coexisting species.

Therefore, the combination of ion-molecule reactivity in an ion trap, following shape selection using a drift-tube ion mobility setup, appears to be the most suitable technique.

In this article, we present a new apparatus designed to study isomer-specific ion-molecule reactions and determine reaction rate coefficients. These capabilities are demonstrated by examples of nucleophilic addition reactions of pyridine (Pyr, C₅H₅N) with various cationic carbon cluster isomers.

## 2. Experimental Section

This new tandem ion mobility-mass spectrometer is conceptually similar to the instrument developed by the Bieske group.[¹⁶,¹⁷] It provides two orthogonal dimensions of selection to identify and discriminate isomers based on their CCS and mass-to-charge ratio. The workflow and a schematic representation of the experimental setup are presented in **Figure 1**. The apparatus consists of four parts: 1) a laser ablation source, 2) a drift region, 3) an octupole, and 4) a quadrupole mass filter (QMF). These components will be described individually below.

### 2.1. Ion Source

Ions are generated by laser vaporization of a graphite target rod (Goodfellow) using the second harmonic of a Nd:YAG laser

(Centurion+, Quantel laser) at 532 nm, with a typical power of 30 mJ per pulse and an adjustable repetition rate ranging from 1 to 100 Hz, depending on the application. The target rotates continuously, and the laser beam is moved vertically by a motorized screw on the last mirror holder along the rod to minimize surface alteration of the sample target.

### 2.2. Drift Region and Isomer Selection

The drift region comprises an extraction stack of lenses, a drift tube, and an ion funnel terminating in a skimmer-shaped electrode. A voltage drop is applied between each component to enable ion-mobility separation. Nitrogen buffer gas is introduced into the drift region via a flowmeter (SLA Series, Brooks Instruments) at a flow rate of 0.2 L min⁻¹, maintaining a pressure of 1.5 mbar, monitored by a baratron (CMR 363, Pfeiffer Vacuum). The chamber is pumped by a rotary pump (Edwards E2M28, Edwards Vacuum).

The extraction stack consists of nine electrodes resistively coupled to function as a voltage divider. The target rod is positioned between the two first electrodes. The typical field applied is 45 V cm⁻¹. The rod itself is polarized at the mean voltage of the two electrodes surrounding it, and the chamber is floated at the average voltage of the entire lens stack to prevent electrical breakdowns.

The central component of the drift region is a 30 cm-long resistive (33 MΩ) glass tube with an inner diameter of 40 mm (Photonis). It is typically operated at an electric field of 35 V cm⁻¹.

After passing through the drift tube, an ion funnel (IF) ensures a good focusing of the ion beam for transfer from the high-pressure to the low-pressure region. The funnel is 15.5 cm long and consists of 28 drilled, printed circuit board electrodes. Their diameter decreases gradually, from 38.5 to 7 mm. The electrodes are connected by 1 MΩ resistors, with suitable potentials applied to the first and last electrodes to create a homogeneous drift field of 10 V cm⁻¹. They are also capacitively coupled to the radio frequency (RF) supply, with a drive amplitude of 150 Vpp and a frequency of 1 MHz.

The end skimmer-shaped electrode situated 1 mm after the last electrode of the IF can function as an ion gate. By applying

<figure><img src="image_6.png" /><figcaption>**Figure 1.** Schematic representation of the setup and the four-step approach to reactivity measurements: (1) ion generation, (2) shape selection, (3) reactivity, and (4) mass analysis.</figcaption></figure>
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a blocking potential, it prevents ion passage, which can be tem-
porarily released for a specific duration (typically 0.5 ms) at a
defined delay after the laser shot (drift time). This allows the
selection of a specific ion population that has been previously
separated by ion mobility. This electrode is also used as a differ-
ential pumping wall between the drift region and the octupole
chamber.

2.3. Octupole Ion Guide/Trap

After exiting the drift region, ions pass through a 51 mm-long octupole RF device made of 2 mm-diameter rods and with a 6 mm inner diameter. This device serves multiple purposes: it can act as an ion guide to the next vacuum chamber, providing an effective differential pumping stage before the mass analysis, or it can be used to trap ions for investigating their reactivity properties. The octupole chamber is pumped by two turbopumps of 380 and 685 L s⁻¹ pumping speed for nitrogen (HiPace 450 and 700, respectively, from Pfeiffer Vacuum).

The pressure inside the octupole chamber is typically main-
tained at approximately 6 × 10⁻⁴ mbar. This is monitored using a
baratron (CMR 375, Pfeiffer Vacuum). The RF amplitude applied
is generally around 100 V but can be adjusted depending on the
m/z of interest. The RF frequency is set at 1.7 MHz

When used as an ion trap, a blocking/releasing potential is
applied to the first electrode after the octupole to trap the ions
within the RF electric field. The chamber is filled with a mixture of
nitrogen and reactive gas. The number density of the reactive gas
is determined based on the partial pressure of the reactant in the
nitrogen flow introduced into the octupole chamber. For Pyr,
we flowed nitrogen at 2.2 bar into a bubbler filled with liquid pyr-
idine, then introduced it into the chamber through a needle
valve. The vapor pressure of pyridine was determined from

the Antoine equation, at a temperature of 293 K (21 mbar).
The mixture is considered homogeneous, typically resulting in
a few percent of Pyr in N₂.

2.4. Quadrupole Mass-Filter and Detection

After passing through the mobility and reactivity regions, ions are
mass-analyzed by the 250 mm-long QMF, driven by an RF power
supply fabricated by JanasCard. The QMF can be operated
with a mass resolution of 1 atomic mass unit up to *m/z* 1800
(see Supporting Information for more details). They are then
deflected off-axis by a quadrupole bender and detected by an elec-
tron multiplier with a conversion dynode (R6984-80, Hamamatsu).
The ion signal is acquired by collecting the analog signal from the
electron multiplier and is visualized on an oscilloscope.

**3. Results and Discussion**

First, we demonstrate how to generate carbon cluster ions and
distinguish between their isomers. Next, we show how, after
selecting the desired isomers, kinetic studies can be performed
on them in an ion trap.

**3.1. Carbon Cluster Generation**

A prototypical mobility spectrum obtained with the described setup
is shown in Panel b of **Figure 2**. In this contour plot, the two dimen-
sions of selection (by mass and by shape) are plotted on the x- and
y-axis, respectively. Each vertical line corresponds to a single arrival
time distribution (ATD). Hence, each spot on the contour plot rep-
resents one isomer at a given mass-to-charge ratio and with a cer-
tain spread in arrival time, which is defined as the time difference

<figure><img src="image_8.png" /><figcaption>**Figure 2.** Panel b provides mass and shape analysis of carbon clusters C<sub>j</sub><sup>+</sup> (n = 9–50) generated from laser-ablated graphite. The mass-to-charge ratio (m/z) is tuned on the x-axis, while the ATD, informing about the shapes of the clusters, is plotted on the y-axis. Panel a shows the corresponding mass spectrum (integration over each ATD).</figcaption></figure>
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between the laser shot and the detection. Typical mobility resolution is ≈20 as can be seen in the SI. The corresponding mass spectrum (integration over each ATD) is displayed in Panel a. No gating on the skimmer-shaped electrode or trapping in the octupole is performed so that all ions are collected without discrimination.

Linear trends in arrival time are observed as the size of the clusters increases, each corresponding to one type of structure: cages, monocyclic and bicyclic rings. The predominant structure for clusters with 20 carbon atoms is a mono-ring. Bicyclic species emerge for cluster sizes between 20 and 30 atoms. Above 30 atoms, cage and ring structures coexist, fullerenic structures becoming prominent as the size of the clusters grows, but are only observed for even numbers of carbon atoms. The smallest fullerene seen in our setup is $C_{32}^+$. These results agree with the well-established knowledge on the size and shape distribution of carbon clusters generated by laser vaporization.[3,18]

## 3.2. Second-Order Rate Coefficient Measurements

The methodology for obtaining second-order rate coefficients was first benchmarked using the reactions of small carbon rings ($C_{11}^+$, $C_{15}^+$, and $C_{17}^+$) with Pyr. These reactions were chosen as they are reported in the literature,[10] and only one isomer of the carbon cluster is expected to exist.

Results are displayed in **Figure 3**. An example of a kinetic profile is provided for the reactions between each carbon cluster and Pyr (Panels a, c, and e). The orange dots represent the ion signal of the parent ions as a function of storage time. The gray and black dots show the ion signal of the two main reaction products, $C_{40}^- - Pyr^+$ and $C_{40}^- - Pyr_2^+$ products, respectively, corresponding to the addition of one and two Pyr molecules. Since typically a few thousand ions at most are trapped, Pyr is present in large excess ($>10^{10}$ molecules), allowing the

<figure><img src="image_10.png" /><figcaption>**Figure 3.** Left panels (a, c, and e): Kinetic profiles of the reactions with Pyr at a Pyr number density of 1.3, 1.5, and $1.9 \times 10^{10} \text{ cm}^{-3}$, respectively. Orange dots show the evolution of the parent ion signal, while gray and black ones represent the signal of the two products. Right panels (b, d, and f): Pseudo-first order rate as a function of pyridine number density. Error bars represent the statistical error from the exponential fit of the kinetic profile, corresponding to two standard deviations (2σ).</figcaption></figure>
<figure><img src="image_11.png" /></figure>

reaction to be treated as pseudo-first order. A kinetic model of two sequential additions was used to interpret the kinetic profiles of the product formation. However, as not all the reactions channels were monitored (as evidenced by the nonconstant total sum of the products signal), but only the two main products, the reaction rates obtained out of this model for products appearance cannot be used for quantitative analysis. Yet, the disappearance of the parent as a function of storage time can be well fitted using a monoexponential decay, providing the pseudo-first-order rate of the reaction. This rate, therefore, accounts for the sum of all reaction channels, and thus only the fits of the parent ion are used to provide reaction rates throughout this article.

<table><caption>**Table 1.** Second order rate coefficients of the reaction of C<sub>11</sub>, C<sub>15</sub>, and C<sub>17</sub> with Pyr. Values obtained in this study are compared with the ones obtained by Pozniak and Dunbar (see ref. [10]).</caption><thead><tr><th>Reaction</th><th>k<sup>a)</sup> (TW<sup>b)</sup></th><th>k<sup>a)</sup> (ref. [10])<sup>c)</sup></th></tr></thead><tbody><tr><td>C<sub>11</sub><sup>+</sup> + Pyr</td><td>24 ± 2</td><td>74 ± 22</td></tr><tr><td>C<sub>15</sub><sup>+</sup> + Pyr</td><td>26 ± 1</td><td>65 ± 20</td></tr><tr><td>C<sub>17</sub><sup>+</sup> + Pyr</td><td>24 ± 2</td><td>74 ± 22</td></tr></tbody></table>

Second-order rate coefficients are measured by repeating this procedure at different Pyr number densities. The entire procedure has been meticulously described in a recent publication.[19] The right panels (b, d, and f) show the pseudo-first-order rates as a function of Pyr number density, which are analyzed using linear regression. The slopes of the fitted lines represent the second-order rate coefficients, which are summarized in **Table 1**.

The relative uncertainties can be estimated from the statistical error of the exponential fit to the kinetic profile, corresponding to twice the standard deviation (2σ). This results in a relative error below 10%. However, the absolute error is much larger, primarily due to uncertainties in the Pyr number density, which contributes an uncertainty of roughly 50%. Therefore, the second-order rate coefficients for all the studied reactions are consistent within these uncertainties with the previous work of Pozniak and Dunbar[10] (see Table 1). Additionally, the relative trends in both studies are similar, with reaction rates for the carbon clusters being nearly identical.

### 3.3. Isomer-Selected Ion-Molecule Reactivity

Unlike smaller carbon clusters, several stable C<sub>40</sub><sup>+</sup> structures coexist. The ATD corresponding to m/z = 480 is shown as a black line in Panel a of **Figure 4**, revealing three distinct families of isomers.

<figure><img src="image_12.png" /><figcaption>**Figure 4.** Panel (a): ATD of C<sub>40</sub><sup>+</sup> with no ion gate (black line) and using the ion gate to select a single isomer (green-, purple-, orange-, and pink-colored areas). Panel (b, c, d, and e): Kinetic profiles of the reactions between the selected isomer and Pyr. The gray dots correspond to the appearance of the reaction product, while the colored dots and lines show the parent signal depletion (experimental and fitted data).</figcaption></figure>

<footnote><sup>a)</sup>Second-order rate coefficients in 10<sup>-10</sup> cm<sup>3</sup> s<sup>-1</sup> <sup>b)</sup>This work: uncertainties given are the relative errors, calculated as ±2σ. We estimate the absolute error to be about 50%. <sup>c)</sup>Absolute uncertainties are within a factor of 2.</footnote>
<figure><img src="image_13.png" /></figure>

Based on trends observed in the pure carbon contour plot in Figure 2 and insights from previous studies,[3,16] these families can be attributed to monorings, birings, and fullerenes. The fullerenes, being the most compact structures, exhibit the fastest arrival times. In contrast, cyclic structures appear at slower arrival times, with monorings being the slowest among them. The method described in this article was used to select each isomer and reveal their reactivity with Pyr.

The colored areas in Panel a show the distributions when the electrical ion gate is used to select only one isomer. The disappearance of the selected structure is then tracked as a function of storage time, as well as the formation of C₄₀ – Pyr⁺. Panels b, c, and e of Figure 4 show the kinetic profiles of the reaction for the monorings, the birings, and the fullerenes, respectively, at a Pyr number density of 4 × 10¹⁰ cm⁻³. The only significant reaction channel with every isomer was the single addition of a Pyr molecule. Unlike reactions with other isomers, the reaction with biring species (Panel c) plateaus and never reaches complete conversion of the parent ions into product ions, indicating the presence of two distinct populations with one being unreactive or very slowly reacting species. This population of almost nonreactive structures was identified in the fastest part of the biring ATD, as shown by the ATD labeled "Unreactive species" in Figure 4 (and also in the Supporting Information), Panel a, and the corresponding kinetic profile of its reaction with Pyr (Panel d). These species could therefore be compact bicyclic or tricyclic rings. To account for their presence within the biring population (blue trace), the kinetic profiles have been fitted using a monoexponential decay for the reactive species, along with a constant background to account for unreactive species.

These results show that each isomer reacts differently with Pyr. Fullerene species react the fastest, and the birings the slowest. This observation is unambiguously confirmed by the second-order rate constant measurements that are presented in Figure 5.

<figure><img src="image_14.png" /><figcaption>**Figure 5.** Pseudo-first order rate as a function of Pyr number density for the fullerenes (red), the birings (blue), and the monorings (green). Data are fitted by a linear trend. Error bars and uncertainties indicate the statistical error from the exponential fit of the kinetic profile (2σ).</figcaption></figure>

They show that the fullerene isomer of C₄₀ exhibits a significantly higher reaction rate than the ring species. The reaction between C₄₀ monocyclic rings and Pyr is also twice as fast as the reaction of biring species.

## 4. Conclusion

We present the capabilities of a novel instrument that combines a laser vaporization source with ion mobility and mass spectrometry. Specifically, we demonstrate its ability to perform isomer-selected ion-molecule reactions and obtain rate coefficients, illustrated through the example of reactions between various cationic carbon clusters and pyridine.

We assessed our method using the reactions of small carbon monorings, for which only one isomer exists. Second-order rate coefficients measurements were performed for the reaction of the three carbon clusters C₁₁, C₁₅, and C₁₇ with pyridine. Our results are consistent with the findings of Pozniak and Dunbar.[10]

The reaction between C₄₀⁺ and pyridine was analyzed in detail. We demonstrated our ability to perform isomer-selected ion-molecule studies and to provide a second-order rate coefficients for each isomer. This method can therefore be used to characterize the reactivity of coexisting isomers, which is particularly valuable for large atomic clusters, for instance.

## Acknowledgements

The work was funded by the French "Agence Nationale de la Recherche" (ANR) under grant no. ANR-22-CE29-0013 (Project iSELECTION). Additional financial support was provided by the Paris Ile-de-France Region (DIM ORIGINES, project DIBsFINDER). This work was also supported by the Programme National "Physique et Chimie du Milieu Interstellaire" (PCMI) and by a research grant (VIL71404) from VILLUM FONDEN. This publication is based upon work from COST Action CA21126 - Carbon molecular nanostructures in space (NanoSpace), supported by COST (European Cooperation in Science and Technology). J.J. would like to thank for the financial support from the Praemium Academiae funding provided by the Czech Academy of Sciences (Project No. AP2102).

## Conflict of Interest

The authors declare no conflict of interest.

## Data Availability Statement

The data that support the findings of this study are available in the supplementary material of this article.

**Keywords:** cluster compounds · gas-phase reactions · isomers · kinetics · mass spectrometry
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Manuscript received: January 29, 2025

Revised manuscript received: April 11, 2025

Version of record online: