Ion-molecule Reactions Research Articles

Shapeshifting Nucleophile Singly Hydrated Hydroperoxide Anion Leads to the Occurrence of the Thermodynamically Unfavored SN2 Product.

Single water molecules alone may introduce unusual features into the kinetics and dynamics of chemical reactions. The singly hydrated hydroperoxide anion, HOO-(H2O), was found to be a shapeshifting nucleophile, which can be transformed to HO- solvated by hydrogen peroxide HO-(HOOH). Herein, we performed direct dynamics simulations of its reaction with methyl iodide to investigate the effect of individual water molecules. In addition to the normal SN2 product CH3OOH, the thermodynamically unfavored proton transfer-induced HO--SN2 path (produces CH3OH) was also observed, contributing ∼4%. The simulated branching ratio of the HO--SN2 path exceeded the statistical estimation (0.6%) based on the free energy barrier difference. The occurrence of the HO--SN2 path was attributed to the shallow entrance channel well before a submerged saddle point, thus providing a region for extensive proton exchange and ultimately leading to the formation of CH3OH. In comparison, changing the leaving group from Cl to I increased the overall reaction rate as well as the proportion of the HO--SN2 path because the CH3I system has a smaller internal barrier. This work elucidates the importance of the dynamic effect introduced by a single solvent molecule to alter the product channel and kinetics of typical ion-molecule SN2 reactions.

Hydrated Formic Acid Clusters and their Interaction with Electrons.

We investigate ion formation in hydrated formic acid (FA) clusters upon collision with electrons of variable energy, focusing on electron ionization at 70 eV (EI) and low-energy (1.5-15 eV) electron attachment (EA). To uncover details about the composition of neutral clusters, we aim to elucidate the ion formation processes in FAM ⋅ WN clusters initiated by interaction with electrons and determine the extent of cluster fragmentation. EI predominantly produces protonated [FAm+H]+ ions, and in FA-rich clusters, the stable ring structures surrounding H3O+ ions are formed. In contrast, EA leads to a competition between the formation of intact [FAm ⋅ Wn]- and dissociated [FAm ⋅ Wn-H]- fragment ions, influenced by the cluster size, level of hydration, and electron energy. Our findings reveal a predisposition of low-energy EA towards forming [FAm ⋅ Wn]-, while higher electron energies tend to favor the formation of [FAm ⋅ Wn-H]- due to intracluster ion-molecule reactions. The comparison of positive and negative ion spectra suggests that the mass spectra of FA-rich clusters may indicate their actual size and composition. On the other hand, the more weakly bound water evaporation from the clusters depends strongly on the ionization. Thus, for the hydrated clusters, the neutral cluster size can hardly be estimated from the mass spectra.

The Magnesium Dication and Water Synergistically Promote the Protonolysis of Two of the B-C Bonds in the Tetraphenylborate Anion.

Analytes are sampled from both solution phase and gas-phase environments during the ESI process, and thus, the mass spectrum that is measured can reflect both solution and gas-phase conditions. In the gas-phase regime, ion-molecule reactions can influence the types of ions that are observed. Herein, the synergistic effects of a Lewis acid (Mg2+) and background water are shown to lead to protonolysis of two of the B-C bonds of the tetraphenylborate ion in the gas phase, giving rise to different ions at different reaction times in ESI-MS/MS experiments in a linear ion trap mass spectrometer. At short reaction times (1 ms), the expected adduct [Mg(BPh4)]+ is observed. At 10 ms, [(HO)Mg(BPh3)]+ and [(HO)2Mg(BPh2)]+ are observed. At 100 ms, the water adducts [(HO)2Mg(BPh2)(H2O)]+ and [(HO)2Mg(BPh2)(H2O)2]+ appear, and these become the dominant ions at longer reaction times. DFT calculations provide a plausible explanation as to why only [(HO)Mg(BPh3)]+ and [(HO)2Mg(BPh2)]+ but not [(HO)3Mg(BPh)]+ are observed.

Decarboxylation of fatty acids by ternary zinc cationic complexes studied by mass spectrometry and theoretical calculations

We have shown that fatty acids can be decarboxylated in the gas phase via collision-induced dissociation (CID) of ternary zinc complexes of the general formula [(L)Zn(OOCR)]+, where RC3H7, C6H13, C7H15, C17H35, C17H33, C17H31 and L = 1,10-phenanthroline or 2,2′:6′,2″-terpyridine. These complexes were formed by electrospray ionization of a solution mixture of zinc(II) salt, fatty acid, and the ligand. Two pathways were mapped for the resulting [(L)ZnR]+ organozinc ion: i) a gas-phase ion-molecule reaction with a neutral carboxylic acid R’COOH in the linear quadrupole ion trap resulted in the production of the alkane RH and formation of [(L)Zn(OOCR’)]+; ii) a second CID stage produced an alkene and the ion [(L)ZnH]+ which underwent a subsequent ion-molecule reaction with R’COOH to form [(L)Zn(OOCR’)]+ ion accompanied by the loss of H2. In the case of RR’ = C3H7 (butyric acid), both processes presented formal catalytic cycles with the overall equations C3H7COOHC3H8+ CO2 or C3H7COOHC3H6 + H2+ CO2. Theoretical DFT calculations provided the energetics of reactants/products as well as transition state energies and were in agreement with the experimental data. The work identifies Zn as a potential catalyst for deoxygenation of fatty acid with no fragmentation of the alkyl chain.

Cold Ion-Molecule Reactions in the Extreme Environment of a Coulomb Crystal.

Coulomb crystals provide a unique environment in which to study ion-neutral gas-phase reactions. In these cold, trapped ensembles, we are able to study the kinetics and dynamics of small molecular systems. These measurements have connections to chemistry in the Interstellar Medium (ISM) and planetary atmospheres. This Feature Article will describe recent work in our laboratory that uses Coulomb crystals to study translationally cold, ion-neutral reactions. We provide a description of how the various affordances of our experimental system allow for detailed studies of the reaction mechanisms and the corresponding products. In particular, we will describe quantum-state resolved reactions, isomer-dependent reactions, and reactions with a rarely studied, astrophysically relevant ion, CCl+.

Nuclear spin ratios of deuterated ammonia in prestellar cores

Context. Molecules containing two or more hydrogen or deuterium atoms have different nuclear spin states which behave as separate chemical species. The relative abundances of these species can give clues to their origin. Formation on grains is believed to yield statistical spin ratios whereas gas-phase reactions are predicted to result in clear deviations from them. This is also true for ammonia and its deuterated forms NH2D, NHD2, and ND3. Aims. Here we aim to determine the ortho/para ratios of NH2D and NHD2 in dense, starless cores, where their formation is supposed to be dominated by gas-phase reactions. Methods. The Large APEX sub-Millimeter Array (LAsMA) multibeam receiver of the Atacama Pathfinder EXperiment (APEX) telescope was used to observe the prestellar cores H-MM1 and Oph D in Ophiuchus in the ground-state lines of ortho and para NH2D and NHD2. The fractional abundances of these molecules were derived employing three-dimensional radiative transfer modelling, using different assumptions about the abundance profiles as functions of density. We also ran gas-grain chemistry models with different scenarios concerning proton or deuteron exchanges and chemical desorption from grains to find out if one of these models can reproduce the observed spin ratios. Results. The observationally deduced ortho/para ratios of NH2D and NHD2 are in both cores within 10% of their statistical values 3 and 2, respectively, and taking 3 σ limits, deviations from these of about 20% are allowed. Of the chemistry models tested here, the model that assumes proton hop (as opposed to full scrambling) in reactions contributing to ammonia formation, and a constant efficiency of chemical desorption, comes nearest to the observed abundances and spin ratios. Conclusions. The nuclear spin ratios derived here are in contrast with spin-state chemistry models that assume full scrambling in proton donation and hydrogen abstraction reactions leading to deuterated ammonia. The efficiency of chemical desorption strongly influences the predicted abundances of NH3, NH2D, and NHD2, but has a lesser effect on their ortho/para ratios. For these the proton exchange scenario in the gas is decisive. We suggest that this is because of rapid re-processing of ammonia and related cations by gas-phase ion-molecule reactions.

A fixed-charge model of the N-protomer of 4-aminobenzoic acid to facilitate the study of the unimolecular and bimolecular chemistry of its "neutral" carboxylic acid group.

There are a growing number of examples of protomers formed via electrospray ionization (ESI) that do not fragment under mobile proton conditions, giving rise to distinct tandem mass spectra. To model the N-protomer of 4-aminobenzoic acid, here we study the gas-phase unimolecular and bimolecular chemistry of the 4-(carboxyphenyl)trimethylammonium ion. 4-(Carboxyphenyl)trimethylammonium iodide was synthesized, purified via recrystallization and transferred to the gas phase via ESI. 4-(Carboxyphenyl)trimethylammonium ion, 7, was mass selected and subjected to collision-induced dissociation and ion-molecule reactions in a linear ion trap mass spectrometer. The major fragmentation channel for the fixed-charge cation 7 is methyl radical loss, whereas loss of trimethylamine and CO2 represents minor pathways. The free carboxylic acid functional group of 7 is unreactive toward a number of neutral reagents (methanol, acetone, acetonitrile, and N,N'-diisopropylcarbodiimide). 7 reacts very slowly with trimethylborate via addition-elimination, consistent with density functional theory (DFT) calculations that show this reaction is slightly endothermic. The deuterated cation 7(D) undergoes slow D/H exchange with ethanol, and DFT calculations reveal that a flip-flop mechanism operates. The free carboxylic group of 7 is not very reactive toward neutral reagents in the gas phase.

Ion molecule reaction dynamics for disentangling competing reactive pathways

ABSTRACT Chemical reactions are by definition dynamical. Reactants move towards each other, collide and products separate again. Therefore, it is important to look beyond the stationary description, and look at how molecules rearrange and how energy is partitioned during a reactive collision. Chemical reactions are complex and often involve competing chemical and/or atomistic pathways whose dominance depends on several factors as for example the involved quantum states or collision energy. Here, we focus on ion molecule reactions which play an important role in gaseous environments even though their steady-state abundance is often much lower than that of their neutral counterparts. We present the use of angle and energy differential cross sections from crossed beam imaging experiments to disentangle competing reaction pathways. The general term pathways includes different effects of specific reactant quantum states on the atomistic mechanism to the competition of different product channels.

To form or not to form a reaction complex: exploring ion-molecule reactions between C3H4 isomers and Xe+ and O2.

Ion-molecule reactions are an essential contributor to the chemistry of a diverse range of environments. While a great deal of work has been done to understand the fundamental mechanisms driving these reactions, there is still much more to discover. Here, we expand upon prior studies on ion-molecule reactions involving two isomers of C3H4, allene (H2C3H2) and propyne (H3C3H). Specifically, we probe the previously observed isomeric dependent reactivity of these molecules by reacting them with two ions with nearly identical ionization potentials, Xe+ and O2+. Our goal is to determine if the isomer-dependent reaction mechanisms previously observed are universal for C3H4 or if they depend on the ion character as well. Through the combination of experimental measurements and theoretical calculations, we found that both isomeric structure and identity of the ion contribute to the propensity of a reaction complex forming or for only long-range charge transfer to occur.

Gas-phase synthesis of [OU-X]+ (X = Cl, Br and I) from a UO22+ precursor using ion-molecule reactions and an [OUCH]+ intermediate.

Difficulty in the preparation of gas-phase ions that include U in middle oxidation states(III,IV) have hampered efforts to investigate intrinsic structure, bonding and reactivity of model species. Our group has used preparative tandem mass spectrometry (PTMS) to synthesize a gas-phase U-methylidyne species, [OUCH]+, by elimination of CO from [UO2(CCH)]+ [M. J. van Stipdonk, I. J. Tatosian, A. C. Iacovino, A. R. Bubas, L. Metzler, M. C. Sherman and A. Somogyi, J. Am. Soc. Mass Spectrom., 2019, 30, 796-805], which has been used as an intermediate to create products such as [OUN]+ and [OUS]+ by ion-molecule reactions. Here, we investigated the reactions of [OUCH]+ with a range of alkyl halides to determine whether the methylidyne is a also a useful intermediate for production and study of the oxy-halide ions [OUX]+, where X = Cl, Br and I, formally U(IV) species for which intrinsic reactivity data is relatively scarce. Our experiments demonstrate that [OUX]+ is the dominant product ion generated by reaction [OUCH]+ with neutral regents such as CH3Cl, CH3CH2Br and CH2CHCH2I.

New light on the imbroglio surrounding the C8H+6 isomers formed from ionized azulene and naphthalene using ion-molecule reactions.

Most polycyclic aromatic hydrocarbons (PAHs) can isomerize with internal energies near to or below the dissociation threshold. The C10H+8 group of ions, made up of the naphthalene (Naph+) and the azulene (Azu+) radical cations, is a prototypical example. C8H+6 isomers are important species in the growth kinetics and formation of complex organic molecules, and more generally fragments from larger PAHs, yet information about C8H+6 structures is scarce and contradictory. Here, ion-molecule reactions were carried out and the tunable photoionization chemical monitoring technique was used to probe the C8H+6 isomers formed upon C2H2-loss from Naph+ and Azu+. The experimental findings were interpreted with the support of ab initio and kinetics calculations. To facilitate the interpretation of these data, chemical reactivity starting from phenylacetylene (PA) was studied. It was found that most of the C8H+6 ions formed from C10H8, in a timescale of 40 μs, are PA+ in the vicinity of the dissociation threshold. No evidence of the pentalene radical cation (PE+) was observed and explanations to reconcile previous results are presented.

Ion molecule reactions in the HBr+ + CH4 system: a combined experimental and theoretical study.

Reactions in the system HBr+ + CH4 have been investigated inside a guided ion-beam apparatus under single-collision conditions. The HBr+ is vibrational and rotational state selected in the electronic X2Π1/2 state created by (2+1)-REMPI. Due to the exitation scheme employed different rotational states of the HBr+ are accessible. Four reaction channels have been observed. The cross section, σ, for the exothermic proton transfer channel (PT) decreases with increasing collision energy, steeper than predicted by the Langevin model. The cross section also decreases with increasing rotational energy in the HBr+, with the effect of the rotational energy being stronger than that of translational energy. The cross section for the endothermic charge transfer (CT) increased with increasing collision energy. The energy dependence is well reproduced by a simple line of center (loc) model. Although the bromine transfer (BT) is exothermic the observed cross section increased with increasing collision energy due to an activation barrier on the potential energy surface (PES). Analysis by a modified loc model suggest the relevance of an angle dependence of σ. The cross section for the endothermic hydrogen atom abstraction (HA) exhibits a maximum at 2 eV Ecm. The measured cross sections are rationalized by means of reaction dynamics simulations which show good agreement with the experimental cross sections. The dynamics simulations are carried out with a machine learning potential that is developed and benchmarked with ab initio molecular dynamics simulation. The absolute cross sections predicted by reaction dynamics simulations are well within the same order of magnitude while reproducing the trends over three different collision energies for all four reaction channels. Furthermore, the simulations demonstrate various reaction mechanisms for these reaction channels, including a very interesting HBr+ orientation selectivity for the BT reaction channel.

Growth mechanism of aromatic prebiotic molecules: insights from different processes of ion-molecule reactions in benzonitrile-ammonia and benzonitrile-methylamine clusters.

Benzonitrile (BN, C6H5CN) has been detected in the cold molecular cloud Taurus molecular cloud-1 (TMC-1) in 2018, which is suggested to be a precursor in the formation of more complex nitrogen-containing aromatic interstellar compounds. In this study, we utilized mass-selected infrared (IR) photodissociation spectroscopy and quantum chemical calculations to investigate the structures and gaseous ion-molecule reactions of benzonitrile-ammonia (BN-NH3) and benzonitrile-methylamine (BN-MA) clusters. The spectral observations indicate that the cyclic hydrogen bonding structure predominates in both neutral clusters. After VUV (118 nm) single-photon ionization, a new C-N covalent bond formed between BN and NH3 in the (BN-NH3)+ cluster. However, proton sharing constitutes the primary structure of the (BN-MA)+ cluster. The two nitrogen-containing interstellar molecules react with BN to yield distinct products due to difference in charge distribution and molecular polarity in the ionized clusters. The reactions of BN with other molecules contribute to our understanding of the growth mechanisms of complex interstellar molecules.

Dynamics of carbene formation in the reaction of methane with the tantalum cation in the gas phase.

The controlled activation of methane has drawn significant attention throughout various disciplines over the last few decades. In gas-phase experiments, the use of model systems with reduced complexity compared to condensed-phase catalytic systems allows us to investigate the intrinsic reactivity of elementary reactions down to the atomic level. Methane is rather inert in chemical reactions, as the weakening or cleavage of a C-H bond is required to make use of methane as C1-building block. The simplest model system for transition-metal-based catalysts is a mono-atomic metal ion. Only a few atomic transition-metal cations activate methane at room temperature. One of the most efficient elements is tantalum, which forms a carbene and releases molecular hydrogen in the reaction with methane: Ta+ + CH4 → TaCH2+ + H2. The reaction takes place at room temperature due to efficient intersystem crossing from the quintet to the triplet surface, i.e., from the electronic ground state of the tantalum cation to the triplet ground state of the tantalum carbene. This multi-state reactivity is often seen for reactions involving transition-metal centres, but leads to their theoretical treatment being a challenge even today. Chemical reactions, or to be precise reactive collisions, are dynamic processes making their description even more of a challenge to experiment and theory alike. Experimental energy- and angle-differential cross sections allow us to probe the rearrangement of atoms during a reactive collision. By interpreting the scattering signatures, we gain insight into the atomistic mechanisms and can move beyond stationary descriptions. Here, we present a study combining collision energy dependent experimentally measured differential cross sections with ab initio calculations of the minimum energy pathway. Product ion velocity distributions were recorded using our crossed-beam velocity map imaging experiment dedicated to studying transition-metal ion molecule reactions. TaCH2+ velocity distributions reveal a significant degree of indirect dynamics. However, the scattering distributions also show signatures of rebound dynamics. We compare the present results to the oxygen transfer reaction between Ta+ and carbon dioxide, which we recently studied.

Reactions of gas-phase uranyl formate/acetate anions: reduction of carboxylate ligands to aldehydes by intra-complex hydride attack.

In a previous study, electrospray ionization, collision-induced dissociation (CID), and gas-phase ion-molecule reactions were used to create and characterize ions derived from homogeneous precursors composed of a uranyl cation (UVIO22+) coordinated by either formate or acetate ligands [E. Perez, C. Hanley, S. Koehler, J. Pestok, N. Polonsky and M. Van Stipdonk, Gas phase reactions of ions derived from anionic uranyl formate and uranyl acetate complexes, J. Am. Soc. Mass Spectrom., 2016, 27, 1989-1998]. Here, we describe a follow-up study of anionic complexes that contain a mix of formate and acetate ligands, namely [UO2(O2C-CH3)2(O2C-H)]- and [UO2(O2C-CH3)(O2C-H)2]-. Initial CID of either anion causes decarboxylation of a formate ligand to create carboxylate-coordinated U-hydride product ions. Subsequent CID of the hydride species causes elimination of acetaldehyde or formaldehyde, consistent with reactions that include intra-complex hydride attack upon bound acetate or formate ligands, respectively. Density functional theory (DFT) calculations reproduce the experimental observations, including the favored elimination of formaldehyde over acetaldehyde by hydride attack during CID of [UO2(H)(O2C-CH3)(O2C-H)]-. We also discovered that MSn CID of the acetate-formate complexes leads to generation of the oxyl-methide species, [UO2(O)(CH3)]-, which reacts with H2O to generate [UO2(O)(OH)]-. DFT calculations support the observation that formation of [UO2(O)(OH)]- by elimination of CH4 is favored over H2O addition and rearrangement to create [UO2(OH)2(CH3)]-.

Time-varying mechanism of ion composition in a pulse-modulated Ar/C4F8/O2 dual-frequency capacitively coupled plasma

The time-varying mechanism of the positive-ion composition in a pulse-modulated Ar/C4F8/O2 dual-frequency capacitively coupled plasma was investigated in detail using a quadrupole mass spectrometer equipped with an electrostatic energy analyzer. Time-resolved measurements of the ion composition with respect to the pulse-off period ( Toff ) revealed that the electron temperature ( Te ) just after turning on the pulse is an important factor in determining the ratio of the ionization rates of the Ar+ and C x F y + ions. The time-varying phenomenon of the ion composition was also investigated through a numerical analysis based on the particle balance model, considering the production and loss rates of ions, ion–ion recombination processes, and ion–molecule reactions. When the VHF power ( PVHF ) was increased, a decrease in the ambipolar diffusion loss time constants of the ions ( τlossi ) was observed, and the change in electronegativity was pointed out as the cause of this phenomenon.

Generation and reactivity of gas-phase phenyloxenium ion

Phenyloxenium ion (POI) is an important intermediate in organic reactions, however, its generation and reactivity have not been extensively investigated. In this study, POI is produced in the gas phase by electrospray ionization tandem mass spectrometry (ESI-MS/MS), isolated for gas phase ion-molecule reactions, and used theoretical calculations to reveal mechanisms to those reactions. It forms adduct ions with H2O, methanol, ethanol, benzene, and toluene, although the structures of the adduct ions are not well-resolved. In contrast, ortho-cyclization with nitriles has been verified by the reaction with acetonitrile and theoretical calculation. Further, Hydride transfer reaction during the reaction with tetrahydrofuran in the gas phase led to experimental values of the hydride affinity and electronic state of POI. Electron transfer studies revealed that the ionization potential of phenoxy radical locates in the range of 8.01–9.19 eV, in line with the calculated value of 8.60 eV for the singlet state POI.

Enhanced Total Vibrational Excitation Yield in a Slow Narrow-Pulsed Hydrogen Molecular Beam.

High-efficiency excitation of a molecular beam is critical for investigating state-selected chemistry. However, achieving vibrational excitation of the entire beam for Raman-active molecules such as H2 proves extremely challenging, primarily because laser pulses are much shorter than the molecular beam. In this study, we achieve a total excitation efficiency of over 20% by employing stimulated Raman pumping (SRP) in a slow, narrow-pulsed molecular beam. Through optimizing the intensity and spot shape of the SRP lasers, we attain saturated excitation within the laser crossing region. Furthermore, by reducing the beam velocity and narrowing the beam pulse using a cold valve and a fast chopper, we significantly enhance the total excitation yield. COMSOL simulation and a newly developed model reveal that a critical velocity allows the chopper to block unexcited molecules and reserve most of the excited ones from the beam, resulting in the highest overall excitation yield. This innovative setup opens new possibilities for state-selected experiments in surface science and ion-molecule reaction dynamics, particularly involving weak transitions and pulsed lasers.

Direct production of molecular oxygen from carbon dioxide and helium ion collisions

The prebiotic mechanism to produce molecular oxygen (O2) in carbon dioxide (CO2)-rich planetary atmospheres is of great importance in understanding astrochemical reactions and is potentially relevant to the origin of life on Earth. Here, we demonstrate that, aside from the direct productions of O2 by photodissociation and dissociative electron attachment, the low-energy ion-molecule reaction between cationic helium in solar winds and molecular CO2 is a noticeable mechanism. Branching ratios of the reaction channels are determined, and their absolute cross-sections are estimated accordingly. The present findings represent a further, indispensable step towards fully understanding the origins of atmospheric O2.

Computational analysis of an electrostatic separator design for removal of volatile organic compounds from indoor air

ABSTRACT Concentrations of volatile organic compounds (VOCs) in air can be reduced in electrostatic separators where VOCs are ionized using ion-molecule reactions, extracted using electric fields, and eliminated in a waste flow. Embodiments for such separator technology have been explored in only a few studies, despite the possible advantage of purification without adsorbent filters. In one design, based on ionization of VOCs in positive polarity with hydrated protons as reactant ions, efficiencies for removal were measured as 30–40% . The results were fitted to a one-dimensional convective diffusion model requiring an unexpectedly high production rate of reactant ions to match both the model and data. A realistic rate of reactant ion production was used in finite element method simulations (COMSOL) and demonstrated that low removal efficiency could be attributed to non-uniform patterns of sample flow and to incomplete mixing of VOCs with reactant ions. In analysis of complex systems, such as this model, even limited computational modeling can outperform a pure analytical approach and bring insights into limiting factors or system bottlenecks. Implications: In this work, we applied modern computational methods to understand the performance of an air purifier based on electrostatics and ionized volatile organic compounds (VOCs). These were described in the publication early 2000s. The model presented was one-dimensional and did not account for the effects of flow. In our multiphysics finite element models, the efficiency and operation of the filter is better explained by the patterns of flow and flow influences on ion distributions in electric fields. In general, this work helps using and applying computational modelling to understand and improve the performance bottlenecks in air purification system designs.