Zero-Point-Energy Driven Isotopic Exchange of the [H3O]- anion Probed by Mid-Infrared Action Spectroscopy

We present the first observation of vibrational transitions in the [H3O]- anion, an intermediate in the anion-molecule reaction of water, H2O, and hydride, H-, using a laser-induced isotopic H/D exchange reaction action spectroscopy scheme applied to anions. The observed bands are assigned as the fundamental and first overtone of the H2O-H- vibrational stretching mode, based on anharmonic calculations within the vibrational perturbation theory and vibrational configuration interaction. Although the D2O·D- species has the lowest energy, our experiments confirm the D2O·H- isotope to be a sink of the H/D exchange reaction. Ab initio calculations corroborate that the formation of D2O·H- is favored, as the zero-point-energy difference is larger between D2 and H2 than between D2O·H- and D2O·D-.

Numerical Analysis and Quantification of Transfer Efficiency Coupled with Capillary and Quadrupole Ion Guide in an API-MS System

Ion trajectory simulation is a significant and useful tool for understanding ion transfer mechanisms within the first vacuum region of the atmospheric pressure ionization mass spectrometer (API-MS). However, the complex dynamic gas field and wide pressure range lead to inaccurate simulation and huge computational costs. In this work, a novel electrohydrodynamic simulation called the statistical diffusion-hard-sphere (SDHS) mixed collision model was developed for characterizing the ion trajectories. For the first time, the influence of the dynamic pressure on the ion trajectory is considered for simulation, which helps to avoid an intolerable computational cost. Comparing with the conventional Monte Carlo collision model, the SDHS method helps to improve the calculation accuracy of ion trajectories under the first vacuum region and reduce the computational cost for at least 12-folds. Simulation results showed that the maximum ion loss came from the gap of the electrodes. The distance of the capillary-quadrupole ion guide was also a non-negligible factor. The trend of quantitative experimental results matches the SDHS simulation results. The maximum ion transfer efficiencies of quantitative experiment and simulation were 55% and 52%, respectively. Moreover, three ions, caffeine, reserpine, and Ultramark 1621, were measured for evaluating the applicability of SDHS in real API-MS. The trend of experimental results showed good agreement with that of computation. And the results of caffeine further illustrated the reason that the small mass ion transfer efficiency decreased with increasing radio frequency voltage. SDHS method is expected to be useful in the design of ion guides for further improvement of the sensitivity of API-MS.

The bond energy of UN+: Guided ion beam studies of the reactions of U+ with N2 and NO

A guided ion beam tandem mass spectrometer was used to study the reactions of U+ with N2 and NO. Reaction cross sections were measured over a wide range of energy for both systems. In each reaction, UN+ is formed by an endothermic process, thereby enabling the direct measurement of the threshold energy and determination of the UN+ bond dissociation energy. For the reaction of U+ + N2, a threshold energy (E0) of 4.02 ± 0.11 eV was measured, leading to D0 (UN+) = 5.73 ± 0.11 eV. The reaction of U+ + NO yields UO+ through an exothermic, barrierless process that proceeds with 94 ± 23% efficiency at the lowest energy. Analysis of the endothermic UN+ cross section in this reaction provides E0 = 0.72 ± 0.11 eV and, therefore, D0 (UN+) = 5.78 ± 0.11 eV. Averaging the values obtained from both reactions, we report D0 (UN+) = 5.76 ± 0.13 eV as our best value (uncertainty of two standard deviations). Combined with precise literature values for the ionization energies of U and UN, we also derive D0 (UN) = 5.86 ± 0.13 eV. Both bond dissociation energies agree well with high-level theoretical treatments in the literature. The formation of UN+ in reaction of U+ with NO also exhibits a considerable increase in reaction probability above ∼3 eV. Theory suggests that this may be consistent with the formation of UN+ in excited quintet spin states, which we hypothesize are dynamically favored because the number of 5f electrons in reactants and products is conserved.

Unveiling Quantum Interference in the D+ + H2 Nonadiabatic Reaction Dynamics at Low Collision Energies

Fully converged nonadiabatic dynamics calculations of the D+ + H2 → H+ + HD reaction are performed at low temperatures using the time-dependent wave packet approach based on a set of precise 3 × 3 diabatic potential energy surfaces (PESs) ( Phys. Chem. Chem. Phys., 2021, 23, 7735-7747, DOI: 10.1039/D0CP04100A). The D+ + H2 reaction is mediated by a dense manifold of resonances associated with the deep potential well on the ground-state PES. The calculated results show that the nonadiabatic coupling can affect the resonance positions, deviating from the expectation based solely on adiabatic considerations. Furthermore, significant forward-backward asymmetry in total differential cross sections (DCSs) is revealed, which is markedly influenced by nonadiabatic effects. The nonadiabatic effects not only affect the contribution of partial waves in the reaction but also make the interference patterns in the DCSs change significantly.

A 22-pole radiofrequency ion trap setup for laboratory astrophysical studies

The formation of large interstellar molecules starting from small reactants constitutes the bottom-up approach in astrochemistry. An experimental setup wherein the ionic reactant is prepared and allowed to react with neutral reactants within a confined interaction space is most desirable for this approach. Here, we present our efforts in constructing a 22-pole radio-frequency ion trap experimental setup that could act as a reaction chamber for the neutral reactant and trapped ions. A compact piezo-based pulsed supersonic expansion discharge source was developed to achieve efficient production of anions, particularly metal-bearing ions. In addition, two other ion sources, namely, the electron impact ion source and the plasma supersonic discharge ion source, were developed to cater to the production of specific ions. The geometry of this experimental setup facilitates photo excitation of trapped ions. The trapping efficiency was studied by trapping SF5+ and SF6- for a few seconds. The control exhibited by various parameters on the efficiency of the trapping is discussed in detail. Potential studies that could be performed with this new experimental setup are also discussed.

Quantitative Aspects of Gas-Phase Metal Ion Chemistry: Conservation of Spin, Participation of f Orbitals, and C-H Activation and C-C Coupling

In this Featured Article, I reflect on over 40 years of guided ion beam tandem mass spectrometry (GIBMS) studies involving atomic metal cations and their clusters throughout the periodic table. Studies that have considered the role of spin conservation (or lack thereof) are a primary focus with a quantitative assessment of the effects examined. A need for state-specific studies of heavier elements is noted, as is a more quantitative assessment of spin-orbit interactions in reactivity. Because GIBMS experiments explicitly evaluate the kinetic energy dependence of reactions over a wide range, several interesting and unusual observations are highlighted. More detailed studies of such unusual reaction events would be welcome. Activation of C-H bonds and ensuing C-C coupling events are reviewed, with future work encouraged. Finally, studies of lanthanides and actinides are examined with an eye on understanding the role of f orbitals in the chemistry, both as participants (or not) in the bonding and as sources/sinks of electron density. This area seems to be ripe for more quantitative experiments.

Advances in high-resolution mass spectrometry techniques for analysis of high mass-to-charge ions

A major challenge in modern mass spectrometry (MS) is achieving high mass resolving power and accuracy for precision analyses in high mass-to-charge (m/z) regions. To advance the capability of MS for increasingly demanding applications, understanding limitations of state-of-the-art techniques and their status in applied sciences is essential. This review summarizes important instruments in high-resolution mass spectrometry (HRMS) and related advances to extend their working range to high m/z regions. It starts with an overview of HRMS techniques that provide adequate performance for macromolecular analysis, including Fourier-transform, time-of-flight (TOF), quadrupole-TOF, and related data-processing techniques. Methodologies and applications of HRMS for characterizing macromolecules in biochemistry and material sciences are summarized, such as top-down proteomics, native MS, drug discovery, structural virology, and polymer analyses.

Vibrational Predissociation Spectra of C2 N- and C3 N- : Bending and Stretching Vibrations

We present infrared predissociation spectra of C2 N- (H2 ) and C 3 N- (H2 ) in the 300-1850 cm-1 range. Measurements were performed using the FELion cryogenic ion trap end user station at the Free Electron Lasers for Infrared eXperiments (FELIX) laboratory. For C2 N- (H2 ), we detected the CCN bending and CC-N stretching vibrations. For the C3 N- (H2 ) system, we detected the CCN bending, the CC-CN stretching, and multiple overtones and/or combination bands. The assignment and interpretation of the presented experimental spectra is validated by calculations of anharmonic spectra within the vibrational configuration interaction (VCI) approach, based on potential energy surfaces calculated at explicitly correlated coupled cluster theory (CCSD(T)-F12/cc-pVTZ-F12). The H2 tag acts as an innocent spectator, not significantly affecting the C2,3 N- bending and stretching mode positions. The recorded infrared predissociation spectra can thus be used as a proxy for the vibrational spectra of the bare anions.

Influence of 2'-Modifications (O-Methylation, Fluorination, and Stereochemical Inversion) on the Base Pairing Energies of Protonated Cytidine Nucleoside Analogue Base Pairs: Implications for the Stabilities of i-Motif Structures

Naturally occurring and chemically engineered modifications are among the most powerful strategies explored for fine-tuning the conformational characteristics and intrinsic stability of nucleic acids topologies. Modifications at the 2'-position of the ribose or 2'-deoxyribose moieties differentiate nucleic acid structures and have a significant impact on their electronic properties and base-pairing interactions. 2'-O-Methylation, a common post-transcriptional modification of tRNA, is directly involved in modulating specific anticodon-codon base-pairing interactions. 2'-Fluorinated and arabino nucleosides possess novel and beneficial medicinal properties and find use as therapeutics for treating viral diseases and cancer. However, the potential to deploy 2'-modified cytidine chemistries for tuning i-motif stability is largely unknown. To address this knowledge gap, the effects of 2'-modifications including O-methylation, fluorination, and stereochemical inversion on the base-pairing interactions of protonated cytidine nucleoside analogue base pairs, the core stabilizing interactions of i-motif structures, are examined using complementary threshold collision-induced dissociation techniques and computational methods. The 2'-modified cytidine nucleoside analogues investigated here include 2'-O-methylcytidine, 2'-fluoro-2'-deoxycytidine, arabinofuranosylcytosine, 2'-fluoro-arabinofuranosylcytosine, and 2',2'-difluoro-2'-deoxycytidine. All five 2'-modifications examined here are found to enhance the base-pairing interactions relative to the canonical DNA and RNA cytidine nucleosides with the greatest enhancements arising from 2'-O-methylation and 2',2'-difluorination, suggesting that these modifications should well be tolerated in the narrow grooves of i-motif conformations.

Charged Ice Particle Beams with Selected Narrow Mass and Kinetic Energy Distributions

Small ice particles play an important role in atmospheric and extraterrestrial chemistry. Circumplanetary ice particles that are encountered by space probes at hypervelocities play a critical role in the determination of surface and subsurface properties of their source bodies. Here we present an apparatus for the generation of low-intensity beams of single mass-selected charged ice particles under vacuum. They are produced via electrospray ionization of water at atmospheric pressure and undergo evaporative cooling when transferred to vacuum through an atmospheric vacuum interface. m/z selection is achieved through two subsequent quadrupole mass filters operated in the variable-frequency mode within a range of m/z values between 8 × 10⁴ and 3 × 10⁷. Velocity and charge of the selected particles are measured using a nondestructive single-pass image charge detector. From the known electrostatic acceleration potentials and settings of the quadrupoles the particle masses could be obtained and be accurately controlled. It has been shown that the droplets are frozen within the transit time of the apparatus such that ice particles are present after the quadrupole stages and finally detected. The demonstrated correspondence between particle mass and specific quadrupole potentials in this device allows preparation of beams of single particles with a repetition rate between 0.1 and 1 Hz with various diameter distributions from 50 to 1000 nm at 30-250 eV of kinetic energy per charge. This corresponds to velocities and particle masses quickly available between 600 m/s (80 nm) and 50 m/s (900 nm) and particle charge numbers (positive) between 10³ and 10⁴[e], depending upon size.

Energetics and mechanisms for decomposition of cationized amino acids and peptides explored using guided ion beam tandem mass spectrometry

Fragmentation studies of cationized amino acids and small peptides as studied using guided ion beam tandem mass spectrometry (GIBMS) are reviewed. After a brief examination of the key attributes of the GIBMS approach, results for a variety of systems are examined, compared, and contrasted. Cationization of amino acids, diglycine, and triglycine with alkali cations generally leads to dissociations in which the intact biomolecule is lost. Exceptions include most lithiated species as well as a few examples for sodiated and one example for potassiated species. Like the lithiated species, cationization by protons leads to numerous dissociation channels. Results for protonated glycine, cysteine, asparagine, diglycine, and a series of tripeptides are reviewed, along with the thermodynamic consequences that can be gleaned. Finally, the important physiological process of the deamidation of asparagine (Asn) residues is explored by the comparison of five dipeptides in which the C-terminal partner (AsnXxx) is altered. The GIBMS thermochemistry is shown to correlate well with kinetic results from solution phase studies.

Ion Mobility Mass Spectrometry (IM-MS) for Structural Biology: Insights Gained by Measuring Mass, Charge, and Collision Cross Section

The investigation of macromolecular biomolecules with ion mobility mass spectrometry (IM-MS) techniques has provided substantial insights into the field of structural biology over the past two decades. An IM-MS workflow applied to a given target analyte provides mass, charge, and conformation, and all three of these can be used to discern structural information. While mass and charge are determined in mass spectrometry (MS), it is the addition of ion mobility that enables the separation of isomeric and isobaric ions and the direct elucidation of conformation, which has reaped huge benefits for structural biology. In this review, where we focus on the analysis of proteins and their complexes, we outline the typical features of an IM-MS experiment from the preparation of samples, the creation of ions, and their separation in different mobility and mass spectrometers. We describe the interpretation of ion mobility data in terms of protein conformation and how the data can be compared with data from other sources with the use of computational tools. The benefit of coupling mobility analysis to activation via collisions with gas or surfaces or photons photoactivation is detailed with reference to recent examples. And finally, we focus on insights afforded by IM-MS experiments when applied to the study of conformationally dynamic and intrinsically disordered proteins.

Periodic trends in the hydration energies and critical sizes of alkaline earth and transition metal dication water complexes

This review encompasses guided ion beam tandem mass spectrometry studies of hydrated metal dication complexes. Metals include the Group 2 alkaline earths (Mg, Ca, Sr, and Ba), late first-row transition metals (Mn, Fe, Co, Ni, Cu, and Zn), along with Cd. In all cases, threshold collision-induced dissociation experiments are used to quantitatively determine the sequential hydration energies for M2+ (H2 O)x complexes ranging in size from one to 11 water molecules. Periodic trends in these bond dissociation energies are examined and discussed. Values are compared to other experimental results when available. In addition to dissociation by simple water ligand loss, complexes at a select size (which differs from metal to metal) are also observed to undergo charge separation to yield a hydrated metal hydroxide cation and a hydrated proton. This leads to the concept of a critical size, xcrit , and the periodic trends in this value are also discussed.

Guided Ion Beam Studies of the Dy + O → DyO+ + e- Chemi-ionization Reaction Thermochemistry and Dysprosium Oxide, Carbide, Sulfide, Dioxide, and Sulfoxide Cation Bond Energies

Guided ion beam tandem mass spectrometry (GIBMS) was used to measure the kinetic energy dependent product ion cross sections for reactions of the lanthanide metal dysprosium cation (Dy⁺) with O₂, SO₂, and CO and reactions of DyO⁺ with CO, O₂, and Xe. DyO⁺ is formed through an exothermic process when Dy⁺ reacts with O₂, whereas all other processes observed are found to be endothermic. The kinetic energy dependences of these cross sections were analyzed to yield 0 K bond dissociation energies (BDEs) for DyO⁺, DyC⁺, DyS⁺, DyO₂⁺, and DySO⁺. The 0 K BDE for DyO⁺ is determined to be 5.60 ± 0.02 eV from the weighted average of six independent thresholds, which are dominated by the slightly endothermic reaction of Dy⁺ with SO₂. Combined with the well-established Dy ionization energy (IE), this value indicates that the chemi-ionization reaction, Dy + O → DyO⁺ + e^-, is endothermic by 0.33 ± 0.02 eV. Theoretical BDEs for Dy⁺-O, Dy⁺-C, Dy⁺-S, ODy⁺-O, and Dy⁺-SO were calculated at several levels of theory and basis sets for comparison with experiment with reasonable agreement achieved.

Influence of 5-Halogenation on the Base-Pairing Energies of Protonated Cytidine Nucleoside Analogue Base Pairs: Implications for the Stabilities of Synthetic i-Motif Structures for DNA Nanotechnology Applications

DNA nanotechnology has been employed to develop devices based on i-motif structures. The protonated cytosine-cytosine base pairs that stabilize i-motif conformations are favored under slightly acidic conditions. This unique property has enabled development of the first DNA molecular motor driven by pH changes. The ability to alter the stability and pH transition range of such DNA molecular motors is desirable. Understanding how i-motif structures are influenced by modifications, and which modifications enhance stability and/or affect the pH characteristics, are therefore of great interest. Here, the influence of 5-halogenation of the cytosine nucleobases on the base pairing of protonated cytidine nucleoside analogue base pairs is examined using complementary threshold collision-induced dissociation techniques and computational methods. The nucleoside analogues examined here include the 5-halogenated forms of the canonical DNA and RNA cytidine nucleosides. Comparisons among these systems and to the analogous canonical base pairs previously examined enable the influence of 5-halogenation and the 2'-hydroxy substituent on the base pairing to be elucidated. 5-Halogenation of the cytosine nucleobases is found to enhance the strength of base pairing of DNA base pairs and generally weakens the base pairing for RNA base pairs. Trends in the strength of base pairing indicate that both inductive and polarizability effects influence the strength of base pairing. Overall, the present results suggest that 5-halogenation, and in particular, 5-fluorination and 5-iodination, provide effective means of stabilizing DNA i-motif conformations for applications in nanotechnology, whereas only 5-iodination is effective for stabilizing RNA i-motif conformations but the enhancement in stability is less significant.

Potassium Binding Interactions with Aliphatic Amino Acids: Thermodynamic and Entropic Effects Analyzed via a Guided Ion Beam and Computational Study

Noncovalent interactions between alkali metals and amino acids are critical for many biological processes, especially for proper function of protein ion channels; however, many precise binding affinities between alkali metals and amino acids still need to be measured. This study addresses this need by using threshold collision-induced dissociation with a guided ion beam tandem mass spectrometer to measure binding affinities between potassium cations and the aliphatic amino acids: Gly, Ala, hAla, Val, Leu, and Ile. These measurements are supplemented by theoretical calculations and include commentary on effects of enthalpy, entropy, and structural preference. Notably, all levels of theory indicate that the lowest-lying isomers at 298 K have K⁺ binding to the carbonyl oxygen in either a monodentate ([CO]) or bidentate ([CO,OH]) fashion, isomers that are linked in a double-well potential. This complicates the analysis of the data, although does not greatly influence the final results. Analysis of the resulting cross sections includes accounting for multiple ion-molecule collisions, internal energy of reactant ions, and unimolecular decay rates. The resulting experimental bond dissociation energies generally increase as the polarizability of the amino acid increases, results that agree well with quantum chemical calculations done at the B3LYP, B3P86, and MP2(full) levels of theory, with B3LYP-GD3BJ predicting systematically larger values.

Rotational Cooling Effect on the Rate Constant in the CH3F + Ca+ Reaction at Low Collision Energies

The rotational cooling effect on the reaction rate constant of the gas-phase ion-polar-molecule reaction CH₃F + Ca⁺ → CH₃ + CaF⁺ was experimentally studied at low collision energies. Fluoromethane molecules showed higher reactivity as the rotational temperature decreased. The experimental rate constants were compared with the capture rate constants which were obtained by the Perturbed Rotational State (PRS) theory assuming the rotational level distribution corresponding to the experimental conditions. The PRS result shows a strong dependence of the capture rate constants on the rotational level distribution in accordance with the experimental findings. However, the PRS capture rate constants deviate from the measurement values as the average collision energy increases especially when the fluoromethane molecules are rotationally cooled far below room temperature. The present paper suggests that the rotational state distribution significantly affects the rate constants of ion-polar-molecule reactions and is one of the important issues to be considered in the study of molecular synthesis in the interstellar medium, where the thermal equilibrium is not necessarily established.

Navigate Flying Molecular Elephants Safely to the Ground: Mass-Selective Soft Landing up to the Mega-Dalton Range by Electrospray Controlled Ion-Beam Deposition

The prototype of a highly versatile and efficient preparative mass spectrometry system used for the deposition of molecules in ultrahigh vacuum (UHV) is presented, along with encouraging performance data obtained using four model species that are thermolabile or not sublimable. The test panel comprises two small organic compounds, a small and very large protein, and a large DNA species covering a 4-log mass range up to 1.7 MDa as part of a broad spectrum of analyte species evaluated to date. Three designs of innovative ion guides, a novel digital mass-selective quadrupole (dQMF), and a standard electrospray ionization (ESI) source are combined to an integrated device, abbreviated electrospray controlled ion-beam deposition (ES-CIBD). Full control is achieved by (i) the square-wave-driven radiofrequency (RF) ion guides with steadily tunable frequencies, including a dQMF allowing for investigation, purification, and deposition of a virtually unlimited m/z range, (ii) the adjustable landing energy of ions down to ∼2 eV/z enabling integrity-preserving soft landing, (iii) the deposition in UHV with high ion beam intensity (up to 3 nA) limiting contaminations and deposition time, and (iv) direct coverage control via the deposited charge. The maximum resolution of R = 650 and overall efficiency up to T_total = 4.4% calculated from the solution to UHV deposition are advantageous, whereby the latter can be further enhanced by optimizing ionization performance. In the setup presented, a scanning tunneling microscope (STM) is attached for in situ UHV investigations of deposited species, demonstrating a selective, structure-preserving process and atomically clean layers.

Reactions of Atomic Thorium and Uranium Cations with SF6 Studied by Guided Ion Beam Tandem Mass Spectrometry

The fundamental chemistry of the thorium and uranium fluorides continues to be an area of interest because of the use of thorium and uranium fluoride compounds in nuclear fuel systems. Here, we study the reaction of thorium cations with sulfur hexafluoride for the first time and revisit the reaction of uranium cations with sulfur hexafluoride. By using guided ion beam tandem mass spectrometry, we explore the reaction pathways that become accessible well above thermal energies (E ∼ 0.04 eV). Overall, we find that both Th⁺ and U⁺ react very efficiently with SF₆, approaching the collision limit at both thermal and elevated energies. The primary products observed at low energies include Th_1-3⁺, UF_1-4⁺, and SF_1-4⁺, all of which are formed in barrierless, exothermic processes. SF₅⁺ was also observed, although the pressure dependence of this channel reveals that SF₅⁺ forms exothermically through secondary reactions, which the energy dependences suggest result from reactions between ThF₂⁺ and UF₃⁺ with SF₆. At higher energies, both AnF₃⁺ products are observed to decay to AnF⁺ + F₂, and both SF₄⁺ and SF₂⁺ exhibit cross sections with endothermic features. For both systems, the rise in SF₄⁺ can be attributed to a secondary collision between AnF⁺ with SF₆ on the basis of the pressure dependence of the SF₄⁺ channel at higher energies, and the rise in SF₂⁺ appears to result from the decomposition of SF₃⁺ to SF₂⁺ + F.

Thermochemistry and mechanisms of the Pt+ + SO2 reaction from guided ion beam tandem mass spectrometry and theory

The kinetic energy dependences of the reactions of Pt⁺ (²D_5/2) with SO₂ were studied using a guided ion beam tandem mass spectrometer and theory. The observed cationic products are PtO⁺ and PtSO⁺, with small amounts of PtS⁺, all formed in endothermic reactions. Modeling the kinetic energy dependent product cross sections allows determination of the product bond dissociation energies (BDEs): D₀(Pt⁺-O) = 3.14 ± 0.11 eV, D₀(Pt⁺-S) = 3.68 ± 0.31 eV, and D₀(Pt⁺-SO) = 3.03 ± 0.12 eV. The oxide BDE agrees well with more precise literature values, whereas the latter two results are the first such measurements. Quantum mechanical calculations were performed for PtO⁺, PtS⁺, PtO₂ ⁺, and PtSO⁺ at the B3LYP and coupled-cluster with single, double, and perturbative triple [CCSD(T)] levels of theory using the def2-XZVPPD (X = T, Q) and aug-cc-pVXZ (X = T, Q, 5) basis sets and complete basis set extrapolations. These theoretical BDEs agree well with the experimental values. After including empirical spin-orbit corrections, the product ground states are determined as PtO⁺ (⁴Σ_3/2), PtS⁺ (⁴Σ_3/2), PtO₂ ⁺ (²Σ_g ⁺), and PtSO⁺ (²A'). Potential energy profiles including intermediates and transition states for each reaction were also calculated at the B3LYP/def2-TZVPPD level. Periodic trends in the thermochemistry of the group 9 metal chalcogenide cations are compared, and the formation of PtO⁺ from the Pt⁺ + SO₂ reaction is compared with those from the Pt⁺ + O₂, CO₂, CO, and NO reactions.

Spectroscopic Detection of Cyano-Cyclopentadiene Ions as Dissociation Products upon Ionization of Aniline

The H-loss products (C₆H₆N⁺) from the dissociative ionization of aniline (C₆H₇N) have been studied by infrared predissociation spectroscopy in a cryogenic ion trap instrument at the free electron laser for infrared experiments (FELIX) laboratory. Broadband and narrow line width vibrational spectra in the spectral fingerprint region of 550–1800 cm^–1 have been recorded. The comparison to calculated spectra of the potential isomeric structures of the fragment ions reveals that the dominant fragments are five-membered cyano-cyclopentadiene ions. Computed C₆H₇N^•+ potential energy surfaces suggest that the dissociation path leading to H loss starts with an isomerization process, following a similar trajectory as the one leading to HNC loss. The possible presence of cyano-cyclopentadiene ions and related five-membered ring species in Titan’s atmosphere and the interstellar medium are discussed.

Activation of CO2 by Actinide Cations (Th+, U+, Pu+, and Am+) as Studied by Guided Ion Beam and Triple Quadrupole Mass Spectrometry

Reactions of CO₂ with Th⁺ have been studied using guided ion beam tandem mass spectrometry (GIBMS) and with An⁺ (An⁺ = Th⁺, U⁺, Pu⁺, and Am⁺) using triple quadrupole inductively coupled plasma mass spectrometry (QQQ-ICP-MS). Additionally, the reactions ThO⁺ + CO and ThO⁺ + CO₂ were examined using GIBMS. Modeling the kinetic energy-dependent GIBMS data allowed the determination of bond dissociation energies (BDEs) for D₀(Th⁺-O) and D₀(OTh⁺-O) that are in reasonable agreement with previous GIBMS measurements. The QQQ-ICP-MS reactions were studied at higher pressures where multiple collisions between An⁺ and the neutral CO₂ occur. As a consequence, both AnO⁺ and AnO₂⁺ products were observed for all An⁺ except Am⁺, where only AmO⁺ was observed. The relative abundances of the observed monoxides compared to the dioxides are consistent with previous reports of the AnO_n⁺ (n = 1, 2) BDEs. A comparison of the periodic trends of the group 4 transition metal, lanthanide (Ln), and actinide atomic cations in reactions with CO₂ (a formally spin-forbidden reaction for most M⁺ ground states) and O₂ (a spin-unrestricted reaction) indicates that spin conservation plays a minor role, if any, for the heavier Ln⁺ and An⁺ metals. Further correlation of Ln⁺ and An⁺ + CO₂ reaction efficiencies with the promotion energy (E_p) to the first electronic state with two valence d-electrons (E_p(5d²) for Ln⁺ and E_p(6d²) for An⁺) indicates that the primary limitation in the activation of CO₂ is the energetic cost to promote from the electronic ground state of the atomic metal ion to a reactive state.

Mass Spectrometry-Based Techniques to Elucidate the Sugar Code

Cells encode information in the sequence of biopolymers, such as nucleic acids, proteins, and glycans. Although glycans are essential to all living organisms, surprisingly little is known about the "sugar code" and the biological roles of these molecules. The reason glycobiology lags behind its counterparts dealing with nucleic acids and proteins lies in the complexity of carbohydrate structures, which renders their analysis extremely challenging. Building blocks that may differ only in the configuration of a single stereocenter, combined with the vast possibilities to connect monosaccharide units, lead to an immense variety of isomers, which poses a formidable challenge to conventional mass spectrometry. In recent years, however, a combination of innovative ion activation methods, commercialization of ion mobility-mass spectrometry, progress in gas-phase ion spectroscopy, and advances in computational chemistry have led to a revolution in mass spectrometry-based glycan analysis. The present review focuses on the above techniques that expanded the traditional glycomics toolkit and provided spectacular insight into the structure of these fascinating biomolecules. To emphasize the specific challenges associated with them, major classes of mammalian glycans are discussed in separate sections. By doing so, we aim to put the spotlight on the most important element of glycobiology: the glycans themselves.

Strong ortho/para effects in the vibrational spectrum of Cl-(H2)

The predissociation spectrum of the Cl-35(H₂) complex is measured between 450 and 800 cm^-1 in a multipole radiofrequency ion trap at different temperatures using the FELIX infrared free electron laser. Above a certain temperature, the removal of the Cl^-(p-H₂) para nuclear spin isomer by ligand exchange to the Cl^-(o-H₂) ortho isomer is suppressed effectively, thereby making it possible to detect the spectrum of this more weakly bound complex. At trap temperatures of 30.5 and 41.5 K, we detect two vibrational bands of Cl^-(p-H₂) at 510(1) and 606(1) cm^-1. Using accurate quantum calculations, these bands are assigned to transitions to the inter-monomer vibrational modes (v₁,v₂ ^l₂ ) = (0, 2⁰) and (1, 2⁰), respectively.

Theoretical description of electric fields in three-dimensional multipole ion traps

In this paper, the principle of forming the spatial distribution of the potential in multipole three-dimensional ion traps of a general type is considered. A matrix method for describing the electric fields in ion traps for the nth order of multipole is proposed. Typical electrode geometries for hexapole and octupole traps are considered.

Ion Guide for Improved Atmosphere to Mass Spectrometer Vacuum Ion Transfer

Various approaches for transmitting ions from atmosphere to the deep vacuum required for mass analysis have been developed with the goal to increase the ion to gas ratio while maintaining high ion transmission efficiency. Since the vast majority of ion losses occurs in the atmospheric pressure ion source, an effective way to improve sampling of those ions is to increase the atmosphere to vacuum aperture diameter. However, as the aperture diameter is increased, the resulting intense free jet gas expansion and subsequent gas beam can scatter ions in the first vacuum region. The interface described here provides an optimized flow field to the second vacuum stage, with a unique geometry to counter the ion losses from scattering collisions with the gas. Two additional differentially pumped quadrupole ion guides are used to further improve the ion to gas ratio, resulting in an ion transfer efficiency improvement of 5-6× over a two-stage differentially pumped interface with quadrupole ion guides. The interface also demonstrates efficient declustering and fragmentation capabilities beneficial for reducing background chemical noise.

Room-Temperature Methane Activation Mediated by Free Tantalum Cluster Cations: Size-by-Size Reactivity

The energetics of small cationic tantalum clusters and their gas-phase adsorption and dehydrogenation reaction pathways with methane are investigated with ion-trap experiments and spin-density-functional-theory calculations. Ta_n⁺ clusters are exposed to methane under multicollision conditions in a cryogenic ring electrode ion-trap. The cluster size affects the reaction efficiency and the number of consecutively dehydrogenated methane molecules. Small clusters (n = 1-4) dehydrogenate CH₄ and concurrently eliminate H₂, while larger clusters (n > 4) demonstrate only molecular adsorption of methane. Unique behavior is found for the Ta⁺ cation, which dehydrogenates consecutively up to four CH₄ molecules and is predicted theoretically to promote formation of a [Ta(CH₂-CH₂-CH₂)(CH₂)]⁺ product, exhibiting C-C coupled groups. Underlying mechanisms, including reaction-enhancing couplings between potential energy surfaces of different spin-multiplicities, are uncovered.

Near-resonant effects in the quantum dynamics of the H + H2 + → H2 + H+ charge transfer reaction and isotopic variants

The non-adiabatic quantum dynamics of the H + H₂ ⁺ → H₂ + H⁺ charge transfer reactions, and some isotopic variants, is studied with an accurate wave packet method. A recently developed 3 × 3 diabatic potential model is used, which is based on very accurate ab initio calculations and includes the long-range interactions for ground and excited states. It is found that for initial H₂ ⁺(v = 0), the quasi-degenerate H₂(v' = 4) non-reactive charge transfer product is enhanced, producing an increase in the reaction probability and cross section. It becomes the dominant channel from collision energies above 0.2 eV, producing a ratio between v' = 4 and the rest of v's, which that increase up to 1 eV. The H + H₂ ⁺ → H₂ ⁺ + H exchange reaction channel is nearly negligible, while the reactive and non-reactive charge transfer reaction channels are of the same order, except that corresponding to H₂(v' = 4), and the two charge transfer processes compete below 0.2 eV. This enhancement is expected to play an important vibrational and isotopic effect that needs to be evaluated. For the three proton case, the problem of the permutation symmetry is discussed when using reactant Jacobi coordinates.

Influence of a Hydroxyl Group on the Deamidation and Dehydration Reactions of Protonated Asparagine-Serine Investigated by Combined Spectroscopic, Guided Ion Beam, and Theoretical Approaches

Deamidation of asparaginyl (Asn) peptides is a spontaneous post-translational modification that plays a significant role in degenerative diseases and other biological processes under physiological conditions. In the gas phase, deamidation of protonated peptides is a major fragmentation channel upon activation by collision-induced dissociation. Here, we present a full description of the deamidation process from protonated asparagine-serine, [AsnSer+H]⁺, via infrared (IR) action spectroscopy and threshold collision-induced dissociation (TCID) experiments in combination with theoretical calculations. The IR results demonstrate that deamidation proceeds via bifurcating reaction pathways leading to furanone- and succinimide-type product ion structures, with a population analysis indicating the latter product dominates. Theory demonstrates that nucleophilic attack of the peptidyl amide oxygen onto the Asn side chain leads to furanone formation, whereas nucleophilic attack by the peptidyl amide nitrogen onto the Asn side-chain carbonyl carbon leads to the formation of the succinimide product structure. TCID experiments find that furanone formation has a threshold energy of 145 ± 12 kJ/mol and succinimide formation occurs with a threshold energy of 131 ± 12 kJ/mol, consistent with theoretical energies and with the spectroscopic results indicating that succinimide dominates. The results provide information regarding the inductive and steric effects of the Ser side chain on the deamidation process. The other major channel observed in the TCID experiments of [AsnSer+H]⁺ is dehydration, where a threshold energy of 104 ± 10 kJ/mol is determined. A complete IR and theoretical analysis of this pathway is also provided. As for deamidation, a bifurcating pathway is found with both dominant oxazoline and minor diketopiperazine products identified. Here, the Ser side chain is directly involved in both pathways.

Charge Transfer Processes for H + H2+ Reaction Employing Coupled 3D Wavepacket Approach on Beyond Born-Oppenheimer Based Ab Initio Constructed Diabatic Potential Energy Surfaces

The dynamics of the H + H₂⁺ reaction has been analyzed from the electronically first excited state of diabatic potential energy surfaces constructed by employing the Beyond Born-Oppenheimer theory [J. Chem. Phys. 2014, 141, 204306]. We have employed the coupled 3D time-dependent wavepacket formalism in hyperspherical coordinates for multisurface reactive scattering problems. To be specific, the charge transfer processes have been investigated extensively by calculating state-to-state as well as total reaction probabilities and integral cross sections, when the reaction process is initiated from the first excited electronic state (2¹A'). We have depicted the convergence profiles of reaction probabilities for the competing charge transfer processes, namely, reactive charge transfer (RCT) and nonreactive charge transfer (NRCT) processes for different total energies with respect to total angular momentum, J. Total and state-to-state integral cross sections are calculated as a function of total energy for the initial rovibrational state, namely, v = 0, j = 0 level of H₂⁺ (²Σ_g⁺) molecule and are compared with previous theoretical calculations. Finally, we have calculated temperature-dependent rate constants using our presently evaluated cross sections and compared their average with the experimentally measured one.

Gas-Phase Binding Energies and Dissociation Dynamics of 1-Alkyl-3-Methylimidazolium Tetrafluoroborate Ionic Liquid Clusters

Ionic liquids (ILs) have become increasingly popular due to their useful and unique properties, yet there are still many unanswered questions regarding their fundamental interactions. In particular, details regarding the nature and strength of the intrinsic cation-anion interactions and how they influence the macroscopic properties of ILs are still largely unknown. Elucidating the molecular-level details of these interactions is essential to the development of better models for describing ILs and enabling the purposeful design of ILs with properties tailored for specific applications. Current uses of ILs are widespread and diverse and include applications for energy storage, electrochemistry, designer/green solvents, separations, and space propulsion. To advance the understanding of the energetics, conformations, and dynamics of gas-phase IL clustering relevant to space propulsion, threshold collision-induced dissociation approaches are used to measure the bond dissociation energies (BDEs) of the 2:1 clusters of 1-alkyl-3-methylimidazolium cations and tetrafluoroborate, [2C_nmim:BF₄]⁺. The cation, [C_nmim]⁺, is varied across the series, 1-ethyl-3-methylimidazolium [C₂mim]⁺, 1-butyl-3-methylimidazolium [C₄mim]⁺, 1-hexyl-3-methylimidazolium [C₆mim]⁺, and 1-octyl-3-methylimidazolium [C₈mim]⁺, to examine the structural and energetic effects of the size of the 1-alkyl substituent on binding. Complementary electronic structure calculations are performed to determine the structures and energetics of the [C_nmim]⁺ and [BF₄]^- ions and their binding preferences in the (C_nmim:BF₄) ion pairs and [2C_nmim:BF₄]⁺ clusters. Several levels of theory, B3LYP, B3LYP-GD3BJ, and M06-2X, using the 6-311+G(d,p) basis set for geometry optimizations and frequency analyses and the 6-311+G(2d,2p) basis set for energetics, are benchmarked to examine their abilities to properly describe the nature of the binding interactions and to reproduce the measured BDEs. The modest structural variation among these [C_nmim]⁺ cations produces only minor structural changes and variation in the measured BDEs of the [2C_nmim:BF₄]⁺ clusters. Present findings indicate that the dominant cation-anion interactions involve the 3-methylimidazolium moieties and that these clusters are sufficiently small that differences in packing effects associated with the variable length of the 1-alkyl substituents are not yet significant.

Weighing synthetic polymers of ultra-high molar mass and polymeric nanomaterials: What can we learn from charge detection mass spectrometry?

Advances in soft ionization techniques for mass spectrometry (MS) of polymeric materials make it possible to determine the masses of intact molecular ions exceeding megadaltons. Interfacing MS with separation and fragmentation methods has additionally led to impressive advances in the ability to structurally characterize polymers. Even if the gap to the megadalton range has been bridged by MS for polymers standards, the MS-based analysis for more complex polymeric materials is still challenging. Charge detection mass spectrometry (CDMS) is a single-molecule method where the mass and the charge of each ion are directly determined from individual measurements. The entire molecular mass distribution of a polymer sample can be thus accurately measured. Described in this perspective paper is how molecular weight distribution as well as charge distribution can provide new insights into the structural and compositional studies of synthetic polymers and polymeric nanomaterials in the megadalton to gigadalton range of molecular weight. The recent multidimensional CDMS studies involving couplings with separation and dissociation techniques will be presented. And, finally, an outlook for the future avenues of the CDMS technique in the field of synthetic polymers of ultra-high molar mass and polymeric nanomaterials will be provided.

Thermometry in a Multipole Ion Trap

We present a characterization of the ions’ translational energy distribution in a multipole ion trap. A linear mapping between the energy distribution of the trapped ions onto the ions’ time-of-flight (TOF) to a detector is demonstrated. For low ion temperatures, a deviation from linearity is observed and can be attributed to the emergence of multiple potential minima. The potential landscape of the trapped ions is modeled via the finite element method, also accounting for subtleties such as surface-charge accumulation. We demonstrate the validity of our thermometry method by simulating the energy distribution of the ion ensemble thermalized with buffer gas using a Molecular Dynamics (MD) simulation. A comparison between the energy distribution of trapped ions in different multipole trap configurations—i.e., with hyperbolic rods, cylindrical rods, and cylindrical wires—is provided. With these findings, one can map the temperature of the trapped ions down to the Kelvin regime using their TOF distributions. This enables future studies on sympathetic cooling and chemical reactions involving ions in multipole traps.

Methane Adducts of Gold Dimer Cations: Thermochemistry and Structure from Collision-Induced Dissociation and Association Kinetics

The bond dissociation energies at 0 K (BDE) of Au₂⁺-CH₄ and Au₂CH₄⁺-CH₄ have been determined using two separate experimental methods. Analyses of collision-induced dissociation cross sections for Au₂CH₄⁺ + Xe and Au₂(CH₄)₂⁺ + Xe measured using a guided ion beam tandem mass spectrometer (GIBMS) yield BDEs of 0.71 ± 0.05 and 0.57 ± 0.07 eV, respectively. Statistical modeling of association kinetics of Au₂(CH₄)_0-2⁺ + CH₄ + He measured from 200 to 400 K and at 0.3-0.9 Torr using a selected-ion flow tube (SIFT) apparatus yields slightly higher values of 0.81 ± 0.21 and 0.75 ± 0.25 eV. The SIFT data also place a lower limit on the BDE of Au₂C₂H₈⁺-CH₄ of 0.35 eV, likely an activated isomer, not Au₂(CH₄)₂⁺-CH₄. Particular emphasis is placed on determining the uncertainty in the derivation from association kinetics measurements, including uncertainties in collisional energy transfer, calculated harmonic frequencies, and possible contribution of isomerization of the association complexes. This evaluation indicates that an uncertainty of ±0.2 eV should be expected and that an uncertainty of better than ±0.1 eV is unlikely to be reasonable.

Cerium Cation (Ce+) Reactions with H2, D2, and HD: CeH+ Bond Energy and Mechanistic Insights from Guided Ion Beam and Theoretical Studies

Reactions of the atomic lanthanide cerium cation (Ce⁺) with H₂, D₂, and HD were studied by using guided ion beam tandem mass spectrometry. Analysis of the kinetic-energy-dependent endothermic reactions to form CeH⁺ (CeD⁺) led to a 0 K bond dissociation energy (BDE) for CeH⁺ of 2.19 ± 0.09 eV. Theoretical calculations for CeH⁺ were performed at the B3LYP, BHLYP, and PBE0 levels of theory and overestimate the experimental BDE. In contrast, extrapolation to the complete basis set limit using coupled-cluster with single, double, and perturbative triple excitations, CCSD(T), gave a value (2.33 eV) in reasonable agreement with the experimental BDE. The branching ratio of the CeH⁺ and CeD⁺ products in the HD reaction suggests that the reaction occurs via a statistical mechanism involving a long-lived intermediate. Relaxed potential energy surfaces for CeH₂⁺ were computed and are consistent with the availability of such an intermediate, but the crossing point between quartet and doublet surfaces helps explain the inefficiency of the association reaction observed in the literature. The reactivity and CeH⁺ BDE are compared with previous results for group 4 transition metal cations (Ti⁺, Zr⁺, and Hf⁺), other lanthanides (La⁺, Sm⁺, Gd⁺, and Lu⁺), and the isovalent actinide Th⁺. Periodic trends and insight into the role of the electronic configuration on metal-hydride bond strength are discussed.

A Cyclic Ion Mobility-Mass Spectrometry System

Improvements in the performance and availability of commercial instrumentation have made ion mobility-mass spectrometry (IM-MS) an increasingly popular approach for the structural analysis of ionic species as well as for separation of complex mixtures. Here, a new research instrument is presented which enables complex experiments, extending the current scope of IM technology. The instrument is based on a Waters SYNAPT G2-S i IM-MS platform, with the IM separation region modified to accept a cyclic ion mobility (cIM) device. The cIM region consists of a 98 cm path length, closed-loop traveling wave (TW)-enabled IM separator positioned orthogonally to the main ion optical axis. A key part of this geometry and its flexibility is the interface between the ion optical axis and the cIM, where a planar array of electrodes provides control over the TW direction and subsequent ion motion. On either side of the array, there are ion guides used for injection, ejection, storage, and activation of ions. In addition to single and multipass separations around the cIM, providing selectable mobility resolution, the instrument design and control software enable a range of "multifunction" experiments such as mobility selection, activation, storage, IMS ⁿ, and importantly custom combinations of these functions. Here, the design and performance of the cIM-MS instrument is highlighted, with a mobility resolving power of approximately 750 demonstrated for 100 passes around the cIM device using a reverse sequence peptide pair. The multifunction capabilities are demonstrated through analysis of three isomeric pentasaccharide species and the small protein ubiquitin.

Photoelectron-Photofragment Coincidence Spectroscopy With Ions Prepared in a Cryogenic Octopole Accumulation Trap: Collisional Excitation and Buffer Gas Cooling

A cryogenic octopole accumulation trap (COAT) has been coupled to a photoelectron-photofragment coincidence (PPC) spectrometer allowing for improved control over anion vibrational excitation. The anions are heated and cooled via collisions with buffer gas <17 K. Shorter trapping times (500 μs) prevent thermalization and result in anions with high internal excitation while longer trapping times (80 ms) at cryogenic temperatures thermalize the ions to the temperature of the buffer gas. The capabilities of the COAT are demonstrated using PPC spectroscopy ofO 3 - at 388 nm (Ehν = 3.20 eV). Cooling the precursor anions with COAT resulted in the elimination of the autodetachment of vibrationally excitedO 2 - produced by the photodissociationO 3 - + hν → O +O 2 - (v ≥ 4). Under heating conditions, a lower limit temperature for the anions was determined to be 1,500 K through Franck-Condon simulations of the photodetachment spectrum ofO 3 - , considering a significant fraction of the ions undergo photodissociation in competition with photodetachment. The ability to cool or heat ions by varying ion injection and trapping duration in COAT provides a new flexibility for studying the spectroscopy of cold ions as well as thermally activated processes.

Two-dimensional mass spectrometry: new perspectives for tandem mass spectrometry

Fourier transform ion cyclotron resonance mass analysers (FT-ICR MS) can offer the highest resolutions and mass accuracies in mass spectrometry. Mass spectra acquired in an FT-ICR MS can yield accurate elemental compositions of all compounds in a complex sample. Fragmentation caused by ion-neutral, ion-electron, or ion-photon interactions leads to more detailed structural information on compounds. The most often used method to correlate compounds and their fragment ions is to isolate the precursor ions from the sample before fragmentation. Two-dimensional mass spectrometry (2D MS) offers a method to correlate precursor and fragment ions without requiring precursor isolation. 2D MS therefore enables easy access to the fragmentation patterns of all compounds from complex samples. In this article, the principles of FT-ICR MS are reviewed and the 2D MS experiment is explained. Data processing for 2D MS is detailed, and the interpretation of 2D mass spectra is described.

A cryogenic cylindrical ion trap velocity map imaging spectrometer

A cryogenic cylindrical ion trap velocity map imaging spectrometer has been developed to study photodissociation spectroscopy and dynamics of gaseous molecular ions and ionic complexes. A cylindrical ion trap made of oxygen-free copper is cryogenically cooled down to ∼7 K by using a closed cycle helium refrigerator and is coupled to a velocity map imaging (VMI) spectrometer. The cold trap is used to cool down the internal temperature of mass selected ions and to reduce the velocity spread of ions after extraction from the trap. For CO₂ ⁺ ions, a rotational temperature of ∼12 K is estimated from the recorded [1 + 1] two-photon dissociation spectrum, and populations in spin-orbit excited X²Π_g,1/2 and vibrationally excited states of CO₂ ⁺ are found to be non-detectable, indicating an efficient internal cooling of the trapped ions. Based on the time-of-flight peak profile and the image of N₃ ⁺, the velocity spread of the ions extracted from the trap, both radially and axially, is interpreted as approximately ±25 m/s. An experimental image of fragmented Ar⁺ from 307 nm photodissociation of Ar₂ ⁺ shows that, benefitting from the well-confined velocity spread of the cold Ar₂ ⁺ ions, a VMI resolution of Δv/v ∼ 2.2% has been obtained. The current instrument resolution is mainly limited by the residual radial speed spread of the parent ions after extraction from the trap.

Correcting symmetry imperfections in linear multipole traps

Multipole radio-frequency (RF) traps are central to collisional experiments in cryogenic environments. They also offer possibilities to generate new type of ion crystals topologies and in particular the potential to create infinite 1D/2D structures: ion rings and ion tubes. However, multipole traps have also been shown to be very sensitive to geometrical misalignment of the trap rods, leading to additional local trapping minima. The present work proposes a method to correct non-ideal potentials, by modifying the applied RF amplitudes for each trap rod. This approach is discussed for the octupole trap, leading to the restitution of the ideal Mexican-Hat-like pseudo-potential, expected in multipole traps. The goodness of the compensation method is quantified in terms of the choice of the diagnosis area, the residual trapping potential variations, the required adaptation of the applied RF voltage amplitudes, and the impact on the trapped ion structures. Experimental implementation for macroscopic multipole traps is also discussed, in order to propose a diagnostic method with respect to the resolution and stability of the trap drive. Using the proposed compensation technique, we discuss the feasibility of generating a homogeneous ion ring crystal, which is a measure of quality for the obtained potential well.

The Use of Mass Spectrometry to Examine IDPs: Unique Insights and Caveats

A sizeable proportion of active protein sequences lack structural motifs making them irresolvable by NMR and crystallography. Such intrinsically disordered proteins (IDPs) or regions (IDRs) play a major role in biological mechanisms. They are often involved in cell regulation processes, and by extension can be the perpetrator or signifier of disease. In light of their importance and the shortcomings of conventional methods of biophysical analysis to identify them and to describe their conformational variance, IDPs and IDRs have been termed "the dark proteome." In this chapter we describe the use of ion mobility-mass spectrometry (IM-MS) coupled with electrospray ionization to analyze the conformational diversity of IDPs. Using the LEA protein COR15A as an exemplar system and contrasting it with the behavior of myoglobin, we outline the methods for analyzing an IDP using nanoelectrospray ionization coupled with IM-MS, covering sample preparation, purification; optimization of mass spectrometry conditions and tuning parameters; data collection and analysis. Following this, we detail the use of a "toy" model that provides a predictive framework for the study of all proteins with ESI-IM-MS.

A cryogenic linear ion trap beamline for providing keV ion bunches

A new cryogenic linear ion trap beamline has been constructed and commissioned, which serves to inject cold molecular and cluster ions into the RIKEN cryogenic electrostatic ring (RICE). Ions are created with an electrospray ion source, and a quadrupole mass filter is used for mass-selection prior to trap injection. The radio frequency octupole ion trap can be continuously loaded with ions and features a fast ion extraction mode to create short ion bunches with tens of μs duration. We report here on the simulations and development of the ion trap beamline and validate performance with the moderately heavy molecular cation methylene blue. Characterization of the novel trap design with additional wedge-shaped electrodes was carried out, which includes the determination of the temporal and spatial shape of the ion bunch and the total number of ions after extraction. Finally, these ion bunches are synchronized with the switching of a pulsed high-voltage acceleration device downstream of the trap, where the ions obtain a kinetic energy of up to 20 keV. The preparation and control of the keV ion beam are demonstrated for the ion injection into RICE.