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 ß-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.

Double Photoionization of Nitrosyl Chloride by Synchrotron Radiation in the 24-70 eV Photon Energy Range.

The behavior of nitrosyl chloride (ClNO) exposed to ionizing radiation was studied by direct probing valence-shell electrons in temporal coincidence with ions originating from the fragmentation process of the transient ClNO2+. Such a molecular dication was produced by double photoionization with synchrotron radiation in the 24-70 eV photon energy range. The experiment has been conducted at the Elettra Synchrotron Facility of Basovizza (Trieste, Italy) using a light beam linearly polarized with the direction of the polarization vector parallel to the ClNO molecular beam axis. ClNO molecules crossing the photon beam at right angles in the scattering region are generated by effusive expansion and randomly oriented. The threshold energy for the double ionization of ClNO (30.1 ± 0.1 eV) and six dissociation channels producing NO+/Cl+, N+/Cl+, N+/O+, O+/Cl+, ClN+/O+, NO+/Cl2+ ion pairs, with their relative abundance and threshold energies, have been measured.

Photochemical Ring-Opening Reaction of 1,3-Cyclohexadiene: Identifying the True Reactive State.

The photochemically induced ring-opening isomerization reaction of 1,3-cyclohexadiene to 1,3,5-hexatriene is a textbook example of a pericyclic reaction and has been amply investigated with advanced spectroscopic techniques. The main open question has been the identification of the single reactive state which drives the process. The generally accepted description of the isomerization pathway starts with a valence excitation to the lowest lying bright state, followed by a passage through a conical intersection to the lowest lying doubly excited state, and finally a branching between either the return to the ground state of the cyclic molecule or the actual ring-opening reaction leading to the open-chain isomer. Here, in a joint experimental and computational effort, we demonstrate that the evolution of the excitation-deexcitation process is much more complex than that usually described. In particular, we show that an initially high-lying electronic state smoothly decreasing in energy along the reaction path plays a key role in the ring-opening reaction.

Electronic state influence on selective bond breaking of core-excited nitrosyl chloride (ClNO).

The potential for selective bond breaking of a small molecule was investigated with electron spectroscopy and electron-ion coincidence experiments on ClNO. The electron spectra were measured upon direct valence photoionization and resonant core excitation at the N 1s- and O 1s-edges, followed by the emission of resonant-Auger (RA) electrons. The RA spectra were analyzed with particular emphasis on the assignment of the participator and spectator states. The states are of special relevance for investigating how distinct electronic configurations influence selective bond breaking. The electron-ion coincidence measurements provided branching fractions of the produced ion fragments as a function of electron binding energy. They explicitly demonstrate how the final electronic states created after photoionization and RA decay influence fragmentation. In particular, we observed a significantly different branching fraction for spectator states compared with participator states. In addition, it was also observed that the bonds broken for the spectator states correlate with the antibonding nature of the spectator-electron orbital.

High-resolution macromolecular crystallography at the FemtoMAX beamline with time-over-threshold photon detection.

Protein dynamics contribute to protein function on different time scales. Ultrafast X-ray diffraction snapshots can visualize the location and amplitude of atom displacements after perturbation. Since amplitudes of ultrafast motions are small, high-quality X-ray diffraction data is necessary for detection. Diffraction from bovine trypsin crystals using single femtosecond X-ray pulses was recorded at FemtoMAX, which is a versatile beamline of the MAX IV synchrotron. The time-over-threshold detection made it possible that single photons are distinguishable even under short-pulse low-repetition-rate conditions. The diffraction data quality from FemtoMAX beamline enables atomic resolution investigation of protein structures. This evaluation is based on the shape of the Wilson plot, cumulative intensity distribution compared with theoretical distribution, I/σ, Rmerge/Rmeas and CC1/2 statistics versus resolution. The FemtoMAX beamline provides an interesting alternative to X-ray free-electron lasers when studying reversible processes in protein crystals.

IRMPD Spectroscopy of Homo- and Heterochiral Asparagine Proton-Bound Dimers in the Gas Phase.

We investigate gas-phase structures of homo- and heterochiral asparagine proton-bound dimers with infrared multiphoton dissociation (IRMPD) spectroscopy and quantum-chemical calculations. Their IRMPD spectra are recorded at room temperature in the range of 500-1875 and 3000-3600 cm-1. Both varieties of asparagine dimers are found to be charge-solvated based on their IRMPD spectra. The location of the principal intramolecular H-bond is discussed in light of harmonic frequency analyses using the B3LYP functional with GD3BJ empirical dispersion. Contrary to theoretical analyses, the two spectra are very similar.

Structure of Proton-Bound Methionine and Tryptophan Dimers in the Gas Phase Investigated with IRMPD Spectroscopy and Quantum Chemical Calculations.

The structures of three proton-bound dimers (Met2H+, MetTrpH+, and Trp2H+) are investigated in the gas phase with infrared multiple photon disassociation (IRMPD) spectroscopy in combination with quantum chemical calculations. Their IRMPD spectra in the range of 600-1850 cm-1 are obtained experimentally using an FT-ICR mass spectrometer and the CLIO free electron laser as an IR light source. The most abundant conformers are elucidated by comparing the IRMPD spectra with harmonic frequencies obtained at the B3LYP-GD3BJ/6-311++G** level of theory. Discrepancies between the experimental and theoretical data in the region of 1500-1700 cm-1 are attributed to the anharmonicity of the amino bending modes. We confirm the result of a previous IRMPD study that the structure of gas-phase Trp2H+ is charge-solvated but find that there are more stable structures than originally reported (Feng, R.; Yin, H.; Kong, X. Rapid Commun. Mass Spectrom. 2016, 30, 24-28). In addition, gas-phase Met2H+ and MetTrpH+ have been revealed to have charge-solvated structures. For all three dimers, the most stable conformer is found to be of type A. The spectrum of Met2H+, however, cannot be explained without some abundance of type B charge-solvated conformers as well as salt-bridged structures.

Theoretical studies of infrared signatures of proton-bound amino acid dimers with homochiral and heterochiral moieties.

Proton-bound homochiral and heterochiral dimers, X-H+ -X, of five amino acids (X = Ser, Ala, Thr, Phe, and Arg) are investigated theoretically using quantum chemical density functional theory (DFT) calculations and molecular dynamics simulations with the aim to unveil diastereomer-specific mid-infrared (mid-IR) absorption bands in the spectral range of 1000 to 1800 cm-1 . The theoretical calculations performed in this work imply that all systems, except Ala2 H+ , have distinct mid-IR absorption bands in homochiral and heterochiral configurations, which make them appropriate systems to be studied experimentally with mid-IR spectroscopy. We show that intermolecular interaction with the side chain, in the form of hydrogen bonding or cation-π interaction, is necessary for chiral effects to be present in the mid-IR spectra of proton-bound dimers of amino acids. We also report new conformers for Ala2 H+ , Thr2 H+ , Phe2 H+ , and Arg2 H+ , which were not found in earlier studies of these dimers.

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

We report the gas phase conformational preferences of laser desorbed Ala-Ala dipeptides probed by action spectroscopy using the IRMPD-VUV method. The molecules were internally cooled through collisional cooling in a supersonic jet environment. An IR spectrum was obtained experimentally in the spectral range of 700-1850 cm-1, and subsequently interpreted with the help of quantum chemical calculations. Although theory predicts that folded structures have lower electronic energies and, thus, are more stable at low temperatures compared to their extended (ß-strand-like) counterparts, analysis of the experimental data concluded the extended conformer to be the most dominant. An explanation to this observation is discussed in this paper and rationalized in terms of collisional conformer relaxation processes occurring in the supersonic jet molecular beam.

Conformational Preferences of Isolated Glycylglycine (Gly-Gly) Investigated with IRMPD-VUV Action Spectroscopy and Advanced Computational Approaches.

In this article, we report the results of gas-phase IR spectroscopy of neutral glycylglycine (Gly-Gly) in the 700-1850 cm-1 frequency range. A combination of laser desorption, jet-cooling, and IR multiple-photon dissociation vacuum-ultraviolet (IRMPD-VUV) action spectroscopy is employed, together with extensive quantum chemical calculations that assist in the analysis of the experimental data. As a result, we determined that the most favorable conformer in the low-temperature environment of the supersonic jet is the nearly planar structure with two C5 hydrogen-bonding interactions. Calculations clearly show that this conformer is favored because of its flexibility (considerable entropy stabilization) as well as efficient conformer relaxation processes in the jet. To gain more understanding into the relative stability of the lowest-energy Gly-Gly conformers, the relative strength of hydrogen bonding and steric interactions is analyzed using the noncovalent interactions (NCI) approach.

Investigating core-excited states of nitrosyl chloride (ClNO) and their break-up dynamics following Auger decay.

The fragmentation of ClNO upon resonant core-electron excitation to the LUMO and LUMO+1 orbitals at the N and O K-edges is investigated. The produced fragment ions were detected in coincidence with a position sensitive ion time-of-flight detector which enables deduction of the angular distribution of the ions. This facilitates a comparison between the two resonances and the two K-edges with respect to fragmentation time, transition dipole moment orientation, fragment yield of single-ion and ion-pair channels, and fragmentation mechanisms. We observe significant correlations between the core-excited site and the location of the bonds that are broken, as well as the dissociation time. Moreover, we observe preferential cleavage of specific bonds upon excitation to the LUMO and LUMO+1 states which can be attributed to their orbital character.

Single Photon Thermal Ionization of C_{60}.

We report on experiments which show that C_{60} can ionize in an indirect, quasithermal boiloff process after absorption of a single photon. The process involves a large number of incoherently excited valence electrons and yields electron spectra with a Boltzmann distribution with temperatures exceeding 10^{4} K. It is expected to be present for other molecules and clusters with a comparatively large number of valence electrons. The astrophysical consequences are briefly discussed.

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

We demonstrate a technique for IR action spectroscopy that enables measuring IR spectra in a background-free fashion for low-temperature neutral gas-phase molecules of arbitrary structure. The method is exemplified experimentally for N-methylacetamide molecules in the mid-IR spectral range of 1000-1800 cm^{-1}, utilizing the free electron laser FELIX. The technique involves the resonant absorption of multiple mid-IR photons, which induces molecular dissociation. The dissociation products are probed with 10.49 eV vacuum ultraviolet photons and analyzed with a mass spectrometer. We also demonstrate the capability of this method to record, with unprecedented ease, mid-IR spectra for the molecular associates, such as clusters and oligomers, present in a molecular beam. In this way the mass-selected spectra of low-temperature gas-phase dimers and trimers of N-methylacetamide are measured in the full amide I-III range.

Aminophenol isomers unraveled by conformer-specific far-IR action spectroscopy.

Spectroscopic studies of molecular structure can strongly benefit from extending the conventional mid-IR range to the far-IR and THz regions, as low-frequency molecular vibrations provide unique fingerprints and high sensitivity to intra- and intermolecular interactions. In this work, the gas-phase conformer specific far-IR spectra of aminophenol isomers, recorded in the spectral range of 220-800 cm(-1) at the free-electron laser laboratory FELIX in Nijmegen (the Netherlands), are reported. Many distinct far-IR vibrational signatures which are specific for the molecular structure of the different aminophenol isomers are revealed and assigned. The observed far-IR transitions of the NH2 wagging (inversion) motion have been treated with a double-minimum harmonic well potential model that has enabled us to obtain the inversion barrier values. Moreover, we discuss the limitations and capability of conventional DFT frequency calculations to describe the far-IR vibrational modes.

Far-infrared spectra of the tryptamine A conformer by IR-UV ion gain spectroscopy.

We present far infrared spectra of the conformer A of tryptamine in the 200 to 500 cm-1 wavenumber range along with resonant photoionization spectra of the far-infrared excited conformer A of tryptamine. We show that single-far-infrared photon excited tryptamine has highly structured resonance enhanced multi-photon ionization spectra, revealing the mode composition of the S1-state. Upon multiple-far-infrared photon absorption, the resonance enhanced multi-photon ionization spectrum broadens allowing ion gain spectroscopy to be performed. In the ion gain spectrum we detect the fundamental far-infrared modes but also combination and overtone bands with high efficiency. The implications to dip spectroscopy using a free electron laser compared to more conventional light sources are discussed.

Experimental and theoretical XPS and NEXAFS studies of N-methylacetamide and N-methyltrifluoroacetamide.

Experimental Near-Edge X-ray Absorption Fine-Structure (NEXAFS) spectra of N-methyltrifluoroacetamide (FNMA), which is a peptide model system, measured at the C, N, O and F K-edges are reported. The features in the spectra have been assigned by Static-Exchange (STEX) calculations. Using the same method, we have also assigned previously measured NEXAFS spectra of another peptide model system, N-methylacetamide (NMA). To facilitate the NEXAFS feature assignments, X-ray Photoelectron Spectroscopy (XPS) measurements for NMA and FNMA have been carried out with the aim of obtaining the 1s electron ionization potentials, which are compared with the values predicted by our Hartree-Fock (ΔHF) and Multi Configuration Self Consistent Field (ΔMCSCF) calculations. We also demonstrate an approach to compensate for screening effects that are neglected in the STEX method. Ion yield measurements of FNMA associated with the excitation of several C, N, O, and F K-shell pre-edge resonances have revealed site-specific fragmentation in some cases which we interpret with the aid of our theoretical calculations.

A Study of H2O2 with Threshold Photoelectron Spectroscopy (TPES) and Electronic Structure Calculations: Redetermination of the First Adiabatic Ionization Energy (AIE).

In this work, hydrogen peroxide has been studied with threshold photoelectron (TPE) spectroscopy and photoelectron (PE) spectroscopy. The TPE spectrum has been recorded in the 10.0-21.0 eV ionization energy region, and the PE spectrum has been recorded at 21.22 eV photon energy. Five bands have been observed which have been assigned on the basis of UCCSD(T)-F12/VQZ-F12 and IP-EOM CCSD calculations. Vibrational structure has only been resolved in the TPE spectrum of the first band, associated with the X̃(2)Bg H2O2(+) ← X̃(1)A H2O2 ionization, on its low energy side. This structure is assigned with the help of harmonic Franck-Condon factor calculations that use the UCCSD(T)-F12a/VQZ-F12 computed adiabatic ionization energy (AIE), and UCCSD(T)-F12a/VQZ-F12 computed equilibrium geometric parameters and harmonic vibrational frequencies for the H2O2 X̃(1)A state and the H2O2(+) X̃(2)Bg state. These calculations show that the main vibrational structure on the leading edge of the first TPE band is in the O-O stretching mode (ω3) and the HOOH deformation mode (ω4), and comparison of the simulated spectrum to the experimental spectrum gives the first AIE of H2O2 as (10.685 ± 0.005) eV and ω4 = (850 ± 30) and ω3 = (1340 ± 30) cm(-1) in the X̃(2)Bg state of H2O2(+). Contributions from ionization of vibrationally excited levels in the torsion mode have been identified in the TPE spectrum of the first band and the need for a vibrationally resolved TPE spectrum from vibrationally cooled molecules, as well as higher level Franck-Condon factors than performed in this work, is emphasized.

Far-infrared amide IV-VI spectroscopy of isolated 2- and 4-Methylacetanilide.

Delocalized molecular vibrations in the far-infrared and THz ranges are highly sensitive to the molecular structure, as well as to intra- and inter-molecular interactions. Thus, spectroscopic studies of biomolecular structures can greatly benefit from an extension of the conventional mid-infrared to the far-infrared wavelength range. In this work, the conformer-specific gas-phase far-infrared spectra of two aromatic molecules containing the peptide -CO-NH- link, namely, 2- and 4-Methylacetanilide, are investigated. The planar conformations with trans configuration of the peptide link have only been observed in the supersonic-jet expansion. The corresponding far-infrared signatures associated with the vibrations of the peptide -CO-NH- moiety, the so-called amide IV-VI bands, have been assigned and compared with the results of density functional theory frequency calculations based on the anharmonic vibrational second-order perturbation theory approach. The analysis of the experimental and theoretical data shows that the amide IV-VI bands are highly diagnostic for the geometry of the peptide moiety and the molecular backbone. They are also strongly blue-shifted upon formation of the NH⋯O-C hydrogen bonding, which is, for example, responsible for the formation of secondary protein structures. Furthermore, the amide IV-VI bands are also diagnostic for the cis configuration of the peptide link, which can be present in cyclic peptides. The experimental gas-phase data presented in this work can assist the vibrational assignment of similar biologically important systems, either isolated or in natural environments.

Mechanisms of site-specific photochemistry following core-shell ionization of chemically inequivalent carbon atoms in acetaldehyde (ethanal).

Site-specific fragmentation upon 1s photoionisation of acetaldehyde has been studied using synchrotron radiation and a multi-electron-ion coincidence technique based on a magnetic bottle. Experimental evidence is presented that bond rupture occurs with highest probability in the vicinity of the initial charge localisation and possible mechanisms are discussed. We find that a significant contribution to site-specific photochemistry is made by different fragmentation patterns of individual quantum states populated at identical ionisation energies.

NEXAFS spectroscopy and site-specific fragmentation of N-methylformamide, N,N-dimethylformamide, and N,N-dimethylacetamide.

Near-edge X-ray absorption fine-structure (NEXAFS) spectra measured at the C, N, and O K-edges for three molecules containing the amide moiety, N-methylformamide (HCONHCH3), N,N-dimethylformamide (HCON(CH3)2), and N,N-dimethylacetamide (CH3CON(CH3)2) are presented. These molecules have similar structures and differ by the number of methyl groups located at the molecular ends. The fragmentation of these molecules after resonant excitation at different K-edge resonances is also investigated, using a 3D-ion imaging time-of-flight spectrometer. A comparison between the molecules with respect to the relative contributions of the fragments created upon excitation at distinct resonances reveals site-specific fragmentation. Further information about the character of the core-excitation and dissociation process is obtained from the angular distributions of the ion fragments.