Article
Chemistry, Multidisciplinary
Maike Lettow, Kim Greis, Eike Mucha, Tyler R. Lambeth, Murat Yaman, Vasilis Kontodimas, Christian Manz, Waldemar Hoffmann, Gerard Meijer, Ryan R. Julian, Gert von Helden, Mateusz Marianski, Kevin Pagel
Summary: Fucose is a signaling carbohydrate attached to the end of glycan processing. It has various roles in processes like leukocyte adhesion and pathogen-receptor interactions. However, the presence of fucose-containing chimeric fragments in mass-spectrometric analysis has complicated the determination of glycans' structure. In this study, various techniques were used to deduce the rearrangement product of fucose in model trisaccharides Lewis x and blood group H2, with the most likely product being fucose attached to galactose through an alpha(1 -> 6) glycosidic bond.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Chemistry, Multidisciplinary
Mathias Paul, Katrin Peckelsen, Thomas Thomulka, Jonathan Martens, Giel Berden, Jos Oomens, Joerg-M. Neudoerfl, Martin Breugst, Anthony J. H. M. Meijer, Mathias Schaefer, Albrecht Berkessel
Summary: The study reported in this paper focuses on the preparation of charge-tagged Breslow intermediates/keto tautomers derived from three different types of NHCs and aldehydes. Using ESI-MS IR ion spectroscopy, it was confirmed that in the gas phase, the Breslow intermediates derived from imidazolidin-2-ylidenes exist as diamino enols, while those derived from 1,2,4-triazolin-5-ylidenes and thiazolin-2-ylidenes exist as keto tautomers. This observation is consistent with findings in solution and in the crystalline state.
CHEMISTRY-A EUROPEAN JOURNAL
(2021)
Article
Chemistry, Multidisciplinary
Niklas F. Eisele, Rene Rahrt, Lamprini Giachanou, Fadi Shikho, Konrad Koszinowski
Summary: The chemistry of alkali-metal enolates, particularly their ion pairing, has been studied. Experiment and quantum chemical calculations reveal that the affinities between alkali-metal cations and enolate anions decrease as the alkali-metal cations increase in size. The electron density of carbonyl and/or nitrile groups of the enolates also affects the affinities.
CHEMISTRY-A EUROPEAN JOURNAL
(2023)
Article
Chemistry, Multidisciplinary
Jaya Mehara, Adarsh Koovakattil Surendran, Teun van Wieringen, Deeksha Setia, Cina Foroutan-Nejad, Michal Straka, Lubomir Rulisek, Jana Roithova
Summary: Gold(II) complexes are not commonly used in catalyzing chemical transformations due to their easy oxidation or reduction to more stable gold(III) or gold(I) complexes. In this study, we investigated the thermodynamics, stability, and spectral properties of [Au-II(L)(X)](+) complexes (L=ligand, X=halogen) in the gas phase. It was found that bidentate and tridentate ligands with nitrogen donor atoms are the best choices for stabilizing gaseous [Au-II(L)(X)](+) complexes. Quantum chemical calculations revealed that the molecular and electronic structures, as well as the spectroscopic properties, of the investigated gold(II) complexes are similar to those of stable copper(II) complexes.
CHEMISTRY-A EUROPEAN JOURNAL
(2022)
Article
Chemistry, Multidisciplinary
Baptiste Moge, Baptiste Schindler, Oznur Yeni, Isabelle Compagnon
Summary: Using ion vibrational spectroscopy, researchers determine the structure and linkage of fucosylated fragments of glycans and discover a new type of fucose migration. This research provides insights into the characterization of glycans and the underlying processes in mass spectrometry.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Chemistry, Multidisciplinary
Edina Sic, Jochen Rohrer, Emmanuel Ricohermoso, Karsten Albe, Emmanuel Ionescu, Ralf Riedel, Hergen Breitzke, Torsten Gutmann, Gerd Buntkowsky
Summary: Polymer-derived silicon oxycarbide ceramics (SiCO) have been investigated as potential anode materials for lithium- and sodium-ion batteries. This study focuses on understanding the local structures of SiCO ceramics with different amounts of carbon. Through various spectroscopic and computational techniques, significant changes in the local structures of SiCO ceramics have been observed, even with small changes in the material composition. These findings will provide valuable insights into the electrochemical storage processes of alkali metal/ions inside polymer-derived ceramics, particularly in the context of future research.
Article
Chemistry, Multidisciplinary
Barbara Chiavarino, Rajeev K. Sinha, Maria Elisa Crestoni, Davide Corinti, Antonello Filippi, Caterina Fraschetti, Debora Scuderi, Philippe Maitre, Simonetta Fornarini
Summary: The structures of proton-bound complexes of 5,7-dimethoxy-4H-chromen-4-one and basic amino acids, histidine and lysine, have been studied using mass spectrometry coupled with IR ion spectroscopy and quantum chemical calculations. These complexes exhibit specific molecular structures where protonated amino acids bind to neutral compounds to form a cooperative hydrogen-bond network.
CHEMISTRY-A EUROPEAN JOURNAL
(2021)
Article
Chemistry, Analytical
Peixi Zhu, Dandan Chen, Kezhi Jiang, Siqi Zhu, Weike Su, Ann Van Schepdael, Erwin Adams
Summary: Tetracyclines and their 4-epimers can be rapidly differentiated by energy resolved mass spectrometry (ERMS) of the sodium adduct ions. The interaction between the drugs and alkali metal ions is achieved through the dimethyl amino group at the C-4 position, and the binding with the hydroxyl group at the C-5 and C-6 positions differs when in contact with lithium ions.
Article
Biochemistry & Molecular Biology
Davide Corinti, Roberto Paciotti, Cecilia Coletti, Nazzareno Re, Barbara Chiavarino, Gilles Frison, Maria Elisa Crestoni, Simonetta Fornarini
Summary: In this study, the reaction products of the inorganic antineoplastic drug cisplatin with dipeptide cysteinylglycine (CysGly) were analyzed using electrospray ionization mass spectrometry (ESI-MS). The results showed that CysGly preferentially binds with platinum(II) via its deprotonated thiolic group to form a monovalent cisplatin complex, and evolves into a chelate structure through the SH and NH2 functionality of the cysteine residue. It was also observed that the platination reaction does not affect the trans configuration of the CysGly peptide bond.
JOURNAL OF INORGANIC BIOCHEMISTRY
(2023)
Article
Physics, Multidisciplinary
Alexander J. Fairchild, Varghese A. Chirayath, Randall W. Gladen, Ali R. Koymen, Alex H. Weiss, Bernardo Barbiellini
Summary: We propose a spectroscopic method that utilizes virtual photons to selectively measure the electronic structure of the topmost atomic layer. The results show that the ejected electrons originate exclusively from the topmost atomic layer and the kinetic energies of the emitted electrons reflect the density of states at the surface. This technique serves as a complementary tool to existing spectroscopic techniques, providing a way to study the electronic structure of 2D materials and fragile systems without subsurface contributions and probe-induced surface damage.
PHYSICAL REVIEW LETTERS
(2022)
Article
Chemistry, Analytical
Ayako Takemori, Philipp T. Kaulich, Liam Cassidy, Nobuaki Takemori, Andreas Tholey
Summary: The combination of liquid chromatography (LC) and gas-phase separation by field-asymmetric ion mobility spectrometry (FAIMS) is a powerful proteoform separation system for top-down proteomics. In this study, an in-depth top-down proteomics workflow, GeLC-FAIMS-MS, was presented, which utilized a molecular-weight-based proteome fractionation approach using SDS-poly-acrylamide gel electrophoresis. The authors optimized the MS parameters for each gel band and compensating voltage (CV) to improve the identification of proteoforms. They also developed a simple and cost-effective method, combining the PEPPI protocol with an AnExSP method, for stain and SDS removal. Results showed that this method was better suited for low-molecular-weight proteoforms, while a methanol-chloroform-water (MCW)-based protocol showed advantages for higher-molecular-weight proteoforms.
ANALYTICAL CHEMISTRY
(2022)
Article
Chemistry, Analytical
Erik Saparbaev, Andrei Zviagin, Oleg Boyarkin
Summary: We propose a universal approach for the quantitative identification of different isomeric biomolecules using infrared fragment cold ion spectroscopy. The method utilizes solvent molecules as natural tags, eliminating the need for any special compounds and allowing for the measurement of relative concentrations of isomers.
ANALYTICAL CHEMISTRY
(2022)
Article
Chemistry, Organic
Kim Greis, Carla Kirschbaum, Giulio Fittolani, Eike Mucha, Rayoon Chang, Gert von Helden, Gerard Meijer, Martina Delbianco, Peter H. Seeberger, Kevin Pagel
Summary: This study investigates the influence of fluorination on the structure of the glycosyl cation, an intermediate in glycosylation reactions. The results reveal that C3 and C6 fluorination of glucosyl building blocks can alter the structure of the glycosyl cation, with neighboring group participation being the dominant motif.
EUROPEAN JOURNAL OF ORGANIC CHEMISTRY
(2022)
Article
Chemistry, Physical
Franco L. Molina, Rafael A. Jara-Toro, Jennifer A. Noble, Claude Dedonder-Lardeux, Christophe Jouvet, Gustavo A. Pino
Summary: The photodetachment and stability of R-Mandelate, the deprotonated form of R-Mandelic acid, were investigated. It was found that R-Mandelate has the possibility to form an intramolecular ionic hydrogen-bond, and the stability of the resulting radicals is dependent on the position of the proton.
Article
Chemistry, Multidisciplinary
Yu-Chieh Huang, Pierre Tremouilhac, An Nguyen, Nicole Jung, Stefan Braese
Summary: ChemSpectra is a web-based software that visualizes and analyzes spectroscopic data, integrating solutions for various types of spectroscopy. It supports open file formats and can be extended to read other formats, making data interoperable and accessible for further analysis and research.
JOURNAL OF CHEMINFORMATICS
(2021)
Article
Endocrinology & Metabolism
Tessa M. A. Peters, Jona Merx, Pieter C. Kooijman, Marek Noga, Siebolt de Boer, Loes A. van Gemert, Guido Salden, Udo F. H. Engelke, Dirk J. Lefeber, Rianne E. van Outersterp, Giel Berden, Thomas J. Boltje, Rafael Artuch, Leticia Pias-Peleteiro, Angeles Garcia-Cazorla, Ivo Baric, Beat Thoeny, Jos Oomens, Jonathan Martens, Ron A. Wevers, Marcel M. Verbeek, Karlien L. M. Coene, Michel A. A. P. Willemsen
Summary: Using next-generation metabolic screening, we identified new biomarkers for improved diagnosis and pathophysiological understanding of glucose transporter type 1 deficiency syndrome (GLUT1DS).
JOURNAL OF INHERITED METABOLIC DISEASE
(2023)
Article
Chemistry, Analytical
Jonathan Martens, Rianne E. van Outersterp, Jitse Oosterhout, Christoph R. Gebhardt, Giel Berden, Udo F. H. Engelke, Ron A. Wevers, Filip Cuyckens, Jos Oomens
Summary: Infrared ion spectroscopy (IRIS) is a useful tool for identifying molecular structures detected in mass spectrometry (MS) experiments. However, coupling LC and IRIS is challenging due to the different timescales. To address this, we propose a heartcutting LC-IRIS approach using two switching valves and two sample loops as an alternative to direct coupling.
ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Inorganic & Nuclear
Marco Giampa, Davide Corinti, Alessandro Maccelli, Simonetta Fornarini, Giel Berden, Jos Oomens, Sabrina Schwarzbich, Thorsten Glaser, Maria Elisa Crestoni
Summary: This study investigates the binding ability of a dinuclear copper complex with phosphate diester ligands, revealing its interaction modes with phosphate groups and mononucleotides. The results suggest that this interaction contributes to the observed anticancer activity.
INORGANIC CHEMISTRY
(2023)
Article
Chemistry, Physical
Bruno Martinez-Haya, Juan Ramon Aviles-Moreno, Francisco Gamez, Jonathan Martens, Jos Oomens, Giel Berden
Summary: The interaction between organic molecules and oxonium cations in their solvation shell can lead to the formation of dynamic supramolecular structures that undergo recurrent changes in their host-guest chemical identity. This phenomenon is illustrated in proton-bonded complexes of water with polyether macrocycles. Despite water's lower proton affinity compared to the ether group, water actually retains the proton as H3O+ with increased stability as the coordination number increases. Hindrance in many-fold coordination induces dynamic reversible interconversion between (ether)·H3O+ (etherH+)·H2O. Infrared action ion spectroscopy reveals the vibrational signatures of loose proton bonding in these systems, which cannot be described by static equilibrium structures but can be accurately modeled using ab initio molecular dynamics.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Chemistry, Analytical
Rianne E. van Outersterp, Pieter C. Kooijman, Jona Merx, Udo F. H. Engelke, Nematollah Omidikia, Mei-Lan H. Tonneijck, Kas J. Houthuijs, Giel Berden, Tessa M. A. Peters, Dirk J. Lefeber, Michel A. A. P. Willemsen, Jasmin Mecinovic, Jeroen J. Jansen, Karlien L. M. Coene, Ron A. Wevers, Thomas J. Boltje, Jos Oomens, Jonathan Martens
Summary: The room-temperature infrared spectra of ion-complexed saccharides recorded in the far-infrared wavelength range can distinguish isomeric saccharides and have high diagnostic value. This approach, combined with liquid chromatography, can identify saccharide biomarkers in complex sample matrices.
ANALYTICAL CHEMISTRY
(2023)
Article
Physics, Atomic, Molecular & Chemical
Yining Jiang, Jean-Xavier Bardaud, Nouha Ayadi, Marc Lecouvey, Chantal Houee-Levin, Giel Berden, Jos Oomens, Debora Scuderi
Summary: The oxidation of single amino acids proline and glutamic acid, as well as Met-containing model peptides, by OH radicals produced by g-radiolysis was studied using tandem mass spectrometry and infrared multiple-photon dissociation spectroscopy. The thioether group of methionine was identified as a common target of OH free radicals, leading to the formation of a S+ radical cation. The final fate of these radicals is still unknown, but the final stable products of oxidation were identified as mostly methionine sulfoxide.
INTERNATIONAL JOURNAL OF MASS SPECTROMETRY
(2023)
Article
Agriculture, Multidisciplinary
Davide Corinti, Lucretia Rotari, Maria Elisa Crestoni, Simonetta Fornarini, Jos Oomens, Giel Berden, Aura Tintaru, Barbara Chiavarino
Summary: In this study, mass spectrometry and spectroscopic techniques were used to analyze naringenin (Nar) and its structural isomer, naringenin chalcone (ChNar). It was found that they have slight structural differences and can be distinguished by specific vibrational features in the infrared spectra.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2023)
Article
Chemistry, Physical
Brandon C. Stevenson, Giel Berden, Jonathan Martens, Jos Oomens, P. B. Armentrout
Summary: Infrared multiple photon dissociation (IRMPD) action spectroscopy was used to evaluate the complexes formed between the aromatic amino acids phenylalanine (Phe), tyrosine (Tyr), and tryptophan (Trp) and cationized ZnCl+ and CdCl+. The results showed that the dominant binding motif for MCl+(Phe) and MCl+(Tyr) is a tridentate structure, where the metal atom coordinates with the backbone amino nitrogen and carbonyl oxygen, as well as the aryl ring. For the ZnCl+(Trp) system, the experimental spectrum indicated 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.
JOURNAL OF PHYSICAL CHEMISTRY A
(2023)
Article
Chemistry, Multidisciplinary
Mathias Paul, Thomas Thomulka, Wacharee Harnying, Joerg-Martin Neudoerfl, Charlie R. Adams, Jonathan Martens, Giel Berden, Jos Oomens, Anthony J. H. M. Meijer, Albrecht Berkessel, Mathias Schaefer
Summary: Hydroxycarbenes can be generated and analyzed in the gas phase through collision-induced decarboxylation of alpha-ketocarboxylic acids. In this study, it was found that the flexible 3-(trimethylammonio)-propylhydroxycarbene exhibited stability and did not undergo H-shift to aldehyde or enol. This novel inhibition of quantum-mechanical hydrogen tunneling is attributed to intramolecular H-bonding between the mildly acidic alpha-ammonio C-H bonds and the hydroxyl carbene's C-atom.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Chemistry, Physical
Laura Finazzi, Jonathan Martens, Giel Berden, Jos Oomens
Summary: Intramolecular radical and proton migration play important roles in dissociation reactions in gas phase tandem mass spectrometry processes. Understanding the mechanism of these processes requires experiments and calculations on ion structures. The combination of ion trap mass spectrometry with IR laser spectroscopy provides an effective method to explore the details of ion structures. In this study, IRMPD spectroscopy and DFT calculations are used to investigate the reactant and product ion structures of a homolytic bond cleavage reaction.
Article
Chemistry, Physical
Yining Jiang, Carine Clavaguera, Suvasthika Indrajith, Chantal Houee-Levin, Giel Berden, Jos Oomens, Debora Scuderi
Summary: This study characterizes the OH*-induced oxidation products of DNA nucleosides and nucleotides using CID-MS2 and IRMPD spectroscopy. The addition of one oxygen atom on the nucleobase moiety is observed by CID-MS2. The gas-phase geometries of the oxidation products are investigated using IRMPD spectroscopy and quantum-chemical calculations. Additionally, IRMPD spectroscopy is employed for the first time to provide direct structural information on oxidative lesions in DNA model systems.
Article
Chemistry, Inorganic & Nuclear
Jing Su, Yu Gong, Enrique R. Batista, Ana F. Lucena, Leonor Maria, Joaquim Marcalo, Michael J. Van Stipdonk, Giel Berden, Jonathan Martens, Jos Oomens, John K. Gibson, Ping Yang
Summary: This study reports a series of actinyl complexes with a N,S-donor redox-active ligand, which can stabilize different oxidation states of radioactive elements. These complexes are isolated and characterized in the gas phase, and high-level electronic structure studies are conducted. These findings are critical for separation science towards sustainable nuclear energy.
INORGANIC CHEMISTRY
(2023)
Article
Chemistry, Physical
Musleh Uddin Munshi, Giel Berden, Jos Oomens
Summary: In this study, we utilized fingerprint infrared multiple-photon dissociation spectra to investigate the monohydrated coordination complex of cobalt(II) and the macrocycle 1,4,7,10,13-pentaoxacyclopentadecane (or 15-crown-5). The metal-ligand complexes were generated through electrospray ionization and their IR action spectra were recorded using a quadrupole ion trap mass spectrometer with the free-electron laser FELIX. By comparing the obtained spectral data with computed vibrational spectra, we determined the electronic structure and chelation motif. We found that the gas-phase complex adopts a quartet spin state and the chelation geometry is pseudo-octahedral.
JOURNAL OF PHYSICAL CHEMISTRY A
(2023)
Article
Chemistry, Multidisciplinary
Rianne E. E. van Outersterp, Jonathan Martens, Giel Berden, Arnaud Lubin, Filip Cuyckens, Jos Oomens
Summary: The identification of biotransformation products of drug compounds is crucial for drug development. Liquid chromatography-mass spectrometry (LC-MS) has become the preferred method for metabolite profiling due to its high sensitivity and selectivity. However, determining the full molecular structure of the detected metabolites, including the exact biotransformation site, remains challenging using MS alone.
Article
Chemistry, Physical
Bruno Martinez-Haya, Juan Ramon Aviles-Moreno, Francisco Gamez, Jonathan Martens, Jos Oomens, Giel Berden
Summary: Proton and hydrogen-bonded networks are crucial for understanding structural and charge transfer processes in supramolecular materials. The study of proton dynamics in 3-hydroxyglutaric acid provides insights into correlated proton dynamics and vibrational signatures.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)