201
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Gu Q, Knee JL. Zero kinetic energy photoelectron spectroscopy of tryptamine and the dissociation pathway of the singly hydrated cation cluster. J Chem Phys 2012; 137:104312. [DOI: 10.1063/1.4752080] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Quanli Gu
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, USA
- Department of Chemistry, Wesleyan University, Middletown, Connecticut 06459, USA
| | - J. L. Knee
- Department of Chemistry, Wesleyan University, Middletown, Connecticut 06459, USA
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202
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Kirk BB, Trevitt AJ, Blanksby SJ, Tao Y, Moore BN, Julian RR. Ultraviolet Action Spectroscopy of Iodine Labeled Peptides and Proteins in the Gas Phase. J Phys Chem A 2012; 117:1228-32. [DOI: 10.1021/jp305470j] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Benjamin B. Kirk
- ARC Centre of Excellence for
Free Radical Chemistry and Biotechnology, School of Chemistry, University of Wollongong, New South Wales 2522, Australia
| | - Adam J. Trevitt
- ARC Centre of Excellence for
Free Radical Chemistry and Biotechnology, School of Chemistry, University of Wollongong, New South Wales 2522, Australia
| | - Stephen J. Blanksby
- ARC Centre of Excellence for
Free Radical Chemistry and Biotechnology, School of Chemistry, University of Wollongong, New South Wales 2522, Australia
| | - Yuanqi Tao
- Department of Chemistry, University of California, Riverside, California 92521,
United States
| | - Benjamin N. Moore
- Department of Chemistry, University of California, Riverside, California 92521,
United States
| | - Ryan R. Julian
- Department of Chemistry, University of California, Riverside, California 92521,
United States
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203
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Kocak A, Austein-Miller G, Pearson WL, Altinay G, Metz RB. Dissociation Energy and Electronic and Vibrational Spectroscopy of Co+(H2O) and Its Isotopomers. J Phys Chem A 2012; 117:1254-64. [DOI: 10.1021/jp305673t] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Abdulkadir Kocak
- Department of Chemistry, University of Massachusetts—Amherst, Amherst,
Massachusetts 01003, United States
| | - Geoff Austein-Miller
- Department of Chemistry, University of Massachusetts—Amherst, Amherst,
Massachusetts 01003, United States
| | - Wright L. Pearson
- Department of Chemistry, University of Massachusetts—Amherst, Amherst,
Massachusetts 01003, United States
| | - Gokhan Altinay
- Department of Chemistry, University of Massachusetts—Amherst, Amherst,
Massachusetts 01003, United States
| | - Ricardo B. Metz
- Department of Chemistry, University of Massachusetts—Amherst, Amherst,
Massachusetts 01003, United States
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204
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Papadopoulos G, Svendsen A, Boyarkin OV, Rizzo TR. Conformational distribution of bradykinin [bk + 2 H]2+ revealed by cold ion spectroscopy coupled with FAIMS. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:1173-81. [PMID: 22528205 DOI: 10.1007/s13361-012-0384-0] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2012] [Revised: 03/22/2012] [Accepted: 03/23/2012] [Indexed: 05/25/2023]
Abstract
We employ cold ion spectroscopy (CIS) in conjunction with high-field asymmetric waveform ion mobility spectrometry (FAIMS) to study the peptide bradykinin in its doubly protonated charge state ([bk + 2 H](2+)). Using FAIMS, we partially separate the electrosprayed [bk + 2 H](2+) ions into two conformational families and selectively introduce one of them at a time into a cold ion trap mass spectrometer, where we probe them by UV photofragment spectroscopy. Although the two conformational families have distinct electronic spectra, some cross-conformer contamination can be observed under certain conditions. We demonstrate that this contamination comes from isomerization of ions energized during and/or after their separation and not from incomplete separation of the initially electrosprayed conformations in the FAIMS stage. By varying the injection voltage of the ions into our mass spectrometer, we can intentionally induce isomerization to produce what seems to be a gas phase equilibrium distribution of conformers. This distribution is different from the one produced initially by electrospray, indicating that some of the conformers are kinetically trapped and may be related to conformers that are more favored in solution.
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Affiliation(s)
- Georgios Papadopoulos
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland
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205
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Wassermann TN, Boyarkin OV, Paizs B, Rizzo TR. Conformation-specific spectroscopy of peptide fragment ions in a low-temperature ion trap. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:1029-1045. [PMID: 22460621 DOI: 10.1007/s13361-012-0368-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2011] [Revised: 02/17/2012] [Accepted: 02/23/2012] [Indexed: 05/31/2023]
Abstract
We have applied conformer-selective infrared-ultraviolet (IR-UV) double-resonance photofragment spectroscopy at low temperatures in an ion trap mass spectrometer for the spectroscopic characterization of peptide fragment ions. We investigate b- and a-type ions formed by collision-induced dissociation from protonated leucine-enkephalin. The vibrational analysis and assignment are supported by nitrogen-15 isotopic substitution of individual amino acid residues and assisted by density functional theory calculations. Under such conditions, b-type ions of different size are found to appear exclusively as linear oxazolone structures with protonation on the N-terminus, while a rearrangement reaction is confirmed for the a (4) ion in which the side chain of the C-terminal phenylalanine residue is transferred to the N-terminal side of the molecule. The vibrational spectra that we present here provide a particularly stringent test for theoretical approaches.
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Affiliation(s)
- Tobias N Wassermann
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, 1015, Lausanne, Switzerland
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206
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Rosu F, Gabelica V, De Pauw E, Antoine R, Broyer M, Dugourd P. UV Spectroscopy of DNA Duplex and Quadruplex Structures in the Gas Phase. J Phys Chem A 2012; 116:5383-91. [DOI: 10.1021/jp302468x] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Frédéric Rosu
- Département de Chimie, Université de Liège, Building B6c, 3, allée de la chimie, 4000 Liège, Belgium
| | - Valérie Gabelica
- Département de Chimie, Université de Liège, Building B6c, 3, allée de la chimie, 4000 Liège, Belgium
| | - Edwin De Pauw
- Département de Chimie, Université de Liège, Building B6c, 3, allée de la chimie, 4000 Liège, Belgium
| | - Rodolphe Antoine
- CNRS and Université Lyon 1, UMR5579, Boulevard du 11 novembre 1918, 69622 Villeurbanne, France
| | - Michel Broyer
- CNRS and Université Lyon 1, UMR5579, Boulevard du 11 novembre 1918, 69622 Villeurbanne, France
| | - Philippe Dugourd
- CNRS and Université Lyon 1, UMR5579, Boulevard du 11 novembre 1918, 69622 Villeurbanne, France
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207
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JIN BING, WANG DONGSHENG, LIU JIANYONG. UNUSUAL LASER-INDUCED ABSORPTIONS OF Ca+-FORMALDEHYDE: MOLECULAR ORBITAL INTERACTION. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2012. [DOI: 10.1142/s0219633611006499] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
We have theoretically studied the photodissociation spectroscopy of Ca +-formaldehyde complex using the TD-B2-PLYP method. The SDD pseudopotential and basis sets for Ca and 6-31++G (2df, 2pd) basis sets for C , H , and O atoms were employed in all calculations. In this way, we have reassigned the photodissociation spectroscopy of this complex. All experimentally observed spectral features can be well explained by our calculation. Besides the charge–dipole interaction, a strong molecule–orbital interaction also exists in the excited states and plays an important role in photoexcitation of the Ca+–CH2O complex.
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Affiliation(s)
- BING JIN
- State Key Laboratory of Molecular Reaction Dynamics Dalian Institute of Chemical Physics Chinese Academy of Sciences Dalian 116023, P. R. China
- Graduate School of the Chinese Academy of Sciences Beijing 100039, P. R. China
| | - DONGSHENG WANG
- State Key Laboratory of Molecular Reaction Dynamics Dalian Institute of Chemical Physics Chinese Academy of Sciences Dalian 116023, P. R. China
| | - JIANYONG LIU
- State Key Laboratory of Molecular Reaction Dynamics Dalian Institute of Chemical Physics Chinese Academy of Sciences Dalian 116023, P. R. China
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208
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Inokuchi Y, Boyarkin OV, Kusaka R, Haino T, Ebata T, Rizzo TR. Ion Selectivity of Crown Ethers Investigated by UV and IR Spectroscopy in a Cold Ion Trap. J Phys Chem A 2012; 116:4057-68. [DOI: 10.1021/jp3011519] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Yoshiya Inokuchi
- Department of Chemistry, Graduate
School of Science, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8526, Japan
| | - Oleg V. Boyarkin
- Laboratoire de Chimie Physique
Moléculaire, École Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland
| | - Ryoji Kusaka
- Department of Chemistry, Graduate
School of Science, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8526, Japan
| | - Takeharu Haino
- Department of Chemistry, Graduate
School of Science, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8526, Japan
| | - Takayuki Ebata
- Department of Chemistry, Graduate
School of Science, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8526, Japan
| | - Thomas R. Rizzo
- Laboratoire de Chimie Physique
Moléculaire, École Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland
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209
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Dunbar RC, Steill JD, Polfer NC, Berden G, Oomens J. Peptide bond tautomerization induced by divalent metal ions: characterization of the iminol configuration. Angew Chem Int Ed Engl 2012; 51:4591-3. [PMID: 22473902 DOI: 10.1002/anie.201200437] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2012] [Indexed: 11/07/2022]
Affiliation(s)
- Robert C Dunbar
- Chemistry Department, Case Western Reserve University, Cleveland, OH 44106, USA.
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210
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Dunbar RC, Steill JD, Polfer NC, Berden G, Oomens J. Peptide Bond Tautomerization Induced by Divalent Metal Ions: Characterization of the Iminol Configuration. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201200437] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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211
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Hurtado P, Gámez F, Hamad S, Martínez–Haya B, Steill JD, Oomens J. Multipodal coordination of a tetracarboxylic crown ether with NH 4+: A vibrational spectroscopy and computational study. J Chem Phys 2012; 136:114301. [DOI: 10.1063/1.3693518] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
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212
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Biswal HS, Gloaguen E, Loquais Y, Tardivel B, Mons M. Strength of NH···S Hydrogen Bonds in Methionine Residues Revealed by Gas-Phase IR/UV Spectroscopy. J Phys Chem Lett 2012; 3:755-9. [PMID: 26286285 DOI: 10.1021/jz300207k] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Despite of being ubiquitous in proteins, NHbackbone···S hydrogen bonds linking the sulfur atom of methionine or cysteine to backbone NH groups remain poorly documented. Here, we report vibrationally resolved IR NH stretch spectra of two methionine-containing dipeptides (Ac-Phe-Met-NH2 and Ac-Met-Phe-NH2). The conformations observed for both molecules, assigned with the help of DFT-D quantum chemistry, provide spectroscopic evidence for the formation of NHbackbone···S H-bonds, surprisingly strong enough to challenge the classical intrabackbone NH···O═C H-bonds. The methionine side chain is found to fold locally, forming a H-bond with the neighboring amide groups (NH(i) or NH(i+1)). Comparison with protein data bank structural information shows that such a local folding is also common in proteins where it concerns 24% of the methionine residues that have a sulfur atom linked to a backbone NH group. This convergence between the strength of these NH···S H-bonds and protein structural data illustrates their contribution to the stability of protein chains.
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Affiliation(s)
- Himansu S Biswal
- CEA, Laboratoire Francis Perrin, DSM/IRAMIS/SPAM, Bât 522, 91191 Gif-sur-Yvette, France
- CNRS, Laboratoire Francis Perrin, URA 2453, 91191 Gif-sur-Yvette, France
| | - Eric Gloaguen
- CEA, Laboratoire Francis Perrin, DSM/IRAMIS/SPAM, Bât 522, 91191 Gif-sur-Yvette, France
- CNRS, Laboratoire Francis Perrin, URA 2453, 91191 Gif-sur-Yvette, France
| | - Yohan Loquais
- CEA, Laboratoire Francis Perrin, DSM/IRAMIS/SPAM, Bât 522, 91191 Gif-sur-Yvette, France
- CNRS, Laboratoire Francis Perrin, URA 2453, 91191 Gif-sur-Yvette, France
| | - Benjamin Tardivel
- CEA, Laboratoire Francis Perrin, DSM/IRAMIS/SPAM, Bât 522, 91191 Gif-sur-Yvette, France
- CNRS, Laboratoire Francis Perrin, URA 2453, 91191 Gif-sur-Yvette, France
| | - Michel Mons
- CEA, Laboratoire Francis Perrin, DSM/IRAMIS/SPAM, Bât 522, 91191 Gif-sur-Yvette, France
- CNRS, Laboratoire Francis Perrin, URA 2453, 91191 Gif-sur-Yvette, France
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213
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Moss CL, Chamot-Rooke J, Nicol E, Brown J, Campuzano I, Richardson K, Williams JP, Bush MF, Bythell B, Paizs B, Turecek F. Assigning Structures to Gas-Phase Peptide Cations and Cation-Radicals. An Infrared Multiphoton Dissociation, Ion Mobility, Electron Transfer, and Computational Study of a Histidine Peptide Ion. J Phys Chem B 2012; 116:3445-56. [DOI: 10.1021/jp3000784] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Christopher L. Moss
- Department of Chemistry, University of Washington, Bagley Hall, Box 351700,
Seattle, Washington 981915-1700, United States
| | - Julia Chamot-Rooke
- Laboratoire des Mécanismes
Réactionnels, CNRS, École Polytechnique, Palaiseau, France
| | - Edith Nicol
- Laboratoire des Mécanismes
Réactionnels, CNRS, École Polytechnique, Palaiseau, France
| | - Jeffery Brown
- Waters Corporation, Floats Road, Wythenshawe, Manchester,
M23 9LZ, United Kingdom
| | - Iain Campuzano
- Waters Corporation, Floats Road, Wythenshawe, Manchester,
M23 9LZ, United Kingdom
| | - Keith Richardson
- Waters Corporation, Floats Road, Wythenshawe, Manchester,
M23 9LZ, United Kingdom
| | - Jonathan P. Williams
- Waters Corporation, Floats Road, Wythenshawe, Manchester,
M23 9LZ, United Kingdom
| | - Matthew F. Bush
- Department of Chemistry, University of Washington, Bagley Hall, Box 351700,
Seattle, Washington 981915-1700, United States
| | | | - Bela Paizs
- German Cancer Research Center, Heidelberg,
Germany
| | - Frantisek Turecek
- Department of Chemistry, University of Washington, Bagley Hall, Box 351700,
Seattle, Washington 981915-1700, United States
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214
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Affiliation(s)
- Timothy S. Zwier
- Department of Chemistry, Purdue University, West Lafayette, IN 47907-2084, USA
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215
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Garand E, Kamrath MZ, Jordan PA, Wolk AB, Leavitt CM, McCoy AB, Miller SJ, Johnson MA. Determination of noncovalent docking by infrared spectroscopy of cold gas-phase complexes. Science 2012; 335:694-8. [PMID: 22267579 PMCID: PMC4038764 DOI: 10.1126/science.1214948] [Citation(s) in RCA: 113] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Multidentate, noncovalent interactions between small molecules and biopolymer fragments are central to processes ranging from drug action to selective catalysis. We present a versatile and sensitive spectroscopic probe of functional groups engaged in hydrogen bonding in such contexts. This involves measurement of the frequency changes in specific covalent bonds upon complex formation, information drawn from otherwise transient complexes that have been extracted from solution and conformationally frozen near 10 kelvin in gas-phase clusters. Resonances closely associated with individual oscillators are easily identified through site-specific isotopic labeling, as demonstrated by application of the method to an archetypal system involving a synthetic tripeptide known to bind biaryl substrates through tailored hydrogen bonding to catalyze their asymmetric bromination. With such data, calculations readily converge on the plausible operative structures in otherwise computationally prohibitive, high-dimensionality landscapes.
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Affiliation(s)
- Etienne Garand
- Sterling Chemistry Laboratory, Yale University, P.O. Box 208107, New Haven, CT 06520
| | - Michael Z. Kamrath
- Sterling Chemistry Laboratory, Yale University, P.O. Box 208107, New Haven, CT 06520
| | - Peter A. Jordan
- Sterling Chemistry Laboratory, Yale University, P.O. Box 208107, New Haven, CT 06520
| | - Arron B. Wolk
- Sterling Chemistry Laboratory, Yale University, P.O. Box 208107, New Haven, CT 06520
| | | | - Anne B. McCoy
- Department of Chemistry, The Ohio State University, Columbus, OH 43210
| | - Scott J. Miller
- Sterling Chemistry Laboratory, Yale University, P.O. Box 208107, New Haven, CT 06520
| | - Mark A. Johnson
- Sterling Chemistry Laboratory, Yale University, P.O. Box 208107, New Haven, CT 06520
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216
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Daluz JS, Kocak A, Metz RB. Photodissociation Studies of the Electronic and Vibrational Spectroscopy of Ni+(H2O). J Phys Chem A 2012; 116:1344-52. [DOI: 10.1021/jp211220v] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jennifer S. Daluz
- Department
of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts
01003, United States
| | - Abdulkadir Kocak
- Department
of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts
01003, United States
| | - Ricardo B. Metz
- Department
of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts
01003, United States
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217
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Fujii M, Dopfer O. Ionisation-induced site switching dynamics in solvated aromatic clusters: phenol–(rare gas)nclusters as prototypical example. INT REV PHYS CHEM 2012. [DOI: 10.1080/0144235x.2012.656013] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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218
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Inokuchi Y, Boyarkin OV, Ebata T, Rizzo TR. UV and IR spectroscopy of cold 1,2-dimethoxybenzene complexes with alkali metal ions. Phys Chem Chem Phys 2012; 14:4457-62. [DOI: 10.1039/c2cp24018a] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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219
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Joshi K, Semrouni D, Ohanessian G, Clavaguéra C. Structures and IR Spectra of the Gramicidin S Peptide: Pushing the Quest for Low-Energy Conformations. J Phys Chem B 2011; 116:483-90. [DOI: 10.1021/jp207102v] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Kaustubh Joshi
- Laboratoire des Mécanismes Réactionnels, Department of Chemistry, Ecole Polytechnique, CNRS, 91128 Palaiseau Cedex, France
| | - David Semrouni
- Laboratoire des Mécanismes Réactionnels, Department of Chemistry, Ecole Polytechnique, CNRS, 91128 Palaiseau Cedex, France
| | - Gilles Ohanessian
- Laboratoire des Mécanismes Réactionnels, Department of Chemistry, Ecole Polytechnique, CNRS, 91128 Palaiseau Cedex, France
| | - Carine Clavaguéra
- Laboratoire des Mécanismes Réactionnels, Department of Chemistry, Ecole Polytechnique, CNRS, 91128 Palaiseau Cedex, France
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220
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James WH, Buchanan EG, Müller CW, Dean JC, Kosenkov D, Slipchenko LV, Guo L, Reidenbach AG, Gellman SH, Zwier TS. Evolution of amide stacking in larger γ-peptides: triamide H-bonded cycles. J Phys Chem A 2011; 115:13783-98. [PMID: 21978283 DOI: 10.1021/jp205527e] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The single-conformation spectroscopy of two model γ-peptides has been studied under jet-cooled conditions in the gas phase. The methyl-capped triamides, Ac-γ(2)-hPhe-γ(2)-hAla-NHMe and Ac-γ(2)-hAla-γ(2)-hPhe-NHMe, were probed by resonant two-photon ionization (R2PI) and resonant ion-dip infrared (RIDIR) spectroscopies. Four conformers of Ac-γ(2)-hPhe-γ(2)-hAla-NHMe and three of Ac-γ(2)-hAla-γ(2)-hPhe-NHMe were observed and spectroscopically interrogated. On the basis of comparison with the predictions of density functional theory calculations employing a dispersion-corrected functional (ωB97X-D/6-311++G(d,p)), all seven conformers have been assigned to particular conformational families. The preference for formation of nine-membered rings (C9) observed in a previous study [James, W. H., III et al., J. Am. Chem. Soc. 2009, 131, 14243] of the smaller analog, Ac-γ(2)-hPhe-NHMe, carries over to these triamides, with four of the seven conformers forming C9/C9 sequential double-ring structures, and one conformer a C9/C14 bifurcated double ring. The remaining two conformers form C7/C7/C14 H-bonded cycles involving all three amide NH groups, unprecedented in other peptides and peptidomimetics. The amide groups in these structures form a H-bonded triangle with the two trimethylene bridges forming loops above and below the molecule's midsection. The structure is a natural extension of amide stacking, with the two terminal amides blocked from forming the amide tristack by formation of the C14 H-bond. Pair interaction energy decomposition analysis based on the fragment molecular orbital method (FMO-PIEDA) is used to determine the nonbonded contributions to the stabilization of these conformers. Natural bond orbital (NBO) analysis identifies amide stacking with a pair of n → π* interactions between the nitrogen lone pairs and π* orbitals on the carbonyl of the opposing amide groups.
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Affiliation(s)
- William H James
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084, USA
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221
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Domin D, Benoit DM. Assessing Spin-Component-Scaled Second-Order Møller-Plesset Theory Using Anharmonic Frequencies. Chemphyschem 2011; 12:3383-91. [DOI: 10.1002/cphc.201100499] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2011] [Indexed: 11/08/2022]
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222
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Stefan SE, Ehsan M, Pearson WL, Aksenov A, Boginski V, Bendiak B, Eyler JR. Differentiation of Closely Related Isomers: Application of Data Mining Techniques in Conjunction with Variable Wavelength Infrared Multiple Photon Dissociation Mass Spectrometry for Identification of Glucose-Containing Disaccharide Ions. Anal Chem 2011; 83:8468-76. [DOI: 10.1021/ac2017103] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Sarah E. Stefan
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611-7200, United States
| | - Mohammad Ehsan
- 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
| | - Alexander Aksenov
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611-7200, United States
| | - Vladimir Boginski
- Department of Industrial & Systems Engineering, University of Florida, 1350 North Poquito Road, Shalimar, Florida 32579-1163, United States
| | - Brad Bendiak
- Department of Cellular and Developmental Biology and Program in Structural Biology and Biophysics, University of Colorado at Denver and Health Sciences Center, Aurora, Colorado 80045, 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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223
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224
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Lorenz UJ, Rizzo TR. Planar Multipole Ion Trap/Time-of-Flight Mass Spectrometer. Anal Chem 2011; 83:7895-901. [DOI: 10.1021/ac201790d] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Ulrich J. Lorenz
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Thomas R. Rizzo
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
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225
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Antoine R, Dugourd P. Visible and ultraviolet spectroscopy of gas phase protein ions. Phys Chem Chem Phys 2011; 13:16494-509. [PMID: 21811728 DOI: 10.1039/c1cp21531k] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Optical spectroscopy has contributed enormously to our knowledge of the structure and dynamics of atoms and molecules and is now emerging as a cornerstone of the gas phase methods available for investigating biomolecular ions. This article focuses on the UV and visible spectroscopy of peptide and protein ions stored in ion traps, with emphasis placed on recent results obtained on protein polyanions, by electron photodetachment experiments. We show that among a large number of possible de-excitation pathways, the relaxation of biomolecular polyanions is mainly achieved by electron emission following photo-excitation in electronically excited states. Electron photodetachment is a fast process that occurs prior to relaxation on vibrational degrees of freedom. Electron photodetachment yield can then be used to record gas phase action spectra for systems as large as entire proteins, without the limitation of system size that would arise from energy redistribution on numerous modes and prevent fragmentation after the absorption of a photon. The optical activity of proteins in the near UV is directly related to the electronic structure and optical absorption of aromatic amino acids (Trp, Phe and Tyr). UV spectra for peptides and proteins containing neutral, deprotonated and radical aromatic amino acids were recorded. They displayed strong bathochromic shifts. In particular, the results outline the privileged role played by open shell ions in molecular spectroscopy which, in the case of biomolecules, is directly related to their reactivity and biological functions. The optical shifts observed are sufficient to provide unambiguous fingerprints of the electronic structure of chromophores without the requirement of theoretical calculations. They constitute benchmarks for calculating the absorption spectra of chromophores embedded in entire proteins and could be used in the future to study biochemical processes in the gas phase involving charge transfer in aromatic amino acids, such as in the mediation of electron transfer or redox reactions. We then addressed the important question of the sensitivity of protein optical spectra to the intrinsic properties of protein ions, including conformation, charge state, etc., and to environmental factors. We report optical spectra for different charge states of insulin, for ubiquitin starting from native and denaturated solutions, and for apo-myoglobin protein. All these spectra are compared critically to spectra recorded in solution, in order to assess solvent effects. We also report the spectra of peptides complexed with metal cations and show that complexation gives rise to new optical transitions related to charge transfer types of excitation. The perspectives of this work include integrative approaches where UV-Vis spectroscopy could, for example, be combined with ion mobility spectrometry and high level calculations for protein structural characterization. It could also be used in spectroscopy to probe biological processes in the gas phase, with different light sources including VUV radiation (to probe different types of excitations) and ultra short pulses with time and phase modulation (to probe and control the dynamics of de-excitation or charge transfer events), and with the derivatization of proteins with chromophores to modulate their optical properties. We also envision that photo-excitation will play an important role in the future to produce intermediates with new chemical and reactive properties. Another promising route is to conduct activated electron photodetachment dissociation experiments.
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226
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Abstract
In the last decade, we have experienced massive progress in spectroscopic methods for mass-selected ions. The aim of this tutorial review is to present action spectroscopy as a powerful tool for the investigation of ionic reaction intermediates. Examples span from ultraviolet and infrared photodissociation spectroscopy of model reaction intermediates to applications of infrared multiphoton dissociation spectroscopy (IRMPD) to intermediates directly sampled from reaction mixtures. The first example of double resonance IR-UV spectroscopy of model intermediates in an organometallic reaction is also mentioned.
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Affiliation(s)
- Jana Roithová
- Charles University in Prague, Faculty of Science, Department of Organic and Nuclear Chemistry, Hlavova 2030, 128 43 Prague 2, Czech Republic.
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227
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Inokuchi Y, Boyarkin OV, Kusaka R, Haino T, Ebata T, Rizzo TR. UV and IR Spectroscopic Studies of Cold Alkali Metal Ion–Crown Ether Complexes in the Gas Phase. J Am Chem Soc 2011; 133:12256-63. [DOI: 10.1021/ja2046205] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Yoshiya Inokuchi
- Department of Chemistry, Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8526, Japan
| | - Oleg V. Boyarkin
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland
| | - Ryoji Kusaka
- Department of Chemistry, Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8526, Japan
| | - Takeharu Haino
- Department of Chemistry, Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8526, Japan
| | - Takayuki Ebata
- Department of Chemistry, Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8526, Japan
| | - Thomas R. Rizzo
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland
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228
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Nagornova NS, Guglielmi M, Doemer M, Tavernelli I, Rothlisberger U, Rizzo TR, Boyarkin OV. Kalte Ionenspektroskopie zur Lösung der Gasphasenstruktur eines Decapeptids. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201100702] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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229
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Bieler NS, Haag MP, Jacob CR, Reiher M. Analysis of the Cartesian Tensor Transfer Method for Calculating Vibrational Spectra of Polypeptides. J Chem Theory Comput 2011; 7:1867-81. [DOI: 10.1021/ct2001478] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Noah S. Bieler
- ETH Zurich, Laboratorium für Physikalische Chemie, Wolfgang-Pauli-Strasse 10, 8093 Zurich, Switzerland
| | - Moritz P. Haag
- ETH Zurich, Laboratorium für Physikalische Chemie, Wolfgang-Pauli-Strasse 10, 8093 Zurich, Switzerland
| | - Christoph R. Jacob
- Karlsruhe Institute of Technology (KIT), Center for Functional Nanostructures, Wolfgang-Gaede-Str. 1a, 76131 Karlsruhe, Germany
| | - Markus Reiher
- ETH Zurich, Laboratorium für Physikalische Chemie, Wolfgang-Pauli-Strasse 10, 8093 Zurich, Switzerland
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230
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Nagornova NS, Guglielmi M, Doemer M, Tavernelli I, Rothlisberger U, Rizzo TR, Boyarkin OV. Cold-Ion Spectroscopy Reveals the Intrinsic Structure of a Decapeptide. Angew Chem Int Ed Engl 2011; 50:5383-6. [DOI: 10.1002/anie.201100702] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2011] [Revised: 03/07/2011] [Indexed: 11/09/2022]
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231
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Kamrath MZ, Garand E, Jordan PA, Leavitt CM, Wolk AB, Van Stipdonk MJ, Miller SJ, Johnson MA. Vibrational characterization of simple peptides using cryogenic infrared photodissociation of H2-tagged, mass-selected ions. J Am Chem Soc 2011; 133:6440-8. [PMID: 21449591 PMCID: PMC3099397 DOI: 10.1021/ja200849g] [Citation(s) in RCA: 123] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
We present infrared photodissociation spectra of two protonated peptides that are cooled in a ~10 K quadrupole ion trap and "tagged" with weakly bound H(2) molecules. Spectra are recorded over the range of 600-4300 cm(-1) using a table-top laser source, and are shown to result from one-photon absorption events. This arrangement is demonstrated to recover sharp (Δν ~6 cm(-1)) transitions throughout the fingerprint region, despite the very high density of vibrational states in this energy range. The fundamentals associated with all of the signature N-H and C=O stretching bands are completely resolved. To address the site-specificity of the C=O stretches near 1800 cm(-1), we incorporated one (13)C into the tripeptide. The labeling affects only one line in the complex spectrum, indicating that each C=O oscillator contributes a single distinct band, effectively "reporting" its local chemical environment. For both peptides, analysis of the resulting band patterns indicates that only one isomeric form is generated upon cooling the ions initially at room temperature into the H(2) tagging regime.
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Affiliation(s)
- Michael Z. Kamrath
- Sterling Chemistry Laboratory, Yale University, P.O. Box 208107, New Haven, CT 06520 USA
| | - Etienne Garand
- Sterling Chemistry Laboratory, Yale University, P.O. Box 208107, New Haven, CT 06520 USA
| | - Peter A. Jordan
- Sterling Chemistry Laboratory, Yale University, P.O. Box 208107, New Haven, CT 06520 USA
| | - Christopher M. Leavitt
- Sterling Chemistry Laboratory, Yale University, P.O. Box 208107, New Haven, CT 06520 USA
| | - Arron B. Wolk
- Sterling Chemistry Laboratory, Yale University, P.O. Box 208107, New Haven, CT 06520 USA
| | | | - Scott J. Miller
- Sterling Chemistry Laboratory, Yale University, P.O. Box 208107, New Haven, CT 06520 USA
| | - Mark A. Johnson
- Sterling Chemistry Laboratory, Yale University, P.O. Box 208107, New Haven, CT 06520 USA
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232
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Plowright RJ, Gloaguen E, Mons M. Compact Folding of Isolated Four-Residue Neutral Peptide Chains: H-Bonding Patterns and Entropy Effects. Chemphyschem 2011; 12:1889-99. [DOI: 10.1002/cphc.201001023] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2010] [Indexed: 11/08/2022]
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233
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Sohn WY, Kim M, Kim SS, Park YD, Kang H. Solvent-assisted conformational isomerization and the conformationally-pure REMPI spectrum of 3-aminophenol. Phys Chem Chem Phys 2011; 13:7037-42. [DOI: 10.1039/c0cp02592e] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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234
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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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235
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Neill JL, Douglass KO, Pate BH, Pratt DW. Next generation techniques in the high resolution spectroscopy of biologically relevant molecules. Phys Chem Chem Phys 2011; 13:7253-62. [DOI: 10.1039/c0cp01573c] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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236
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Sakota K, Shimazaki Y, Sekiya H. Entropy-driven rearrangement of the water network at the hydrated amide group of the trans-formanilide–water cluster in the gas phase. Phys Chem Chem Phys 2011; 13:6411-5. [DOI: 10.1039/c0cp02836c] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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237
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Papadopoulos G, Svendsen A, Boyarkin OV, Rizzo TR. Spectroscopy of mobility-selected biomolecular ions. Faraday Discuss 2011; 150:243-55; discussion 257-92. [DOI: 10.1039/c0fd00004c] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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238
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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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239
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McKay AR, Sanz ME, Mooney CRS, Minns RS, Gill EM, Fielding HH. Development of a new photoelectron spectroscopy instrument combining an electrospray ion source and photoelectron imaging. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2010; 81:123101. [PMID: 21198008 DOI: 10.1063/1.3505097] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
A new apparatus has been constructed that combines electrospray ionization with a quadrupole mass filter, hexapole ion trap, and velocity-map imaging. The purpose is to record photoelectron images of isolated chromophore anions. To demonstrate the capability of our instrument we have recorded the photodetachment spectra of isolated deprotonated phenol and indole anions. To our knowledge, this is the first time that the photodetachment energy of the deprotonated indole anion has been recorded.
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Affiliation(s)
- A R McKay
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, United Kingdom
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240
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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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241
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Alata I, Dedonder C, Broquier M, Marceca E, Jouvet C. Role of the Charge-Transfer State in the Electronic Absorption of Protonated Hydrocarbon Molecules. J Am Chem Soc 2010; 132:17483-9. [DOI: 10.1021/ja106424f] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ivan Alata
- Centre Laser de l’Université Paris Sud (LUMAT FR 2764), Bât. 106, and Institut des Sciences Moléculaires d’Orsay, Bât. 210, Université Paris-Sud 11, 91405 Orsay Cedex, France, Atomic Energy Commission of Syria, P.O. Box 6091, Damascus, Syria, and INQUIMAE-FCEN,UBA, Ciudad Universitaria, 3er piso, Pab. II, 1428 Buenos Aires, Argentina
| | - Claude Dedonder
- Centre Laser de l’Université Paris Sud (LUMAT FR 2764), Bât. 106, and Institut des Sciences Moléculaires d’Orsay, Bât. 210, Université Paris-Sud 11, 91405 Orsay Cedex, France, Atomic Energy Commission of Syria, P.O. Box 6091, Damascus, Syria, and INQUIMAE-FCEN,UBA, Ciudad Universitaria, 3er piso, Pab. II, 1428 Buenos Aires, Argentina
| | - Michel Broquier
- Centre Laser de l’Université Paris Sud (LUMAT FR 2764), Bât. 106, and Institut des Sciences Moléculaires d’Orsay, Bât. 210, Université Paris-Sud 11, 91405 Orsay Cedex, France, Atomic Energy Commission of Syria, P.O. Box 6091, Damascus, Syria, and INQUIMAE-FCEN,UBA, Ciudad Universitaria, 3er piso, Pab. II, 1428 Buenos Aires, Argentina
| | - Ernesto Marceca
- Centre Laser de l’Université Paris Sud (LUMAT FR 2764), Bât. 106, and Institut des Sciences Moléculaires d’Orsay, Bât. 210, Université Paris-Sud 11, 91405 Orsay Cedex, France, Atomic Energy Commission of Syria, P.O. Box 6091, Damascus, Syria, and INQUIMAE-FCEN,UBA, Ciudad Universitaria, 3er piso, Pab. II, 1428 Buenos Aires, Argentina
| | - Christophe Jouvet
- Centre Laser de l’Université Paris Sud (LUMAT FR 2764), Bât. 106, and Institut des Sciences Moléculaires d’Orsay, Bât. 210, Université Paris-Sud 11, 91405 Orsay Cedex, France, Atomic Energy Commission of Syria, P.O. Box 6091, Damascus, Syria, and INQUIMAE-FCEN,UBA, Ciudad Universitaria, 3er piso, Pab. II, 1428 Buenos Aires, Argentina
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242
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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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243
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Smolarek S, Brauer NB, Buma WJ, Drabbels M. IR Spectroscopy of Molecular Ions by Nonthermal Ion Ejection from Helium Nanodroplets. J Am Chem Soc 2010; 132:14086-91. [DOI: 10.1021/ja1034655] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Szymon Smolarek
- University of Amsterdam, P.O. Box 94157, 1090 GD Amsterdam, The Netherlands, and Laboratoire de Chimie Physique Moléculaire, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Nils B. Brauer
- University of Amsterdam, P.O. Box 94157, 1090 GD Amsterdam, The Netherlands, and Laboratoire de Chimie Physique Moléculaire, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Wybren J. Buma
- University of Amsterdam, P.O. Box 94157, 1090 GD Amsterdam, The Netherlands, and Laboratoire de Chimie Physique Moléculaire, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Marcel Drabbels
- University of Amsterdam, P.O. Box 94157, 1090 GD Amsterdam, The Netherlands, and Laboratoire de Chimie Physique Moléculaire, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
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244
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Fedorov A, Couzijn EPA, Nagornova NS, Boyarkin OV, Rizzo TR, Chen P. Structure and Bonding of Isoleptic Coinage Metal (Cu, Ag, Au) Dimethylaminonitrenes in the Gas Phase. J Am Chem Soc 2010; 132:13789-98. [DOI: 10.1021/ja104649k] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Alexey Fedorov
- Laboratorium für Organische Chemie, ETH Zürich, Wolfgang-Pauli-Strasse 10, CH-8093 Zürich, Switzerland, and Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Erik P. A. Couzijn
- Laboratorium für Organische Chemie, ETH Zürich, Wolfgang-Pauli-Strasse 10, CH-8093 Zürich, Switzerland, and Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Natalia S. Nagornova
- Laboratorium für Organische Chemie, ETH Zürich, Wolfgang-Pauli-Strasse 10, CH-8093 Zürich, Switzerland, and Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Oleg V. Boyarkin
- Laboratorium für Organische Chemie, ETH Zürich, Wolfgang-Pauli-Strasse 10, CH-8093 Zürich, Switzerland, and Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Thomas R. Rizzo
- Laboratorium für Organische Chemie, ETH Zürich, Wolfgang-Pauli-Strasse 10, CH-8093 Zürich, Switzerland, and Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Peter Chen
- Laboratorium für Organische Chemie, ETH Zürich, Wolfgang-Pauli-Strasse 10, CH-8093 Zürich, Switzerland, and Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
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245
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Svendsen A, Lorenz UJ, Boyarkin OV, Rizzo TR. A new tandem mass spectrometer for photofragment spectroscopy of cold, gas-phase molecular ions. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2010; 81:073107. [PMID: 20687705 DOI: 10.1063/1.3458014] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
We present here the design of a new tandem mass spectrometer that combines an electrospray ion source with a cryogenically cooled ion trap for spectroscopic studies of cold, gas-phase ions. The ability to generate large ions in the gas phase without fragmentation, cool them to approximately 10 K in an ion trap, and perform photofragment spectroscopy opens up new possibilities for spectroscopic characterization of large biomolecular ions. The incorporation of an ion funnel, together with a number of small enhancements, significantly improves the sensitivity, signal stability, and ease of use compared with the previous instrument built in our laboratory.
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Affiliation(s)
- Annette Svendsen
- Laboratoire de Chimie Physique Moléculaire, Ecole Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland
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246
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Gaigeot MP. Infrared spectroscopy of the alanine dipeptide analog in liquid water with DFT-MD. Direct evidence for P(II)/beta conformations. Phys Chem Chem Phys 2010; 12:10198-209. [PMID: 20539891 DOI: 10.1039/c003485a] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Following our previous work [J. Phys. Chem. B. Lett., 2009, 113, 10059], DFT-based molecular dynamics (DFTMD) simulations of 2-Ala peptide (i.e. Ac-Ala-NHMe dialanine peptide analog with methyl group caps at the extremities) immersed in liquid water at room temperature are reported. Our goal here is the theoretical calculation of the infrared spectrum of aqueous 2-Ala, in order to provide a definitive understanding of the average conformation adopted by this peptide in the liquid phase, taking into account solute and solvent at the same theoretical level of representation. We find that the experimental Amide I-II band predominantly results from a mixture of partially unfolded P(II) and unfolded beta conformational equilibrium of aqueous 2-Ala at room temperature.
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Affiliation(s)
- Marie-Pierre Gaigeot
- Université d'Evry val d'Essonne, LAMBE UMR8587 Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement, Blvd F. Mitterrand, Bât. Maupertuis, 91025 Evry, France.
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Baer T, Dunbar RC. Ion spectroscopy: where did it come from; where is it now; and where is it going? JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2010; 21:681-693. [PMID: 20189827 DOI: 10.1016/j.jasms.2010.01.028] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2009] [Revised: 01/27/2010] [Accepted: 01/27/2010] [Indexed: 05/28/2023]
Abstract
The ASMS conference on ion spectroscopy brought together at Asilomar on October 16-20, 2009 a large group of mass spectrometrists working in the area of ion spectroscopy. In this introduction to the field, we provide a brief history, its current state, and where it is going. Ion spectroscopy of intermediate size molecules began with photoelectron spectroscopy in the 1960s, while electronic spectroscopy of ions using the photodissociation "action spectroscopic" mode became active in the next decade. These approaches remained for many years the main source of information about ionization energies, electronic states, and electronic transitions of ions. In recent years, high-resolution laser techniques coupled with pulsed field ionization and sample cooling in molecular beams have provided high precision ionization energies and vibrational frequencies of small to intermediate sized molecules, including a number of radicals. More recently, optical parametric oscillator (OPO) IR lasers and free electron lasers have been developed and employed to record the IR spectra of molecular ions in either molecular beams or ion traps. These results, in combination with theoretical ab initio molecular orbital (MO) methods, are providing unprecedented structural and energetic information about gas-phase ions.
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Affiliation(s)
- Tomas Baer
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599-3290, USA.
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248
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Gaigeot MP. Theoretical spectroscopy of floppy peptides at room temperature. A DFTMD perspective: gas and aqueous phase. Phys Chem Chem Phys 2010; 12:3336-59. [PMID: 20336243 DOI: 10.1039/b924048a] [Citation(s) in RCA: 135] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Theoretical spectroscopy is mandatory for a precise understanding and assignment of experimental spectra recorded at finite temperature. We review here room temperature DFT-based molecular dynamics simulations for the purpose of interpreting finite temperature infrared spectra of peptides of increasing size and complexity, in terms of temperature-dependent conformational dynamics and flexibility, and vibrational anharmonicities (potential energy surface anharmonicities, vibrational mode couplings and dipole anharmonicities). We take examples from our research projects in order to illustrate the main key-points and strengths of dynamical spectra modeling in that context. The calculations are presented in relation to room temperature gas phase IR-MPD experiments and room temperature liquid phase IR absorption experiments. These illustrations of floppy polypeptides have been chosen in order to convey the following ideas: temperature-dependent spectra modeling is pivotal for a precise understanding of gas phase spectra recorded at room temperature, including conformational dynamics and vibrational anharmonicities; harmonic spectroscopy (as commonly performed in the literature) can be misleading and even erroneous for a proper interpretation of spectra recorded at finite temperature; taking into account vibrational anharmonicities is pivotal for a proper interplay between theory and experiments; amide I-III bands are not necessarily the most relevant fingerprints for unraveling the local structures of peptides and more complex systems; liquid phase simulations have unraveled relationships between the zwitterionic properties of the peptide bonds and infrared signatures. The review presents a state-of-the-art account of the domain and offers perspectives and new developments for future still more challenging applications.
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Affiliation(s)
- Marie-Pierre Gaigeot
- Université d'Evry val d'Essonne, LAMBE UMR8587 Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement, Blvd F. Mitterrand, Bat Maupertuis, 91025 Evry, France.
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249
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Nagornova NS, Rizzo TR, Boyarkin OV. Highly Resolved Spectra of Gas-Phase Gramicidin S: A Benchmark for Peptide Structure Calculations. J Am Chem Soc 2010; 132:4040-1. [DOI: 10.1021/ja910118j] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Natalia S. Nagornova
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Thomas R. Rizzo
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Oleg V. Boyarkin
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
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250
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Cocinero EJ, Lesarri A, Écija P, Grabow JU, Fernández JA, Castaño F. Conformational equilibria in vanillin and ethylvanillin. Phys Chem Chem Phys 2010; 12:12486-93. [DOI: 10.1039/c0cp00585a] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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