Infrared action spectroscopy of the deprotonated formic acid trimer, trapped in helium nanodroplets.

Hydrogen bonding interactions are essential in the structural stabilization and physicochemical properties of complex molecular systems, and carboxylic acid functional groups are common participants in these motifs. Consequently, the neutral formic acid (FA) dimer has been extensively investigated in the past, as it represents a useful model system to investigate proton donor-acceptor interactions. The analogous deprotonated dimers, in which two carboxylate groups are bound by a single proton, have also served as informative model systems. In these complexes, the position of the shared proton is mainly determined by the proton affinity of the carboxylate units. However, very little is known about the nature of the hydrogen bonding interactions in systems containing more than two carboxylate units. Here we report a study on the deprotonated (anionic) FA trimer. IR spectra are recorded in the 400-2000 cm-1 spectral range by means of vibrational action spectroscopy of FA trimer ions embedded in helium nanodroplets. Characterization of the gas-phase conformer and assignment of the vibrational features is achieved by comparing the experimental results with electronic structure calculations. To assist in the assignments, the 2H and 18O FA trimer anion isotopologues are also measured under the same experimental conditions. Comparison between the experimental and computed spectra, especially the observed shifts in spectral line positions upon isotopic substitution of the exchangeable protons, suggests that the prevalent conformer, under the experimental conditions, exhibits a planar structure that resembles the crystalline structure of formic acid.

Establishing carbon-carbon double bond position and configuration in unsaturated fatty acids by gas-phase infrared spectroscopy.

Fatty acids are an abundant class of lipids that are characterised by wide structural variation including isomeric diversity arising from the position and configuration of functional groups. Traditional approaches to fatty acid characterisation have combined chromatography and mass spectrometry for a description of the composition of individual fatty acids while infrared (IR) spectroscopy has provided insights into the functional groups and bond configurations at the bulk level. Here we exploit universal 3-pyridylcarbinol ester derivatization of fatty acids to acquire IR spectra of individual lipids as mass-selected gas-phase ions. Intramolecular interactions between the protonated pyridine moiety and carbon-carbon double bonds present highly sensitive probes for regiochemistry and configuration through promotion of strong and predictable shifts in IR resonances. Gas-phase IR spectra obtained from unsaturated fatty acids are shown to discriminate between isomers and enable the first unambiguous structural assignment of 6Z-octadecenoic acid in human-derived cell lines. Compatibility of 3-pyridylcarbinol ester derivatization with conventional chromatography-mass spectrometry and now gas-phase IR spectroscopy paves the way for comprehensive structure elucidation of fatty acids that is sensitive to regio- and stereochemical variations and with the potential to uncover new pathways in lipid metabolism.

Adatom Bonding Sites in a Nickel-Fe3 O4 (001) Single-Atom Model Catalyst and O2 Reactivity Unveiled by Surface Action Spectroscopy with Infrared Free-Electron Laser Light.

Single-atom (SA) catalysis presently receives much attention with its promise to decrease the cost of the active material while increasing the catalyst's performance. However, key details such as the exact location of SA species and their stability are often unclear due to a lack of atomic level information. Here, we show how vibrational spectra measured with surface action spectroscopy (SAS) and density functional theory (DFT) simulations can differentiate between different adatom binding sites and determine the location of Ni and Au single atoms on Fe3 O4 (001). We reveal that Ni and Au adatoms selectively bind to surface oxygen ions which are octahedrally coordinated to Fe ions. In addition, we find that the Ni adatoms can activate O2 to superoxide in contrast to the bare surface and Ni in subsurface positions. Overall, we unveil the advantages of combining SAS and DFT for improving the understanding of single-atom catalysts.

Studying the Key Intermediate of RNA Autohydrolysis by Cryogenic Gas-Phase Infrared Spectroscopy.

Over the course of the COVID-19 pandemic, mRNA-based vaccines have gained tremendous importance. The development and analysis of modified RNA molecules benefit from advanced mass spectrometry and require sufficient understanding of fragmentation processes. Analogous to the degradation of RNA in solution by autohydrolysis, backbone cleavage of RNA strands was equally observed in the gas phase; however, the fragmentation mechanism remained elusive. In this work, autohydrolysis-like intermediates were generated from isolated RNA dinucleotides in the gas phase and investigated using cryogenic infrared spectroscopy in helium nanodroplets. Data from both experiment and density functional theory provide evidence for the formation of a five-membered cyclic phosphate intermediate and rule out linear or six-membered structures. Furthermore, the experiments show that another prominent condensed-phase reaction of RNA nucleotides can be induced in the gas phase: the tautomerization of cytosine. Both observed reactions are therefore highly universal and intrinsic properties of the investigated molecules.

Cryogenic infrared spectroscopy provides mechanistic insight into the fragmentation of phospholipid silver adducts.

Tandem mass spectrometry is arguably the most important analytical tool for structure elucidation of lipids and other metabolites. By fragmenting intact lipid ions, valuable structural information such as the lipid class and fatty acyl composition are readily obtainable. The information content of a fragment spectrum can often be increased by the addition of metal cations. In particular, the use of silver ions is deeply rooted in the history of lipidomics due to their propensity to coordinate both electron-rich heteroatoms and C = C bonds in aliphatic chains. Not surprisingly, coordination of silver ions was found to enable the distinction of sn-isomers in glycerolipids by inducing reproducible intensity differences in the fragment spectra, which could, however, not be rationalized. Here, we investigate the fragmentation behaviors of silver-adducted sn- and double bond glycerophospholipid isomers by probing fragment structures using cryogenic gas-phase infrared (IR) spectroscopy. Our results confirm that neutral headgroup loss from silver-adducted glycerophospholipids leads to dioxolane-type fragments generated by intramolecular cyclization. By combining high-resolution IR spectroscopy and computational modelling of silver-adducted fragments, we offer qualitative explanations for different fragmentation behaviors of glycerophospholipid isomers. Overall, the results demonstrate that gas-phase IR spectroscopy of fragment ions can significantly contribute to our understanding of lipid dissociation mechanisms and the influence of coordinating cations.

Unveiling Glycerolipid Fragmentation by Cryogenic Infrared Spectroscopy.

Mass spectrometry is routinely employed for structure elucidation of molecules. Structural information can be retrieved from intact molecular ions by fragmentation; however, the interpretation of fragment spectra is often hampered by poor understanding of the underlying dissociation mechanisms. For example, neutral headgroup loss from protonated glycerolipids has been postulated to proceed via an intramolecular ring closure but the mechanism and resulting ring size have never been experimentally confirmed. Here we use cryogenic gas-phase infrared (IR) spectroscopy in combination with computational chemistry to unravel the structures of fragment ions and thereby shed light on elusive dissociation mechanisms. Using the example of glycerolipid fragmentation, we study the formation of protonated five-membered dioxolane and six-membered dioxane rings and show that dioxolane rings are predominant throughout different glycerolipid classes and fragmentation channels. For comparison, pure dioxolane and dioxane ions were generated from tailor-made dehydroxyl derivatives inspired by natural 1,2- and 1,3-diacylglycerols and subsequently interrogated using IR spectroscopy. Furthermore, the cyclic structure of an intermediate fragment occurring in the phosphatidylcholine fragmentation pathway was spectroscopically confirmed. Overall, the results contribute substantially to the understanding of glycerolipid fragmentation and showcase the value of vibrational ion spectroscopy to mechanistically elucidate crucial fragmentation pathways in lipidomics.

Surface oxygen Vacancies on Reduced Co3 O4 (100): Superoxide Formation and Ultra-Low-Temperature CO Oxidation.

The activation of molecular oxygen is a fundamental step in almost all catalytic oxidation reactions. We have studied this topic and the role of surface vacancies for Co3 O4 (100) films with a synergistic combination of experimental and theoretical methods. We show that the as-prepared surface is B-layer terminated and that mild reduction produces oxygen single and double vacancies in this layer. Oxygen adsorption experiments clearly reveal different superoxide species below room temperature. The superoxide desorbs below ca. 120 K from a vacancy-free surface and is not active for CO oxidation while superoxide on a surface with oxygen vacancies is stable up to ca. 270 K and can oxidize CO already at the low temperature of 120 K. The vacancies are not refilled by oxygen from the superoxide, which makes them suitable for long-term operation. Our joint experimental/theoretical effort highlights the relevance of surface vacancies in catalytic oxidation reactions.

Non-covalent double bond sensors for gas-phase infrared spectroscopy of unsaturated fatty acids.

The position and configuration of carbon-carbon double bonds in unsaturated fatty acids is crucial for their biological functions and influences health and disease. However, double bond isomers are not routinely distinguished by classical mass spectrometry workflows. Instead, they require sophisticated analytical approaches usually based on chemical derivatization and/or instrument modification. In this work, a novel strategy to investigate fatty acid double bond isomers (18:1) without prior chemical treatment or modification of the ion source was implemented by non-covalent adduct formation in the gas phase. Fatty acid adducts with sodium, pyridinium, trimethylammonium, dimethylammonium, and ammonium cations were characterized by a combination of cryogenic gas-phase infrared spectroscopy, ion mobility-mass spectrometry, and computational modeling. The results reveal subtle differences between double bond isomers and confirm three-dimensional geometries constrained by non-covalent ion-molecule interactions. Overall, this study on fatty acid adducts in the gas phase explores new avenues for the distinction of lipid double bond isomers and paves the way for further investigations of coordinating cations to increase resolution.

Unravelling the structural complexity of glycolipids with cryogenic infrared spectroscopy.

Glycolipids are complex glycoconjugates composed of a glycan headgroup and a lipid moiety. Their modular biosynthesis creates a vast amount of diverse and often isomeric structures, which fulfill highly specific biological functions. To date, no gold-standard analytical technique can provide a comprehensive structural elucidation of complex glycolipids, and insufficient tools for isomer distinction can lead to wrong assignments. Herein we use cryogenic gas-phase infrared spectroscopy to systematically investigate different kinds of isomerism in immunologically relevant glycolipids. We show that all structural features, including isomeric glycan headgroups, anomeric configurations and different lipid moieties, can be unambiguously resolved by diagnostic spectroscopic fingerprints in a narrow spectral range. The results allow for the characterization of isomeric glycolipid mixtures and biological applications.

Direct Experimental Characterization of the Ferrier Glycosyl Cation in the Gas Phase.

The Ferrier rearrangement reaction is crucial for the synthesis of pharmaceuticals. Although its mechanism was described more than 50 years ago, the structure of the intermediate remains elusive. Two structures have been proposed for this Ferrier glycosyl cation: a 1,2-unsaturated cation that is resonance-stabilized within the pyranose ring or a cation that is stabilized by the anchimeric assistance of a neighboring acetyl group. Using a combination of gas-phase cryogenic infrared spectroscopy in helium nanodroplets and first-principles density functional theory, we provide the first direct structural characterization of Ferrier cations. The data show that both acetylated glucal and galactal lead to glycosyl cations of the dioxolenium type.

Probing the conformational landscape and thermochemistry of DNA dinucleotide anions via helium nanodroplet infrared action spectroscopy.

Isolation of biomolecules in vacuum facilitates characterization of the intramolecular interactions that determine three-dimensional structure, but experimental quantification of conformer thermochemistry remains challenging. Infrared spectroscopy of molecules trapped in helium nanodroplets is a promising methodology for the measurement of thermochemical parameters. When molecules are captured in a helium nanodroplet, the rate of cooling to an equilibrium temperature of ca. 0.4 K is generally faster than the rate of isomerization, resulting in "shock-freezing" that kinetically traps molecules in local conformational minima. This unique property enables the study of temperature-dependent conformational equilibria via infrared spectroscopy at 0.4 K, thereby avoiding the deleterious effects of spectral broadening at higher temperatures. Herein, we demonstrate the first application of this approach to ionic species by coupling electrospray ionization mass spectrometry (ESI-MS) with helium nanodroplet infrared action spectroscopy to probe the structure and thermochemistry of deprotonated DNA dinucleotides. Dinucleotide anions were generated by ESI, confined in an ion trap at temperatures between 90 and 350 K, and entrained in traversing helium nanodroplets. The infrared action spectra of the entrained ions show a strong dependence on pre-pickup ion temperature, consistent with the preservation of conformer population upon cooling to 0.4 K. Non-negative matrix factorization was utilized to identify component conformer infrared spectra and determine temperature-dependent conformer populations. Relative enthalpies and entropies of conformers were subsequently obtained from a van't Hoff analysis. IR spectra and conformer thermochemistry are compared to results from ion mobility spectrometry (IMS) and electronic structure methods. The implementation of ESI-MS as a source of dopant molecules expands the diversity of molecules accessible for thermochemical measurements, enabling the study of larger, non-volatile species.

Resolving Sphingolipid Isomers Using Cryogenic Infrared Spectroscopy.

1-Deoxysphingolipids are a recently described class of sphingolipids that have been shown to be associated with several disease states including diabetic and hereditary neuropathy. The identification and characterization of 1-deoxysphingolipids and their metabolites is therefore highly important. However, exact structure determination requires a combination of sophisticated analytical techniques due to the presence of various isomers, such as ketone/alkenol isomers, carbon-carbon double-bond (C=C) isomers and hydroxylation regioisomers. Here we demonstrate that cryogenic gas-phase infrared (IR) spectroscopy of ionized 1-deoxysphingolipids enables the identification and differentiation of isomers by their unique spectroscopic fingerprints. In particular, C=C bond positions and stereochemical configurations can be distinguished by specific interactions between the charged amine and the double bond. The results demonstrate the power of gas-phase IR spectroscopy to overcome the challenge of isomer resolution in conventional mass spectrometry and pave the way for deeper analysis of the lipidome.

Elucidating Surface Structure with Action Spectroscopy.

Surface Action Spectroscopy, a vibrational spectroscopy method developed in recent years at the Fritz Haber Institute is employed for structure determination of clean and H2O-dosed (111) magnetite surfaces. Surface structural information is revealed by using the microscopic surface vibrations as a fingerprint of the surface structure. Such vibrations involve just the topmost atomic layers, and therefore the structural information is truly surface related. Our results strongly support the view that regular Fe3O4(111)/Pt(111) is terminated by the so-called Fetet1 termination, that the biphase termination of Fe3O4(111)/Pt(111) consists of FeO and Fe3O4(111) terminated areas, and we show that the method can differentiate between different water structures in H2O-derived adsorbate layers on Fe3O4(111)/Pt(111). With this, we conclude that the method is a capable new member in the set of techniques providing crucial information to elucidate surface structures. The method does not rely on translational symmetry and can therefore also be applied to systems which are not well ordered. Even an application to rough surfaces is possible.

Surface action spectroscopy with rare gas messenger atoms.

Action spectroscopy with inert gas messengers is commonly used for the characterization of aggregates in the gas phase. The messengers, often rare gas atoms or D2 molecules, are attached to the gas phase aggregates at low temperature. Vibrational spectra of the aggregates are measured via detection of inert gas desorption following a vibrational excitation by variable-energy infrared light. We have constructed an apparatus for the application of action spectroscopy to surfaces of solids with the aim of establishing a new method for the vibrational spectroscopy of surfaces and deposited clusters. Experiments performed for neon covered V2O3(0001) show that this method can provide information about surface vibrations. Besides the surface sensitive channel, there is also a bulk sensitive one as demonstrated with the example of CeO2(111) thin film data. Unlike infrared reflection absorption spectroscopy, normalization to a reference spectrum is not required for action spectroscopy data, and unlike high resolution electron energy loss spectroscopy, the action spectroscopy method does not suffer from moderate resolution nor from multiple excitations. Selective decoration of specific surface features with messenger atoms may be utilized to focus the spectroscopic information onto these features.

Vibrational Spectroscopy of Fluoroformate, FCO2-, Trapped in Helium Nanodroplets.

Fluoroformate, also known as carbonofluoridate, is an intriguing molecule readily formed by the reductive derivatization of carbon dioxide. In spite of its well-known stability, a detailed structural characterization of the isolated anion has yet to be reported. Presented in this work is the vibrational spectrum of fluoroformate obtained by infrared action spectroscopy of ions trapped in helium nanodroplets, the first application of this technique to a molecular anion. The experimental method yields narrow spectral lines, providing experimental constraints on the structure that can be accurately reproduced using high-level ab initio methods. In addition, two notable Fermi resonances between a fundamental and combination band are observed. The electrostatic potential map of fluoroformate reveals substantial charge density on fluorine as well as on the oxygen atoms, suggesting multiple sites for interaction with hydrogen bond donors and electrophiles, which may in turn lead to intriguing solvation structures and reaction pathways.

Hydrogen Chemisorption on Singly Vanadium-Doped Aluminum Clusters.

The effect of vanadium doping on the hydrogen adsorption capacity of aluminum clusters (Aln+ , n=2-18) is studied experimentally by mass spectrometry and infrared multiple photon dissociation (IRMPD) spectroscopy. We find that vanadium doping enhances the reactivity of the clusters towards hydrogen, albeit in a size-dependent way. IRMPD spectra, which provide a fingerprint of the hydrogen binding geometry, show that H2 dissociates upon adsorption. Density functional theory (DFT) calculations for the smaller Aln V+ (n=2-8,10) clusters are in good agreement with the observed reactivity pattern and underline the importance of activation barriers in the chemisorption process. Orbital analysis shows that the activation barriers are due to an unfavorable overlap between cluster and hydrogen orbitals.

Excess charge driven dissociative hydrogen adsorption on Ti2O4.

The mechanism of dissociative D2 adsorption on Ti2O4-, which serves as a model for an oxygen vacancy on a titania surface, is studied using infrared photodissociation spectroscopy in combination with density functional theory calculations and a recently developed single-component artificial force induced reaction method. Ti2O4- readily reacts with D2 under multiple collision conditions in a gas-filled ion trap held at 16 K forming a global minimum-energy structure (DO-Ti-(O)2-Ti(D)-O)-. The highly exergonic reaction proceeds quasi barrier-free via several intermediate species, involving heterolytic D2-bond cleavage followed by D-atom migration. We show that, compared to neutral Ti2O4, the excess negative charge in Ti2O4- is responsible for the substantial lowering of the D2 dissociation barrier, but does not affect the molecular D2 adsorption energy in the initial physisorption step.

Glycan Fingerprinting via Cold-Ion Infrared Spectroscopy.

The diversity of stereochemical isomers present in glycans and glycoconjugates poses a formidable challenge for comprehensive structural analysis. Typically, sophisticated mass spectrometry (MS)-based techniques are used in combination with chromatography or ion-mobility separation. However, coexisting structurally similar isomers often render an unambiguous identification impossible. Other powerful techniques such as gas-phase infrared (IR) spectroscopy have been limited to smaller glycans, since conformational flexibility and thermal activation during the measurement result in poor spectral resolution. This limitation can be overcome by using cold-ion spectroscopy. The vibrational fingerprints of cold oligosaccharide ions exhibit a wealth of well-resolved absorption features that are diagnostic for minute structural variations. The unprecedented resolution of cold-ion spectroscopy coupled with tandem MS may render this the key technology to unravel complex glycomes.

Dissociative Water Adsorption by Al3O4+ in the Gas Phase.

We use cryogenic ion trap vibrational spectroscopy in combination with density functional theory (DFT) to study the adsorption of up to four water molecules on Al3O4+. The infrared photodissociation spectra of [Al3O4(D2O)1-4]+ are measured in the O-D stretching (3000-2000 cm-1) as well as the fingerprint spectral region (1300-400 cm-1) and are assigned based on a comparison with simulated harmonic infrared spectra for global minimum-energy structures obtained with DFT. We find that dissociative water adsorption is favored in all cases. The unambiguous assignment of the vibrational spectra of these gas phase model systems allows identifying characteristic spectral regions for O-D and O-H stretching modes of terminal (µ1) and bridging (µ2) hydroxyl groups in aluminum oxide/water systems, which sheds new light on controversial assignments for solid Al2O3 phases.

Gas-Phase Vibrational Spectroscopy of the Aluminum Oxide Anions (Al2 O3 )1-6 AlO2.

We use cryogenic ion trap vibrational spectroscopy in combination with density functional theory to probe how the structural variability of alumina manifests itself in the structures of the gas-phase clusters (Al2 O3 )n AlO2- with n=1-6. The infrared photodissociation spectra of the D2 -tagged complexes, measured in the fingerprint spectral range (400-1200 cm-1 ), are rich in spectral features and start approaching the vibrational spectrum of amorphous alumina particles for n>4. Aided by a genetic algorithm, we find a trend towards the formation of irregular structures for larger n, with the exception of n=4, which exhibits a C3v ground-state structure. Locating the global minima of the larger systems proves challenging.