1
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Stevenson BC, Berden G, Martens J, Oomens J, Armentrout PB. Spectroscopic Investigation of the Metal Coordination of the Aromatic Amino Acids with Zinc and Cadmium. J Phys Chem A 2023; 127:3560-3569. [PMID: 37053556 DOI: 10.1021/acs.jpca.2c08940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
The aromatic amino acids (AAA), phenylalanine (Phe), tyrosine (Tyr), and tryptophan (Trp), were cationized with ZnCl+ and CdCl+, and the complexes were evaluated using infrared multiple photon dissociation (IRMPD) action spectroscopy. Specifically, the ZnCl+(Phe), CdCl+(Phe), ZnCl+(Tyr), CdCl+(Tyr), and ZnCl+(Trp) species were examined because the CdCl+(Trp) IRMPD spectrum is available in the literature. Several low-energy conformers for all complexes were found using quantum chemical calculations, and their simulated vibrational spectra were compared to the experimental IRMPD spectra to identify dominant isomers formed. In the case of MCl+(Phe) and MCl+(Tyr), these comparisons indicated the dominant binding motif is a tridentate structure, where the metal atom coordinates with the backbone amino nitrogen and carbonyl oxygen, as well as the aryl ring. These observations are consistent with the predicted ground states at the B3LYP, B3P86, B3LYP-GD3BJ, and MP2 levels of theory. For the ZnCl+(Trp) system, the experimental spectrum indicates a similar binding motif, with the zinc atom coordinating with the backbone nitrogen and carbonyl oxygen and either the pyrrole ring or the benzene ring of the indole side chain. These observations are consistent with the predicted low-lying conformers identified by the aforementioned levels of theory, with the B3LYP and B3P86 levels predicting the metal-pyrrole ring interaction is more favorable than the metal-benzene ring interactions and the opposite at the B3LYP-GD3BJ and MP2 levels.
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Affiliation(s)
- Brandon C Stevenson
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
| | - Giel Berden
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
| | - Jonathan Martens
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
| | - Jos Oomens
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
- van't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, NL-1098 XH Amsterdam, The Netherlands
| | - P B Armentrout
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
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2
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Differentiation between Isomeric 4,5-Functionalized 1,2,3-Thiadiazoles and 1,2,3-Triazoles by ESI-HRMS and IR Ion Spectroscopy. Molecules 2023; 28:molecules28030977. [PMID: 36770641 PMCID: PMC9920699 DOI: 10.3390/molecules28030977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 01/14/2023] [Accepted: 01/16/2023] [Indexed: 01/21/2023] Open
Abstract
A large variety of 1,2,3-thiadiazoles and 1,2,3-triazoles are used extensively in modern pure and applied organic chemistry as important structural blocks of numerous valuable products. Creation of new methods of synthesis of these isomeric compounds requires the development of reliable analytical tools to reveal the structural characteristics of these novel compounds, which are able to distinguish between isomers. Mass spectrometry (MS) is a clear choice for this task due to its selectivity, sensitivity, informational capacity, and reliability. Here, the application of electrospray ionization (ESI) with ion detection in positive and negative modes was demonstrated to be useful in structural studies. Additionally, interconversion of isomeric 4,5-functionalized 1,2,3-triazoles and 1,2,3-thiadiazoles was demonstrated. Application of accurate mass measurements and tandem mass spectrometry in MS2 and MS3 modes indicated the occurrence of gas-phase rearrangement of 1,2,3-triazoles into 1,2,3-thiadiazoles under (+)ESI-MS/MS conditions, independent of the nature of substituents, in line with the reaction in the condensed phase. Infrared multiple photon dissociation (IRMPD) spectroscopy enabled the establishment of structures of some of the most crucial common fragment ions, including [M+H-N2]+ and [M+H-N2-RSO2]+ species. The (-)ESI-MS/MS experiments were significantly more informative for the sulfonyl alkyl derivatives compared to the sulfonyl aryl ones. However, there was insufficient evidence to confirm the solution-phase transformation of 1,2,3-thiadiazoles into the corresponding 1,2,3-triazoles.
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3
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Munshi MU, Berden G, Oomens J. Facial vs. meridional coordination in gaseous Ni(II)-hexacyclen complexes revealed with infrared ion spectroscopy. Phys Chem Chem Phys 2022; 24:26890-26897. [PMID: 36317665 PMCID: PMC9644429 DOI: 10.1039/d2cp03871d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 10/21/2022] [Indexed: 08/20/2023]
Abstract
We report fingerprint infrared multiple-photon dissociation (IRMPD) spectra of the isolated gaseous hexa-coordinated complex of the macrocycle hexa-aza-18-crown-6 (hexacyclen, 1,4,7,10,13,16-hexaazacyclooctadecane, 18-azacrown-6) with Ni2+. The metal-ligand complexes are generated using electrospray ionization (ESI) and IR action spectra are recorded in a Fourier transform ion cyclotron resonance mass spectrometer (FTICR) MS coupled to the infrared free-electron laser FELIX. We investigate geometric structure of the complexes and in particular the chelation motif, by comparison with computed vibrational spectra, obtained using density functional theory (DFT) at the B3LYP/6-31++G(d,p) level. The quasi-octahedral chelation motif of the complex has been well documented in condensed-phase studies, and we focus here on the gas-phase structure, addressing in particular the question of a facial (fac) versus a meridional (mer) octahedral chelation geometry. Based on the good agreement between calculated linear IR spectra and experimental IRMPD spectra, we conclude that the gas-phase complex adopts a mer chelation geometry and we exclude significant contribution of the fac isomer, which is computed to lie about 10 kJ mol-1 higher in energy. We also address the possible presence of both meridional diastereomers and of higher energy conformers of meridional isomers. Finally, as expected for the d8 Ni2+-ion in an octahedral ligand environment, the IR spectrum also shows that the complexes are in a high-spin electron configuration.
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Affiliation(s)
| | - Giel Berden
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands.
| | - Jos Oomens
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands.
- University of Amsterdam, Science Park 904, 1098XH Amsterdam, The Netherlands
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4
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Mikawy NN, Roy HA, Israel E, Hamlow LA, Zhu Y, Berden G, Oomens J, Frieler CE, Rodgers MT. 5-Halogenation of Uridine Suppresses Protonation-Induced Tautomerization and Enhances Glycosidic Bond Stability of Protonated Uridine: Investigations via IRMPD Action Spectroscopy, ER-CID Experiments, and Theoretical Calculations. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:2165-2180. [PMID: 36279168 DOI: 10.1021/jasms.2c00231] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Uridine (Urd), a canonical nucleoside of RNA, is the most commonly modified nucleoside among those that occur naturally. Uridine has also been an important target for the development of modified nucleoside analogues for pharmaceutical applications. In this work, the effects of 5-halogenation of uracil on the structures and glycosidic bond stabilities of protonated uridine nucleoside analogues are examined using tandem mass spectrometry and computational methods. Infrared multiple photon dissociation (IRMPD) action spectroscopy experiments and theoretical calculations are performed to probe the structural influences of these modifications. Energy-resolved collision-induced dissociation experiments along with survival yield analyses are performed to probe glycosidic bond stability. The measured IRMPD spectra are compared to linear IR spectra predicted for the stable low-energy conformations of these species computed at the B3LYP/6-311+G(d,p) level of theory to determine the conformations experimentally populated. Spectral signatures in the IR fingerprint and hydrogen-stretching regions allow the 2,4-dihydroxy protonated tautomers (T) and O4- and O2-protonated conformers to be readily differentiated. Comparisons between the measured and predicted spectra indicate that parallel to findings for uridine, both T and O4-protonated conformers of the 5-halouridine nucleoside analogues are populated, whereas O2-protonated conformers are not. Variations in yields of the spectral signatures characteristic of the T and O4-protonated conformers indicate that the extent of protonation-induced tautomerization is suppressed as the size of the halogen substituent increases. Trends in the energy-dependence of the survival yield curves find that 5-halogenation strengthens the glycosidic bond and that the enhancement in stability increases with the size of the halogen substituent.
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Affiliation(s)
- Neven N Mikawy
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - H A Roy
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - E Israel
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - L A Hamlow
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - Y Zhu
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - G Berden
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525ED Nijmegen, The Netherlands
| | - J Oomens
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525ED Nijmegen, The Netherlands
| | - C E Frieler
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - M T Rodgers
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
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5
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Armentrout PB, Stevenson BC, Ghiassee M, Boles GC, Berden G, Oomens J. Infrared multiple-photon dissociation spectroscopy of cationized glycine: effects of alkali metal cation size on gas-phase conformation. Phys Chem Chem Phys 2022; 24:22950-22959. [PMID: 36125205 DOI: 10.1039/d2cp03469g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The gas-phase structures of cationized glycine (Gly), including complexes with Li+, Na+, K+, Rb+, and Cs+, are examined using infrared multiple-photon dissociation (IRMPD) spectroscopy utilizing light generated by a free electron laser, in conjunction with ab initio calculations. To identify the structures present in the experimental studies, measured IRMPD spectra are compared to spectra calculated at B3LYP/6-311+G(d,p) for the Li+, Na+, and K+ complexes and at B3LYP/def2TZVP for the Rb+ and Cs+ complexes. Single-point energy calculations were carried out at the B3LYP, B3P86, and MP2(full) levels using the 6-311+G(2d,2p) basis set for Li+, Na+, K+ and the def2TZVPP basis set for Rb+ and Cs+. The Li+ and Na+ complexes are identified as metal cation coordination to the amino nitrogen and carbonyl oxygen, [N,CO]-tt, although Na+(Gly) may have contributions from additional structures. The heavier metal cations coordinate to either the carbonyl oxygen, [CO]-cc, or the carbonyl oxygen and hydroxy oxygen, [CO,OH]-cc, with the former apparently preferred for Rb+ and Cs+ and the latter for K+. These two structures reside in a double-well potential and different levels of theory predict very different relative stabilities. Some experimental evidence is provided that MP2(full) theory provides the most accurate relative energies.
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Affiliation(s)
- P B Armentrout
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, USA.
| | - Brandon C Stevenson
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, USA.
| | - Maryam Ghiassee
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, USA.
| | - Georgia C Boles
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, USA.
| | - Giel Berden
- Radboud University, FELIX Laboratory, Institute for Molecules and Materials, Toernooiveld 7, NL-6525 ED Nijmegen, The Netherlands
| | - Jos Oomens
- Radboud University, FELIX Laboratory, Institute for Molecules and Materials, Toernooiveld 7, NL-6525 ED Nijmegen, The Netherlands.,van't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, NL-1098 XH Amsterdam, The Netherlands
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6
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McNary CP, Demireva M, Martens J, Berden G, Oomens J, Hamlow LA, Rodgers MT, Armentrout PB. Infrared multiple photon dissociation action spectroscopy of protonated unsymmetrical dimethylhydrazine and proton-bound dimers of hydrazine and unsymmetrical dimethylhydrazine. Phys Chem Chem Phys 2021; 23:25877-25885. [PMID: 34766618 DOI: 10.1039/d1cp03781a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The gas-phase structures of protonated unsymmetrical 1,1-dimethylhydrazine (UDMH) and the proton-bound dimers of UDMH and hydrazine are examined by infrared multiple photon dissociation (IRMPD) action spectroscopy utilizing light generated by a free electron laser and an optical parametric oscillator laser system. To identify the structures present in the experimental studies, the measured IRMPD spectra are compared to spectra calculated at the B3LYP-GD3BJ/6-311+G(d,p) level of theory. These comparisons show that protonated UDMH binds the proton at the methylated nitrogen atom (α) with two low-lying α conformers probably being populated. For (UDMH)2H+, the proton is shared between the methylated nitrogen atoms with several low-lying α conformers likely to be populated. Higher-lying conformers of (UDMH)2H+ in which the proton is shared between α and β (unmethylated) nitrogen atoms cannot be ruled out on the basis of the IRPMD spectrum. For (N2H4)2H+, there are four low-lying conformers that all reproduce the IRMPD spectrum reasonably well. As hydrazine and UDMH see usage as fuels for rocket engines, such spectra are potentially useful as a means of remotely monitoring rocket launches, especially in cases of unsuccessful launches where environmental hazards need to be assessed.
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Affiliation(s)
| | - Maria Demireva
- Department of Chemistry, University of Utah, Salt Lake City, UT 84112, USA.
| | - Jonathan Martens
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525ED Nijmegen, The Netherlands
| | - Giel Berden
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525ED Nijmegen, The Netherlands
| | - Jos Oomens
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525ED Nijmegen, The Netherlands.,Van't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098XH Amsterdam, The Netherlands
| | - L A Hamlow
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA
| | - M T Rodgers
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA
| | - P B Armentrout
- Department of Chemistry, University of Utah, Salt Lake City, UT 84112, USA.
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7
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Andersson Å, Poline M, Houthuijs KJ, van Outersterp RE, Berden G, Oomens J, Zhaunerchyk V. IRMPD Spectroscopy of Homo- and Heterochiral Asparagine Proton-Bound Dimers in the Gas Phase. J Phys Chem A 2021; 125:7449-7456. [PMID: 34428065 PMCID: PMC8419839 DOI: 10.1021/acs.jpca.1c05667] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Revised: 08/11/2021] [Indexed: 12/16/2022]
Abstract
We investigate gas-phase structures of homo- and heterochiral asparagine proton-bound dimers with infrared multiphoton dissociation (IRMPD) spectroscopy and quantum-chemical calculations. Their IRMPD spectra are recorded at room temperature in the range of 500-1875 and 3000-3600 cm-1. Both varieties of asparagine dimers are found to be charge-solvated based on their IRMPD spectra. The location of the principal intramolecular H-bond is discussed in light of harmonic frequency analyses using the B3LYP functional with GD3BJ empirical dispersion. Contrary to theoretical analyses, the two spectra are very similar.
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Affiliation(s)
- Åke Andersson
- Department
of Physics, University of Gothenburg, 41296 Gothenburg, Sweden
| | - Mathias Poline
- Department
of Physics, Stockholm University, 10691 Stockholm, Sweden
| | - Kas J. Houthuijs
- FELIX
Laboratory, Institute for Molecules and Materials, Radboud University, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
| | - Rianne E. van Outersterp
- FELIX
Laboratory, Institute for Molecules and Materials, Radboud University, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
| | - Giel Berden
- FELIX
Laboratory, Institute for Molecules and Materials, Radboud University, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
| | - Jos Oomens
- FELIX
Laboratory, Institute for Molecules and Materials, Radboud University, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
| | - Vitali Zhaunerchyk
- Department
of Physics, University of Gothenburg, 41296 Gothenburg, Sweden
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8
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Armentrout PB, Boles GC, Ghiassee M, Berden G, Oomens J. Infrared Multiple-Photon Dissociation Spectra of Sodiated Complexes of the Aliphatic Amino Acids. J Phys Chem A 2021; 125:6348-6355. [PMID: 34270243 DOI: 10.1021/acs.jpca.1c04708] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Sodiated complexes of the aliphatic amino acids, Gly, Ala, Val, Leu, and Ile, were examined with infrared multiple-photon dissociation action spectroscopy utilizing light from a free-electron laser. To identify structures, the experimental spectra were compared to linear spectra calculated at the B3LYP/6-311+G(d,p) level of theory. Relative energetics of all complexes were calculated at B3LYP, B3P86, MP2(full), B3LYP-GD3BJ, and M06-2X levels using a 6-311+G(2d,2p) basis set. Spectral comparison for all complexes indicates that the dominant conformation, [N, CO], binds to the amino nitrogen and carbonyl oxygen. For all complexes except Gly, contributions are observed from [CO2-] structures, where the sodium cation binds to both oxygens of the carboxylate group in the zwitterionic form of the amino acid. The semiquantitative distribution between these two structures appears to be best-predicted by the B3LYP and MP2(full) levels of theory, with predictions from the other three levels inconsistent with the experiment.
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Affiliation(s)
- P B Armentrout
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
| | - Georgia C Boles
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
| | - Maryam Ghiassee
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
| | - Giel Berden
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7, NL-6525 ED Nijmegen, The Netherlands
| | - Jos Oomens
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7, NL-6525 ED Nijmegen, The Netherlands.,Van't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
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9
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Affiliation(s)
- Martin Mayer
- Wilhelm-Ostwald-Institut für Physikalische und Theoretische Chemie, Universität Leipzig, Linnéstraße 2, 04103 Leipzig, Germany
| | - Knut R. Asmis
- Wilhelm-Ostwald-Institut für Physikalische und Theoretische Chemie, Universität Leipzig, Linnéstraße 2, 04103 Leipzig, Germany
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10
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Eremin DB, Boiko DA, Kostyukovich AY, Burykina JV, Denisova EA, Anania M, Martens J, Berden G, Oomens J, Roithová J, Ananikov VP. Mechanistic Study of Pd/NHC-Catalyzed Sonogashira Reaction: Discovery of NHC-Ethynyl Coupling Process. Chemistry 2020; 26:15672-15681. [PMID: 32881095 DOI: 10.1002/chem.202003533] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Indexed: 11/07/2022]
Abstract
The product of a revealed transformation-NHC-ethynyl coupling-was observed as a catalyst transformation pathway in the Sonogashira cross-coupling, catalyzed by Pd/NHC complexes. The 2-ethynylated azolium salt was isolated in individual form and fully characterized, including X-ray analysis. A number of possible intermediates of this transformation with common formulae (NHC)n Pd(C2 Ph) (n=1,2) were observed and subjected to collision-induced dissociation (CID) and infrared multiphoton dissociation (IRMPD) experiments to elucidate their structure. Measured bond dissociation energies (BDEs) and IRMPD spectra were in an excellent agreement with quantum calculations for coupling product π-complexes with Pd0 . Molecular dynamics simulations confirmed the observed multiple CID fragmentation pathways. An unconventional methodology to study catalyst evolution suggests the reported transformation to be considered in the development of new catalytic systems for alkyne functionalization reactions.
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Affiliation(s)
- Dmitry B Eremin
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Pr. 47, Moscow, 119991, Russia.,The Bridge@USC, University of Southern California, 1002 Childs Way, Los Angeles, CA, 90089-3502, USA
| | - Daniil A Boiko
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Pr. 47, Moscow, 119991, Russia
| | - Alexander Yu Kostyukovich
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Pr. 47, Moscow, 119991, Russia
| | - Julia V Burykina
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Pr. 47, Moscow, 119991, Russia
| | - Ekaterina A Denisova
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Pr. 47, Moscow, 119991, Russia
| | - Mariarosa Anania
- Department for Spectroscopy and Catalysis, Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, Netherlands
| | - Jonathan Martens
- FELIX Laboratory, Institute for Molecules and Materials, Radboud University, Toernooiveld 7, 6525 ED, Nijmegen, Netherlands
| | - Giel Berden
- FELIX Laboratory, Institute for Molecules and Materials, Radboud University, Toernooiveld 7, 6525 ED, Nijmegen, Netherlands
| | - Jos Oomens
- FELIX Laboratory, Institute for Molecules and Materials, Radboud University, Toernooiveld 7, 6525 ED, Nijmegen, Netherlands
| | - Jana Roithová
- Department for Spectroscopy and Catalysis, Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, Netherlands
| | - Valentine P Ananikov
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Pr. 47, Moscow, 119991, Russia
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11
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Oomens J, Kempkes LJM, Geurts TPJ, van Dijk L, Martens J, Berden G, Armentrout PB. Water Loss from Protonated XxxSer and XxxThr Dipeptides Gives Oxazoline-Not Oxazolone-Product Ions. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:2111-2123. [PMID: 32876444 PMCID: PMC7552115 DOI: 10.1021/jasms.0c00239] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 08/31/2020] [Accepted: 09/02/2020] [Indexed: 06/11/2023]
Abstract
Neutral loss of water and ammonia are often significant fragmentation channels upon collisional activation of protonated peptides. Here, we deploy infrared ion spectroscopy to investigate the dehydration reactions of protonated AlaSer, AlaThr, GlySer, GlyThr, PheSer, PheThr, ProSer, ProThr, AsnSer, and AsnThr, focusing on the question of the structure of the resulting [M + H - H2O]+ fragment ion and the site from which H2O is expelled. In all cases, the second residue of the selected peptides contains a hydroxyl moiety, so that H2O loss can potentially occur from this side-chain, as an alternative to loss from the C-terminal free acid of the dipeptide. Infrared action spectra of the product ions along with quantum-chemical calculations unambiguously show that dehydration consistently produces fragment ions containing an oxazoline moiety. This contrasts with the common oxazolone structure that would result from dehydration at the C-terminus analogous to the common b/y dissociation forming regular b2-type sequence ions. The oxazoline product structure suggests a reaction mechanism involving water loss from the Ser/Thr side-chain with concomitant nucleophilic attack of the amide carbonyl oxygen at its β-carbon, forming an oxazoline ring. However, an extensive quantum-chemical investigation comparing the potential energy surfaces for three entirely different dehydration reaction pathways indicates that it is actually the backbone amide oxygen atom that leaves as the water molecule.
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Affiliation(s)
- Jos Oomens
- FELIX Laboratory, Institute of Molecules and
Materials, Radboud University, Toernooiveld 7, 6525 ED
Nijmegen, The Netherlands
- Van’t Hoff Institute for Molecular Sciences,
University of Amsterdam, Science Park 904, 1098 XH Amsterdam,
The Netherlands
| | - Lisanne J. M. Kempkes
- FELIX Laboratory, Institute of Molecules and
Materials, Radboud University, Toernooiveld 7, 6525 ED
Nijmegen, The Netherlands
| | - Thijs P. J. Geurts
- FELIX Laboratory, Institute of Molecules and
Materials, Radboud University, Toernooiveld 7, 6525 ED
Nijmegen, The Netherlands
| | - Luuk van Dijk
- FELIX Laboratory, Institute of Molecules and
Materials, Radboud University, Toernooiveld 7, 6525 ED
Nijmegen, The Netherlands
| | - Jonathan Martens
- FELIX Laboratory, Institute of Molecules and
Materials, Radboud University, Toernooiveld 7, 6525 ED
Nijmegen, The Netherlands
| | - Giel Berden
- FELIX Laboratory, Institute of Molecules and
Materials, Radboud University, Toernooiveld 7, 6525 ED
Nijmegen, The Netherlands
| | - P. B. Armentrout
- Department of Chemistry, University of
Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112,
United States
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12
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Boles GC, Stevenson BC, Hightower RL, Berden G, Oomens J, Armentrout PB. Zinc and cadmium complexation of L-methionine: An infrared multiple photon dissociation spectroscopy and theoretical study. JOURNAL OF MASS SPECTROMETRY : JMS 2020; 56:e4580. [PMID: 32677757 DOI: 10.1002/jms.4580] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 05/14/2020] [Accepted: 05/20/2020] [Indexed: 06/11/2023]
Abstract
Methionine (Met) cationized with Zn2+ , forming Zn (Met-H)+ (ACN) where ACN = acetonitrile, Zn (Met-H)+ , and ZnCl+ (Met), as well as Cd2+ , forming CdCl+ (Met), were examined by infrared multiple photon dissociation (IRMPD) action spectroscopy using light generated from the FELIX free electron laser. A series of low-energy conformers for each complex was found using quantum-chemical calculations in order to identify the structures formed experimentally. For all four complexes, spectral comparison indicated that the main binding motif observed is a charge solvated, tridentate structure where the metal center binds to the backbone amino group nitrogen, backbone carbonyl oxygen (where the carboxylic acid is deprotonated in two of the Zn2+ complexes), and side-chain sulfur. For all species, the predicted ground structures reproduce the experimental spectra well, although low-lying conformers characterized by similar binding motifs may also contribute in each system. The current work provides valuable information regarding the binding interaction between Met and biologically relevant metals. Further, the comparison between the current work and previous analyses involving alkali metal cationized Met as well as cysteine (the other sulfur containing amino acid) cationized with Zn2+ and Cd2+ allows for the elucidation of important metal dependent trends associated with physiologically important metal-sulfur binding.
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Affiliation(s)
- Georgia C Boles
- Department of Chemistry, University of Utah, Salt Lake City, Utah, USA
| | | | - Randy L Hightower
- Department of Chemistry, University of Utah, Salt Lake City, Utah, USA
| | - Giel Berden
- FELIX Laboratory, Institute for Molecules and Materials, Radboud University, Nijmegen, The Netherlands
| | - Jos Oomens
- FELIX Laboratory, Institute for Molecules and Materials, Radboud University, Nijmegen, The Netherlands
- Van't Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - P B Armentrout
- Department of Chemistry, University of Utah, Salt Lake City, Utah, USA
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13
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Avilés-Moreno JR, Gámez F, Berden G, Martens J, Oomens J, Martínez-Haya B. Multipodal coordination and mobility of molecular cations inside the macrocycle valinomycin. Phys Chem Chem Phys 2020; 22:19725-19734. [DOI: 10.1039/d0cp02996c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Small cations (K+, NH4+) occupy the center of the valinomycin cavity. Bulkier cations like H4PO4+ stretch the valinomycin backbone, which adopts barrel-like and funnel-like configurations, depending on the dynamically varying position of the cation.
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Affiliation(s)
| | - Francisco Gámez
- Department of Applied Physical Chemistry
- Universidad Autónoma de Madrid
- Madrid
- Spain
| | - Giel Berden
- Radboud University
- Institute for Molecules and Materials
- FELIX Laboratory
- 6525ED Nijmegen
- The Netherlands
| | - Jonathan Martens
- Radboud University
- Institute for Molecules and Materials
- FELIX Laboratory
- 6525ED Nijmegen
- The Netherlands
| | - Jos Oomens
- Radboud University
- Institute for Molecules and Materials
- FELIX Laboratory
- 6525ED Nijmegen
- The Netherlands
| | - Bruno Martínez-Haya
- Department of Physical
- Chemical and Natural Systems
- Universidad Pablo de Olavide
- 41013 Seville
- Spain
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14
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Maitre P, Scuderi D, Corinti D, Chiavarino B, Crestoni ME, Fornarini S. Applications of Infrared Multiple Photon Dissociation (IRMPD) to the Detection of Posttranslational Modifications. Chem Rev 2019; 120:3261-3295. [PMID: 31809038 DOI: 10.1021/acs.chemrev.9b00395] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Infrared multiple photon dissociation (IRMPD) spectroscopy allows for the derivation of the vibrational fingerprint of molecular ions under tandem mass spectrometry (MS/MS) conditions. It provides insight into the nature and localization of posttranslational modifications (PTMs) affecting single amino acids and peptides. IRMPD spectroscopy, which takes advantage of the high sensitivity and resolution of MS/MS, relies on a wavelength specific fragmentation process occurring on resonance with an IR active vibrational mode of the sampled species and is well suited to reveal the presence of a PTM and its impact in the molecular environment. IRMPD spectroscopy is clearly not a proteomics tool. It is rather a valuable source of information for fixed wavelength IRMPD exploited in dissociation protocols of peptides and proteins. Indeed, from the large variety of model PTM containing amino acids and peptides which have been characterized by IRMPD spectroscopy, specific signatures of PTMs such as phosphorylation or sulfonation can be derived. High throughput workflows relying on the selective fragmentation of modified peptides within a complex mixture have thus been proposed. Sequential fragmentations can be observed upon IR activation, which do not only give rise to rich fragmentation patterns but also overcome low mass cutoff limitations in ion trap mass analyzers. Laser-based vibrational spectroscopy of mass-selected ions holding various PTMs is an increasingly expanding field both in the variety of chemical issues coped with and in the technological advancements and implementations.
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Affiliation(s)
- Philippe Maitre
- Laboratoire de Chimie Physique (UMR8000), Université Paris-Sud, CNRS, Université Paris Saclay, 91405, Orsay, France
| | - Debora Scuderi
- Laboratoire de Chimie Physique (UMR8000), Université Paris-Sud, CNRS, Université Paris Saclay, 91405, Orsay, France
| | - Davide Corinti
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma "La Sapienza", I-00185 Roma, Italy
| | - Barbara Chiavarino
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma "La Sapienza", I-00185 Roma, Italy
| | - Maria Elisa Crestoni
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma "La Sapienza", I-00185 Roma, Italy
| | - Simonetta Fornarini
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma "La Sapienza", I-00185 Roma, Italy
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15
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He CC, Hamlow LA, Zhu Y, Nei YW, Fan L, McNary CP, Maître P, Steinmetz V, Schindler B, Compagnon I, Armentrout PB, Rodgers MT. Structural and Energetic Effects of O2'-Ribose Methylation of Protonated Pyrimidine Nucleosides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:2318-2334. [PMID: 31435890 DOI: 10.1007/s13361-019-02300-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 07/18/2019] [Accepted: 07/23/2019] [Indexed: 06/10/2023]
Abstract
The 2'-substituents distinguish DNA from RNA nucleosides. 2'-O-methylation occurs naturally in RNA and plays important roles in biological processes. Such 2'-modifications may alter the hydrogen-bonding interactions of the nucleoside and thus may affect the conformations of the nucleoside in an RNA chain. Structures of the protonated 2'-O-methylated pyrimidine nucleosides were examined by infrared multiple photon dissociation (IRMPD) action spectroscopy, assisted by electronic structure calculations. The glycosidic bond stabilities of the protonated 2'-O-methylated pyrimidine nucleosides, [Nuom+H]+, were also examined and compared to their DNA and RNA nucleoside analogues via energy-resolved collision-induced dissociation (ER-CID). The preferred sites of protonation of the 2'-O-methylated pyrimidine nucleosides parallel their canonical DNA and RNA nucleoside analogues, [dNuo+H]+ and [Nuo+H]+, yet their nucleobase orientation and sugar puckering differ. The glycosidic bond stabilities of the protonated pyrimidine nucleosides follow the order: [dNuo+H]+ < [Nuo+H]+ < [Nuom+H]+. The slightly altered structures help explain the stabilization induced by 2'-O-methylation of the pyrimidine nucleosides.
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Affiliation(s)
- C C He
- Department of Chemistry, Wayne State University, Detroit, MI, 48202, USA
| | - L A Hamlow
- Department of Chemistry, Wayne State University, Detroit, MI, 48202, USA
| | - Y Zhu
- Department of Chemistry, Wayne State University, Detroit, MI, 48202, USA
| | - Y-W Nei
- Department of Chemistry, Wayne State University, Detroit, MI, 48202, USA
| | - L Fan
- Department of Chemistry, Wayne State University, Detroit, MI, 48202, USA
| | - C P McNary
- Department of Chemistry, University of Utah, Salt Lake City, UT, 84112, USA
| | - P Maître
- Laboratoire de Chimie Physique (UMR8000), Université Paris-Sud, CNRS, Université Paris Saclay, 91405, Orsay, France
| | - V Steinmetz
- Laboratoire de Chimie Physique (UMR8000), Université Paris-Sud, CNRS, Université Paris Saclay, 91405, Orsay, France
| | - B Schindler
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, F-69622, Villeurbanne, France
| | - I Compagnon
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, F-69622, Villeurbanne, France
| | - P B Armentrout
- Department of Chemistry, University of Utah, Salt Lake City, UT, 84112, USA
| | - M T Rodgers
- Department of Chemistry, Wayne State University, Detroit, MI, 48202, USA.
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16
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Martens J, van Outersterp RE, Vreeken RJ, Cuyckens F, Coene KLM, Engelke UF, Kluijtmans LAJ, Wevers RA, Buydens LMC, Redlich B, Berden G, Oomens J. Infrared ion spectroscopy: New opportunities for small-molecule identification in mass spectrometry - A tutorial perspective. Anal Chim Acta 2019; 1093:1-15. [PMID: 31735202 DOI: 10.1016/j.aca.2019.10.043] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 10/19/2019] [Accepted: 10/21/2019] [Indexed: 01/21/2023]
Abstract
Combining the individual analytical strengths of mass spectrometry and infrared spectroscopy, infrared ion spectroscopy is increasingly recognized as a powerful tool for small-molecule identification in a wide range of analytical applications. Mass spectrometry is itself a leading analytical technique for small-molecule identification on the merit of its outstanding sensitivity, selectivity and versatility. The foremost shortcoming of the technique, however, is its limited ability to directly probe molecular structure, especially when contrasted against spectroscopic techniques. In infrared ion spectroscopy, infrared vibrational spectra are recorded for mass-isolated ions and provide a signature that can be matched to reference spectra, either measured from standards or predicted using quantum-chemical calculations. Here we present an overview of the potential for this technique to develop into a versatile analytical method for identifying molecular structures in mass spectrometry-based analytical workflows. In this tutorial perspective, we introduce the reader to the technique of infrared ion spectroscopy and highlight a selection of recent experimental advances and applications in current analytical challenges, in particular in the field of untargeted metabolomics. We report on the coupling of infrared ion spectroscopy with liquid chromatography and present experiments that serve as proof-of-principle examples of strategies to address outstanding challenges.
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Affiliation(s)
- Jonathan Martens
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525 ED, Nijmegen, the Netherlands.
| | - Rianne E van Outersterp
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525 ED, Nijmegen, the Netherlands
| | - Rob J Vreeken
- Drug Metabolism & Pharmacokinetics, Janssen R&D, Beerse, Belgium
| | - Filip Cuyckens
- Drug Metabolism & Pharmacokinetics, Janssen R&D, Beerse, Belgium
| | - Karlien L M Coene
- Department of Laboratory Medicine, Translational Metabolic Laboratory, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Udo F Engelke
- Department of Laboratory Medicine, Translational Metabolic Laboratory, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Leo A J Kluijtmans
- Department of Laboratory Medicine, Translational Metabolic Laboratory, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Ron A Wevers
- Department of Laboratory Medicine, Translational Metabolic Laboratory, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Lutgarde M C Buydens
- Radboud University, Institute for Molecules and Materials, Chemometrics, Heyendaalseweg 135, 6525AJ, Nijmegen, the Netherlands
| | - Britta Redlich
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525 ED, Nijmegen, the Netherlands
| | - Giel Berden
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525 ED, Nijmegen, the Netherlands
| | - Jos Oomens
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525 ED, Nijmegen, the Netherlands; van't Hoff Institute for Molecular Sciences, University of Amsterdam, 1098XH, Amsterdam, Science Park 908, the Netherlands.
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17
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Boles GC, Hightower RL, Berden G, Oomens J, Armentrout PB. Zinc and Cadmium Complexation of l-Threonine: An Infrared Multiple Photon Dissociation Spectroscopy and Theoretical Study. J Phys Chem B 2019; 123:9343-9354. [DOI: 10.1021/acs.jpcb.9b08184] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Georgia C. Boles
- Department of Chemistry, University of Utah, 315 South 1400 East Room 2020, Salt Lake City, Utah 84112, United States
| | - Randy L. Hightower
- Department of Chemistry, University of Utah, 315 South 1400 East Room 2020, Salt Lake City, Utah 84112, United States
| | - Giel Berden
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, NL-6525 ED Nijmegen, The Netherlands
| | - Jos Oomens
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, NL-6525 ED Nijmegen, The Netherlands
- van’t Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, NL-1098 XH Amsterdam, The Netherlands
| | - P. B. Armentrout
- Department of Chemistry, University of Utah, 315 South 1400 East Room 2020, Salt Lake City, Utah 84112, United States
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18
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Munshi MU, Martens J, Berden G, Oomens J. Gas-Phase Infrared Ion Spectroscopy Characterization of Cu(II/I)Cyclam and Cu(II/I)2,2'-Bipyridine Redox Pairs. J Phys Chem A 2019; 123:4149-4157. [PMID: 31021091 PMCID: PMC6526468 DOI: 10.1021/acs.jpca.9b00793] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
![]()
We report the fingerprint
IR spectra of mass-isolated gaseous coordination
complexes of 2,2′-bipyridine (bpy) and 1,4,8,11-tetra-azacyclotetradecane
(cyclam) with a copper ion in its I and II oxidation states. Experiments
are carried out in a quadrupole ion trap (QIT) mass spectrometer coupled
to the FELIX infrared free-electron laser. Dications are prepared
using electrospray ionization (ESI), while monocations are generated
by charge reduction of the dication using electron transfer-reduction
(ETR) in the QIT. Interestingly, [Cu(bpy)2]+ can also be generated directly using ESI, so that its geometries
as produced from ETR and ESI can be compared. The effects of charge
reduction on the IR spectra are investigated by comparing the experimental
spectra with the IR spectra modeled by density functional theory.
Reduction of Cu(II) to the closed-shell Cu(I) ion retains the square-planar
geometry of the Cu–cyclam complex. In contrast, for the bis–bpy
complex with Cu, charge reduction induces a conversion from a near-square-planar
to a tetrahedral geometry. The geometry of [Cu(bpy)2]+ is identical to that of the complex generated directly from
ESI as a native structure, which indicates that the ETR product ion
thermalizes. For [Cu(cyclam)]+, however, the square-planar
geometry of the 2+ complex is retained upon charge reduction, although
a (distorted) tetrahedral geometry was predicted to be lower in energy.
These differences are attributed to different barriers to rearrangement.
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Affiliation(s)
- Musleh Uddin Munshi
- Radboud University , Institute for Molecules and Materials, FELIX Laboratory , Toernooiveld 7 , 6525 ED Nijmegen , The Netherlands
| | - Jonathan Martens
- Radboud University , Institute for Molecules and Materials, FELIX Laboratory , Toernooiveld 7 , 6525 ED Nijmegen , The Netherlands
| | - Giel Berden
- Radboud University , Institute for Molecules and Materials, FELIX Laboratory , Toernooiveld 7 , 6525 ED Nijmegen , The Netherlands
| | - Jos Oomens
- Radboud University , Institute for Molecules and Materials, FELIX Laboratory , Toernooiveld 7 , 6525 ED Nijmegen , The Netherlands.,University of Amsterdam , Science Park 904 , 1098 XH Amsterdam , The Netherlands
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19
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Hamlow LA, Devereaux ZJ, Roy HA, Cunningham NA, Berden G, Oomens J, Rodgers MT. Impact of the 2'- and 3'-Sugar Hydroxyl Moieties on Gas-Phase Nucleoside Structure. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:832-845. [PMID: 30850972 DOI: 10.1007/s13361-019-02155-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 02/12/2019] [Accepted: 02/12/2019] [Indexed: 06/09/2023]
Abstract
Modified nucleosides have been an important target for pharmaceutical development for the treatment of cancer, herpes simplex virus, and the human immunodeficiency virus (HIV). Amongst these nucleoside analogues, those based on 2',3'-dideoxyribose sugars are quite common, particularly in anti-HIV applications. The gas-phase structures of several protonated 2',3'-dideoxyribose nucleosides are examined in this work and compared with those of the analogous protonated DNA, RNA, and arabinose nucleosides to elucidate the influence of the 2'- and combined 2',3'-hydroxyl groups on intrinsic structure. Infrared multiple photon dissociation (IRMPD) action spectra are collected for the protonated 2',3'-dideoxy forms of adenosine, guanosine, cytidine, thymidine and uridine, [ddAdo+H]+, [ddGuo+H]+, [ddCyd+H]+, [ddThd+H]+, and [ddUrd+H]+, in the IR fingerprint and hydrogen-stretching regions. Molecular mechanics conformational searching followed by electronic structure calculations generates low-energy conformers of the protonated 2',3'-dideoxynucleosides and corresponding predicted linear IR spectra to facilitate interpretation of the measured IRMPD action spectra. These experimental IRMPD spectra and theoretical calculations indicate that the absence of the 2'- and 3'-hydroxyls largely preserves the protonation preferences of the canonical forms. The spectra and calculated structures indicate a slight preference for C3'-endo sugar puckering. The presence of the 3'- and further 2'-hydroxyl increases the available intramolecular hydrogen-bonding opportunities and shifts the sugar puckering modes for all nucleosides but the guanosine analogues to a slight preference for C2'-endo over C3'-endo. Graphical Abstract.
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Affiliation(s)
- L A Hamlow
- Department of Chemistry, Wayne State University, 5101 Cass Ave, Detroit, MI, 48202, USA
| | - Zachary J Devereaux
- Department of Chemistry, Wayne State University, 5101 Cass Ave, Detroit, MI, 48202, USA
| | - H A Roy
- Department of Chemistry, Wayne State University, 5101 Cass Ave, Detroit, MI, 48202, USA
| | - N A Cunningham
- Department of Chemistry, Wayne State University, 5101 Cass Ave, Detroit, MI, 48202, USA
| | - G Berden
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7c, 6525ED, Nijmegen, The Netherlands
| | - J Oomens
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7c, 6525ED, Nijmegen, The Netherlands
| | - M T Rodgers
- Department of Chemistry, Wayne State University, 5101 Cass Ave, Detroit, MI, 48202, USA.
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Piatkivskyi A, Lau JKC, Berden G, Oomens J, Hopkinson AC, Siu KM, Ryzhov V. Hydrogen atom transfer in the radical cations of tryptophan-containing peptides AW and WA studied by mass spectrometry, infrared multiple-photon dissociation spectroscopy, and theoretical calculations. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2019; 25:112-121. [PMID: 30282467 DOI: 10.1177/1469066718802547] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Two types of radical cations of tryptophan-the π-radical cation and the protonated tryptophan-N radical-have been studied in dipeptides AW and WA. The π-radical cation produced by removal of an electron during collision-induced dissociation of a ternary Cu(II) complex was only observed for the AW peptide. In the case of WA, only the ion corresponding to the loss of ammonia, [WA-NH3] •+, was observed from the copper complex. Both protonated tryptophan-N radicals were produced by N-nitrosylation of the neutral peptides followed by transfer to the gas phase via electrospray ionization and subsequent collision-induced dissociation. The regiospecifically formed N• species were characterized by infrared multiple-photon dissociation spectroscopy which revealed that the WA tryptophan-N• radical remains the nitrogen radical, while the AW nitrogen radical rearranges into the π-radical cation. These findings are supported by the density functional theory calculations that suggest a relatively high barrier for the radical rearrangement (N• to π) in WA (156.3 kJ mol-1) and a very low barrier in AW (6.1 kJ mol-1). The facile hydrogen atom migration in the AW system is also supported by the collision-induced dissociation of the tryptophan-N radical species that produces fragments characteristic of the tryptophan π-radical cation. Gas-phase ion-molecule reactions with n-propyl thiol have also been used to differentiate between the π-radical cations (react by hydrogen abstraction) and the tryptophan-N• species (unreactive) of AW.
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Affiliation(s)
- Andrii Piatkivskyi
- 1 Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL, USA
| | - Justin Kai-Chi Lau
- 2 Department of Chemistry and Centre for Research in Mass Spectrometry, York University, Ontario, Canada
- 3 Department of Chemistry and Biochemistry, University of Windsor, Ontario, Canada
| | - Giel Berden
- 4 Institute for Molecules and Materials, FELIX Laboratory Radboud University, ED Nijmegen, The Netherlands
| | - Jos Oomens
- 4 Institute for Molecules and Materials, FELIX Laboratory Radboud University, ED Nijmegen, The Netherlands
| | - Alan C Hopkinson
- 2 Department of Chemistry and Centre for Research in Mass Spectrometry, York University, Ontario, Canada
| | - Kw Michael Siu
- 2 Department of Chemistry and Centre for Research in Mass Spectrometry, York University, Ontario, Canada
- 3 Department of Chemistry and Biochemistry, University of Windsor, Ontario, Canada
| | - Victor Ryzhov
- 1 Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL, USA
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21
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Perez E, Corcovilos TA, Gibson JK, Martens J, Berden G, Oomens J, Van Stipdonk MJ. Isotope labeling and infrared multiple-photon photodissociation investigation of product ions generated by dissociation of [ZnNO 3(CH 3OH) 2] +: Conversion of methanol to formaldehyde. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2019; 25:58-72. [PMID: 30773924 DOI: 10.1177/1469066718809881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Electrospray ionization was used to generate species such as [ZnNO3(CH3OH)2]+ from Zn(NO3)2•XH2O dissolved in a mixture of CH3OH and H2O. Collision-induced dissociation of [ZnNO3(CH3OH)2]+ causes elimination of CH3OH to form [ZnNO3(CH3OH)]+. Subsequent collision-induced dissociation of [ZnNO3(CH3OH)]+ causes elimination of 47 mass units (u), consistent with ejection of HNO2. The neutral loss shifts to 48 u for collision-induced dissociation of [ZnNO3(CD3OH)]+, demonstrating the ejection of HNO2 involves intra-complex transfer of H from the methyl group methanol ligand. Subsequent collision-induced dissociation causes the elimination of 30 u (32 u for the complex with CD3OH), suggesting the elimination of formaldehyde (CH2 = O). The product ion is [ZnOH]+. Collision-induced dissociation of a precursor complex created using CH3-18OH shows the isotope label is retained in CH2 = O. Density functional theory calculations suggested that the "rearranged" product, ZnOH with bound HNO2 and formaldehyde is significantly lower in energy than ZnNO3 with bound methanol. We therefore used infrared multiple-photon photodissociation spectroscopy to determine the structures of both [ZnNO3(CH3OH)2]+ and [ZnNO3(CH3OH)]+. The infrared spectra clearly show that both ions contain intact nitrate and methanol ligands, which suggests that rearrangement occurs during collision-induced dissociation of [ZnNO3(CH3OH)]+. Based on the density functional theory calculations, we propose that transfer of H, from the methyl group of the CH3OH ligand to nitrate, occurs in concert with the formation of a Zn-C bond. After dissociation to release HNO2, the product rearranges with the insertion of the remaining O atom into the Zn-C bond. Subsequent C-O bond cleavage, with H transfer, produces an ion-molecule complex composed of [ZnOH]+ and O = CH2.
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Affiliation(s)
- Evan Perez
- 1 Department of Chemistry and Biochemistry, Duquesne University, Pittsburgh, PA, USA
| | | | - John K Gibson
- 3 Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jonathan Martens
- 4 Institute for Molecules and Materials, FELIX Facility, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Giel Berden
- 4 Institute for Molecules and Materials, FELIX Facility, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Jos Oomens
- 4 Institute for Molecules and Materials, FELIX Facility, Radboud University Nijmegen, Nijmegen, The Netherlands
- 5 van't Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam, The Netherlands
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22
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Owen CJ, Boles GC, Berden G, Oomens J, Armentrout PB. Experimental and theoretical investigations of infrared multiple photon dissociation spectra of lysine complexes with Zn 2+ and Cd 2. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2019; 25:97-111. [PMID: 30526028 DOI: 10.1177/1469066718792902] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The gas-phase structures of zinc and cadmium complexes of lysine (Lys) are investigated via a combination of infrared multiple photon dissociation action spectroscopy and ab initio quantum chemical calculations. In order to unambiguously identify the experimentally observed species, [Zn(Lys-H)]+ and CdCl+(Lys), the action spectra were compared to linear absorption spectra calculated at the B3LYP level of theory, using 6-311+G(d,p) and def2-TVZP basis sets for the zinc and cadmium systems, respectively. Single point energies were also calculated at the B3LYP, B3P86, MP2, and B3LYP-GD3BJ (accounting for empirical dispersion) levels of theory using larger basis sets. Identification of the experimentally formed isomers is possible through good agreement between infrared multiple photon dissociation action spectra and the theoretically predicted spectra. The [Zn(Lys-H)]+ complex adopts a tridentate orientation involving the amino acid backbone amine and deprotonated carboxylic acid groups as well as the side-chain amine group, [Nα,CO-,Nɛ]. The CdCl+(Lys) complex similarly adopts a tridentate chelation involving the amino acid backbone amine and carbonyl groups, as well as the side-chain amine group, [Nα,CO,Nɛ]. In both cases, the identified complexes are the lowest energy gas-phase structures at all levels of theory.
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Affiliation(s)
- Cameron J Owen
- 1 Department of Chemistry, University of Utah, Salt Lake City, USA
| | - Georgia C Boles
- 1 Department of Chemistry, University of Utah, Salt Lake City, USA
| | - Giel Berden
- 2 FELIX Laboratory, Institute for Molecules and Materials, Radboud University, Nijmegen, The Netherlands
| | - Jos Oomens
- 2 FELIX Laboratory, Institute for Molecules and Materials, Radboud University, Nijmegen, The Netherlands
- 3 Van't Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - P B Armentrout
- 1 Department of Chemistry, University of Utah, Salt Lake City, USA
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23
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Kempkes LJM, Martens J, Berden G, Oomens J. w-Type ions formed by electron transfer dissociation of Cys-containing peptides investigated by infrared ion spectroscopy. JOURNAL OF MASS SPECTROMETRY : JMS 2018; 53:1207-1213. [PMID: 30281881 PMCID: PMC6283004 DOI: 10.1002/jms.4298] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Revised: 08/24/2018] [Accepted: 09/26/2018] [Indexed: 06/08/2023]
Abstract
In mass spectrometry-based peptide sequencing, electron transfer dissociation (ETD) and electron capture dissociation (ECD) have become well-established fragmentation methods complementary to collision-induced dissociation. The dominant fragmentation pathways during ETD and ECD primarily involve the formation of c- and z• -type ions by cleavage of the peptide backbone at the N─Cα bond, although neutral losses from amino acid side chains have also been observed. Residue-specific neutral side chain losses provide useful information when conducting database searching and de novo sequencing. Here, we use a combination of infrared ion spectroscopy and quantum-chemical calculations to assign the structures of two ETD-generated w-type fragment ions. These ions are spontaneously formed from ETD-generated z• -type fragments by neutral loss of 33 Da in peptides containing a cysteine residue. Analysis of the infrared ion spectra confirms that these z• -ions expel a thiol radical (SH• ) and that a vinyl C═C group is formed at the cleavage site. z• -type fragments containing a Cys residue but not at the cleavage site do not spontaneously expel a thiol radical, but only upon additional collisional activation after ETD.
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Affiliation(s)
- Lisanne J. M. Kempkes
- Radboud University, Institute for Molecules and Materials, FELIX LaboratoryNijmegenThe Netherlands
| | - Jonathan Martens
- Radboud University, Institute for Molecules and Materials, FELIX LaboratoryNijmegenThe Netherlands
| | - Giel Berden
- Radboud University, Institute for Molecules and Materials, FELIX LaboratoryNijmegenThe Netherlands
| | - Jos Oomens
- Radboud University, Institute for Molecules and Materials, FELIX LaboratoryNijmegenThe Netherlands
- Van't Hoff Institute for Molecular SciencesUniversity of AmsterdamAmsterdamThe Netherlands
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24
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Kempkes LM, Martens J, Berden G, Oomens J. Spectroscopic Characterization of an Extensive Set of c-Type Peptide Fragment Ions Formed by Electron Transfer Dissociation Suggests Exclusive Formation of Amide Isomers. J Phys Chem Lett 2018; 9:6404-6411. [PMID: 30343579 PMCID: PMC6240889 DOI: 10.1021/acs.jpclett.8b02850] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2018] [Accepted: 10/18/2018] [Indexed: 06/08/2023]
Abstract
Electron attachment dissociation (electron capture dissociation (ECD) and electron transfer dissociation (ETD)) applied to gaseous multiply protonated peptides leads predominantly to backbone N-Cα bond cleavages and the formation of c- and z-type fragment ions. The mechanisms involved in the formation of these ions have been the subject of much discussion. Here, we determine the molecular structures of an extensive set of c-type ions produced by ETD using infrared ion spectroscopy. Nine c3- and c4-ions are investigated to establish their C-terminal structure as either enol-imine or amide isomers by comparison of the experimental infrared spectra with quantum-chemically predicted spectra for both structural variants. The spectra suggest that all c-ions investigated possess an amide structure; the absence of the NH bending mode at approximately 1000-1200 cm-1 serves as an important diagnostic feature.
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Affiliation(s)
- Lisanne
J. M. Kempkes
- FELIX
Laboratory, Institute for Molecules and Materials, Radboud University, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
| | - Jonathan Martens
- FELIX
Laboratory, Institute for Molecules and Materials, Radboud University, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
| | - Giel Berden
- FELIX
Laboratory, Institute for Molecules and Materials, Radboud University, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
| | - Jos Oomens
- FELIX
Laboratory, Institute for Molecules and Materials, Radboud University, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
- Van’t
Hoff Institute for Molecular Sciences, University
of Amsterdam, Science
Park 904, 1098 XH Amsterdam, The Netherlands
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25
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Hamlow LA, Zhu Y, Devereaux ZJ, Cunningham NA, Berden G, Oomens J, Rodgers MT. Modified Quadrupole Ion Trap Mass Spectrometer for Infrared Ion Spectroscopy: Application to Protonated Thiated Uridines. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:2125-2137. [PMID: 30136214 DOI: 10.1007/s13361-018-2047-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 07/31/2018] [Accepted: 08/01/2018] [Indexed: 05/17/2023]
Abstract
Modifications to a Paul-type quadrupole ion trap mass spectrometer providing optical access to the trapped ion cloud as well as hardware and software for coupling to a table-top IR optical parametric oscillator laser (OPO) are detailed. Critical experimental parameters for infrared multiple photon dissociation (IRMPD) on this instrument are characterized. IRMPD action spectra, collected in the hydrogen-stretching region with this instrument, complemented by spectra in the IR fingerprint region acquired at the FELIX facility, are employed to characterize the structures of the protonated forms of 2-thiouridine, [s2Urd+H]+, and 4-thiouridine, [s4Urd+H]+. The measured spectra are compared with predicted linear IR spectra calculated at the B3LYP/6-311+G(d,p) level of theory to determine the conformers populated in the experiments. This comparison indicates that thiation at the 2- or 4-positions shifts the protonation preference between the 2,4-H tautomer and 4-protonation in opposite directions versus canonical uridine, which displays a roughly equal preference for the 2,4-H tautomer and O4 protonation. As found for canonical uridine, protonation leads to a mixture of conformers exhibiting C2'-endo and C3'-endo sugar puckering with an anti nucleobase orientation being populated for both 2- and 4-thiated uridine. Graphical Abstract ᅟ.
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Affiliation(s)
- L A Hamlow
- Department of Chemistry, Wayne State University, 5101 Cass Ave., Detroit, MI, 48202, USA
| | - Y Zhu
- Department of Chemistry, Wayne State University, 5101 Cass Ave., Detroit, MI, 48202, USA
| | - Zachary J Devereaux
- Department of Chemistry, Wayne State University, 5101 Cass Ave., Detroit, MI, 48202, USA
| | - N A Cunningham
- Department of Chemistry, Wayne State University, 5101 Cass Ave., Detroit, MI, 48202, USA
| | - G Berden
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7c, 6525 ED, Nijmegen, The Netherlands
| | - J Oomens
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7c, 6525 ED, Nijmegen, The Netherlands
| | - M T Rodgers
- Department of Chemistry, Wayne State University, 5101 Cass Ave., Detroit, MI, 48202, USA.
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26
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He CC, Hamlow LA, Devereaux ZJ, Zhu Y, Nei YW, Fan L, McNary CP, Maitre P, Steinmetz V, Schindler B, Compagnon I, Armentrout PB, Rodgers MT. Structural and Energetic Effects of O2'-Ribose Methylation of Protonated Purine Nucleosides. J Phys Chem B 2018; 122:9147-9160. [PMID: 30203656 DOI: 10.1021/acs.jpcb.8b07687] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The chemical difference between DNA and RNA nucleosides is their 2'-hydrogen versus 2'-hydroxyl substituents. Modification of the ribosyl moiety at the 2'-position and 2'-O-methylation in particular, is common among natural post-transcriptional modifications of RNA. 2'-Modification may alter the electronic properties and hydrogen-bonding characteristics of the nucleoside and thus may lead to enhanced stabilization or malfunction. The structures and relative glycosidic bond stabilities of the protonated forms of the 2'-O-methylated purine nucleosides, 2'-O-methyladenosine (Adom) and 2'-O-methylguanosine (Guom), were examined using two complementary tandem mass spectrometry approaches, infrared multiple photon dissociation action spectroscopy and energy-resolved collision-induced dissociation. Theoretical calculations were also performed to predict the structures and relative stabilities of stable low-energy conformations of the protonated forms of the 2'-O-methylated purine nucleosides and their infrared spectra in the gas phase. Low-energy conformations highly parallel to those found for the protonated forms of the canonical DNA and RNA purine nucleosides are also found for the protonated 2'-O-methylated purine nucleosides. Importantly, the preferred site of protonation, nucleobase orientation, and sugar puckering are preserved among the DNA, RNA, and 2'-O-methylated variants of the protonated purine nucleosides. The 2'-substituent does however influence hydrogen-bond stabilization as the 2'-O-methyl and 2'-hydroxyl substituents enable a hydrogen-bonding interaction between the 2'- and 3'-substituents, whereas a 2'-hydrogen atom does not. Further, 2'-O-methylation reduces the number of stable low-energy hydrogen-bonded conformations possible and importantly inverts the preferred polarity of this interaction versus that of the RNA analogues. Trends in the CID50% values extracted from survival yield analyses of the 2'-O-methylated and canonical DNA and RNA forms of the protonated purine nucleosides are employed to elucidate their relative glycosidic bond stabilities. The glycosidic bond stability of Adom is found to exceed that of its DNA and RNA analogues. The glycosidic bond stability of Guom is also found to exceed that of its DNA analogue; however, this modification weakens this bond relative to its RNA counterpart. The glycosidic bond stability of the protonated purine nucleosides appears to be correlated with the hydrogen-bond stabilization of the sugar moiety.
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Affiliation(s)
- C C He
- Department of Chemistry , Wayne State University , Detroit , Michigan 48202 , United States
| | - L A Hamlow
- Department of Chemistry , Wayne State University , Detroit , Michigan 48202 , United States
| | - Zachary J Devereaux
- Department of Chemistry , Wayne State University , Detroit , Michigan 48202 , United States
| | - Y Zhu
- Department of Chemistry , Wayne State University , Detroit , Michigan 48202 , United States
| | - Y-W Nei
- Department of Chemistry , Wayne State University , Detroit , Michigan 48202 , United States
| | - L Fan
- Department of Chemistry , Wayne State University , Detroit , Michigan 48202 , United States
| | - C P McNary
- Department of Chemistry , University of Utah , Salt Lake City , Utah 84112 , United States
| | - P Maitre
- Laboratoire de Chimie Physique (UMR8000), CNRS, Université Paris-Sud, Université Paris-Saclay , 91405 Orsay , France
| | - V Steinmetz
- Laboratoire de Chimie Physique (UMR8000), CNRS, Université Paris-Sud, Université Paris-Saclay , 91405 Orsay , France
| | - B Schindler
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière , F-69622 Villeurbanne , France
| | - I Compagnon
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière , F-69622 Villeurbanne , France
| | - P B Armentrout
- Department of Chemistry , University of Utah , Salt Lake City , Utah 84112 , United States
| | - M T Rodgers
- Department of Chemistry , Wayne State University , Detroit , Michigan 48202 , United States
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27
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Avilés-Moreno JR, Berden G, Oomens J, Martínez-Haya B. Complexes of Crown Ether Macrocycles with Methyl Guanidinium: Insights into the Capture of Charge in Peptides. Chemphyschem 2018; 19:2169-2175. [PMID: 29944200 DOI: 10.1002/cphc.201800596] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Indexed: 11/08/2022]
Abstract
Crown ethers are well known as modulating agents of protein function and interactions. The action of crown ethers is driven by an alteration of the charged moieties of proteins through the capping of cationic amino acid side chains. This study evaluates the conformational features involved in the binding of crown ethers to the side chain of arginine. For this purpose, isolated complexes of methyl guanidinium with 12-crown-4 and 18-crown-6 are characterized with infrared action vibrational spectroscopy and quantum chemical computations. The conformational landscapes of the two complexes comprise an extensive ensemble of conformations close in energy. In the 12-crown-4 complex, the crown ether has the plane of its backbone approximately perpendicular to that of the guanidinium moiety and coordinates to two or three of its NHδ+ bonds. In the 18-crown-6 complex, the crown ether backbone is partially folded and tilted with respect to guanidinium and fixes its position in order to facilitate up to a four-fold coordination in the complex. The access of the complexes to multiple conformations leads to broad band structures in the N-H stretching region of their vibrational spectra.
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Affiliation(s)
- Juan Ramón Avilés-Moreno
- Department of Physical, Chemical and Natural Systems, Universidad Pablo de Olavide, 41013, Seville, Spain
| | - Giel Berden
- Radboud University, Institute for Molecules and Materials FELIX Laboratory, Toernooiveld 7c, 6525ED, Nijmegen, The Netherlands
| | - Jos Oomens
- Radboud University, Institute for Molecules and Materials FELIX Laboratory, Toernooiveld 7c, 6525ED, Nijmegen, The Netherlands
| | - Bruno Martínez-Haya
- Department of Physical, Chemical and Natural Systems, Universidad Pablo de Olavide, 41013, Seville, Spain
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28
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Iacobucci C, Reale S, Aschi M, Oomens J, Berden G, De Angelis F. An Unprecedented Retro-Mumm Rearrangement Revealed by ESI-MS/MS, IRMPD Spectroscopy, and DFT Calculations. Chemistry 2018. [DOI: 10.1002/chem.201800347] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Claudio Iacobucci
- Current address: Institute of Pharmacy; Martin Luther University Halle-Wittenberg; Wolfgang-Langenbeck-Strasse 4 06120 Halle (Saale) Germany
- Dipartimento di Scienze Fisiche e Chimiche; Università degli Studi dell'Aquila; Via Vetoio, Coppito 67100 L'Aquila Italy
| | - Samantha Reale
- Dipartimento di Scienze Fisiche e Chimiche; Università degli Studi dell'Aquila; Via Vetoio, Coppito 67100 L'Aquila Italy
| | - Massimiliano Aschi
- Dipartimento di Scienze Fisiche e Chimiche; Università degli Studi dell'Aquila; Via Vetoio, Coppito 67100 L'Aquila Italy
| | - Jos Oomens
- Radboud University Nijmegen; Institute for Molecules and Materials, FELIX Laboratory; Toernooiveld 7c 6525 ED Nijmegen The Netherlands
| | - Giel Berden
- Radboud University Nijmegen; Institute for Molecules and Materials, FELIX Laboratory; Toernooiveld 7c 6525 ED Nijmegen The Netherlands
| | - Francesco De Angelis
- Dipartimento di Scienze Fisiche e Chimiche; Università degli Studi dell'Aquila; Via Vetoio, Coppito 67100 L'Aquila Italy
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29
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Tóbiás R, Császár AG, Gyevi-Nagy L, Tasi G. Definitive thermochemistry and kinetics of the interconversions among conformers of n-butane and n-pentane. J Comput Chem 2018; 39:424-437. [PMID: 29239472 DOI: 10.1002/jcc.25130] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 10/27/2017] [Accepted: 10/31/2017] [Indexed: 11/09/2022]
Abstract
The focal-point analysis (FPA) technique is used for the definitive characterization of conformational interconversion parameters, including activation energy barriers, activation free energies, and kinetic rate coefficients at 298 K, of two n-alkanes, n-butane, and n-pentane, yielding the first complete analysis of their interconversion kinetics. The FPA implementation developed in this study is based on geometry optimizations and harmonic frequency computations carried out with density functional theory methods and single-point energy computations up to the CCSD(T) level of electronic structure theory using atom-centered Gaussian basis sets as large as cc-pV5Z. The anharmonic vibrational computations are carried out, at the MP2/6-31G* level of theory. Reflecting the convergence behavior of the Gibbs free-energy terms and the interconversion parameters, well-defined uncertainties, mostly neglected in previous theoretical studies, are provided. Finally, the effect of these uncertainties on the concentrations of the conformers of n-butane and n-pentane is examined via a global Monte-Carlo uncertainty analysis. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Roland Tóbiás
- MTA-ELTE Complex Chemical Systems Research Group, H-1518 Budapest 112, P.O. Box 32, Hungary
| | - Attila G Császár
- MTA-ELTE Complex Chemical Systems Research Group, H-1518 Budapest 112, P.O. Box 32, Hungary.,Laboratory of Molecular Structure and Dynamics, Institute of Chemistry, Eötvös Loránd University, H-1117 Budapest, Pázmány Péter sétány 1/A, Hungary
| | - László Gyevi-Nagy
- Department of Physical Chemistry and Materials Science, University of Szeged, H-6720 Szeged, Rerrich B. tér 1, Hungary
| | - Gyula Tasi
- Department of Applied and Environmental Chemistry, University of Szeged, H-6720 Szeged, Rerrich B. tér 1, Hungary
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30
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Avilés-Moreno JR, Berden G, Oomens J, Martínez-Haya B. Intra-cavity proton bonding and anharmonicity in the anionophore cyclen. Phys Chem Chem Phys 2018; 20:8968-8975. [PMID: 29557457 DOI: 10.1039/c8cp00660a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Proton bonding drives the supramolecular chemistry of a broad range of materials with polar moieties. Proton delocalization and electronic charge redistribution have a profound impact on the structure of proton-bound molecular frameworks, and pose fundamental challenges to quantum chemical modelling. This study provides insights into the structural and spectral signatures of the intramolecular proton bond formed in a benchmark polyazamacrocycle anionophore (cyclen, 1,4,7,10-tetraazacyclododecane). Infrared action spectroscopy is employed to characterize the macrocycle, isolated in protonated form. In its most stable configuration, protonated cyclen adopts an open arrangement of Cs symmetry with a particularly strong NHδ+N bond across the cavity. The quantum chemical analysis of the infrared spectrum reveals intrinsic difficulties for the accurate description of the vibrational modes of the system. The reconciliation of the computational predictions with experiment demands a careful anharmonic treatment of the proton motion, which exposes the limitations of current methods. Best results are obtained with the incorporation of anharmonicity only to the fundamental modes directly related to motions of the proton. However, the full anharmonic treatment of the system fails to describe correctly the vibrations related to the macrocycle backbone. The results should serve as motivation for new developments in the modelling of proton bonded systems.
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Affiliation(s)
- Juan Ramón Avilés-Moreno
- Department of Physical, Chemical and Natural Systems, Universidad Pablo de Olavide, E-41013 Seville, Spain.
| | - Giel Berden
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7c, 6525ED Nijmegen, The Netherlands
| | - Jos Oomens
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7c, 6525ED Nijmegen, The Netherlands
| | - Bruno Martínez-Haya
- Department of Physical, Chemical and Natural Systems, Universidad Pablo de Olavide, E-41013 Seville, Spain.
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31
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Kempkes LJ, Boles GC, Martens J, Berden G, Armentrout PB, Oomens J. Deamidation of Protonated Asparagine-Valine Investigated by a Combined Spectroscopic, Guided Ion Beam, and Theoretical Study. J Phys Chem A 2018; 122:2424-2436. [PMID: 29436829 PMCID: PMC5846081 DOI: 10.1021/acs.jpca.7b12348] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 02/12/2018] [Indexed: 11/28/2022]
Abstract
Peptide deamidation of asparaginyl residues is a spontaneous post-translational modification that is believed to play a role in aging and several diseases. It is also a well-known small-molecule loss channel in the MS/MS spectra of protonated peptides. Here we investigate the deamidation reaction, as well as other decomposition pathways, of the protonated dipeptide asparagine-valine ([AsnVal + H]+) upon low-energy activation in a mass spectrometer. Using a combination of infrared ion spectroscopy, guided ion beam tandem mass spectrometry, and theoretical calculations, we have been able to identify product ion structures and determine the energetics and mechanisms for decomposition. Deamidation proceeds via ammonia loss from the asparagine side chain, initiated by a nucleophilic attack of the peptide bond oxygen on the γ-carbon of the Asn side chain. This leads to the formation of a furanone ring containing product ion characterized by a threshold energy of 129 ± 5 kJ/mol (15 kJ/mol higher in energy than dehydration of [AsnVal + H]+, the lowest energy dissociation channel available to the system). Competing formation of a succinimide ring containing product, as has been observed for protonated asparagine-glycine ([AsnGly + H]+) and asparagine-alanine ([AsnAla + H]+), was not observed here. Quantum-chemical modeling of the reaction pathways confirms these subtle differences in dissociation behavior. Measured reaction thresholds are in agreement with predicted theoretical reaction energies computed at several levels of theory.
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Affiliation(s)
- L. J.
M. Kempkes
- FELIX
Laboratory, Institute for Molecules and Materials, Radboud University, Toernooiveld 7c, 6525 ED, Nijmegen, The Netherlands
| | - G. C. Boles
- Department
of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
| | - J. Martens
- FELIX
Laboratory, Institute for Molecules and Materials, Radboud University, Toernooiveld 7c, 6525 ED, Nijmegen, The Netherlands
| | - G. Berden
- FELIX
Laboratory, Institute for Molecules and Materials, Radboud University, Toernooiveld 7c, 6525 ED, Nijmegen, The Netherlands
| | - P. B. Armentrout
- Department
of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
| | - J. Oomens
- FELIX
Laboratory, Institute for Molecules and Materials, Radboud University, Toernooiveld 7c, 6525 ED, Nijmegen, The Netherlands
- Van‘t
Hoff Institute for Molecular Sciences, University
of Amsterdam, Science
Park 904, 1098 XH Amsterdam, The Netherlands
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32
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Boles GC, Hightower RL, Coates RA, McNary CP, Berden G, Oomens J, Armentrout PB. Experimental and Theoretical Investigations of Infrared Multiple Photon Dissociation Spectra of Aspartic Acid Complexes with Zn2+ and Cd2+. J Phys Chem B 2018; 122:3836-3853. [DOI: 10.1021/acs.jpcb.8b00801] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Georgia C. Boles
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
| | - Randy L. Hightower
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
| | - Rebecca A. Coates
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
| | - Christopher P. McNary
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
| | - Giel Berden
- Radboud University, FELIX Laboratory, Institute for Molecules and Materials, Toernooiveld 7c, NL-6525 ED Nijmegen, The Netherlands
| | - Jos Oomens
- Radboud University, FELIX Laboratory, Institute for Molecules and Materials, Toernooiveld 7c, NL-6525 ED Nijmegen, The Netherlands
- van’t Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, NL-1098 XH Amsterdam, The Netherlands
| | - P. B. Armentrout
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
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33
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Wu RR, Hamlow LA, He CC, Nei YW, Berden G, Oomens J, Rodgers MT. The intrinsic basicity of the phosphate backbone exceeds that of uracil and thymine residues: protonation of the phosphate moiety is preferred over the nucleobase for pdThd and pUrd. Phys Chem Chem Phys 2018; 19:30351-30361. [PMID: 29099122 DOI: 10.1039/c7cp05521h] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The gas-phase conformations of the protonated forms of thymidine-5'-monophosphate and uridine-5'-monophosphate, [pdThd+H]+ and [pUrd+H]+, are investigated by infrared multiple photon dissociation (IRMPD) action spectroscopy and electronic structure calculations. The IRMPD action spectra of [pdThd+H]+ and [pUrd+H]+ are measured over the IR fingerprint and hydrogen-stretching regions using the FELIX free electron laser and an OPO/OPA laser system. Low-energy conformations of [pdThd+H]+ and [pUrd+H]+ and their relative stabilities are computed at the MP2(full)/6-311+G(2d,2p)//B3LYP/6-311+G(d,p) and B3LYP/6-311+G(2d,2p)//B3LYP/6-311+G(d,p) levels of theory. Comparisons of the measured IRMPD action spectra and B3LYP/6-311+G(d,p) linear IR spectra computed for the low-energy conformers indicate that the dominant conformers of [pdThd+H]+ and [pUrd+H]+ populated in the experiments are protonated at the phosphate oxo oxygen atom, with a syn nucleobase orientation that is stabilized by strong P[double bond, length as m-dash]OH+O2 and P-OHO4' hydrogen-bonding interactions, and C2'-endo sugar puckering. Minor abundance of conformers protonated at the O2 carbonyl of the nucleobase residue may also contribute for [pdThd+H]+, but do not appear to be important for [pUrd+H]+. Comparisons to previous IRMPD spectroscopy investigations of the protonated forms of thymidine and uridine, [dThd+H]+ and [Urd+H]+, and the deprotonated forms of pdThd and pUrd, [pdThd-H]- and [pUrd-H]-, provide insight into the effects of the phosphate moiety and protonation on the conformational features of the nucleobase and sugar moieties. Most interestingly, the thymine and uracil nucleobases remain in their canonical forms for [pdThd+H]+ and [pUrd+H]+, unlike [dThd+H]+ and [Urd+H]+, where protonation occurs on the nucleobases and induces tautomerization of the thymine and uracil residues.
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Affiliation(s)
- R R Wu
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA.
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34
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Wu RR, He CC, Hamlow LA, Nei YW, Berden G, Oomens J, Rodgers MT. Protonation induces base rotation of purine nucleotides pdGuo and pGuo. Phys Chem Chem Phys 2018; 18:15081-90. [PMID: 27197049 DOI: 10.1039/c6cp01354f] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Infrared multiple photon dissociation (IRMPD) action spectra of the protonated forms of 2'-deoxyguanosine-5'-monophosphate and guanosine-5'-monophosphate, [pdGuo+H](+) and [pGuo+H](+), are measured over the IR fingerprint and hydrogen-stretching regions using the FELIX free electron laser and an OPO/OPA laser system. Electronic structure calculations are performed to generate low-energy conformations of [pdGuo+H](+) and [pGuo+H](+) and determine their relative stabilities at the B3LYP/6-311+G(2d,2p)//B3LYP/6-311+G(d,p) and MP2(full)/6-311+G(2d,2p)//B3LYP/6-311+G(d,p) levels of theory. Comparative analyses of the measured IRMPD action spectra and B3LYP/6-311+G(d,p) linear IR spectra computed for the low-energy conformers are performed to determine the most favorable site of protonation and the conformers present in the experiments. These comparisons and the computed energetics find that N7 protonation is considerably preferred over O6 and N3, and the N7 protonated ground-state conformers of [pdGuo+H](+) and [pGuo+H](+) are populated in the experiments. The 2'-hydroxyl substituent does not significantly impact the stable low-energy conformers of [pdGuo+H](+)vs. those of [pGuo+H](+). The effect of the 2'-hydroxyl substituent is primarily reflected in the relative intensities of the measured IRMPD bands, as the IRMPD profiles of [pdGuo+H](+) and [pGuo+H](+) are quite similar. Comparisons to previous IRMPD spectroscopy investigations of the protonated forms of the guanine nucleosides, [dGuo+H](+) and [Guo+H](+), and deprotonated forms of the guanine nucleotides, [pdGuo-H](-) and [pGuo-H](-), provide insight into the effects of the phosphate moiety and protonation on the conformational features of the nucleobase and sugar moieties. Protonation is found to induce base rotation of the guanine residue to an anti orientation vs. the syn orientation found for the deprotonated forms of the guanine nucleotides.
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Affiliation(s)
- R R Wu
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA.
| | - C C He
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA.
| | - L A Hamlow
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA.
| | - Y-W Nei
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA.
| | - G Berden
- FELIX Laboratory, Institute for Molecules and Materials, Radboud University, Toernooiveld 7c, 6525 ED, Nijmegen, The Netherlands
| | - J Oomens
- FELIX Laboratory, Institute for Molecules and Materials, Radboud University, Toernooiveld 7c, 6525 ED, Nijmegen, The Netherlands and van't Hoff Institute for Molecular Sciences, University of Amsterdam, 1090 GD, Amsterdam, The Netherlands
| | - M T Rodgers
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA.
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35
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Rabus JM, Simmons DR, Maître P, Bythell BJ. Deprotonated carbohydrate anion fragmentation chemistry: structural evidence from tandem mass spectrometry, infra-red spectroscopy, and theory. Phys Chem Chem Phys 2018; 20:27897-27909. [DOI: 10.1039/c8cp02620c] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We investigate the gas-phase structures and fragmentation chemistry of deprotonated carbohydrate anions using combined tandem mass spectrometry, infrared spectroscopy, regioselective labelling, and theory.
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Affiliation(s)
- Jordan M. Rabus
- Department of Chemistry and Biochemistry
- University of Missouri-St. Louis
- St. Louis
- USA
| | - Daniel R. Simmons
- Department of Chemistry and Biochemistry
- University of Missouri-St. Louis
- St. Louis
- USA
| | - Philippe Maître
- Laboratoire de Chimie Physique (UMR8000)
- CNRS
- Univ. Paris-Sud
- Université Paris-Saclay
- Orsay
| | - Benjamin J. Bythell
- Department of Chemistry and Biochemistry
- University of Missouri-St. Louis
- St. Louis
- USA
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36
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Avilés-Moreno JR, Berden G, Oomens J, Martínez-Haya B. Guanidinium/ammonium competition and proton transfer in the interaction of the amino acid arginine with the tetracarboxylic 18-crown-6 ionophore. Phys Chem Chem Phys 2018; 20:4067-4073. [DOI: 10.1039/c7cp07975c] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The binding of arginine by the 18-crown-6 tetracarboxylic ionophore relies on extensive host–guest redistribution of electronic charge and proton transfer.
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Affiliation(s)
- Juan Ramón Avilés-Moreno
- Department of Physical
- Chemical and Natural Systems
- Universidad Pablo de Olavide
- E-41013 Seville
- Spain
| | - Giel Berden
- Radboud University
- Institute for Molecules and Materials
- FELIX Laboratory
- Toernooiveld 7c
- The Netherlands
| | - Jos Oomens
- Radboud University
- Institute for Molecules and Materials
- FELIX Laboratory
- Toernooiveld 7c
- The Netherlands
| | - Bruno Martínez-Haya
- Department of Physical
- Chemical and Natural Systems
- Universidad Pablo de Olavide
- E-41013 Seville
- Spain
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37
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Chalifoux AM, Boles GC, Berden G, Oomens J, Armentrout PB. Experimental and theoretical investigations of infrared multiple photon dissociation spectra of arginine complexes with Zn2+ and Cd2+. Phys Chem Chem Phys 2018; 20:20712-20725. [DOI: 10.1039/c8cp03484b] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Arginine (Arg) complexes with Zn2+ and Cd2+ were examined by infrared multiple photon dissociation (IRMPD) action spectroscopy using light from a free electron laser.
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Affiliation(s)
| | | | - Giel Berden
- Radboud University
- FELIX Laboratory
- Institute for Molecules and Materials
- NL-6525 ED Nijmegen
- The Netherlands
| | - Jos Oomens
- Radboud University
- FELIX Laboratory
- Institute for Molecules and Materials
- NL-6525 ED Nijmegen
- The Netherlands
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38
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Akinyemi TE, Wu RR, Nei YW, Cunningham NA, Roy HA, Steill JD, Berden G, Oomens J, Rodgers MT. Influence of Transition Metal Cationization versus Sodium Cationization and Protonation on the Gas-Phase Tautomeric Conformations and Stability of Uracil: Application to [Ura+Cu] + and [Ura+Ag]<sup/>. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:2438-2453. [PMID: 28895083 DOI: 10.1007/s13361-017-1771-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 07/22/2017] [Accepted: 07/22/2017] [Indexed: 05/17/2023]
Abstract
The gas-phase conformations of transition metal cation-uracil complexes, [Ura+Cu]+ and [Ura+Ag]+, were examined via infrared multiple photon dissociation (IRMPD) action spectroscopy and theoretical calculations. IRMPD action spectra were measured over the IR fingerprint and hydrogen-stretching regions. Structures and linear IR spectra of the stable tautomeric conformations of these complexes were initially determined at the B3LYP/6-31G(d) level. The four most stable structures computed were also examined at the B3LYP/def2-TZVPPD level to improve the accuracy of the predicted IR spectra. Two very favorable modes of binding are found for [Ura+Cu]+ and [Ura+Ag]+ that involve O2N3 bidentate binding to the 2-keto-4-hydroxy minor tautomer and O4 monodentate binding to the canonical 2,4-diketo tautomer of Ura. Comparisons between the measured IRMPD and calculated IR spectra enable elucidation of the conformers present in the experiments. These comparisons indicate that both favorable binding modes are represented in the experimental tautomeric conformations of [Ura+Cu]+ and [Ura+Ag]+. B3LYP suggests that Cu+ exhibits a slight preference for O4 binding, whereas Ag+ exhibits a slight preference for O2N3 binding. In contrast, MP2 suggests that both Cu+ and Ag+ exhibit a more significant preference for O2N3 binding. The relative band intensities suggest that O4 binding conformers comprise a larger portion of the population for [Ura+Ag]+ than [Ura+Cu]+. The dissociation behavior and relative stabilities of the [Ura+M]+ complexes, M+ = Cu+, Ag+, H+, and Na+) are examined via energy-resolved collision-induced dissociation experiments. The IRMPD spectra, dissociation behaviors, and binding preferences of Cu+ and Ag+ are compared with previous and present results for those of H+ and Na+. Graphical Abstract ᅟ.
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Affiliation(s)
- T E Akinyemi
- Department of Chemistry, Wayne State University, Detroit, MI, 48202, USA
| | - R R Wu
- Department of Chemistry, Wayne State University, Detroit, MI, 48202, USA
| | - Y-W Nei
- Department of Chemistry, Wayne State University, Detroit, MI, 48202, USA
| | - N A Cunningham
- Department of Chemistry, Wayne State University, Detroit, MI, 48202, USA
| | - H A Roy
- Department of Chemistry, Wayne State University, Detroit, MI, 48202, USA
| | - J D Steill
- Institute for Molecules and Materials, FELIX Facility, Radboud University Nijmegen, Toernooiveld 7, 6525 ED, Nijmegen, The Netherlands
| | - G Berden
- Institute for Molecules and Materials, FELIX Facility, Radboud University Nijmegen, Toernooiveld 7, 6525 ED, Nijmegen, The Netherlands
| | - J Oomens
- Institute for Molecules and Materials, FELIX Facility, Radboud University Nijmegen, Toernooiveld 7, 6525 ED, Nijmegen, The Netherlands
- van't Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - M T Rodgers
- Department of Chemistry, Wayne State University, Detroit, MI, 48202, USA.
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39
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Zhu Y, Roy HA, Cunningham NA, Strobehn SF, Gao J, Munshi MU, Berden G, Oomens J, Rodgers MT. IRMPD Action Spectroscopy, ER-CID Experiments, and Theoretical Studies of Sodium Cationized Thymidine and 5-Methyluridine: Kinetic Trapping During the ESI Desolvation Process Preserves the Solution Structure of [Thd+Na]<sup/>. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:2423-2437. [PMID: 28836109 DOI: 10.1007/s13361-017-1753-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 07/01/2017] [Accepted: 07/02/2017] [Indexed: 05/25/2023]
Abstract
Thymidine (dThd) is a fundamental building block of DNA nucleic acids, whereas 5-methyluridine (Thd) is a common modified nucleoside found in tRNA. In order to determine the conformations of the sodium cationized thymine nucleosides [dThd+Na]+ and [Thd+Na]+ produced by electrospray ionization, their infrared multiple photon dissociation (IRMPD) action spectra are measured. Complementary electronic structure calculations are performed to determine the stable low-energy conformations of these complexes. Geometry optimizations and frequency analyses are performed at the B3LYP/6-311+G(d,p) level of theory, whereas energies are calculated at the B3LYP/6-311+G(2d,2p) level of theory. As protonation preferentially stabilizes minor tautomers of dThd and Thd, tautomerization facilitated by Na+ binding is also considered. Comparisons of the measured IRMPD and computed IR spectra find that [dThd+Na]+ prefers tridentate (O2,O4',O5') coordination to the canonical 2,4-diketo form of dThd with thymine in a syn orientation. In contrast, [Thd+Na]+ prefers bidentate (O2,O2') coordination to the canonical 2,4-diketo tautomer of Thd with thymine in an anti orientation. Although 2,4-dihydroxy tautomers and O2 protonated thymine nucleosides coexist in the gas phase, no evidence for minor tautomers is observed for the sodium cationized species. Consistent with experimental observations, the computational results confirm that the sodium cationized thymine nucleosides exhibit a strong preference for the canonical form of the thymine nucleobase. Survival yield analyses based on energy-resolved collision-induced dissociation (ER-CID) experiments suggest that the relative stabilities of protonated and sodium cationized dThd and Thd follow the order [dThd+H]+ < [Thd+H]+ < [dThd+Na]+ < [Thd+Na]+. Graphical Abstract ᅟ.
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Affiliation(s)
- Y Zhu
- Department of Chemistry, Wayne State University, Detroit, MI, 48202, USA
| | - H A Roy
- Department of Chemistry, Wayne State University, Detroit, MI, 48202, USA
| | - N A Cunningham
- Department of Chemistry, Wayne State University, Detroit, MI, 48202, USA
| | - S F Strobehn
- Department of Chemistry, Wayne State University, Detroit, MI, 48202, USA
| | - J Gao
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7c, 6525ED, Nijmegen, The Netherlands
| | - M U Munshi
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7c, 6525ED, Nijmegen, The Netherlands
| | - G Berden
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7c, 6525ED, Nijmegen, The Netherlands
| | - J Oomens
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7c, 6525ED, Nijmegen, The Netherlands
| | - M T Rodgers
- Department of Chemistry, Wayne State University, Detroit, MI, 48202, USA.
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40
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Wu RR, Hamlow LA, He CC, Nei YW, Berden G, Oomens J, Rodgers MT. N3 and O2 Protonated Conformers of the Cytosine Mononucleotides Coexist in the Gas Phase. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:1638-1646. [PMID: 28497356 DOI: 10.1007/s13361-017-1653-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Revised: 03/06/2017] [Accepted: 03/07/2017] [Indexed: 06/07/2023]
Abstract
The gas-phase conformations of the protonated forms of the DNA and RNA cytosine mononucleotides, [pdCyd+H]+ and [pCyd+H]+, are examined by infrared multiple photon dissociation (IRMPD) action spectroscopy over the IR fingerprint and hydrogen-stretching regions complemented by electronic structure calculations. The low-energy conformations of [pdCyd+H]+ and [pCyd+H]+ and their relative stabilities are computed at the B3LYP/6-311+G(2d,2p)//B3LYP/6-311+G(d,p) and MP2(full)/6-311+G(2d,2p)//B3LYP/6-311+G(d,p) levels of theory. Comparisons of the measured IRMPD action spectra and B3LYP/6-311+G(d,p) linear IR spectra computed for the low-energy conformers allow the conformers present in the experiments to be determined. Similar to that found in previous IRMPD action spectroscopy studies of the protonated forms of the cytosine nucleosides, [dCyd+H]+ and [Cyd+H]+, both N3 and O2 protonated cytosine mononucleotides exhibiting an anti orientation of cytosine are found to coexist in the experimental population. The 2'-hydroxyl substituent does not significantly influence the most stable conformations of [pCyd+H]+ versus those of [pdCyd+H]+, as the IRMPD spectral profiles of [pdCyd+H]+ and [pCyd+H]+ are similar. However, the presence of the 2'-hydroxyl substituent does influence the relative intensities of the measured IRMPD bands. Comparisons to IRMPD spectroscopy studies of the deprotonated forms of the cytosine mononucleotides, [pdCyd-H]- and [pCyd-H]-, provide insight into the effects of protonation versus deprotonation on the conformational features of the nucleobase and sugar moieties. Likewise, comparisons to results of IRMPD spectroscopy studies of the protonated cytosine nucleosides provide insight into the influence of the phosphate moiety on structure. Comparison with previous ion mobility results shows the superiority of IRMPD spectroscopy for distinguishing various protonation sites. Graphical Abstract ᅟ.
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Affiliation(s)
- R R Wu
- Department of Chemistry, Wayne State University, Detroit, MI, 48202, USA
| | - L A Hamlow
- Department of Chemistry, Wayne State University, Detroit, MI, 48202, USA
| | - C C He
- Department of Chemistry, Wayne State University, Detroit, MI, 48202, USA
| | - Y-W Nei
- Department of Chemistry, Wayne State University, Detroit, MI, 48202, USA
| | - G Berden
- FELIX Laboratory, Institute for Molecules and Materials, Radboud University, Toernooiveld 7, 6525 ED, Nijmegen, The Netherlands
| | - J Oomens
- FELIX Laboratory, Institute for Molecules and Materials, Radboud University, Toernooiveld 7, 6525 ED, Nijmegen, The Netherlands
- van't Hoff Institute for Molecular Sciences, University of Amsterdam, 1090 GD, Amsterdam, The Netherlands
| | - M T Rodgers
- Department of Chemistry, Wayne State University, Detroit, MI, 48202, USA.
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41
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Zhu Y, Hamlow LA, He CC, Lee JK, Gao J, Berden G, Oomens J, Rodgers MT. Gas-Phase Conformations and N-Glycosidic Bond Stabilities of Sodium Cationized 2'-Deoxyguanosine and Guanosine: Sodium Cations Preferentially Bind to the Guanine Residue. J Phys Chem B 2017; 121:4048-4060. [PMID: 28355483 DOI: 10.1021/acs.jpcb.7b02906] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
2'-Deoxyguanosine (dGuo) and guanosine (Guo) are fundamental building blocks of DNA and RNA nucleic acids. In order to understand the effects of sodium cationization on the gas-phase conformations and stabilities of dGuo and Guo, infrared multiple photon dissociation (IRMPD) action spectroscopy experiments and complementary electronic structure calculations are performed. The measured IRMPD spectra of [dGuo+Na]+ and [Guo+Na]+ are compared to calculated IR spectra predicted for the stable low-energy structures computed for these species to determine the most favorable sodium cation binding sites, identify the structures populated in the experiments, and elucidate the influence of the 2'-hydroxyl substituent on the structures and IRMPD spectral features. These results are compared with those from a previous IRMPD study of the protonated guanine nucleosides to elucidate the differences between sodium cationization and protonation on structure. Energy-resolved collision-induced dissociation (ER-CID) experiments and survival yield analyses of protonated and sodium cationized dGuo and Guo are performed to compare the effects of these cations toward activating the N-glycosidic bonds of these nucleosides. For both [dGuo+Na]+ and [Guo+Na]+, the gas-phase structures populated in the experiments are found to involve bidentate binding of the sodium cation to the O6 and N7 atoms of guanine, forming a 5-membered chelation ring, with guanine found in both anti and syn orientations and C2'-endo (2T3 or 3T2) puckering of the sugar. The ER-CID results, IRMPD yields and the computed C1'-N9 bond lengths indicate that sodium cationization activates the N-glycosidic bond less effectively than protonation for both dGuo and Guo. The 2'-hydroxyl substituent of Guo is found to impact the preferred structures very little except that it enables a 2'OH···3'OH hydrogen bond to be formed, and stabilizes the N-glycosidic bond relative to that of dGuo in both the sodium cationized and protonated complexes.
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Affiliation(s)
- Y Zhu
- Department of Chemistry, Wayne State University , Detroit, Michigan 48202, United States
| | - L A Hamlow
- Department of Chemistry, Wayne State University , Detroit, Michigan 48202, United States
| | - C C He
- Department of Chemistry, Wayne State University , Detroit, Michigan 48202, United States
| | - J K Lee
- Department of Chemistry, Wayne State University , Detroit, Michigan 48202, United States
| | - J Gao
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University , Toernooiveld 7c, 6525ED Nijmegen, The Netherlands
| | - G Berden
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University , Toernooiveld 7c, 6525ED Nijmegen, The Netherlands
| | - J Oomens
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University , Toernooiveld 7c, 6525ED Nijmegen, The Netherlands
| | - M T Rodgers
- Department of Chemistry, Wayne State University , Detroit, Michigan 48202, United States
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42
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Avilés-Moreno JR, Berden G, Oomens J, Martínez-Haya B. Benchmark Ditopic Binding of Cl−
and Cs+
by the Macrocycle Hexacyclen. Chemphyschem 2017; 18:1324-1332. [DOI: 10.1002/cphc.201700091] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 02/17/2017] [Indexed: 01/05/2023]
Affiliation(s)
- Juan Ramón Avilés-Moreno
- Department of Physical, Chemical and Natural Systems; Universidad Pablo de Olavide; 41013 Seville Spain
| | - Giel Berden
- Institute for Molecules and Materials; FELIX Laboratory; Radboud University; Toernooiveld 7c 6525 ED Nijmegen The Netherlands
| | - Jos Oomens
- Institute for Molecules and Materials; FELIX Laboratory; Radboud University; Toernooiveld 7c 6525 ED Nijmegen The Netherlands
| | - Bruno Martínez-Haya
- Department of Physical, Chemical and Natural Systems; Universidad Pablo de Olavide; 41013 Seville Spain
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43
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Boles GC, Owen CJ, Berden G, Oomens J, Armentrout PB. Experimental and theoretical investigations of infrared multiple photon dissociation spectra of glutamic acid complexes with Zn2+and Cd2+. Phys Chem Chem Phys 2017; 19:12394-12406. [DOI: 10.1039/c7cp01786c] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
IRMPD of [Zn(Glu-H)ACN]+was particularly interesting because fragmentation of the amino acid was favored, rather than dissociation of the ACN ligand.
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Affiliation(s)
| | | | - Giel Berden
- Radboud University
- Institute for Molecules and Materials
- FELIX Laboratory
- NL-6525 ED Nijmegen
- The Netherlands
| | - Jos Oomens
- Radboud University
- Institute for Molecules and Materials
- FELIX Laboratory
- NL-6525 ED Nijmegen
- The Netherlands
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44
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Carita Correra T, Santos Fernandes A, Mota Reginato M, Colucci Ducati L, Berden G, Oomens J. Probing the geometry reorganization from solution to gas-phase in putrescine derivatives by IRMPD, 1H-NMR and theoretical calculations. Phys Chem Chem Phys 2017; 19:24330-24340. [DOI: 10.1039/c7cp04617k] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Geometry reorganization of ESI formed ions are demonstrated and explicit calculations of the solution phase are shown to be relevant.
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Affiliation(s)
- Thiago Carita Correra
- Department of Fundamental Chemistry
- Institute of Chemistry
- University of São Paulo
- São Paulo
- Brazil
| | - André Santos Fernandes
- Department of Fundamental Chemistry
- Institute of Chemistry
- University of São Paulo
- São Paulo
- Brazil
| | - Marcelo Mota Reginato
- Department of Fundamental Chemistry
- Institute of Chemistry
- University of São Paulo
- São Paulo
- Brazil
| | - Lucas Colucci Ducati
- Department of Fundamental Chemistry
- Institute of Chemistry
- University of São Paulo
- São Paulo
- Brazil
| | - Giel Berden
- Radboud University
- Institute for Molecules and Materials
- FELIX Laboratory
- 6525 ED Nijmegen
- The Netherlands
| | - Jos Oomens
- Radboud University
- Institute for Molecules and Materials
- FELIX Laboratory
- 6525 ED Nijmegen
- The Netherlands
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45
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Avilés-Moreno JR, Gámez F, Berden G, Oomens J, Martínez-Haya B. Isolated alkali cation complexes of the antibiotic ionophore nonactin: correlation with crystalline structures. Phys Chem Chem Phys 2017; 19:14984-14991. [DOI: 10.1039/c7cp02438j] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The stabilization of the nonactin–Na+ complex in a S4 or C2 conformation constitutes a challenging benchmark for experimental and modelling methods.
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Affiliation(s)
- Juan Ramón Avilés-Moreno
- Department of Physical
- Chemical and Natural Systems
- Universidad Pablo de Olavide
- E-41013 Seville
- Spain
| | - Francisco Gámez
- Department of Physical
- Chemical and Natural Systems
- Universidad Pablo de Olavide
- E-41013 Seville
- Spain
| | - Giel Berden
- Radboud University
- Institute for Molecules and Materials
- FELIX Laboratory
- 6525ED Nijmegen
- The Netherlands
| | - Jos Oomens
- Radboud University
- Institute for Molecules and Materials
- FELIX Laboratory
- 6525ED Nijmegen
- The Netherlands
| | - Bruno Martínez-Haya
- Department of Physical
- Chemical and Natural Systems
- Universidad Pablo de Olavide
- E-41013 Seville
- Spain
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46
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Peckelsen K, Martens J, Czympiel L, Oomens J, Berden G, Gründemann D, Meijer AJHM, Schäfer M. Ergothioneine and related histidine derivatives in the gas phase: tautomer structures determined by IRMPD spectroscopy and theory. Phys Chem Chem Phys 2017; 19:23362-23372. [DOI: 10.1039/c7cp03843g] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Gas-phase analysis of ergothioneine molecular ions allows differentiating thiol from thione tautomer structures.
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Affiliation(s)
- Katrin Peckelsen
- Department für Chemie
- Institut für Organische Chemie
- Universität zu Köln
- Greinstrasse 4
- Köln
| | - Jonathan Martens
- Radboud University
- Institute for Molecules and Materials
- FELIX Laboratory
- Toernooiveld 7c
- Nijmegen
| | - Lisa Czympiel
- Department für Chemie
- Institut für Organische Chemie
- Universität zu Köln
- Greinstrasse 4
- Köln
| | - Jos Oomens
- Radboud University
- Institute for Molecules and Materials
- FELIX Laboratory
- Toernooiveld 7c
- Nijmegen
| | - Giel Berden
- Radboud University
- Institute for Molecules and Materials
- FELIX Laboratory
- Toernooiveld 7c
- Nijmegen
| | - Dirk Gründemann
- Department of Pharmacology
- University of Cologne
- Gleueler Straße 24
- Cologne
- Germany
| | | | - Mathias Schäfer
- Department für Chemie
- Institut für Organische Chemie
- Universität zu Köln
- Greinstrasse 4
- Köln
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47
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Munshi MU, Berden G, Martens J, Oomens J. Gas-phase vibrational spectroscopy of triphenylamine: the effect of charge on structure and spectra. Phys Chem Chem Phys 2017. [DOI: 10.1039/c7cp02638b] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The effect of ionization by oxidation and protonation on the structure and IR spectrum of isolated, gas-phase triphenylamine (TPA) has been investigated by infrared multiple photon dissociation (IRMPD) spectroscopy in the fingerprint range from 600 cm−1 to 1800 cm−1 using an infrared free electron laser.
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Affiliation(s)
- Musleh Uddin Munshi
- Radboud University
- Institute for Molecules and Materials
- FELIX Laboratory
- 6525 ED Nijmegen
- The Netherlands
| | - Giel Berden
- Radboud University
- Institute for Molecules and Materials
- FELIX Laboratory
- 6525 ED Nijmegen
- The Netherlands
| | - Jonathan Martens
- Radboud University
- Institute for Molecules and Materials
- FELIX Laboratory
- 6525 ED Nijmegen
- The Netherlands
| | - Jos Oomens
- Radboud University
- Institute for Molecules and Materials
- FELIX Laboratory
- 6525 ED Nijmegen
- The Netherlands
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48
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Boles GC, Coates RA, Berden G, Oomens J, Armentrout PB. Experimental and Theoretical Investigations of Infrared Multiple Photon Dissociation Spectra of Asparagine Complexes with Zn2+ and Cd2+ and Their Deamidation Processes. J Phys Chem B 2016; 120:12486-12500. [DOI: 10.1021/acs.jpcb.6b10326] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Georgia C. Boles
- Department
of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
| | - Rebecca A. Coates
- Department
of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
| | - Giel Berden
- Radboud University, Institute for Molecules and
Materials, FELIX Laboratory, Toernooiveld 7c, NL-6525 ED Nijmegen, The Netherlands
| | - Jos Oomens
- Radboud University, Institute for Molecules and
Materials, FELIX Laboratory, Toernooiveld 7c, NL-6525 ED Nijmegen, The Netherlands
- van‘t
Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - P. B. Armentrout
- Department
of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
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49
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Kempkes LJM, Martens J, Grzetic J, Berden G, Oomens J. Deamidation Reactions of Asparagine- and Glutamine-Containing Dipeptides Investigated by Ion Spectroscopy. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:1855-1869. [PMID: 27624159 PMCID: PMC5059420 DOI: 10.1007/s13361-016-1462-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 07/21/2016] [Accepted: 07/22/2016] [Indexed: 05/27/2023]
Abstract
Deamidation is a major fragmentation channel upon activation by collision induced dissociation (CID) for protonated peptides containing glutamine (Gln) and asparagine (Asn) residues. Here, we investigate these NH3-loss reactions for four Asn- and Gln-containing protonated peptides in terms of the resulting product ion structures using infrared ion spectroscopy with the free electron laser FELIX. The influence of the side chain length (Asn versus Gln) and of the amino acid sequence on the deamidation reaction has been examined. Molecular structures for the product ions are determined by comparison of experimental IR spectra with spectra predicted by density functional theory (DFT). The reaction mechanisms identified for the four dipeptides AlaAsn, AsnAla, AlaGln, and GlnAla are not the same. For all four dipeptides, primary deamidation takes place from the amide side chain (and not from the N-terminus) and, in most cases, resembles the mechanisms previously identified for the protonated amino acids asparagine and glutamine. Secondary fragmentation reactions of the deamidation products have also been characterized and provide further insight in - and confirmation of - the identified mechanisms. Overall, this study provides a comprehensive molecular structure map of the deamidation chemistry of this series of dipeptides. Graphical Abstract ᅟ.
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Affiliation(s)
- Lisanne J M Kempkes
- FELIX Laboratory, Institute for Molecules and Materials, Radboud University, Toernooiveld 7c, 6525 ED, Nijmegen, The Netherlands
| | - Jonathan Martens
- FELIX Laboratory, Institute for Molecules and Materials, Radboud University, Toernooiveld 7c, 6525 ED, Nijmegen, The Netherlands
| | - Josipa Grzetic
- FELIX Laboratory, Institute for Molecules and Materials, Radboud University, Toernooiveld 7c, 6525 ED, Nijmegen, The Netherlands
| | - Giel Berden
- FELIX Laboratory, Institute for Molecules and Materials, Radboud University, Toernooiveld 7c, 6525 ED, Nijmegen, The Netherlands
| | - Jos Oomens
- FELIX Laboratory, Institute for Molecules and Materials, Radboud University, Toernooiveld 7c, 6525 ED, Nijmegen, The Netherlands.
- Van 't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands.
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50
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Martens J, Berden G, Gebhardt CR, Oomens J. Infrared ion spectroscopy in a modified quadrupole ion trap mass spectrometer at the FELIX free electron laser laboratory. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2016; 87:103108. [PMID: 27802712 DOI: 10.1063/1.4964703] [Citation(s) in RCA: 124] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
We report on modifications made to a Paul-type quadrupole ion trap mass spectrometer and discuss its application in infrared ion spectroscopy experiments. Main modifications involve optical access to the trapped ions and hardware and software coupling to a variety of infrared laser sources at the FELIX infrared free electron laser laboratory. In comparison to previously described infrared ion spectroscopy experiments at the FELIX laboratory, we find significant improvements in efficiency and sensitivity. Effects of the trapping conditions of the ions on the IR multiple photon dissociation spectra are explored. Enhanced photo-dissociation is found at lower pressures in the ion trap. Spectra obtained under reduced pressure conditions are found to more closely mimic those obtained in the high-vacuum conditions of an Fourier transform ion cyclotron resonance mass spectrometer. A gas-mixing system is described enabling the controlled addition of a secondary gas into helium buffer gas flowing into the trap and allows for ion/molecule reactions in the trap. The electron transfer dissociation (ETD) option of the mass spectrometer allows for IR structure characterization of ETD-generated peptide dissociation products.
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Affiliation(s)
- Jonathan Martens
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7c, 6525ED Nijmegen, The Netherlands
| | - Giel Berden
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7c, 6525ED Nijmegen, The Netherlands
| | | | - Jos Oomens
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7c, 6525ED Nijmegen, The Netherlands
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