Infrared multiple photon dissociation spectroscopy of ions in Penning traps

Cryo IR spectroscopy and cryo kinetics of dinitrogen activation and cleavage by small tantalum cluster cations

We investigate small tantalum clusters Tan+, n = 2-4, for their capability to cleave N2 adsorption spontaneously. We utilize infrared photon dissociation (IR-PD) spectroscopy of isolated and size selected clusters under cryogenic conditions within a buffer gas filled ion trap, and we augment our experiments by quantum chemical simulations (at DFT level). All Tan+ clusters, n = 2-4, seem to cleave N2 efficiently. We confirm and extend a previous study under ambient conditions on Ta2+ cluster [Geng et al., Proc. Natl. Acad. Sci. U. S. A. 115, 11680-11687 (2018)]. Our cryo studies and the concomitant DFT simulations of the tantalum trimer Ta3+ suggest cleavage of the first and activation of the second and third N2 molecule across surmountable barriers and along much-involved multidimensional reaction paths. We unravel the underlying reaction processes and the intermediates involved. The study of the N2 adsorbate complexes of Ta4+ presented here extends our earlier study and previously published spectra from (4,m), m = 1-5 [Fries et al., Phys. Chem. Chem. Phys. 23(19), 11345-11354 (2021)], up to m = 12. We confirm the priory published double activation and nitride formation, succeeded by single side-on N2 coordination. Significant red shifts of IR-PD bands from these side-on coordinated μ2-κN:κN,N N2 ligands correlate with the degree of tilting towards the second coordinating Ta center. All subsequently attaching N2 adsorbates onto Ta4+ coordinate in an end-on fashion, and we find clear evidence for co-existence of end-on coordination isomers. The study of stepwise N2 adsorption revealed adsorption limits m(max) of [Tan(N2)m]+ which increase with n, and kinetic fits revealed significant N2 desorption rates upon higher N2 loads. The enhanced absolute rate constants of the very first adsorbate steps kabs(n,0) of the small Ta3+ and Ta4+ clusters independently suggest dissociative N2 adsorption and likely N2 cleavage into Ta nitrides.

IRMPD spectroscopy and quantum-chemical simulations of the reaction products of cisplatin with the dipeptide CysGly

The inorganic antineoplastic drug cisplatin was made to react in solution with the dipeptide cysteinylglycine (CysGly), chosen as a functional model of glutathione, and the reaction products were analyzed using electrospray ionization mass spectrometry (ESI-MS). Selected complexes, i.e., the primary substitution product cis-[PtCl(NH3)2(CysGly)]+ and the chelate cis-[PtCl(NH3)(CysGly)]+, were submitted to IR multiple photon dissociation (IRMPD) spectroscopy obtaining their vibrational features. The experimental IR ion spectra were compared with the calculated IR absorptions of different plausible isomeric families, finding CysGly to bind preferentially platinum(II) via its deprotonated thiolic group in the monovalent complex, cis-[PtCl(NH3)2(CysGly)]+, and to evolve in the S,N-bound chelate structure cis-[PtCl(NH3)(CysGly)]+ through the SH and NH2 functionality of the cysteine residue. Moreover, our findings indicate that the platination reaction does not affect the CysGly peptide bond, which remains in its trans configuration. These results provide additional insights into the reactivity of Pt(II)-complexes with glutathione which is involved in cellular cisplatin resistance.

Probing the binding and activation of small molecules by gas-phase transition metal clusters via IR spectroscopy

Isolated transition metal clusters have been established as useful models for extended metal surfaces or deposited metal particles, to improve the understanding of their surface chemistry and of catalytic reactions. For this objective, an important milestone has been the development of experimental methods for the size-specific structural characterization of clusters and cluster complexes in the gas phase. This review focusses on the characterization of molecular ligands, their binding and activation by small transition metal clusters, using cluster-size specific infrared action spectroscopy. A comprehensive overview and a critical discussion of the experimental data available to date is provided, reaching from the initial results obtained using line-tuneable CO₂ lasers to present-day studies applying infrared free electron lasers as well as other intense and broadly tuneable IR laser sources.

UV-vis spectroscopy of gas-phase ions

Photodissociation action spectroscopy has made a great progress in expanding investigations of gas-phase ion structures. This review deals with aspects of gas-phase ion electronic excitations that result in wavelength-dependent dissociation and light emission via fluorescence, chiefly covering the ultraviolet and visible regions of the spectrum. The principles are briefly outlined and a few examples of instrumentation are presented. The main thrust of the review is to collect and selectively present applications of UV-vis action spectroscopy to studies of stable gas-phase ion structures and combinations of spectroscopy with ion mobility, collision-induced dissociation, and ion-ion reactions leading to the generation of reactive intermediates and electronic energy transfer.

Elusive intermediates in cisplatin reaction with target amino acids: Platinum(II)-cysteine complexes assayed by IR ion spectroscopy and DFT calculations

The reactivity of a widely used metal based antineoplastic drug, cisplatin, cis-PtCl₂(NH₃)₂, with L-cysteine (Cys) has been investigated using a combination of electrospray ionization mass spectrometry (ESI-MS), IRMPD gas phase ion spectroscopy and DFT calculations. The cysteine lateral chain represents one of the main platination sites in proteins, which is believed to be related to the resistance mechanisms to cisplatin. The vibrational features of the mass-selected substitution product cis-[PtCl(NH₃)₂(Cys)]⁺ and the intercepted cis-[PtCl(NH₃)₂(H₂O)(Cys)]⁺ intermediate complex were compared to calculated IR spectra, enabling the assessment of the sampled ions structures. In cis-[PtCl(NH₃)₂(Cys)]⁺, cysteine was found to bind platinum through the sulfur atom as a thiolate zwitterion, highlighting the enhanced acidity of the cysteine thiol group upon metal coordination. The cis-[PtCl(NH₃)₂(H₂O)(Cys)]⁺ structure complies with the non-covalent encounter complex, formed by cis-[PtCl(NH₃)₂(H₂O)]⁺ and neutral cysteine. This species is able to undergo the substitution process to produce cis-[PtCl(NH₃)₂(Cys)]⁺ when activated as a mass-isolated ion suggesting its participation in the reaction mechanism of cisplatin with cysteine in solution. Finally, the DFT-calculated energy profile for the substitution reaction was correlated with the peculiar gas-phase reactivity of this non-covalent complex, resulting to be 10-fold less reactive toward substitution than the corresponding methionine complex.

Ligation Motifs in Zinc-Bound Sulfonamide Drugs Assayed by IR Ion Spectroscopy

The sulfonamide–zinc ion interaction, performing a key role in various biological contexts, is the focus of the present study, with the aim of elucidating ligation motifs in zinc complexes of sulfa drugs, namely sulfadiazine (SDZ) and sulfathiazole (STZ), in a perturbation-free environment. To this end, an approach is exploited based on mass spectrometry coupled with infrared multiple photon dissociation (IRMPD) spectroscopy backed by quantum chemical calculations. IR spectra of Zn(H2O+SDZ−H)+ and Zn(H2O+STZ−H)+ ions are consistent with a three-coordinate zinc complex, where ZnOH+ binds to the uncharged sulfonamide via N(heterocycle) and O(sulfonyl) donor atoms. Alternative prototropic isomers Zn(OH2)(SDZ−H)+ and Zn(OH2)(STZ−H)+ lie 63 and 26 kJ mol−1 higher in free energy, respectively, relative to the ground state Zn(OH)(SDZ)+ and Zn(OH)(STZ)+ species and do not contribute to any significant extent in the sampled population.

A novel method for photon unfolding spectroscopy of protein ions in the gas phase

In this study, a new experimental method for photon unfolding spectroscopy of protein ions based on a Fourier transform ion cyclotron resonance (FT ICR) mass spectrometer was developed. The method of short-time Fourier transform has been applied here to obtain decay curves of target ions trapped in the cell of the FT ICR mass spectrometer. Based on the decay constants, the collision cross sections (CCSs) of target ions were calculated using the energetic hard-sphere model. By combining a tunable laser to the FT ICR mass spectrometer, the changes of CCSs of the target ions were recorded as a function of the wavelengths; thus, the photon isomerization spectrum was obtained. As one example, the photon isomerization spectrum of [Cyt c + 13H]¹³⁺ was recorded as the decay constants relative to the applied wavelengths of the laser in the 410-480 nm range. The spectrum shows a maximum at 426 nm, where an unfolded structure induced by a 4 s irradiation can be deduced. The strong peak at 426 nm was also observed for another ion of [Cyt c + 15H]¹⁵⁺, although some difference at 410 nm between the two spectra was found at the same time. This novel method can be expanded to ultraviolet or infrared region, making the experimental study of wavelength-dependent photon-induced structural variation of a variety of organic or biological molecules possible.

Comment on "Microhydration of Biomolecules: Revealing the Native Structures by Cold Ion IR Spectroscopy"

This Viewpoint presents a re-examination of the conclusions of a study reported in The Journal of Physical Chemistry Letters (Saparbaev, et al. 2021, 12, 907) that compared the structure of microsolvated ions formed by electrospray ionization to those formed in the gas-phase via a previously published cryogenic ion trap approach. We conducted additional experiments that clearly show that most of the observed differences in the IR spectra can be accounted for by considering the different spectroscopic action schemes used to obtain them. In particular, the presence of the D₂-tag induces shifts in some of the N-H and O-H peaks which need to be carefully considered before comparing spectra. Once these spectral effects are taken into account, we show that both clustering approaches yield similar cluster structures for the small GlyH⁺(H₂O)_n species. Using unimolecular reaction rate theory, we also show that for the small complexes considered here, only the gas-phase equilibrium distribution of conformers should be expected in both experimental approaches. In addition, the barrier heights necessary to kinetically trap high-energy conformers at 298 K is explored using a series of model polyalanine chains.

Infrared multiple photon dissociation (IRMPD) spectroscopy and its potential for the clinical laboratory

Infrared multiple photon dissociation (IRMPD) spectroscopy is a powerful tool used to probe the vibrational modes-and, by extension, the structure-of an ion within an ion trap mass spectrometer. Compared to traditional FTIR spectroscopy, IRMPD spectroscopy has advantages including its sensitivity and its relative ability to handle complex mixtures. While IRMPD has historically been a technique for fundamental analyses, it is increasingly being applied in a more analytical fashion. Notable recent demonstrations pertinent to the clinical laboratory and adjacent interests include analysis of modified amino acids/residues and carbohydrates, structural elucidation (including isomeric differentiation) of metabolites, identification of novel illicit drugs, and structural studies of various biomolecules and pharmaceuticals. Improvements in analysis time, coupling to commercial instruments, and integration with separations methods are all drivers toward the realization of these analytical applications. Additional improvements in these areas, along with advances in benchtop tunable IR sources and increased cross-discipline collaboration, will continue to drive innovation and widespread adoption. The goal of this tutorial article is to briefly present the fundamentals and instrumentation of IRMPD spectroscopy, as an overview of the utility of this technique for helping to answer questions relevant to clinical analysis, and to highlight limitations to widespread adoption, as well as promising directions in which the field may be heading.

Rapid IRMPD (InfraRed multiple photon dissociation) analysis for glycomics

Infrared vibrational spectroscopy in the gas phase has emerged as a powerful tool to determine complex molecular structures with high precision. Among the different approaches IRMPD (InfraRed multiple photon dissociation), which requires the use of an intense pulsed tuneable laser in the InfraRed (IR) domain, has been broadly applied to the study of complex (bio)molecules. Recently, it also emerged as a highly relevant approach for analytical purposes especially in the field of glycomics in which structural analysis is still a tremendous challenge. This opens the perspective to develop new analytical tools allowing for the determination of molecular structures with atomic precision, and to address advanced questions in the field. However, IRMPD experiments require non commercial equipment or/and long acquisition time which limits the data output. Here we show that it is possible to improve the IRMPD performances by optimizing the combination between a linear ion trap mass spectrometer and a high repetition tuneable laser. Two orders of magnitude are gained with this approach compared to the usual experiments ultimately leading to a completely resolved spectrum acquired in less than one minute. These results open the way to many new applications in glycomics with the possibility to include IRMPD in complex analytical workflows.

Evaluation of table-top lasers for routine infrared ion spectroscopy in the analytical laboratory

Infrared ion spectroscopy is increasingly recognized as a method to identify mass spectrometry-detected analytes in many (bio)chemical areas and its integration in analytical laboratories is now on the horizon. Commercially available quadrupole ion trap mass spectrometers are attractive ion spectroscopy platforms but operate at relatively high pressures. This promotes collisional deactivation which directly interferes with the multiple-photon excitation process required for ion spectroscopy. To overcome this, infrared lasers having a high instantaneous power are required and therefore a majority of analytical studies have been performed at infrared free electron laser facilities. Proliferation of the technique to routine use in analytical laboratories requires table-top infrared lasers and optical parametric oscillators (OPOs) are the most suitable candidates, offering both relatively high intensities and reasonable spectral tuning ranges. Here, we explore the potential of a range of commercially available high-power OPOs for ion spectroscopy, comparing systems with repetition rates of 10 Hz, 20 kHz, 80 MHz and a continuous-wave (cw) system. We compare the performance for various molecular ions and show that the kHz and MHz repetition-rate systems outperform cw and 10 Hz systems in photodissociation efficiency and offer several advantages in terms of cost-effectiveness and practical implementation in an analytical laboratory not specialized in laser spectroscopy.

Molecular Basis for the Remarkably Different Gas-Phase Behavior of Deprotonated Thyroid Hormones Triiodothyronine (T3) and Reverse Triiodothyronine (rT3): A Clue for Their Discrimination?

Thyroid hormones are biologically active small molecules responsible for growth and development regulation, basal metabolic rate, and lipid and carbohydrate metabolism. Liquid chromatography mass spectrometry (LC–MS) can be used to quantify thyroid hormones blood level with high speed and selectivity, aiming to improve the diagnosis and treatment of the severe pathological conditions in which they are implicated, i.e., hypo- and hyperthyroidism. In this work, the gas-phase behavior of the isomeric thyroid hormones triiodothyronine (T3) and reverse triiodothyronine (rT3) in their deprotonated form was studied at a molecular level using MS-based techniques. Previously reported collision-induced dissociation experiments yielded distinct spectra despite the high structural similarity of the two compounds, suggesting different charge sites to be responsible. Infrared multiple photon dissociation spectroscopy on [T3-H]⁻ and [rT3-H]⁻ was performed, and the results were interpreted using DFT and MP2 calculations, assessing the prevalence of T3 in the carboxylate form and rT3 as a phenolate isomer. The different deprotonation sites of the two isomers were also found to drive their ion-mobility behavior. In fact, [T3-H]⁻ and [rT3-H]⁻ were successfully separated. Drift times were correlated with collisional cross section values of 209 and 215 Ų for [T3-H]⁻ and [rT3-H]⁻, respectively. Calculations suggested the charge site to be the main parameter involved in the different mobilities of the two anions. Finally, bare [T3-H]⁻ and [rT3-H]⁻ were made to react with neutral acetylacetone and trifluoroacetic acid, confirming rT3 to be more acidic than T3 in agreement with the calculated gas-phase acidities of T3 and rT3 equal to 1345 and 1326 kJ mol^–1, respectively.

Mass Spectrometry of Nucleic Acid Noncovalent Complexes

Nucleic acids have been among the first targets for antitumor drugs and antibiotics. With the unveiling of new biological roles in regulation of gene expression, specific DNA and RNA structures have become very attractive targets, especially when the corresponding proteins are undruggable. Biophysical assays to assess target structure as well as ligand binding stoichiometry, affinity, specificity, and binding modes are part of the drug development process. Mass spectrometry offers unique advantages as a biophysical method owing to its ability to distinguish each stoichiometry present in a mixture. In addition, advanced mass spectrometry approaches (reactive probing, fragmentation techniques, ion mobility spectrometry, ion spectroscopy) provide more detailed information on the complexes. Here, we review the fundamentals of mass spectrometry and all its particularities when studying noncovalent nucleic acid structures, and then review what has been learned thanks to mass spectrometry on nucleic acid structures, self-assemblies (e.g., duplexes or G-quadruplexes), and their complexes with ligands.

From Preassociation to Chelation: A Survey of Cisplatin Interaction with Methionine at Molecular Level by IR Ion Spectroscopy and Computations

Methionine (Met) plays an important role in the metabolism of cisplatin anticancer drug. Yet, methionine platination in aqueous solution presents a highly complex pattern of interconnected paths and intermediates. This study reports on the reaction of methionine with the active aqua form of cisplatin, cis-[PtCl(NH₃)₂(H₂O)]⁺, isolating the encounter complex of the reactant pair, {cis-[PtCl(NH₃)₂(H₂O)]⁺·Met}, by electrospray ionization. In the unsolvated state, charged intermediates are characterized for their structure and photofragmentation behavior by IR ion spectroscopy combined with quantum-chemical calculations, obtaining an outline of the cisplatin-methionine reaction at a molecular level. To summarize the major findings: (i) the {cis-[PtCl(NH₃)₂(H₂O)]⁺·Met} encounter complex, lying on the reaction coordinate of the Eigen-Wilkins preassociation mechanism for ligand substitution, is delivered in the gas phase and characterized by IR ion spectroscopy; (ii) upon vibrational excitation, ligand exchange occurs within {cis-[PtCl(NH₃)₂(H₂O)]⁺·Met}, releasing water and cis-[PtCl(NH₃)₂(Met)]⁺, along the calculated energy profile; (iii) activated cis-[PtCl(NH₃)₂(Met)]⁺ ions undergo NH₃ departure, forming a chelate complex, [PtCl(NH₃)(Met)]⁺, whose structure is congruent with overwhelming S-Met ligation as the primary coordination step. The latter process involving ammonia loss marks a difference with the prevailing chloride replacement in protic solvent, pointing to the effect of a low-polarity environment.

Charge-Tagged Nucleosides in the Gas Phase: UV-Vis Action Spectroscopy and Structures of Cytidine Cations, Dications, and Cation Radicals

Cytidine ribonucleosides were furnished at O5' with fixed-charge 6-trimethylammoniumhexan-1-aminecarbonyl tags and studied by UV-vis photodissociation action spectroscopy in the gas phase to probe isolated nucleobase chromophores in their neutral, protonated, and hydrogen-adduct radical forms. The action spectrum of the doubly charged cytidine conjugate showed bands at 310 and 270 nm that were assigned to the N3- and O2-protonated cytosine tautomers formed by electrospray, respectively. In contrast, cytidine conjugates coordinated to dibenzo-18-crown-6-ether (DBCE) in a noncovalent complex were found to strongly favor protonation at N3, forming a single-ion tautomer. This allowed us to form cytidine N3-H radicals by electron transfer dissociation of the complex and study their action spectra. Cytidine radicals showed only very weak absorption in the visible region of the spectrum for dipole-disallowed transitions to the low (A and B) excited states. The main bands were observed at 360, 300, and 250 nm that were assigned with the help of theoretical vibronic spectra obtained by time-dependent density functional theory calculations of multiple (>300) radical vibrational configurations. Collision-induced dissociations of cytidine radicals proceeded by major cleavage of the N1-C1' glycosidic bond leading to loss of cytosine and competitive loss of N3-hydrogen atom. These dissociations were characterized by calculations of transition-state structures and energies using combined Born-Oppenheimer molecular dynamics and DFT calculations. Overall, cytidine radicals were found to be kinetically and thermodynamically more stable than previously reported analogous adenosine and guanosine radicals.

Versatile Double-Beam Confocal Laser System Combined with a Fourier Transform Ion Cyclotron Resonance Mass Spectrometer for Photodissociation Mass Spectrometry and Spectroscopy

Both infrared multiphoton dissociation (IRMPD) and ultraviolet photodissociation (UVPD) play important roles in tandem mass spectrometry and the action spectroscopy of organic and biological molecules. A flexible combination of the two methods may provide researchers with more versatile and powerful ion activation/dissociation choices for structural characterization and spectroscopic studies. Here, we report the integration of two tunable lasers with a Fourier transform ion cyclotron resonance mass spectrometer in a confocal mode, which offers multiple capabilities for photon activation/dissociation experiments. The two overlapped beams can be introduced into the cell individually, sequentially, or simultaneously, providing highly flexible and diverse activation schemes. The setup can also measure the UVPD or IRMPD action spectra of fragment ions generated by previous photon dissociation processes. In addition, the multistage tandem-in-time mass spectrometry performance up to MS⁴, including three different activation methods in a single cell, has also been demonstrated.

Molecular Properties of Bare and Microhydrated Vitamin B5-Calcium Complexes

Pantothenic acid, also called vitamin B5, is an essential nutrient involved in several metabolic pathways. It shows a characteristic preference for interacting with Ca(II) ions, which are abundant in the extracellular media and act as secondary mediators in the activation of numerous biological functions. The bare deprotonated form of pantothenic acid, [panto-H]⁻, its complex with Ca(II) ion, [Ca(panto-H)]⁺, and singly charged micro-hydrated calcium pantothenate [Ca(panto-H)(H₂O)]⁺ adduct have been obtained in the gas phase by electrospray ionization and assayed by mass spectrometry and IR multiple photon dissociation spectroscopy in the fingerprint spectral range. Quantum chemical calculations at the B3LYP(-D3) and MP2 levels of theory were performed to simulate geometries, thermochemical data, and linear absorption spectra of low-lying isomers, allowing us to assign the experimental absorptions to particular structural motifs. Pantothenate was found to exist in the gas phase as a single isomeric form showing deprotonation on the carboxylic moiety. On the contrary, free and monohydrated calcium complexes of deprotonated pantothenic acid both present at least two isomers participating in the gas-phase population, sharing the deprotonation of pantothenate on the carboxylic group and either a fourfold or fivefold coordination with calcium, thus justifying the strong affinity of pantothenate for the metal.

Application of Infrared Multiple Photon Dissociation (IRMPD) Spectroscopy in Chiral Analysis

In recent years, methods based on photodissociation in the gas phase have become powerful means in the field of chiral analysis. Among them, infrared multiple photon dissociation (IRMPD) spectroscopy is a very attractive one, since it can provide valuable spectral and structural information of chiral complexes in addition to chiral discrimination. Experimentally, the method can be fulfilled by the isolation of target diastereomeric ions in an ion trap followed by the irradiation of a tunable IR laser. Chiral analysis is performed by comparing the difference existing in the spectra of enantiomers. Combined with theoretical calculations, their structures can be further understood on the molecular scale. By now, lots of chiral molecules, including amino acids and peptides, have been studied with the method combined with theoretical calculations. This review summarizes the relative experimental results obtained, and discusses the limitation and prospects of the method.

Development of a photoinduced fragmentation ion trap for infrared multiple photon dissociation spectroscopy

RATIONALE

Methods for isomer discrimination by mass spectroscopy are of increasing interest. Here we describe the development of a three-dimensional ion trap for infrared multiple photon dissociation (IRMPD) spectroscopy that enables the acquisition of the infrared spectrum of selected ions in the gas phase. This system is suitable for the study of a myriad of chemical systems, including isomer mixtures.

METHODS

A modified three-dimensional ion trap was coupled to a CO₂ laser and an optical parametric oscillator/optical parametric amplifier (OPO/OPA) system operating in the range 2300 to 4000 cm^-1 . Density functional theory vibrational frequency calculations were carried out to support spectral assignments.

RESULTS

Detailed descriptions of the interface between the laser and the mass spectrometer, the hardware to control the laser systems, the automated system for IRMPD spectrum acquisition and data management are presented. The optimization of the crystal position of the OPO/OPA system to maximize the spectroscopic response under low-power laser radiation is also discussed.

CONCLUSIONS

OPO/OPA and CO₂ laser-assisted dissociation of gas-phase ions was successfully achieved. The system was validated by acquiring the IRMPD spectra of model species and comparing with literature data. Two isomeric alkaloids of high economic importance were characterized to demonstrate the potential of this technique, which is now available as an open IRMPD spectroscopy facility in Brazil.

A Combined Infrared Ion Spectroscopy and Computational Chemistry Study of Hydroxyproline Isomers

Hydroxyproline is a common variation of proline, with diverse biological roles. The hydroxylation of proline gives rise to several (natural and/or synthetic) isomeric forms, including both positional isomers and stereoisomers. While mass spectrometry is widely touted as a very selective analytical technique, the identification of closely related isomers often poses a challenge. In these cases, allied technologies become helpful in providing full characterization. Here, infrared multiple photon dissociation (IRMPD) spectroscopy is used to differentiate between three isomers, namely cis-3-hydroxyproline, cis-4-hydroxyproline, and trans-4-hydroxyproline. In contrast to the protonated species which show only minor variations in their IRMPD spectra, lithiated species were found to display significant spectral differences, making their differentiation more straightforward. The conformational origin of these spectral differences was investigated by complementary quantum-chemical calculations.

Mass-Spectrometry-Based Identification of Synthetic Drug Isomers Using Infrared Ion Spectroscopy

Infrared ion spectroscopy (IRIS), a mass-spectrometry-based technique exploiting resonant infrared multiple photon dissociation (IRMPD), has been applied for the identification of novel psychoactive substances (NPS). Identification of the precise isomeric forms of NPS is of significant forensic relevance since legal controls are dependent on even minor molecular differences such as a single ring-substituent position. Using three isomers of fluoroamphetamine and two ring-isomers of both MDA and MDMA, we demonstrate the ability of IRIS to distinguish closely related NPS. Computationally predicted infrared (IR) spectra are shown to correspond with experimental spectra and could explain the molecular origins of their distinctive IR absorption bands. IRIS was then used to investigate a confiscated street sample containing two unknown substances. One substance could easily be identified by comparison to the IR spectra of reference standards. For the other substance, however, this approach proved inconclusive due to incomplete mass spectral databases as well as a lack of available reference compounds, two common analytical limitations resulting from the rapid development of NPS. Most excitingly, the second unknown substance could nevertheless be identified by using computationally predicted IR spectra of several potential candidate structures instead of their experimental reference spectra.

Applications of Infrared Multiple Photon Dissociation (IRMPD) to the Detection of Posttranslational Modifications

Infrared multiple photon dissociation (IRMPD) spectroscopy allows for the derivation of the vibrational fingerprint of molecular ions under tandem mass spectrometry (MS/MS) conditions. It provides insight into the nature and localization of posttranslational modifications (PTMs) affecting single amino acids and peptides. IRMPD spectroscopy, which takes advantage of the high sensitivity and resolution of MS/MS, relies on a wavelength specific fragmentation process occurring on resonance with an IR active vibrational mode of the sampled species and is well suited to reveal the presence of a PTM and its impact in the molecular environment. IRMPD spectroscopy is clearly not a proteomics tool. It is rather a valuable source of information for fixed wavelength IRMPD exploited in dissociation protocols of peptides and proteins. Indeed, from the large variety of model PTM containing amino acids and peptides which have been characterized by IRMPD spectroscopy, specific signatures of PTMs such as phosphorylation or sulfonation can be derived. High throughput workflows relying on the selective fragmentation of modified peptides within a complex mixture have thus been proposed. Sequential fragmentations can be observed upon IR activation, which do not only give rise to rich fragmentation patterns but also overcome low mass cutoff limitations in ion trap mass analyzers. Laser-based vibrational spectroscopy of mass-selected ions holding various PTMs is an increasingly expanding field both in the variety of chemical issues coped with and in the technological advancements and implementations.

UV-Vis Photodissociation Action Spectroscopy on Thermo LTQ-XL ETD and Bruker amaZon Ion Trap Mass Spectrometers: a Practical Guide

We report automated procedures for multiple tandem mass spectra acquisition allowing UV-Vis photodissociation action spectroscopy measurements of ions and radicals. The procedures were developed for two commercial ion trap mass spectrometers and applied to collision-induced and electron-transfer dissociation tandem mass spectrometry modes of ion generation.

Gas-Phase Infrared Ion Spectroscopy Characterization of Cu(II/I)Cyclam and Cu(II/I)2,2'-Bipyridine Redox Pairs

We report the fingerprint IR spectra of mass-isolated gaseous coordination complexes of 2,2′-bipyridine (bpy) and 1,4,8,11-tetra-azacyclotetradecane (cyclam) with a copper ion in its I and II oxidation states. Experiments are carried out in a quadrupole ion trap (QIT) mass spectrometer coupled to the FELIX infrared free-electron laser. Dications are prepared using electrospray ionization (ESI), while monocations are generated by charge reduction of the dication using electron transfer-reduction (ETR) in the QIT. Interestingly, [Cu(bpy)₂]⁺ can also be generated directly using ESI, so that its geometries as produced from ETR and ESI can be compared. The effects of charge reduction on the IR spectra are investigated by comparing the experimental spectra with the IR spectra modeled by density functional theory. Reduction of Cu(II) to the closed-shell Cu(I) ion retains the square-planar geometry of the Cu–cyclam complex. In contrast, for the bis–bpy complex with Cu, charge reduction induces a conversion from a near-square-planar to a tetrahedral geometry. The geometry of [Cu(bpy)₂]⁺ is identical to that of the complex generated directly from ESI as a native structure, which indicates that the ETR product ion thermalizes. For [Cu(cyclam)]⁺, however, the square-planar geometry of the 2+ complex is retained upon charge reduction, although a (distorted) tetrahedral geometry was predicted to be lower in energy. These differences are attributed to different barriers to rearrangement.

Binding motifs of cisplatin interaction with simple biomolecules and aminoacid targets probed by IR ion spectroscopy

The primary intermediates resulting from the interaction of cisplatin, cis-(PtCl2(NH3)2], most widespread antitumor drug, with biomolecular targets are characterized. Electrospray ionization is used to deliver ions formed in solution into the gas phase where they are structurally interrogated by vibrational “action” spectroscopy in conjunction with quantum chemical calculations. The aquation products, cis-[PtX(NH3)2(H2O)]+ (X = Cl, OH), lying along the path responsible for biological activity, are shown to display distinctive features responding to ligation pattern and optimized geometry. The IR spectra of trans-[PtX(NH3)2(H2O)]+ are different, testifying that cis and trans complexes are stable, non interconverting species both in solution and in the gas phase. Ligand substitution by simple nucleophiles (L = pyridine, 4(5)-methylimidazole, thioanisole, trimethylphosphate, acetamide, dimethylacetamide, urea and thiourea) yields cis-[PtCl(NH3)2(L)]+ complexes displaying remarkable regioselectivity whenever L presents multiple candidate platination sites. The incipient formation of cisplatin-derived complexes with the recognized biological amino acid targets L-histidine (His) and L-methionine (Met) has been investigated revealing the primary platination event to be mainly directed at the Nπ atom of the imidazole side chain of His and to the thiomethyl sulfur of Met. The isomer and conformer population of the ensuing cis-[PtCl(NH3)2(Met/His)]+ complexes, sampled in the gas phase, can be ascertained by photofragmentation kinetics on isomer/conformer specific resonances.

Gas-phase metal ion chelation investigated with IRMPD spectroscopy: A brief review of Robert Dunbar's contributions

With the passing of Prof. Robert C. Dunbar on 31 October 2017, the field of ion chemistry lost one of its modern heroes. Throughout his career in mass spectrometry, two of his main research interests involved the interaction of trapped ions with electromagnetic radiation and the chelation motifs of metal ions with organic ligands. The focus of his early career was on the fundamental processes that take place in molecules upon ultraviolet and infrared excitation. From 2003 to 2017, his scientific interests shifted to more structural questions, notably to resolving the structures and binding motifs of metal ion chelation complexes by application of infrared photodissociation spectroscopy. These experiments were carried out during numerous visits to the (Free Electron Laser for Infrared eXperiments) (FELIX) facility in the Netherlands and were complemented by extensive theoretical investigations by Rob. As a tribute to our friend, we present in this contribution a brief review of this work.

Probing the gas-phase structure of charge-tagged intermediates of a proline catalyzed aldol reaction – vibrational spectroscopy distinguishes oxazolidinone from enamine species

Charge-tagging enables the detection of reaction intermediates which are probed by IRMPD spectroscopy in combination with theory.

Chiral differentiation of d- and l-isoleucine using permethylated β-cyclodextrin: infrared multiple photon dissociation spectroscopy, ion-mobility mass spectrometry, and DFT calculations

Chiral differentiation of protonated isoleucine (Ile) using permethylated β-cyclodextrin (perCD) in the gas-phase was studied using infrared multiple photon dissociation (IRMPD) spectroscopy, ion-mobility, and density functional theory (DFT) calculations. The gaseous protonated non-covalent complexes of perCD and d-Ile or l-Ile produced by electrospray ionization were interrogated by laser pulses in the wavenumber region of 2650 to 3800 cm-1. The IRMPD spectra showed remarkably different IR spectral features for the d-Ile or l-Ile and perCD non-covalent complexes. However, drift-tube ion-mobility experiments provided only a small difference in their collision cross-sections, and thus a limited separation of the d- and l-Ile complexes. DFT calculations revealed that the chiral distinction of the d- and l-complexes by IRMPD spectroscopy resulted from local interactions of the protonated Ile with perCD. Furthermore, the theoretical results showed that the IR absorption spectra of higher energy conformers (by ∼13.7 kcal mol-1) matched best with the experimentally observed IRMPD spectra. These conformers are speculated to be formed from kinetic-trapping of the solution-phase conformers. This study demonstrated that IRMPD spectroscopy provides an excellent platform for differentiating the subtle chiral difference of a small amino acid in a cyclodextrin-complexation environment; however, drift-tube ion-mobility did not have sufficient resolution to distinguish the chiral difference.

Proton Transfer Accounting for Anomalous Collision-Induced Dissociation of Proton-Bound Hoogsteen Base Pair of Cytosine and Guanine

To understand the anomalous collision-induced dissociation (CID) behavior of the proton-bound Hoogsteen base pair of cytosine (C) and guanine (G), C:H⁺∙∙∙G, we investigated CID of a homologue series of proton-bound heterodimers of C, 1-methylcytosine, and 5-methylcytosine with G as a common base partner. The CID experiments were performed in an energy-resolved way (ER-CID) under both multiple and near-single collision conditions. The relative stabilities of the protonated complexes examined by ER-CID suggested that the proton-bound complexes produced by electrospray ionization in this study are proton-bound Hoogsteen base pairs. On the other hand, in contrast to the other base pairs, CID of C:H⁺∙∙∙G exhibited more abundant productions of C:H⁺, the fragment protonated on the moiety with a smaller proton affinity, than that of G:H⁺. This appeared to contradict general prediction based on the kinetic method. However, further theoretical exploration of potential energy surfaces found that there can be facile proton transfers in the proton-bound Hoogsteen base pairs during the CID process, which makes the process accessible to an additional product state of O-protonated C for C:H⁺ fragments. The presence of an additional dissociation channel, which in other words corresponds to twofold degeneracy in the transition state leading to C:H⁺ fragments, effectively doubles the apparent reaction rate for production of C:H⁺. In this way, the process gives rise to the anomaly, the observed pronounced formation of C:H⁺ in the CID of the proton-bound Hoogsteen base pair, C:H⁺∙∙∙G. Graphical Abstract ᅟ.

Modified Quadrupole Ion Trap Mass Spectrometer for Infrared Ion Spectroscopy: Application to Protonated Thiated Uridines

Modifications to a Paul-type quadrupole ion trap mass spectrometer providing optical access to the trapped ion cloud as well as hardware and software for coupling to a table-top IR optical parametric oscillator laser (OPO) are detailed. Critical experimental parameters for infrared multiple photon dissociation (IRMPD) on this instrument are characterized. IRMPD action spectra, collected in the hydrogen-stretching region with this instrument, complemented by spectra in the IR fingerprint region acquired at the FELIX facility, are employed to characterize the structures of the protonated forms of 2-thiouridine, [s²Urd+H]⁺, and 4-thiouridine, [s⁴Urd+H]⁺. The measured spectra are compared with predicted linear IR spectra calculated at the B3LYP/6-311+G(d,p) level of theory to determine the conformers populated in the experiments. This comparison indicates that thiation at the 2- or 4-positions shifts the protonation preference between the 2,4-H tautomer and 4-protonation in opposite directions versus canonical uridine, which displays a roughly equal preference for the 2,4-H tautomer and O4 protonation. As found for canonical uridine, protonation leads to a mixture of conformers exhibiting C2'-endo and C3'-endo sugar puckering with an anti nucleobase orientation being populated for both 2- and 4-thiated uridine. Graphical Abstract ᅟ.

Protonated glycine supramolecular systems: the need for quantum dynamics

Quantum mechanical simulations unequivocally explain experimental IR spectra of protonated supramolecular systems.

IR spectroscopy is one of the most commonly employed techniques to study molecular vibrations and interactions. However, characterization of experimental IR spectra is not always straightforward. This is the case of protonated glycine supramolecular systems like Gly₂H⁺ and (GlyH + nH₂), whose IR spectra raise questions which have still to find definitive answers even after theoretical spectroscopy investigations. Specifically, the assignment of the conformer responsible for the spectrum of the protonated glycine dimer (Gly₂H⁺) has led to much controversy and it is still debated, while structural hypotheses formulated to explain the main experimental spectral features of (GlyH + nH₂) systems have not been theoretically confirmed. We demonstrate that simulations must account for quantum dynamical effects in order to resolve these open issues. This is achieved by means of our divide-and-conquer semiclassical initial value representation technique, which approximates the quantum dynamics of high dimensional systems with remarkable accuracy and outperforms not only the commonly employed but unfit scaled-harmonic approaches, but also pure classical dynamics simulations. Besides the specific insights concerning the two particular cases presented here, the general conclusion is that, due to the widespread presence of protonated systems in chemistry, quantum dynamics may play a prominent role and should not be totally overlooked even when dealing with large systems including biological structures.

Infrared Multiple Photon Dissociation Spectroscopy of Cationized Canavanine: Side-Chain Substitution Influences Gas-Phase Zwitterion Formation†

Infrared multiple photon dissociation spectroscopy was performed on protonated and cationized canavanine (Cav), a non-protein amino acid oxy-analog of arginine. Infrared spectra in the XH stretching region (3000 - 4000 cm^-1) were obtained at the Centre Laser Infrarouge d'Orsay (CLIO) facility. Comparison of the experimental infrared spectra with scaled harmonic frequencies at the B3LYP/6-31+G(d,p) level of theory indicates that canavanine is in a canonical neutral form in CavH⁺, CavLi⁺, and CavNa⁺; therefore, these cations are charge-solvated structures. The infrared spectrum of CavK⁺ is consistent with a mixture of Cav in canonical and zwitterionic forms leading to both charge-solvated and salt-bridged cationic structures. The Cav moiety in CavCs⁺ is shown to be zwitterionic, forming a salt-bridged structure for the cation. Infrared spectra in the fingerprint region (1000 - 2000 cm^-1) obtained at the FELIX Laboratory in Nijmegen, Netherlands support these assignments. These results show that that a single oxygen atom substitution in the side chain reduces the stability of the zwitterion compared to that of the protein amino acid arginine (Arg), which has been shown previously to adopt a zwitterionic structure in ArgNa⁺ and ArgK⁺. This difference can be explained in part due to the decreased basicity of Cav (PA = 1001 kJ/mol) as compared to arginine (PA = 1051 kJ/mol), but not entirely, as lysine, which has nearly the same proton affinity as Cav, (~993 kJ/mol) forms only canonical structures with Na⁺, K⁺, and Cs⁺. A major difference between the zwitterionic forms of ArgM⁺ and CavM⁺ is that the protonation site is on the side chain for Arg and on the N-terminus for Cav. This results in systematically weaker salt bridges in the Cav zwitterions. In addition, the presence of another hydrogen-bonding acceptor atom in the side chain contributes to the stability of the canonical structures for the smaller alkali cations.

Infrared Multiphoton Dissociation Spectroscopy with Free-Electron Lasers: On the Road from Small Molecules to Biomolecules

Infrared multiphoton dissociation (IRMPD) spectroscopy is commonly used to determine the structure of isolated, mass-selected ions in the gas phase. This method has been widely used since it became available at free-electron laser (FEL) user facilities. Thus, in this Minireview, we examine the use of IRMPD/FEL spectroscopy for investigating ions derived from small molecules, metal complexes, organometallic compounds and biorelevant ions. Furthermore, we outline new applications of IRMPD spectroscopy to study biomolecules.

Chiral differentiation of d- and l-alanine by permethylated β-cyclodextrin: IRMPD spectroscopy and DFT methods

The gaseous chiral differentiation of alanine by permethylated β-cyclodextrin was studied using IRMPD spectroscopy and density functional theory calculations. The protonated non-covalent complexes of permethylated β-cyclodextrin and d- or l-alanine were mass-selected and investigated by IR laser pulses in the wavelength region of 2650-3800 cm^-1. The remarkably different features of the IRMPD spectra for d- and l-alanine are described, and their origin is elucidated by quantum chemical calculations. We show that the differentiation of the experimentally observed spectral features is the result of different local interactions of d- and l-alanine with permethylated β-cyclodextrin. We also assign the extremely high-frequency (>3700 cm^-1) bands in the observed spectra to the stretch motions of completely isolated alanine -OH groups.

Protonation induces base rotation of purine nucleotides pdGuo and pGuo

Infrared multiple photon dissociation (IRMPD) action spectra of the protonated forms of 2'-deoxyguanosine-5'-monophosphate and guanosine-5'-monophosphate, [pdGuo+H](+) and [pGuo+H](+), are measured over the IR fingerprint and hydrogen-stretching regions using the FELIX free electron laser and an OPO/OPA laser system. Electronic structure calculations are performed to generate low-energy conformations of [pdGuo+H](+) and [pGuo+H](+) and determine their relative stabilities at the B3LYP/6-311+G(2d,2p)//B3LYP/6-311+G(d,p) and MP2(full)/6-311+G(2d,2p)//B3LYP/6-311+G(d,p) levels of theory. Comparative analyses of the measured IRMPD action spectra and B3LYP/6-311+G(d,p) linear IR spectra computed for the low-energy conformers are performed to determine the most favorable site of protonation and the conformers present in the experiments. These comparisons and the computed energetics find that N7 protonation is considerably preferred over O6 and N3, and the N7 protonated ground-state conformers of [pdGuo+H](+) and [pGuo+H](+) are populated in the experiments. The 2'-hydroxyl substituent does not significantly impact the stable low-energy conformers of [pdGuo+H](+)vs. those of [pGuo+H](+). The effect of the 2'-hydroxyl substituent is primarily reflected in the relative intensities of the measured IRMPD bands, as the IRMPD profiles of [pdGuo+H](+) and [pGuo+H](+) are quite similar. Comparisons to previous IRMPD spectroscopy investigations of the protonated forms of the guanine nucleosides, [dGuo+H](+) and [Guo+H](+), and deprotonated forms of the guanine nucleotides, [pdGuo-H](-) and [pGuo-H](-), provide insight into the effects of the phosphate moiety and protonation on the conformational features of the nucleobase and sugar moieties. Protonation is found to induce base rotation of the guanine residue to an anti orientation vs. the syn orientation found for the deprotonated forms of the guanine nucleotides.

Charge-state Resolved Infrared Multiple Photon Dissociation (IRMPD) Spectroscopy of Ubiquitin Ions in the Gas Phase

In this study, we obtained for the first time the direct infrared multiple photon dissociation (IRMPD) spectra of ubiquitin ions in the range 2700-3750 cm-1. Ubiquitin ions with different charge states showed absorption in the two regions of 2940-3000 cm-1 and 3280-3400 cm-1. The increase of the charge state of ubiquitin ions broadened the absorption peak on the high-frequency side in the second region, indicating some hydrogen bonds were weakened due to Coulomb interaction. It is also found that the relative intensity of the absorption peak in the first region compared to the absorption peak in the second region increased with increasing charge state, making the IRMPD spectra charge-state resolved. Although it is usually reasonable to suggest the origin of the absorption in the range 2940-3000 cm-1 as the C-H bond stretching modes, the results show significantly reduced absorption after the deuteration of all labile hydrogen atoms. A possible explanation for this is that the coupling coefficients between the C-H vibrational mode and other selective modes decreased greatly after the deuteration, reducing the rate of energy redistribution and probability of consecutive IR absorption.

Undervalued N3 Coordination Revealed in the Cisplatin Complex with 2'-Deoxyadenosine-5'-monophosphate by a Combined IRMPD and Theoretical Study

The complex obtained by the reaction of cisplatin and 2'-deoxyadenosine-5'-monophosphate (5'-dAMP) in water has been isolated and detected by electrospray ionization mass spectrometry. The so-formed cis-[PtCl(NH₃)₂(5'-dAMP)]⁺ complex has been studied in detail by infrared multiple photon dissociation (IRMPD) spectroscopy in two spectral ranges, namely, 700-1900 and 2800-3800 cm^-1, backed by quantum-chemical calculations at the B3LYP/LACV3P/6-311G** level of theory. In agreement with the computational results, the vibrational spectroscopic characterization of cis-[PtCl(NH₃)₂(5'-dAMP)]⁺ shows that the sampled ionic population comprises two major isomers, differentiated in the X-H stretching region by their distinct fragmentation patterns. One of these species presents coordination of the platinum moiety at the N3 position of adenine, whereas in the second one, platinum is bound at the N1 position of adenine. IRMPD kinetics have allowed an estimation of their relative proportions. Surprisingly, the most abundant component of cis-[PtCl(NH₃)₂(5'-dAMP)]⁺ is the N3 isomer, although it is slightly less stable than the other potential isomers in the gas phase. In contrast, the lowest-energy species, namely, the one showing cisplatin binding to the N7 position of adenine, seems to be the one less represented in the sampled ionic population. These findings suggest that the reaction of cisplatin with 5'-dAMP is governed by the kinetics of the process occurring in solution rather than by the thermodynamic factors.

Effects of ESI conditions on kinetic trapping of the solution-phase protonation isomer of p-aminobenzoic acid in the gas phase

The effects of electrospray ionization (ESI) solvent and source temperature on the relative abundance of the preferred solution-phase (N-protonated; i.e. amine) versus preferred gas-phase (O-protonated; i.e., acid) isomers of p-aminobenzoic acid (PABA) were investigated. When PABA was electrosprayed from protic solvents (i.e., methanol/water), the infrared multiple photon dissociation (IRMPD) spectrum recorded was consistent with that for O-protonation, according to both calculations and previous studies. When aprotic solvent (i.e., acetonitrile) was used, a different spectrum was recorded and was assigned to the N-protonated isomer. As the amine is the preferred protonation site in solution, this suggests that an isomerization takes place under certain conditions. Photodissociation at the diagnostic band for the O-protonated isomer (NH₂ stretching mode) was used to quantify the relative contributions of each isomer to ion signal as a function of ESI conditions. For mixtures of methanol and acetonitrile, the relative contribution of the O-protonated gas-phase structure increased as a function of methanol content. Yet, substituting methanol for water resulted in a marked decrease of isomerization to the O-protonated structure. The source temperature (i.e., temperature of a heated desolvation capillary) was found to play a key role in determining the extent of isomerization, with higher temperatures yielding increased presence of gas-phase structures. These results are consistent with a protic bridge mechanism, in which the ESI droplet temperatures, dependent on endothermic desolvation and radiative heating from the capillary, may determine the isomerization yield.

Near-UV Photodissociation of Tryptic Peptide Cation Radicals. Scope and Effects of Amino Acid Residues and Radical Sites

Peptide cation-radical fragment ions of the z-type, [^●AXAR⁺], [^●AXAK⁺], and [^●XAR⁺], where X = A, C, D, E, F, G, H, K, L, M, N, P, Y, and W, were generated by electron transfer dissociation of peptide dications and investigated by MS³-near-ultraviolet photodissociation (UVPD) at 355 nm. Laser-pulse dependence measurements indicated that the ion populations were homogeneous for most X residues except phenylalanine. UVPD resulted in dissociations of backbone CO─NH bonds that were accompanied by hydrogen atom transfer, producing fragment ions of the [y_n]⁺ type. Compared with collision-induced dissociation, UVPD yielded less side-chain dissociations even for residues that are sensitive to radical-induced side-chain bond cleavages. The backbone dissociations are triggered by transitions to second (B) excited electronic states in the peptide ion R-CH^●-CONH- chromophores that are resonant with the 355-nm photon energy. Electron promotion increases the polarity of the B excited states, R-CH⁺-C^●(O^-)NH-, and steers the reaction to proceed by transfer of protons from proximate acidic C_α and amide nitrogen positions. Graphical Abstract ᅟ.

Probing the geometry reorganization from solution to gas-phase in putrescine derivatives by IRMPD, 1H-NMR and theoretical calculations

Geometry reorganization of ESI formed ions are demonstrated and explicit calculations of the solution phase are shown to be relevant.

Hydrolysis of cis- and transplatin: structure and reactivity of the aqua complexes in a solvent free environment

Vibrational spectroscopy and ligand exchange reactivity allows unambiguous discrimination of singly and doubly aquated species from cis- and transplatin, highlighting elementary events at the basis of anticancer action.

Cisplatin and transplatin interaction with methionine: bonding motifs assayed by vibrational spectroscopy in the isolated ionic complexes

IRMPD spectroscopy discloses N- versus S-platination.