151
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Schubert F, Rossi M, Baldauf C, Pagel K, Warnke S, von Helden G, Filsinger F, Kupser P, Meijer G, Salwiczek M, Koksch B, Scheffler M, Blum V. Exploring the conformational preferences of 20-residue peptides in isolation: Ac-Ala19-Lys + H+vs. Ac-Lys-Ala19 + H+ and the current reach of DFT. Phys Chem Chem Phys 2015; 17:7373-85. [DOI: 10.1039/c4cp05541a] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Using a high-level density functional and an exhaustive search of conformation space, the predicted conformation of a 20-amino acid peptide explains two seemingly contradictory experiments.
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Affiliation(s)
| | - Mariana Rossi
- Fritz-Haber-Institut der Max-Planck-Gesellschaft
- D-14195 Berlin
- Germany
- Physical and Theoretical Chemistry Laboratory
- University of Oxford
| | - Carsten Baldauf
- Fritz-Haber-Institut der Max-Planck-Gesellschaft
- D-14195 Berlin
- Germany
| | - Kevin Pagel
- Fritz-Haber-Institut der Max-Planck-Gesellschaft
- D-14195 Berlin
- Germany
- Institut für Chemie und Biochemie - Organische Chemie
- Freie Universität Berlin
| | - Stephan Warnke
- Fritz-Haber-Institut der Max-Planck-Gesellschaft
- D-14195 Berlin
- Germany
| | - Gert von Helden
- Fritz-Haber-Institut der Max-Planck-Gesellschaft
- D-14195 Berlin
- Germany
| | - Frank Filsinger
- Fritz-Haber-Institut der Max-Planck-Gesellschaft
- D-14195 Berlin
- Germany
| | - Peter Kupser
- Fritz-Haber-Institut der Max-Planck-Gesellschaft
- D-14195 Berlin
- Germany
| | - Gerard Meijer
- Fritz-Haber-Institut der Max-Planck-Gesellschaft
- D-14195 Berlin
- Germany
- Radboud University Nijmegen
- 65000 HC Nijmegen
| | - Mario Salwiczek
- Institut für Chemie und Biochemie - Organische Chemie
- Freie Universität Berlin
- D-14195 Berlin
- Germany
| | - Beate Koksch
- Institut für Chemie und Biochemie - Organische Chemie
- Freie Universität Berlin
- D-14195 Berlin
- Germany
| | | | - Volker Blum
- Fritz-Haber-Institut der Max-Planck-Gesellschaft
- D-14195 Berlin
- Germany
- Department Mechanical Engineering and Material Science and Center for Materials Genomics
- Duke University
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152
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Voronina L, Rizzo TR. Spectroscopic studies of kinetically trapped conformations in the gas phase: the case of triply protonated bradykinin. Phys Chem Chem Phys 2015; 17:25828-36. [DOI: 10.1039/c5cp01651g] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
We explore conformational space of triply protonated bradykinin. Three conformational families are mobility-separated and spectroscopically characterized. Kinetically trapped structures are identified via annealing.
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Affiliation(s)
- Liudmila Voronina
- Laboratoire de Chimie Physique Moléculaire
- École Polytechnique Fédérale de Lausanne
- EPFL SB ISIC LCPM
- CH-1015 Lausanne
- Switzerland
| | - Thomas R. Rizzo
- Laboratoire de Chimie Physique Moléculaire
- École Polytechnique Fédérale de Lausanne
- EPFL SB ISIC LCPM
- CH-1015 Lausanne
- Switzerland
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153
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Féraud G, Esteves-López N, Dedonder-Lardeux C, Jouvet C. UV spectroscopy of cold ions as a probe of the protonation site. Phys Chem Chem Phys 2015; 17:25755-60. [DOI: 10.1039/c5cp01122a] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Where does the proton go?
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Affiliation(s)
- Géraldine Féraud
- CNRS, Aix Marseille Université
- PIIM
- Physique des Interactions Ioniques et Moléculaires (UMR-7345)
- 13397 Marseille Cedex 20
- France
| | - Natalia Esteves-López
- CNRS, Aix Marseille Université
- PIIM
- Physique des Interactions Ioniques et Moléculaires (UMR-7345)
- 13397 Marseille Cedex 20
- France
| | - Claude Dedonder-Lardeux
- CNRS, Aix Marseille Université
- PIIM
- Physique des Interactions Ioniques et Moléculaires (UMR-7345)
- 13397 Marseille Cedex 20
- France
| | - Christophe Jouvet
- CNRS, Aix Marseille Université
- PIIM
- Physique des Interactions Ioniques et Moléculaires (UMR-7345)
- 13397 Marseille Cedex 20
- France
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154
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Broquier M, Soorkia S, Grégoire G. A comprehensive study of cold protonated tyramine: UV photodissociation experiments and ab initio calculations. Phys Chem Chem Phys 2015; 17:25854-62. [DOI: 10.1039/c5cp01375e] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Excited state properties of cold protonated ions are revealed by a combination of laser spectroscopy and ab initio calculations.
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Affiliation(s)
- Michel Broquier
- CNRS
- Université Paris Sud
- Institut des Sciences Moléculaires d'Orsay (ISMO) UMR 8214
- 91405 Orsay Cedex
- France
| | - Satchin Soorkia
- CNRS
- Université Paris Sud
- Institut des Sciences Moléculaires d'Orsay (ISMO) UMR 8214
- 91405 Orsay Cedex
- France
| | - Gilles Grégoire
- CNRS
- Université Paris Sud
- Institut des Sciences Moléculaires d'Orsay (ISMO) UMR 8214
- 91405 Orsay Cedex
- France
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155
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Soorkia S, Broquier M, Grégoire G. Conformer- and Mode-Specific Excited State Lifetimes of Cold Protonated Tyrosine Ions. J Phys Chem Lett 2014; 5:4349-4355. [PMID: 26273986 DOI: 10.1021/jz502387q] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The excited state lifetimes of conformer- and mode-selected cold protonated tyrosine have been measured for the first time through a picosecond pump-probe photodissociation scheme. Whereas the photofragmentation mechanism of protonated tyrosine ions strongly depends upon the interaction of the carboxylic acid group with the phenol ring, their excited state lifetimes are quite similar and decrease as the excess energy increases from 1.5 ns at the band origin to 900 ps and less than 500 ps for the 10(1) and 10(2) bands, respectively. Surprisingly, the excited state lifetime of the conformer with the anti orientation of the hydroxyl oxygen lone pair with respect to the ammonium group dramatically increases as compared to the others conformers up to 10 ns at the band origin and by more than a factor of 2 for the 10(1) band. The present experimental results clearly emphasize the subtle effect of the structural conformation on the excited state properties of molecular ions.
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Affiliation(s)
- Satchin Soorkia
- †CNRS, Université Paris Sud, Institut des Sciences Moléculaires d'Orsay (ISMO) UMR 8624, 91405 Orsay Cedex, France
| | - Michel Broquier
- †CNRS, Université Paris Sud, Institut des Sciences Moléculaires d'Orsay (ISMO) UMR 8624, 91405 Orsay Cedex, France
- ‡Université Paris Sud, CLUPS (Centre Laser de l'Université Paris Sud) LUMAT FR 2764, 91405 Orsay Cedex, France
| | - Gilles Grégoire
- §CNRS, Université Paris 13, Sorbonne Paris Cité, Laboratoire de Physique des Lasers, UMR 7538, F-93430 Villetaneuse, France
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156
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Site-specific vibrational spectral signatures of water molecules in the magic H3O+ (H2O)20 and Cs+ (H2O)20 clusters. Proc Natl Acad Sci U S A 2014; 111:18132-7. [PMID: 25489068 DOI: 10.1073/pnas.1420734111] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Theoretical models of proton hydration with tens of water molecules indicate that the excess proton is embedded on the surface of clathrate-like cage structures with one or two water molecules in the interior. The evidence for these structures has been indirect, however, because the experimental spectra in the critical H-bonding region of the OH stretching vibrations have been too diffuse to provide band patterns that distinguish between candidate structures predicted theoretically. Here we exploit the slow cooling afforded by cryogenic ion trapping, along with isotopic substitution, to quench water clusters attached to the H3O(+) and Cs(+) ions into structures that yield well-resolved vibrational bands over the entire 215- to 3,800-cm(-1) range. The magic H3O(+)(H2O)20 cluster yields particularly clear spectral signatures that can, with the aid of ab initio predictions, be traced to specific classes of network sites in the predicted pentagonal dodecahedron H-bonded cage with the hydronium ion residing on the surface.
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157
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Jašík J, Gerlich D, Roithová J. Two-Color Infrared Predissociation Spectroscopy of C6H62+ Isomers Using Helium Tagging. J Phys Chem A 2014; 119:2532-42. [DOI: 10.1021/jp5088064] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Juraj Jašík
- Department
of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 2030/8, 12843 Prague 2, Czech Republic
| | - Dieter Gerlich
- Department
of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 2030/8, 12843 Prague 2, Czech Republic
- Department
of Physics, University of Technology, 09107 Chemnitz, Germany
| | - Jana Roithová
- Department
of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 2030/8, 12843 Prague 2, Czech Republic
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158
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Adamson BD, Coughlan NJA, Markworth PB, Continetti RE, Bieske EJ. An ion mobility mass spectrometer for investigating photoisomerization and photodissociation of molecular ions. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2014; 85:123109. [PMID: 25554274 DOI: 10.1063/1.4903753] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
An ion mobility mass spectrometry apparatus for investigating the photoisomerization and photodissociation of electrosprayed molecular ions in the gas phase is described. The device consists of a drift tube mobility spectrometer, with access for a laser beam that intercepts the drifting ion packet either coaxially or transversely, followed by a quadrupole mass filter. An ion gate halfway along the drift region allows the instrument to be used as a tandem ion mobility spectrometer, enabling mobility selection of ions prior to irradiation, with the photoisomer ions being separated over the second half of the drift tube. The utility of the device is illustrated with photoisomerization and photodissociation action spectra of carbocyanine molecular cations. The mobility resolution of the device for singly charged ions is typically 80 and it has a mass range of 100-440 Da, with the lower limit determined by the drive frequency for the ion funnels, and the upper limit by the quadrupole mass filter.
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Affiliation(s)
- B D Adamson
- School of Chemistry, The University of Melbourne, Victoria 3010, Australia
| | - N J A Coughlan
- School of Chemistry, The University of Melbourne, Victoria 3010, Australia
| | - P B Markworth
- School of Chemistry, The University of Melbourne, Victoria 3010, Australia
| | - R E Continetti
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, USA
| | - E J Bieske
- School of Chemistry, The University of Melbourne, Victoria 3010, Australia
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159
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Loquais Y, Gloaguen E, Habka S, Vaquero-Vara V, Brenner V, Tardivel B, Mons M. Secondary Structures in Phe-Containing Isolated Dipeptide Chains: Laser Spectroscopy vs Quantum Chemistry. J Phys Chem A 2014; 119:5932-41. [DOI: 10.1021/jp509494c] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Yohan Loquais
- CEA,
IRAMIS, Laboratoire
Interactions, Dynamique et Lasers, CEA Saclay, Bât 522, 91191 Gif-sur-Yvette, France
- CNRS, INP, Laboratoire
Francis Perrin, URA 2453, CEA Saclay,
Bât 522, 91191 Gif-sur-Yvette, France
| | - Eric Gloaguen
- CEA,
IRAMIS, Laboratoire
Interactions, Dynamique et Lasers, CEA Saclay, Bât 522, 91191 Gif-sur-Yvette, France
- CNRS, INP, Laboratoire
Francis Perrin, URA 2453, CEA Saclay,
Bât 522, 91191 Gif-sur-Yvette, France
| | - Sana Habka
- CEA,
IRAMIS, Laboratoire
Interactions, Dynamique et Lasers, CEA Saclay, Bât 522, 91191 Gif-sur-Yvette, France
- CNRS, INP, Laboratoire
Francis Perrin, URA 2453, CEA Saclay,
Bât 522, 91191 Gif-sur-Yvette, France
| | - Vanesa Vaquero-Vara
- CEA,
IRAMIS, Laboratoire
Interactions, Dynamique et Lasers, CEA Saclay, Bât 522, 91191 Gif-sur-Yvette, France
- CNRS, INP, Laboratoire
Francis Perrin, URA 2453, CEA Saclay,
Bât 522, 91191 Gif-sur-Yvette, France
| | - Valérie Brenner
- CEA,
IRAMIS, Laboratoire
Interactions, Dynamique et Lasers, CEA Saclay, Bât 522, 91191 Gif-sur-Yvette, France
- CNRS, INP, Laboratoire
Francis Perrin, URA 2453, CEA Saclay,
Bât 522, 91191 Gif-sur-Yvette, France
| | - Benjamin Tardivel
- CEA,
IRAMIS, Laboratoire
Interactions, Dynamique et Lasers, CEA Saclay, Bât 522, 91191 Gif-sur-Yvette, France
- CNRS, INP, Laboratoire
Francis Perrin, URA 2453, CEA Saclay,
Bât 522, 91191 Gif-sur-Yvette, France
| | - Michel Mons
- CEA,
IRAMIS, Laboratoire
Interactions, Dynamique et Lasers, CEA Saclay, Bât 522, 91191 Gif-sur-Yvette, France
- CNRS, INP, Laboratoire
Francis Perrin, URA 2453, CEA Saclay,
Bât 522, 91191 Gif-sur-Yvette, France
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160
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Giuliani A, Milosavljević AR, Canon F, Nahon L. Contribution of synchrotron radiation to photoactivation studies of biomolecular ions in the gas phase. MASS SPECTROMETRY REVIEWS 2014; 33:424-441. [PMID: 24375654 DOI: 10.1002/mas.21398] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Photon activation of ions in the visible and ultraviolet range attracts a growing interest, partly for its promising applications in tandem mass spectrometry. However, this task is not trivial, as it requires notably high brilliance photon sources. Hence, most of the work in that field has been performed using lasers. Synchrotron radiation is a source continuously tunable over a wide photon energy range and which possesses the necessary characteristics for ion activation. This review focuses on the array of applications of synchrotron radiation in photon activation of ions ranging from near UV to soft X-rays.
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Affiliation(s)
- Alexandre Giuliani
- Synchrotron SOLEIL, L'Orme des Merisiers, Saint Aubin, 91192, Gif-sur-Yvette, France; UAR1008 CEPIA, INRA, 44316, Nantes, France
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161
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Zabuga AV, Kamrath MZ, Boyarkin OV, Rizzo TR. Fragmentation mechanism of UV-excited peptides in the gas phase. J Chem Phys 2014; 141:154309. [DOI: 10.1063/1.4897158] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Aleksandra V. Zabuga
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland
| | - Michael Z. Kamrath
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland
| | - Oleg V. Boyarkin
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland
| | - Thomas R. Rizzo
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland
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162
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Dedonder C, Féraud G, Jouvet C. Communication: Identification of daughter ions through their electronic spectroscopy at low temperature. J Chem Phys 2014; 141:131101. [DOI: 10.1063/1.4896981] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Affiliation(s)
- Claude Dedonder
- Aix-Marseille Université, CNRS, PIIM, UMR-7345, Marseille Cedex 20, France
| | - Géraldine Féraud
- Aix-Marseille Université, CNRS, PIIM, UMR-7345, Marseille Cedex 20, France
| | - Christophe Jouvet
- Aix-Marseille Université, CNRS, PIIM, UMR-7345, Marseille Cedex 20, France
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163
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Lorenz UJ, Rizzo TR. Structural melting of an amino acid dimer upon intersystem crossing. J Am Chem Soc 2014; 136:14974-80. [PMID: 25250642 DOI: 10.1021/ja507981p] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
We present a spectroscopic investigation of the excited-state dynamics of the phenylalanine (Phe)/serine (Ser) protonated dimer in the gas phase. Using an ultraviolet (UV) laser pulse, we promote individual isomers to the S1 state and probe their fate with an infrared (IR) pulse. We find that the S1 state has a lifetime of ~70 ns and undergoes intersystem crossing (ISC) to the T1 state. Time-resolved IR spectra allow us to follow the structural evolution of the dimer. In the S1 state, the different isomers retain the hydrogen-bonding pattern of the ground state. Intersystem crossing triggers a sudden increase of the vibrational energy, so that the dimers can overcome isomerization barriers and explore large parts of the potential energy surface (PES). Their broad IR spectra largely resemble one another and indicate that the dimers adopt a molten structure.
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Affiliation(s)
- Ulrich J Lorenz
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne , CH-1015 Lausanne, Switzerland
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164
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Leavitt CM, Moore KB, Raston PL, Agarwal J, Moody GH, Shirley CC, Schaefer HF, Douberly GE. Liquid Hot NAGMA Cooled to 0.4 K: Benchmark Thermochemistry of a Gas-Phase Peptide. J Phys Chem A 2014; 118:9692-700. [DOI: 10.1021/jp5092653] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | | | - Paul L. Raston
- Department
of Chemistry, University of Adelaide, Adelaide, SA 5005, Australia
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165
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Féraud G, Dedonder-Lardeux C, Soorkia S, Jouvet C. Photo-fragmentation spectroscopy of benzylium and 1-phenylethyl cations. J Chem Phys 2014; 140:024302. [PMID: 24437872 DOI: 10.1063/1.4858409] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The electronic spectra of cold benzylium (C6H5-CH2 (+)) and 1-phenylethyl (C6H5-CH-CH3 (+)) cations have been recorded via photofragment spectroscopy. Benzylium and 1-phenylethyl cations produced from electrosprayed benzylamine and phenylethylamine solutions, respectively, were stored in a cryogenically cooled quadrupole ion trap and photodissociated by an OPO laser, scanned in parts of the UV and visible regions (600-225 nm). The electronic states and active vibrational modes of the benzylium and 1-phenylethyl cations as well as those of their tropylium or methyl tropylium isomers have been calculated with ab initio methods for comparison with the spectra observed. Sharp vibrational progressions are observed in the visible region while the absorption features are much broader in the UV. The visible spectrum of the benzylium cation is similar to that obtained in an argon tagging experiment [V. Dryza, N. Chalyavi, J. A. Sanelli, and E. J. Bieske, J. Chem. Phys. 137, 204304 (2012)], with an additional splitting assigned to Fermi resonances. The visible spectrum of the 1-phenylethyl cation also shows vibrational progressions. For both cations, the second electronic transition is observed in the UV, around 33,000 cm(-1) (4.1 eV) and shows a broadened vibrational progression. In both cases the S2 optimized geometry is non-planar. The third electronic transition observed around 40,000 cm(-1) (5.0 eV) is even broader with no apparent vibrational structures, which is indicative of either a fast non-radiative process or a very large change in geometry between the excited and the ground states. The oscillator strengths calculated for tropylium and methyl tropylium are weak. Therefore, these isomeric structures are most likely not responsible for these absorption features. Finally, the fragmentation pattern changes in the second and third electronic states: C2H2 loss becomes predominant at higher excitation energies, for both cations.
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Affiliation(s)
- Géraldine Féraud
- Physique des Interactions Ioniques et Moleculaires, UMR CNRS 7345, Aix-Marseille Université, Avenue Escadrille Normandie-Niémen, 13397 Marseille Cedex 20, France
| | - Claude Dedonder-Lardeux
- Physique des Interactions Ioniques et Moleculaires, UMR CNRS 7345, Aix-Marseille Université, Avenue Escadrille Normandie-Niémen, 13397 Marseille Cedex 20, France
| | - Satchin Soorkia
- Institut des Sciences Moléculaires d'Orsay, CNRS UMR 8214, Université Paris Sud 11, 91405 Orsay Cedex, France
| | - Christophe Jouvet
- Physique des Interactions Ioniques et Moleculaires, UMR CNRS 7345, Aix-Marseille Université, Avenue Escadrille Normandie-Niémen, 13397 Marseille Cedex 20, France
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166
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Kang H, Féraud G, Dedonder-Lardeux C, Jouvet C. New Method for Double-Resonance Spectroscopy in a Cold Quadrupole Ion Trap and Its Application to UV-UV Hole-Burning Spectroscopy of Protonated Adenine Dimer. J Phys Chem Lett 2014; 5:2760-2764. [PMID: 26277976 DOI: 10.1021/jz5012466] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
A novel method for double-resonance spectroscopy in a cold quadrupole ion trap is presented, which utilizes dipolar resonant excitation of fragment ions in the quadrupole ion trap. Photofragments by a burn laser are removed by applying an auxiliary RF to the trap, and a probe laser detects the depletion of photofragments by the burn laser. By scanning the wavelength of the burn laser, conformation-specific UV spectrum of a cold ion is obtained. This simple and powerful method is applicable to any type of double-resonance spectroscopy in a cold quadrupole ion trap and was applied to UV-UV hole-burning spectroscopy of protonated adenine dimer. It was found that protonated adenine dimer has multiple conformers/tautomers, each with multiple excited states with drastically different excited state dynamics.
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Affiliation(s)
- Hyuk Kang
- †Department of Chemistry, Ajou University, San5, Wonchon-dong, Youngtong-gu, Suwon 443-749, Korea
| | - Géraldine Féraud
- ‡CNRS, Aix-Marseille Université, Physique des Interactions Ioniques et Moléculaire (PIIM) UMR 7345, 13397 Marseille Cedex, France
| | - Claude Dedonder-Lardeux
- ‡CNRS, Aix-Marseille Université, Physique des Interactions Ioniques et Moléculaire (PIIM) UMR 7345, 13397 Marseille Cedex, France
| | - Christophe Jouvet
- ‡CNRS, Aix-Marseille Université, Physique des Interactions Ioniques et Moléculaire (PIIM) UMR 7345, 13397 Marseille Cedex, France
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167
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Mosley JD, Young JW, Duncan MA. Infrared spectroscopy of the acetyl cation and its protonated ketene isomer. J Chem Phys 2014; 141:024306. [DOI: 10.1063/1.4887074] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- J. D. Mosley
- Department of Chemistry, University of Georgia, Athens, Georgia 30602, USA
| | - J. W. Young
- Department of Chemistry, University of Georgia, Athens, Georgia 30602, USA
| | - M. A. Duncan
- Department of Chemistry, University of Georgia, Athens, Georgia 30602, USA
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168
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Eibenberger S, Cheng X, Cotter JP, Arndt M. Absolute absorption cross sections from photon recoil in a matter-wave interferometer. PHYSICAL REVIEW LETTERS 2014; 112:250402. [PMID: 25014795 DOI: 10.1103/physrevlett.112.250402] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Indexed: 06/03/2023]
Abstract
We measure the absolute absorption cross section of molecules using a matter-wave interferometer. A nanostructured density distribution is imprinted onto a dilute molecular beam through quantum interference. As the beam crosses the light field of a probe laser some molecules will absorb a single photon. These absorption events impart a momentum recoil which shifts the position of the molecule relative to the unperturbed beam. Averaging over the shifted and unshifted components within the beam leads to a reduction of the fringe visibility, enabling the absolute absorption cross section to be extracted with high accuracy. This technique is independent of the molecular density, it is minimally invasive and successfully eliminates many problems related to photon cycling, state mixing, photobleaching, photoinduced heating, fragmentation, and ionization. It can therefore be extended to a wide variety of neutral molecules, clusters, and nanoparticles.
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Affiliation(s)
- Sandra Eibenberger
- Faculty of Physics, University of Vienna, VCQ & QuNaBioS, Boltzmanngasse 5, A-1090 Vienna, Austria
| | - Xiaxi Cheng
- Faculty of Physics, University of Vienna, VCQ & QuNaBioS, Boltzmanngasse 5, A-1090 Vienna, Austria
| | - J P Cotter
- Faculty of Physics, University of Vienna, VCQ & QuNaBioS, Boltzmanngasse 5, A-1090 Vienna, Austria
| | - Markus Arndt
- Faculty of Physics, University of Vienna, VCQ & QuNaBioS, Boltzmanngasse 5, A-1090 Vienna, Austria
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169
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Schinle F, Jacob CR, Wolk AB, Greisch JF, Vonderach M, Weis P, Hampe O, Johnson MA, Kappes MM. Ion mobility spectrometry, infrared dissociation spectroscopy, and ab initio computations toward structural characterization of the deprotonated leucine-enkephalin peptide anion in the gas phase. J Phys Chem A 2014; 118:8453-63. [PMID: 24884600 DOI: 10.1021/jp501772d] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Although the sequencing of protonated proteins and peptides with tandem mass spectrometry has blossomed into a powerful means of characterizing the proteome, much less effort has been directed at their deprotonated analogues, which can offer complementary sequence information. We present a unified approach to characterize the structure and intermolecular interactions present in the gas-phase pentapeptide leucine-enkephalin anion by several vibrational spectroscopy schemes as well as by ion-mobility spectrometry, all of which are analyzed with the help of quantum-chemical computations. The picture emerging from this study is that deprotonation takes place at the C terminus. In this configuration, the excess charge is stabilized by strong intramolecular hydrogen bonds to two backbone amide groups and thus provides a detailed picture of a potentially common charge accommodation motif in peptide anions.
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Affiliation(s)
- Florian Schinle
- Institute of Nanotechnology, Karlsruhe Institute of Technology (KIT) , 76021 Karlsruhe, Germany
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170
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Servage KA, Silveira JA, Fort KL, Russell DH. Evolution of Hydrogen-Bond Networks in Protonated Water Clusters H(+)(H2O)n (n = 1 to 120) Studied by Cryogenic Ion Mobility-Mass Spectrometry. J Phys Chem Lett 2014; 5:1825-1830. [PMID: 26273860 DOI: 10.1021/jz500693k] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Cryogenic (80 K) ion mobility-mass spectrometry (cryo-IM-MS) is employed to study structural transitions of protonated water clusters in both the small, H(+)(H2O)n (n = 1 to 30), and large, (n = 31 to ∼120), size regions. In agreement with previous studies, we find compelling evidence of regions of uniform cluster decay in the small size region, accompanied by sharp transition points whereby the loss of a single water monomer induces a different H-bonding motif. The investigation of the isomeric distribution of each species at 80 K reveals experimental evidence supporting the notion that H(+)(H2O)n (n = 6) is the smallest system to possess both Eigen- (H3O(+)) and Zundel- (H5O2(+)) centered structures. Cryo-IM-MS is particularly well-suited for studying clusters in the large size region, for which previous spectroscopic experimental studies are scarce.
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171
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Marsh BM, Duffy EM, Soukup MT, Zhou J, Garand E. Intramolecular Hydrogen Bonding Motifs in Deprotonated Glycine Peptides by Cryogenic Ion Infrared Spectroscopy. J Phys Chem A 2014; 118:3906-12. [DOI: 10.1021/jp501936b] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Brett M. Marsh
- Department
of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Erin M. Duffy
- Department
of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Michael T. Soukup
- Department
of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Jia Zhou
- Department
of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Etienne Garand
- Department
of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
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172
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Rösch D, Willitsch S, Chang YP, Küpper J. Chemical reactions of conformationally selected 3-aminophenol molecules in a beam with Coulomb-crystallized Ca+ ions. J Chem Phys 2014; 140:124202. [PMID: 24697433 DOI: 10.1063/1.4869100] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Daniel Rösch
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056 Basel, Switzerland
| | - Stefan Willitsch
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056 Basel, Switzerland
| | - Yuan-Pin Chang
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Jochen Küpper
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
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173
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Dopfer O, Patzer A, Chakraborty S, Alata I, Omidyan R, Broquier M, Dedonder C, Jouvet C. Electronic and vibrational spectra of protonated benzaldehyde-water clusters, [BZ-(H2O)n≤5]H+: Evidence for ground-state proton transfer to solvent for n ≥ 3. J Chem Phys 2014; 140:124314. [DOI: 10.1063/1.4869341] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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174
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Ziegler BE, Marta RA, Burt MB, Martens SM, Martens JK, McMahon TB. Structural investigation of protonated azidothymidine and protonated dimer. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2014; 25:176-185. [PMID: 24306778 DOI: 10.1007/s13361-013-0767-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2013] [Revised: 09/29/2013] [Accepted: 10/07/2013] [Indexed: 06/02/2023]
Abstract
Infrared multiple photon dissociation (IRMPD) spectroscopy experiments and quantum chemical calculations have been used to explore the possible structures of protonated azidothymidine and the corresponding protonated dimer. Many interesting differences between the protonated and neutral forms of azidothymidine were found, particularly associated with keto-enol tautomerization. Comparison of computational vibrational and the experimental IMRPD spectra show good agreement and give confidence that the dominant protonated species has been identified. The protonated dimer of azidothymidine exhibits three intramolecular hydrogen bonds. The IRMPD spectrum of the protonated dimer is consistent with the spectrum of the most stable computational structure. This work brings to light interesting keto-enol tautomerization and exocyclic hydrogen bonding involving azidothymidine and its protonated dimer. The fact that one dominant protonated species is observed in the gas phase, despite both the keto and enol structures being similar in energy, is proposed to be the direct result of the electrospray ionization process in which the dominant protonated dimer structure dissociates in the most energetically favorable way.
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Affiliation(s)
- Blake E Ziegler
- Department of Chemistry, University of Waterloo, Waterloo, Ontario, N2L 3G1, Canada
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175
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Inokuchi Y, Ebata T, Rizzo TR, Boyarkin OV. Microhydration Effects on the Encapsulation of Potassium Ion by Dibenzo-18-Crown-6. J Am Chem Soc 2014; 136:1815-24. [DOI: 10.1021/ja4086066] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yoshiya Inokuchi
- Department
of Chemistry, Graduate School of Science, Hiroshima University, Higashi-Hiroshima,
Hiroshima 739-8526, Japan
| | - Takayuki Ebata
- Department
of Chemistry, Graduate School of Science, Hiroshima University, Higashi-Hiroshima,
Hiroshima 739-8526, Japan
| | - Thomas R. Rizzo
- Laboratoire
de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland
| | - Oleg V. Boyarkin
- Laboratoire
de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland
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176
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Wolk AB, Leavitt CM, Garand E, Johnson MA. Cryogenic ion chemistry and spectroscopy. Acc Chem Res 2014; 47:202-10. [PMID: 23972279 DOI: 10.1021/ar400125a] [Citation(s) in RCA: 229] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The use of mass spectrometry in macromolecular analysis is an incredibly important technique and has allowed efficient identification of secondary and tertiary protein structures. Over 20 years ago, Chemistry Nobelist John Fenn and co-workers revolutionized mass spectrometry by developing ways to non-destructively extract large molecules directly from solution into the gas phase. This advance, in turn, enabled rapid sequencing of biopolymers through tandem mass spectrometry at the heart of the burgeoning field of proteomics. In this Account, we discuss how cryogenic cooling, mass selection, and reactive processing together provide a powerful way to characterize ion structures as well as rationally synthesize labile reaction intermediates. This is accomplished by first cooling the ions close to 10 K and condensing onto them weakly bound, chemically inert small molecules or rare gas atoms. This assembly can then be used as a medium in which to quench reactive encounters by rapid evaporation of the adducts, as well as provide a universal means for acquiring highly resolved vibrational action spectra of the embedded species by photoinduced mass loss. Moreover, the spectroscopic measurements can be obtained with readily available, broadly tunable pulsed infrared lasers because absorption of a single photon is sufficient to induce evaporation. We discuss the implementation of these methods with a new type of hybrid photofragmentation mass spectrometer involving two stages of mass selection with two laser excitation regions interfaced to the cryogenic ion source. We illustrate several capabilities of the cryogenic ion spectrometer by presenting recent applications to peptides, a biomimetic catalyst, a large antibiotic molecule (vancomycin), and reaction intermediates pertinent to the chemistry of the ionosphere. First, we demonstrate how site-specific isotopic substitution can be used to identify bands due to local functional groups in a protonated tripeptide designed to stereoselectively catalyze bromination of biaryl substrates. This procedure directly reveals the particular H-bond donor and acceptor groups that enforce the folded structure of the bare ion as well as provide contact points for noncovalent interaction with substrates. We then show how photochemical hole-burning involving only vibrational excitations can be used in a double-resonance mode to systematically disentangle overlapping spectra that arise when several conformers of a dipeptide are prepared in the ion source. Finally, we highlight our ability to systematically capture reaction intermediates and spectroscopically characterize their structures. Through this method, we can identify the pathway for water-network-mediated, proton-coupled transformation of nitrosonium, NO(+) to HONO, a key reaction controlling the cations present in the ionosphere. Through this work, we reveal the critical role played by water molecules occupying the second solvation shell around the ion, where they stabilize the emergent product ion in a fashion reminiscent of the solvent coordinate responsible for the barrier to charge transfer in solution. Looking to the future, we predict that the capture and characterization of fleeting intermediate complexes in the homogeneous catalytic activation of small molecules like water, alkanes, and CO2 is a likely avenue rich with opportunity.
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Affiliation(s)
- Arron B. Wolk
- Sterling Chemistry Laboratory, Yale University, P. O. Box 208107, New Haven, Connecticut 06520, United States
| | - Christopher M. Leavitt
- Sterling Chemistry Laboratory, Yale University, P. O. Box 208107, New Haven, Connecticut 06520, United States
| | - Etienne Garand
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Mark A. Johnson
- Sterling Chemistry Laboratory, Yale University, P. O. Box 208107, New Haven, Connecticut 06520, United States
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177
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Loquais Y, Gloaguen E, Alauddin M, Brenner V, Tardivel B, Mons M. On the near UV photophysics of a phenylalanine residue: conformation-dependent ππ* state deactivation revealed by laser spectroscopy of isolated neutral dipeptides. Phys Chem Chem Phys 2014; 16:22192-200. [DOI: 10.1039/c4cp03401e] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The primary step of the near UV photophysics is investigated in pump–probe R2PI ns experiments carried out on specific conformers of model peptide chains.
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Affiliation(s)
- Yohan Loquais
- CEA
- IRAMIS
- Laboratoire Interactions
- Dynamique et Lasers
- 91191 Gif-sur-Yvette, France
| | - Eric Gloaguen
- CNRS
- INP
- Laboratoire Francis Perrin
- URA 2453
- 91191 Gif-sur-Yvette, France
| | - Mohammad Alauddin
- CEA
- IRAMIS
- Laboratoire Interactions
- Dynamique et Lasers
- 91191 Gif-sur-Yvette, France
| | - Valérie Brenner
- CEA
- IRAMIS
- Laboratoire Interactions
- Dynamique et Lasers
- 91191 Gif-sur-Yvette, France
| | - Benjamin Tardivel
- CEA
- IRAMIS
- Laboratoire Interactions
- Dynamique et Lasers
- 91191 Gif-sur-Yvette, France
| | - Michel Mons
- CEA
- IRAMIS
- Laboratoire Interactions
- Dynamique et Lasers
- 91191 Gif-sur-Yvette, France
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178
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179
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Féraud G, Broquier M, Dedonder-Lardeux C, Grégoire G, Soorkia S, Jouvet C. Photofragmentation spectroscopy of cold protonated aromatic amines in the gas phase. Phys Chem Chem Phys 2014; 16:5250-9. [DOI: 10.1039/c3cp54736a] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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180
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Dunbar RC. Spectroscopy of Metal-Ion Complexes with Peptide-Related Ligands. Top Curr Chem (Cham) 2014; 364:183-223. [DOI: 10.1007/128_2014_578] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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181
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Marshall DL, Hansen CS, Trevitt AJ, Oh HB, Blanksby SJ. Photodissociation of TEMPO-modified peptides: new approaches to radical-directed dissociation of biomolecules. Phys Chem Chem Phys 2014; 16:4871-9. [DOI: 10.1039/c3cp54825b] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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182
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Lang J, Gaffga M, Menges F, Niedner-Schatteburg G. Two-color delay dependent IR probing of torsional isomerization in a [AgL1L2]+complex. Phys Chem Chem Phys 2014; 16:17417-21. [DOI: 10.1039/c4cp02045f] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Two-color infrared multiple photon dissociation (2c-IR-MPD) spectroscopy with delayed pulses indicates a torsional isomerization in a “ligand–metal–chelate” complex [AgL1L2]+.
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Affiliation(s)
- Johannes Lang
- Fachbereich Chemie and Forschungszentrum OPTIMAS
- Technische Universität Kaiserslautern
- 67663 Kaiserslautern, Germany
| | - Maximilian Gaffga
- Fachbereich Chemie and Forschungszentrum OPTIMAS
- Technische Universität Kaiserslautern
- 67663 Kaiserslautern, Germany
| | - Fabian Menges
- Fachbereich Chemie and Forschungszentrum OPTIMAS
- Technische Universität Kaiserslautern
- 67663 Kaiserslautern, Germany
| | - Gereon Niedner-Schatteburg
- Fachbereich Chemie and Forschungszentrum OPTIMAS
- Technische Universität Kaiserslautern
- 67663 Kaiserslautern, Germany
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183
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Li H, Bendiak B, Siems WF, Gang DR, Hill HH. Ion mobility mass spectrometry analysis of isomeric disaccharide precursor, product and cluster ions. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2013; 27:2699-709. [PMID: 24591031 PMCID: PMC4317727 DOI: 10.1002/rcm.6720] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2013] [Revised: 08/22/2013] [Accepted: 08/23/2013] [Indexed: 05/11/2023]
Abstract
RATIONALE Carbohydrates are highly variable in structure owing to differences in their anomeric configurations, monomer stereochemistry, inter-residue linkage positions and general branching features. The separation of carbohydrate isomers poses a great challenge for current analytical techniques. METHODS The isomeric heterogeneity of disaccharide ions and monosaccharide-glycolaldehyde product ions was evaluated using electrospray traveling wave ion mobility mass spectrometry (Synapt G2 high-definition mass spectrometer) in both positive and negative ion modes. RESULTS The separation of isomeric disaccharide ions was observed but not fully achieved based on their mobility profiles. The mobilities of isomeric product ions, the monosaccharide-glycolaldehydes, derived from different disaccharide isomers were measured. Multiple mobility peaks were observed for both monosaccharide-glycolaldehyde cations and anions, indicating that there was more than one structural configuration in the gas phase as verified by NMR in solution. More importantly, the mobility patterns for isomeric monosaccharide-glycolaldehyde product ions were different, which enabled partial characterization of their respective disaccharide ions. Abundant disaccharide cluster ions were also observed. The results showed that a majority of isomeric cluster ions had different drift times and, moreover, more than one mobility peak was detected for a number of specific cluster ions. CONCLUSIONS It is demonstrated that ion mobility mass spectrometry is an advantageous method to assess the isomeric heterogeneity of carbohydrate compounds. It is capable of differentiating different types of carbohydrate ions having identical m/z values as well as multiple structural configurations of single compounds.
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Affiliation(s)
- Hongli Li
- Department of Chemistry, Washington State University, Pullman, Washington, USA
| | - Brad Bendiak
- Department of Cell and Developmental Biology, Program in Structural Biology and Biophysics, University of Colorado, Health Sciences Center, Anschutz Medical Campus, Aurora, Colorado, USA
| | - William F. Siems
- Department of Chemistry, Washington State University, Pullman, Washington, USA
| | - David R. Gang
- Institute of Biological Chemistry, Washington State University, Pullman, Washington, USA
| | - Herbert H. Hill
- Department of Chemistry, Washington State University, Pullman, Washington, USA
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184
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Johnson CJ, Fournier JA, Wolke CT, Johnson MA. Ionic liquids from the bottom up: Local assembly motifs in [EMIM][BF4] through cryogenic ion spectroscopy. J Chem Phys 2013; 139:224305. [DOI: 10.1063/1.4838475] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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185
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Chang YP, Długołęcki K, Küpper J, Rösch D, Wild D, Willitsch S. Specific Chemical Reactivities of Spatially Separated 3-Aminophenol Conformers with Cold Ca+ Ions. Science 2013; 342:98-101. [DOI: 10.1126/science.1242271] [Citation(s) in RCA: 119] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Many molecules exhibit multiple rotational isomers (conformers) that interconvert thermally and are difficult to isolate. Consequently, a precise characterization of their role in chemical reactions has proven challenging. We have probed the reactivity of specific conformers by using an experimental technique based on their spatial separation in a molecular beam by electrostatic deflection. The separated conformers react with a target of Coulomb-crystallized ions in a trap. In the reaction of Ca+ with 3-aminophenol, we find a twofold larger rate constant for the cis compared with the trans conformer (differentiated by the O–H bond orientation). This result is explained by conformer-specific differences in the long-range ion-molecule interaction potentials. Our approach demonstrates the possibility of controlling reactivity through selection of conformational states.
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186
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Dunbar RC, Oomens J, Berden G, Lau JKC, Verkerk UH, Hopkinson AC, Siu KWM. Metal Ion Complexes with HisGly: Comparison with PhePhe and PheGly. J Phys Chem A 2013; 117:5335-43. [DOI: 10.1021/jp4021917] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Robert C. Dunbar
- Chemistry
Department, Case Western Reserve University, Cleveland, Ohio 44106,
United States
| | - Jos Oomens
- Radboud University Nijmegen, Institute
for Molecules and Materials, FELIX Facility, Toernooiveld 7, 6525
ED Nijmegen, The Netherlands
- University of Amsterdam, Science Park
904, 1098XH Amsterdam, The Netherlands
| | - Giel Berden
- Radboud University Nijmegen, Institute
for Molecules and Materials, FELIX Facility, Toernooiveld 7, 6525
ED Nijmegen, The Netherlands
| | - Justin Kai-Chi Lau
- Department of Chemistry and
Centre for Research in Mass Spectrometry, York University, 4700 Keele Street, Toronto, Ontario, M3J 1P3, Canada
| | - Udo H. Verkerk
- Department of Chemistry and
Centre for Research in Mass Spectrometry, York University, 4700 Keele Street, Toronto, Ontario, M3J 1P3, Canada
| | - Alan C. Hopkinson
- Department of Chemistry and
Centre for Research in Mass Spectrometry, York University, 4700 Keele Street, Toronto, Ontario, M3J 1P3, Canada
| | - K. W. Michael Siu
- Department of Chemistry and
Centre for Research in Mass Spectrometry, York University, 4700 Keele Street, Toronto, Ontario, M3J 1P3, Canada
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187
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Hansen CS, Kirk BB, Blanksby SJ, O'Hair RAJ, Trevitt AJ. UV photodissociation action spectroscopy of haloanilinium ions in a linear quadrupole ion trap mass spectrometer. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2013; 24:932-940. [PMID: 23609184 DOI: 10.1007/s13361-013-0615-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2013] [Revised: 03/05/2013] [Accepted: 03/10/2013] [Indexed: 06/02/2023]
Abstract
UV-vis photodissociation action spectroscopy is becoming increasingly prevalent because of advances in, and commercial availability of, ion trapping technologies and tunable laser sources. This study outlines in detail an instrumental arrangement, combining a commercial ion-trap mass spectrometer and tunable nanosecond pulsed laser source, for performing fully automated photodissociation action spectroscopy on gas-phase ions. The components of the instrumentation are outlined, including the optical and electronic interfacing, in addition to the control software for automating the experiment and performing online analysis of the spectra. To demonstrate the utility of this ensemble, the photodissociation action spectra of 4-chloroanilinium, 4-bromoanilinium, and 4-iodoanilinium cations are presented and discussed. Multiple photoproducts are detected in each case and the photoproduct yields are followed as a function of laser wavelength. It is shown that the wavelength-dependent partitioning of the halide loss, H loss, and NH3 loss channels can be broadly rationalized in terms of the relative carbon-halide bond dissociation energies and processes of energy redistribution. The photodissociation action spectrum of (phenyl)Ag2 (+) is compared with a literature spectrum as a further benchmark.
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188
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Fujii A, Mizuse K. Infrared spectroscopic studies on hydrogen-bonded water networks in gas phase clusters. INT REV PHYS CHEM 2013. [DOI: 10.1080/0144235x.2012.760836] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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189
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Alata I, Bert J, Broquier M, Dedonder C, Feraud G, Grégoire G, Soorkia S, Marceca E, Jouvet C. Electronic Spectra of the Protonated Indole Chromophore in the Gas Phase. J Phys Chem A 2013; 117:4420-7. [DOI: 10.1021/jp402298y] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ivan Alata
- Atomic Energy Commission of Syria, P.O. Box 6091, Damascus, Syria
| | - Johan Bert
- PIIM, Aix-Marseille Université, UMR-CNRS 7345, Avenue Escadrille
Normandie-Niémen, 13397 Marseille cedex 20, France
| | | | - Claude Dedonder
- PIIM, Aix-Marseille Université, UMR-CNRS 7345, Avenue Escadrille
Normandie-Niémen, 13397 Marseille cedex 20, France
| | - Géraldine Feraud
- PIIM, Aix-Marseille Université, UMR-CNRS 7345, Avenue Escadrille
Normandie-Niémen, 13397 Marseille cedex 20, France
| | - Gilles Grégoire
- Laboratoire de Physique des
Lasers, Université Paris 13, Sorbonne Paris Cité, CNRS, 93430 Villetaneuse, France
| | | | - Ernesto Marceca
- INQUIMAE-FCEN, UBA, Ciudad Universitaria, 3er piso, Pabellón II, 1428 Buenos
Aires, Argentina
| | - Christophe Jouvet
- PIIM, Aix-Marseille Université, UMR-CNRS 7345, Avenue Escadrille
Normandie-Niémen, 13397 Marseille cedex 20, France
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190
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Nagornova NS, Rizzo TR, Boyarkin OV. Exploring the Mechanism of IR-UV Double-Resonance for Quantitative Spectroscopy of Protonated Polypeptides and Proteins. Angew Chem Int Ed Engl 2013; 52:6002-5. [DOI: 10.1002/anie.201301656] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Indexed: 11/11/2022]
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191
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Nagornova NS, Rizzo TR, Boyarkin OV. Exploring the Mechanism of IR-UV Double-Resonance for Quantitative Spectroscopy of Protonated Polypeptides and Proteins. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201301656] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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192
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Nosenko Y, Menges F, Riehn C, Niedner-Schatteburg G. Investigation by two-color IR dissociation spectroscopy of Hoogsteen-type binding in a metalated nucleobase pair mimic. Phys Chem Chem Phys 2013; 15:8171-8. [PMID: 23612714 DOI: 10.1039/c3cp44283g] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Two Ag(I) ions, deprotonated 1-methyl-thymine (1MT-H)(-) and 1,3-dideaza-adenine (DDA), self-assemble in methanolic solution to a cationic [(Ag)2(1MT-H)(DDA)](+) complex as identified by electrospray ionization mass spectrometry. Assignment of vibrational bands and identification of the silver coordination pattern arise from comparison of one- and two-color Infrared Multiple Photon Dissociation (IRMPD) spectra (1000-4000 cm(-1)) of isolated and trapped complexes to calculated spectra from density functional theory. This approach reveals two structurally and energetically close isomers that resemble a metalated Hoogsteen-like binding motif. The two color IR/IR double resonance scheme proved in particular useful to observe weakly absorbing or weakly fragmenting vibrational modes.
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Affiliation(s)
- Yevgeniy Nosenko
- Fachbereich Chemie and Forschungszentrum OPTIMAS, Technische Universität Kaiserslautern, Erwin-Schrödinger-Str. 52, Kaiserslautern 67663, Germany.
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193
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Stedwell CN, Galindo JF, Roitberg AE, Polfer NC. Structures of biomolecular ions in the gas phase probed by infrared light sources. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2013; 6:267-285. [PMID: 23560933 DOI: 10.1146/annurev-anchem-062012-092700] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Infrared (IR) spectroscopy of biomolecular ions combines mass spectrometry's high sensitivity and ability to analyze complex mixtures with the enhanced structural information available from vibrational spectroscopy. IR spectroscopy is in principle well placed to distinguish isomers and allow chemical classification of unknown molecules. This review gives an outline of current instrumentation, spectroscopic approaches, and potential bottlenecks. We discuss the most promising applications in bioanalytical mass spectrometry in view of recent experimental results, as well as future applications based on bioinformatics.
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Affiliation(s)
- Corey N Stedwell
- Department of Chemistry, University of Florida, Gainesville, Florida 32611-7200, USA.
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194
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Patzer A, Schütz M, Jouvet C, Dopfer O. Experimental Observation and Quantum Chemical Characterization of the S1 ← S0 Transition of Protonated Naphthalene–Argon Clusters. J Phys Chem A 2013; 117:9785-93. [DOI: 10.1021/jp312581v] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Alexander Patzer
- Institut für Optik und
Atomare Physik, Technische Universität Berlin, Hardenbergstraße 36, 10623 Berlin, Germany
| | - Markus Schütz
- Institut für Optik und
Atomare Physik, Technische Universität Berlin, Hardenbergstraße 36, 10623 Berlin, Germany
| | - Christophe Jouvet
- Laboratoire de Physique des Interactions
Ioniques et Moléculaires
(PIIM/UMR CNRS 7345), Aix Marseille Université, Avenue Escadrille Normandie-Niémen, 13397 Marseille cedex
20, France
| | - Otto Dopfer
- Institut für Optik und
Atomare Physik, Technische Universität Berlin, Hardenbergstraße 36, 10623 Berlin, Germany
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195
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Wolk AB, Garand E, Jones IM, Hamilton AD, Johnson MA. Quantifying Intrinsic Ion-Driven Conformational Changes in Diphenylacetylene Supramolecular Switches with Cryogenic Ion Vibrational Spectroscopy. J Phys Chem A 2013; 117:5962-9. [DOI: 10.1021/jp3111925] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Arron B. Wolk
- Sterling Chemistry Laboratory, Department of Chemistry, Yale University, P.O. Box 208107, New
Haven, Connecticut 06520, United States
| | - Etienne Garand
- Department of Chemistry, University of Wisconsin, 1101 University
Avenue, Madison, Wisconsin 53706, United States
| | - Ian M. Jones
- Department of Chemistry
and Biochemistry, The University of Texas at Austin, 1 University Station A5300, Austin, Texas
78712, United States
| | - Andrew D. Hamilton
- Department of Chemistry, University of Oxford, 12 Mansfield Road,
Oxford OX1 3TA, Great Britain
| | - Mark A. Johnson
- Sterling Chemistry Laboratory, Department of Chemistry, Yale University, P.O. Box 208107, New
Haven, Connecticut 06520, United States
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196
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197
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Mališ M, Loquais Y, Gloaguen E, Biswal HS, Piuzzi F, Tardivel B, Brenner V, Broquier M, Jouvet C, Mons M, Došlić N, Ljubić I. Unraveling the Mechanisms of Nonradiative Deactivation in Model Peptides Following Photoexcitation of a Phenylalanine Residue. J Am Chem Soc 2012; 134:20340-51. [DOI: 10.1021/ja3054942] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Momir Mališ
- Division
of Physical Chemistry, Ruđer Bošković Institute, Bijenička
cesta 54, HR-10002 Zagreb, Croatia
| | - Yohan Loquais
- CEA, IRAMIS, SPAM, Lab. Francis
Perrin, URA 2453, CEA-Saclay, Bât
522, Gif-sur-Yvette, F-91191, France
- CNRS, INC & INP, Lab. Francis Perrin, URA 2453, CEA-Saclay, Bât 522, Gif-sur-Yvette, F-91191, France
| | - Eric Gloaguen
- CEA, IRAMIS, SPAM, Lab. Francis
Perrin, URA 2453, CEA-Saclay, Bât
522, Gif-sur-Yvette, F-91191, France
- CNRS, INC & INP, Lab. Francis Perrin, URA 2453, CEA-Saclay, Bât 522, Gif-sur-Yvette, F-91191, France
| | - Himansu S. Biswal
- CEA, IRAMIS, SPAM, Lab. Francis
Perrin, URA 2453, CEA-Saclay, Bât
522, Gif-sur-Yvette, F-91191, France
- CNRS, INC & INP, Lab. Francis Perrin, URA 2453, CEA-Saclay, Bât 522, Gif-sur-Yvette, F-91191, France
| | - François Piuzzi
- CEA, IRAMIS, SPAM, Lab. Francis
Perrin, URA 2453, CEA-Saclay, Bât
522, Gif-sur-Yvette, F-91191, France
- CNRS, INC & INP, Lab. Francis Perrin, URA 2453, CEA-Saclay, Bât 522, Gif-sur-Yvette, F-91191, France
| | - Benjamin Tardivel
- CEA, IRAMIS, SPAM, Lab. Francis
Perrin, URA 2453, CEA-Saclay, Bât
522, Gif-sur-Yvette, F-91191, France
- CNRS, INC & INP, Lab. Francis Perrin, URA 2453, CEA-Saclay, Bât 522, Gif-sur-Yvette, F-91191, France
| | - Valérie Brenner
- CEA, IRAMIS, SPAM, Lab. Francis
Perrin, URA 2453, CEA-Saclay, Bât
522, Gif-sur-Yvette, F-91191, France
- CNRS, INC & INP, Lab. Francis Perrin, URA 2453, CEA-Saclay, Bât 522, Gif-sur-Yvette, F-91191, France
| | - Michel Broquier
- Université Paris-Sud 11, CLUPS / CNRS, LUMAT FR 2764, Bât
106, Orsay, F-91405, France
- CNRS, Université Paris-Sud 11, ISMO, UMR 8624, Bât 210, Orsay,
F-91405, France
| | - Christophe Jouvet
- Université Paris-Sud 11, CLUPS / CNRS, LUMAT FR 2764, Bât
106, Orsay, F-91405, France
- CNRS, Université Paris-Sud 11, ISMO, UMR 8624, Bât 210, Orsay,
F-91405, France
| | - Michel Mons
- CEA, IRAMIS, SPAM, Lab. Francis
Perrin, URA 2453, CEA-Saclay, Bât
522, Gif-sur-Yvette, F-91191, France
- CNRS, INC & INP, Lab. Francis Perrin, URA 2453, CEA-Saclay, Bât 522, Gif-sur-Yvette, F-91191, France
| | - Nađa Došlić
- Division
of Physical Chemistry, Ruđer Bošković Institute, Bijenička
cesta 54, HR-10002 Zagreb, Croatia
| | - Ivan Ljubić
- Division
of Physical Chemistry, Ruđer Bošković Institute, Bijenička
cesta 54, HR-10002 Zagreb, Croatia
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198
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Inokuchi Y, Kusaka R, Ebata T, Boyarkin OV, Rizzo TR. Laser Spectroscopic Study of Cold Host–Guest Complexes of Crown Ethers in the Gas Phase. Chemphyschem 2012. [DOI: 10.1002/cphc.201200746] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Yoshiya Inokuchi
- Department of Chemistry, Graduate School of Science, Hiroshima University, Higashi‐Hiroshima 739‐8526 (Japan)
| | - Ryoji Kusaka
- Department of Chemistry, Graduate School of Science, Hiroshima University, Higashi‐Hiroshima 739‐8526 (Japan)
| | - Takayuki Ebata
- Department of Chemistry, Graduate School of Science, Hiroshima University, Higashi‐Hiroshima 739‐8526 (Japan)
| | - Oleg V. Boyarkin
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, Lausanne 1015 (Switzerland)
| | - Thomas R. Rizzo
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, Lausanne 1015 (Switzerland)
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199
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Hyung SJ, Ruotolo BT. Integrating mass spectrometry of intact protein complexes into structural proteomics. Proteomics 2012; 12:1547-64. [PMID: 22611037 DOI: 10.1002/pmic.201100520] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
MS analysis of intact protein complexes has emerged as an established technology for assessing the composition and connectivity within dynamic, heterogeneous multiprotein complexes at low concentrations and in the context of mixtures. As this technology continues to move forward, one of the main challenges is to integrate the information content of such intact protein complex measurements with other MS approaches in structural biology. Methods such as H/D exchange, oxidative foot-printing, chemical cross-linking, affinity purification, and ion mobility separation add complementary information that allows access to every level of protein structure and organization. Here, we survey the structural information that can be retrieved by such experiments, demonstrate the applicability of integrative MS approaches in structural proteomics, and look to the future to explore upcoming innovations in this rapidly advancing area.
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Affiliation(s)
- Suk-Joon Hyung
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
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200
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Dean JC, Buchanan EG, Zwier TS. Mixed 14/16 Helices in the Gas Phase: Conformation-Specific Spectroscopy of Z-(Gly)n, n = 1, 3, 5. J Am Chem Soc 2012; 134:17186-201. [PMID: 23039317 DOI: 10.1021/ja306652c] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Jacob C. Dean
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084,
United States
| | - Evan G. Buchanan
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084,
United States
| | - Timothy S. Zwier
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084,
United States
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