Studying the Intrinsic Reactivity of Chromanes by Gas-Phase Infrared Spectroscopy.

Tandem mass spectrometry is routinely used for the structural analysis of organic molecules, but many fragmentation reactions are not well understood. Because several potential structures can correspond to a measured mass, the assignment of product ions is ambiguous using mass spectrometry alone. Here, we combine mass spectrometry with high-resolution gas-phase infrared spectroscopy and computational chemistry tools to identify product ion structures and derive collision-induced fragmentation mechanisms of the chromane derivatives Trolox and Methyltrolox. We find that protonated Trolox and Methyltrolox fragment identically via dehydration and decarbonylation, while deprotonated ions display substantially diverging reactivities. For deprotonated Methyltrolox, we observe unusual radical fragmentation reactions and suggest a [1,2]-Wittig rearrangement involving aryl migration in the gas phase. Overall, the combined experimental and theoretical approach presented here revealed complex proton dynamics and intramolecular rearrangement reactions, which expand our understanding on structure-reactivity relationships of isolated molecules in different protonation states.

Structure and Conformation Determine Gas-Phase Infrared Spectra of Detergents.

Native mass spectrometry of membrane proteins relies on non-ionic detergents which protect the protein during transfer from solution into the gas phase. Once in the gas phase, the detergent micelle must be efficiently removed, which is usually achieved by collision-induced dissociation (CID). Recently, infrared multiple photon dissociation (IRMPD) has emerged as an alternative activation method for the analysis of membrane proteins, which has led to a growing interest in detergents that efficiently absorb infrared light. Here we investigate whether the absorption properties of synthetic detergents can be tailored by merging structural motifs of existing detergents into new hybrid detergents. We combine gas-phase infrared ion spectroscopy with density functional theory to investigate and rationalize the absorption properties of three established detergents and two hybrid detergents with fused headgroups. We show that, although the basic intramolecular interactions in the parent and hybrid detergents are similar, the three-dimensional structures differ significantly and so do the infrared spectra. Our results outline a roadmap for guiding the synthesis of tailored detergents with computational chemistry for future mass spectrometry applications.

Diffractive mirrors for neutral-atom matter-wave optics.

Mirrors for atoms and molecules are essential tools for matter-wave optics with neutral particles. Their realization has required either a clean and atomically smooth crystal surface, sophisticated tailored electromagnetic fields, nanofabrication, or particle cooling because of the inherently short de Broglie wavelengths and strong interactions of atoms with surfaces. Here, we demonstrate reflection of He atoms from inexpensive, readily available, and robust gratings designed for light waves. Using different types of blazed gratings with different periods, we study how microscopic and macroscopic grating properties affect the mirror performance. A holographic grating with 417 nm period shows reflectivity up to 47% for He atoms, demonstrating that commercial gratings can serve as mirrors for thermal energy atoms and molecules. We also observe reflection of He2 and He3 which implies that the grating might also function as a mirror for other breakable particles that, under typical conditions, do not scatter nondestructively from a solid surface such as, e.g., metastable atoms or antihydrogen atoms.

IR spectra and structures of saturated ruthenium cluster carbonyl cations Run(CO)m+ (n = 1-6).

A series of saturated ruthenium cluster carbonyls (Ru(CO)5+, Ru2(CO)9+, Ru3(CO)12+, Ru4(CO)14+, Ru5(CO)16+ and Ru6(CO)18+) have been synthesized in the gas phase and subsequently characterized by infrared spectroscopy. Their size-specific IR spectra in the region of the carbonyl stretch vibration (1900-2150 cm-1) and in the region of the Ru-C-O bending modes (420-620 cm-1) are obtained by infrared multiple photon dissociation spectroscopy. The structures of these cluster carbonyls are assigned by comparison with results from density functional calculations. A multitude of differently activated CO ligands are identified in these cationic cluster carbonyls, reaching from terminal, over non-symmetrically bridging (semi-bridging) ligands with varying degrees of interaction to additional Ru atoms towards symmetrically bridging CO ligands.

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.

Dinitrogen Activation in the Gas Phase: Spectroscopic Characterization of C-N Coupling in the V3 C+ +N2 Reaction.

We report on cluster-mediated C-N bond formation in the gas phase using N2 as a nitrogen source. The V3 C+ +N2 reaction is studied by a combination of ion-trap mass spectrometry with infrared photodissociation (IRPD) spectroscopy and complemented by electronic structure calculations. The proposed reaction mechanism is spectroscopically validated by identifying the structures of the reactant and product ions. V3 C+ exhibits a pyramidal structure of C1 -symmetry. N2 activation is initiated by adsorption in an end-on fashion at a vanadium site, followed by spontaneous cleavage of the N≡N triple bond and subsequent C-N coupling. The IRPD spectrum of the metal nitride product [NV3 (C=N)]+ exhibits characteristic C=N double bond (1530 cm-1 ) and V-N single bond (770, 541 and 522 cm-1 ) stretching bands.

Enhanced elastic scattering of He2 and He3 from solids by multiple-edge diffraction.

We report on a method of enhanced elastic and coherent reflection of 4He2 and 4He3 from a micro-structured solid surface under grazing incidence conditions. The van der Waals bound ground-state helium clusters exhibit fundamental quantum effects: 4He2, characterized by a single ro-vibrational bound state of 10-7 eV dissociation energy, is known to be a quantum halo state; and 4He3 is the only electronic ground-state triatomic system possessing an Efimov state in addition to the ro-vibrational ground state. Classical methods to select and manipulate these clusters by interaction with a solid surface fail due to their exceedingly fragile bonds. Quantum reflection under grazing incidence conditions was demonstrated as a viable tool for elastic scattering from a solid surface but suffers from small reflection probabilities for typical conditions. Here we demonstrate that multiple-edge diffraction enables enhanced elastic scattering of the clusters from a solid. A dual-period reflection grating, where the strips consist of micro-structured edge arrays, shows an up to ten fold increased reflection probability as compared to its conventional counterpart where the strips are plane patches enabling quantum reflection of the clusters. The observed diffraction patterns of the clusters provide evidence of the coherent and elastic nature of scattering by multiple-edge diffraction.

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.

Gas-Phase Mechanism of O.- /Ni2+ -Mediated Methane Conversion to Formaldehyde.

The gas-phase reaction of NiAl2 O4 + with CH4 is studied by mass spectrometry in combination with vibrational action spectroscopy and density functional theory (DFT). Two product ions, NiAl2 O4 H+ and NiAl2 O3 H2 + , are identified in the mass spectra. The DFT calculations predict that the global minimum-energy isomer of NiAl2 O4 + contains Ni in the +II oxidation state and features a terminal Al-O.- oxygen radical site. They show that methane can react along two competing pathways leading to formation of either a methyl radical (CH3 ⋅) or formaldehyde (CH2 O). Both reactions are initiated by hydrogen atom transfer from methane to the terminal O.- site, followed by either CH3 ⋅ loss or CH3 ⋅ migration to an O2- site next to the Ni2+ center. The CH3 ⋅ attaches as CH3 + to O2- and its unpaired electron is transferred to the Ni-center reducing it to Ni+ . The proposed mechanism is experimentally confirmed by vibrational spectroscopy of the reactant and two different product ions.

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.

Atomic Cluster Au_{10}

We report an intense broadband midinfrared absorption band in the Au_{10}^{+} cluster in a region in which only molecular vibrations would normally be expected. Observed in the infrared multiple photon dissociation spectra of Au_{10}Ar^{+}, Au_{10}(N_{2}O)^{+}, and Au_{10}(OCS)^{+}, the smooth feature stretches 700-3400 cm^{-1} (λ=14-2.9 µm). Calculations confirm unusually low-energy allowed electronic excitations consistent with the observed spectra. In Au_{10}(OCS)^{+}, IR absorption throughout the band drives OCS decomposition resulting in CO loss, providing an alternative method of bond activation or breaking.

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.

Experimental test of Babinet's principle in matter-wave diffraction.

We report on an experimental test of Babinet's principle in quantum reflection of an atom beam from diffraction gratings. The He beam is reflected and diffracted from a square-wave grating at near grazing-incidence conditions. According to Babinet's principle the diffraction peak intensities (except for the specular-reflected beam) are expected to be identical for any pair of gratings of complementary geometry. We observe conditions where Babinet's principle holds and also where it fails. Our data indicate breakdown conditions when either the incident or a diffracted beam propagates close to the grating surface. At these conditions, the incident or the diffracted He beam is strongly affected by the dispersive interaction between the atoms and the grating surface. Babinet's principle is also found to break down, when the complementary grating pair shows a large asymmetry in the strip widths. For very small strip widths, edge diffraction from half planes becomes dominant, whereas for the complementary wide strips the atom-surface interactions leads to a strong reduction of all non-specular diffraction peak intensities.

Infrared action spectroscopy of nitrous oxide on cationic gold and cobalt clusters.

Understanding the catalytic decomposition of nitrous oxide on finely divided transition metals is an important environmental issue. In this study, we present the results of a combined infrared action spectroscopy and quantum chemical investigation of molecular N2O binding to isolated Aun+ (n ≤ 7) and Con+ (n ≤ 5) clusters. Infrared multiple-photon dissociation spectra have been recorded in the regions of both the N[double bond, length as m-dash]O (1000-1400 cm-1) and N[double bond, length as m-dash]N (2100-2450 cm-1) stretching modes of nitrous oxide. In the case of Aun+ clusters only the ground electronic state plays a role, while the involvement of energetically low-lying excited states in binding to the Con+ clusters cannot be ruled out. There is a clear preference for N-binding to clusters of both metals but some O-bound isomers are observed in the case of smaller Con(N2O)+ clusters.

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.