Faculty of Science
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Molecular Structure and Dynamics research group

Molecular Structure and Dynamics research group

Our group combines and integrates mass spectrometry with IR spectroscopy, enabling us to obtain infrared spectral fingerprints for mass-selected ions inside the mass spectrometer. We apply infrared ion spectroscopy in various analytical challenges of identifying molecular structures of low-abundance compounds within complex mixtures, e.g. in biomarker discovery. In more fundamental studies, we investigate molecular spectra and structures of ionized molecules, e.g. to pin down the molecular structure of MS/MS product ions or for applications in astrochemistry.

Jos Oomens on the local channel RN7 on his research (in Dutch)

Latest news & research

Group members


Prof. dr. Jos Oomens
dr. Giel Berden
dr. Jonathan Martens


Kas Houthuijs, MSc
Matthias Vink, MSc
Jelle Schuurman, MSc
Laura Finazzi, MSc
Lara van Tetering,MSc
Teun van Wieringen, MSc

MSD Alumni

MSD Group Photos

Research web pages

Analytical Infrared Ion Spectroscopy (biomarkers, environmental, forensic, etc)

Ion chemistry & mass spectrometry


Recent publications

Characterization of Solar Radiation-Induced Degradation Products of the Plant Sunscreen Sinapoyl Malate. Matthias J.A. Vink, J.J. Schermer, J. Martens, W. J. Buma, G. Berden and J. Oomens: (2023) ACS Agric. Sci. Technol., 3, 171-180.  [PDF]

Targeted Small-Molecule Identification Using Heartcutting Liquid Chromatography–Infrared Ion Spectroscopy. R.E. van Outersterp, Jitse Oosterhout, Christoph R. Gebhardt, G. Berden, U. F. Engelke, R. A. Wevers, F. Cuyckens, J. Oomens and J. Martens: (2023) Anal. Chem., 95, 3406-3413.  [PDF]

A Dynamic Proton Bond: MH+·H2O ⇌ M·H3O+ Interconversion in Loosely Coordinated Environments. B. Martinez-Haya, J.R. Avilés-Moreno, F. Gamez, J. Martens, J. Oomens and G. Berden: (2023) J. Phys. Chem. Letters, 14, 1294-1300.

Binding Modes of a Cytotoxic Dinuclear Copper(II) Complex with Phosphate Ligands Probed by Vibrational Photodissociation Ion Spectroscopy. Marco Giampà, Davide Corinti, Alessandro Maccelli, Simonetta Fornarini, G. Berden, J. Oomens, Sabrina Schwarzbich, Thorsten Glaser and Maria Elisa Crestoni: (2023) Inorganic Chemistry, 62, 1341–1353.  [PDF]

Differentiation between Isomeric 4,5-Functionalized 1,2,3-Thiadiazoles and 1,2,3-Triazoles by ESI-HRMS and IR Ion Spectroscopy. Dmitrii M. Mazur, E.L. Piacentino, G. Berden, J. Oomens, V. Ryzhov, Vasiliy A. Bakulev and Albert T. Lebedev: (2023) Molecules, 28, 977-1 - 977-14.  [PDF]

Novel cerebrospinal fluid biomarkers of glucose transporter type 1 deficiency syndrome: Implications beyond the brain's energy defici. Tessa M.A. Peters, J. Merx, Pieter C. Kooijman, Marek Noga, de Siebolt Boer, Loes A. Gemert van, Guido Salden, U. F. Engelke, Dirk J. Lefeber, R.E. van Outersterp, T.J. Boltje, Rafael Artuch, Leticia Pias-Peleteiro, Ángeles Garcia-Cazorla, Ivo Barić, Thöny Beat, J. Oomens, J. Martens, R. A. Wevers, Marcel M. Verbeek, K. L. M. Coene and Michèl A. A. P. Willemsen: (2023) Journal of Inherited Metabolic Disease, 46, 66-75.  [PDF]

Final Products of One-Electron Oxidation of Cyclic Dipeptides Containing Methionine Investigated by IRMPD Spectroscopy: Does the Free Radical Choose the Final Compound? Yining Jian, Suvashika Indrajith, Ariel Franzis Perez Mellor, Thomas Bürgi, Marc Lecouvey, Carine Clavaguéra, Enrico Bodo, Chantal Houeé-Levin, Estelle Loire, G. Berden, J. Oomens and Debora Scuderi: (2022)J. Phys. Chem. B, 2022, 10055 - 10068.

Identification of Δ-1-pyrroline-5-carboxylate derived biomarkers for hyperprolinemia type II. . J. Merx, R.E. van Outersterp, U.F Engelke, V. Hendriks, R.A. Wevers, M.C.D.G. Huigen, F.P.J.T. Rutjes, J. Oomens, K.L.M. Coene, H. Waterval, I. Korver-Keularts, J.K. Martens and T.J.  Boltje: (2022) Communications Biology, 5, 1-8.  [PDF]

Characterization of Elusive Reaction Intermediates Using Infrared Ion Spectroscopy: Application to the Experimental Characterization of Glycosyl Cations. Floor ter Braak, H. Elferink, Kas J. Houthuijs, J. Oomens, J. Martens and Thomas J. Boltje: (2022) Accounts of Chemical Research, 55, 1669-1679.  [PDF]

Structural Determination of Lysine-Linked Cisplatin Complexes via IRMPD Action Spectroscopy: NNs and NO– Binding Modes of Lysine to Platinum Coexist. C. C. He, L. A. Hamlow, H. A. Roy, Z. J. Devereaux, M.A. Hasan, E. Israel, N. A. Cunningham, J. Martens, G. Berden, J. Oomens and M. T. Rodgers: (2022) J. Phys. Chem. B., 126, 9246-9260.

Structural Elucidation of Agrochemicals and Related Derivatives Using Infrared Ion Spectroscopy. Matthias J.A. Vink, F.A.M.G. Geenen, G. Berden, Timothy J.C. O' Riordan, Peter Howe, W.A., J. Oomens, Simon J. Perry and J. Martens: (2022) Environ. Sci. Technol., 56, 15563-15572.  [PDF]

Competing C-4 and C-5-Acyl Stabilization of Uronic Acid Glycosyl Cations. H. Elferink, W.A. Remmerswaal, Kas J. Houthuijs, Oscar Jansen, T. Hansen, M. Rijs Anouk, G. Berden, J. Martens, J. Oomens, J. D.C. Codée and Thomas J. Boltje: (2022) Chem. Eur. J., 28, e202201742-1 - e202201742-8.  [PDF]

Facial vs. meridional coordination in gaseous Ni(II)–hexacyclen complexes revealed with infrared ion spectroscopy. Munshi Mushleh Uddin, Berden Giel and J. Oomens: (2022) Phys Chem Chem Phys, 24, 26890-26897. [PDF]

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. Neven N. Mikawy, H. A. Roy, E. Israel, L. A. Hamlow, Y. Zhu, G. Berden, J. Oomens, C. E. Frieler and M. T. Rodgers: (2022) J Am Soc Mass Spectrom, 33, 2165-2180.  [PDF]

Infrared multiple-photon dissociation spectroscopy of cationized glycine: effects of alkali metal cation size on gas-phase conformation. P. B. Armentrout, B.C. Stevenson, Maryam Ghiassee, G. C. Boles, G. Berden and J. Oomens: (2022) Phys Chem Chem Phys, 24, 22950-22959.  [PDF]

Unidirectional Double- and Triple-Hydrogen Rearrangement Reactions Probed by Infrared Ion Spectroscopy. Dennis Zeh, Marcel Bast, J. Martens, G. Berden, J. Oomens, Sandra Brünken, S. Schlemmer, Mathias Schäfer and Dietmar Kuck: (2022) J Am Soc Mass Spectrom, 33, 1377-1392.

Characterization of Cyclic N-Acyliminium ions by infrared ion spectroscopy. Jona Merx, Kas J. Houthuijs, Hidde Elferink, Eva Witlox, Jasmin Mecinović, J. Oomens, J. Martens, Thomas J. Boltje and Floris P. J. T. Rutjes: (2022)Chem. Eur. J., 28, e202104078-1 - e202104078-7.[PDF]

Infrared multiple photon dissociation action spectroscopy of protonated unsymmetrical dimethylhydrazine and proton-bound dimers of
hydrazine and unsymmetrical dimethylhydrazine. C. P. McNary, M. Demireva, J. Martens, G. Berden, J. Oomens, L. A. Hamlow, M. T. Rodgers and P. B. Armentrout: (2021) Phys Chem Chem Phys, 23, 25877-25885.  [PDF]

IRMPD spectroscopy of [PC (4:0/4:0) + M]+ (M = H, Na, K) and corresponding CID fragment ions. Simon Becher, G. Berden, J. Martens, J. Oomens and Sven Heiles: (2021) J Am Soc Mass Spectrom, 32, 2874-2884.

Evaluation of table-top lasers for routine infrared ion spectroscopy in the analytical laboratory. van Rianne E. Outersterp, J. Martens, A. Peremans, L. Lamard, F. Cuyckens, J. Oomens and G. Berden: (2021) Analyst, 146, 7218-7229.  [PDF]

Untargeted metabolomics and infrared ion spectroscopy identify biomarkers for pyridoxine-dependent epilepsy. U. F. Engelke, J. Martens and K. L. M. Coene: (2021) J. Clin, Invest., 131, e148272-1 - e148272-15.  [PDF]

Infrared multiple-photon dissociation spectra of sodiated complexes of the aliphatic amino acids. P. B. Armentrout, G. C. Boles, Maryam Ghiassee, G. Berden and J. Oomens: (2021) J. Phys. Chem. A., 125, 6348-6355.

Characterization of uranyl coordinated by equatorial Oxygen: Oxo in UO3 versus Oxyl in UO3+. Eric Renault, Jiwen Jian, Rémi Maurice, Michael J. Stipdonk van, Irena Bubas Tatosian, Amanda R. Martens, Jonathan, G. Berden, J. Oomens and J. K. Gibson: (2021) Journal of Physical Chemistry A, 125, 5544-5555.  [PDF]

Generation, characterization, and dissociation of radical cations derived from prolyl-glycyl-glycine. J. K. C. Lau, Francis Esuon, G. Berden, J. Oomens, A. C. Hopkinson, V. Ryzhov and K.W. Michael Siu: (2021) J. Phys. Chem. B, 125, 6121-6129.  [PDF]

Laboratory IR spectroscopy of protonated hexa-peri-hexabenzocoronene and dicoronylene. Julianna Palotás, J. Martens, G. Berden and J Oomens: (2021) Journal of Molecular Spectroscopy, 378, 11474-1 - 11474-9.  [PDF]

Radical‐pairing interactions in a molecular switch evidenced by ion mobility spectrometry and infrared ion spectroscopy. Emeline Hanozin, Benoit Mignolet, J. Martens, G. Berden, Damien Sluysman, Anne-Sophie Duwez, J. Fraser Stoddart, Gauthier Eppe, J. Oomens, E. de Pauw and Denis Morsa: (2021) Angew Chem Int Ed Engl, 60, 10049-10055.  [PDF]

UV/Vis and IRMPD spectroscopic analysis of the absorption properties of methylglyoxal brown carbon. Lemai Vo, Emily Legaard, Corey Thrasher, Aron Jaffe, G. Berden, J. Martens, J. Oomens and R. E O' Brien: (2021) ACS Earth Space Chem., 5, 910–919.  [PDF]

Amadori rearrangement products as potential biomarkers for inborn errors of amino-acid metabolism. van Rianne E. Outersterp, Sam. J. Moons, U. F. Engelke, Herman Bentlage, Tessa M.A. Peters, van Arno Rooij, Marleen C.D.G. Huigen, de Siebolt Boer, van der Ed Heeft, L. A. J. Kluijtmans, Clara D.M. Karnebeek, R. A. Wevers, G. Berden, J. Oomens, Thomas J. Boltje, K. L. M. Coene and J. Martens: (2021) Communications Biology, 4, 367-1 - 367-8.  [PDF]

Mechanistic examination of Cα–Cβ tyrosyl bond cleavage: Spectroscopic investigation of the generation of α‐glycyl radical cations from tyrosyl (glycyl/alanyl)tryptophan. Li Yinan, Li Mengzhu, D.M. Spencer, J. Martens, G. Berden, J. Oomens, Chi-Kit Siu and Ivan K. Chu: (2021) Journal of Mass Spectrometry, 56, e4630-1- e4630-9.  [PDF]

A vibrational spectroscopic and computational study of the structures of protonated imidacloprid and its fragmentation products in the gas phase. Kelsey Menard, J., J. Martens and Travis D. Fridgen: (2021) Phys Chem Chem Phys, 23, 3377-3388.  [PDF]

Zinc and cadmium complexation of L‐methionine: An infrared multiple photon dissociation spectroscopy and theoretical study. G. C. Boles, B.C. Stevenson, R. L. Hightower, G. Berden, J. Oomens and P. B. Armentrout: (2021) Journal of Mass Spectrometry, 56, e4580-1 - e458017.  [PDF]

The infrared spectrum of protonated C70. Julianna Palotás, J. Martens, G. Berden and J Oomens: (2021) Astrophysical Journal Letters, 909, L17-1 - L17-9. https://doi.org/10.3847/2041-8213/abe874 [PDF]

Influence of a hydroxyl group on the deamidation and dehydration reactions of protonated asparagine-serine investigated by combined spectroscopic, guided ion beam, and theoretical approaches. G. C. Boles, L. J. M. Kempkes, J. Martens, G. Berden, J Oomens and P. B. Armentrout: (2021) J Am Soc Mass Spectrom, 32, 786-805.  [PDF]

IR photofragmentation of the phenyl cation: spectroscopy and fragmentation pathways. Sandra D. Wiersma, A. Candian, J. Bakker, G. Berden, J. R. Eyler, J Oomens, A. G. G. M. Tielens and A. Petrignani: (2021) Phys Chem Chem Phys, 23, 4334-4343.  [PDF]

Breslow intermediates (amino enols) and their keto tautomers: First gas‐phase characterization by IR ion spectroscopy. Mathias Paul, Katrin Peckelsen, Thomas Thomulka, J. Martens, G. Berden, J. Oomens, Jörg M Neudörf, M Breugst, A. J. H. M. Meijer, M Schäfer and Albrecht Berkessel: (2021) Chemistry – A European Journal, 27, 2662-2669.  [PDF]

Isomer-specific two-color double-resonance IR2MS3 ion spectroscopy using a single laser: Application in the identification of novel psychoactive substances. van F.A.M.G. Geenen, R.F. Kranenburg, A.C. van Asten, J. Martens, Jos Oomens and G. Berden: (2021) Anal. Chem., 93, 2687-2693.  [PDF]

Preferred protonation site of a series of sulfa drugs in the gas phase revealed by IR spectroscopy. Thomas Uhlemann, Berden  Giel and Jos Oomens: (2021) The European Physical Journal D, 75, 23-1 - 23-13.  [PDF]