Infrared Action Spectroscopy of Low-Temperature Neutral Gas-Phase Molecules of Arbitrary Structure

Probing the structure and dynamics of the heterocyclic PAH xanthene and its water complexes with infrared and microwave spectroscopy

To assess the presence of oxygen-containing polycyclic aromatic hydrocarbons (OPAHs) in the interstellar medium and understand how water aggregates on an OPAH surface, we present a comprehensive gas-phase spectroscopy investigation of the OPAH xanthene (C13H10O) and its complexes with water using IR-UV ion dip spectroscopy and chirped-pulse Fourier transform microwave spectroscopy. The infrared spectrum of xanthene shows weak features at 3.42, 3.43, and 3.47 μm, which have been suggested to partly originate from vibrational modes of PAHs containing sp3 hybridized carbon atoms, in agreement with the molecular structure of xanthene. The high resolution of rotational spectroscopy reveals a tunneling splitting of the rotational transitions, which can be explained with an out-of-plane bending motion of the two lateral benzene rings of xanthene. The nature of the tunnelling motion is elucidated by observing a similar splitting pattern in the rotational transitions of the singly-substituted 13C isotopologues. The rotational spectroscopy investigation is extended to hydrates of xanthene with up to four water molecules. Different xanthene-water binding motifs are observed based on the degree of hydration, with O-H⋯π interactions becoming preferred over O-H⋯Oxanthene interactions as the degree of hydration increases. A structural comparison with water complexes of related molecular systems highlights the impact of the substrate's shape and chemical composition on the arrangement of the surrounding water molecules.

Laboratory infrared spectra and fragmentation chemistry of sulfur allotropes

Sulfur is one of six life-essential elements, but its path from interstellar clouds to planets and their atmospheres is not well known. Astronomical observations in dense clouds have so far been able to trace only 1 percent of cosmic sulfur, in the form of gas phase molecules and volatile ices, with the missing sulfur expected to be locked in a currently unidentified form. The high sulfur abundances inferred in icy and rocky solar system bodies indicate that an efficient pathway must exist from volatile atomic sulfur in the diffuse interstellar medium to some form of refractory sulfur. One hypothesis is the formation of sulfur allotropes, particularly of the stable S8. However, experimental information about sulfur allotropes under astrochemically relevant conditions, needed to constrain their abundance, is lacking. Here, we report the laboratory far-infrared spectra of sulfur allotropes and examine their fragmentation pathways. The spectra, including that of cold, isolated S8 with three bands at 53.5, 41.3 and 21.1 µm, form a benchmark for computational modelling, which show a near-perfect match with the experiments. The experimental fragmentation pathways of sulfur allotropes, key information for astrochemical formation/destruction models, evidence a facile fragmentation of S8. These findings suggest the presence of sulfur allotropes distributions in interstellar space or in the atmosphere of planets, dependent on the environmental conditions.

Infrared bands of neutral gas-phase carbon clusters in a broad spectral range

The identification of species in the interstellar medium requires precise and molecule-specific spectroscopic information in the laboratory framework, in broad spectral ranges and under conditions relevant to interstellar environments. In this work, we measure the gas-phase infrared spectra of neutral carbon clusters, CN (N = 6-11), in a molecular beam. The CN distribution is formed by photofragmentation of C60 molecules, concurrently showing a top-down formation mechanism. A broad spectral range in the infrared between 500-3200 cm-1 (20-3.125 μm) is investigated. We observe strong bands between 5 and 6 μm, in conjunction with novel features in the 3 μm region. Density functional theory calculations reveal that these short wavelength modes correspond to combination bands with significant infrared intensity. Moreover, we identify the N ≤ 10 clusters as linear, while C11 adopts a ring configuration, placing the linear-to-ring transition at N = 11 under our molecular beam conditions. The linearity of C10 is discussed based on the formation pathway from larger clusters in energetic conditions. Given the vast and very precise infrared information already been released from the James Webb Space Telescope mission, this infrared spectroscopic data set in conjunction with information on formation mechanisms is of major relevance for identifying neutral carbon clusters in astronomical environments.

The infrared absorption spectrum of phenylacetylene and its deuterated isotopologue in the mid- to far-IR

Anharmonicity strongly influences the absorption and emission spectra of polycyclic aromatic hydrocarbon (PAH) molecules. Here, IR-UV ion-dip spectroscopy experiments together with detailed anharmonic computations reveal the presence of fundamental, overtone, as well as 2- and 3-quanta combination band transitions in the far- and mid-infrared absorption spectra of phenylacetylene and its singly deuterated isotopologue. Strong absorption features in the 400-900 cm-1 range originate from CH(D) in-plane and out-of-plane wags and bends, as well as bending motions including the C≡C and CH bonds of the acetylene substituent and the aromatic ring. For phenylacetylene, every absorption feature is assigned either directly or indirectly to a single or multiple vibrational mode(s). The measured spectrum is dense, broad, and structureless in many regions but well characterized by computations. Upon deuteration, large isotopic shifts are observed. At frequencies above 1500 cm-1 for d1-phenylacetylene, a one-to-one match is seen when comparing computations and experiments with all features assigned to combination bands and overtones. The C≡C stretch observed in phenylacetylene is not observed in d1-phenylacetylene due to a computed 40-fold drop in intensity. Overall, a careful treatment of anharmonicity that includes 2- and 3-quanta modes is found to be crucial to understand the rich details of the infrared spectrum of phenylacetylene. Based on these results, it can be expected that such an all-inclusive anharmonic treatment will also be key for unraveling the infrared spectra of PAHs in general.

Indication of 310-Helix Structure in Gas-Phase Neutral Pentaalanine

We investigate the gas-phase structure of the neutral pentaalanine peptide. The IR spectrum in the 340-1820 cm^-1 frequency range is obtained by employing supersonic jet cooling, infrared multiphoton dissociation, and vacuum-ultraviolet action spectroscopy. Comparison with quantum chemical spectral calculations suggests that the molecule assumes multiple stable conformations, mainly of two structure types. In the most stable conformation theoretically found, the N-terminus forms a C5 ring and the backbone resembles that of an 3₁₀-helix with two β-turns. Additionally, the conformational preferences of pentaalanine have been evaluated using Born-Oppenheimer molecular dynamics, showing that a nonzero simulation time step causes a systematic frequency shift.

Some opinions on MD-based vibrational spectroscopy of gas phase molecules and their assembly: An overview of what has been achieved and where to go

We hereby review molecular dynamics simulations for anharmonic gas phase spectroscopy and provide some of our opinions of where the field is heading. With these new directions, the theoretical IR/Raman spectroscopy of large (bio)-molecular systems will be more easily achievable over longer time-scale MD trajectories for an increase in accuracy of the MD-IR and MD-Raman calculated spectra. With the new directions presented here, the high throughput 'decoding' of experimental IR/Raman spectra into 3D-structures should thus be possible, hence advancing e.g. the field of MS-IR for structural characterization by spectroscopy. We also review the assignment of vibrational spectra in terms of anharmonic molecular modes from the MD trajectories, and especially introduce our recent developments based on Graph Theory algorithms. Graph Theory algorithmic is also introduced in this review for the identification of the molecular 3D-structures sampled over MD trajectories.

Neutral Peptides in the Gas Phase: Conformation and Aggregation Issues

Combined IR and UV laser spectroscopic techniques in molecular beams merged with theoretical approaches have proven to be an ideal tool to elucidate intrinsic structural properties on a molecular level. It offers the possibility to analyze structural changes, in a controlled molecular environment, when successively adding aggregation partners. By this, it further makes these techniques a valuable starting point for a bottom-up approach in understanding the forces shaping larger molecular systems. This bottom-up approach was successfully applied to neutral amino acids starting around the 1990s. Ever since, experimental and theoretical methods developed further, and investigations could be extended to larger peptide systems. Against this background, the review gives an introduction to secondary structures and experimental methods as well as a summary on theoretical approaches. Vibrational frequencies being characteristic probes of molecular structure and interactions are especially addressed. Archetypal biologically relevant secondary structures investigated by molecular beam spectroscopy are described, and the influences of specific peptide residues on conformational preferences as well as the competition between secondary structures are discussed. Important influences like microsolvation or aggregation behavior are presented. Beyond the linear α-peptides, the main results of structural analysis on cyclic systems as well as on β- and γ-peptides are summarized. Overall, this contribution addresses current aspects of molecular beam spectroscopy on peptides and related species and provides molecular level insights into manifold issues of chemical and biochemical relevance.

Polycyclic aromatic hydrocarbon formation chemistry in a plasma jet revealed by IR-UV action spectroscopy

Large polycyclic aromatic hydrocarbons (PAHs) are the most abundant complex molecules in the interstellar medium; however, their possible formation pathways from small molecular species are still elusive. In the present work, we follow and characterize the formation of PAHs in an electrical discharge, specifically the PAH naphthalene in a molecular beam of argon. The fragments, products and reaction intermediates are unambiguously structurally identified by mass-selective IR-UV spectroscopy combined with quantum chemical calculations. This experiment provides evidence of the formation of larger PAHs containing up to four cyclic rings in the gas phase originating from a non-radical PAH molecule as a precursor. In addition to PAH formation, key resonance stabilized radical intermediates and intermediates containing di-acetylenic side groups are unambiguously identified in our experiment. We thereby not only reveal competing formation pathways to larger PAHs, but also identify intermediate species to PAH formation that are candidates for detection in radio-astronomy.

Polycyclic aromatic hydrocarbons (PAHs) are present in the interstellar medium but their origin is unclear. Here the authors investigate large PAH formation from smaller PAHs in a plasma jet by mass-selective IR and UV laser spectroscopy, uncovering diacetylene radical addition as formation mechanism.

Interactions of aggregating peptides probed by IR-UV action spectroscopy

The interplay between intramolecular and formed inter-sheet hydrogen bonds and the effect of dispersion interactions on the formation of peptide dimers is studied using IR-UV action spectroscopy.

Competition between folded and extended structures of alanylalanine (Ala-Ala) in a molecular beam

Structural analysis of the neutral dipeptide Ala-Ala by action spectroscopy using IRMPD-VUV spectroscopy reveals predominance of extended structure.

Conformational assignment of gas phase peptides and their H-bonded complexes using far-IR/THz: IR-UV ion dip experiment, DFT-MD spectroscopy, and graph theory for mode assignment

Graph theory based vibrational modes as new entities for vibrational THz spectroscopy.

Correcting the record: the dimers and trimers of trans-N-methylacetamide

Raman jet spectroscopy reveals three N-methylacetamide molecules organizing into a ring structure, previously overlooked in computations.