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Lau JKC, Hopkinson AC, Siu KWM. Phosphate Migration versus the Loss of Phosphoric Acid in Protonated Phosphopeptides: A Computational Study. J Phys Chem B 2024; 128:504-514. [PMID: 38190618 DOI: 10.1021/acs.jpcb.3c06767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2024]
Abstract
Residue-specific phosphorylation is a protein post-translational modification that regulates cellular functions. Experimental determination of the exact sites of protein phosphorylation provides an understanding of the signaling and processes at work for a given cellular state. Any experimental artifact that involves migration of the phosphate group during measurement is a concern, as the outcome can lead to erroneous conclusions that may confound studies on cellular signal transduction. Herein, we examine computationally the mechanism by which a phosphate group migrates from one serine residue to another serine in monoprotonated pentapeptides [BA-pSer-Gly-Ser-BB + H]+ → [BA-Ser-Gly-pSer-BB + H]+ (where BA and BB are different combinations of the three basic amino acids, histidine, lysine, and arginine). In addition to moving the phosphate group, the overall mechanism involves transferring a proton from the N-terminal amino acid, BA, to the C-terminal amino acid, BB. This is not a synchronous process, and there is a key high-energy intermediate, structure C, that is zwitterionic with both the basic amino acids protonated and the phosphate group attached to both serine residues and carrying a negative charge. The barriers to moving the phosphate group are calculated to be in the range of 219-274 kJ mol-1 at the B3LYP/6-31G(d) level. These barriers are systematically slightly lower and in good agreement with single-point energy calculations at both M06-2X/6-311++G(d,p) and MP2/6-31++G(d,p) levels. The competitive reaction, loss of phosphoric acid from the protonated pentapeptides, has a barrier in the range of 176-202 kJ mol-1 at the B3LYP/6-31G(d) level. Extension of the theory to M06-2X/6-311++G(d,p)//B3LYP/6-31G(d) and MP2/6-31++G(d,p)// B3LYP/6-31G(d) gives higher values for the loss of phosphoric acid, falling in the range of 196-226 kJ mol-1; these are comparable to the barriers against phosphate migration at the same levels of theory. For larger peptides His-pSer-(Gly)n-Ser-His, where n has values from 2 to 5, the barriers against the loss of phosphoric acid are higher than those against the phosphate group migration. This difference is most pronounced and significant when n = 4 and 5 (the differences are approximately 80 kJ mol-1 under the single-point energy calculations at the M06-2X and MP2 levels). Energy differences using two more recent functionals, M08-HX and MN15, on His-pSer-(Gly)n-Ser-His, where n = 1 and 5, are in good agreement with the M06-2X and MP2 calculations. These results provide the mechanistic rationale for phosphate migration versus other competing reactions in the gas phase under tandem mass spectrometry conditions.
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Affiliation(s)
- Justin Kai-Chi Lau
- Department of Chemistry and Centre for Research in Mass Spectrometry, York University, 4700 Keele Street, Toronto, ON M3J 1P3, Canada
- Department of Chemistry and Biochemistry, University of Windsor, 401 Sunset Avenue, Windsor, ON N9B 3P4, Canada
| | - Alan C Hopkinson
- Department of Chemistry and Centre for Research in Mass Spectrometry, York University, 4700 Keele Street, Toronto, ON M3J 1P3, Canada
| | - K W Michael Siu
- Department of Chemistry and Centre for Research in Mass Spectrometry, York University, 4700 Keele Street, Toronto, ON M3J 1P3, Canada
- Department of Chemistry and Biochemistry, University of Windsor, 401 Sunset Avenue, Windsor, ON N9B 3P4, Canada
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2
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A computational and experimental examination of the CID of phosphorylated serine-H +. Chem Phys Lett 2023. [DOI: 10.1016/j.cplett.2023.140442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2023]
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3
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Giampà M, Corinti D, Maccelli A, Fornarini S, Berden G, Oomens J, Schwarzbich S, Glaser T, Crestoni ME. Binding Modes of a Cytotoxic Dinuclear Copper(II) Complex with Phosphate Ligands Probed by Vibrational Photodissociation Ion Spectroscopy. Inorg Chem 2023; 62:1341-1353. [PMID: 36655890 PMCID: PMC9890465 DOI: 10.1021/acs.inorgchem.2c02091] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The dinuclear copper complex bearing a 2,7-disubstituted-1,8-naphthalenediol ligand, [(HtomMe){Cu(OAc)}2](OAc), a potential anticancer drug able to bind to two neighboring phosphates in the DNA backbone, is endowed with stronger cytotoxic effects and inhibition ability of DNA synthesis in human cancer cells as compared to cisplatin. In this study, the intrinsic binding ability of the charged complex [(HtomMe){Cu(OAc)}2]+ is investigated with representative phosphate diester ligands with growing chemical complexity, ranging from simple inorganic phosphate up to mononucleotides. An integrated method based on high-resolution mass spectrometry (MS), tandem MS, and infrared multiple photon dissociation (IRMPD) spectroscopy in the 600-1800 cm-1 spectral range, backed by quantum chemical calculations, has been used to characterize complexes formed in solution and delivered as bare species by electrospray ionization. The structural features revealed by IRMPD spectroscopy have been interpreted by comparison with linear IR spectra of the lowest-energy structures, revealing diagnostic signatures of binding modes of the dinuclear copper(II) complex with phosphate groups, whereas the possible competitive interaction with the nucleobase is silenced in the gas phase. This result points to the prevailing interaction of [(HtomMe){Cu(OAc)}2]+ with phosphate diesters and mononucleotides as a conceivable contribution to the observed anticancer activity.
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Affiliation(s)
- Marco Giampà
- Department
of Clinical and Molecular Medicine, Norwegian
University of Science and Technology, Olav Kyrres Gate 9, 7030 Trondheim, Norway
| | - Davide Corinti
- Dipartimento
di Chimica e Tecnologie del Farmaco, Università
di Roma “La Sapienza”, I-00185 Roma, Italy,
| | - Alessandro Maccelli
- 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
| | - Giel Berden
- Institute
for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
| | - Jos Oomens
- Institute
for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
| | - Sabrina Schwarzbich
- Lehrstuhl
für Anorganische Chemie I, Fakultät für Chemie, Universität Bielefeld, D-33615 Bielefeld, Germany
| | - Thorsten Glaser
- Lehrstuhl
für Anorganische Chemie I, Fakultät für Chemie, Universität Bielefeld, D-33615 Bielefeld, Germany
| | - Maria Elisa Crestoni
- Dipartimento
di Chimica e Tecnologie del Farmaco, Università
di Roma “La Sapienza”, I-00185 Roma, Italy,
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4
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Corinti D, Chiavarino B, Scuderi D, Fraschetti C, Filippi A, Fornarini S, Crestoni ME. Molecular Properties of Bare and Microhydrated Vitamin B5-Calcium Complexes. Int J Mol Sci 2021; 22:E692. [PMID: 33445631 PMCID: PMC7826572 DOI: 10.3390/ijms22020692] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 01/06/2021] [Accepted: 01/08/2021] [Indexed: 12/22/2022] Open
Abstract
Pantothenic acid, also called vitamin B5, is an essential nutrient involved in several metabolic pathways. It shows a characteristic preference for interacting with Ca(II) ions, which are abundant in the extracellular media and act as secondary mediators in the activation of numerous biological functions. The bare deprotonated form of pantothenic acid, [panto-H]-, its complex with Ca(II) ion, [Ca(panto-H)]+, and singly charged micro-hydrated calcium pantothenate [Ca(panto-H)(H2O)]+ adduct have been obtained in the gas phase by electrospray ionization and assayed by mass spectrometry and IR multiple photon dissociation spectroscopy in the fingerprint spectral range. Quantum chemical calculations at the B3LYP(-D3) and MP2 levels of theory were performed to simulate geometries, thermochemical data, and linear absorption spectra of low-lying isomers, allowing us to assign the experimental absorptions to particular structural motifs. Pantothenate was found to exist in the gas phase as a single isomeric form showing deprotonation on the carboxylic moiety. On the contrary, free and monohydrated calcium complexes of deprotonated pantothenic acid both present at least two isomers participating in the gas-phase population, sharing the deprotonation of pantothenate on the carboxylic group and either a fourfold or fivefold coordination with calcium, thus justifying the strong affinity of pantothenate for the metal.
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Affiliation(s)
- Davide Corinti
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma “La Sapienza”, Piazzale Aldo Moro, 5, I-00185 Roma, Italy; (D.C.); (B.C.); (C.F.); (A.F.); (S.F.)
| | - Barbara Chiavarino
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma “La Sapienza”, Piazzale Aldo Moro, 5, I-00185 Roma, Italy; (D.C.); (B.C.); (C.F.); (A.F.); (S.F.)
| | - Debora Scuderi
- Institut de Chimie Physique (UMR8000), CNRS, Université Paris-Saclay, 91405 Orsay, France;
| | - Caterina Fraschetti
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma “La Sapienza”, Piazzale Aldo Moro, 5, I-00185 Roma, Italy; (D.C.); (B.C.); (C.F.); (A.F.); (S.F.)
| | - Antonello Filippi
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma “La Sapienza”, Piazzale Aldo Moro, 5, I-00185 Roma, Italy; (D.C.); (B.C.); (C.F.); (A.F.); (S.F.)
| | - Simonetta Fornarini
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma “La Sapienza”, Piazzale Aldo Moro, 5, I-00185 Roma, Italy; (D.C.); (B.C.); (C.F.); (A.F.); (S.F.)
| | - Maria Elisa Crestoni
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma “La Sapienza”, Piazzale Aldo Moro, 5, I-00185 Roma, Italy; (D.C.); (B.C.); (C.F.); (A.F.); (S.F.)
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5
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Lucas K, Barnes GL. Modeling the Effects of O-Sulfonation on the CID of Serine. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:1114-1122. [PMID: 32202776 DOI: 10.1021/jasms.0c00037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
We present the results of direct dynamics simulations and DFT calculations aimed at elucidating the effect of O-sulfonation on the collision-induced dissociation for serine. Toward this end, direct dynamics simulations of both serine and sulfoserine were performed at multiple collision energies and theoretical mass spectra obtained. Comparisons to experimental results are favorable for both systems. Peaks related to the sulfo group are identified and the reaction dynamics explored. In particular, three significant peaks (m/z 106, 88, and 81) seen in the theoretical mass spectrum directly related to the sulfo group are analyzed as well as major peaks shared by both systems. Our analysis shows that the m/z 106 peaks result from intramolecular rearrangements, intermolecular proton transfer among complexes composed of initial fragmentation products, and at high energy side-chain fragmentation. The m/z 88 peak was found to contain multiple constitutional isomers, including a previously unconsidered, low energy structure. It was also observed that the RM1 semiempirical method was not able to obtain all of the major peaks seen in experimens for sulfoserine. In contrast, PM6 did obtain all major experimental peaks.
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Affiliation(s)
- Kenneth Lucas
- Department of Chemistry and Biochemistry Siena College 515 Loudon Road Loudonville, New York 12211, United States
| | - George L Barnes
- Department of Chemistry and Biochemistry Siena College 515 Loudon Road Loudonville, New York 12211, United States
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6
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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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7
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Tripodi GL, Correra TC, Angolini CFF, Ferreira BRV, Maître P, Eberlin MN, Roithová J. The Intermediates in Lewis Acid Catalysis with Lanthanide Triflates. European J Org Chem 2019; 2019:3560-3566. [PMID: 31680777 PMCID: PMC6813638 DOI: 10.1002/ejoc.201900171] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Indexed: 01/27/2023]
Abstract
Lanthanide triflates are effective Lewis acid catalysts in reactions involving carbonyl compounds due to their high oxophilicity and water stability. Despite the growing interest, the identity of the catalytic species formed in lanthanide catalysed reactions is still unknown. We have therefore used mass spectrometry and ion spectroscopy to intercept and characterize the intermediates in a reaction catalysed by ytterbium and dysprosium triflates. We were able to identify a number of lanthanide intermediates formed in a simple condensation reaction between a C-acid and an aldehyde. Results show correlation between the reactivity of lanthanide complexes and their charge state and suggest that the triply charged complexes play a key role in lanthanide catalysed reactions. Spectroscopic data of the gaseous ions accompanied by theoretical calculations reveal that the difference between catalytic efficiencies of ytterbium and dysprosium ions can be explained by their different electrophilicity.
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Affiliation(s)
- Guilherme L. Tripodi
- Institute for Molecules and MaterialsRadboud UniversityHeyendaalseweg 1356525 AJ NijmegenThe Netherlands
| | - Thiago C. Correra
- Departament of Organic ChemistryInstitute of ChemistryUniversity of São Paulo05508–000São Paulo‐SPBrazil
| | - Célio F. F. Angolini
- Center for Natural and Human SciencesFederal University of ABC (UFABC)09210–580Santo André ‐SPBrazil
| | - Bruno R. V. Ferreira
- Instituto Federal do Norte de Minas GeraisCampus Salinas39560–000Salinas‐MGBrazil
| | - Philippe Maître
- Laboratoire de Chimie Physique, URM8000, CNRS, Univ. Paris‐SudUniversité Paris‐Saclay91405OrsayFrance
| | - Marcos N. Eberlin
- ThoMSon Mass Spectrometry Laboratory, Institute of ChemistryState University of Campinas13084–971Campinas‐SPBrazil
- School of EngeneeringMackenzie Presbiterian University01302907São Paulo‐SPBrazil
| | - Jana Roithová
- Institute for Molecules and MaterialsRadboud UniversityHeyendaalseweg 1356525 AJ NijmegenThe Netherlands
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8
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Santos Fernandes A, Maître P, Carita Correra T. Evaluation of the Katsuki–Sharpless Epoxidation Precatalysts by ESI-FTMS, CID, and IRMPD Spectroscopy. J Phys Chem A 2019; 123:1022-1029. [DOI: 10.1021/acs.jpca.8b09979] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- André Santos Fernandes
- Department of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes, 748, 05508-000, São Paulo, SP, Brazil
| | - Philippe Maître
- Laboratoire de Chimie Physique, URM8000, CNRS, Université Paris-Sud, Université Paris-Saclay, 91405, Orsay, France
| | - Thiago Carita Correra
- Department of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes, 748, 05508-000, São Paulo, SP, Brazil
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9
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Affiliation(s)
- Clement
M. Potel
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584
CH Utrecht, The Netherlands
- Netherlands
Proteomics Centre, Padualaan
8, 3584 CH Utrecht, The Netherlands
| | - Simone Lemeer
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584
CH Utrecht, The Netherlands
- Netherlands
Proteomics Centre, Padualaan
8, 3584 CH Utrecht, The Netherlands
| | - Albert J. R. Heck
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584
CH Utrecht, The Netherlands
- Netherlands
Proteomics Centre, Padualaan
8, 3584 CH Utrecht, The Netherlands
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10
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Willms JA, Vidic J, Barthelmes J, Steinmetz V, Bredow T, Maître P, Engeser M. Probing the gas-phase structure of charge-tagged intermediates of a proline catalyzed aldol reaction – vibrational spectroscopy distinguishes oxazolidinone from enamine species. Phys Chem Chem Phys 2019; 21:2578-2586. [DOI: 10.1039/c8cp04905j] [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
Charge-tagging enables the detection of reaction intermediates which are probed by IRMPD spectroscopy in combination with theory.
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Affiliation(s)
- J. Alexander Willms
- Kekulé-Institute of Organic Chemistry and Biochemistry
- University of Bonn
- D-53121 Bonn
- Germany
| | - Jandro Vidic
- Mulliken Center for Theoretical Chemistry
- Institute of Physical und Theoretical Chemistry
- University of Bonn
- D-53115 Bonn
- Germany
| | - Janosch Barthelmes
- Kekulé-Institute of Organic Chemistry and Biochemistry
- University of Bonn
- D-53121 Bonn
- Germany
| | - Vincent Steinmetz
- Laboratoire de Chimie Physique
- Université Paris-Sud
- CNRS, Université Paris-Saclay
- Orsay
- France
| | - Thomas Bredow
- Mulliken Center for Theoretical Chemistry
- Institute of Physical und Theoretical Chemistry
- University of Bonn
- D-53115 Bonn
- Germany
| | - Philippe Maître
- Laboratoire de Chimie Physique
- Université Paris-Sud
- CNRS, Université Paris-Saclay
- Orsay
- France
| | - Marianne Engeser
- Kekulé-Institute of Organic Chemistry and Biochemistry
- University of Bonn
- D-53121 Bonn
- Germany
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Tesler LF, Cismesia AP, Bell MR, Bailey LS, Polfer NC. Operation and Performance of a Mass-Selective Cryogenic Linear Ion Trap. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:2115-2124. [PMID: 30062479 PMCID: PMC6301008 DOI: 10.1007/s13361-018-2026-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 06/26/2018] [Accepted: 06/27/2018] [Indexed: 06/08/2023]
Abstract
We report on the performance of a cryogenic 2D linear ion trap (cryoLIT) that is shown to be mass-selective in the temperature range of 17-295 K. As the cryoLIT is cooled, the ejection voltages during the mass instability scan decrease, which results in an effective mass shift to lower m/z relative to room temperature. This is attributed to a decrease in trap radius caused by thermal contraction. Additionally, the cryoLIT generates reproducible mass spectra from day-to-day, and is capable of performing stored waveform inverse Fourier transform (SWIFT) mass isolation of fragile N2-tagged ions for the purpose of background-free infrared dissociation spectroscopy. Graphical Abstract ᅟ.
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Affiliation(s)
- Larry F Tesler
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, FL, 32611-7200, USA
| | - Adam P Cismesia
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, FL, 32611-7200, USA
| | - Matthew R Bell
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, FL, 32611-7200, USA
| | - Laura S Bailey
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, FL, 32611-7200, USA
| | - Nicolas C Polfer
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, FL, 32611-7200, USA.
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12
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Bell MR, Cruzeiro VWD, Cismesia AP, Tesler LF, Roitberg AE, Polfer NC. Probing the Structures of Solvent-Complexed Ions Formed in Electrospray Ionization Using Cryogenic Infrared Photodissociation Spectroscopy. J Phys Chem A 2018; 122:7427-7436. [DOI: 10.1021/acs.jpca.8b05896] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Matthew R. Bell
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611-7200, United States
| | - Vinícius Wilian D. Cruzeiro
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611-7200, United States
| | - Adam P. Cismesia
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611-7200, United States
| | - Larry F. Tesler
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611-7200, United States
| | - Adrian E. Roitberg
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611-7200, United States
| | - Nicolas C. Polfer
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611-7200, United States
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13
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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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14
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Cismesia AP, Bell MR, Tesler LF, Alves M, Polfer NC. Infrared ion spectroscopy: an analytical tool for the study of metabolites. Analyst 2018; 143:1615-1623. [PMID: 29497730 PMCID: PMC6186386 DOI: 10.1039/c8an00087e] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Vibrational ion spectroscopy techniques coupled with mass spectrometry are applied to standard metabolites as a proof-of-principle demonstration for the structural identification of unknown metabolites. The traditional room temperature infrared multiple photon dissociation (IRMPD) spectroscopy technique is shown to differentiate chemical moieties in isobaric and isomeric variants. These results are compared to infrared spectra of cryogenically cooled analyte ions, showing enhanced spectral resolution, and thus also improved differentiation between closely related molecules, such as isomers. The cryogenic spectroscopy is effected in a recently developed mass-selective cryogenic linear ion trap, which is capable of high sensitivity and the ability to measure the IR spectra of multiple analytes simultaneously.
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Affiliation(s)
- Adam P Cismesia
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, FL 32611-7200, USA.
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15
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Corinti D, Gregori B, Guidoni L, Scuderi D, McMahon TB, Chiavarino B, Fornarini S, Crestoni ME. Complexation of halide ions to tyrosine: role of non-covalent interactions evidenced by IRMPD spectroscopy. Phys Chem Chem Phys 2018; 20:4429-4441. [PMID: 29372198 DOI: 10.1039/c7cp06657k] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The binding motifs in the halide adducts with tyrosine ([Tyr + X]-, X = Cl, Br, I) have been investigated and compared with the analogues with 3-nitrotyrosine (nitroTyr), a biomarker of protein nitration, in a solvent-free environment by mass-selected infrared multiple photon dissociation (IRMPD) spectroscopy over two IR frequency ranges, namely 950-1950 and 2800-3700 cm-1. Extensive quantum chemical calculations at B3LYP, B3LYP-D3 and MP2 levels of theory have been performed using the 6-311++G(d,p) basis set to determine the geometry, relative energy and vibrational properties of likely isomers and interpret the measured spectra. A diagnostic carbonyl stretching band at ∼1720 cm-1 from the intact carboxylic group characterizes the IRMPD spectra of both [Tyr + X]- and [nitroTyr + X]-, revealing that the canonical isomers (maintaining intact amino and carboxylic functions) are the prevalent structures. The spectroscopic evidence reveals the presence of multiple non-covalent forms. The halide complexes of tyrosine conform to a mixture of plane and phenol isomers. The contribution of phenol-bound isomers is sensitive to anion size, increasing from chloride to iodide, consistent with the decreasing basicity of the halide, with relative amounts depending on the relative energies of the respective structures. The stability of the most favorable phenol isomer with respect to the reference plane geometry is in fact 1.3, -2.1, -6.8 kJ mol-1, for X = Cl, Br, I, respectively. The change in π-acidity by ring nitration also stabilizes anion-π interactions yielding ring isomers for [nitroTyr + X]-, where the anion is placed above the face of the aromatic ring.
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Affiliation(s)
- Davide Corinti
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma "La Sapienza", P.le A. Moro 5, I-00185 Roma, Italy.
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16
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Cismesia AP, Tesler LF, Bell MR, Bailey LS, Polfer NC. Infrared ion spectroscopy inside a mass-selective cryogenic 2D linear ion trap. JOURNAL OF MASS SPECTROMETRY : JMS 2017; 52:720-727. [PMID: 28750482 PMCID: PMC5690808 DOI: 10.1002/jms.3975] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Revised: 07/18/2017] [Accepted: 07/20/2017] [Indexed: 06/07/2023]
Abstract
We demonstrate operation of the first cryogenic 2D linear ion trap (LIT) with mass-selective capabilities. This trap presents a number of advantages for infrared ion "action" spectroscopy studies, particularly those employing the "tagging/messenger" spectroscopy approach. The high trapping efficiencies, trapping capacities, and low detection limits make 2D LITs a highly suitable choice for low-concentration analytes from scarce biological samples. In our trap, ions can be cooled down to cryogenic temperatures to achieve higher-resolution infrared spectra, and individual ions can be mass selected prior to irradiation for a background-free photodissociation scheme. Conveniently, multiple tagged analyte ions can be mass isolated and efficiently irradiated in the same experiment, allowing their infrared spectra to be recorded in parallel. This multiplexed approach is critical in terms of increasing the duty cycle of infrared ion spectroscopy, which is currently a key weakness of the technique. The compact design of this instrument, coupled with powerful mass selection capabilities, set the stage for making cryogenic infrared ion spectroscopy viable as a bioanalytical tool in small molecule identification.
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Affiliation(s)
| | | | | | | | - Nicolas C. Polfer
- Correspondence to Nicolas C. Polfer, Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, FL 32611-7200, USA.
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17
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Patrick AL, Cismesia AP, Tesler LF, Polfer NC. Effects of ESI conditions on kinetic trapping of the solution-phase protonation isomer of p-aminobenzoic acid in the gas phase. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2017; 418:148-155. [PMID: 28781574 PMCID: PMC5542407 DOI: 10.1016/j.ijms.2016.09.022] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The effects of electrospray ionization (ESI) solvent and source temperature on the relative abundance of the preferred solution-phase (N-protonated; i.e. amine) versus preferred gas-phase (O-protonated; i.e., acid) isomers of p-aminobenzoic acid (PABA) were investigated. When PABA was electrosprayed from protic solvents (i.e., methanol/water), the infrared multiple photon dissociation (IRMPD) spectrum recorded was consistent with that for O-protonation, according to both calculations and previous studies. When aprotic solvent (i.e., acetonitrile) was used, a different spectrum was recorded and was assigned to the N-protonated isomer. As the amine is the preferred protonation site in solution, this suggests that an isomerization takes place under certain conditions. Photodissociation at the diagnostic band for the O-protonated isomer (NH2 stretching mode) was used to quantify the relative contributions of each isomer to ion signal as a function of ESI conditions. For mixtures of methanol and acetonitrile, the relative contribution of the O-protonated gas-phase structure increased as a function of methanol content. Yet, substituting methanol for water resulted in a marked decrease of isomerization to the O-protonated structure. The source temperature (i.e., temperature of a heated desolvation capillary) was found to play a key role in determining the extent of isomerization, with higher temperatures yielding increased presence of gas-phase structures. These results are consistent with a protic bridge mechanism, in which the ESI droplet temperatures, dependent on endothermic desolvation and radiative heating from the capillary, may determine the isomerization yield.
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Cismesia AP, Nicholls GR, Polfer NC. Amine vs. carboxylic acid protonation in ortho-, meta-, and para-aminobenzoic acid: An IRMPD spectroscopy study. JOURNAL OF MOLECULAR SPECTROSCOPY 2017; 332:79-85. [PMID: 28439142 PMCID: PMC5400370 DOI: 10.1016/j.jms.2016.10.020] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Infrared multiple photon dissociation (IRMPD) spectroscopy and computational chemistry are applied to the ortho-, meta-, and para- positional isomers of aminobenzoic acid to investigate whether the amine or the carboxylic acid are the favored sites of proton attachment in the gas phase. The NH and OH stretching modes yield distinct patterns that establish the carboxylic acid as the site of protonation in para-aminobenzoic acid, as opposed to the amine group in ortho- and meta-aminobenzoic acid, in agreement with computed thermochemistries. The trends for para- and meta-substitutions can be rationalized simplistically by inductive effects and resonant stabilization, and will be discussed in light of computed charge distributions based from electrostatic potentials. In ortho-aminobenzoic acid, the close proximity of the amine and acid groups allow a simultaneous interaction of the proton with both groups, thus stabilizing and delocalizing the charge more effectively, and compensating for some of the resonance stabilization effects.
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Scuderi D, Bodo E, Chiavarino B, Fornarini S, Crestoni ME. Amino Acid Oxidation: A Combined Study of Cysteine Oxo Forms by IRMPD Spectroscopy and Simulations. Chemistry 2016; 22:17239-17250. [PMID: 27808437 DOI: 10.1002/chem.201603298] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Indexed: 01/02/2023]
Abstract
The redox activity of cysteine sulfur allows numerous post-translational protein modifications involved in the oxidative regulation of metabolism, in metal binding, and in signal transduction. A combined approach based on infrared multiple photon dissociation spectroscopy at the Centre Laser Infrarouge d'Orsay (CLIO) free electron laser facility, calculations of IR frequencies, and finite temperature ab initio molecular dynamics simulations has been employed to characterize the gas-phase structures of deprotonated cysteine sulfenic, sulfinic, and sulfonic acids, [cysSOx ]- (x=1, 2, 3, representing the number of S-bound oxygen atoms), which are key intermediates in the redox-switching chemistry of proteins. The ions show different structural motifs owing to preferential binding of the proton to either the carboxylate or sulfur-containing group. Due to the decreasing basicity of the sulfenic, sulfinic, and sulfonic terminals, the proton bound to SO- in [cysSO]- migrates to the carboxylate in [cysSO3 ]- , whereas it turns out to be shared in [cysSO2 ]- . Evidence is gathered that a mixture of close-lying low-energy conformers is sampled for each cysteine oxo form in a Paul ion trap at room temperature.
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Affiliation(s)
- Debora Scuderi
- Laboratoire de Chimie Physique d'Orsay, Faculté des Sciences, Université Paris Sud, UMR8000 CNRS, Bât 350, 91405, Orsay Cedex, France
| | - Enrico Bodo
- Dipartimento di Chimica, Università degli Studi di Roma La Sapienza, P.le A. Moro 5, 00185, Roma, Italy
| | - Barbara Chiavarino
- Dipartimento di Chimica e Tecnologie del Farmaco, Università degli Studi di Roma La Sapienza, P.le A. Moro 5, 00185, Roma, Italy
| | - Simonetta Fornarini
- Dipartimento di Chimica e Tecnologie del Farmaco, Università degli Studi di Roma La Sapienza, P.le A. Moro 5, 00185, Roma, Italy
| | - Maria Elisa Crestoni
- Dipartimento di Chimica e Tecnologie del Farmaco, Università degli Studi di Roma La Sapienza, P.le A. Moro 5, 00185, Roma, Italy
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20
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Paciotti R, Coletti C, Re N, Scuderi D, Chiavarino B, Fornarini S, Crestoni ME. Serine O-sulfation probed by IRMPD spectroscopy. Phys Chem Chem Phys 2016; 17:25891-904. [PMID: 26027702 DOI: 10.1039/c5cp01409c] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The sulfation of amino acids is a frequent post-translational modification. It is highly labile, though, and characterizing it by mass spectrometry, an otherwise powerful and widely exploited tool in analytical proteomics, is a challenge. The presently reported study is aimed at revealing the O-sulfation of l-serine and elucidating the effects of protonation and deprotonation on the structure and stability of the ensuing ionic species, [sSer + H](+) and [sSer - H](-). These ions are obtained as gaseous, isolated species by electrospray ionization, trapped in a Paul ion-trap, and sampled by IR multiple photon dissociation (IRMPD) spectroscopy in either the 750-1900 cm(-1) fingerprint range, or the 2900 and 3700 cm(-1) range encompassing the N-H and O-H stretching modes. The recorded IRMPD spectra present diagnostic signatures of the sulfate modification which are missing in the spectra of the native serine ions, [Ser + H](+) and [Ser - H](-). The experimental IRMPD features have been interpreted by comparison with the linear IR spectra of the lowest energy structures that are likely candidates for the sampled ions, calculated at the M06-2X/6-311+G(d,p) level of theory. Evidence is gathered that the most stable conformations of [sSer + H](+) are stabilized by hydrogen bonding interactions between the protonated amino group and both the carbonyl and sulfate oxygens. [sSer - H](-) ions possess a negatively charged sulfate group involved in either a S=O···HN or a S=O···HO hydrogen bond. The experimental IRMPD spectra are consistent with the presence of multiple low-lying structures in a thermally equilibrated population of several species particularly in the case of [sSer - H](-) ions, where the high structural flexibility combined with the presence of a negative charge favors the co-existence of several different H-bonding motifs.
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Affiliation(s)
- Roberto Paciotti
- Dipartimento di Farmacia, Università G. D'Annunzio, Via dei Vestini 31, I-66100 Chieti, Italy
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Corinti D, Mannina L, Chiavarino B, Steinmetz V, Fornarini S, Crestoni ME. IRMPD signature of protonated pantothenic acid, an ubiquitous nutrient. Chem Phys Lett 2016. [DOI: 10.1016/j.cplett.2016.01.032] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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22
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Masson A, Williams ER, Rizzo TR. Molecular hydrogen messengers can lead to structural infidelity: A cautionary tale of protonated glycine. J Chem Phys 2015; 143:104313. [DOI: 10.1063/1.4930196] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Antoine Masson
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland
| | - Evan R. Williams
- Department of Chemistry, University of California, Berkeley, California 94720-1460, USA
| | - Thomas R. Rizzo
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland
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23
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Alahmadi YJ, Gholami A, Fridgen TD. The protonated and sodiated dimers of proline studied by IRMPD spectroscopy in the N-H and O-H stretching region and computational methods. Phys Chem Chem Phys 2015; 16:26855-63. [PMID: 25375752 DOI: 10.1039/c4cp03104k] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
IRMPD spectroscopy and computational chemistry techniques have been used to determine that the proton- and sodium-bound dimers of proline exist as a mixture of a number of different structures. Simulated annealing computations were found to be helpful in determining the unique structures of the protonated and sodiated dimers, augmenting chemical intuition. The experimental and computational results are consistent with the proton-bound dimer of N-protonated proline bound to zwitterionic proline. There was no spectroscopic evidence in the 3200-3800 cm(-1) region for a canonical structure which is predicted to have a weak N-H stretch at about 3440 cm(-1). A well resolved band at 1733 cm(-1) from a previous spectroscopic study (DOI: 10.1021/ja068715a ) was reassigned from a high energy canonical isomer to the C=O stretch of a lower energy zwitterionic structure. This band is a free carboxylate C=O stretch where protonated proline is hydrogen bonded to the other carboxylate oxygen which is also involved in an intramolecular hydrogen bond. Fifteen structures of the sodium bound proline dimer were computed to be within 10 kJ mol(-1) of Gibbs energy and eight structures were within 5 kJ mol(-1). None of these structures can be ruled out based on the experimental IRMPD spectrum. They all have an N-H stretching band predicted in a position that agrees with the experimental spectrum. However, only structures where one of the proline monomers is in the canonical form and having a free O-H bond can produce the band at ∼3600 cm(-1).
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24
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Chiavarino B, Crestoni ME, Fornarini S, Scuderi D, Salpin JY. Interaction of cisplatin with 5'-dGMP: a combined IRMPD and theoretical study. Inorg Chem 2015; 54:3513-22. [PMID: 25798661 DOI: 10.1021/acs.inorgchem.5b00070] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
IR multiple photon dissociation (IRMPD) spectroscopy of cis-[Pt(NH3)2(5'-dGMP-H)](+) and cis-[PtCl(NH3)2(5'-dGMP)](+) ions (where 5'-dGMP is 2'-deoxyguanosine-5'-monophosphate), generated in the gas phase by electrospray ionization, was performed in two spectral regions, namely, 700-1900 cm(-1) and 2800-3800 cm(-1). For structural assignment, experimental IRMPD spectra were compared to IR spectra computed at the B3LYP/LACV3P/6-311G** level of theory. In agreement with computational results, the vibrational spectroscopic characterization of the cis-[Pt(NH3)2(5'-dGMP-H)](+) ion points to macrochelate species resulting from the simultaneous interaction of the metal with both the N7 atom of the guanine residue and an O atom of the phosphate group, structures that bear features in common with those characterized in solution by NMR spectroscopy. Concerning the cis-[PtCl(NH3)2(5'-dGMP)](+) ion, our study points to a monodentate complex involving exclusively the N7 position of guanine, as observed in solution. Also this species exhibits a compact form due to the formation of two hydrogen bonds involving the same ammonia ligand. For both complexes, IRMPD experiments show that a strong intramolecular hydrogen bond is established between one ammonia hydrogen and the carbonyl group of guanine. The strength of this particular interaction can be qualitatively estimated by looking at the redshift of the CO vibration with respect to an unperturbed C═O stretching mode in the fingerprint region. This point is also highlighted in the X-H (X = N, O) stretch region, by the shift of the N-H stretch frequency as a function of the number of hydrogen bonds involving the ammonia ligand.
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Affiliation(s)
- Barbara Chiavarino
- †Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma "La Sapienza", P.le A. Moro 5, I-00185 Roma, Italy
| | - Maria Elisa Crestoni
- †Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma "La Sapienza", P.le A. Moro 5, I-00185 Roma, Italy
| | - Simonetta Fornarini
- †Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma "La Sapienza", P.le A. Moro 5, I-00185 Roma, Italy
| | | | - Jean-Yves Salpin
- ∥Université d'Evry Val d'Essonne, Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement, Boulevard François Mitterrand, 91025 Evry, France
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Qian JQ, Correra TC, Li J, Maître P, Song DQ, Hu CQ. Differentiation of cefaclor and its delta-3 isomer by electrospray mass spectrometry, infrared multiple photon dissociation spectroscopy and theoretical calculations. JOURNAL OF MASS SPECTROMETRY : JMS 2015; 50:265-269. [PMID: 25601701 DOI: 10.1002/jms.3510] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Revised: 09/08/2014] [Accepted: 09/12/2014] [Indexed: 06/04/2023]
Affiliation(s)
- Jian-Qin Qian
- Institute of Medicinal Biotechnology, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100050, China; National Institutes for Food and Drug Control, Beijing, 100050, China
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26
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Chiavarino B, Crestoni ME, Schütz M, Bouchet A, Piccirillo S, Steinmetz V, Dopfer O, Fornarini S. Cation-π interactions in protonated phenylalkylamines. J Phys Chem A 2014; 118:7130-8. [PMID: 25061749 DOI: 10.1021/jp505037n] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Phenylalkylamines of the general formula C6H5(CH2)nNH2 (n = 1-4) have been delivered to the gas phase as protonated species using electrospray ionization. The ions thus formed have been assayed by IRMPD spectroscopy in two different spectroscopic domains, namely, the 600-1800 and the 3000-3500 cm(-1) regions using either an IR free electron laser or a tabletop OPO/OPA laser source. The interpretation of the experimental spectra is aided by density functional theory calculations of candidate species and vibrational frequency analyses. Protonated benzylamine presents a relatively straightforward instance of a single stable conformer, providing a trial case for the adopted approach. Turning to the higher homologues, C6H5(CH2)nNH3(+) (n = 2-4), more conformations become accessible. For each C6H5(CH2)nNH3(+) ion (n = 2-4), the most stable geometry is characterized by cation-π interactions between the positively charged ammonium group and the aromatic π-electronic system, permitted by the folding of the polymethylene chain. The IRMPD spectra of the sampled ions confirm the presence of the folded structures by comparison with the calculated IR spectra of the various possible conformers. An inspection of the NH stretching region is helpful in this regard.
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Affiliation(s)
- Barbara Chiavarino
- Dipartimento di Chimica e Tecnologie del Farmaco, Università degli Studi di Roma La Sapienza , P. le A. Moro 5, I-00185 Roma, Italy
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Patrick AL, Stedwell CN, Polfer NC. Differentiating sulfopeptide and phosphopeptide ions via resonant infrared photodissociation. Anal Chem 2014; 86:5547-52. [PMID: 24823797 DOI: 10.1021/ac500992f] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The post-translational modifications sulfation and phosphorylation pose special challenges to mass spectral analysis due to their isobaric nature and their lability in the gas phase, as both types of peptides dissociate through similar channels upon collisional activation. Here, we present resonant infrared photodissociation based on diagnostic sulfate and phosphate OH stretches, as a means to differentiate sulfated from phosphorylated peptides within the framework of a mass spectrometry platform. The approach is demonstrated for a number of tyrosine-containing peptides, ranging from dipeptides (YG, pYG, and sYG) over tripeptides (GYR, GpYR, and GsYR), to more biologically relevant enkephalin peptides (YGGFL, pYGGFL, and sYGGFL). In all cases, the diagnostic ranges for sulfate OH stretches are established as 3580-3600 cm(-1) and can thus be distinguished from other characteristic hydrogen stretches, such as carboxylic acid OH, alcohol OH, and phosphate OH stretches.
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Affiliation(s)
- Amanda L Patrick
- Department of Chemistry, University of Florida , P.O. Box 117200, Gainesville, Florida 32611, United States
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