1
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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2
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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3
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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4
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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5
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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6
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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7
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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8
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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9
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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10
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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11
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Su J, Gong Y, Batista ER, Lucena AF, Maria L, Marçalo J, Van Stipdonk MJ, Berden G, Martens J, Oomens J, Gibson JK, Yang P. Unusual Actinyl Complexes with a Redox-Active N,S-Donor Ligand. Inorg Chem 2023. [PMID: 37390399 DOI: 10.1021/acs.inorgchem.3c00990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/02/2023]
Abstract
Understanding the fundamental chemistry of soft N,S-donor ligands with actinides across the series is critical for separation science toward sustainable nuclear energy. This task is particularly challenging when the ligands are redox active. We herein report a series of actinyl complexes with a N,S-donor redox-active ligand that stabilizes different oxidation states across the actinide series. These complexes are isolated and characterized in the gas phase, along with high-level electronic structure studies. The redox-active N,S-donor ligand in the products, C5H4NS, acts as a monoanion in [UVIO2(C5H4NS-)]+ but as a neutral radical with unpaired electrons localized on the sulfur atom in [NpVO2(C5H4NS•)]+ and [PuVO2(C5H4NS•)]+, resulting in different oxidation states for uranium and transuranic elements. This is rationalized by considering the relative energy levels of actinyl(VI) 5f orbitals and S 3p lone pair orbitals of the C5H4NS- ligand and the cooperativity between An-N and An-S bonds that provides additional stability for the transuranic elements.
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Affiliation(s)
- Jing Su
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
- College of Chemistry, Sichuan University, Chengdu 610064, China
| | - Yu Gong
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Enrique R Batista
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Ana F Lucena
- Centro de Química Estrutural, Institute of Molecular Sciences, Instituto Superior Técnico, Universidade de Lisboa, 2695-066 Bobadela LRS, Portugal
| | - Leonor Maria
- Centro de Química Estrutural, Institute of Molecular Sciences, Instituto Superior Técnico, Universidade de Lisboa, 2695-066 Bobadela LRS, Portugal
| | - Joaquim Marçalo
- Centro de Química Estrutural, Institute of Molecular Sciences, Instituto Superior Técnico, Universidade de Lisboa, 2695-066 Bobadela LRS, Portugal
| | - Michael J Van Stipdonk
- Department of Chemistry and Biochemistry, Duquesne University, 600 Forbes Avenue, Pittsburgh, Pennsylvania 15282, United States
| | - Giel Berden
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7c, 6525ED Nijmegen, The Netherlands
| | - Jonathan Martens
- van't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098XH Amsterdam, The Netherlands
| | - Jos Oomens
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7c, 6525ED Nijmegen, The Netherlands
- van't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098XH Amsterdam, The Netherlands
| | - John K Gibson
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Ping Yang
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
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12
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van Outersterp RE, Kooijman PC, Merx J, Engelke UFH, Omidikia N, Tonneijck MLH, Houthuijs KJ, Berden G, Peters TMA, Lefeber DJ, Willemsen MAAP, Mecinovic J, Jansen JJ, Coene KLM, Wevers RA, Boltje TJ, Oomens J, Martens J. Distinguishing Oligosaccharide Isomers Using Far-Infrared Ion Spectroscopy: Identification of Biomarkers for Inborn Errors of Metabolism. Anal Chem 2023. [PMID: 37341384 DOI: 10.1021/acs.analchem.3c00363] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/22/2023]
Abstract
Distinguishing isomeric saccharides poses a major challenge for analytical workflows based on (liquid chromatography) mass spectrometry (LC-MS). In recent years, many studies have proposed infrared ion spectroscopy as a possible solution as the orthogonal, spectroscopic characterization of mass-selected ions can often distinguish isomeric species that remain unresolved using conventional MS. However, the high conformational flexibility and extensive hydrogen bonding in saccharides cause their room-temperature fingerprint infrared spectra to have broad features that often lack diagnostic value. Here, we show that room-temperature infrared spectra of ion-complexed saccharides recorded in the previously unexplored far-infrared wavelength range (300-1000 cm-1) provide well-resolved and highly diagnostic features. We show that this enables distinction of isomeric saccharides that differ either by their composition of monosaccharide units and/or the orientation of their glycosidic linkages. We demonstrate the utility of this approach from single monosaccharides up to isomeric tetrasaccharides differing only by the configuration of a single glycosidic linkage. Furthermore, through hyphenation with hydrophilic interaction liquid chromatography, we identify oligosaccharide biomarkers in patient body fluid samples, demonstrating a generalized and highly sensitive MS-based method for the identification of saccharides found in complex sample matrices.
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Affiliation(s)
- Rianne E van Outersterp
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University, 6525 ED Nijmegen, The Netherlands
| | - Pieter C Kooijman
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University, 6525 ED Nijmegen, The Netherlands
| | - Jona Merx
- Institute for Molecules and Materials, Synthetic Organic Chemistry, Radboud University, 6525 AJ Nijmegen, The Netherlands
| | - Udo F H Engelke
- Department of Laboratory Medicine, Translational Metabolic Laboratory, Radboud University Medical Centre, 6525 GA Nijmegen, The Netherlands
| | - Nematollah Omidikia
- Department of Analytical Chemistry and Chemometrics, Institute for Molecules and Materials, Radboud University, 6525 AJ Nijmegen, The Netherlands
| | - Mei-Lan H Tonneijck
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University, 6525 ED Nijmegen, The Netherlands
| | - Kas J Houthuijs
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University, 6525 ED Nijmegen, The Netherlands
| | - Giel Berden
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University, 6525 ED Nijmegen, The Netherlands
| | - Tessa M A Peters
- Department of Laboratory Medicine, Translational Metabolic Laboratory, Radboud University Medical Centre, 6525 GA Nijmegen, The Netherlands
- Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Centre, 6500 HB Nijmegen, The Netherlands
| | - Dirk J Lefeber
- Department of Laboratory Medicine, Translational Metabolic Laboratory, Radboud University Medical Centre, 6525 GA Nijmegen, The Netherlands
- Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Centre, 6500 HB Nijmegen, The Netherlands
| | - Michel A A P Willemsen
- Amalia Children's Hospital, Department of Pediatric Neurology & Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Centre, 6500 HB Nijmegen, The Netherlands
| | - Jasmin Mecinovic
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, 5230 Odense, Denmark
| | - Jeroen J Jansen
- Department of Analytical Chemistry and Chemometrics, Institute for Molecules and Materials, Radboud University, 6525 AJ Nijmegen, The Netherlands
| | - Karlien L M Coene
- Department of Laboratory Medicine, Translational Metabolic Laboratory, Radboud University Medical Centre, 6525 GA Nijmegen, The Netherlands
- Department of Clinical Chemistry and Hematology, Elisabeth-TweeSteden Hospital, 5042 AD Tilburg, The Netherlands
| | - Ron A Wevers
- Department of Laboratory Medicine, Translational Metabolic Laboratory, Radboud University Medical Centre, 6525 GA Nijmegen, The Netherlands
| | - Thomas J Boltje
- Institute for Molecules and Materials, Synthetic Organic Chemistry, Radboud University, 6525 AJ Nijmegen, The Netherlands
| | - Jos Oomens
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University, 6525 ED Nijmegen, The Netherlands
- van't Hoff Institute for Molecular Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
| | - Jonathan Martens
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University, 6525 ED Nijmegen, The Netherlands
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13
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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14
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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15
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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16
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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] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
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17
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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. J Agric Food Chem 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] [What about the content of this article? (0)] [Affiliation(s)] [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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18
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Kotobi A, Schwob L, Vonbun-Feldbauer GB, Rossi M, Gasparotto P, Feiler C, Berden G, Oomens J, Oostenrijk B, Scuderi D, Bari S, Meißner RH. Reconstructing the infrared spectrum of a peptide from representative conformers of the full canonical ensemble. Commun Chem 2023; 6:46. [PMID: 36869192 PMCID: PMC9984374 DOI: 10.1038/s42004-023-00835-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 02/08/2023] [Indexed: 03/05/2023] Open
Abstract
Leucine enkephalin (LeuEnk), a biologically active endogenous opioid pentapeptide, has been under intense investigation because it is small enough to allow efficient use of sophisticated computational methods and large enough to provide insights into low-lying minima of its conformational space. Here, we reproduce and interpret experimental infrared (IR) spectra of this model peptide in gas phase using a combination of replica-exchange molecular dynamics simulations, machine learning, and ab initio calculations. In particular, we evaluate the possibility of averaging representative structural contributions to obtain an accurate computed spectrum that accounts for the corresponding canonical ensemble of the real experimental situation. Representative conformers are identified by partitioning the conformational phase space into subensembles of similar conformers. The IR contribution of each representative conformer is calculated from ab initio and weighted according to the population of each cluster. Convergence of the averaged IR signal is rationalized by merging contributions in a hierarchical clustering and the comparison to IR multiple photon dissociation experiments. The improvements achieved by decomposing clusters containing similar conformations into even smaller subensembles is strong evidence that a thorough assessment of the conformational landscape and the associated hydrogen bonding is a prerequisite for deciphering important fingerprints in experimental spectroscopic data.
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Affiliation(s)
- Amir Kotobi
- grid.7683.a0000 0004 0492 0453Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Lucas Schwob
- Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany.
| | - Gregor B. Vonbun-Feldbauer
- grid.6884.20000 0004 0549 1777Hamburg University of Technology, Institute of Advanced Ceramics, Hamburg, Germany
| | - Mariana Rossi
- grid.469852.40000 0004 1796 3508Max Planck Institute for the Structure and Dynamics of Matter, Hamburg, Germany
| | - Piero Gasparotto
- grid.5991.40000 0001 1090 7501Scientific Computing Division, Paul Scherrer Institute, Villigen, Switzerland
| | - Christian Feiler
- grid.24999.3f0000 0004 0541 3699Helmholtz-Zentrum Hereon, Institute of Surface Science, Geesthacht, Germany
| | - Giel Berden
- grid.5590.90000000122931605Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Nijmegen, The Netherlands
| | - Jos Oomens
- grid.5590.90000000122931605Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Nijmegen, The Netherlands
| | - Bart Oostenrijk
- grid.7683.a0000 0004 0492 0453Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany ,grid.9026.d0000 0001 2287 2617The Hamburg Centre for Ultrafast Imaging, Hamburg, Germany
| | - Debora Scuderi
- grid.503243.3Institut de Chimie Physique, CNRS UMR8000, Université Paris-Saclay, Orsay, France
| | - Sadia Bari
- Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany. .,The Hamburg Centre for Ultrafast Imaging, Hamburg, Germany. .,Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands.
| | - Robert H. Meißner
- grid.24999.3f0000 0004 0541 3699Helmholtz-Zentrum Hereon, Institute of Surface Science, Geesthacht, Germany ,grid.6884.20000 0004 0549 1777Hamburg University of Technology, Institute of Polymers and Composites, Hamburg, Germany
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19
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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20
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van Outersterp R, Oosterhout J, Gebhardt CR, Berden G, Engelke UFH, Wevers RA, Cuyckens F, Oomens J, Martens J. Targeted Small-Molecule Identification Using Heartcutting Liquid Chromatography-Infrared Ion Spectroscopy. Anal Chem 2023; 95:3406-3413. [PMID: 36735826 PMCID: PMC9933049 DOI: 10.1021/acs.analchem.2c04904] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Infrared ion spectroscopy (IRIS) can be used to identify molecular structures detected in mass spectrometry (MS) experiments and has potential applications in a wide range of analytical fields. However, MS-based approaches are often combined with orthogonal separation techniques, in many cases liquid chromatography (LC). The direct coupling of LC and IRIS is challenging due to the mismatching timescales of the two technologies: an IRIS experiment typically takes several minutes, whereas an LC fraction typically elutes in several seconds. To resolve this discrepancy, we present a heartcutting LC-IRIS approach using a setup consisting of two switching valves and two sample loops as an alternative to direct online LC-IRIS coupling. We show that this automated setup enables us to record multiple IR spectra for two LC-features from a single injection without degrading the LC-separation performance. We demonstrate the setup for application in drug metabolism research by recording six m/z-selective IR spectra for two drug metabolites from a single 2 μL sample of cell incubation extract. Additionally, we measure the IR spectra of two closely eluting diastereomeric biomarkers for the inborn error of metabolism pyridoxine-dependent epilepsy (PDE-ALDH7A1), which shows that the heartcutting LC-IRIS setup has good sensitivity (requiring ∼μL injections of ∼μM samples) and that the separation between closely eluting isomers is maintained. We envision applications in a range of research fields, where the identification of molecular structures detected by LC-MS is required.
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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
| | - Jitse Oosterhout
- Radboud
University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
| | | | - Giel Berden
- Radboud
University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
| | - Udo F. H. Engelke
- Department
of Laboratory Medicine, Translational Metabolic Laboratory, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Ron A. Wevers
- Department
of Laboratory Medicine, Translational Metabolic Laboratory, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Filip Cuyckens
- Drug
Metabolism & Pharmacokinetics, Janssen R&D, Beerse 2340, 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, 1098XH Amsterdam, The Netherlands
| | - Jonathan Martens
- Radboud
University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands,
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21
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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22
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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 Agric Sci Technol 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] [What about the content of this article? (0)] [Affiliation(s)] [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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23
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Peters TMA, Merx J, Kooijman PC, Noga M, de Boer S, van Gemert LA, Salden G, Engelke UFH, Lefeber DJ, van Outersterp RE, Berden G, Boltje TJ, Artuch R, Pías-Peleteiro L, García-Cazorla Á, Barić I, Thöny B, Oomens J, Martens J, Wevers RA, Verbeek MM, Coene KLM, Willemsen MAAP. Novel cerebrospinal fluid biomarkers of glucose transporter type 1 deficiency syndrome: Implications beyond the brain's energy deficit. J Inherit Metab Dis 2023; 46:66-75. [PMID: 36088537 PMCID: PMC10091941 DOI: 10.1002/jimd.12554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 08/26/2022] [Accepted: 09/07/2022] [Indexed: 01/19/2023]
Abstract
We used next-generation metabolic screening to identify new biomarkers for improved diagnosis and pathophysiological understanding of glucose transporter type 1 deficiency syndrome (GLUT1DS), comparing metabolic cerebrospinal fluid (CSF) profiles from 12 patients to those of 116 controls. This confirmed decreased CSF glucose and lactate levels in patients with GLUT1DS and increased glutamine at group level. We identified three novel biomarkers significantly decreased in patients, namely gluconic + galactonic acid, xylose-α1-3-glucose, and xylose-α1-3-xylose-α1-3-glucose, of which the latter two have not previously been identified in body fluids. CSF concentrations of gluconic + galactonic acid may be reduced as these metabolites could serve as alternative substrates for the pentose phosphate pathway. Xylose-α1-3-glucose and xylose-α1-3-xylose-α1-3-glucose may originate from glycosylated proteins; their decreased levels are hypothetically the consequence of insufficient glucose, one of two substrates for O-glucosylation. Since many proteins are O-glucosylated, this deficiency may affect cellular processes and thus contribute to GLUT1DS pathophysiology. The novel CSF biomarkers have the potential to improve the biochemical diagnosis of GLUT1DS. Our findings imply that brain glucose deficiency in GLUT1DS may cause disruptions at the cellular level that go beyond energy metabolism, underlining the importance of developing treatment strategies that directly target cerebral glucose uptake.
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Affiliation(s)
- Tessa M A Peters
- Department of Neurology, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Laboratory Medicine, Translational Metabolic Laboratory (TML), Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jona Merx
- Institute for Molecules and Materials, Synthetic Organic Chemistry, Radboud University, Nijmegen, The Netherlands
| | - Pieter C Kooijman
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University, Nijmegen, The Netherlands
| | - Marek Noga
- Department of Laboratory Medicine, Translational Metabolic Laboratory (TML), Radboud University Medical Center, Nijmegen, The Netherlands
| | - Siebolt de Boer
- Department of Laboratory Medicine, Translational Metabolic Laboratory (TML), Radboud University Medical Center, Nijmegen, The Netherlands
| | - Loes A van Gemert
- Amalia Children's Hospital, Department of Pediatric Neurology & Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Guido Salden
- Department of Neurology, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Laboratory Medicine, Translational Metabolic Laboratory (TML), Radboud University Medical Center, Nijmegen, The Netherlands
| | - Udo F H Engelke
- Department of Laboratory Medicine, Translational Metabolic Laboratory (TML), Radboud University Medical Center, Nijmegen, The Netherlands
| | - Dirk J Lefeber
- Department of Neurology, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Laboratory Medicine, Translational Metabolic Laboratory (TML), Radboud University Medical Center, Nijmegen, The Netherlands
| | - Rianne E van Outersterp
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University, Nijmegen, The Netherlands
| | - Giel Berden
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University, Nijmegen, The Netherlands
| | - Thomas J Boltje
- Institute for Molecules and Materials, Synthetic Organic Chemistry, Radboud University, Nijmegen, The Netherlands
| | - Rafael Artuch
- Clinical Biochemistry Department, Institut de Recerca Sant Joan de Déu, CIBERER and MetabERN Hospital Sant Joan de Déu, Barcelona, Spain
| | - Leticia Pías-Peleteiro
- Clinical Biochemistry Department, Institut de Recerca Sant Joan de Déu, CIBERER and MetabERN Hospital Sant Joan de Déu, Barcelona, Spain
| | - Ángeles García-Cazorla
- Clinical Biochemistry Department, Institut de Recerca Sant Joan de Déu, CIBERER and MetabERN Hospital Sant Joan de Déu, Barcelona, Spain
| | - Ivo Barić
- Department of Pediatrics, University Hospital Center Zagreb & University of Zagreb, School of Medicine, Zagreb, Croatia
| | - Beat Thöny
- Division of Metabolism, University Children's Hospital Zürich, Zürich, Switzerland
| | - Jos Oomens
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University, Nijmegen, The Netherlands
| | - Jonathan Martens
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University, Nijmegen, The Netherlands
| | - Ron A Wevers
- Department of Laboratory Medicine, Translational Metabolic Laboratory (TML), Radboud University Medical Center, Nijmegen, The Netherlands
| | - Marcel M Verbeek
- Department of Neurology, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Laboratory Medicine, Translational Metabolic Laboratory (TML), Radboud University Medical Center, Nijmegen, The Netherlands
| | - Karlien L M Coene
- Department of Laboratory Medicine, Translational Metabolic Laboratory (TML), Radboud University Medical Center, Nijmegen, The Netherlands
- Laboratory of Clinical Chemistry and Hematology, Elisabeth TweeSteden Hospital, Tilburg, The Netherlands
| | - Michèl A A P Willemsen
- Amalia Children's Hospital, Department of Pediatric Neurology & Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, The Netherlands
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24
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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25
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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26
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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. Environ Sci Technol 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] [What about the content of this article? (0)] [Affiliation(s)] [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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27
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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28
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Munshi MU, Berden G, Oomens J. Facial vs. meridional coordination in gaseous Ni(II)-hexacyclen complexes revealed with infrared ion spectroscopy. Phys Chem Chem Phys 2022; 24:26890-26897. [PMID: 36317665 PMCID: PMC9644429 DOI: 10.1039/d2cp03871d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 10/21/2022] [Indexed: 08/20/2023]
Abstract
We report fingerprint infrared multiple-photon dissociation (IRMPD) spectra of the isolated gaseous hexa-coordinated complex of the macrocycle hexa-aza-18-crown-6 (hexacyclen, 1,4,7,10,13,16-hexaazacyclooctadecane, 18-azacrown-6) with Ni2+. The metal-ligand complexes are generated using electrospray ionization (ESI) and IR action spectra are recorded in a Fourier transform ion cyclotron resonance mass spectrometer (FTICR) MS coupled to the infrared free-electron laser FELIX. We investigate geometric structure of the complexes and in particular the chelation motif, by comparison with computed vibrational spectra, obtained using density functional theory (DFT) at the B3LYP/6-31++G(d,p) level. The quasi-octahedral chelation motif of the complex has been well documented in condensed-phase studies, and we focus here on the gas-phase structure, addressing in particular the question of a facial (fac) versus a meridional (mer) octahedral chelation geometry. Based on the good agreement between calculated linear IR spectra and experimental IRMPD spectra, we conclude that the gas-phase complex adopts a mer chelation geometry and we exclude significant contribution of the fac isomer, which is computed to lie about 10 kJ mol-1 higher in energy. We also address the possible presence of both meridional diastereomers and of higher energy conformers of meridional isomers. Finally, as expected for the d8 Ni2+-ion in an octahedral ligand environment, the IR spectrum also shows that the complexes are in a high-spin electron configuration.
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Affiliation(s)
| | - Giel Berden
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands.
| | - Jos Oomens
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands.
- University of Amsterdam, Science Park 904, 1098XH Amsterdam, The Netherlands
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29
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Mikawy NN, Roy HA, Israel E, Hamlow LA, Zhu Y, Berden G, Oomens J, Frieler CE, Rodgers MT. 5-Halogenation of Uridine Suppresses Protonation-Induced Tautomerization and Enhances Glycosidic Bond Stability of Protonated Uridine: Investigations via IRMPD Action Spectroscopy, ER-CID Experiments, and Theoretical Calculations. J Am Soc Mass Spectrom 2022; 33:2165-2180. [PMID: 36279168 DOI: 10.1021/jasms.2c00231] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Uridine (Urd), a canonical nucleoside of RNA, is the most commonly modified nucleoside among those that occur naturally. Uridine has also been an important target for the development of modified nucleoside analogues for pharmaceutical applications. In this work, the effects of 5-halogenation of uracil on the structures and glycosidic bond stabilities of protonated uridine nucleoside analogues are examined using tandem mass spectrometry and computational methods. Infrared multiple photon dissociation (IRMPD) action spectroscopy experiments and theoretical calculations are performed to probe the structural influences of these modifications. Energy-resolved collision-induced dissociation experiments along with survival yield analyses are performed to probe glycosidic bond stability. The measured IRMPD spectra are compared to linear IR spectra predicted for the stable low-energy conformations of these species computed at the B3LYP/6-311+G(d,p) level of theory to determine the conformations experimentally populated. Spectral signatures in the IR fingerprint and hydrogen-stretching regions allow the 2,4-dihydroxy protonated tautomers (T) and O4- and O2-protonated conformers to be readily differentiated. Comparisons between the measured and predicted spectra indicate that parallel to findings for uridine, both T and O4-protonated conformers of the 5-halouridine nucleoside analogues are populated, whereas O2-protonated conformers are not. Variations in yields of the spectral signatures characteristic of the T and O4-protonated conformers indicate that the extent of protonation-induced tautomerization is suppressed as the size of the halogen substituent increases. Trends in the energy-dependence of the survival yield curves find that 5-halogenation strengthens the glycosidic bond and that the enhancement in stability increases with the size of the halogen substituent.
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Affiliation(s)
- Neven N Mikawy
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - H A Roy
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - E Israel
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - L A Hamlow
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - Y Zhu
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - G Berden
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525ED Nijmegen, The Netherlands
| | - J Oomens
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525ED Nijmegen, The Netherlands
| | - C E Frieler
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - M T Rodgers
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
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30
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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31
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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32
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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. J Am Soc Mass Spectrom 2022; 33:1377-1392. [PMID: 35471836 DOI: 10.1021/jasms.2c00039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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33
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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34
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Braak FT, Elferink H, Houthuijs KJ, Oomens J, Martens J, Boltje TJ. Characterization of Elusive Reaction Intermediates Using Infrared Ion Spectroscopy: Application to the Experimental Characterization of Glycosyl Cations. Acc Chem Res 2022; 55:1669-1679. [PMID: 35616920 PMCID: PMC9219114 DOI: 10.1021/acs.accounts.2c00040] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
![]()
A detailed
understanding of the reaction mechanism(s) leading to
stereoselective product formation is crucial to understanding and
predicting product formation and driving the development of new synthetic
methodology. One way to improve our understanding of reaction mechanisms
is to characterize the reaction intermediates involved in product
formation. Because these intermediates are reactive, they are often
unstable and therefore difficult to characterize using experimental
techniques. For example, glycosylation reactions are critical steps
in the chemical synthesis of oligosaccharides and need to be stereoselective
to provide the desired α- or β-diastereomer. It remains
challenging to predict and control the stereochemical outcome of glycosylation
reactions, and their reaction mechanisms remain a hotly debated topic.
In most cases, glycosylation reactions take place via reaction mechanisms
in the continuum between SN1- and SN2-like pathways.
SN2-like pathways proceeding via the displacement of a
contact ion pair are relatively well understood because the reaction
intermediates involved can be characterized by low-temperature NMR
spectroscopy. In contrast, the SN1-like pathways proceeding
via the solvent-separated ion pair, also known as the glycosyl cation,
are poorly understood. SN1-like pathways are more challenging
to investigate because the glycosyl cation intermediates involved
are highly reactive. The highly reactive nature of glycosyl cations
complicates their characterization because they have a short lifetime
and rapidly equilibrate with the corresponding contact ion pair. To
overcome this hurdle and enable the study of glycosyl cation stability
and structure, they can be generated in a mass spectrometer in the
absence of a solvent and counterion in the gas phase. The ease of
formation, stability, and fragmentation of glycosyl cations have been
studied using mass spectrometry (MS). However, MS alone provides little
information about the structure of glycosyl cations. By combining
mass spectrometry (MS) with infrared ion spectroscopy (IRIS), the
determination of the gas-phase structures of glycosyl cations has
been achieved. IRIS enables the recording of gas-phase infrared spectra
of glycosyl cations, which can be assigned by matching to reference
spectra predicted from quantum chemically calculated vibrational spectra.
Here, we review the experimental setups that enable IRIS of glycosyl
cations and discuss the various glycosyl cations that have been characterized
to date. The structure of glycosyl cations depends on the relative
configuration and structure of the monosaccharide substituents, which
can influence the structure through both steric and electronic effects.
The scope and relevance of gas-phase glycosyl cation structures in
relation to their corresponding condensed-phase structures are also
discussed. We expect that the workflow reviewed here to study glycosyl
cation structure and reactivity can be extended to many other reaction
types involving difficult-to-characterize ionic intermediates.
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Affiliation(s)
- Floor ter Braak
- Radboud University, Institute for Molecules and Materials, Synthetic Organic Chemistry, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Hidde Elferink
- Radboud University, Institute for Molecules and Materials, Synthetic Organic Chemistry, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Kas J. Houthuijs
- Radboud University, FELIX Laboratory, Institute of Molecules and Materials, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
| | - Jos Oomens
- Radboud University, FELIX Laboratory, Institute of Molecules and Materials, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
| | - Jonathan Martens
- Radboud University, FELIX Laboratory, Institute of Molecules and Materials, 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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35
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Abstract
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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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36
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Avilés-Moreno JR, Gámez F, Berden G, Oomens J, Martínez-Haya B. Inclusion complexes of the macrocycle nonactin with benchmark protonated amines: aniline and serine. Phys Chem Chem Phys 2022; 24:8422-8431. [PMID: 35343526 DOI: 10.1039/d2cp00264g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The biological activity of the macrocycle nonactin is intimately related to its ionophore properties and ability to act as a selective cation carrier. While the focus of most investigations on nonactin has been on the binding of metal cations and small molecular ions, this study pursues the characterization of its inclusion complexes with primary amines with bulky structured side groups of different polarity. To this end, the complexes of nonactin with aniline and with the amino acid L-serine, both in protonated form, are considered as case studies and their relevant coordination arrangements are assessed by means of infrared action spectroscopy, quantum chemical density functional theory and Born-Oppenheimer molecular dynamics. The study suggests that the oxygen atoms from the oxolane (tetrahydrofuran) groups of nonactin constitute the preferential docking sites of the ammonium moiety of the guest cation, although conformational constraints promote interactions with the ester carbonyl backbone groups. In the aniline complex, the benzyl side ring is oriented outwards from the cavity, whereas in the case of L-serine, the side carboxylic acid and alcohol groups participate actively in the coordination process. Interestingly, the accommodation of L-serine is favoured when nonactin adopts an enantiomeric-selective folding, that promotes the tripodal coordination of the protonated amine group with oxolane rings from three nonactinic acid blocks with enantiomeric sequence (+)-(-)-(+), which allows for a facile coordination of the serine side groups. This is recognized as a general feature associated with the alternation of chiral domains in globally achiral natural nonactin, yielding mirror-symmetric complexes with the enantiomers of chiral amines.
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Affiliation(s)
| | - Francisco Gámez
- Departamento de Química Física, Universidad Complutense, 28040 Madrid, Spain
| | - 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
| | - Bruno Martínez-Haya
- Department of Physical, Chemical and Natural Systems, Universidad Pablo de Olavide, 41013 Seville, Spain.
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37
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Avilés-Moreno JR, Berden G, Oomens J, Martínez-Haya B. Insights into the binding of arginine to adenosine phosphate from mimetic complexes. Phys Chem Chem Phys 2022; 24:27136-27145. [DOI: 10.1039/d2cp04371h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The recognition of adenosine monophosphate (AMP) by arginine-rich proteins is conditioned by the competitive binding of the guanidinium side group with metal cations, as derived from vibrational spectroscopy and modelling of mimetic complexes.
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Affiliation(s)
| | - 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
| | - Bruno Martínez-Haya
- Department of Physical, Chemical and Natural Systems, Universidad Pablo de Olavide, 41013, Seville, Spain
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38
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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39
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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. J Am Soc Mass Spectrom 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] [What about the content of this article? (0)] [Affiliation(s)] [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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40
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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41
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van Outersterp RE, Engelke UFH, Merx J, Berden G, Paul M, Thomulka T, Berkessel A, Huigen MCDG, Kluijtmans LAJ, Mecinović J, Rutjes FPJT, van Karnebeek CDM, Wevers RA, Boltje TJ, Coene KLM, 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] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [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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42
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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43
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Gámez F, Avilés-Moreno JR, Berden G, Oomens J, Martínez-Haya B. Proton in the ring: spectroscopy and dynamics of proton bonding in macrocycle cavities. Phys Chem Chem Phys 2021; 23:21532-21543. [PMID: 34549205 DOI: 10.1039/d1cp03033g] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The proton bond is a paradigmatic quantum molecular interaction and a major driving force of supramolecular chemistry. The ring cavities of crown ethers provide an intriguing environment, promoting competitive proton sharing with multiple coordination anchors. This study shows that protons confined in crown ether cavities form dynamic bonds that migrate to varying pairs of coordinating atoms when allowed by the flexibility of the macrocycle backbone. Prototypic native crown ethers (12-crown-4, 15-crown-5 and 18-crown-6) and aza-crown ethers (cyclen, 1-aza-18-crown-6 and hexacyclen) are investigated. For each system, Infrared action spectroscopy experiments and ab initio Molecular Dynamics computations are employed to elucidate the structural effects associated with proton diffusion and its entanglement with the conformational and vibrational dynamics of the protonated host.
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Affiliation(s)
- Francisco Gámez
- Department of Physical Chemistry, Universidad de Granada, Avenida de la Fuente Nueva s/n, 18071, Granada, Spain
| | - Juan R Avilés-Moreno
- Department of Applied Physical Chemistry, Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - Giel Berden
- FELIX Laboratory, Institute for Molecules and Materials, Radboud University, Toernooiveld 7, 6525ED Nijmegen, The Netherlands
| | - Jos Oomens
- FELIX Laboratory, Institute for Molecules and Materials, Radboud University, Toernooiveld 7, 6525ED Nijmegen, The Netherlands
| | - Bruno Martínez-Haya
- Department of Physical, Chemical and Natural Systems, Universidad Pablo de Olavide, Ctra. de Utrera, km. 1, 41013 Seville, Spain.
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44
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He CC, Hamlow LA, Kimutai B, Roy HA, Devereaux ZJ, Cunningham NA, Martens J, Berden G, Oomens J, Chow CS, Rodgers MT. Structural determination of arginine-linked cisplatin complexes via IRMPD action spectroscopy: arginine binds to platinum via NO - binding mode. Phys Chem Chem Phys 2021; 23:21959-21971. [PMID: 34569570 DOI: 10.1039/d1cp03407c] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Cisplatin, (NH3)2PtCl2, has been known as a successful metal-based anticancer drug for more than half a century. Its analogue, Argplatin, arginine-linked cisplatin, (Arg)PtCl2, is being investigated because it exhibits reactivity towards DNA and RNA that differs from that of cisplatin. In order to understand the basis for its altered reactivity, the deprotonated and sodium cationized forms of Argplatin, [(Arg-H)PtCl2]- and [(Arg)PtCl2 + Na]+, are examined by infrared multiple photon dissociation (IRMPD) action spectroscopy in the IR fingerprint and hydrogen-stretching regions. Complementary electronic structure calculations are performed using density functional theory approaches to characterize the stable structures of these complexes and to predict their infrared spectra. Comparison of the theoretical IR spectra predicted for various stable conformations of these Argplatin complexes to their measured IRMPD spectra enables determination of the binding mode(s) of Arg to the Pt metal center to be identified. Arginine is found to bind to Pt in a bidentate fashion to the backbone amino nitrogen and carboxylate oxygen atoms in both the [(Arg-H)PtCl2]- and [(Arg)PtCl2 + Na]+ complexes, the NO- binding mode. The neutral side chain of Arg also interacts with the Pt center to achieve additional stabilization in the [(Arg-H)PtCl2]- complex. In contrast, Na+ binds to both chlorido ligands in the [(Arg)PtCl2 + Na]+ complex and the protonated side chain of Arg is stabilized via hydrogen-bonding interactions with the carboxylate moiety. These findings are consistent with condensed-phase results, indicating that the NO- binding mode of arginine to Pt is preserved in the electrospray ionization process even under variable pH and ionic strength.
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Affiliation(s)
- C C He
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA.
| | - L A Hamlow
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA.
| | - B Kimutai
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA.
| | - H A Roy
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA.
| | - Zachary J Devereaux
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA.
| | - N A Cunningham
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA.
| | - J Martens
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525ED Nijmegen, The Netherlands
| | - G Berden
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525ED Nijmegen, The Netherlands
| | - J Oomens
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525ED Nijmegen, The Netherlands.,van't Hoff Institute for Molecular Sciences, University of Amsterdam, The Netherlands
| | - C S Chow
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA.
| | - M T Rodgers
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA.
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Andersson Å, Poline M, Houthuijs KJ, van Outersterp RE, Berden G, Oomens J, Zhaunerchyk V. IRMPD Spectroscopy of Homo- and Heterochiral Asparagine Proton-Bound Dimers in the Gas Phase. J Phys Chem A 2021; 125:7449-7456. [PMID: 34428065 PMCID: PMC8419839 DOI: 10.1021/acs.jpca.1c05667] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
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We investigate gas-phase structures of homo- and heterochiral
asparagine proton-bound dimers
with infrared multiphoton dissociation (IRMPD) spectroscopy and quantum-chemical
calculations. Their IRMPD spectra are recorded at room temperature
in the range of 500–1875 and 3000–3600 cm–1. Both varieties of asparagine dimers are found to be charge-solvated
based on their IRMPD spectra. The location of the principal intramolecular
H-bond is discussed in light of harmonic frequency analyses using
the B3LYP functional with GD3BJ empirical dispersion. Contrary to
theoretical analyses, the two spectra are very similar.
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Affiliation(s)
- Åke Andersson
- Department of Physics, University of Gothenburg, 41296 Gothenburg, Sweden
| | - Mathias Poline
- Department of Physics, Stockholm University, 10691 Stockholm, Sweden
| | - Kas J Houthuijs
- FELIX Laboratory, Institute for Molecules and Materials, Radboud University, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
| | - Rianne E van Outersterp
- FELIX Laboratory, Institute for Molecules and Materials, Radboud University, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
| | - Giel Berden
- FELIX Laboratory, Institute for Molecules and Materials, Radboud University, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
| | - Jos Oomens
- FELIX Laboratory, Institute for Molecules and Materials, Radboud University, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
| | - Vitali Zhaunerchyk
- Department of Physics, University of Gothenburg, 41296 Gothenburg, Sweden
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Engelke UF, van Outersterp RE, Merx J, van Geenen FA, van Rooij A, Berden G, Huigen MC, Kluijtmans LA, Peters TM, Al-Shekaili HH, Leavitt BR, de Vrieze E, Broekman S, van Wijk E, Tseng LA, Kulkarni P, Rutjes FP, Mecinović J, Struys EA, Jansen LA, Gospe SM, Mercimek-Andrews S, Hyland K, Willemsen MA, Bok LA, van Karnebeek CD, Wevers RA, Boltje TJ, Oomens J, Martens J, Coene KL. Untargeted metabolomics and infrared ion spectroscopy identify biomarkers for pyridoxine-dependent epilepsy. J Clin Invest 2021; 131:e148272. [PMID: 34138754 DOI: 10.1172/jci148272] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 06/16/2021] [Indexed: 12/30/2022] Open
Abstract
BackgroundPyridoxine-dependent epilepsy (PDE-ALDH7A1) is an inborn error of lysine catabolism that presents with refractory epilepsy in newborns. Biallelic ALDH7A1 variants lead to deficiency of α-aminoadipic semialdehyde dehydrogenase/antiquitin, resulting in accumulation of piperideine-6-carboxylate (P6C), and secondary deficiency of the important cofactor pyridoxal-5'-phosphate (PLP, active vitamin B6) through its complexation with P6C. Vitamin B6 supplementation resolves epilepsy in patients, but intellectual disability may still develop. Early diagnosis and treatment, preferably based on newborn screening, could optimize long-term clinical outcome. However, no suitable PDE-ALDH7A1 newborn screening biomarkers are currently available.MethodsWe combined the innovative analytical methods untargeted metabolomics and infrared ion spectroscopy to discover and identify biomarkers in plasma that would allow for PDE-ALDH7A1 diagnosis in newborn screening.ResultsWe identified 2S,6S-/2S,6R-oxopropylpiperidine-2-carboxylic acid (2-OPP) as a PDE-ALDH7A1 biomarker, and confirmed 6-oxopiperidine-2-carboxylic acid (6-oxoPIP) as a biomarker. The suitability of 2-OPP as a potential PDE-ALDH7A1 newborn screening biomarker in dried bloodspots was shown. Additionally, we found that 2-OPP accumulates in brain tissue of patients and Aldh7a1-knockout mice, and induced epilepsy-like behavior in a zebrafish model system.ConclusionThis study has opened the way to newborn screening for PDE-ALDH7A1. We speculate that 2-OPP may contribute to ongoing neurotoxicity, also in treated PDE-ALDH7A1 patients. As 2-OPP formation appears to increase upon ketosis, we emphasize the importance of avoiding catabolism in PDE-ALDH7A1 patients.FundingSociety for Inborn Errors of Metabolism for Netherlands and Belgium (ESN), United for Metabolic Diseases (UMD), Stofwisselkracht, Radboud University, Canadian Institutes of Health Research, Dutch Research Council (NWO), and the European Research Council (ERC).
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Affiliation(s)
- Udo Fh Engelke
- Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud University Medical Center, Nijmegen, Netherlands
| | | | - Jona Merx
- Institute for Molecules and Materials, Synthetic Organic Chemistry, Radboud University, Nijmegen, Netherlands
| | | | - Arno van Rooij
- Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud University Medical Center, Nijmegen, Netherlands
| | - Giel Berden
- Institute for Molecules and Materials, FELIX Laboratory and
| | - Marleen Cdg Huigen
- Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud University Medical Center, Nijmegen, Netherlands
| | - Leo Aj Kluijtmans
- Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud University Medical Center, Nijmegen, Netherlands
| | - Tessa Ma Peters
- Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud University Medical Center, Nijmegen, Netherlands.,Department of Neurology, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, Netherlands
| | - Hilal H Al-Shekaili
- Centre for Molecular Medicine and Therapeutics, British Columbia Children's Hospital Research Institute, Department of Medical Genetics, University of British Columbia Vancouver, British Columbia, Canada
| | - Blair R Leavitt
- Centre for Molecular Medicine and Therapeutics, British Columbia Children's Hospital Research Institute, Department of Medical Genetics, University of British Columbia Vancouver, British Columbia, Canada
| | - Erik de Vrieze
- Department of Otorhinolaryngology, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, Netherlands
| | - Sanne Broekman
- Department of Otorhinolaryngology, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, Netherlands
| | - Erwin van Wijk
- Department of Otorhinolaryngology, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, Netherlands
| | - Laura A Tseng
- Department of Pediatrics, Emma Children's Hospital, Amsterdam University Medical Centers, Amsterdam, Netherlands
| | - Purva Kulkarni
- Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud University Medical Center, Nijmegen, Netherlands
| | - Floris Pjt Rutjes
- Institute for Molecules and Materials, Synthetic Organic Chemistry, Radboud University, Nijmegen, Netherlands
| | - Jasmin Mecinović
- Institute for Molecules and Materials, Synthetic Organic Chemistry, Radboud University, Nijmegen, Netherlands.,Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense, Denmark
| | - Eduard A Struys
- Department of Clinical Chemistry, Amsterdam University Medical Centers, location VU Medical Centre, Amsterdam, Netherlands
| | - Laura A Jansen
- Division of Pediatric Neurology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Sidney M Gospe
- Departments of Neurology and Pediatrics, University of Washington, Seattle, Washington, USA.,Department of Pediatrics, Duke University, Durham, North Carolina, USA
| | - Saadet Mercimek-Andrews
- Division of Clinical and Metabolic Genetics, Department of Pediatrics, University of Toronto, Toronto, Ontario, Canada.,Department of Medical Genetics, University of Alberta, Edmonton, Alberta, Canada
| | - Keith Hyland
- Medical Neurogenetics Laboratories, Atlanta, Georgia, USA
| | - Michèl Aap Willemsen
- Department of Pediatric Neurology, Radboud University Medical Centre, Nijmegen, Netherlands
| | - Levinus A Bok
- Department of Pediatrics, Máxima Medical Centre, Veldhoven, Netherlands
| | - Clara Dm van Karnebeek
- Department of Pediatrics, Emma Children's Hospital, Amsterdam University Medical Centers, Amsterdam, Netherlands.,Department of Pediatrics-Metabolic Diseases, Radboud Center for Mitochondrial Medicine, Radboud University Medical Center, Nijmegen, Netherlands.,United for Metabolic Diseases (UMD), Netherlands
| | - Ron A Wevers
- Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud University Medical Center, Nijmegen, Netherlands
| | - Thomas J Boltje
- Institute for Molecules and Materials, Synthetic Organic Chemistry, Radboud University, Nijmegen, Netherlands
| | - Jos Oomens
- Institute for Molecules and Materials, FELIX Laboratory and.,Van't Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam, Netherlands
| | | | - Karlien Lm Coene
- Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud University Medical Center, Nijmegen, Netherlands
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47
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Armentrout PB, Boles GC, Ghiassee M, Berden G, Oomens J. Infrared Multiple-Photon Dissociation Spectra of Sodiated Complexes of the Aliphatic Amino Acids. J Phys Chem A 2021; 125:6348-6355. [PMID: 34270243 DOI: 10.1021/acs.jpca.1c04708] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Sodiated complexes of the aliphatic amino acids, Gly, Ala, Val, Leu, and Ile, were examined with infrared multiple-photon dissociation action spectroscopy utilizing light from a free-electron laser. To identify structures, the experimental spectra were compared to linear spectra calculated at the B3LYP/6-311+G(d,p) level of theory. Relative energetics of all complexes were calculated at B3LYP, B3P86, MP2(full), B3LYP-GD3BJ, and M06-2X levels using a 6-311+G(2d,2p) basis set. Spectral comparison for all complexes indicates that the dominant conformation, [N, CO], binds to the amino nitrogen and carbonyl oxygen. For all complexes except Gly, contributions are observed from [CO2-] structures, where the sodium cation binds to both oxygens of the carboxylate group in the zwitterionic form of the amino acid. The semiquantitative distribution between these two structures appears to be best-predicted by the B3LYP and MP2(full) levels of theory, with predictions from the other three levels inconsistent with the experiment.
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Affiliation(s)
- P B Armentrout
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
| | - Georgia C Boles
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
| | - Maryam Ghiassee
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
| | - Giel Berden
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7, NL-6525 ED Nijmegen, The Netherlands
| | - Jos Oomens
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7, NL-6525 ED Nijmegen, The Netherlands.,Van't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
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48
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Renault E, Jian J, Maurice R, van Stipdonk MJ, Tatosian IJ, Bubas AR, Martens J, Berden G, Oomens J, Gibson JK. Characterization of Uranyl Coordinated by Equatorial Oxygen: Oxo in UO 3 versus Oxyl in UO 3. J Phys Chem A 2021; 125:5544-5555. [PMID: 34138571 DOI: 10.1021/acs.jpca.1c03818] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Uranium trioxide, UO3, has a T-shaped structure with bent uranyl, UO22+, coordinated by an equatorial oxo, O2-. The structure of cation UO3+ is similar but with an equatorial oxyl, O•-. Neutral and cationic uranium trioxide coordinated by nitrates were characterized by collision induced dissociation (CID), infrared multiple-photon dissociation (IRMPD) spectroscopy, and density functional theory. CID of uranyl nitrate, [UO2(NO3)3]- (complex A1), eliminates NO2 to produce nitrate-coordinated UO3+, [UO2(O•)(NO3)2]- (B1), which ejects NO3 to yield UO3 in [UO2(O)(NO3)]- (C1). Finally, C1 associates with H2O to afford uranyl hydroxide in [UO2(OH)2(NO3)]- (D1). IRMPD of B1, C1, and D1 confirms uranyl equatorially coordinated by nitrate(s) along with the following ligands: (B1) radical oxyl O•-; (C1) oxo O2-; and (D1) two hydroxyls, OH-. As the nitrates are bidentate, the equatorial coordination is six in A1, five in B1, four in D1, and three in C1. Ligand congestion in low-coordinate C1 suggests orbital-directed bonding. Hydrolysis of the equatorial oxo in C1 epitomizes the inverse trans influence in UO3, which is uranyl with inert axial oxos and a reactive equatorial oxo. The uranyl ν3 IR frequencies indicate the following donor ordering: O2-[best donor] ≫ O•-> OH-> NO3-.
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Affiliation(s)
- Eric Renault
- CEISAM UMR 6230, CNRS, Université de Nantes, F-44000 Nantes, France
| | - Jiwen Jian
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Rémi Maurice
- SUBATECH, UMR CNRS 6457, IN2P3/IMT Atlantique/Université de Nantes, 4 rue Alfred Kastler, BP 20722, 44307 Nantes Cedex 3, France
| | - Michael J van Stipdonk
- Department of Chemistry and Biochemistry, Duquesne University, 600 Forbes Avenue, Pittsburgh, Pennsylvania 15282, United States
| | - Irena J Tatosian
- Department of Chemistry and Biochemistry, Duquesne University, 600 Forbes Avenue, Pittsburgh, Pennsylvania 15282, United States
| | - Amanda R Bubas
- Department of Chemistry and Biochemistry, Duquesne University, 600 Forbes Avenue, Pittsburgh, Pennsylvania 15282, United States
| | - Jonathan Martens
- Radboud University Nijmegen, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525ED Nijmegen, The Netherlands
| | - Giel Berden
- Radboud University Nijmegen, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525ED Nijmegen, The Netherlands
| | - Jos Oomens
- Radboud University Nijmegen, 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
| | - John K Gibson
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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49
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Lau JKC, Esuon F, Berden G, Oomens J, Hopkinson AC, Ryzhov V, Siu KWM. Generation, Characterization, and Dissociation of Radical Cations Derived from Prolyl-glycyl-glycine. J Phys Chem B 2021; 125:6121-6129. [PMID: 34097420 DOI: 10.1021/acs.jpcb.1c01732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Radical cations of an aliphatic tripeptide prolyl-glycyl-glycine (PGG•+) and its sequence ions [a3 + H]•+ and [b2 - H]•+ have been generated by collision-induced dissociation of the [Cu(Phen)(PGG)]•2+ complex, where Phen = 1,10-phenanthroline. Infrared multiple photon dissociation spectroscopy, ion-molecule reaction experiments, and theoretical calculations have been used to investigate the structures of these ions. The unpaired electron in these three radical cations is located at different α-carbons. The PGG•+ radical cation has a captodative structure with the radical at the α-carbon of the proline residue and the proton on the oxygen of the first amide group. This structure is at the global minimum on the potential energy surface (PES). By contrast, the [a3 + H]•+ and [b2 - H]•+ ions are not the lowest-energy structures on their respective PESs, and their radicals are formally located at the C-terminal and second α-carbons, respectively. Density functional theory calculations on the structures of the ternary copper(II) complex ion suggest that the charge-solvated isomer of the metal complex is the precursor ion that dissociates to give the PGG•+ radical cation. The isomer of the complex in which PGG is bound as a zwitterion dissociates to give the [a3 + H]•+ and [b2 - H]•+ ions.
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Affiliation(s)
- Justin Kai-Chi Lau
- Department of Chemistry and Centre for Research in Mass Spectrometry, York University, 4700 Keele Street, Toronto, Ontario M3J 1P3, Canada.,Department of Chemistry and Biochemistry, University of Windsor, 401 Sunset Avenue, Windsor, Ontario N9B 3P4, Canada
| | - Francis Esuon
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, Illinois 60115, United States
| | - Giel Berden
- FELIX Laboratory, Institute for Molecules and Materials, Radboud University, Toernooiveld 7, Nijmegen 6525 ED, the Netherlands
| | - Jos Oomens
- FELIX Laboratory, Institute for Molecules and Materials, Radboud University, Toernooiveld 7, Nijmegen 6525 ED, the Netherlands
| | - Alan C Hopkinson
- Department of Chemistry and Centre for Research in Mass Spectrometry, York University, 4700 Keele Street, Toronto, Ontario M3J 1P3, Canada
| | - Victor Ryzhov
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, Illinois 60115, United States
| | - K W Michael Siu
- Department of Chemistry and Centre for Research in Mass Spectrometry, York University, 4700 Keele Street, Toronto, Ontario M3J 1P3, Canada.,Department of Chemistry and Biochemistry, University of Windsor, 401 Sunset Avenue, Windsor, Ontario N9B 3P4, Canada
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50
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van Outersterp RE, Martens J, Berden G, Koppen V, Cuyckens F, Oomens J. Mass spectrometry-based identification of ortho-, meta- and para-isomers using infrared ion spectroscopy. Analyst 2021; 145:6162-6170. [PMID: 32924040 DOI: 10.1039/d0an01119c] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Distinguishing positional isomers, such as compounds having different substitution patterns on an aromatic ring, presents a significant challenge for mass spectrometric analyses and is a frequently encountered difficulty in, for example, drug metabolism research. In contrast to mass spectrometry, IR spectroscopy is a well-known and powerful tool in the distinction of ortho-, meta- and para-isomers, but is not applicable to low-abundance compounds in complex mixtures such as often targeted in bioanalytical studies. Here, we demonstrate the use of infrared ion spectroscopy (IRIS) as a novel method that facilitates the differentiation between positional isomers of disubstituted phenyl-containing compounds and that can be applied in mass spectrometry-based complex mixture analysis. By analyzing different substitution patterns over several sets of isomeric compounds, we show that IRIS is able to consistently probe the diagnostic CH out-of-plane vibrations that are sensitive to positional isomerism. We show that these modes are largely independent of the chemical functionality contained in the ring substituents and of the type of ionization. We also show that IRIS spectra often identify the positional isomer directly, even in the absence of reference spectra obtained from physical standards or from computational prediction. We foresee that this method will be generally applicable to the identification of disubstituted phenyl-containing compounds.
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Affiliation(s)
- Rianne E van Outersterp
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525ED Nijmegen, The Netherlands.
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