101
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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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102
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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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103
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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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104
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Chingin K, Balabin RM, Barylyuk K, Chen H, Frankevich V, Zenobi R. Rhodamines in the gas phase: cations, neutrals, anions, and adducts with metal cations. Phys Chem Chem Phys 2010; 12:11710-4. [DOI: 10.1039/c000807a] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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105
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Carl DR, Cooper TE, Oomens J, Steill JD, Armentrout PB. Infrared multiple photon dissociation spectroscopy of cationized methionine: effects of alkali-metal cation size on gas-phase conformation. Phys Chem Chem Phys 2010; 12:3384-98. [DOI: 10.1039/b919039b] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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106
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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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107
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Däschlein C, Bauer J, Strohmann C. From the Selective Cleavage of the Si-O-Si Bond in Disiloxanes to Zwitterionic, Water-Stable Zinc Silanolates. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200902318] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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108
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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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109
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Chiavarino B, Crestoni M, Fornarini S, Lanucara F, Lemaire J, Maître P, Scuderi D. Molecular Complexes of Simple Anions with Electron-Deficient Arenes: Spectroscopic Evidence for Two Types of Structural Motifs for Anion-Arene Interactions. Chemistry 2009; 15:8185-95. [DOI: 10.1002/chem.200900822] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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110
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Drayβ MK, Blunk D, Oomens J, Gao B, Wyttenbach T, Bowers MT, Schäfer M. Systematic Study of the Structures of Potassiated Tertiary Amino Acids: Salt Bridge Structures Dominate. J Phys Chem A 2009; 113:9543-50. [DOI: 10.1021/jp903036t] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Miriam K. Drayβ
- Department of Chemistry, University of Cologne, Greinstraβe 4, 50939 Köln, Germany, FOM Institute for Plasmaphysics Rijnhuizen, Edisonbaan 14, NL-3439 MN Nieuwegein, The Netherlands,University of Amsterdam, Nieuwe Achtergracht 166, 1018WV Amsterdam, The Netherlands, and Department of Chemistry and Biochemistry, University of California, Santa Barbara, California
| | - Dirk Blunk
- Department of Chemistry, University of Cologne, Greinstraβe 4, 50939 Köln, Germany, FOM Institute for Plasmaphysics Rijnhuizen, Edisonbaan 14, NL-3439 MN Nieuwegein, The Netherlands,University of Amsterdam, Nieuwe Achtergracht 166, 1018WV Amsterdam, The Netherlands, and Department of Chemistry and Biochemistry, University of California, Santa Barbara, California
| | - Jos Oomens
- Department of Chemistry, University of Cologne, Greinstraβe 4, 50939 Köln, Germany, FOM Institute for Plasmaphysics Rijnhuizen, Edisonbaan 14, NL-3439 MN Nieuwegein, The Netherlands,University of Amsterdam, Nieuwe Achtergracht 166, 1018WV Amsterdam, The Netherlands, and Department of Chemistry and Biochemistry, University of California, Santa Barbara, California
| | - Bing Gao
- Department of Chemistry, University of Cologne, Greinstraβe 4, 50939 Köln, Germany, FOM Institute for Plasmaphysics Rijnhuizen, Edisonbaan 14, NL-3439 MN Nieuwegein, The Netherlands,University of Amsterdam, Nieuwe Achtergracht 166, 1018WV Amsterdam, The Netherlands, and Department of Chemistry and Biochemistry, University of California, Santa Barbara, California
| | - Thomas Wyttenbach
- Department of Chemistry, University of Cologne, Greinstraβe 4, 50939 Köln, Germany, FOM Institute for Plasmaphysics Rijnhuizen, Edisonbaan 14, NL-3439 MN Nieuwegein, The Netherlands,University of Amsterdam, Nieuwe Achtergracht 166, 1018WV Amsterdam, The Netherlands, and Department of Chemistry and Biochemistry, University of California, Santa Barbara, California
| | - Michael T. Bowers
- Department of Chemistry, University of Cologne, Greinstraβe 4, 50939 Köln, Germany, FOM Institute for Plasmaphysics Rijnhuizen, Edisonbaan 14, NL-3439 MN Nieuwegein, The Netherlands,University of Amsterdam, Nieuwe Achtergracht 166, 1018WV Amsterdam, The Netherlands, and Department of Chemistry and Biochemistry, University of California, Santa Barbara, California
| | - Mathias Schäfer
- Department of Chemistry, University of Cologne, Greinstraβe 4, 50939 Köln, Germany, FOM Institute for Plasmaphysics Rijnhuizen, Edisonbaan 14, NL-3439 MN Nieuwegein, The Netherlands,University of Amsterdam, Nieuwe Achtergracht 166, 1018WV Amsterdam, The Netherlands, and Department of Chemistry and Biochemistry, University of California, Santa Barbara, California
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111
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Prell JS, O’Brien JT, Steill JD, Oomens J, Williams ER. Structures of Protonated Dipeptides: The Role of Arginine in Stabilizing Salt Bridges. J Am Chem Soc 2009; 131:11442-9. [DOI: 10.1021/ja901870d] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- James S. Prell
- Department of Chemistry, University of California, Berkeley, California 94720-1460, and FOM Institute for Plasma Physics “Rijnhuizen”, Edisonbaan 14, 3439 MN Nieuwegein, The Netherlands
| | - Jeremy T. O’Brien
- Department of Chemistry, University of California, Berkeley, California 94720-1460, and FOM Institute for Plasma Physics “Rijnhuizen”, Edisonbaan 14, 3439 MN Nieuwegein, The Netherlands
| | - Jeffrey D. Steill
- Department of Chemistry, University of California, Berkeley, California 94720-1460, and 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, and 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, and FOM Institute for Plasma Physics “Rijnhuizen”, Edisonbaan 14, 3439 MN Nieuwegein, The Netherlands
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112
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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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113
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Tian SX, Li HB, Yang J. Monoanion BH4−Can Stabilize Zwitterionic Glycine with Dihydrogen Bonds. Chemphyschem 2009; 10:1435-7. [DOI: 10.1002/cphc.200900158] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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114
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Dunbar RC, Hopkinson AC, Oomens J, Siu CK, Siu KWM, Steill JD, Verkerk UH, Zhao J. Conformation Switching in Gas-Phase Complexes of Histidine with Alkaline Earth Ions. J Phys Chem B 2009; 113:10403-8. [DOI: 10.1021/jp903064w] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Robert C. Dunbar
- Chemistry Department, Case Western Reserve University, Cleveland, Ohio 44106, Department of Chemistry and Centre for Research in Mass Spectrometry, York University, 4700 Keele Street, Toronto, Ontario M3J 1P3, Canada, and FOM-Institute for Plasma Physics Rijnhuizen, Edisonbaan 14, NL-3439 MN Nieuwegein, The Netherlands
| | - Alan C. Hopkinson
- Chemistry Department, Case Western Reserve University, Cleveland, Ohio 44106, Department of Chemistry and Centre for Research in Mass Spectrometry, York University, 4700 Keele Street, Toronto, Ontario M3J 1P3, Canada, and FOM-Institute for Plasma Physics Rijnhuizen, Edisonbaan 14, NL-3439 MN Nieuwegein, The Netherlands
| | - Jos Oomens
- Chemistry Department, Case Western Reserve University, Cleveland, Ohio 44106, Department of Chemistry and Centre for Research in Mass Spectrometry, York University, 4700 Keele Street, Toronto, Ontario M3J 1P3, Canada, and FOM-Institute for Plasma Physics Rijnhuizen, Edisonbaan 14, NL-3439 MN Nieuwegein, The Netherlands
| | - Chi-Kit Siu
- Chemistry Department, Case Western Reserve University, Cleveland, Ohio 44106, Department of Chemistry and Centre for Research in Mass Spectrometry, York University, 4700 Keele Street, Toronto, Ontario M3J 1P3, Canada, and FOM-Institute for Plasma Physics Rijnhuizen, Edisonbaan 14, NL-3439 MN Nieuwegein, The Netherlands
| | - K. W. Michael Siu
- Chemistry Department, Case Western Reserve University, Cleveland, Ohio 44106, Department of Chemistry and Centre for Research in Mass Spectrometry, York University, 4700 Keele Street, Toronto, Ontario M3J 1P3, Canada, and FOM-Institute for Plasma Physics Rijnhuizen, Edisonbaan 14, NL-3439 MN Nieuwegein, The Netherlands
| | - Jeffrey D. Steill
- Chemistry Department, Case Western Reserve University, Cleveland, Ohio 44106, Department of Chemistry and Centre for Research in Mass Spectrometry, York University, 4700 Keele Street, Toronto, Ontario M3J 1P3, Canada, and FOM-Institute for Plasma Physics Rijnhuizen, Edisonbaan 14, NL-3439 MN Nieuwegein, The Netherlands
| | - Udo H. Verkerk
- Chemistry Department, Case Western Reserve University, Cleveland, Ohio 44106, Department of Chemistry and Centre for Research in Mass Spectrometry, York University, 4700 Keele Street, Toronto, Ontario M3J 1P3, Canada, and FOM-Institute for Plasma Physics Rijnhuizen, Edisonbaan 14, NL-3439 MN Nieuwegein, The Netherlands
| | - Junfang Zhao
- Chemistry Department, Case Western Reserve University, Cleveland, Ohio 44106, Department of Chemistry and Centre for Research in Mass Spectrometry, York University, 4700 Keele Street, Toronto, Ontario M3J 1P3, Canada, and FOM-Institute for Plasma Physics Rijnhuizen, Edisonbaan 14, NL-3439 MN Nieuwegein, The Netherlands
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115
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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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116
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Wu R, McMahon TB. Protonation Sites and Conformations of Peptides of Glycine (Gly1−5H+) by IRMPD Spectroscopy. J Phys Chem B 2009; 113:8767-75. [DOI: 10.1021/jp811468q] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ronghu Wu
- Department of Chemistry, University of Waterloo, Waterloo, Ontario, Canada N2L 3G1
| | - Terry B. McMahon
- Department of Chemistry, University of Waterloo, Waterloo, Ontario, Canada N2L 3G1
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117
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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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118
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Burke RM, Dessent CEH. Effect of cation complexation on the structure of a conformationally flexible multiply charged anion: stabilization of excess charge in the Na+ x adenosine 5'-triphosphate dianion ion-pair complex. J Phys Chem A 2009; 113:2683-92. [PMID: 19249856 DOI: 10.1021/jp805868u] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
We report a computational study of the conformationally and tautomerically flexible cation-dianion complex of Na(+) with doubly deprotonated adenosine 5'-triphosphate (ATP) using a hierarchical selection method. The method uses molecular dynamics to generate initial conformeric structures, followed by a classification process that groups conformers into five "families" to ensure that a representative sample of structures is retained for further analysis, while very similar conformational structures are eliminated. Hierarchical ab initio calculations (DFT and MP2) of typical conformers of the families are then performed to identify the lowest-energy conformeric structures. The procedure described should provide a useful methodology for conducting higher-level ab initio calculations of medium-sized gas-phase biological molecules for interpreting contemporary laser spectroscopy measurements. For Na(+) x [ATP-2H](2) (considering tautomers where the phosphate chain of ATP is doubly deprotonated), the calculations reveal that the sodium cation interacts directly with the negatively charged phosphates (maximum distance = 2.54 A) in all of the low-energy conformers, while a number of the structures also display close cation-adenine interactions producing compact ball-like structures. These compact structures generally correspond to the lowest-energy conformers. The structural variation between the bare [ATP-2H](2-) molecular ion (Burke et al. J. Phys. Chem. A 2005 , 109 , 9775-9785) and the Na(+) x [ATP-2H](2-) cluster is discussed in detail, including the effect of sodiation on the intramolecular hydrogen-bonding network within ATP in a gas-phase environment.
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Affiliation(s)
- Ruth M Burke
- Department of Chemistry, University of York, Heslington, York YO10 5DD, UK
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119
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Heaton AL, Bowman VN, Oomens J, Steill JD, Armentrout PB. Infrared Multiple Photon Dissociation Spectroscopy of Cationized Asparagine: Effects of Metal Cation Size on Gas-Phase Conformation. J Phys Chem A 2009; 113:5519-30. [DOI: 10.1021/jp9008064] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- A. L. Heaton
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112 and FOM Institute for Plasma Physics “Rijnhuizen”, Edisonbaan 14, 3439 MN Nieuwegein, The Netherlands
| | - V. N. Bowman
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112 and FOM Institute for Plasma Physics “Rijnhuizen”, Edisonbaan 14, 3439 MN Nieuwegein, The Netherlands
| | - J. Oomens
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112 and FOM Institute for Plasma Physics “Rijnhuizen”, Edisonbaan 14, 3439 MN Nieuwegein, The Netherlands
| | - J. D. Steill
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112 and FOM Institute for Plasma Physics “Rijnhuizen”, Edisonbaan 14, 3439 MN Nieuwegein, The Netherlands
| | - P. B. Armentrout
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112 and FOM Institute for Plasma Physics “Rijnhuizen”, Edisonbaan 14, 3439 MN Nieuwegein, The Netherlands
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120
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Bush MF, Oomens J, Williams ER. Proton affinity and zwitterion stability: new results from infrared spectroscopy and theory of cationized lysine and analogues in the gas phase. J Phys Chem A 2009; 113:431-8. [PMID: 19128186 DOI: 10.1021/jp807470p] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The gas-phase structures of alkali metal cationized lysine (Lys), alpha-N-methyllysine (NMeLys), and epsilon-N,N-dimethyllysine (Lys(Me)(2)) are investigated using infrared multiple photon dissociation (IRMPD) spectroscopy utilizing light generated by a free electron laser and ab initio calculations. The proton affinities of the compounds span a range of approximately 20 kJ/mol. For NMeLys x M(+), experiment and theory indicate that NMeLys is nonzwitterionic for M = Li and zwitterionic for M = Na and K. For Lys(Me)(2) x M(+), experiment and theory indicate that Lys(Me)(2) is zwitterionic for M = Li, Na, and K. This is the first spectroscopic observation of the zwitterionic form of an amino acid complexed with Li(+). The results are compared with IRMPD spectra reported previously for Lys and -N-methyllysine (Lys(Me)) complexed with Li, Na, and K, and new calculations performed at higher levels of theory for those ions. The combined experimental and theoretical results indicate that protonation in the zwitterionic forms of the these amino acids is favored at the more basic methylated amine site, but that any relationship between the proton affinity of the amino acid and the relative zwitterion stability of the alkali metal cationized amino acid is only indirect. These results provide additional evidence that proton affinities are not a reliable indicator of zwitterion stability for cationized amino acids because side chains can have very different effects on the stability of different conformers in the neutral, protonated, and metal cationized forms.
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Affiliation(s)
- Matthew F Bush
- Department of Chemistry, University of California, Berkeley, California 94720-1460, USA
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121
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Oomens J, Steill JD, Redlich B. Gas-Phase IR Spectroscopy of Deprotonated Amino Acids. J Am Chem Soc 2009; 131:4310-9. [DOI: 10.1021/ja807615v] [Citation(s) in RCA: 155] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jos Oomens
- FOM Institute for Plasma Physics “Rijnhuizen”, Edisonbaan 14, 3439MN Nieuwegein, The Netherlands
| | - Jeffrey D. Steill
- FOM Institute for Plasma Physics “Rijnhuizen”, Edisonbaan 14, 3439MN Nieuwegein, The Netherlands
| | - Britta Redlich
- FOM Institute for Plasma Physics “Rijnhuizen”, Edisonbaan 14, 3439MN Nieuwegein, The Netherlands
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122
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O’Brien JT, Prell JS, Steill JD, Oomens J, Williams ER. Changes in Binding Motif of Protonated Heterodimers Containing Valine and Amines Investigated Using IRMPD Spectroscopy between 800 and 3700 cm−1 and Theory. J Am Chem Soc 2009; 131:3905-12. [DOI: 10.1021/ja809928h] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jeremy T. O’Brien
- Department of Chemistry, University of California, Berkeley, California 94720-1460, and FOM Institute for Plasma Physics “Rijnhuizen”, Edisonbaan 14, 3439 MN Nieuwegein, The Netherlands
| | - James S. Prell
- Department of Chemistry, University of California, Berkeley, California 94720-1460, and FOM Institute for Plasma Physics “Rijnhuizen”, Edisonbaan 14, 3439 MN Nieuwegein, The Netherlands
| | - Jeffrey D. Steill
- Department of Chemistry, University of California, Berkeley, California 94720-1460, and 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, and 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, and FOM Institute for Plasma Physics “Rijnhuizen”, Edisonbaan 14, 3439 MN Nieuwegein, The Netherlands
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123
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Gaigeot MP. Alanine polypeptide structural fingerprints at room temperature: what can be gained from non-harmonic Car-Parrinello molecular dynamics simulations. J Phys Chem A 2009; 112:13507-17. [PMID: 19053558 DOI: 10.1021/jp807550j] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Structural infrared fingerprints of neutral gas phase alanine peptides of increasing size and complexity (dipeptide, octapeptide, and beta-strand peptide) are characterized through DFT-based Car-Parrinello molecular dynamics simulations. Harmonic and nonharmonic vibrational signatures are calculated from the time correlation of the dipole moment of the gas phase peptide in a direct way (without any approximation) respectively from low temperature (20 K) and room temperature (300 K) molecular dynamics. Our main purpose is to answer the two following questions: (i) Is the direct inclusion of temperature for the calculation of infrared spectra mandatory for the comprehension of the vibrational signatures experimentally recorded at room temperature? (ii) To what extent is the amide I, II, and III domain sensitive enough to the local structure of the peptides, to provide vibrational signatures that can be definitely used to assess the peptide conformation at 300 K?
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Affiliation(s)
- M-P Gaigeot
- LAMBE UMR8587 Laboratoire Analyse et Modelisation pour la Biologie et l'Environnement, Universite d'Evry val d'Essonne, Boulevard F. Mitterrand, Batiment Maupertuis, 91025 Evry, France.
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124
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Dunbar RC, Steill JD, Polfer NC, Oomens J. Dimeric Complexes of Tryptophan with M2+ Metal Ions. J Phys Chem A 2009; 113:845-51. [DOI: 10.1021/jp8087176] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Robert C. Dunbar
- FOM Institute for Plasma Physics “Rijnhuizen”, Edisonbaan 14, 3439MN Nieuwegein, The Netherlands, Department of Chemistry, Case Western Reserve University, Cleveland, Ohio 44106, and Department of Chemistry, The University of Florida, Gainesville, Florida 32611
| | - Jeffrey D. Steill
- FOM Institute for Plasma Physics “Rijnhuizen”, Edisonbaan 14, 3439MN Nieuwegein, The Netherlands, Department of Chemistry, Case Western Reserve University, Cleveland, Ohio 44106, and Department of Chemistry, The University of Florida, Gainesville, Florida 32611
| | - Nick C. Polfer
- FOM Institute for Plasma Physics “Rijnhuizen”, Edisonbaan 14, 3439MN Nieuwegein, The Netherlands, Department of Chemistry, Case Western Reserve University, Cleveland, Ohio 44106, and Department of Chemistry, The University of Florida, Gainesville, Florida 32611
| | - Jos Oomens
- FOM Institute for Plasma Physics “Rijnhuizen”, Edisonbaan 14, 3439MN Nieuwegein, The Netherlands, Department of Chemistry, Case Western Reserve University, Cleveland, Ohio 44106, and Department of Chemistry, The University of Florida, Gainesville, Florida 32611
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125
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Shimazaki Y, Takani M, Yamauchi O. Metal complexes of amino acids and amino acid side chain groups. Structures and properties. Dalton Trans 2009:7854-69. [PMID: 19771344 DOI: 10.1039/b905871k] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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126
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Prell JS, Demireva M, Oomens J, Williams ER. Role of Sequence in Salt-Bridge Formation for Alkali Metal Cationized GlyArg and ArgGly Investigated with IRMPD Spectroscopy and Theory. J Am Chem Soc 2008; 131:1232-42. [DOI: 10.1021/ja808177z] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- James S. Prell
- Department of Chemistry, University of California, Berkeley, California 94720-1460, and FOM Institute for Plasma Physics “Rijnhuizen,” Edisonbaan 14, 3439 MN Nieuwegein, The Netherlands
| | - Maria Demireva
- Department of Chemistry, University of California, Berkeley, California 94720-1460, and 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, and 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, and FOM Institute for Plasma Physics “Rijnhuizen,” Edisonbaan 14, 3439 MN Nieuwegein, The Netherlands
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127
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Tian SX, Sun X, Cao R, Yang J. Thermal Stabilities of the Microhydrated Zwitterionic Glycine: A Kinetics and Dynamics Study. J Phys Chem A 2008; 113:480-3. [DOI: 10.1021/jp8092594] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Shan Xi Tian
- Hefei National Laboratory for Physical Sciences at Microscale, and Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Xiang Sun
- Hefei National Laboratory for Physical Sciences at Microscale, and Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Rui Cao
- Hefei National Laboratory for Physical Sciences at Microscale, and Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Jinlong Yang
- Hefei National Laboratory for Physical Sciences at Microscale, and Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
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128
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O’Brien JT, Prell JS, Steill JD, Oomens J, Williams ER. Interactions of Mono- and Divalent Metal Ions with Aspartic and Glutamic Acid Investigated with IR Photodissociation Spectroscopy and Theory. J Phys Chem A 2008; 112:10823-30. [DOI: 10.1021/jp805787e] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jeremy T. O’Brien
- Department of Chemistry, University of California, Berkeley, California 94720-1460, and FOM Institute for Plasma Physics “Rijnhuizen”, Edisonbaan 14, 3439 MN Nieuwegein, The Netherlands
| | - James S. Prell
- Department of Chemistry, University of California, Berkeley, California 94720-1460, and FOM Institute for Plasma Physics “Rijnhuizen”, Edisonbaan 14, 3439 MN Nieuwegein, The Netherlands
| | - Jeff D. Steill
- Department of Chemistry, University of California, Berkeley, California 94720-1460, and 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, and 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, and FOM Institute for Plasma Physics “Rijnhuizen”, Edisonbaan 14, 3439 MN Nieuwegein, The Netherlands
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129
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Bush MF, Oomens J, Saykally RJ, Williams ER. Alkali Metal Ion Binding to Glutamine and Glutamine Derivatives Investigated by Infrared Action Spectroscopy and Theory. J Phys Chem A 2008; 112:8578-84. [DOI: 10.1021/jp803121w] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Matthew F. Bush
- Department of Chemistry, University of California, Berkeley, California 94720-1460, and 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, and FOM Institute for Plasma Physics “Rijnhuizen”, Edisonbaan 14, 3439 MN Nieuwegein, The Netherlands
| | - Richard J. Saykally
- Department of Chemistry, University of California, Berkeley, California 94720-1460, and 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, and FOM Institute for Plasma Physics “Rijnhuizen”, Edisonbaan 14, 3439 MN Nieuwegein, The Netherlands
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