1
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Spencer RJ, Zhanserkeev AA, Yang EL, Steele RP. The Near-Sightedness of Many-Body Interactions in Anharmonic Vibrational Couplings. J Am Chem Soc 2024; 146:15376-15392. [PMID: 38771156 DOI: 10.1021/jacs.4c03198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Couplings between vibrational motions are driven by electronic interactions, and these couplings carry special significance in vibrational energy transfer, multidimensional spectroscopy experiments, and simulations of vibrational spectra. In this investigation, the many-body contributions to these couplings are analyzed computationally in the context of clathrate-like alkali metal cation hydrates, including Cs+(H2O)20, Rb+(H2O)20, and K+(H2O)20, using both analytic and quantum-chemistry potential energy surfaces. Although the harmonic spectra and one-dimensional anharmonic spectra depend strongly on these many-body interactions, the mode-pair couplings were, perhaps surprisingly, found to be dominated by one-body effects, even in cases of couplings to low-frequency modes that involved the motion of multiple water molecules. The origin of this effect was traced mainly to geometric distortion within water monomers and cancellation of many-body effects in differential couplings, and the effect was also shown to be agnostic to the identity of the ion. These outcomes provide new understanding of vibrational couplings and suggest the possibility of improved computational methods for the simulation of infrared and Raman spectra.
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Affiliation(s)
- Ryan J Spencer
- Department of Chemistry and Henry Eyring Center for Theoretical Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Asylbek A Zhanserkeev
- Department of Chemistry and Henry Eyring Center for Theoretical Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Emily L Yang
- Department of Chemistry and Henry Eyring Center for Theoretical Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Ryan P Steele
- Department of Chemistry and Henry Eyring Center for Theoretical Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
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2
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Schleier D, Kamer J, Martens J, Berden G, Oomens J, Bouwman J. Exploring the Scaling Factors for Infrared Modes of PANHs - A Case Study on Cationic 3-Azafluoranthene⋅ + and Protonated 3-Azafluoranthene. Chemphyschem 2024:e202300915. [PMID: 38758018 DOI: 10.1002/cphc.202300915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 05/15/2024] [Accepted: 05/16/2024] [Indexed: 05/18/2024]
Abstract
Infrared (IR) emission bands by interstellar polycyclic aromatic hydrocarbons (PAHs) and polycyclic aromatic nitrogen heterocycles (PANHs) are observed towards a large variety of interstellar objects and offer detailed insights into the chemistry and physics of the interstellar medium. The analysis of the emission bands, and thus the interpretation of the molecular characteristics of the carriers, heavily relies on the use of density functional theory (DFT) calculated IR spectra. However, there are significant challenges in accurately predicting the experimental IR band positions, particularly for PANH emission vibrational modes around 6 μm. In this work, we present gas-phase mid-infrared (mid-IR) spectra of cationic 3-azafluoranthene (3AF⋅+) and protonated 3-azafluoranthene (3AFH+) to investigate their experimental IR band positions in relation to DFT calculated bands. The experimental spectra are compared to DFT simulated spectra, where different approaches were followed to correct for anharmonicities. The best agreement is achieved by scaling frequencies of modes with large nitrogen displacements with a different factor. Even though our findings might be limited to a small number of PANH structures, they indicate, that nitrogen atom incorporation needs to be accounted for by carefully adjusting the corresponding scaling factors while computing IR spectra of PANHs on DFT level.
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Affiliation(s)
- Domenik Schleier
- Laboratory for Astrophysics, Leiden Observatory, University Leiden, Einsteinweg 55, 2333 CA, Leiden, The, Netherlands
- Lehrstuhl Technische Thermodynamik, Fakultät für Maschinenbau, Universität Paderborn, Warburger Str. 100, 33098, Paderborn, Germany
| | - Jerry Kamer
- Laboratory for Astrophysics, Leiden Observatory, University Leiden, Einsteinweg 55, 2333 CA, Leiden, The, Netherlands
| | - Jonathan Martens
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University Nijmegen, Toernooiveld 7, 6525 ED, Nijmegen, The, Netherlands
| | - Giel Berden
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University Nijmegen, Toernooiveld 7, 6525 ED, Nijmegen, The, Netherlands
| | - Jos Oomens
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University Nijmegen, Toernooiveld 7, 6525 ED, Nijmegen, The, Netherlands
- University of Amsterdam, 1098 XH, Amsterdam, The Netherlands
| | - Jordy Bouwman
- Laboratory for Atmospheric and Space Physics, University of Colorado, Boulder, Colorado, 80303, USA
- Department of Chemistry, University of Colorado, Boulder, Colorado, 80309, USA
- Institute for Modeling Plasma, Atmospheres and Cosmic Dust (IMPACT), NASA/SSERVI, Boulder, Colorado, 80309, USA
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3
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Kelly JT, McNamara LE, Hoover ME, Rubenstein HM, Houthuijs K, Martens J. Development of Nontargeted Workflow of Occupational Exposure by Infrared Ion Spectroscopy and Silicone Wristbands' Passive Sampling. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:829-833. [PMID: 38564189 DOI: 10.1021/jasms.3c00400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
A new approach using orthogonal analytical techniques is developed for chemical identification. High resolution mass spectrometry and infrared ion spectroscopy are applied through a 5-level confidence paradigm to demonstrate the effectiveness of nontargeted workflow for the identification of hazardous organophosphates. Triphenyl phosphate is used as a surrogate organophosphate for occupational exposure, and silicone wristbands are used to represent personal samplers. Spectral data of a target compound is combined with spectral data of the sodium adduct and quantum chemical calculations to achieve a confirmed identification. Here, we demonstrate a nontargeted workflow that identifies organophosphate exposure and provides a mechanism for selecting validated methods for quantitative analyses.
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Affiliation(s)
- John T Kelly
- Savannah River National Laboratory, 301 Gateway Drive, Aiken, South Carolina 29803, United States
| | - Louis E McNamara
- Savannah River National Laboratory, 301 Gateway Drive, Aiken, South Carolina 29803, United States
| | - Megan E Hoover
- Savannah River National Laboratory, 301 Gateway Drive, Aiken, South Carolina 29803, United States
| | - H Mitchell Rubenstein
- United States Air Force - Air Force Research Laboratory, 711th Human Performance Wing, 2510 Fifth Street, Area B, Building 840, Wright-Patterson AFB, Ohio 45433, United States
| | - Kas Houthuijs
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7c, 6525ED Nijmegen, The Netherlands
| | - Jonathan Martens
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7c, 6525ED Nijmegen, The Netherlands
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4
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Lee AE, Featherstone J, Martens J, McMahon TB, Hopkins WS. Fluorinated Propionic Acids Unmasked: Puzzling Fragmentation Phenomena of the Deprotonated Species. J Phys Chem Lett 2024; 15:3029-3036. [PMID: 38466046 DOI: 10.1021/acs.jpclett.3c03400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Environmental contamination by per- and polyfluorinated substances (PFAS) is an emerging concern for the public. In this study, short-chain PFAS such as deprotonated per- and polyfluorinated propionic acids are investigated using a combination of infrared multiple-photon dissociation (IRMPD) spectroscopy, collision-induced dissociation (CID), and density functional theory calculations. IRMPD and CID proceed via multiple competing pathways: (1) production of fluoroformate (FCO2-) and the associated ethylene derivative, (2) production of HF and the associated carbanion, or (3) loss of CO2 and the associated carbanion. Fluorinated propionic acids with at least one fluorine atom bound to the terminal carbon yield FCO2-, whereas loss of HF is observed in polyfluorinated species with at least one fluorine atom bound to the α-carbon. To explore the reaction pathways of the various fluorinated propionic acids, the nudged elastic band method is employed. The relative energy of the four-membered ring transition state leading to FCO2- dictates which product channel is observed in dissociation.
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Affiliation(s)
- Arthur E Lee
- Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Josh Featherstone
- Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Jonathan Martens
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525ED Nijmegen, The Netherlands
| | - Terrance B McMahon
- Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - W Scott Hopkins
- Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
- Watermine Innovation, Waterloo, Ontario N0B 2T0, Canada
- Centre for Eye and Vision Research, Hong Kong Science Park, New Territories 999077, Hong Kong SAR, China
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5
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Moons PH, Ter Braak F, de Kleijne FFJ, Bijleveld B, Corver SJR, Houthuijs KJ, Almizori HR, Berden G, Martens J, Oomens J, White PB, Boltje TJ. Characterization of elusive rhamnosyl dioxanium ions and their application in complex oligosaccharide synthesis. Nat Commun 2024; 15:2257. [PMID: 38480691 PMCID: PMC10937939 DOI: 10.1038/s41467-024-46522-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 02/29/2024] [Indexed: 03/17/2024] Open
Abstract
Attaining complete anomeric control is still one of the biggest challenges in carbohydrate chemistry. Glycosyl cations such as oxocarbenium and dioxanium ions are key intermediates of glycosylation reactions. Characterizing these highly-reactive intermediates and understanding their glycosylation mechanisms are essential to the stereoselective synthesis of complex carbohydrates. Although C-2 acyl neighbouring-group participation has been well-studied, the reactive intermediates in more remote participation remain elusive and are challenging to study. Herein, we report a workflow that is utilized to characterize rhamnosyl 1,3-bridged dioxanium ions derived from C-3 p-anisoyl esterified donors. First, we use a combination of quantum-chemical calculations and infrared ion spectroscopy to determine the structure of the cationic glycosylation intermediate in the gas-phase. In addition, we establish the structure and exchange kinetics of highly-reactive, low-abundance species in the solution-phase using chemical exchange saturation transfer, exchange spectroscopy, correlation spectroscopy, heteronuclear single-quantum correlation, and heteronuclear multiple-bond correlation nuclear magnetic resonance spectroscopy. Finally, we apply C-3 acyl neighbouring-group participation to the synthesis of complex bacterial oligosaccharides. This combined approach of finding answers to fundamental physical-chemical questions and their application in organic synthesis provides a robust basis for elucidating highly-reactive intermediates in glycosylation reactions.
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Affiliation(s)
- Peter H Moons
- Synthetic Organic Chemistry, Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Floor Ter Braak
- Synthetic Organic Chemistry, Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Frank F J de Kleijne
- Synthetic Organic Chemistry, Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Bart Bijleveld
- Synthetic Organic Chemistry, Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Sybren J R Corver
- Synthetic Organic Chemistry, Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Kas J Houthuijs
- FELIX laboratory, Institute for Molecules and Materials, Radboud University Nijmegen, Toernooiveld 7, 6525 ED, Nijmegen, The Netherlands
| | - Hero R Almizori
- Synthetic Organic Chemistry, Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Giel Berden
- FELIX laboratory, Institute for Molecules and Materials, Radboud University Nijmegen, Toernooiveld 7, 6525 ED, Nijmegen, The Netherlands
| | - Jonathan Martens
- FELIX laboratory, Institute for Molecules and Materials, Radboud University Nijmegen, Toernooiveld 7, 6525 ED, Nijmegen, The Netherlands
| | - Jos Oomens
- FELIX laboratory, Institute for Molecules and Materials, Radboud University Nijmegen, Toernooiveld 7, 6525 ED, Nijmegen, The Netherlands
| | - Paul B White
- Synthetic Organic Chemistry, Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands.
| | - Thomas J Boltje
- Synthetic Organic Chemistry, Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands.
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6
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Gámez F, Avilés-Moreno JR, Martens J, Berden G, Oomens J, Martínez-Haya B. Vibrational signatures of dynamic excess proton storage between primary amine and carboxylic acid groups. J Chem Phys 2024; 160:094311. [PMID: 38450729 DOI: 10.1063/5.0192331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 02/20/2024] [Indexed: 03/08/2024] Open
Abstract
Ammonium and carboxylic moieties play a central role in proton-mediated processes of molecular recognition, charge transfer or chemical change in (bio)materials. Whereas both chemical groups constitute acid-base pairs in organic salt-bridge structures, they may as well host excess protons in acidic environments. The binding of excess protons often precedes proton transfer reactions and it is therefore of fundamental interest, though challenging from a quantum chemical perspective. As a benchmark for this process, we investigate proton storage in the amphoteric compound 5-aminovaleric acid (AV), within an intramolecular proton bond shared by its primary amine and carboxylic acid terminal groups. Infrared ion spectroscopy is combined with ab initio Molecular Dynamics (AIMD) calculations to expose and rationalize the spectral signatures of protonated AV and its deuterated isotopologues. The dynamic character of the proton bond confers a fluxional structure to the molecular framework, leading to wide-ranging bands in the vibrational spectrum. These features are reproduced with remarkable accuracy by AIMD computations, which serves to lay out microscopic insights into the excess proton binding scenario.
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Affiliation(s)
- F Gámez
- Department of Physical Chemistry, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - J R Avilés-Moreno
- Department of Applied Physical Chemistry, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - J Martens
- FELIX Laboratory, Institute for Molecules and Materials, Radboud University, Toernooiveld 7, 6525ED Nijmegen, The Netherlands
| | - G Berden
- FELIX Laboratory, Institute for Molecules and Materials, Radboud University, Toernooiveld 7, 6525ED Nijmegen, The Netherlands
| | - J Oomens
- FELIX Laboratory, Institute for Molecules and Materials, Radboud University, Toernooiveld 7, 6525ED Nijmegen, The Netherlands
| | - B Martínez-Haya
- Center for Nanoscience and Sustainable Technologies (CNATS), Universidad Pablo de Olavide, 41013 Seville, Spain
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7
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van Tetering L, Spies S, Wildeman QDK, Houthuijs KJ, van Outersterp RE, Martens J, Wevers RA, Wishart DS, Berden G, Oomens J. A spectroscopic test suggests that fragment ion structure annotations in MS/MS libraries are frequently incorrect. Commun Chem 2024; 7:30. [PMID: 38355930 PMCID: PMC10867025 DOI: 10.1038/s42004-024-01112-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Accepted: 01/22/2024] [Indexed: 02/16/2024] Open
Abstract
Modern untargeted mass spectrometry (MS) analyses quickly detect and resolve thousands of molecular compounds. Although features are readily annotated with a molecular formula in high-resolution small-molecule MS applications, the large majority of them remains unidentified in terms of their full molecular structure. Collision-induced dissociation tandem mass spectrometry (CID-MS2) provides a diagnostic molecular fingerprint to resolve the molecular structure through a library search. However, for de novo identifications, one must often rely on in silico generated MS2 spectra as reference. The ability of different in silico algorithms to correctly predict MS2 spectra and thus to retrieve correct molecular structures is a topic of lively debate, for instance in the CASMI contest. Underlying the predicted MS2 spectra are the in silico generated product ion structures, which are normally not used in de novo identification, but which can serve to critically assess the fragmentation algorithms. Here we evaluate in silico generated MSn product ion structures by comparison with structures established experimentally by infrared ion spectroscopy (IRIS). For a set of three dozen product ion structures from five precursor molecules, we find that virtually all fragment ion structure annotations in three major in silico MS2 libraries (HMDB, METLIN, mzCloud) are incorrect and caution the reader against their use for structure annotation of MS/MS ions.
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Affiliation(s)
- Lara van Tetering
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525ED, Nijmegen, The Netherlands
| | - Sylvia Spies
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525ED, Nijmegen, The Netherlands
| | - Quirine D K Wildeman
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525ED, Nijmegen, The Netherlands
| | - Kas J Houthuijs
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525ED, Nijmegen, The Netherlands
| | - Rianne E van Outersterp
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525ED, Nijmegen, The Netherlands
| | - Jonathan Martens
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525ED, Nijmegen, The Netherlands
| | - Ron A Wevers
- Department of Laboratory Medicine, Translational Metabolic Laboratory, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525GA, Nijmegen, The Netherlands
| | - David S Wishart
- Departments of Computing Science and Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - 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.
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8
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Wan J, Nytka M, Qian H, Vu K, Lemr K, Tureček F. Nitrile Imines as Peptide and Oligonucleotide Photo-Cross-Linkers in Gas-Phase Ions. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:344-356. [PMID: 38252626 DOI: 10.1021/jasms.3c00379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Nitrile imines produced by photodissociation of 2,5-diaryltetrazoles undergo cross-linking reactions with amide groups in peptide-tetrazole (tet-peptide) conjugates and a tet-peptide-dinucleotide complex. Tetrazole photodissociation in gas-phase ions is efficient, achieving ca. 50% conversion with 2 laser pulses at 250 nm. The formation of cross-links was detected by CID-MS3 that showed structure-significant dissociations by loss of side-chain groups and internal peptide segments. The structure and composition of cross-linking products were established by a combination of UV-vis action spectroscopy and cyclic ion mobility mass spectrometry (c-IMS). The experimental absorption bands were found to match the bands calculated for vibronic absorption spectra of nitrile imines and cross-linked hydrazone isomers. The calculated collision cross sections (CCSth) for these ions were related to the matching experimental CCSexp from multipass c-IMS measurements. Loss of N2 from tet-peptide conjugates was calculated to be a mildly endothermic reaction with ΔH0 = 80 kJ mol-1 in the gas phase. The excess energy in the photolytically formed nitrile imine is thought to drive endothermic proton transfer, followed by exothermic cyclization to a sterically accessible peptide amide group. The exothermic nitrile imine reaction with peptide amides is promoted by proton transfer and may involve an initial [3 + 2] cycloaddition followed by cleavage of the oxadiazole intermediate. Nucleophilic groups, such as cysteine thiol, did not compete with the amide cyclization. Nitrile imine cross-linking to 2'-deoxycytidylguanosine was found to be >80% efficient and highly specific in targeting guanine. The further potential for exploring nitrile-imine cross-linking for biomolecular structure analysis is discussed.
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Affiliation(s)
- Jiahao Wan
- Department of Chemistry, Bagley Hall, Box 351700, University of Washington, Seattle, Washington 98195-1700, United States
| | - Marianna Nytka
- Department of Analytical Chemistry, Faculty of Science, Palacky University, 17. listopadu 12, Olomouc 779 00, Czech Republic
| | - Haocheng Qian
- Department of Chemistry, Bagley Hall, Box 351700, University of Washington, Seattle, Washington 98195-1700, United States
| | - Kim Vu
- Department of Chemistry, Bagley Hall, Box 351700, University of Washington, Seattle, Washington 98195-1700, United States
| | - Karel Lemr
- Department of Analytical Chemistry, Faculty of Science, Palacky University, 17. listopadu 12, Olomouc 779 00, Czech Republic
- Institute of Microbiology of the Czech Academy of Sciences, Prague 142 20, Czech Republic
| | - František Tureček
- Department of Chemistry, Bagley Hall, Box 351700, University of Washington, Seattle, Washington 98195-1700, United States
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9
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Remmerswaal W, Elferink H, Houthuijs KJ, Hansen T, ter Braak F, Berden G, van der Vorm S, Martens J, Oomens J, van der Marel GA, Boltje TJ, Codée JDC. Anomeric Triflates versus Dioxanium Ions: Different Product-Forming Intermediates from 3-Acyl Benzylidene Mannosyl and Glucosyl Donors. J Org Chem 2024; 89:1618-1625. [PMID: 38235652 PMCID: PMC10845153 DOI: 10.1021/acs.joc.3c02262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 12/19/2023] [Accepted: 12/28/2023] [Indexed: 01/19/2024]
Abstract
Minimal structural differences in the structure of glycosyl donors can have a tremendous impact on their reactivity and the stereochemical outcome of their glycosylation reactions. Here, we used a combination of systematic glycosylation reactions, the characterization of potential reactive intermediates, and in-depth computational studies to study the disparate behavior of glycosylation systems involving benzylidene glucosyl and mannosyl donors. While these systems have been studied extensively, no satisfactory explanations are available for the differences observed between the 3-O-benzyl/benzoyl mannose and glucose donor systems. The potential energy surfaces of the different reaction pathways available for these donors provide an explanation for the contrasting behavior of seemingly very similar systems. Evidence has been provided for the intermediacy of benzylidene mannosyl 1,3-dioxanium ions, while the formation of the analogous 1,3-glucosyl dioxanium ions is thwarted by a prohibitively strong flagpole interaction of the C-2-O-benzyl group with the C-5 proton in moving toward the transition state, in which the glucose ring adopts a B2,5-conformation. This study provides an explanation for the intermediacy of 1,3-dioxanium ions in the mannosyl system and an answer to why these do not form from analogous glucosyl donors.
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Affiliation(s)
- Wouter
A. Remmerswaal
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2300 RA, The Netherlands
| | - Hidde Elferink
- Institute
for Molecules and Materials, Radboud University, Heyendaalseweg 135, Nijmegen 6525 AJ, The Netherlands
| | - Kas J. Houthuijs
- Institute
for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7, Nijmegen 6525 ED, The Netherlands
| | - Thomas Hansen
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2300 RA, The Netherlands
- Department
of Chemistry and Pharmaceutical Sciences, Amsterdam Institute of Molecular
and Life Sciences (AIMMS), Vrije Universiteit
Amsterdam, De Boelelaan
1108, Amsterdam 1081 HZ, The Netherlands
| | - Floor ter Braak
- Institute
for Molecules and Materials, Radboud University, Heyendaalseweg 135, Nijmegen 6525 AJ, The Netherlands
| | - Giel Berden
- Institute
for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7, Nijmegen 6525 ED, The Netherlands
| | - Stefan van der Vorm
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2300 RA, The Netherlands
| | - Jonathan Martens
- Institute
for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7, Nijmegen 6525 ED, The Netherlands
| | - Jos Oomens
- Institute
for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7, Nijmegen 6525 ED, The Netherlands
| | | | - Thomas J. Boltje
- Institute
for Molecules and Materials, Radboud University, Heyendaalseweg 135, Nijmegen 6525 AJ, The Netherlands
| | - Jeroen D. C. Codée
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2300 RA, The Netherlands
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10
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Vink MA, Alarcan J, Martens J, Buma WJ, Braeuning A, Berden G, Oomens J. Structural Elucidation of Agrochemical Metabolic Transformation Products Based on Infrared Ion Spectroscopy to Improve In Silico Toxicity Assessment. Chem Res Toxicol 2024; 37:81-97. [PMID: 38118149 PMCID: PMC10792670 DOI: 10.1021/acs.chemrestox.3c00316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 12/03/2023] [Accepted: 12/05/2023] [Indexed: 12/22/2023]
Abstract
Toxicological assessments of newly developed agrochemical agents consider chemical modifications and their metabolic and biotransformation products. To carry out an in silico hazard assessment, understanding the type of chemical modification and its location on the original compound can greatly enhance the reliability of the evaluation. Here, we present and apply a method based on liquid chromatography-mass spectrometry (LC-MS) enhanced with infrared ion spectroscopy (IRIS) to better delineate the molecular structures of transformation products before in silico toxicology evaluation. IRIS facilitates the recording of IR spectra directly in the mass spectrometer for features selected by retention time and mass-to-charge ratio. By utilizing quantum-chemically predicted IR spectra for candidate molecular structures, one can either derive the actual structure or significantly reduce the number of (isomeric) candidate structures. This approach can assist in making informed decisions. We apply this method to a plant growth stimulant, digeraniol sinapoyl malate (DGSM), that is currently under development. Incubation of the compound in Caco-2 and HepaRG cell lines in multiwell plates and analysis by LC-MS reveals oxidation, glucuronidation, and sulfonation metabolic products, whose structures were elucidated by IRIS and used as input for an in silico toxicology assessment. The toxicity of isomeric metabolites predicted by in silico tools was also assessed, which revealed that assigning the right metabolite structure is an important step in the overall toxicity assessment of the agrochemical. We believe this identification approach can be advantageous when specific isomers are significantly more hazardous than others and can help better understand metabolic pathways.
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Affiliation(s)
- Matthias
J. A. Vink
- Institute
for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
| | - Jimmy Alarcan
- Department
of Food Safety, German Federal Institute
for Risk Assessment, Max-Dohrn-Str. 8-10, 10589 Berlin, Germany
| | - Jonathan Martens
- Institute
for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
| | - Wybren Jan Buma
- Institute
for Molecules and Materials, FELIX Laboratory, 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
| | - Albert Braeuning
- Department
of Food Safety, German Federal Institute
for Risk Assessment, Max-Dohrn-Str. 8-10, 10589 Berlin, Germany
| | - 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
- van’t
Hoff Institute for Molecular Sciences, University
of Amsterdam, Science
Park 904, 1098 XH Amsterdam, The Netherlands
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11
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Ribeiro FWM, Omari I, Thomas GT, Paul M, Williams PJH, McIndoe JS, Correra TC. Microstructural Analysis of Benzoxazine Cationic Ring-Opening Polymerization Pathways. Macromol Rapid Commun 2024; 45:e2300470. [PMID: 37716013 DOI: 10.1002/marc.202300470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 09/06/2023] [Indexed: 09/18/2023]
Abstract
Herein, an evaluation of the initial step of benzoxazine polymerization is presented by mass spectrometry, with a focus on differentiating the phenoxy and phenolic products formed by distinct pathways of the cationic ring opening polymerization (ROP) mechanism of polybenzoxazine formation. The use of infrared multiple photon dissociation (IRMPD) and ion mobility spectrometry (IMS) techniques allows for differentiation of the two pathways and provides valuable insights into the ROP mechanism. The results suggest that type I pathway is favored in the initial stages of the reaction yielding the phenoxy product, while type II product should be observed at later stages when the phenoxy product would interconvert to the most stable type II phenolic product. Overall, the findings presented here provide important information on the initial step of the benzoxazine polymerization, allowing the development of optimal polymerization conditions and represents a way to evaluate other multifunctional polymerization processes.
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Affiliation(s)
- Francisco W M Ribeiro
- Department of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes, 748, Cidade Universitária, São Paulo, SP, 05508-000, Brazil
| | - Isaac Omari
- Department of Chemistry, University of Victoria, P. O. Box 3065, Victoria, BC V8W 3V6, Canada
| | - Gilian T Thomas
- Department of Chemistry, University of Victoria, P. O. Box 3065, Victoria, BC V8W 3V6, Canada
| | - Mathias Paul
- Department of Chemistry, University of Victoria, P. O. Box 3065, Victoria, BC V8W 3V6, Canada
| | - Peter J H Williams
- Department of Chemistry, University of Victoria, P. O. Box 3065, Victoria, BC V8W 3V6, Canada
| | - J Scott McIndoe
- Department of Chemistry, University of Victoria, P. O. Box 3065, Victoria, BC V8W 3V6, Canada
| | - Thiago C Correra
- Department of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes, 748, Cidade Universitária, São Paulo, SP, 05508-000, Brazil
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12
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Martínez-Haya B, Avilés-Moreno JR, Gámez F, Martens J, Oomens J, Berden G. Correlated proton dynamics in hydrogen bonding networks: the benchmark case of 3-hydroxyglutaric acid. Phys Chem Chem Phys 2023; 26:198-208. [PMID: 38053486 DOI: 10.1039/d3cp04514e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
Proton and hydrogen-bonded networks sustain a broad range of structural and charge transfer processes in supramolecular materials. The modelling of proton dynamics is however challenging and demands insights from prototypical benchmark systems. The intramolecular H-bonding networks induced by either protonation or deprotonation of 3-hydroxyglutaric acid provide intriguing case studies of correlated proton dynamics. The vibrational signatures associated with the fluxional proton bonding and its coupling with the hydroxyglutaric backbone are investigated here with infrared action ion spectroscopy experiments and Born-Oppenheimer molecular dynamics (BOMD) computations. Despite the formally similar symmetry of protonated and deprotonated hydroxyglutaric acid, the relative proton affinities of the oxygen centers of the carboxylic and carboxylate groups with respect to that of the central hydroxyl group lead to distinct proton dynamics. In the protonated acid, a tautomeric arrangement of the type HOCO·[HOH]+·OCOH is preferred with the proton binding tighter to the central hydroxyl moiety and the electronic density being shared between the two nearly symmetric H-bonds with the carboxylic end groups. In the deprotonated acid, the asymmetric [OCO]-·HO·HOCO configuration is more stable, with a stronger H-bonding on the bare carboxylate end. Both systems display active backbone dynamics and concerted Grothuss-like proton motions, leading to diffuse band structures in their vibrational spectra. These features are accurately reproduced by the BOMD computations.
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Affiliation(s)
- Bruno Martínez-Haya
- Center for Nanoscience and Sustainable Technologies (CNATS), Universidad Pablo de Olavide, E-41013 Seville, Spain.
| | - Juan Ramón Avilés-Moreno
- Department of Applied Physical Chemistry, Universidad Autónoma de Madrid, E-28049, Madrid, Spain
| | - Francisco Gámez
- Departamento de Química Física, Universidad Complutense, E-28040 Madrid, Spain
| | - Jonathan Martens
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7, 6525ED Nijmegen, The Netherlands
| | - Jos Oomens
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7, 6525ED Nijmegen, The Netherlands
| | - Giel Berden
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7, 6525ED Nijmegen, The Netherlands
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13
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Rioux B, Mouterde LMM, Alarcan J, Abiola TT, Vink MJA, Woolley JM, Peru AAM, Mention MM, Brunissen F, Berden G, Oomens J, Braeuning A, Stavros VG, Allais F. An expeditive and green chemo-enzymatic route to diester sinapoyl-l-malate analogues: sustainable bioinspired and biosourced UV filters and molecular heaters. Chem Sci 2023; 14:13962-13978. [PMID: 38075651 PMCID: PMC10699562 DOI: 10.1039/d3sc04836e] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 11/21/2023] [Indexed: 06/03/2024] Open
Abstract
Sinapoyl malate, naturally present in plants, has proved to be an exceptional UV filter and molecular heater for plants. Although there are nowadays industrially relevant sustainable synthetic routes to sinapoyl malate, its incorporation into certain cosmetic formulations, as well as its adsorption on plant leaves, is limited by its hydrophilicity. To overcome these obstacles, it is important to find a way to effectively control the hydrophilic-lipophilic balance of sinapoyl malate to make it readily compatible with the cosmetic formulations and stick on the waxy cuticle of leaves. To this end, herein, we describe a highly regioselective chemo-enzymatic synthesis of sinapoyl malate analogues possessing fatty aliphatic chains of variable length, enabling the lipophilicity of the compounds to be modulated. The potential toxicity (i.e., mutagenicity, carcinogenicity, endocrine disruption, acute and repeated-dose toxicity), bioaccumulation, persistence and biodegradability potential of these new analogues were evaluated in silico, along with the study of their transient absorption spectroscopy, their photostability as well as their photodegradation products.
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Affiliation(s)
- Benjamin Rioux
- URD Agro-Biotechnologies Industrielles (ABI), CEBB, AgroParisTech 51110 Pomacle France
| | - Louis M M Mouterde
- URD Agro-Biotechnologies Industrielles (ABI), CEBB, AgroParisTech 51110 Pomacle France
| | - Jimmy Alarcan
- Department of Food Safety, German Federal Institute for Risk Assessment Max-Dohrn-Str. 8-10 10589 Berlin Germany
| | - Temitope T Abiola
- Department of Chemistry, University of Warwick Gibbet Hill Road CV4 7AL Coventry UK
- Department of Chemistry, Lash Miller Chemical Laboratories 80 St. George Street Toronto ON M5S 3H6 Canada
| | - Matthias J A Vink
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University Toernooiveld 7 6525ED Nijmegen Netherlands
| | - Jack M Woolley
- Department of Chemistry, University of Warwick Gibbet Hill Road CV4 7AL Coventry UK
| | - Aurélien A M Peru
- URD Agro-Biotechnologies Industrielles (ABI), CEBB, AgroParisTech 51110 Pomacle France
| | - Matthieu M Mention
- URD Agro-Biotechnologies Industrielles (ABI), CEBB, AgroParisTech 51110 Pomacle France
| | - Fanny Brunissen
- URD Agro-Biotechnologies Industrielles (ABI), CEBB, AgroParisTech 51110 Pomacle France
| | - Giel Berden
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University Toernooiveld 7 6525ED Nijmegen Netherlands
| | - Jos Oomens
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University Toernooiveld 7 6525ED Nijmegen Netherlands
| | - Albert Braeuning
- Department of Food Safety, German Federal Institute for Risk Assessment Max-Dohrn-Str. 8-10 10589 Berlin Germany
| | - Vasilios G Stavros
- Department of Chemistry, University of Warwick Gibbet Hill Road CV4 7AL Coventry UK
- School of Chemistry, University of Birmingham Edgbaston Birmingham B15 2TT UK
| | - Florent Allais
- URD Agro-Biotechnologies Industrielles (ABI), CEBB, AgroParisTech 51110 Pomacle France
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14
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Jiang Y, Clavaguéra C, Indrajith S, Houée-Levin C, Berden G, Oomens J, Scuderi D. OH Radical-Induced Oxidation in Nucleosides and Nucleotides Unraveled by Tandem Mass Spectrometry and Infrared Multiple Photon Dissociation Spectroscopy. Chemphyschem 2023; 24:e202300534. [PMID: 37713246 DOI: 10.1002/cphc.202300534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 09/14/2023] [Accepted: 09/15/2023] [Indexed: 09/16/2023]
Abstract
OH⋅-induced oxidation products of DNA nucleosides and nucleotides have been structurally characterized by collision-induced dissociation tandem mass spectrometry (CID-MS2 ) and Infrared Multiple Photon Dissociation (IRMPD) spectroscopy. CID-MS2 results have shown that the addition of one oxygen atom occurs on the nucleobase moiety. The gas-phase geometries of +16 mass increment products of 2'-deoxyadenosine (dA(O)H+ ), 2'-deoxyadenosine 5'-monophosphate (dAMP(O)H+ ), 2'-deoxycytidine (dC(O)H+ ), and 2'-deoxycytidine 5'-monophosphate (dCMP(O)H+ ) are extensively investigated by IRMPD spectroscopy and quantum-chemical calculations. We show that a carbonyl group is formed at the C8 position after oxidation of 2'-deoxyadenosine and its monophosphate derivative. For 2'-deoxycytidine and its monophosphate derivative, the oxygen atom is added to the C5 position to form a C-OH group. IRMPD spectroscopy has been employed for the first time to provide direct structural information on oxidative lesions in DNA model systems.
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Affiliation(s)
- Yining Jiang
- Université Paris-Saclay, CNRS, Institut de Chimie Physique, 91405, Orsay, France
| | - Carine Clavaguéra
- Université Paris-Saclay, CNRS, Institut de Chimie Physique, 91405, Orsay, France
| | - Suvasthika Indrajith
- Stockholm University, Roslagstullsbacken 21 C, plan 4, Albano, Fysikum, 106 91, Stockholm, Sweden
| | - Chantal Houée-Levin
- Université Paris-Saclay, CNRS, Institut de Chimie Physique, 91405, Orsay, France
| | - Giel Berden
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, Nijmegen, 6525 ED, The Netherlands
| | - Jos Oomens
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, Nijmegen, 6525 ED, The Netherlands
- Van't Hoff Institute for Molecular Sciences, University of Amsterdam, P.O. Box, 94157, Amsterdam, 1090 GD, The Netherlands
| | - Debora Scuderi
- Université Paris-Saclay, CNRS, Institut de Chimie Physique, 91405, Orsay, France
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15
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Yang EL, Talbot JJ, Spencer RJ, Steele RP. Pitfalls in the n-mode representation of vibrational potentials. J Chem Phys 2023; 159:204104. [PMID: 38010326 DOI: 10.1063/5.0176612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 10/19/2023] [Indexed: 11/29/2023] Open
Abstract
Simulations of anharmonic vibrational motion rely on computationally expedient representations of the governing potential energy surface. The n-mode representation (n-MR)-effectively a many-body expansion in the space of molecular vibrations-is a general and efficient approach that is often used for this purpose in vibrational self-consistent field (VSCF) calculations and correlated analogues thereof. In the present analysis, a lack of convergence in many VSCF calculations is shown to originate from negative and unbound potentials at truncated orders of the n-MR expansion. For cases of strong anharmonic coupling between modes, the n-MR can both dip below the true global minimum of the potential surface and lead to effective single-mode potentials in VSCF that do not correspond to bound vibrational problems, even for bound total potentials. The present analysis serves mainly as a pathology report of this issue. Furthermore, this insight into the origin of VSCF non-convergence provides a simple, albeit ad hoc, route to correct the problem by "painting in" the full representation of groups of modes that exhibit these negative potentials at little additional computational cost. Somewhat surprisingly, this approach also reasonably approximates the results of the next-higher n-MR order and identifies groups of modes with particularly strong coupling. The method is shown to identify and correct problematic triples of modes-and restore SCF convergence-in two-mode representations of challenging test systems, including the water dimer and trimer, as well as protonated tropine.
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Affiliation(s)
- Emily L Yang
- Department of Chemistry, The University of Utah, 315 S 1400 E, Salt Lake City, Utah 84112, USA
- Henry Eyring Center for Theoretical Chemistry, The University of Utah, Salt Lake City, Utah 84112, USA
| | - Justin J Talbot
- Department of Chemistry, University of California-Berkeley, 420 Latimer Hall, Berkeley, California 94720, USA
| | - Ryan J Spencer
- Department of Chemistry, The University of Utah, 315 S 1400 E, Salt Lake City, Utah 84112, USA
- Henry Eyring Center for Theoretical Chemistry, The University of Utah, Salt Lake City, Utah 84112, USA
| | - Ryan P Steele
- Department of Chemistry, The University of Utah, 315 S 1400 E, Salt Lake City, Utah 84112, USA
- Henry Eyring Center for Theoretical Chemistry, The University of Utah, Salt Lake City, Utah 84112, USA
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16
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Cucchiaro A, Scherfler A, Corinti D, Berden G, Oomens J, Wurst K, Gust R, Crestoni ME, Kircher B, Cziferszky M. Amino Acids as Chelating Ligands for Platinum: Enhanced Stability in an Aqueous Environment Promoted by Biocompatible Molecules. J Med Chem 2023; 66:15256-15268. [PMID: 37937969 PMCID: PMC10683014 DOI: 10.1021/acs.jmedchem.3c01340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 09/21/2023] [Accepted: 10/25/2023] [Indexed: 11/09/2023]
Abstract
Platinum-based chemotherapeutics are a cornerstone in the treatment of many malignancies. However, their dose-limiting side effects have rooted efforts to develop new drug candidates with higher selectivity for tumor tissues and less problematic side effects. Here, we developed a cytotoxic platinum(II) complex based on Zeise's salt, containing the nonsteroidal anti-inflammatory drug acetylsalicylic acid and alanine as ligands (4). The previously developed complex (5) displayed high reactivity against sulfur-containing biomolecules; therefore, we put the focus on the optimization of the structure regarding its stability. Different amino acids were used as biocompatible chelating ligands to achieve this aim. Differences in the coordination sphere caused pronounced changes in the stability of Zeise-type precursors 1-3. Coordination with l-Ala through N in the trans position to ethylene showed the most promising results and was employed to stabilize 5. As a result, complex 4 showed improved stability and cytotoxicity, outperforming both 5 and 1.
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Affiliation(s)
- Andrea Cucchiaro
- Institute
of Pharmacy, Pharmaceutical Chemistry, Center for Molecular Biosciences
Innsbruck, University of Innsbruck, Innrain 80-82, A-6020 Innsbruck, Austria
| | - Amelie Scherfler
- Institute
of Pharmacy, Pharmaceutical Chemistry, Center for Molecular Biosciences
Innsbruck, University of Innsbruck, Innrain 80-82, A-6020 Innsbruck, Austria
| | - Davide Corinti
- Dipartimento
di Chimica e Tecnologie del Farmaco, Università
di Roma “La Sapienza”, P. le A. Moro 5, I-00185 Roma, Italy
| | - Giel Berden
- Institute
for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7, 6525ED Nijmegen, The Netherlands
| | - Jos Oomens
- Institute
for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7, 6525ED Nijmegen, The Netherlands
| | - Klaus Wurst
- Institute
of General, Inorganic and Theoretical Chemistry, CCB-Centrum for Chemistry
and Biomedicine, University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Ronald Gust
- Institute
of Pharmacy, Pharmaceutical Chemistry, Center for Molecular Biosciences
Innsbruck, University of Innsbruck, Innrain 80-82, A-6020 Innsbruck, Austria
| | - Maria Elisa Crestoni
- Dipartimento
di Chimica e Tecnologie del Farmaco, Università
di Roma “La Sapienza”, P. le A. Moro 5, I-00185 Roma, Italy
| | - Brigitte Kircher
- Tyrolean
Cancer Research Institute, Innrain 66, 6020 Innsbruck, Austria
- Immunobiology
and Stem Cell Laboratory, Department of Internal Medicine V (Hematology
and Oncology), Medical University of Innsbruck, Anichstraße 35, 6020 Innsbruck, Austria
| | - Monika Cziferszky
- Institute
of Pharmacy, Pharmaceutical Chemistry, Center for Molecular Biosciences
Innsbruck, University of Innsbruck, Innrain 80-82, A-6020 Innsbruck, Austria
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17
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Houthuijs KJ, Horn M, Vughs D, Martens J, Brunner AM, Oomens J, Berden G. Identification of organic micro-pollutants in surface water using MS-based infrared ion spectroscopy. CHEMOSPHERE 2023; 341:140046. [PMID: 37660788 DOI: 10.1016/j.chemosphere.2023.140046] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/29/2023] [Accepted: 08/31/2023] [Indexed: 09/05/2023]
Abstract
Comprehensive monitoring of organic micro-pollutants (OMPs) in drinking water sources relies on non-target screening (NTS) using liquid-chromatography and high-resolution mass spectrometry (LC-HRMS). Identification of OMPs is typically based on accurate mass and tandem mass spectrometry (MS/MS) data by matching against entries in compound databases and MS/MS spectral libraries. MS/MS spectra are, however, not always diagnostic for the full molecular structure and, moreover, emerging OMPs or OMP transformation products may not be present in libraries. Here we demonstrate how infrared ion spectroscopy (IRIS), an emerging MS-based method for structural elucidation, can aid in the identification of OMPs. IRIS measures the IR spectrum of an m/z-isolated ion in a mass spectrometer, providing an orthogonal diagnostic for molecular identification. Here, we demonstrate the workflow for identification of OMPs in river water and show how quantum-chemically predicted IR spectra can be used to screen potential candidates and suggest structural assignments. A crucial step herein is to define a set of candidate structures, presumably including the actual OMP, for which we present several strategies based on domain knowledge, the IR spectrum and MS/MS spectrum.
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Affiliation(s)
- Kas J Houthuijs
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525 ED, Nijmegen, the Netherlands
| | - Marijke Horn
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525 ED, Nijmegen, the Netherlands
| | - Dennis Vughs
- KWR Water Research Institute, Chemical Water Quality and Health, P.O. Box 1072, 3430 BB, Nieuwegein, the Netherlands
| | - Jonathan Martens
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525 ED, Nijmegen, the Netherlands
| | - Andrea M Brunner
- KWR Water Research Institute, Chemical Water Quality and Health, P.O. Box 1072, 3430 BB, Nieuwegein, the Netherlands; TNO, Environmental Modelling, Sensing and Analysis (EMSA), Princetonlaan 8, 3584 CB, Utrecht, 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, 1098 XH, Amsterdam, the Netherlands
| | - Giel Berden
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525 ED, Nijmegen, the Netherlands.
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18
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Munshi MU, Berden G, Oomens J. Infrared Ion Spectroscopic Characterization of the Gaseous [Co(15-crown-5)(H 2O)] 2+ Complex. J Phys Chem A 2023; 127:7256-7263. [PMID: 37595154 PMCID: PMC10476210 DOI: 10.1021/acs.jpca.3c04241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 08/04/2023] [Indexed: 08/20/2023]
Abstract
We report fingerprint infrared multiple-photon dissociation spectra of the gaseous monohydrated coordination complex of cobalt(II) and the macrocycle 1,4,7,10,13-pentaoxacyclopentadecane (or 15-crown-5), [Co(15-crown-5)(H2O)]2+. The metal-ligand complexes are generated using electrospray ionization, and their IR action spectra are recorded in a quadrupole ion trap mass spectrometer using the free-electron laser FELIX. The electronic structure and chelation motif are derived from spectral comparison with computed vibrational spectra obtained at the density functional theory level. We focus here on the gas-phase structure, addressing the question of doublet versus quartet spin multiplicity and the chelation geometry. We conclude that the gas-phase complex adopts a quartet spin state, excluding contributions of doublet species, and that the chelation geometry is pseudo-octahedral with the six oxygen centers of 15-crown-5 and H2O coordinated to the metal ion. We also address the possible presence of higher-energy conformers based on the IR spectral evidence and calculated thermodynamics.
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Affiliation(s)
| | - Giel Berden
- FELIX
Laboratory, Radboud University, Institute
for Molecules and Materials, Toernooiveld 7, 6525
ED Nijmegen, The
Netherlands
| | - Jos Oomens
- FELIX
Laboratory, Radboud University, Institute
for Molecules and Materials, Toernooiveld 7, 6525
ED Nijmegen, The
Netherlands
- University
of Amsterdam, Science
Park 904, 1098XH Amsterdam, The Netherlands
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19
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Zhanserkeev AA, Yang EL, Steele RP. Accelerating Anharmonic Spectroscopy Simulations via Local-Mode, Multilevel Methods. J Chem Theory Comput 2023; 19:5572-5585. [PMID: 37555634 DOI: 10.1021/acs.jctc.3c00589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/10/2023]
Abstract
Ab initio computer simulations of anharmonic vibrational spectra provide nuanced insight into the vibrational behavior of molecules and complexes. The computational bottleneck in such simulations, particularly for ab initio potentials, is often the generation of mode-coupling potentials. Focusing specifically on two-mode couplings in this analysis, the combination of a local-mode representation and multilevel methods is demonstrated to be particularly symbiotic. In this approach, a low-level quantum chemistry method is employed to predict the pairwise couplings that should be included at the target level of theory in vibrational self-consistent field (and similar) calculations. Pairs that are excluded by this approach are "recycled" at the low level of theory. Furthermore, because this low-level pre-screening will eventually become the computational bottleneck for sufficiently large chemical systems, distance-based truncation is applied to these low-level predictions without substantive loss of accuracy. This combination is demonstrated to yield sub-wavenumber fidelity with reference vibrational transitions when including only a small fraction of target-level couplings; the overhead of predicting these couplings, particularly when employing distance-based, local-mode cutoffs, is a trivial added cost. This combined approach is assessed on a series of test cases, including ethylene, hexatriene, and the alanine dipeptide. Vibrational self-consistent field (VSCF) spectra were obtained with an RI-MP2/cc-pVTZ potential for the dipeptide, at approximately a 5-fold reduction in computational cost. Considerable optimism for increased accelerations for larger systems and higher-order couplings is also justified, based on this investigation.
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Affiliation(s)
- Asylbek A Zhanserkeev
- Department of Chemistry and Henry Eyring Center for Theoretical Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
| | - Emily L Yang
- Department of Chemistry and Henry Eyring Center for Theoretical Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
| | - Ryan P Steele
- Department of Chemistry and Henry Eyring Center for Theoretical Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
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20
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Karunaratne E, Hill DW, Dührkop K, Böcker S, Grant DF. Combining Experimental with Computational Infrared and Mass Spectra for High-Throughput Nontargeted Chemical Structure Identification. Anal Chem 2023; 95:11901-11907. [PMID: 37540774 DOI: 10.1021/acs.analchem.3c00937] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/06/2023]
Abstract
The inability to identify the structures of most metabolites detected in environmental or biological samples limits the utility of nontargeted metabolomics. The most widely used analytical approaches combine mass spectrometry and machine learning methods to rank candidate structures contained in large chemical databases. Given the large chemical space typically searched, the use of additional orthogonal data may improve the identification rates and reliability. Here, we present results of combining experimental and computational mass and IR spectral data for high-throughput nontargeted chemical structure identification. Experimental MS/MS and gas-phase IR data for 148 test compounds were obtained from NIST. Candidate structures for each of the test compounds were obtained from PubChem (mean = 4444 candidate structures per test compound). Our workflow used CSI:FingerID to initially score and rank the candidate structures. The top 1000 ranked candidates were subsequently used for IR spectra prediction, scoring, and ranking using density functional theory (DFT-IR). Final ranking of the candidates was based on a composite score calculated as the average of the CSI:FingerID and DFT-IR rankings. This approach resulted in the correct identification of 88 of the 148 test compounds (59%). 129 of the 148 test compounds (87%) were ranked within the top 20 candidates. These identification rates are the highest yet reported when candidate structures are used from PubChem. Combining experimental and computational MS/MS and IR spectral data is a potentially powerful option for prioritizing candidates for final structure verification.
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Affiliation(s)
- Erandika Karunaratne
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Dennis W Hill
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Kai Dührkop
- Chair for Bioinformatics, Faculty of Mathematics and Computer Science, Friedrich Schiller University Jena, Jena 07743, Germany
| | - Sebastian Böcker
- Chair for Bioinformatics, Faculty of Mathematics and Computer Science, Friedrich Schiller University Jena, Jena 07743, Germany
| | - David F Grant
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, Connecticut 06269, United States
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21
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Fernandes AS, Obeid G, Laureno TJN, Correra TC. Protonated and Sodiated Cyclophosphamide Fragmentation Pathways Evaluation by Infrared Multiple Photon Dissociation Spectroscopy. J Phys Chem A 2023. [PMID: 37285455 DOI: 10.1021/acs.jpca.3c01323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Cyclophosphamide (CP or CTX) is a widely used antineoplastic agent, and the evaluation of its efficacy and its impacts on the environment are dependent on tandem mass spectrometry (MSn) techniques. Because there is no dedicated experimental study to characterize the actual molecular nature of the CP fragments upon collision-induced dissociation, this work evaluated the chemical structure of the fragments of protonated and sodiated CP and CP protonation sites by infrared multiple photon dissociation spectroscopy supported by density functional theory calculations. This study allowed us to propose a new fragment structure and confirm the nature of multiple fragments, including those relevant for transitions used for CP quantitative and qualitative analyses. Our results also show that there is no spectroscopic evidence that can rule out the existence of aziridinium fragments, making it clear that further studies on the nature of iminium/aziridinium fragments in the gas phase are necessary.
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Affiliation(s)
- André S Fernandes
- Department of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes, 748, Cidade Universitária, São Paulo 05508-000, São Paulo, Brazil
| | - Guilherme Obeid
- Department of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes, 748, Cidade Universitária, São Paulo 05508-000, São Paulo, Brazil
| | - Tiago J N Laureno
- Department of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes, 748, Cidade Universitária, São Paulo 05508-000, São Paulo, Brazil
| | - Thiago C Correra
- Department of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes, 748, Cidade Universitária, São Paulo 05508-000, São Paulo, Brazil
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22
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Houthuijs KJ, Berden G, Engelke UFH, Gautam V, Wishart DS, Wevers RA, Martens J, Oomens J. An In Silico Infrared Spectral Library of Molecular Ions for Metabolite Identification. Anal Chem 2023. [PMID: 37262385 DOI: 10.1021/acs.analchem.3c01078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Infrared ion spectroscopy (IRIS) continues to see increasing use as an analytical tool for small-molecule identification in conjunction with mass spectrometry (MS). The IR spectrum of an m/z selected population of ions constitutes a unique fingerprint that is specific to the molecular structure. However, direct translation of an IR spectrum to a molecular structure remains challenging, as reference libraries of IR spectra of molecular ions largely do not exist. Quantum-chemically computed spectra can reliably be used as reference, but the challenge of selecting the candidate structures remains. Here, we introduce an in silico library of vibrational spectra of common MS adducts of over 4500 compounds found in the human metabolome database. In total, the library currently contains more than 75,000 spectra computed at the DFT level that can be queried with an experimental IR spectrum. Moreover, we introduce a database of 189 experimental IRIS spectra, which is employed to validate the automated spectral matching routines. This demonstrates that 75% of the metabolites in the experimental data set are correctly identified, based solely on their exact m/z and IRIS spectrum. Additionally, we demonstrate an approach for specifically identifying substructures by performing a search without m/z constraints to find structural analogues. Such an unsupervised search paves the way toward the de novo identification of unknowns that are absent in spectral libraries. We apply the in silico spectral library to identify an unknown in a plasma sample as 3-hydroxyhexanoic acid, highlighting the potential of the method.
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Affiliation(s)
- Kas J Houthuijs
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University, Nijmegen 6525 ED, The Netherlands
| | - Giel Berden
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University, Nijmegen 6525 ED, The Netherlands
| | - Udo F H Engelke
- Department of Genetics, Translational Metabolic Laboratory, Radboud University Medical Center, Nijmegen 6525 GA, The Netherlands
| | - Vasuk Gautam
- Department of Biological Sciences, University of Alberta, Edmonton AB T6G 2E9, Canada
| | - David S Wishart
- Department of Biological Sciences, University of Alberta, Edmonton AB T6G 2E9, Canada
- Department of Computing Science, University of Alberta, Edmonton, AB T6G 2E8, Canada
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB T6G 2B7, Canada
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Ron A Wevers
- Department of Genetics, Translational Metabolic Laboratory, Radboud University Medical Center, Nijmegen 6525 GA, The Netherlands
| | - Jonathan Martens
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University, Nijmegen 6525 ED, The Netherlands
| | - Jos Oomens
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University, Nijmegen 6525 ED, The Netherlands
- van 't Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam 1098 XH, The Netherlands
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23
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Paul M, Thomulka T, Harnying W, Neudörfl JM, Adams CR, Martens J, Berden G, Oomens J, Meijer AJHM, Berkessel A, Schäfer M. Hydrogen Bonding Shuts Down Tunneling in Hydroxycarbenes: A Gas-Phase Study by Tandem-Mass Spectrometry, Infrared Ion Spectroscopy, and Theory. J Am Chem Soc 2023. [PMID: 37235775 DOI: 10.1021/jacs.3c01698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Hydroxycarbenes can be generated and structurally characterized in the gas phase by collision-induced decarboxylation of α-keto carboxylic acids, followed by infrared ion spectroscopy. Using this approach, we have shown earlier that quantum-mechanical hydrogen tunneling (QMHT) accounts for the isomerization of a charge-tagged phenylhydroxycarbene to the corresponding aldehyde in the gas phase and above room temperature. Herein, we report the results of our current study on aliphatic trialkylammonio-tagged systems. Quite unexpectedly, the flexible 3-(trimethylammonio)propylhydroxycarbene turned out to be stable─no H-shift to either aldehyde or enol occurred. As supported by density functional theory calculations, this novel QMHT inhibition is due to intramolecular H-bonding of a mildly acidic α-ammonio C-H bonds to the hydroxyl carbene's C-atom (C:···H-C). To further support this hypothesis, (4-quinuclidinyl)hydroxycarbenes were synthesized, whose rigid structure prevents this intramolecular H-bonding. The latter hydroxycarbenes underwent "regular" QMHT to the aldehyde at rates comparable to, e.g., methylhydroxycarbene studied by Schreiner et al. While QMHT has been shown for a number of biological H-shift processes, its inhibition by H-bonding disclosed here may serve for the stabilization of highly reactive intermediates such as carbenes, even as a mechanism for biasing intrinsic selectivity patterns.
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Affiliation(s)
- Mathias Paul
- Department of Chemistry, Organic Chemistry, University of Cologne, Greinstraße 4, Cologne 50939, Germany
| | - Thomas Thomulka
- Department of Chemistry, Organic Chemistry, University of Cologne, Greinstraße 4, Cologne 50939, Germany
| | - Wacharee Harnying
- Department of Chemistry, Organic Chemistry, University of Cologne, Greinstraße 4, Cologne 50939, Germany
| | - Jörg-Martin Neudörfl
- Department of Chemistry, Organic Chemistry, University of Cologne, Greinstraße 4, Cologne 50939, Germany
| | - Charlie R Adams
- Department of Chemistry, University of Sheffield, Sheffield S3 7HF, U.K
| | - Jonathan Martens
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7, Nijmegen 6525 ED, The Netherlands
| | - Giel Berden
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7, Nijmegen 6525 ED, The Netherlands
| | - Jos Oomens
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7, Nijmegen 6525 ED, The Netherlands
- Van't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, Amsterdam 1098 XH, The Netherlands
| | | | - Albrecht Berkessel
- Department of Chemistry, Organic Chemistry, University of Cologne, Greinstraße 4, Cologne 50939, Germany
| | - Mathias Schäfer
- Department of Chemistry, Organic Chemistry, University of Cologne, Greinstraße 4, Cologne 50939, Germany
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24
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Fielicke A. Probing the binding and activation of small molecules by gas-phase transition metal clusters via IR spectroscopy. Chem Soc Rev 2023. [PMID: 37162518 DOI: 10.1039/d2cs00104g] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Isolated transition metal clusters have been established as useful models for extended metal surfaces or deposited metal particles, to improve the understanding of their surface chemistry and of catalytic reactions. For this objective, an important milestone has been the development of experimental methods for the size-specific structural characterization of clusters and cluster complexes in the gas phase. This review focusses on the characterization of molecular ligands, their binding and activation by small transition metal clusters, using cluster-size specific infrared action spectroscopy. A comprehensive overview and a critical discussion of the experimental data available to date is provided, reaching from the initial results obtained using line-tuneable CO2 lasers to present-day studies applying infrared free electron lasers as well as other intense and broadly tuneable IR laser sources.
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Affiliation(s)
- André Fielicke
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, 14195 Berlin, Germany.
- Institut für Optik und Atomare Physik, Technische Universität Berlin, 10623 Berlin, Germany
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25
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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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26
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Finazzi L, Martens J, Berden G, Oomens J. Probing radical versus proton migration in the aniline cation with IRMPD spectroscopy. Mol Phys 2023. [DOI: 10.1080/00268976.2023.2192307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
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27
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Corinti D, Rotari L, Crestoni ME, Fornarini S, Oomens J, Berden G, Tintaru A, Chiavarino B. Protonated Forms of Naringenin and Naringenin Chalcone: Proteiform Bioactive Species Elucidated by IRMPD Spectroscopy, IMS, CID-MS, and Computational Approaches. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:4005-4015. [PMID: 36849438 PMCID: PMC9999425 DOI: 10.1021/acs.jafc.2c07453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 02/08/2023] [Accepted: 02/17/2023] [Indexed: 06/18/2023]
Abstract
Naringenin (Nar) and its structural isomer, naringenin chalcone (ChNar), are two natural phytophenols with beneficial health effects belonging to the flavonoids family. A direct discrimination and structural characterization of the protonated forms of Nar and ChNar, delivered into the gas phase by electrospray ionization (ESI), was performed by mass spectrometry-based methods. In this study, we exploit a combination of electrospray ionization coupled to (high-resolution) mass spectrometry (HR-MS), collision-induced dissociation (CID) measurements, IR multiple-photon dissociation (IRMPD) action spectroscopy, density functional theory (DFT) calculations, and ion mobility-mass spectrometry (IMS). While IMS and variable collision-energy CID experiments hardly differentiate the two isomers, IRMPD spectroscopy appears to be an efficient method to distinguish naringenin from its related chalcone. In particular, the spectral range between 1400 and 1700 cm-1 is highly specific in discriminating between the two protonated isomers. Selected vibrational signatures in the IRMPD spectra have allowed us to identify the nature of the metabolite present in methanolic extracts of commercial tomatoes and grapefruits. Furthermore, comparisons between experimental IRMPD and calculated IR spectra have clarified the geometries adopted by the two protonated isomers, allowing a conformational analysis of the probed species.
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Affiliation(s)
- Davide Corinti
- Dipartimento
di Chimica e Tecnologie del Farmaco, Sapienza
Università di Roma, Piazzale Aldo Moro 5, 00185 Roma, Italy
| | - Lucretia Rotari
- Dipartimento
di Chimica e Tecnologie del Farmaco, Sapienza
Università di Roma, Piazzale Aldo Moro 5, 00185 Roma, Italy
| | - Maria Elisa Crestoni
- Dipartimento
di Chimica e Tecnologie del Farmaco, Sapienza
Università di Roma, Piazzale Aldo Moro 5, 00185 Roma, Italy
| | - Simonetta Fornarini
- Dipartimento
di Chimica e Tecnologie del Farmaco, Sapienza
Università di Roma, Piazzale Aldo Moro 5, 00185 Roma, Italy
| | - Jos Oomens
- FELIX
Laboratory, Institute for Molecules and Materials, Radboud University, Toernooiveld 7, Nijmegen 6525ED, Netherlands
| | - Giel Berden
- FELIX
Laboratory, Institute for Molecules and Materials, Radboud University, Toernooiveld 7, Nijmegen 6525ED, Netherlands
| | - Aura Tintaru
- CNRS,
Centre Interdisciplinaire de Nanoscience de Marseille, CINaM UMR 7325, Aix Marseille University, Marseille 13288, France
| | - Barbara Chiavarino
- Dipartimento
di Chimica e Tecnologie del Farmaco, Sapienza
Università di Roma, Piazzale Aldo Moro 5, 00185 Roma, Italy
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28
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Martínez-Haya B, Avilés-Moreno JR, Gámez F, Martens J, Oomens J, Berden G. A Dynamic Proton Bond: MH +·H 2O ⇌ M·H 3O + Interconversion in Loosely Coordinated Environments. J Phys Chem Lett 2023; 14:1294-1300. [PMID: 36723385 PMCID: PMC9923742 DOI: 10.1021/acs.jpclett.2c03832] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Accepted: 01/26/2023] [Indexed: 06/18/2023]
Abstract
The interaction of organic molecules with oxonium cations within their solvation shell may lead to the emergence of dynamic supramolecular structures with recurrently changing host-guest chemical identity. We illustrate this phenomenon in benchmark proton-bonded complexes of water with polyether macrocyles. Despite the smaller proton affinity of water versus the ether group, water in fact retains the proton in the form of H3O+, with increasing stability as the coordination number increases. Hindrance in many-fold coordination induces dynamic reversible (ether)·H3O+ ⇌ (etherH+)·H2O interconversion. We perform infrared action ion spectroscopy over a broad spectral range to expose the vibrational signatures of the loose proton bonding in these systems. Remarkably, characteristic bands for the two limiting proton bonding configurations are observed in the experimental vibrational spectra, superimposed onto diffuse bands associated with proton delocalization. These features cannot be described by static equilibrium structures but are accurately modeled within the framework of ab initio molecular dynamics.
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Affiliation(s)
- Bruno Martínez-Haya
- Department
of Physical, Chemical and Natural Systems, Universidad Pablo de Olavide, 41013 Seville, Spain
| | | | - Francisco Gámez
- Departamento
de Química Física, Universidad Complutense, 28040 Madrid, Spain
| | - Jonathan Martens
- Institute
for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7, 6525ED Nijmegen, The Netherlands
| | - Jos Oomens
- Institute
for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7, 6525ED Nijmegen, The Netherlands
| | - Giel Berden
- Institute
for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7, 6525ED Nijmegen, The Netherlands
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29
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Schüssler L, Israil RGE, Hütchen P, Thiel WR, Diller R, Riehn C. Ultrafast spectroscopy of Ru II polypyridine complexes in the gas phase and the liquid phase: [Ru(2,2'-bipyridine) 2(nicotinamide) 2] 2. Phys Chem Chem Phys 2023; 25:4899-4914. [PMID: 36722394 DOI: 10.1039/d2cp03765c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
[Ru(bipyridine)2(nicotinamide)2]2+ (1) and its monoaqua-complex [Ru(bipyridine)2(nicotinamide)(H2O)]2+ (2) were spectroscopically studied for the first time in the gas phase by static and time resolved UV photodissociation spectroscopy, observing nicotinamide and H2O ligand dissociation for 1 and 2, respectively. Both processes and their ultrafast dynamics were investigated in parallel by transient absorption spectroscopy in aqueous solution. The latter data were newly acquired for the long-wavelength MLCT band excitation of 1 and provide novel ultrafast ligand dissociation results for 2, confirming the gas phase results, i.e., exclusive H2O cleavage over nicotinamide loss. Similar apparent time constants in the sub-ps and few ps ranges were obtained for 1 in both phases, whereas a larger time constant of ca. two hundreds of ps for the ground state recovery was observed exclusively in the solution phase. Our reaction scheme accounts for faster dissociation dynamics in the gas phase by energetical lowering of the 3MC vs. the 3MLCT states by lack of solvent stabilization of the latter. Based on the apparent time constants, we favour, for the solution dynamics, a fast bimodal vibrational deactivation in the 3MLCT/3MC manifolds and a slow dissociation obfuscated by the ground state recovery. This is substantiated by a similar reaction scheme proposed for the ultrafast dynamics of 2, resulting in a new assignment for transient absorption features with λ > 550 nm to the 3MC manifold, and a common kinetic description for 1 and 2. Computations at the TD-DFT/cc-PVTZ/MDF28 level support our spectroscopic findings and the suggested deactivation pathways.
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Affiliation(s)
- L Schüssler
- Department of Physics, Technische Universität Kaiserslautern (TUK), Erwin-Schrödinger-Str. 46, D-67663 Kaiserslautern, Germany.
| | - R G E Israil
- Department of Chemistry, Technische Universität Kaiserslautern (TUK), Erwin-Schrödinger-Str. 52, D-67663 Kaiserslautern, Germany.
| | - P Hütchen
- Department of Chemistry, Technische Universität Kaiserslautern (TUK), Erwin-Schrödinger-Str. 54, D-67663 Kaiserslautern, Germany
| | - W R Thiel
- Department of Chemistry, Technische Universität Kaiserslautern (TUK), Erwin-Schrödinger-Str. 54, D-67663 Kaiserslautern, Germany
| | - R Diller
- Department of Physics, Technische Universität Kaiserslautern (TUK), Erwin-Schrödinger-Str. 46, D-67663 Kaiserslautern, Germany.
| | - C Riehn
- Department of Chemistry, Technische Universität Kaiserslautern (TUK), Erwin-Schrödinger-Str. 52, D-67663 Kaiserslautern, Germany. .,Research Center OPTIMAS, Erwin-Schrödinger Str. 46, D-67663 Kaiserslautern, Germany
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30
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Reinwardt S, Baev I, Linß F, Cieslik P, Raberg O, Buhr T, Perry-Sassmannshausen A, Schippers S, Müller A, Trinter F, Guda A, Laasch R, Martins M. An integrated ion trap for the photon-ion spectrometer at PETRA III. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2023; 94:023201. [PMID: 36859035 DOI: 10.1063/5.0111097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 01/22/2023] [Indexed: 06/18/2023]
Abstract
We have added a multipole ion trap to the existing photon-ion spectrometer at PETRA III (PIPE). Its hybrid structure combines a ring-electrode trap with a segmented 16-pole trap. The interaction of gases and ions with extreme ultraviolet radiation from the beamline P04 is planned to be investigated with the newly installed multipole trap. The research focus lies on radiation-induced chemical reactions that take place in the interstellar medium or in the atmospheres of planets, including natural as well as man-made processes that are important in the Earth's atmosphere. In order to determine the mass-to-charge ratio of the stored ions as efficiently as possible, we are using an ion time-of-flight spectrometer. With this technique, all stored ions can be detected simultaneously. To demonstrate the possibilities of the trap setup, two experiments have been carried out: The photoionization of xenon and the ion-impact ionization of norbornadiene. This type of ion-impact ionization can, in principle, also take place in planetary atmospheres. In addition to ionization by photon or ion impact, chemical reactions of the trapped ions with neutral atoms or molecules in the gas phase have been observed. The operation of the trap enables us to simulate conditions similar to those in the ionosphere.
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Affiliation(s)
- S Reinwardt
- Institut für Experimentalphysik, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - I Baev
- Institut für Experimentalphysik, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - F Linß
- Institut für Experimentalphysik, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - P Cieslik
- Institut für Experimentalphysik, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - O Raberg
- Institut für Experimentalphysik, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - T Buhr
- I. Physikalisches Institut, Justus-Liebig-Universität Gießen, Heinrich-Buff-Ring 16, 35392 Giessen, Germany
| | - A Perry-Sassmannshausen
- I. Physikalisches Institut, Justus-Liebig-Universität Gießen, Heinrich-Buff-Ring 16, 35392 Giessen, Germany
| | - S Schippers
- I. Physikalisches Institut, Justus-Liebig-Universität Gießen, Heinrich-Buff-Ring 16, 35392 Giessen, Germany
| | - A Müller
- I. Physikalisches Institut, Justus-Liebig-Universität Gießen, Heinrich-Buff-Ring 16, 35392 Giessen, Germany
| | - F Trinter
- Institut für Kernphysik, Goethe-Universität Frankfurt, Max-von-Laue-Straße 1, 60438 Frankfurt am Main, Germany
| | - A Guda
- The Smart Materials Research Institute, Southern Federal University, Sladkova 178/24, 344090 Rostov-on-Don, Russia
| | - R Laasch
- Brookhaven National Laboratory, 98 Rochester St, Upton, New York 11973, USA
| | - M Martins
- Institut für Experimentalphysik, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
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31
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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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32
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Vink MA, Schermer JJ, Martens J, Buma WJ, Berden G, Oomens J. Characterization of Solar Radiation-Induced Degradation Products of the Plant Sunscreen Sinapoyl Malate. ACS AGRICULTURAL SCIENCE & TECHNOLOGY 2023; 3:171-180. [PMID: 36846518 PMCID: PMC9945346 DOI: 10.1021/acsagscitech.2c00279] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 01/05/2023] [Accepted: 01/05/2023] [Indexed: 01/20/2023]
Abstract
Agricultural activities at lower temperatures lead to lower yields due to reduced plant growth. Applying photomolecular heater agrochemicals could boost yields under these conditions, but UV-induced degradation of these compounds needs to be assessed. In this study, we employ liquid chromatography-mass spectrometry (LC-MS) coupled with infrared ion spectroscopy (IRIS) to detect and identify the degradation products generated upon simulated solar irradiation of sinapoyl malate, a proposed photomolecular heater/UV filter compound. All major irradiation-induced degradation products are identified in terms of their full molecular structure by comparing the IRIS spectra obtained after LC fractionation and mass isolation with reference IR spectra obtained from quantum-chemical calculations. In cases where physical standards are available, a direct experimental-to-experimental comparison is possible for definitive structure identification. We find that the major degradation products originate from trans-to-cis isomerization, ester cleavage, and esterification reactions of sinapoyl malate. Preliminary in silico toxicity investigations using the VEGAHUB platform suggest no significant concerns for these degradation products' human and environmental safety. The identification workflow presented here can analogously be applied to break down products from other agrochemical compounds. As the method records IR spectra with the sensitivity of LC-MS, application to agricultural samples, e.g., from field trials, is foreseen.
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Affiliation(s)
- Matthias
J. A. Vink
- Institute
for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
| | - John J. Schermer
- Institute
for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Jonathan Martens
- Institute
for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
| | - Wybren Jan Buma
- Institute
for Molecules and Materials, FELIX Laboratory, 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
| | - 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,
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33
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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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34
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Jiang Y, Indrajith S, Perez Mellor AF, Bürgi T, Lecouvey M, Clavaguéra C, Bodo E, Houée-Levin C, Loire E, Berden G, Oomens J, Scuderi D. Final Products of One-Electron Oxidation of Cyclic Dipeptides Containing Methionine Investigated by IRMPD Spectroscopy: Does the Free Radical Choose the Final Compound? J Phys Chem B 2022; 126:10055-10068. [PMID: 36417492 DOI: 10.1021/acs.jpcb.2c06541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Reactive oxygen species (ROS) such as hydrogen peroxide (H2O2) and the hydroxyl radical (•OH) have specific functions in biological processes, while their uncontrolled production and reactivity are known to be determining factors in pathophysiology. Methionine (Met) residues act as endogenous antioxidants, when they are oxidized into methionine sulfoxide (MetSO), thus depleting ROS and protecting the protein. We employed tandem mass spectrometry combined with IR multiple photon dissociation spectroscopy to study the oxidation induced by OH radicals produced by γ radiolysis on model cyclic dipeptides c(LMetLMet), c(LMetDMet), and c(GlyMet). Our aim was to characterize the geometries of the oxidized peptides in the gas phase and to understand the relationship between the structure of the 2-center 3-electron (2c-3e) free radical formed in the first step of the oxidation process and the final compound. Density functional theory calculations were performed to characterize the lowest energy structures of the final product of oxidation and to interpret the IR spectra. Collision-induced dissociation tandem mass spectrometry (CID-MS2) experiments of oxidized c(LMetLMet)H+ and c(LMetDMet)H+ led to the loss of one or two oxidized sulfenic acid molecules, indicating that the addition of one or two oxygen atoms occurs on the sulfur atom of both methionine side chains and no sulfone formation was observed. The CID-MS2 fragmentation mass spectrum of oxidized c(GlyMet)H+ showed only the loss of one oxidized sulfenic acid molecule. Thus, the final products of oxidation are the same regardless of the structure of the precursor sulfur-centered free radical.
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Affiliation(s)
- Yining Jiang
- Université Paris-Saclay, CNRS, Institut de Chimie Physique, UMR 8000, 91405 Orsay, France
| | - Suvasthika Indrajith
- Université Paris-Saclay, CNRS, Institut de Chimie Physique, UMR 8000, 91405 Orsay, France.,Stockholm University, Roslagstullsbacken 21 C, plan 4, Albano, Fysikum, 106 91 Stockholm, Sweden
| | - Ariel Francis Perez Mellor
- Faculté des Sciences, Section de Chimie et Biologie, Département de Chimie Physique, Université de Genève, 30 Quai Ernest-Ansermet, CH-1211 Genève, Switzerland
| | - Thomas Bürgi
- Faculté des Sciences, Section de Chimie et Biologie, Département de Chimie Physique, Université de Genève, 30 Quai Ernest-Ansermet, CH-1211 Genève, Switzerland
| | - Marc Lecouvey
- Department of Chemistry, Université Sorbonne Paris Nord, CSPBAT, CNRS, UMR 7244, 1 rue de Chablis, F-93000 Bobigny, France
| | - Carine Clavaguéra
- Université Paris-Saclay, CNRS, Institut de Chimie Physique, UMR 8000, 91405 Orsay, France
| | - Enrico Bodo
- Departement of Chemistry, Università di Roma La Sapienza, P. Aldo Moro 5, 00185 Rome, Italy
| | - Chantal Houée-Levin
- Université Paris-Saclay, CNRS, Institut de Chimie Physique, UMR 8000, 91405 Orsay, France
| | - Estelle Loire
- Université Paris-Saclay, CNRS, Institut de Chimie Physique, UMR 8000, 91405 Orsay, France
| | - 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, P.O. Box 94157, 1090 GD Amsterdam, The Netherlands
| | - Debora Scuderi
- Université Paris-Saclay, CNRS, Institut de Chimie Physique, UMR 8000, 91405 Orsay, France
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35
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He CC, Hamlow LA, Roy HA, Devereaux ZJ, Hasan MA, Israel E, Cunningham NA, Martens J, Berden G, Oomens J, Rodgers MT. Structural Determination of Lysine-Linked Cisplatin Complexes via IRMPD Action Spectroscopy: NN s and NO - Binding Modes of Lysine to Platinum Coexist. J Phys Chem B 2022; 126:9246-9260. [PMID: 36326184 DOI: 10.1021/acs.jpcb.2c06234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Despite its success as an anticancer drug, cisplatin suffers from resistance and produces side effects. To overcome these limitations, amino-acid-linked cisplatin analogues have been investigated. Lysine-linked cisplatin, Lysplatin, (Lys)PtCl2, exhibited outstanding reactivity toward DNA and RNA that differs from that of cisplatin. To gain insight into its differing reactivity, the structure of Lysplatin is examined here using infrared multiple photon dissociation (IRMPD) action spectroscopy. To probe the influence of the local chemical environment on structure, the deprotonated and sodium-cationized Lysplatin complexes are examined. Electronic structure calculations are performed to explore possible modes of binding of Lys to Pt, their relative stabilities, and to predict their infrared spectra. Comparisons of the measured IRMPD and predicted IR spectra elucidate the structures contributing to the experimental spectra. Coexistence of two modes of binding of Lys to Pt is found where Lys binds via the backbone and side-chain amino nitrogen atoms, NNs, or to the backbone amino and carboxylate oxygen atoms, NO-. Glycine-linked cisplatin and arginine-linked cisplatin complexes have previously been found to bind only via the NO- binding mode. Present results suggest that the NNs binding conformers may be key to the outstanding reactivity of Lysplatin toward DNA and RNA.
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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
| | - H A Roy
- 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
| | - M A Hasan
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - E Israel
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - N A Cunningham
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - J Martens
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
| | - G Berden
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
| | - J Oomens
- Institute for Molecules and Materials, FELIX Laboratory, 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
| | - M T Rodgers
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
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36
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Vink M, van Geenen FA, Berden G, O’Riordan TJC, Howe PW, Oomens J, Perry SJ, Martens J. Structural Elucidation of Agrochemicals and Related Derivatives Using Infrared Ion Spectroscopy. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:15563-15572. [PMID: 36214158 PMCID: PMC9671053 DOI: 10.1021/acs.est.2c03210] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 09/15/2022] [Accepted: 09/19/2022] [Indexed: 06/03/2023]
Abstract
Agrochemicals frequently undergo various chemical and metabolic transformation reactions in the environment that often result in a wide range of derivates that must be comprehensively characterized to understand their toxicity profiles and their persistence and outcome in the environment. In the development phase, this typically involves a major effort in qualitatively identifying the correct chemical isomer(s) of these derivatives from the many isomers that could potentially be formed. Liquid chromatography-mass spectrometry and nuclear magnetic resonance (NMR) spectroscopy are often used in attempts to characterize such environment transformation products. However, challenges in confidently correlating chemical structures to detected compounds in mass spectrometry data and sensitivity/selectivity limitations of NMR frequently lead to bottlenecks in identification. In this study, we use an alternative approach, infrared ion spectroscopy, to demonstrate the identification of hydroxylated derivatives of two plant protection compounds (azoxystrobin and benzovindiflupyr) contained at low levels in tomato and spinach matrices. Infrared ion spectroscopy is an orthogonal tandem mass spectrometry technique that combines the sensitivity and selectivity of mass spectrometry with structural information obtained by infrared spectroscopy. Furthermore, IR spectra can be computationally predicted for candidate molecular structures, enabling the tentative identification of agrochemical derivatives and other unknowns in the environment without using physical reference standards.
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Affiliation(s)
- Matthias
J.A. Vink
- FELIX
Laboratory, Institute for Molecules and Materials, Radboud University, Toernooiveld 7, 6525ED Nijmegen, the Netherlands
| | - Fred A.M.G. van Geenen
- FELIX
Laboratory, Institute for Molecules and Materials, Radboud University, Toernooiveld 7, 6525ED Nijmegen, the Netherlands
| | - Giel Berden
- FELIX
Laboratory, Institute for Molecules and Materials, Radboud University, Toernooiveld 7, 6525ED Nijmegen, the Netherlands
| | - Timothy J. C. O’Riordan
- Syngenta,
Jealott’s Hill International Research Centre, RG42 6EY, Bracknell, Berkshire, United Kingdom
| | - Peter W.A. Howe
- Syngenta,
Jealott’s Hill International Research Centre, RG42 6EY, Bracknell, Berkshire, United Kingdom
| | - Jos Oomens
- FELIX
Laboratory, Institute for Molecules and Materials, Radboud University, Toernooiveld 7, 6525ED Nijmegen, the Netherlands
| | - Simon J. Perry
- Syngenta,
Jealott’s Hill International Research Centre, RG42 6EY, Bracknell, Berkshire, United Kingdom
| | - Jonathan Martens
- FELIX
Laboratory, Institute for Molecules and Materials, Radboud University, Toernooiveld 7, 6525ED Nijmegen, the Netherlands
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37
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Elferink H, Remmerswaal WA, Houthuijs KJ, Jansen O, Hansen T, Rijs AM, Berden G, Martens J, Oomens J, Codée JDC, Boltje TJ. Competing C-4 and C-5-Acyl Stabilization of Uronic Acid Glycosyl Cations. Chemistry 2022; 28:e202201724. [PMID: 35959853 PMCID: PMC9825916 DOI: 10.1002/chem.202201724] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Indexed: 01/11/2023]
Abstract
Uronic acids are carbohydrates carrying a terminal carboxylic acid and have a unique reactivity in stereoselective glycosylation reactions. Herein, the competing intramolecular stabilization of uronic acid cations by the C-5 carboxylic acid or the C-4 acetyl group was studied with infrared ion spectroscopy (IRIS). IRIS reveals that a mixture of bridged ions is formed, in which the mixture is driven towards the C-1,C-5 dioxolanium ion when the C-5,C-2-relationship is cis, and towards the formation of the C-1,C-4 dioxepanium ion when this relation is trans. Isomer-population analysis and interconversion barrier computations show that the two bridged structures are not in dynamic equilibrium and that their ratio parallels the density functional theory computed stability of the structures. These studies reveal how the intrinsic interplay of the different functional groups influences the formation of the different regioisomeric products.
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Affiliation(s)
- Hidde Elferink
- Institute for Molecules and MaterialsSynthetic Organic ChemistryRadboud University NijmegenHeyendaalseweg 1356525 AJNijmegen (TheNetherlands
| | - Wouter A. Remmerswaal
- Leiden Institute of ChemistryLeiden UniversityEinsteinweg 552333 CCLeiden (TheNetherlands
| | - Kas J. Houthuijs
- Institute for Molecules and MaterialsFELIX LaboratoryRadboud University NijmegenToernooiveld 76525 EDNijmegen (TheNetherlands
| | - Oscar Jansen
- Institute for Molecules and MaterialsFELIX LaboratoryRadboud University NijmegenToernooiveld 76525 EDNijmegen (TheNetherlands
| | - Thomas Hansen
- Leiden Institute of ChemistryLeiden UniversityEinsteinweg 552333 CCLeiden (TheNetherlands,Departament de Química Inorgànica i Orgànica & IQTUBUniversitat de Barcelona08028BarcelonaSpain
| | - Anouk M. Rijs
- Institute for Molecules and MaterialsFELIX LaboratoryRadboud University NijmegenToernooiveld 76525 EDNijmegen (TheNetherlands,Division of BioAnalytical ChemistryDepartment of Chemistry and Pharmaceutical SciencesAIMMS Amsterdam Institute of Molecular and Life SciencesVrije Univeristeit AmsterdamDe Boelelaan 10851081 HVAmsterdam (TheNetherlands
| | - Giel Berden
- Institute for Molecules and MaterialsFELIX LaboratoryRadboud University NijmegenToernooiveld 76525 EDNijmegen (TheNetherlands
| | - Jonathan Martens
- Institute for Molecules and MaterialsFELIX LaboratoryRadboud University NijmegenToernooiveld 76525 EDNijmegen (TheNetherlands
| | - Jos Oomens
- Institute for Molecules and MaterialsFELIX LaboratoryRadboud University NijmegenToernooiveld 76525 EDNijmegen (TheNetherlands
| | - Jeroen D. C. Codée
- Leiden Institute of ChemistryLeiden UniversityEinsteinweg 552333 CCLeiden (TheNetherlands
| | - Thomas J. Boltje
- Institute for Molecules and MaterialsSynthetic Organic ChemistryRadboud University NijmegenHeyendaalseweg 1356525 AJNijmegen (TheNetherlands
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38
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Di Sabato A, D’Acunzo F, Filippini D, Vetica F, Brasiello A, Corinti D, Bodo E, Michenzi C, Panzetta E, Gentili P. Unusually Chemoselective Photocyclization of 2-(Hydroxyimino)aldehydes to Cyclobutanol Oximes: Synthetic, Stereochemical, and Mechanistic Aspects. J Org Chem 2022; 87:13803-13818. [PMID: 36198009 PMCID: PMC9639046 DOI: 10.1021/acs.joc.2c01503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Photocyclization of carbonyl compounds (known as the Norrish-Yang reaction) to yield cyclobutanols is, in general, accompanied by fragmentation reactions. The latter are predominant in the case of aldehydes so that secondary cyclobutanols are not considered accessible via the straightforward Norrish-Yang reaction. A noteworthy exception has been reported in our laboratory, where cyclobutanols bearing a secondary alcohol function were observed upon UV light irradiation of 2-(hydroxyimino)aldehydes (HIAs). This reaction is here investigated in detail by combining synthesis, spectroscopic data, molecular dynamics, and DFT calculations. The synthetic methodology is generally applicable to a series of HIAs, affording the corresponding cyclobutanol oximes (CBOs) chemoselectively (i.e., without sizable fragmentation side-reactions), diastereoselectively (up to >99:1), and in good to excellent yields (up to 95%). CBO oxime ether derivatives can be purified and diastereomers isolated by standard column chromatography. The mechanistic and stereochemical picture of this photocyclization reaction, as well as of the postcyclization E/Z isomerization of the oxime double bond is completed.
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Affiliation(s)
- Antonio Di Sabato
- Department
of Chemistry, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy,Institute
of Biological Systems (ISB), Sezione Meccanismi di Reazione, Italian
National Research Council (CNR), c/o Department of Chemistry, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Francesca D’Acunzo
- Institute
of Biological Systems (ISB), Sezione Meccanismi di Reazione, Italian
National Research Council (CNR), c/o Department of Chemistry, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Dario Filippini
- Department
of Chemistry, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Fabrizio Vetica
- Department
of Chemistry, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy,
| | - Antonio Brasiello
- Department
of Chemical Engineering Materials Environment, Sapienza University of Rome, via Eudossiana 18, 00184 Rome, Italy
| | - Davide Corinti
- Department
of Chemistry and Technology of Drugs, Sapienza
University of Rome, Piazzale
Aldo Moro 5, 00185 Rome, Italy
| | - Enrico Bodo
- Department
of Chemistry, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Cinzia Michenzi
- Department
of Chemistry, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Edoardo Panzetta
- Department
of Chemistry, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Patrizia Gentili
- Department
of Chemistry, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy,Institute
of Biological Systems (ISB), Sezione Meccanismi di Reazione, Italian
National Research Council (CNR), c/o Department of Chemistry, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy,
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39
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Schmid PC, Asvany O, Salomon T, Thorwirth S, Schlemmer S. Leak-Out Spectroscopy, A Universal Method of Action Spectroscopy in Cold Ion Traps. J Phys Chem A 2022; 126:8111-8117. [DOI: 10.1021/acs.jpca.2c05767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Philipp C. Schmid
- I. Physikalisches Institut der Universität zu Köln, Köln 50937, Germany
| | - Oskar Asvany
- I. Physikalisches Institut der Universität zu Köln, Köln 50937, Germany
| | - Thomas Salomon
- I. Physikalisches Institut der Universität zu Köln, Köln 50937, Germany
| | - Sven Thorwirth
- I. Physikalisches Institut der Universität zu Köln, Köln 50937, Germany
| | - Stephan Schlemmer
- I. Physikalisches Institut der Universität zu Köln, Köln 50937, Germany
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40
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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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41
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Merx J, van Outersterp RE, Engelke UFH, Hendriks V, Wevers RA, Huigen MCDG, Waterval HWAH, Körver-Keularts IMLW, Mecinović J, Rutjes FPJT, Oomens J, Coene KLM, Martens J, Boltje TJ. Identification of Δ-1-pyrroline-5-carboxylate derived biomarkers for hyperprolinemia type II. Commun Biol 2022; 5:997. [PMID: 36131087 PMCID: PMC9492674 DOI: 10.1038/s42003-022-03960-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 09/07/2022] [Indexed: 11/10/2022] Open
Abstract
Hyperprolinemia type II (HPII) is an inborn error of metabolism due to genetic variants in ALDH4A1, leading to a deficiency in Δ-1-pyrroline-5-carboxylate (P5C) dehydrogenase. This leads to an accumulation of toxic levels of P5C, an intermediate in proline catabolism. The accumulating P5C spontaneously reacts with, and inactivates, pyridoxal 5’-phosphate, a crucial cofactor for many enzymatic processes, which is thought to be the pathophysiological mechanism for HPII. Here, we describe the use of a combination of LC-QTOF untargeted metabolomics, NMR spectroscopy and infrared ion spectroscopy (IRIS) to identify and characterize biomarkers for HPII that result of the spontaneous reaction of P5C with malonic acid and acetoacetic acid. We show that these biomarkers can differentiate between HPI, caused by a deficiency of proline oxidase activity, and HPII. The elucidation of their molecular structures yields insights into the disease pathophysiology of HPII. Combined metabolomics, NMR, and, IRIS identify biomarkers of hyperprolinemia type II (HPII) distinct from HPI and similar metabolic signatures as in patients with pyridoxine-dependent epilepsy.
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Affiliation(s)
- Jona Merx
- Radboud University, Institute for Molecules and Materials, Synthetic Organic Chemistry, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Rianne E van Outersterp
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525 ED, Nijmegen, the Netherlands
| | - Udo F H Engelke
- Department of Laboratory Medicine, Translational Metabolic Laboratory, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA, Nijmegen, the Netherlands
| | - Veronique Hendriks
- Radboud University, Institute for Molecules and Materials, Synthetic Organic Chemistry, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Ron A Wevers
- Department of Laboratory Medicine, Translational Metabolic Laboratory, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA, Nijmegen, the Netherlands.,United for Metabolic Disease, UMD, Amsterdam, The Netherlands
| | - Marleen C D G Huigen
- Department of Laboratory Medicine, Translational Metabolic Laboratory, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA, Nijmegen, the Netherlands.,United for Metabolic Disease, UMD, Amsterdam, The Netherlands
| | - Huub W A H Waterval
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Irene M L W Körver-Keularts
- United for Metabolic Disease, UMD, Amsterdam, The Netherlands.,Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Jasmin Mecinović
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense, Denmark
| | - Floris P J T Rutjes
- Radboud University, Institute for Molecules and Materials, Synthetic Organic Chemistry, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Jos Oomens
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525 ED, Nijmegen, the Netherlands
| | - Karlien L M Coene
- Department of Laboratory Medicine, Translational Metabolic Laboratory, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA, Nijmegen, the Netherlands.,United for Metabolic Disease, UMD, Amsterdam, The Netherlands.,Department of Clinical Chemistry and Hematology, Elisabeth-TweeSteden Hospital, Tilburg, The Netherlands
| | - Jonathan Martens
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525 ED, Nijmegen, the Netherlands.
| | - Thomas J Boltje
- Radboud University, Institute for Molecules and Materials, Synthetic Organic Chemistry, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands.
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42
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Zeh D, Bast M, Martens J, Berden G, Oomens J, Brünken S, Schlemmer S, Schäfer M, Kuck D. Unidirectional Double- and Triple-Hydrogen Rearrangement Reactions Probed by Infrared Ion Spectroscopy. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:1377-1392. [PMID: 35471836 DOI: 10.1021/jasms.2c00039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Unidirectional double-hydrogen (2H) and triple-hydrogen (3H) rearrangement reactions occur upon electron-ionization-induced fragmentation of trans-2-(4-N,N-dimethylaminobenzyl)-1-indanol (1), trans-2-(4-methoxybenzyl)-1-indanol (2), 4-(4-N,N-dimethylaminophenyl)-2-butanol (3), and related compounds, as reported some 35 years ago (Kuck, D.; Filges, U. Org. Mass Spectrom. 1988, 23, 643-653). These unusual intramolecular redox processes were found to dominate the mass spectra of long-lived, metastable ions. The present report provides independent evidence for the structures of the product ions formed by the 2H and 3H rearrangement in an ion trap instrument. The radical cations 1•+ and 3•+ as well as ionized 1-(4-N,N-dimethylaminophenyl)-5-(4-methoxyphenyl)-3-pentanol, 5•+, were generated by electrospray ionization from anhydrous acetonitrile solutions. The 2H and 3H fragment ions were obtained by collision-induced dissociation and characterized by IR ion spectroscopy and density functional theory calculations. Comparison of the experimental and calculated infrared ion spectra enabled the identification of the 2H rearrangement product ion, C9H14N+ (m/z 136), as an N,N-dimethyl-para-toluidinium ion bearing the extra proton ortho to the amino group, a tautomer which was calculated to be 31 kJ/mol less stable than the corresponding N-protonated form. The 3H rearrangement product ion, C8H13N•+ (m/z 123), formerly assumed to be a distonic ammonium ion bearing a cyclohexadienyl radical, was now identified as a conventional radical cation, ionized N,N-dimethyl-2,3-dihydro-para-toluidine. Thus, the 3H rearrangement represents an intramolecular transfer hydrogenation between a secondary alcohol and an ionized aromatic ring. Based on these structural assignments, more detailed mechanisms for the unidirectional 2H and 3H rearrangement reactions are proposed.
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Affiliation(s)
- Dennis Zeh
- Department of Chemistry, Institute of Organic Chemistry, University of Cologne, Greinstraße 4, 50939 Köln, Germany
| | - Marcel Bast
- I. Physikalisches Institut, University of Cologne, Zülpicher Straße 77, 50937 Köln, Germany
| | - Jonathan Martens
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
| | - 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
| | - Sandra Brünken
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
| | - Stephan Schlemmer
- I. Physikalisches Institut, University of Cologne, Zülpicher Straße 77, 50937 Köln, Germany
| | - Mathias Schäfer
- Department of Chemistry, Institute of Organic Chemistry, University of Cologne, Greinstraße 4, 50939 Köln, Germany
| | - Dietmar Kuck
- Department of Chemistry, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
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43
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Remmerswaal WA, Houthuijs KJ, van de Ven R, Elferink H, Hansen T, Berden G, Overkleeft HS, van der Marel GA, Rutjes FPJT, Filippov DV, Boltje TJ, Martens J, Oomens J, Codée JDC. Stabilization of Glucosyl Dioxolenium Ions by "Dual Participation" of the 2,2-Dimethyl-2-( ortho-nitrophenyl)acetyl (DMNPA) Protection Group for 1,2- cis-Glucosylation. J Org Chem 2022; 87:9139-9147. [PMID: 35748115 PMCID: PMC9295149 DOI: 10.1021/acs.joc.2c00808] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
![]()
The stereoselective
introduction of glycosidic bonds is of paramount
importance to oligosaccharide synthesis. Among the various chemical
strategies to steer stereoselectivity, participation by either neighboring
or distal acyl groups is used particularly often. Recently, the use
of the 2,2-dimethyl-2-(ortho-nitrophenyl)acetyl (DMNPA)
protection group was shown to offer enhanced stereoselective steering
compared to other acyl groups. Here, we investigate the origin of
the stereoselectivity induced by the DMNPA group through systematic
glycosylation reactions and infrared ion spectroscopy (IRIS) combined
with techniques such as isotopic labeling of the anomeric center and
isomer population analysis. Our study indicates that the origin of
the DMNPA stereoselectivity does not lie in the direct participation
of the nitro moiety but in the formation of a dioxolenium ion that
is strongly stabilized by the nitro group.
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Affiliation(s)
- Wouter A Remmerswaal
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Kas J Houthuijs
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
| | - Roel van de Ven
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
| | - Hidde Elferink
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Thomas Hansen
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands.,Departament de Química Inorgànica i Orgànica & IQTUB, Universitat de Barcelona, 08028 Barcelona, Spain
| | - Giel Berden
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
| | - Herman S Overkleeft
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Gijsbert A van der Marel
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Floris P J T Rutjes
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Dmitri V Filippov
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Thomas J Boltje
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Jonathan Martens
- 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
| | - Jeroen D C Codée
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
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44
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Palotás J, Martens J, Berden G, Oomens J. Laboratory IR Spectra of the Ionic Oxidized Fullerenes C 60O + and C 60OH . J Phys Chem A 2022; 126:2928-2935. [PMID: 35533303 PMCID: PMC9125688 DOI: 10.1021/acs.jpca.2c01329] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
![]()
We present the first
experimental vibrational spectra of gaseous
oxidized derivatives of C60 in protonated and radical cation
forms, obtained through infrared multiple-photon dissociation spectroscopy
using the FELIX free-electron laser. Neutral C60O has two
nearly iso-energetic isomers: the epoxide isomer in which the O atom
bridges a CC bond that connects two six-membered rings and the annulene
isomer in which the O atom inserts into a CC bond connecting a five-
and a six-membered ring. To determine the isomer formed for C60O+ in our experiment—a question that cannot
be confidently answered on the basis of the DFT-computed stabilities
alone—we compare our experimental IR spectra to vibrational
spectra predicted by DFT calculations. We conclude that the annulene-like
isomer is formed in our experiment. For C60OH+, a strong OH stretch vibration observed in the 3 μm range
of the spectrum immediately reveals its structure as C60 with a hydroxyl group attached, which is further confirmed by the
spectrum in the 400–1600 cm–1 range. We compare
the experimental spectra of C60O+ and C60OH+ to the astronomical IR emission spectrum of
a fullerene-rich planetary nebula and discuss their astrophysical
relevance.
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Affiliation(s)
- Julianna Palotás
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7, 6525ED Nijmegen, The Netherlands
| | - Jonathan Martens
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7, 6525ED Nijmegen, The Netherlands
| | - Giel Berden
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7, 6525ED Nijmegen, The Netherlands
| | - Jos Oomens
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7, 6525ED Nijmegen, The Netherlands.,van 't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098XH Amsterdam, The Netherlands
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45
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Carlo MJ, Patrick AL. Infrared multiple photon dissociation (IRMPD) spectroscopy and its potential for the clinical laboratory. J Mass Spectrom Adv Clin Lab 2022; 23:14-25. [PMID: 34993503 PMCID: PMC8713122 DOI: 10.1016/j.jmsacl.2021.12.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 12/09/2021] [Accepted: 12/09/2021] [Indexed: 11/29/2022] Open
Abstract
Infrared multiple photon dissociation (IRMPD) spectroscopy is a powerful tool used to probe the vibrational modes-and, by extension, the structure-of an ion within an ion trap mass spectrometer. Compared to traditional FTIR spectroscopy, IRMPD spectroscopy has advantages including its sensitivity and its relative ability to handle complex mixtures. While IRMPD has historically been a technique for fundamental analyses, it is increasingly being applied in a more analytical fashion. Notable recent demonstrations pertinent to the clinical laboratory and adjacent interests include analysis of modified amino acids/residues and carbohydrates, structural elucidation (including isomeric differentiation) of metabolites, identification of novel illicit drugs, and structural studies of various biomolecules and pharmaceuticals. Improvements in analysis time, coupling to commercial instruments, and integration with separations methods are all drivers toward the realization of these analytical applications. Additional improvements in these areas, along with advances in benchtop tunable IR sources and increased cross-discipline collaboration, will continue to drive innovation and widespread adoption. The goal of this tutorial article is to briefly present the fundamentals and instrumentation of IRMPD spectroscopy, as an overview of the utility of this technique for helping to answer questions relevant to clinical analysis, and to highlight limitations to widespread adoption, as well as promising directions in which the field may be heading.
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Key Words
- 2-AEP, 2-aminoethylphosphonic acid
- 2P1EA, 2-phenyl-1-ethanolamine
- CIVP, cryogenic ion vibrational predissociation spectroscopy
- CLIO, Centre Laser Infrarouge d’Orsay
- DFT, density functional theory
- FA, fluoroamphetamine
- FEL, free electron laser
- FELIX, Free Electron Laser for Infrared eXperiments
- FMA, fluoromethamphetamine
- FTICR, Fourier transform ion cyclotron resonance
- GC–MS, gas chromatography-mass spectrometry
- GSNO, S- nitro glutathione
- GlcNAc, n-Acetylglucosamine
- IR, infrared
- IR2MS3, infrared-infrared double-resonance multi-stage mass spectrometry
- IRMPD, infrared multiple photon dissociation (IRMPD)
- IRMPD-MS, infrared multiple photon dissociation spectroscopy mass spectrometry
- IRPD, infrared predissociation spectroscopy
- IVR, intramolecular vibrational redistribution
- Infrared multiple photon dissociation spectroscopy
- LC, liquid chromatography
- LC-MS, liquid chromatography-mass spectrometry
- LC-MS/MS, liquid chromatography-tandem mass spectrometry
- MDA, methylenedioxyamphetamine
- MDMA, methylenedioxymethamphetamine
- MMC, methylmethcathinone
- MS/MS, tandem mass spectrometry
- MSn, multi-stage mass spectrometry
- Mass spectrometry
- Metabolites
- NANT, N-acetyl-N-nitrosotryptophan
- OPO/A, optical parametric oscillator/amplifier
- PTM, post-translational modification
- Pharmaceuticals
- Post-translational modifications
- SNOCys, S-nitrosocysteine
- UV, ultraviolet
- UV-IR, ultraviolet-infrared
- Vibrational spectroscopy
- cw, continuous wave
- α-PVP, alpha-pyrrolidinovalerophenone
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Affiliation(s)
- Matthew J. Carlo
- Department of Chemistry, Mississippi State University, Mississippi State, MS 39762, USA
| | - Amanda L. Patrick
- Department of Chemistry, Mississippi State University, Mississippi State, MS 39762, USA
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46
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Merx J, Houthuijs KJ, Elferink H, Witlox E, Mecinović J, Oomens J, Martens J, Boltje TJ, Rutjes FPJT. Characterization of Cyclic N-Acyliminium Ions by Infrared Ion Spectroscopy. Chemistry 2021; 28:e202104078. [PMID: 34911145 PMCID: PMC9302692 DOI: 10.1002/chem.202104078] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Indexed: 11/10/2022]
Abstract
N‐Acyliminium ions are highly reactive intermediates that are important for creating CC‐bonds adjacent to nitrogen atoms. Here we report the characterization of cyclic N‐acyliminium ions in the gas phase, generated by collision induced dissociation tandem mass spectrometry followed by infrared ion spectroscopy using the FELIX infrared free electron laser. Comparison of DFT calculated spectra with the experimentally observed IR spectra provided valuable insights in the conformations of the N‐acyliminium ions.
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Affiliation(s)
- Jona Merx
- Institute for Molecules and Materials, Synthetic Organic Chemistry, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Kas J Houthuijs
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Hidde Elferink
- Institute for Molecules and Materials, Synthetic Organic Chemistry, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Eva Witlox
- Institute for Molecules and Materials, Synthetic Organic Chemistry, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Jasmin Mecinović
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense, Denmark
| | - Jos Oomens
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Jonathan Martens
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Thomas J Boltje
- Institute for Molecules and Materials, Synthetic Organic Chemistry, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Floris P J T Rutjes
- Institute for Molecules and Materials, Synthetic Organic Chemistry, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
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47
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Becher S, Berden G, Martens J, Oomens J, Heiles S. IRMPD Spectroscopy of [PC (4:0/4:0) + M] + (M = H, Na, K) and Corresponding CID Fragment Ions. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:2874-2884. [PMID: 34723538 DOI: 10.1021/jasms.1c00277] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Glycerophospholipids (GPs) are highly abundant in eukaryotic cells and take part in numerous fundamental physiological processes such as molecular signaling. The GP composition of samples is often analyzed using mass spectrometry (MS), but identification of some structural features, for example, differentiation of stereospecific numbering (sn) isomers by well-established tandem MS (MS2) methods, is challenging. In particular, the formation of 1,3-dioxolane over 1,3-dioxane intermediates proposed to be responsible for the sn-selectivity of these tandem MS strategies has not been validated by spectroscopic methods. In this work, we present infrared multiple photon dissociation (IRMPD) spectra of phosphatidylcholine (PC) ions [PC 4:0/4:0 + H/Na/K]+ and [PC 4:0/4:0 + Na/K - 183]+ fragments generated by electrospray ionization (ESI)-MS and collision-induced dissociation (CID), respectively. IRMPD spectra of protonated, sodiated, and potassiated PC 4:0/4:0 differ in the phosphate- and ester-related bands, which are increasingly shifted to lower wavenumbers with higher adduct masses. Comparison of calculated and experimental IR spectra indicates the presence of multiple, two and one isomer(s) for [PC 4:0/4:0 + H]+, [PC 4:0/4:0 + Na]+, and [PC 4:0/4:0 + K]+, respectively. Isomers exhibiting pronounced sn-1 ester-ion interactions are computationally predicted to be energetically preferred for all species and are in line with experimental results. IRMPD spectra of [PC 4:0/4:0 + Na/K - 183]+ are presented and shed the first light on the fragment ion structures, rationalizing MS-based lipidomics strategies that aim to characterize the sn-isomerism of GPs.
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Affiliation(s)
- Simon Becher
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University Giessen, 35392 Giessen, Germany
| | - Giel Berden
- FELIX Laboratory, Institute for Molecules and Materials, Radboud University, 6525 ED Nijmegen, The Netherlands
| | - Jonathan Martens
- FELIX Laboratory, Institute for Molecules and Materials, Radboud University, 6525 ED Nijmegen, The Netherlands
| | - Jos Oomens
- FELIX Laboratory, Institute for Molecules and Materials, Radboud University, 6525 ED Nijmegen, The Netherlands
| | - Sven Heiles
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University Giessen, 35392 Giessen, Germany
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48
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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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49
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van Outersterp R, Engelke UF, Merx J, Berden G, Paul M, Thomulka T, Berkessel A, Huigen MC, Kluijtmans LA, Mecinović J, Rutjes FP, van Karnebeek CD, Wevers RA, Boltje TJ, Coene KL, Martens J, Oomens J. Metabolite Identification Using Infrared Ion Spectroscopy─Novel Biomarkers for Pyridoxine-Dependent Epilepsy. Anal Chem 2021; 93:15340-15348. [PMID: 34756024 PMCID: PMC8613736 DOI: 10.1021/acs.analchem.1c02896] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 10/25/2021] [Indexed: 11/30/2022]
Abstract
Untargeted liquid chromatography-mass spectrometry (LC-MS)-based metabolomics strategies are being increasingly applied in metabolite screening for a wide variety of medical conditions. The long-standing "grand challenge" in the utilization of this approach is metabolite identification─confidently determining the chemical structures of m/z-detected unknowns. Here, we use a novel workflow based on the detection of molecular features of interest by high-throughput untargeted LC-MS analysis of patient body fluids combined with targeted molecular identification of those features using infrared ion spectroscopy (IRIS), effectively providing diagnostic IR fingerprints for mass-isolated targets. A significant advantage of this approach is that in silico-predicted IR spectra of candidate chemical structures can be used to suggest the molecular structure of unknown features, thus mitigating the need for the synthesis of a broad range of physical reference standards. Pyridoxine-dependent epilepsy (PDE-ALDH7A1) is an inborn error of lysine metabolism, resulting from a mutation in the ALDH7A1 gene that leads to an accumulation of toxic levels of α-aminoadipic semialdehyde (α-AASA), piperideine-6-carboxylate (P6C), and pipecolic acid in body fluids. While α-AASA and P6C are known biomarkers for PDE in urine, their instability makes them poor candidates for diagnostic analysis from blood, which would be required for application in newborn screening protocols. Here, we use combined untargeted metabolomics-IRIS to identify several new biomarkers for PDE-ALDH7A1 that can be used for diagnostic analysis in urine, plasma, and cerebrospinal fluids and that are compatible with analysis in dried blood spots for newborn screening. The identification of these novel metabolites has directly provided novel insights into the pathophysiology of PDE-ALDH7A1.
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Affiliation(s)
- Rianne
E. van Outersterp
- Institute
for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
| | - Udo F.H. Engelke
- Department
of Laboratory Medicine, Translational Metabolic Laboratory, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands
| | - Jona Merx
- Institute
for Molecules and Materials, Synthetic Organic Chemistry, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Giel Berden
- Institute
for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
| | - Mathias Paul
- Department
of Chemistry, University of Cologne, Greinstrasse 4, 50939 Cologne, Germany
| | - Thomas Thomulka
- Department
of Chemistry, University of Cologne, Greinstrasse 4, 50939 Cologne, Germany
| | - Albrecht Berkessel
- Department
of Chemistry, University of Cologne, Greinstrasse 4, 50939 Cologne, Germany
| | - Marleen C.D.G. Huigen
- Department
of Laboratory Medicine, Translational Metabolic Laboratory, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands
| | - Leo A.J. Kluijtmans
- Department
of Laboratory Medicine, Translational Metabolic Laboratory, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands
| | - Jasmin Mecinović
- University
of Southern Denmark, Department of Physics,
Chemistry and Pharmacy, Campusvej 55, 5230 Odense, Denmark
| | - Floris P.J.T. Rutjes
- Institute
for Molecules and Materials, Synthetic Organic Chemistry, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Clara D.M. van Karnebeek
- Department
of Pediatrics-Metabolic Diseases, Radboud Center for Mitochondrial
Medicine, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands
| | - Ron A. Wevers
- Department
of Laboratory Medicine, Translational Metabolic Laboratory, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands
| | - Thomas J. Boltje
- Institute
for Molecules and Materials, Synthetic Organic Chemistry, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Karlien L.M. Coene
- Department
of Laboratory Medicine, Translational Metabolic Laboratory, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands
| | - Jonathan Martens
- 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
- van’t
Hoff Institute for Molecular Sciences, University
of Amsterdam, Science
Park 908, 1098XH Amsterdam, The Netherlands
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50
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van Outersterp RE, Martens J, Peremans A, Lamard L, Cuyckens F, Oomens J, Berden G. Evaluation of table-top lasers for routine infrared ion spectroscopy in the analytical laboratory. Analyst 2021; 146:7218-7229. [PMID: 34724520 PMCID: PMC8607882 DOI: 10.1039/d1an01406d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 10/20/2021] [Indexed: 01/12/2023]
Abstract
Infrared ion spectroscopy is increasingly recognized as a method to identify mass spectrometry-detected analytes in many (bio)chemical areas and its integration in analytical laboratories is now on the horizon. Commercially available quadrupole ion trap mass spectrometers are attractive ion spectroscopy platforms but operate at relatively high pressures. This promotes collisional deactivation which directly interferes with the multiple-photon excitation process required for ion spectroscopy. To overcome this, infrared lasers having a high instantaneous power are required and therefore a majority of analytical studies have been performed at infrared free electron laser facilities. Proliferation of the technique to routine use in analytical laboratories requires table-top infrared lasers and optical parametric oscillators (OPOs) are the most suitable candidates, offering both relatively high intensities and reasonable spectral tuning ranges. Here, we explore the potential of a range of commercially available high-power OPOs for ion spectroscopy, comparing systems with repetition rates of 10 Hz, 20 kHz, 80 MHz and a continuous-wave (cw) system. We compare the performance for various molecular ions and show that the kHz and MHz repetition-rate systems outperform cw and 10 Hz systems in photodissociation efficiency and offer several advantages in terms of cost-effectiveness and practical implementation in an analytical laboratory not specialized in laser spectroscopy.
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Affiliation(s)
- Rianne E van Outersterp
- 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.
| | - André Peremans
- Laboratoire Physique de la Matière et du Rayonnement (P.M.R), Université de Namur, 5000 Namur, Belgium
| | | | - Filip Cuyckens
- Drug Metabolism & Pharmacokinetics, Janssen R&D, Beerse, Belgium
| | - 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, P.O. Box 94157, 1090 GD Amsterdam, The Netherlands
| | - Giel Berden
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands.
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