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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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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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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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Obstarczyk P, Pniakowska A, Nonappa, Grzelczak MP, Olesiak-Bańska J. Crown Ether-Capped Gold Nanoclusters as a Multimodal Platform for Bioimaging. ACS Omega 2023; 8:11503-11511. [PMID: 37008092 PMCID: PMC10061685 DOI: 10.1021/acsomega.3c00426] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 03/02/2023] [Indexed: 12/01/2023]
Abstract
The distinct polarity of biomolecule surfaces plays a pivotal role in their biochemistry and functions as it is involved in numerous processes, such as folding, aggregation, or denaturation. Therefore, there is a need to image both hydrophilic and hydrophobic bio-interfaces with markers of distinct responses to hydrophobic and hydrophilic environments. In this work, we present a synthesis, characterization, and application of ultrasmall gold nanoclusters capped with a 12-crown-4 ligand. The nanoclusters present an amphiphilic character and can be successfully transferred between aqueous and organic solvents and have their physicochemical integrity retained. They can serve as probes for multimodal bioimaging with light (as they emit near-infrared luminescence) and electron microscopy (due to the high electron density of gold). In this work, we used protein superstructures, namely, amyloid spherulites, as a hydrophobic surface model and individual amyloid fibrils with a mixed hydrophobicity profile. Our nanoclusters spontaneously stained densely packed amyloid spherulites as observed under fluorescence microscopy, which is limited for hydrophilic markers. Moreover, our clusters revealed structural features of individual amyloid fibrils at a nanoscale as observed under a transmission electron microscope. We show the potential of crown ether-capped gold nanoclusters in multimodal structural characterization of bio-interfaces where the amphiphilic character of the supramolecular ligand is required.
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Affiliation(s)
- Patryk Obstarczyk
- Institute
of Advanced Materials, Wroclaw University
of Science and Technology, 50-370 Wrocław, Poland
| | - Anna Pniakowska
- Institute
of Advanced Materials, Wroclaw University
of Science and Technology, 50-370 Wrocław, Poland
| | - Nonappa
- Faculty
of Engineering and Natural Sciences, Tampere
University, FI-33720 Tampere, Finland
| | - Marcin P. Grzelczak
- Institute
of Advanced Materials, Wroclaw University
of Science and Technology, 50-370 Wrocław, Poland
| | - Joanna Olesiak-Bańska
- Institute
of Advanced Materials, Wroclaw University
of Science and Technology, 50-370 Wrocław, Poland
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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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