151
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Rummel JL, Steill JD, Oomens J, Contreras CS, Pearson WL, Szczepanski J, Powell DH, Eyler JR. Structural Elucidation of Direct Analysis in Real Time Ionized Nerve Agent Simulants with Infrared Multiple Photon Dissociation Spectroscopy. Anal Chem 2011; 83:4045-52. [DOI: 10.1021/ac102973a] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Julia L. Rummel
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611-7200, United States
| | - Jeffrey D. Steill
- FOM Institute for Plasma Physics “Rijnhuizen”, Edisonbaan 14, 3439 MN Nieuwegein, The Netherlands
| | - Jos Oomens
- FOM Institute for Plasma Physics “Rijnhuizen”, Edisonbaan 14, 3439 MN Nieuwegein, The Netherlands
- Van‘t Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Cesar S. Contreras
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611-7200, United States
| | - Wright L. Pearson
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611-7200, United States
| | - Jan Szczepanski
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611-7200, United States
| | - David H. Powell
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611-7200, United States
| | - John R. Eyler
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611-7200, United States
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152
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Gulyuz K, Stedwell CN, Wang D, Polfer NC. Hybrid quadrupole mass filter∕quadrupole ion trap∕time-of-flight-mass spectrometer for infrared multiple photon dissociation spectroscopy of mass-selected ions. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2011; 82:054101. [PMID: 21639521 DOI: 10.1063/1.3585982] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
We present a laboratory-constructed mass spectrometer optimized for recording infrared multiple photon dissociation (IRMPD) spectra of mass-selected ions using a benchtop tunable infrared optical parametric oscillator∕amplifier (OPO∕A). The instrument is equipped with two ionization sources, an electrospray ionization source, as well as an electron ionization source for troubleshooting. This hybrid mass spectrometer is composed of a quadrupole mass filter for mass selection, a reduced pressure (∼10(-5) Torr) quadrupole ion trap (QIT) for OPO irradiation, and a reflectron time-of-flight drift tube for detecting the remaining precursor and photofragment ions. A helium gas pulse is introduced into the QIT to temporarily increase the pressure and hence enhance the trapping efficiency of axially injected ions. After a brief pump-down delay, the compact ion cloud is subjected to the focused output from the continuous wave OPO. In a recent study, we implemented this setup in the study of protonated tryptophan, TrpH(+), as well as collision-induced dissociation products of this protonated amino acid [W. K. Mino, Jr., K. Gulyuz, D. Wang, C. N. Stedwell, and N. C. Polfer, J. Phys. Chem. Lett. 2, 299 (2011)]. Here, we give a more detailed account on the figures of merit of such IRMPD experiments. The appreciable photodissociation yields in these measurements demonstrate that IRMPD spectroscopy of covalently bound ions can be routinely carried out using benchtop OPO setups.
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Affiliation(s)
- Kerim Gulyuz
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611, USA
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153
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Jang S, Song MJ, Kim H, Choi SS. Formation of metal complex ions from amino acid in the presence of Li+, Na+ and K+ by electrospray ionization: metal replacement of hydrogen in the ligands. JOURNAL OF MASS SPECTROMETRY : JMS 2011; 46:496-501. [PMID: 21500307 DOI: 10.1002/jms.1916] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Alkali metal cations easily form complexes with proteins in biological systems; understanding amino acid clusters with these cations can provide useful insight into their behaviors at the molecular level including diagnosis and therapy of related diseases. For the purpose of characterization of basic interaction between amino acids and alkali metal, each of the 20 naturally occurring amino acids were ionized in the presence of lithium, sodium and potassium cations by electrospray ionization, and the resulting product ions were analyzed. We focus our attention on the gas phase alkali metal ion-proton exchanged complexes in current study, specifically complexes with serine, threonine, asparagine and glutamine, which share characteristic pattern unlike other amino acids. All amino acids generated [M + H](+) and [M + Na](+) ions, where M stands for the neutral amino acid. Serine, threonine, asparagine and glutamine generated cluster ions of [nM - nH + (n + 1)Na](+) and [nM - (n - 1)H + (n - 1)Na + K](+) , where n = 1-7. While the (M - H + Li) and (M - H + K) species were not observed, the neutral (M - H + Na) species formed by proton-sodium cation exchange had a highly stable cyclic structure with ketone and amine ligand sites, suggesting that (M - H + Na) serves as a building block in cluster ion formation. Cluster ion intensity distributions of [nM - nH + (n + 1)Na](+) and [nM - (n - 1)H + (n - 1)Na + K](+) showed a magic number at n = 3 and 4, respectively. Extensive B3LYP-DFT quantum mechanical calculations were carried out to elucidate the geometry and energy of the cluster ions, and they provided a reasonable explanation for the stability and structure of the cluster ions.
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Affiliation(s)
- Soonmin Jang
- Department of Chemistry and Institute for Chemical Biology, Sejong University, 98 Gunja-dong, Gwangjin-gu, Seoul 143-747, Korea
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154
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Lanucara F, Chiavarino B, Crestoni ME, Scuderi D, Sinha RK, Maı̂tre P, Fornarini S. Naked Five-Coordinate FeIII(NO) Porphyrin Complexes: Vibrational and Reactivity Features. Inorg Chem 2011; 50:4445-52. [DOI: 10.1021/ic200073v] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Francesco Lanucara
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma “La Sapienza”, P.le A. Moro 5, I-00185, Roma, Italy
| | - Barbara Chiavarino
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma “La Sapienza”, P.le A. Moro 5, I-00185, Roma, Italy
| | - Maria Elisa Crestoni
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma “La Sapienza”, P.le A. Moro 5, I-00185, Roma, Italy
| | - Debora Scuderi
- Laboratoire de Chimie Physique, UMR8000 CNRS, Faculté des Sciences, Université Paris Sud, Bâtiment 350, 91405 Orsay Cedex, France
| | - Rajeev K. Sinha
- Laboratoire de Chimie Physique, UMR8000 CNRS, Faculté des Sciences, Université Paris Sud, Bâtiment 350, 91405 Orsay Cedex, France
| | - Philippe Maı̂tre
- Laboratoire de Chimie Physique, UMR8000 CNRS, Faculté des Sciences, Université Paris Sud, Bâtiment 350, 91405 Orsay Cedex, France
| | - Simonetta Fornarini
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma “La Sapienza”, P.le A. Moro 5, I-00185, Roma, Italy
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155
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156
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Chakraborty S, Dopfer O. Infrared spectrum of the Ag(+)-(pyridine)2 ionic complex: probing interactions in artificial metal-mediated base pairing. Chemphyschem 2011; 12:1999-2008. [PMID: 21442717 DOI: 10.1002/cphc.201001052] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2010] [Indexed: 11/11/2022]
Abstract
The isolated pyridine-Ag(+)-pyridine unit (Py-Ag(+)-Py) is employed as a model system to characterize the recently observed Ag(+)-mediated base pairing in DNA oligonucleotides at the molecular level. The structure and infrared (IR) spectrum of the Ag(+)-Py(2) cationic complex are investigated in the gas phase by IR multiple-photon dissociation (IRMPD) spectroscopy and quantum chemical calculations to determine the preferred metal-ion binding site and other salient properties of the potential-energy surface. The IRMPD spectrum has been obtained in the 840-1720 cm(-1) fingerprint region by coupling the IR free electron laser at the Centre Laser Infrarouge d'Orsay (CLIO) with a Fourier-transform ion cyclotron resonance (FT-ICR) mass spectrometer equipped with an electrospray ionization source. The spectroscopic results are interpreted with quantum chemical calculations conducted at the B3LYP/aug-cc-pVDZ level. The analysis of the IRMPD spectrum is consistent with a σ complex, in which the Ag(+) ion binds to the nitrogen lone pairs of the two Py ligands in a linear configuration. The binding motif of Py-Ag(+)-Py in the gas phase is the same as that observed in Ag(+)-mediated base pairing in solution. Ag(+) bonding to the π-electron system of the aromatic ring is predicted to be a substantially less-favorable binding motif.
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Affiliation(s)
- Shamik Chakraborty
- Institut für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstr. 36, 10623 Berlin, Germany
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157
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Prell JS, Chang TM, Biles JA, Berden G, Oomens J, Williams ER. Isomer Population Analysis of Gaseous Ions From Infrared Multiple Photon Dissociation Kinetics. J Phys Chem A 2011; 115:2745-51. [DOI: 10.1021/jp2004166] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- James S. Prell
- Department of Chemistry, University of California, Berkeley, California 94720-1460, United States
| | - Terrence M. Chang
- Department of Chemistry, University of California, Berkeley, California 94720-1460, United States
| | - Jeffrey A. Biles
- Department of Chemistry, University of California, Berkeley, California 94720-1460, United States
| | - Giel Berden
- FOM Institute for Plasma Physics Rijnhuizen, Edisonbaan 14, 3439 MN Nieuwegein, The Netherlands
| | - Jos Oomens
- FOM Institute for Plasma Physics Rijnhuizen, Edisonbaan 14, 3439 MN Nieuwegein, The Netherlands
- University of Amsterdam, Science Park 904, 1098XH Amsterdam, The Netherlands
| | - Evan R. Williams
- Department of Chemistry, University of California, Berkeley, California 94720-1460, United States
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158
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Brodbelt JS. Shedding light on the frontier of photodissociation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2011; 22:197-206. [PMID: 21472579 DOI: 10.1007/s13361-010-0023-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2010] [Revised: 10/11/2010] [Accepted: 10/13/2010] [Indexed: 05/30/2023]
Abstract
The development of new ion activation/dissociation methods is motivated by the need for more versatile ways to characterize structures of ions, especially in the growing arena of biological mass spectrometry in which better tools for determining sequences, modifications, interactions, and conformations of biopolymers are essential. Although most agree that collision-induced dissociation (CID) remains the gold standard for ion activation/dissociation, recent inroads in electron- and photon-based activation methods have cemented their role as outstanding alternatives. This article will focus on the impact of photodissociation, including its strengths and drawbacks as an analytical tool, and its potential for further development in the next decade. Moreover, the discussion will emphasize photodissociation in quadrupole ion traps, because that platform has been used for one of the greatest arrays of new applications over the past decade.
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Affiliation(s)
- Jennifer S Brodbelt
- Department of Chemistry and Biochemistry, University of Texas, Austin, TX 78712, USA.
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159
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Structural characterization by infrared multiple photon dissociation spectroscopy of protonated gas-phase ions obtained by electrospray ionization of cysteine and dopamine. Anal Bioanal Chem 2011; 399:2463-73. [DOI: 10.1007/s00216-010-4582-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2010] [Revised: 12/03/2010] [Accepted: 12/06/2010] [Indexed: 01/23/2023]
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160
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Lagutschenkov A, Langer J, Berden G, Oomens J, Dopfer O. Infrared spectra of protonated neurotransmitters: dopamine. Phys Chem Chem Phys 2011; 13:2815-23. [DOI: 10.1039/c0cp02133d] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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161
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162
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Polfer NC. Infrared multiple photon dissociation spectroscopy of trapped ions. Chem Soc Rev 2011; 40:2211-21. [DOI: 10.1039/c0cs00171f] [Citation(s) in RCA: 229] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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163
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Massah AR, Dreiocker F, Jackson RFW, Pickup BT, Oomens J, Meijer AJHM, Schäfer M. Gas-phase study of new organozinc reagents by IRMPD-spectroscopy, computational modelling and tandem-MS. Phys Chem Chem Phys 2011; 13:13255-67. [DOI: 10.1039/c1cp20747d] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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164
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Lagutschenkov A, Langer J, Berden G, Oomens J, Dopfer O. Infrared spectra of the protonated neurotransmitter histamine: competition between imidazolium and ammonium isomers in the gas phase. Phys Chem Chem Phys 2011; 13:15644-56. [DOI: 10.1039/c1cp21681c] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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165
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Lagutschenkov A, Langer J, Berden G, Oomens J, Dopfer O. Infrared Spectra of Protonated Neurotransmitters: Serotonin. J Phys Chem A 2010; 114:13268-76. [DOI: 10.1021/jp109337a] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Anita Lagutschenkov
- Institut für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstrasse 36, 10623 Berlin, Germany, FOM Institute for Plasma Physics Rijnhuizen, Edisonbaan 14, 3439 MN Nieuwegein, The Netherlands, and University of Amsterdam, Science Park 904, Amsterdam 1098XH, The Netherlands
| | - Judith Langer
- Institut für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstrasse 36, 10623 Berlin, Germany, FOM Institute for Plasma Physics Rijnhuizen, Edisonbaan 14, 3439 MN Nieuwegein, The Netherlands, and University of Amsterdam, Science Park 904, Amsterdam 1098XH, The Netherlands
| | - Giel Berden
- Institut für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstrasse 36, 10623 Berlin, Germany, FOM Institute for Plasma Physics Rijnhuizen, Edisonbaan 14, 3439 MN Nieuwegein, The Netherlands, and University of Amsterdam, Science Park 904, Amsterdam 1098XH, The Netherlands
| | - Jos Oomens
- Institut für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstrasse 36, 10623 Berlin, Germany, FOM Institute for Plasma Physics Rijnhuizen, Edisonbaan 14, 3439 MN Nieuwegein, The Netherlands, and University of Amsterdam, Science Park 904, Amsterdam 1098XH, The Netherlands
| | - Otto Dopfer
- Institut für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstrasse 36, 10623 Berlin, Germany, FOM Institute for Plasma Physics Rijnhuizen, Edisonbaan 14, 3439 MN Nieuwegein, The Netherlands, and University of Amsterdam, Science Park 904, Amsterdam 1098XH, The Netherlands
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166
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Patzer A, Zimmermann M, Alata I, Jouvet C, Dopfer O. Electronic Spectra of Protonated Benzaldehyde Clusters with Ar and N2: Effect of ππ* Excitation on the Intermolecular Potential. J Phys Chem A 2010; 114:12600-4. [DOI: 10.1021/jp109949y] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Alexander Patzer
- Institut für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstrasse 36, 10623 Berlin, Germany, and Centre Laser de l’Université Paris Sud (EA. 4127) and Institut des Sciences Moleculaires d’Orsay CNRS (FRE 3363), Universite Paris-Sud 11, 91405 Orsay Cedex, France
| | - Max Zimmermann
- Institut für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstrasse 36, 10623 Berlin, Germany, and Centre Laser de l’Université Paris Sud (EA. 4127) and Institut des Sciences Moleculaires d’Orsay CNRS (FRE 3363), Universite Paris-Sud 11, 91405 Orsay Cedex, France
| | - Ivan Alata
- Institut für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstrasse 36, 10623 Berlin, Germany, and Centre Laser de l’Université Paris Sud (EA. 4127) and Institut des Sciences Moleculaires d’Orsay CNRS (FRE 3363), Universite Paris-Sud 11, 91405 Orsay Cedex, France
| | - Christophe Jouvet
- Institut für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstrasse 36, 10623 Berlin, Germany, and Centre Laser de l’Université Paris Sud (EA. 4127) and Institut des Sciences Moleculaires d’Orsay CNRS (FRE 3363), Universite Paris-Sud 11, 91405 Orsay Cedex, France
| | - Otto Dopfer
- Institut für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstrasse 36, 10623 Berlin, Germany, and Centre Laser de l’Université Paris Sud (EA. 4127) and Institut des Sciences Moleculaires d’Orsay CNRS (FRE 3363), Universite Paris-Sud 11, 91405 Orsay Cedex, France
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167
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Assignment of the stereochemistry and anomeric configuration of structurally informative product ions derived from disaccharides: infrared photodissociation of glycosyl-glycolaldehydes in the negative ion mode. Carbohydr Res 2010; 345:2390-400. [DOI: 10.1016/j.carres.2010.09.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2010] [Revised: 08/29/2010] [Accepted: 09/01/2010] [Indexed: 12/30/2022]
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168
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Talbot FO, Rullo A, Yao H, Jockusch RA. Fluorescence Resonance Energy Transfer in Gaseous, Mass-Selected Polyproline Peptides. J Am Chem Soc 2010; 132:16156-64. [DOI: 10.1021/ja1067405] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Francis O. Talbot
- Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada
| | - Anthony Rullo
- Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada
| | - Huihui Yao
- Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada
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169
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Prell JS, Chang TM, O'Brien JT, Williams ER. Hydration isomers of protonated phenylalanine and derivatives: relative stabilities from infrared photodissociation. J Am Chem Soc 2010; 132:7811-9. [PMID: 20469865 DOI: 10.1021/ja102765w] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The binding sites of water molecules to protonated Phe and its derivatives are investigated using infrared photodissociation (IRPD) spectroscopy and kinetics as well as by computational chemistry. Calculated relative energies for hydration of PheH(+) at various sites on the N- and C-termini depend on the type of theory and basis set used, and no one hydration site was consistently calculated to be most favorable. Infrared photodissociation (IRPD) spectra between approximately 2650 and 3850 cm(-1) are reported for PheH(+)(H(2)O)(1-4) at 133 K and compared to calculated absorption spectra of low-energy hydration isomers, which do not resemble the IRPD spectra closely enough to unambiguously assign spectral bands. The IRPD spectra of PheH(+)(H(2)O)(1-4) are instead compared to those of N,N-Me(2)PheH(+)(H(2)O)(1,2), N-MePheH(+)(H(2)O)(1-3), and PheOMeH(+)(H(2)O)(1-3) at 133 K, which makes possible systematic band assignments. A unique band associated with a binding site not previously reported for PheH(+)(H(2)O), in which the water molecule accepts a hydrogen bond from the N-terminus of PheH(+) and donates a weak hydrogen bond to the pi-system of the side chain, is identified in the IRPD spectra. IRPD kinetics at laser frequencies resonant with specific hydration isomers are found to be biexponential for N,N-Me(2)PheH(+)(H(2)O), N-MePheH(+)(H(2)O), and PheH(+)(H(2)O). Relative populations of ions with water molecules attached at various binding sites are determined from fitting these kinetic data, and relative energies for hydration of these competitive binding sites at 133 K are obtained from these experimental values.
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Affiliation(s)
- James S Prell
- Department of Chemistry, University of California, Berkeley, California 94720, USA
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170
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Gucinski AC, Somogyi A, Chamot-Rooke J, Wysocki VH. Separation and identification of structural isomers by quadrupole collision-induced dissociation-hydrogen/deuterium exchange-infrared multiphoton dissociation (QCID-HDX-IRMPD). JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2010; 21:1329-1338. [PMID: 20452240 DOI: 10.1016/j.jasms.2010.03.036] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2009] [Revised: 03/08/2010] [Accepted: 03/10/2010] [Indexed: 05/29/2023]
Abstract
A new approach that uses a hybrid Q-FTICR instrument and combines quadrupole collision-induced dissociation, hydrogen-deuterium exchange, and infrared multiphoton dissociation (QCID-HDX-IRMPD) has been shown to effectively separate and differentiate isomeric fragment ion structures present at the same m/z. This method was used to study protonated YAGFL-OH (free acid), YAGFL-NH(2) (amide), cyclic YAGFL, and YAGFL-OCH(3) (methyl ester). QCID-HDX of m/z 552.28 (C(29)H(38)N(5)O(6)) from YAGFL-OH reveals at least two distributions of ions corresponding to the b(5) ion and a non-C-terminal water loss ion structure. Subsequent IRMPD fragmentation of each population shows distinct fragmentation patterns, reflecting the different structures from which they arise. This contrasts with data for YAGFL-NH(2) and YAGFL-OCH(3), which do not show two distinct H/D exchange populations for the C(29)H(38)N(5)O(6) structure formed by NH(3) and HOCH(3) loss, respectively. Relative extents of exchange for C(29)H(38)N(5)O(6) ions from six sequence isomers (YAGFL, AGFLY, GFLYA, FLYAG, LYAGF, and LFGAY) show a sequence dependence of relative isomer abundance. Supporting action IRMPD spectroscopy data are also presented herein and also show that multiple structures are present for the C(29)H(38)N(5)O(6) species from YAGFL-OH.
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Affiliation(s)
- Ashley C Gucinski
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721, USA
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171
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Chen X, Steill JD, Oomens J, Polfer NC. Oxazolone versus macrocycle structures for Leu-enkephalin b2-b4: insights from infrared multiple-photon dissociation spectroscopy and gas-phase hydrogen/deuterium exchange. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2010; 21:1313-1321. [PMID: 20236836 DOI: 10.1016/j.jasms.2010.02.022] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2009] [Revised: 02/11/2010] [Accepted: 02/11/2010] [Indexed: 05/28/2023]
Abstract
The collision-induced dissociation (CID) products b(2)-b(4) from Leu-enkephalin are examined with infrared multiple-photon dissociation (IR-MPD) spectroscopy and gas-phase hydrogen/deuterium exchange (HDX). Infrared spectroscopy reveals that b(2) exclusively adopts oxazolone structures, protonated at the N-terminus and at the oxazolone ring N, based on the presence and absence of diagnostic infrared vibrations. This is correlated with the presence of a single HDX rate. For the larger b(3) and b(4), the IR-MPD measurements display diagnostic bands compatible with a mixture of oxazolone and macrocycle structures. This result is supported by HDX experiments, which show a bimodal distribution in the HDX spectra and two distinct rates in the HDX kinetic fitting. The kinetic fitting of the HDX data is employed to derive the relative abundances of macrocycle and oxazolone structures for b(3) and b(4), using a procedure recently implemented by our group for a series of oligoglycine b fragments (Chen et al. J. Am. Chem. Soc.2009, 131(51), 18272-18282. doi: 10.1021/ja9030837). In analogy to that study, the results suggest that the relative abundance of the macrocycle structure increases as a function of b fragment size, going from 0% for b(2) to approximately 6% for b(3), and culminating in 31% for b(4). Nonetheless, there are also surprising differences between both studies, both in the exchange kinetics and the propensity in forming macrocycle structures. This indicates that the chemistry of "head-to-tail" cyclization depends on subtle differences in the sequence as well as the size of the b fragment.
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Affiliation(s)
- Xian Chen
- Department of Chemistry, University of Florida, Gainesville, Florida 32611-7200, USA
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172
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Li X, Oomens J, Eyler JR, Moore DT, Iyengar SS. Isotope dependent, temperature regulated, energy repartitioning in a low-barrier, short-strong hydrogen bonded cluster. J Chem Phys 2010; 132:244301. [DOI: 10.1063/1.3430525] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Xiaohu Li
- Department of Chemistry, Indiana University, 800 E. Kirkwood Ave., Bloomington, Indiana 47405, USA
| | - Jos Oomens
- FOM Institute for Plasma Physics ‘Rijnhuizen’, Edisonbaan 14, 3439 MN Nieuwegein, The Netherlands
| | - John R. Eyler
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, USA
| | - David T. Moore
- Department of Chemistry, Lehigh University, Bethlehem, Pennsylvania 18015, USA
| | - Srinivasan S. Iyengar
- Department of Chemistry, Indiana University, 800 E. Kirkwood Ave., Bloomington, Indiana 47405, USA
- Department of Physics, Indiana University, 727 E. Third St., Bloomington, Indiana 47405, USA
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173
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Triuret as a potential hypokalemic agent: Structure characterization of triuret and triuret-alkali metal adducts by mass spectrometric techniques. Arch Biochem Biophys 2010; 498:23-34. [PMID: 20371222 DOI: 10.1016/j.abb.2010.03.023] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2010] [Accepted: 03/31/2010] [Indexed: 02/07/2023]
Abstract
Triuret (also known as carbonyldiurea, dicarbamylurea, or 2,4-diimidotricarbonic diamide) is a byproduct of purine degradation in living organisms. An abundant triuret precursor is uric acid, whose level is altered in multiple metabolic pathologies. Triuret can be generated via urate oxidation by peroxynitrite, the latter being produced by the reaction of nitric oxide radical with superoxide radical anion. From this standpoint, an excess production of superoxide radical anions could indirectly favor triuret formation; however very little is known about the potential in vivo roles of this metabolite. Triuret's structure is suggestive of its ability to adopt various conformations and act as a flexible ligand for metal ions. In the current study, HPLC-MS/MS, energy-resolved mass spectrometry, selected ion monitoring, collision-induced dissociation, IRMPD spectroscopy, Fourier transform-ion cyclotron resonance mass spectrometry and computational methods were employed to characterize the structure of triuret and its metal complexes, to determine the triuret-alkali metal binding motif, and to evaluate triuret affinity toward alkali metal ions, as well as its affinity for Na(+) and K(+) relative to other organic ligands. The most favored binding motif was determined to be a bidentate chelation of triuret with the alkali metal cation involving two carbonyl oxygens. Using the complexation selectivity method, it was observed that in solution triuret has an increased affinity for potassium ions, compared to sodium and other alkali metal ions. We propose that triuret may act as a potential hypokalemic agent under pathophysiological conditions conducive to its excessive formation and thus contribute to electrolyte disorders. The collision- or photo-induced fragmentation channels of deprotonated and protonated triuret, as well as its alkali metal adducts, are likely to mimic the triuret degradation pathways in vivo.
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174
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Prell JS, O'Brien JT, Williams ER. IRPD spectroscopy and ensemble measurements: effects of different data acquisition and analysis methods. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2010; 21:800-9. [PMID: 20185332 DOI: 10.1016/j.jasms.2010.01.010] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2009] [Revised: 01/06/2010] [Accepted: 01/10/2010] [Indexed: 05/17/2023]
Abstract
Three different commonly used infrared photodissociation (IRPD) spectroscopy acquisition and analysis methods are described, and results from these methods are compared using the same dataset for an extensively hydrated metal cation, La(3+)(H(2)O)(36). Using the first-order laser-induced photodissociation rate constant as an IRPD intensity has several advantages over photodissociation yield and depletion/appearance methods in that intensities can be more directly compared with calculated infrared absorption spectra, and the intensities can be readily corrected for changes in laser power or irradiation times used for optimum data acquisition at each frequency. Extending IRPD spectroscopy to large clusters can be complicated when blackbody infrared radiative dissociation competes strongly with laser-induced photodissociation. A new method to obtain IRPD spectra of single precursor ions or ensembles of precursor ions that is nearly equivalent to the photodissociation rate constant method for single precursor ions is demonstrated. The ensemble IRPD spectra represent the "average" structure of clusters of a given size range, and this method has the advantage that spectra with improved signal-to-noise ratios can be obtained with no increase in data acquisition time. Results using this new method for a precursor ensemble consisting of La(3+)(H(2)O)(35-37) are compared with results for La(3+)(H(2)O)(36).
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Affiliation(s)
- James S Prell
- Department of Chemistry, University of California, Berkeley, California 94720-1460, USA
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175
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Lagutschenkov A, Sinha RK, Maitre P, Dopfer O. Structure and Infrared Spectrum of the Ag+−Phenol Ionic Complex. J Phys Chem A 2010; 114:11053-9. [DOI: 10.1021/jp100853m] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Anita Lagutschenkov
- Institut für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstrasse 36, 10623 Berlin, Germany, and Laboratoire de Chimie Physique, Faculté des Sciences, Université Paris-Sud 11, UMR8000 CNRS, Bât. 350, 91405 Orsay Cedex, France
| | - Rajeev K. Sinha
- Institut für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstrasse 36, 10623 Berlin, Germany, and Laboratoire de Chimie Physique, Faculté des Sciences, Université Paris-Sud 11, UMR8000 CNRS, Bât. 350, 91405 Orsay Cedex, France
| | - Philippe Maitre
- Institut für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstrasse 36, 10623 Berlin, Germany, and Laboratoire de Chimie Physique, Faculté des Sciences, Université Paris-Sud 11, UMR8000 CNRS, Bât. 350, 91405 Orsay Cedex, France
| | - Otto Dopfer
- Institut für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstrasse 36, 10623 Berlin, Germany, and Laboratoire de Chimie Physique, Faculté des Sciences, Université Paris-Sud 11, UMR8000 CNRS, Bât. 350, 91405 Orsay Cedex, France
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176
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Chen X, Yu L, Steill JD, Oomens J, Polfer NC. Effect of peptide fragment size on the propensity of cyclization in collision-induced dissociation: oligoglycine b(2)-b(8). J Am Chem Soc 2010; 131:18272-82. [PMID: 19947633 DOI: 10.1021/ja9030837] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The chemistry of peptide fragmentation by collision-induced dissociation (CID) is currently being reviewed, as a result of observations that the amino acid sequence of peptide fragments can change upon activation. This rearrangement mechanism is thought to be due to a head-to-tail cyclization reaction, where the N-terminal and C-terminal part of the fragment are fused into a macrocycle (= cyclic peptide) structure, thus "losing" the memory of the original sequence. We present a comprehensive study for a series of b fragment ions, from b(2) to b(8), based on the simplest amino acid residue glycine, to investigate the effect of peptide chain length on the appearance of macrocycle fragment structures. The CID product ions are structurally characterized with a range of gas-phase techniques, including isotope labeling, infrared photodissociation spectroscopy, gas-phase hydrogen/deuterium exchange (using CH(3)OD), and computational structure approaches. The combined insights from these results yield compelling evidence that smaller b(n) fragments (n = 2, 3) exclusively adopt oxazolone-type structures, whereas a mixture of oxazolone and macrocycle b fragment structures are formed for midsized b(n) fragments, where n = 4-7. As each of these chemical structures exchanges at different rates, it is possible to approximate the relative abundances using kinetic fits to the H/D exchange data. Under the conditions used here, the "slow"-exchanging macrocycle structure represents approximately 30% of the b ion population for b(6)-b(7), while the "fast"-exchanging oxazolone structure represents the remainder (70%). Intriguingly, for b(8) only the macrocycle structure is identified, which is also consistent with the "slow" kinetic rate in the HDX results. In a control experiment, a protonated cyclic peptide with 6 amino acid residues, cyclo(Gln-Trp-Phe-Gly-Leu-Met), is confirmed not to adopt an oxazolone structure, even upon collisional activation. These results demonstrate that in some cases larger macrocycle structures are surprisingly stable. While more studies are required to establish the general propensity for cyclization in b fragments, the implications from this study are troubling in terms of faulty sequence identification.
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Affiliation(s)
- Xian Chen
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, USA
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177
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Chingin K, Frankevich V, Balabin R, Barylyuk K, Chen H, Wang R, Zenobi R. Direct Access to Isolated Biomolecules under Ambient Conditions. Angew Chem Int Ed Engl 2010; 49:2358-61. [DOI: 10.1002/anie.200906213] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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178
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Chingin K, Frankevich V, Balabin R, Barylyuk K, Chen H, Wang R, Zenobi R. Direct Access to Isolated Biomolecules under Ambient Conditions. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.200906213] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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179
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Lagutschenkov A, Springer A, Lorenz UJ, Maitre P, Dopfer O. Structure of Zirconocene Complexes Relevant for Olefin Catalysis: Infrared Fingerprint of the Zr(C5H5)2(OH)(CH3CN)+ Cation in the Gas Phase. J Phys Chem A 2010; 114:2073-9. [DOI: 10.1021/jp910035w] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Anita Lagutschenkov
- Institut für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstrasse 36, 10623 Berlin, Germany, Institut für Chemie und Biochemie, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany, Laboratoire de Chimie Physique Moléculaire, Ecole Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland, and Laboratoire de Chimie Physique, Faculté des Sciences, Université Paris-Sud 11, UMR8000 CNRS, Faculté des Sciences, Bât. 350, 91405 Orsay Cedex,
| | - Andreas Springer
- Institut für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstrasse 36, 10623 Berlin, Germany, Institut für Chemie und Biochemie, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany, Laboratoire de Chimie Physique Moléculaire, Ecole Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland, and Laboratoire de Chimie Physique, Faculté des Sciences, Université Paris-Sud 11, UMR8000 CNRS, Faculté des Sciences, Bât. 350, 91405 Orsay Cedex,
| | - Ulrich Joseph Lorenz
- Institut für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstrasse 36, 10623 Berlin, Germany, Institut für Chemie und Biochemie, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany, Laboratoire de Chimie Physique Moléculaire, Ecole Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland, and Laboratoire de Chimie Physique, Faculté des Sciences, Université Paris-Sud 11, UMR8000 CNRS, Faculté des Sciences, Bât. 350, 91405 Orsay Cedex,
| | - Philippe Maitre
- Institut für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstrasse 36, 10623 Berlin, Germany, Institut für Chemie und Biochemie, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany, Laboratoire de Chimie Physique Moléculaire, Ecole Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland, and Laboratoire de Chimie Physique, Faculté des Sciences, Université Paris-Sud 11, UMR8000 CNRS, Faculté des Sciences, Bât. 350, 91405 Orsay Cedex,
| | - Otto Dopfer
- Institut für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstrasse 36, 10623 Berlin, Germany, Institut für Chemie und Biochemie, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany, Laboratoire de Chimie Physique Moléculaire, Ecole Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland, and Laboratoire de Chimie Physique, Faculté des Sciences, Université Paris-Sud 11, UMR8000 CNRS, Faculté des Sciences, Bât. 350, 91405 Orsay Cedex,
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180
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Sinha RK, Maître P, Piccirillo S, Chiavarino B, Crestoni ME, Fornarini S. Cysteine radical cation: A distonic structure probed by gas phase IR spectroscopy. Phys Chem Chem Phys 2010; 12:9794-800. [DOI: 10.1039/c003576a] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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181
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Cagmat EB, Szczepanski J, Pearson WL, Powell DH, Eyler JR, Polfer NC. Vibrational signatures of metal-chelated monosaccharide epimers: gas-phase infrared spectroscopy of Rb+-tagged glucuronic and iduronic acid. Phys Chem Chem Phys 2010; 12:3474-9. [DOI: 10.1039/b924027f] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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182
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Coletti C, Re N, Scuderi D, Maître P, Chiavarino B, Fornarini S, Lanucara F, Sinha RK, Crestoni ME. IRMPD spectroscopy of protonated S-nitrosocaptopril, a biologically active, synthetic amino acid. Phys Chem Chem Phys 2010; 12:13455-67. [DOI: 10.1039/c0cp00671h] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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183
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Dunbar RC, Steill JD, Oomens J. Cationized phenylalanine conformations characterized by IRMPD and computation for singly and doubly charged ions. Phys Chem Chem Phys 2010; 12:13383-93. [DOI: 10.1039/c0cp00784f] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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184
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Erlekam U, Bythell BJ, Scuderi D, Van Stipdonk M, Paizs B, Maître P. Infrared spectroscopy of fragments of protonated peptides: direct evidence for macrocyclic structures of b5 ions. J Am Chem Soc 2009; 131:11503-8. [PMID: 19637928 DOI: 10.1021/ja903390r] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
b ions are of fundamental importance in peptide sequencing using tandem mass spectrometry. These ions have generally been assumed to exist as protonated oxazolone derivatives. Recent work indicates that medium-sized b ions can rearrange by head-to-tail cyclization of the oxazolone structures generating macrocyclic protonated peptides as intermediates. Here, we show using infrared spectroscopy and density functional theory calculations that the b(5) ion of protonated G(5)R exists in the mass spectrometer as an amide oxygen protonated cyclic peptide rather than fleetingly as a transient intermediate. This assignment is supported by our DFT calculations which show this macrocyclic isomer to be energetically preferred over the open oxazolone form despite the entropic constraints the cyclic form introduces.
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Affiliation(s)
- Undine Erlekam
- Laboratoire de Chimie Physique, Université Paris-Sud 11, UMR8000 CNRS, Faculté des Sciences, 91405 Orsay Cedex, France
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185
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Prell JS, Flick TG, Oomens J, Berden G, Williams ER. Coordination of Trivalent Metal Cations to Peptides: Results from IRMPD Spectroscopy and Theory. J Phys Chem A 2009; 114:854-60. [DOI: 10.1021/jp909366a] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- James S. Prell
- Department of Chemistry, University of California, Berkeley, California 94720-1460, FOM Institute for Plasma Physics “Rijnhuizen,” Edisonbaan 14, 3439 MN Nieuwegein, The Netherlands
| | - Tawnya G. Flick
- Department of Chemistry, University of California, Berkeley, California 94720-1460, FOM Institute for Plasma Physics “Rijnhuizen,” Edisonbaan 14, 3439 MN Nieuwegein, The Netherlands
| | - Jos Oomens
- Department of Chemistry, University of California, Berkeley, California 94720-1460, FOM Institute for Plasma Physics “Rijnhuizen,” Edisonbaan 14, 3439 MN Nieuwegein, The Netherlands
| | - Giel Berden
- Department of Chemistry, University of California, Berkeley, California 94720-1460, FOM Institute for Plasma Physics “Rijnhuizen,” Edisonbaan 14, 3439 MN Nieuwegein, The Netherlands
| | - Evan R. Williams
- Department of Chemistry, University of California, Berkeley, California 94720-1460, FOM Institute for Plasma Physics “Rijnhuizen,” Edisonbaan 14, 3439 MN Nieuwegein, The Netherlands
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186
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Zhao D, Langer J, Oomens J, Dopfer O. Infrared spectra of protonated polycyclic aromatic hydrocarbon molecules: Azulene. J Chem Phys 2009; 131:184307. [DOI: 10.1063/1.3262720] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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187
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Atkins CG, Banu L, Rowsell M, Blagojevic V, Bohme DK, Fridgen TD. Structure of [Pb(Gly-H)]+ and the Monosolvated Water and Methanol Solvated Species by Infrared Multiple-Photon Dissociation Spectroscopy, Energy-Resolved Collision-Induced Dissociation, and Electronic Structure Calculations. J Phys Chem B 2009; 113:14457-64. [DOI: 10.1021/jp905654v] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Chad G. Atkins
- Department of Chemistry, Memorial University, St. John’s, Newfoundland, A1B 3X7 Canada, and Department of Chemistry and Centre for Research in Mass Spectrometry, York University, Toronto, Ontario, M3J 1P3 Canada
| | - Laura Banu
- Department of Chemistry, Memorial University, St. John’s, Newfoundland, A1B 3X7 Canada, and Department of Chemistry and Centre for Research in Mass Spectrometry, York University, Toronto, Ontario, M3J 1P3 Canada
| | - Mark Rowsell
- Department of Chemistry, Memorial University, St. John’s, Newfoundland, A1B 3X7 Canada, and Department of Chemistry and Centre for Research in Mass Spectrometry, York University, Toronto, Ontario, M3J 1P3 Canada
| | - Voislav Blagojevic
- Department of Chemistry, Memorial University, St. John’s, Newfoundland, A1B 3X7 Canada, and Department of Chemistry and Centre for Research in Mass Spectrometry, York University, Toronto, Ontario, M3J 1P3 Canada
| | - Diethard K. Bohme
- Department of Chemistry, Memorial University, St. John’s, Newfoundland, A1B 3X7 Canada, and Department of Chemistry and Centre for Research in Mass Spectrometry, York University, Toronto, Ontario, M3J 1P3 Canada
| | - Travis D. Fridgen
- Department of Chemistry, Memorial University, St. John’s, Newfoundland, A1B 3X7 Canada, and Department of Chemistry and Centre for Research in Mass Spectrometry, York University, Toronto, Ontario, M3J 1P3 Canada
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188
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Dunbar RC, Steill JD, Polfer NC, Oomens J. Peptide Length, Steric Effects, and Ion Solvation Govern Zwitterion Stabilization in Barium-Chelated Di- and Tripeptides. J Phys Chem B 2009; 113:10552-4. [DOI: 10.1021/jp905060n] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Robert C. Dunbar
- Chemistry Department, Case Western Reserve University, Cleveland, Ohio 44106, FOM-Institute for Plasmaphysics Rijnhuizen, Edisonbaan 14, NL-3439 MN Nieuwegein, The Netherlands, Chemistry Department, University of Florida, Gainesville, Florida 32611, and University of Amsterdam, Nieuwe Achtergracht 166, 1018WV Amsterdam, The Netherlands
| | - Jeffrey D. Steill
- Chemistry Department, Case Western Reserve University, Cleveland, Ohio 44106, FOM-Institute for Plasmaphysics Rijnhuizen, Edisonbaan 14, NL-3439 MN Nieuwegein, The Netherlands, Chemistry Department, University of Florida, Gainesville, Florida 32611, and University of Amsterdam, Nieuwe Achtergracht 166, 1018WV Amsterdam, The Netherlands
| | - Nick C. Polfer
- Chemistry Department, Case Western Reserve University, Cleveland, Ohio 44106, FOM-Institute for Plasmaphysics Rijnhuizen, Edisonbaan 14, NL-3439 MN Nieuwegein, The Netherlands, Chemistry Department, University of Florida, Gainesville, Florida 32611, and University of Amsterdam, Nieuwe Achtergracht 166, 1018WV Amsterdam, The Netherlands
| | - Jos Oomens
- Chemistry Department, Case Western Reserve University, Cleveland, Ohio 44106, FOM-Institute for Plasmaphysics Rijnhuizen, Edisonbaan 14, NL-3439 MN Nieuwegein, The Netherlands, Chemistry Department, University of Florida, Gainesville, Florida 32611, and University of Amsterdam, Nieuwe Achtergracht 166, 1018WV Amsterdam, The Netherlands
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189
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Fridgen TD. Infrared consequence spectroscopy of gaseous protonated and metal ion cationized complexes. MASS SPECTROMETRY REVIEWS 2009; 28:586-607. [PMID: 19343731 DOI: 10.1002/mas.20224] [Citation(s) in RCA: 135] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
In this article, the new and exciting techniques of infrared consequence spectroscopy (sometimes called action spectroscopy) of gaseous ions are reviewed. These techniques include vibrational predissociation spectroscopy and infrared multiple photon dissociation spectroscopy and they typically complement one another in the systems studied and the information gained. In recent years infrared consequence spectroscopy has provided long-awaited direct evidence into the structures of gaseous ions from organometallic species to strong ionic hydrogen bonded structures to large biomolecules. Much is being learned with respect to the structures of ions without their stabilizing solvent which can be used to better understand the effect of solvent on their structures. This review mainly covers the topics with which the author has been directly involved in research: structures of proton-bound dimers, protonated amino acids and DNA bases, amino acid and DNA bases bound to metal ions and, more recently, solvated ionic complexes. It is hoped that this review reveals the impact that infrared consequence spectroscopy has had on the field of gaseous ion chemistry.
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Affiliation(s)
- Travis D Fridgen
- Department of Chemistry, Memorial University of Newfoundland, St. John's, Newfoundland and Labrador, Canada A1B 3X7.
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190
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Rajabi K, Theel K, Gillis EAL, Beran G, Fridgen TD. The Structure of the Protonated Adenine Dimer by Infrared Multiple Photon Dissociation Spectroscopy and Electronic Structure Calculations. J Phys Chem A 2009; 113:8099-107. [DOI: 10.1021/jp9033062] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Khadijeh Rajabi
- Department of Chemistry, Memorial University of Newfoundland, St. John’s, Newfoundland, Canada, A1B 3X7, and Department of Chemistry, University of California, Riverside, California 92521
| | - Kelly Theel
- Department of Chemistry, Memorial University of Newfoundland, St. John’s, Newfoundland, Canada, A1B 3X7, and Department of Chemistry, University of California, Riverside, California 92521
| | - Elizabeth A. L. Gillis
- Department of Chemistry, Memorial University of Newfoundland, St. John’s, Newfoundland, Canada, A1B 3X7, and Department of Chemistry, University of California, Riverside, California 92521
| | - Gregory Beran
- Department of Chemistry, Memorial University of Newfoundland, St. John’s, Newfoundland, Canada, A1B 3X7, and Department of Chemistry, University of California, Riverside, California 92521
| | - Travis D. Fridgen
- Department of Chemistry, Memorial University of Newfoundland, St. John’s, Newfoundland, Canada, A1B 3X7, and Department of Chemistry, University of California, Riverside, California 92521
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191
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Polfer NC, Oomens J. Vibrational spectroscopy of bare and solvated ionic complexes of biological relevance. MASS SPECTROMETRY REVIEWS 2009; 28:468-494. [PMID: 19241457 DOI: 10.1002/mas.20215] [Citation(s) in RCA: 261] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
The low density of ions in mass spectrometers generally precludes direct infrared (IR) absorption measurements. The IR spectrum of an ion can nonetheless be obtained by inducing photodissociation of the ion using a high-intensity tunable laser. The emergence of free electron lasers (FELs) and recent breakthroughs in bench-top lasers based on nonlinear optics have now made it possible to routinely record IR spectra of gas-phase ions. As the energy of one IR photon is insufficient to cause dissociation of molecules and strongly bound complexes, two main experimental strategies have been developed to effect photodissociation. In infrared multiple-photon dissociation (IR-MPD) many photons are absorbed resonantly and their energy is stored in the bath of vibrational modes, leading to dissociation. In the "messenger" technique a weakly bound van der Waals atom is detached upon absorption of a single photon. Fundamental, historical, and practical aspects of these methods will be presented. Both of these approaches make use of very different methods of ion preparation and manipulation. While in IR-MPD ions are irradiated in trapping mass spectrometers, the "messenger" technique is generally carried out in molecular beam instruments. The main focus of this review is the application of IR spectroscopy to biologically relevant molecular systems (amino acids, peptides, proteins). Particular issues that will be addressed here include gas-phase zwitterions, the (chemical) structures of peptides and their collision-induced dissociation (CID) products, IR spectra of gas-phase proteins, and the chelation of metal-ligand complexes. Another growing area of research is IR spectroscopy on solvated clusters, which offer a bridge between the gas-phase and solution environments. The development of state-of-the-art computational approaches has gone hand-in-hand with advances in experimental techniques. The main advantage of gas-phase cluster research, as opposed to condensed-phase experiments, is that the systems of interest can be understood in detail and structural effects can be studied in isolation. It will be shown that IR spectroscopy of mass-selected (bio)molecular systems is now well-placed to address specific questions on the individual effect of charge carriers (protons and metal ions), as well as solvent molecules on the overall structure.
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Affiliation(s)
- Nick C Polfer
- Chemistry Department, University of Florida, Gainesville, Florida 32611, USA.
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