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17. Structure and fragmentation chemistry of the peptide radical cations of glycylphenylalanylglycine (GFG).

Author

Li, Yinan, Lau, Justin Kai-Chi, van Wieringen, Teun, Martens, Jonathan, Berden, Giel, Oomens, Jos, Hopkinson, Alan C., Siu, K. W. Michael, and Chu, Ivan K.

Subjects
RADICAL cations, ACTION spectrum, FRAGMENTATION reactions, RADICALS (Chemistry), DAUGHTER ions
Abstract

Herein, we explore the generation and characterization of the radical cations of glycylphenylalanylglycine, or [GFG]•+, formed via dissociative electron-transfer reaction from the tripeptide to copper(II) within a ternary complex. A comprehensive investigation employing isotopic labeling, infrared multiple-photon dissociation (IRMPD) spectroscopy, and density functional theory (DFT) calculations elucidated the details and energetics in formation of the peptide radical cations as well as their dissociation products. Unlike conventional aromatic-containing peptide radical cations that primarily form canonical π-radicals, our findings reveal that 75% of the population of the experimentally produced [GFG]•+ precursors are [GFα•G]+, where the radical resides on the middle α-carbon of the phenylalanyl residue. This unexpected isomeric ion has an enthalpy of 6.8 kcal/mol above the global minimum, which has an N-terminal captodative structure, [Gα•FG]+, comprising 25% of the population. The [b₂-H]•+ product ions are also present in a ratio of 75/25 from [GFα•G]+/ [Gα•FG]+, the results of which are obtained from matches between the IRMPD action spectrum and predicted IR absorption spectra of the [b₂-H]•+ candidate structures, as well as from IRMPD isomer population analyses. [ABSTRACT FROM AUTHOR]

Published
2024
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40. Correlated proton dynamics in hydrogen bonding networks: the benchmark case of 3-hydroxyglutaric acid.

Author

Martínez-Haya, Bruno, Avilés-Moreno, Juan Ramón, Gámez, Francisco, Martens, Jonathan, Oomens, Jos, and Berden, Giel

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. [ABSTRACT FROM AUTHOR]

Published
2024
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41. Probing radical versus proton migration in the aniline cation with IRMPD spectroscopy.

Author

Finazzi, Laura, Martens, Jonathan, Berden, Giel, and Oomens, Jos

Subjects
COLLISION induced dissociation, RADICALS (Chemistry), IONS, MOLECULAR structure, LASER spectroscopy, TANDEM mass spectrometry
Abstract

Intramolecular radical and proton migration in the gas phase are important processes driving the dissociation reactions underlying common tandem mass spectrometry processes, such as collision-induced and electron-induced dissociation reactions (CID and ExD). Mechanistic insights in these processes requires experiments that probe the molecular structures of ions along the reaction pathways, usually combined with quantum-chemical calculations. The combination of ion trap mass spectrometry with IR laser spectroscopy, pioneered among others by Dieter Gerlich, provides a particularly effective method to explore details of the ion structures. In this work, we employ infrared multiple-photon dissociation (IRMPD) spectroscopy and density functional theory (DFT) calculations to probe the reactant and product ion structures of a homolytic bond cleavage reaction. First, we employ IRMPD spectroscopy to establish that protonation of the 4-bromoaniline precursor occurs on the amine moiety and then that C-Br homolytic cleavage produces the π-radical cation of aniline. Transition-state calculations are performed to compare the various pathways that connect reactant and product ions, including both proton and radical transfer mechanisms. [ABSTRACT FROM AUTHOR]

Published
2024
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44. Untargeted metabolomics and infrared ion spectroscopy identify biomarkers for pyridoxine-dependent epilepsy

Author

Engelke, Udo F.H., van Outersterp, Rianne E., Merx, Jona, van Geenen, Fred A.M.G., van Rooij, Arno, Berden, Giel, Huigen, Marleen C.D.G., Kluijtmans, Leo A.J., Peters, Tessa M.A., Shekaili, Hilal H. Al-, Leavitt, Blair R., de Vrieze, Erik, Broekman, Sanne, van Wijk, Erwin, Tseng, Laura A., Kulkarni, Purva, Rutjes, Floris P.J.T., Mecinovic, Jasmin, Struys, Eduard A., Jansen, Laura A., Gospe, Sidney M., Jr., Mercimek-Andrews, Saadet, Hyland, Keith, Willemsen, Michel A.A.P., Bok, Levinus A., van Karnebeek, Clara D.M., Wevers, Ron A., Boltje, Thomas J., Oomens, Jos, Martens, Jonathan, and Coene, Karlien L.M.

Subjects
Infrared spectroscopy -- Methods, Metabolism, Inborn errors of -- Diagnosis, Biological markers -- Identification and classification, Epilepsy -- Diagnosis, Vitamin B6 -- Health aspects, Metabolomics -- Methods, Health care industry
Abstract

Background. Pyridoxine-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 a-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. Methods. We 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. Results. We 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. Conclusion. This 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. Funding. Society 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)., Introduction Pyridoxine-dependent epilepsy due to biallelic ALDH7A1 variants (OMIM 266100, PDE-ALDH7A1) is an inborn error of metabolism (IEM) that presents with refractory seizures in early infancy. These seizures are typically [...]

Published
2021
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