1
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Greis K, Kirschbaum C, Ober K, Taccone MI, Torres-Boy A, Meijer G, Pagel K, von Helden G. Infrared Spectroscopy of Fluorenyl Cations at Cryogenic Temperatures. J Phys Chem Lett 2023; 14:11313-11317. [PMID: 38064287 PMCID: PMC10749476 DOI: 10.1021/acs.jpclett.3c02928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 12/01/2023] [Accepted: 12/05/2023] [Indexed: 12/22/2023]
Abstract
The notion of (anti)aromaticity is a successful concept in chemistry to explain the structure and stability of polycyclic hydrocarbons. Cyclopentadienyl and fluorenyl cations are among the most studied classical antiaromatic systems. In this work, fluorenyl cations are investigated by high-resolution gas-phase infrared spectroscopy in helium droplets. Bare fluorenyl cations are generated in the gas phase by electrospray ionization. After mass-to-charge selection, ions are captured in ultracold helium nanodroplets and probed by infrared spectroscopy using a widely tunable free-electron laser in the 600-1700 cm-1 range. The highly resolved cryogenic infrared spectra confirm, in combination with DFT computations, that all cations are present in their singlet states.
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Affiliation(s)
- Kim Greis
- Fritz
Haber Institute of the Max Planck Society, Berlin, Faradayweg 4-6, 14195 Berlin, Germany
- Institute
of Chemistry and Biochemistry, Freie Universität
Berlin, Altensteinstraße 23A, 14195 Berlin, Germany
| | - Carla Kirschbaum
- Fritz
Haber Institute of the Max Planck Society, Berlin, Faradayweg 4-6, 14195 Berlin, Germany
- Institute
of Chemistry and Biochemistry, Freie Universität
Berlin, Altensteinstraße 23A, 14195 Berlin, Germany
| | - Katja Ober
- Fritz
Haber Institute of the Max Planck Society, Berlin, Faradayweg 4-6, 14195 Berlin, Germany
| | - Martín I. Taccone
- Fritz
Haber Institute of the Max Planck Society, Berlin, Faradayweg 4-6, 14195 Berlin, Germany
| | - América
Y. Torres-Boy
- Fritz
Haber Institute of the Max Planck Society, Berlin, Faradayweg 4-6, 14195 Berlin, Germany
| | - Gerard Meijer
- Fritz
Haber Institute of the Max Planck Society, Berlin, Faradayweg 4-6, 14195 Berlin, Germany
| | - Kevin Pagel
- Fritz
Haber Institute of the Max Planck Society, Berlin, Faradayweg 4-6, 14195 Berlin, Germany
- Institute
of Chemistry and Biochemistry, Freie Universität
Berlin, Altensteinstraße 23A, 14195 Berlin, Germany
| | - Gert von Helden
- Fritz
Haber Institute of the Max Planck Society, Berlin, Faradayweg 4-6, 14195 Berlin, Germany
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2
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Safferthal M, Greis K, Chang R, Kirschbaum C, Hoffmann W, Meijer G, von Helden G, Pagel K. Cryogenic infrared spectroscopy reveals remarkably short NH +⋯F hydrogen bonds in fluorinated phenylalanines. Phys Chem Chem Phys 2023; 25:24783-24788. [PMID: 37671576 DOI: 10.1039/d3cp03776b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/07/2023]
Abstract
In past decades, hydrogen bonds involving organic fluorine have been a highly disputed topic. Obtaining clear evidence for the presence of fluorine-specific interactions is generally difficult because of their weak nature. Today, the existence of hydrogen bonds with organic fluorine is widely accepted and supported by numerous studies. However, strong bonds with short H⋯F distances remain scarce and are primarily found in designed model compounds. Using a combination of cryogenic gas-phase infrared spectroscopy and density functional theory, we here analyze a series of conformationally unrestrained fluorinated phenylalanine compounds as protonated species. The results suggest proximal NH+⋯F hydrogen bonds with an exceptionally close H⋯F distance (1.79 Å) in protonated ortho-fluorophenylalanine.
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Affiliation(s)
- Marc Safferthal
- Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, Altensteinstraße 23a, 14195 Berlin, Germany.
- Fritz Haber Institute of the Max Planck Society, Faradayweg 4-6, 14195 Berlin, Germany
| | - Kim Greis
- Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, Altensteinstraße 23a, 14195 Berlin, Germany.
- Fritz Haber Institute of the Max Planck Society, Faradayweg 4-6, 14195 Berlin, Germany
| | - Rayoon Chang
- Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, Altensteinstraße 23a, 14195 Berlin, Germany.
- Fritz Haber Institute of the Max Planck Society, Faradayweg 4-6, 14195 Berlin, Germany
| | - Carla Kirschbaum
- Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, Altensteinstraße 23a, 14195 Berlin, Germany.
- Fritz Haber Institute of the Max Planck Society, Faradayweg 4-6, 14195 Berlin, Germany
| | - Waldemar Hoffmann
- Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, Altensteinstraße 23a, 14195 Berlin, Germany.
- Fritz Haber Institute of the Max Planck Society, Faradayweg 4-6, 14195 Berlin, Germany
| | - Gerard Meijer
- Fritz Haber Institute of the Max Planck Society, Faradayweg 4-6, 14195 Berlin, Germany
| | - Gert von Helden
- Fritz Haber Institute of the Max Planck Society, Faradayweg 4-6, 14195 Berlin, Germany
| | - Kevin Pagel
- Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, Altensteinstraße 23a, 14195 Berlin, Germany.
- Fritz Haber Institute of the Max Planck Society, Faradayweg 4-6, 14195 Berlin, Germany
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3
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Albertini S, Gruber E, Zappa F, Krasnokutski S, Laimer F, Scheier P. Chemistry and physics of dopants embedded in helium droplets. MASS SPECTROMETRY REVIEWS 2022; 41:529-567. [PMID: 33993543 DOI: 10.1002/mas.21699] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 04/20/2021] [Accepted: 04/20/2021] [Indexed: 05/18/2023]
Abstract
Helium droplets represent a cold inert matrix, free of walls with outstanding properties to grow complexes and clusters at conditions that are perfect to simulate cold and dense regions of the interstellar medium. At sub-Kelvin temperatures, barrierless reactions triggered by radicals or ions have been observed and studied by optical spectroscopy and mass spectrometry. The present review summarizes developments of experimental techniques and methods and recent results they enabled.
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Affiliation(s)
- Simon Albertini
- Institut für Ionenphysik und Angewandte Physik, Universität Innsbruck, Innsbruck, Austria
| | - Elisabeth Gruber
- Institut für Ionenphysik und Angewandte Physik, Universität Innsbruck, Innsbruck, Austria
| | - Fabio Zappa
- Institut für Ionenphysik und Angewandte Physik, Universität Innsbruck, Innsbruck, Austria
| | - Serge Krasnokutski
- Laboratory Astrophysics Group of the MPI for Astronomy, University of Jena, Jena, Germany
| | - Felix Laimer
- Institut für Ionenphysik und Angewandte Physik, Universität Innsbruck, Innsbruck, Austria
| | - Paul Scheier
- Institut für Ionenphysik und Angewandte Physik, Universität Innsbruck, Innsbruck, Austria
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4
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Greis K, Kirschbaum C, Fittolani G, Mucha E, Chang R, von Helden G, Meijer G, Delbianco M, Seeberger PH, Pagel K. Neighboring Group Participation of Benzoyl Protecting Groups in C3- and C6-Fluorinated Glucose. European J Org Chem 2022; 2022:e202200255. [PMID: 35915640 PMCID: PMC9321577 DOI: 10.1002/ejoc.202200255] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 03/23/2022] [Indexed: 11/17/2022]
Abstract
Fluorination is a potent method to modulate chemical properties of glycans. Here, we study how C3- and C6-fluorination of glucosyl building blocks influence the structure of the intermediate of the glycosylation reaction, the glycosyl cation. Using a combination of gas-phase infrared spectroscopy and first-principles theory, glycosyl cations generated from fluorinated and non-fluorinated monosaccharides are structurally characterized. The results indicate that neighboring group participation of the C2-benzoyl protecting group is the dominant structural motif for all building blocks, correlating with the β-selectivity observed in glycosylation reactions. The infrared signatures indicate that participation of the benzoyl group in enhanced by resonance effects. Participation of remote acyl groups such as Fmoc or benzyl on the other hand is unfavored. The introduction of the less bulky fluorine leads to a change in the conformation of the ring pucker, whereas the structure of the active dioxolenium site remains unchanged.
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Affiliation(s)
- Kim Greis
- Institute of Chemistry and BiochemistryFreie Universität BerlinArnimallee 2214195BerlinGermany
- Fritz Haber Institute of the Max Planck SocietyFaradayweg 4–614195BerlinGermany
| | - Carla Kirschbaum
- Institute of Chemistry and BiochemistryFreie Universität BerlinArnimallee 2214195BerlinGermany
- Fritz Haber Institute of the Max Planck SocietyFaradayweg 4–614195BerlinGermany
| | - Giulio Fittolani
- Institute of Chemistry and BiochemistryFreie Universität BerlinArnimallee 2214195BerlinGermany
- Max Planck Institute of Colloids and InterfacesAm Mühlenberg 114476PotsdamGermany
| | - Eike Mucha
- Fritz Haber Institute of the Max Planck SocietyFaradayweg 4–614195BerlinGermany
| | - Rayoon Chang
- Institute of Chemistry and BiochemistryFreie Universität BerlinArnimallee 2214195BerlinGermany
- Fritz Haber Institute of the Max Planck SocietyFaradayweg 4–614195BerlinGermany
| | - Gert von Helden
- Fritz Haber Institute of the Max Planck SocietyFaradayweg 4–614195BerlinGermany
| | - Gerard Meijer
- Fritz Haber Institute of the Max Planck SocietyFaradayweg 4–614195BerlinGermany
| | - Martina Delbianco
- Max Planck Institute of Colloids and InterfacesAm Mühlenberg 114476PotsdamGermany
| | - Peter H. Seeberger
- Institute of Chemistry and BiochemistryFreie Universität BerlinArnimallee 2214195BerlinGermany
- Max Planck Institute of Colloids and InterfacesAm Mühlenberg 114476PotsdamGermany
| | - Kevin Pagel
- Institute of Chemistry and BiochemistryFreie Universität BerlinArnimallee 2214195BerlinGermany
- Fritz Haber Institute of the Max Planck SocietyFaradayweg 4–614195BerlinGermany
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5
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Martini P, Albertini S, Laimer F, Meyer M, Gatchell M, Echt O, Zappa F, Scheier P. Splashing of Large Helium Nanodroplets upon Surface Collisions. PHYSICAL REVIEW LETTERS 2021; 127:263401. [PMID: 35029473 DOI: 10.1103/physrevlett.127.263401] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 07/15/2021] [Accepted: 11/12/2021] [Indexed: 05/18/2023]
Abstract
In the present work we observe that helium nanodroplets colliding with surfaces can exhibit splashing in a way that is analogous to classical liquids. We use transmission electron microscopy and mass spectrometry to demonstrate that neutral and ionic dopants embedded in the droplets are efficiently backscattered in such events. High abundances of weakly bound He-tagged ions of both polarities indicate a gentle extraction mechanism of these ions from the droplets upon collision with a solid surface. This backscattering process is observed for dopant particles with masses up to 400 kilodaltons, indicating an unexpected mechanism that effectively lowers deposition rates of nanoparticles formed in helium droplets.
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Affiliation(s)
- Paul Martini
- Institut für Ionenphysik und Angewandte Physik, Universität Innsbruck, A-6020 Innsbruck, Austria
- Department of Physics, Stockholm University, 106 91 Stockholm, Sweden
| | - Simon Albertini
- Institut für Ionenphysik und Angewandte Physik, Universität Innsbruck, A-6020 Innsbruck, Austria
- Management Center Innsbruck, Department Biotechnology & Food Engineering, A-6020 Innsbruck, Austria
| | - Felix Laimer
- Institut für Ionenphysik und Angewandte Physik, Universität Innsbruck, A-6020 Innsbruck, Austria
| | - Miriam Meyer
- Institut für Ionenphysik und Angewandte Physik, Universität Innsbruck, A-6020 Innsbruck, Austria
| | - Michael Gatchell
- Institut für Ionenphysik und Angewandte Physik, Universität Innsbruck, A-6020 Innsbruck, Austria
- Department of Physics, Stockholm University, 106 91 Stockholm, Sweden
| | - Olof Echt
- Institut für Ionenphysik und Angewandte Physik, Universität Innsbruck, A-6020 Innsbruck, Austria
- Department of Physics, University of New Hampshire, Durham, New Hampshire 03824, USA
| | - Fabio Zappa
- Institut für Ionenphysik und Angewandte Physik, Universität Innsbruck, A-6020 Innsbruck, Austria
- Departamento de Física, Universidade Federal de Juiz de Fora, MG 36036-900 Minas Gerais, Brazil
| | - Paul Scheier
- Institut für Ionenphysik und Angewandte Physik, Universität Innsbruck, A-6020 Innsbruck, Austria
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6
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Stabilizing the Exotic Carbonic Acid by Bisulfate Ion. MOLECULES (BASEL, SWITZERLAND) 2021; 27:molecules27010008. [PMID: 35011240 PMCID: PMC8746525 DOI: 10.3390/molecules27010008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 12/15/2021] [Accepted: 12/16/2021] [Indexed: 01/08/2023]
Abstract
Carbonic acid is an important species in a variety of fields and has long been regarded to be non-existing in isolated state, as it is thermodynamically favorable to decompose into water and carbon dioxide. In this work, we systematically studied a novel ionic complex [H2CO3·HSO4]- using density functional theory calculations, molecular dynamics simulations, and topological analysis to investigate if the exotic H2CO3 molecule could be stabilized by bisulfate ion, which is a ubiquitous ion in various environments. We found that bisulfate ion could efficiently stabilize all the three conformers of H2CO3 and reduce the energy differences of isomers with H2CO3 in three different conformations compared to the isolated H2CO3 molecule. Calculated isomerization pathways and ab initio molecular dynamics simulations suggest that all the optimized isomers of the complex have good thermal stability and could exist at finite temperatures. We also explored the hydrogen bonding properties in this interesting complex and simulated their harmonic infrared spectra to aid future infrared spectroscopic experiments. This work could be potentially important to understand the fate of carbonic acid in certain complex environments, such as in environments where both sulfuric acid (or rather bisulfate ion) and carbonic acid (or rather carbonic dioxide and water) exist.
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7
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Gaigeot MP. 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. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 260:119864. [PMID: 34052762 DOI: 10.1016/j.saa.2021.119864] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 04/13/2021] [Accepted: 04/18/2021] [Indexed: 06/12/2023]
Abstract
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.
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Affiliation(s)
- Marie-Pierre Gaigeot
- Université Paris-Saclay, Univ Evry, CNRS, LAMBE UMR8587, 91025 Evry-Courcouronnes, France.
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8
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Thomas DA, Taccone M, Ober K, Mucha E, Meijer G, von Helden G. Helium Nanodroplet Infrared Action Spectroscopy of the Proton-Bound Dimer of Hydrogen Sulfate and Formate: Examining Nuclear Quantum Effects. J Phys Chem A 2021; 125:9279-9287. [PMID: 34652165 PMCID: PMC8558860 DOI: 10.1021/acs.jpca.1c05705] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The proton-bound dimer of hydrogen sulfate and formate is an archetypal structure for ionic hydrogen-bonding complexes that contribute to biogenic aerosol nucleation. Of central importance for the structure and properties of this complex is the location of the bridging proton connecting the two conjugate base moieties. The potential energy surface for bridging proton translocation features two local minima, with the proton localized at either the formate or hydrogen sulfate moiety. However, electronic structure methods reveal a shallow potential energy surface governing proton translocation, with a barrier on the order of the zero-point energy. This shallow potential complicates structural assignment and necessitates a consideration of nuclear quantum effects. In this work, we probe the structure of this complex and its isotopologues, utilizing infrared (IR) action spectroscopy of ions captured in helium nanodroplets. The IR spectra indicate a structure in which a proton is shared between the hydrogen sulfate and formate moieties, HSO4-···H+···-OOCH. However, because of the nuclear quantum effects and vibrational anharmonicities associated with the shallow potential for proton translocation, the extent of proton displacement from the formate moiety remains unclear, requiring further experiments or more advanced theoretical treatments for additional insight.
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Affiliation(s)
- Daniel A Thomas
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
| | - Martín Taccone
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
| | - Katja Ober
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
| | - Eike Mucha
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
| | - Gerard Meijer
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
| | - Gert von Helden
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
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9
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Lettow M, Greis K, Grabarics M, Horlebein J, Miller RL, Meijer G, von Helden G, Pagel K. Chondroitin Sulfate Disaccharides in the Gas Phase: Differentiation and Conformational Constraints. J Phys Chem A 2021; 125:4373-4379. [PMID: 33979516 PMCID: PMC8279649 DOI: 10.1021/acs.jpca.1c02463] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
![]()
Glycosaminoglycans
(GAGs) are a family of complex carbohydrates
vital to all mammalian organisms and involved in numerous biological
processes. Chondroitin and dermatan sulfate, an important class of
GAGs, are linear macromolecules consisting of disaccharide building
blocks of N-acetylgalactosamine and two different
uronic acids. The varying degree and the site of sulfation render
their characterization challenging. Here, we combine mass spectrometry
with cryogenic infrared spectroscopy in the wavenumber range from
1000 to 1800 cm–1. Fingerprint spectra were recorded
for a comprehensive set of disaccharides bearing all known motifs
of sulfation. In addition, state-of-the-art quantum chemical calculations
were performed to aid the understanding of the differences in the
experimental fingerprint spectra. The results show that the degree
and position of charged sulfate groups define the size of the conformational
landscape in the gas phase. The detailed understanding of cryogenic
infrared spectroscopy for acidic and often highly sulfated glycans
may pave the way to utilize the technique in fragment-based sequencing
approaches.
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Affiliation(s)
- Maike Lettow
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany.,Institut für Chemie und Biochemie, Freie Universität Berlin, Arnimallee 22, 14195 Berlin, Germany
| | - Kim Greis
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany.,Institut für Chemie und Biochemie, Freie Universität Berlin, Arnimallee 22, 14195 Berlin, Germany
| | - Márkó Grabarics
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany.,Institut für Chemie und Biochemie, Freie Universität Berlin, Arnimallee 22, 14195 Berlin, Germany
| | - Jan Horlebein
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany.,Institut für Chemie und Biochemie, Freie Universität Berlin, Arnimallee 22, 14195 Berlin, Germany
| | - Rebecca L Miller
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Gerard Meijer
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
| | - Gert von Helden
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
| | - Kevin Pagel
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany.,Institut für Chemie und Biochemie, Freie Universität Berlin, Arnimallee 22, 14195 Berlin, Germany
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10
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Thomas DA, Chang R, Mucha E, Lettow M, Greis K, Gewinner S, Schöllkopf W, Meijer G, von Helden G. Probing the conformational landscape and thermochemistry of DNA dinucleotide anions via helium nanodroplet infrared action spectroscopy. Phys Chem Chem Phys 2020; 22:18400-18413. [PMID: 32797142 DOI: 10.1039/d0cp02482a] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
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.
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Affiliation(s)
- Daniel A Thomas
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany.
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11
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Lettow M, Grabarics M, Greis K, Mucha E, Thomas DA, Chopra P, Boons GJ, Karlsson R, Turnbull JE, Meijer G, Miller RL, von Helden G, Pagel K. Cryogenic Infrared Spectroscopy Reveals Structural Modularity in the Vibrational Fingerprints of Heparan Sulfate Diastereomers. Anal Chem 2020; 92:10228-10232. [PMID: 32658472 DOI: 10.1021/acs.analchem.0c02048] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Heparan sulfate and heparin are highly acidic polysaccharides with a linear sequence, consisting of alternating glucosamine and hexuronic acid building blocks. The identity of hexuronic acid units shows a variability along their sequence, as d-glucuronic acid and its C5 epimer, l-iduronic acid, can both occur. The resulting backbone diversity represents a major challenge for an unambiguous structural assignment by mass spectrometry-based techniques. Here, we employ cryogenic infrared spectroscopy on mass-selected ions to overcome this challenge and distinguish isomeric heparan sulfate tetrasaccharides that differ only in the configuration of their hexuronic acid building blocks. High-resolution infrared spectra of a systematic set of synthetic heparan sulfate stereoisomers were recorded in the fingerprint region from 1000 to 1800 cm-1. The experiments reveal a characteristic combination of spectral features for each of the four diastereomers studied and imply structural modularity in the vibrational fingerprints. Strong spectrum-structure correlations were found and rationalized by state-of-the-art quantum chemical calculations. The findings demonstrate the potential of cryogenic infrared spectroscopy to extend the mass spectrometry-based toolkit for the sequencing of heparan sulfate and structurally related biomolecules.
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Affiliation(s)
- Maike Lettow
- Department of Molecular Physics, Fritz Haber Institute of the Max Planck Society, Faradayweg 4-6, 14195 Berlin, Germany.,Institut für Chemie und Biochemie, Freie Universität Berlin, Arnimallee 22, 14195 Berlin, Germany
| | - Márkó Grabarics
- Department of Molecular Physics, Fritz Haber Institute of the Max Planck Society, Faradayweg 4-6, 14195 Berlin, Germany.,Institut für Chemie und Biochemie, Freie Universität Berlin, Arnimallee 22, 14195 Berlin, Germany
| | - Kim Greis
- Department of Molecular Physics, Fritz Haber Institute of the Max Planck Society, Faradayweg 4-6, 14195 Berlin, Germany.,Institut für Chemie und Biochemie, Freie Universität Berlin, Arnimallee 22, 14195 Berlin, Germany
| | - Eike Mucha
- Department of Molecular Physics, Fritz Haber Institute of the Max Planck Society, Faradayweg 4-6, 14195 Berlin, Germany
| | - Daniel A Thomas
- Department of Molecular Physics, Fritz Haber Institute of the Max Planck Society, Faradayweg 4-6, 14195 Berlin, Germany
| | - Pradeep Chopra
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, Georgia 30602, United States
| | - Geert-Jan Boons
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, Georgia 30602, United States.,Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Science, and Bijvoet Center for Biomolecular Research, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
| | - Richard Karlsson
- Copenhagen Centre for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen N 2200, Denmark
| | - Jeremy E Turnbull
- Copenhagen Centre for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen N 2200, Denmark.,Centre for Glycobiology, Department of Biochemistry, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | - Gerard Meijer
- Department of Molecular Physics, Fritz Haber Institute of the Max Planck Society, Faradayweg 4-6, 14195 Berlin, Germany
| | - Rebecca L Miller
- Copenhagen Centre for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen N 2200, Denmark
| | - Gert von Helden
- Department of Molecular Physics, Fritz Haber Institute of the Max Planck Society, Faradayweg 4-6, 14195 Berlin, Germany
| | - Kevin Pagel
- Department of Molecular Physics, Fritz Haber Institute of the Max Planck Society, Faradayweg 4-6, 14195 Berlin, Germany.,Institut für Chemie und Biochemie, Freie Universität Berlin, Arnimallee 22, 14195 Berlin, Germany
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Zhang H, Cao W, Yuan Q, Wang L, Zhou X, Liu S, Wang XB. Spectroscopic evidence for intact carbonic acid stabilized by halide anions in the gas phase. Phys Chem Chem Phys 2020; 22:19459-19467. [DOI: 10.1039/d0cp02338h] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The whole series of halide anions can stabilize elusive carbonic acid in the gas phase through dual hydrogen bonds.
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Affiliation(s)
- Hanhui Zhang
- Hefei National Laboratory for Physical Sciences at the Microscale
- Department of Chemical Physics
- University of Science and Technology of China
- Hefei
- P. R. China
| | - Wenjin Cao
- Physical Sciences Division
- Pacific Northwest National Laboratory
- Richland
- USA
| | - Qinqin Yuan
- Physical Sciences Division
- Pacific Northwest National Laboratory
- Richland
- USA
| | - Lei Wang
- Hefei National Laboratory for Physical Sciences at the Microscale
- Department of Chemical Physics
- University of Science and Technology of China
- Hefei
- P. R. China
| | - Xiaoguo Zhou
- Hefei National Laboratory for Physical Sciences at the Microscale
- Department of Chemical Physics
- University of Science and Technology of China
- Hefei
- P. R. China
| | - Shilin Liu
- Hefei National Laboratory for Physical Sciences at the Microscale
- Department of Chemical Physics
- University of Science and Technology of China
- Hefei
- P. R. China
| | - Xue-Bin Wang
- Physical Sciences Division
- Pacific Northwest National Laboratory
- Richland
- USA
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Shirman E, Shahi A, Continetti RE, Strasser D. Dissociative detachment of the fluoroformate anion. Phys Chem Chem Phys 2020; 22:27666-27672. [DOI: 10.1039/d0cp04283h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
3D fragment imaging of the fluoroformate anion (FCO2−) dissociative photodetachment products shows reductive fragmentation, forming FCO + O, as well as a dominant cleavage of the CF bond.
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Affiliation(s)
- Eugene Shirman
- Institute of Chemistry
- The Hebrew University of Jerusalem
- 91904 Jerusalem
- Israel
| | - Abhishek Shahi
- Institute of Chemistry
- The Hebrew University of Jerusalem
- 91904 Jerusalem
- Israel
| | - Robert E. Continetti
- Department of Chemistry and Biochemistry
- University of California San Diego
- La Jolla
- USA
| | - Daniel Strasser
- Institute of Chemistry
- The Hebrew University of Jerusalem
- 91904 Jerusalem
- Israel
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