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Kotobi A, Singh K, Höche D, Bari S, Meißner RH, Bande A. Integrating Explainability into Graph Neural Network Models for the Prediction of X-ray Absorption Spectra. J Am Chem Soc 2023; 145:22584-22598. [PMID: 37807700 PMCID: PMC10591337 DOI: 10.1021/jacs.3c07513] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Indexed: 10/10/2023]
Abstract
The use of sophisticated machine learning (ML) models, such as graph neural networks (GNNs), to predict complex molecular properties or all kinds of spectra has grown rapidly. However, ensuring the interpretability of these models' predictions remains a challenge. For example, a rigorous understanding of the predicted X-ray absorption spectrum (XAS) generated by such ML models requires an in-depth investigation of the respective black-box ML model used. Here, this is done for different GNNs based on a comprehensive, custom-generated XAS data set for small organic molecules. We show that a thorough analysis of the different ML models with respect to the local and global environments considered in each ML model is essential for the selection of an appropriate ML model that allows a robust XAS prediction. Moreover, we employ feature attribution to determine the respective contributions of various atoms in the molecules to the peaks observed in the XAS spectrum. By comparing this peak assignment to the core and virtual orbitals from the quantum chemical calculations underlying our data set, we demonstrate that it is possible to relate the atomic contributions via these orbitals to the XAS spectrum.
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Affiliation(s)
- Amir Kotobi
- Helmholtz-Zentrum
Hereon, Institute of Surface
Science, Geesthacht, DE 21502, Germany
| | - Kanishka Singh
- Helmholtz-Zentrum
Berlin für Materialien und Energie GmbH, Berlin, DE 10409, Germany
- Institute
of Chemistry and Biochemistry, Freie Universität
Berlin, Berlin, DE 14195, Germany
| | - Daniel Höche
- Helmholtz-Zentrum
Hereon, Institute of Surface
Science, Geesthacht, DE 21502, Germany
| | - Sadia Bari
- Deutsches
Elektronen-Synchrotron DESY, Hamburg, DE 22607, Germany
- Zernike
Institute for Advanced Materials, University
of Groningen, Groningen 9712, Netherlands
| | - Robert H. Meißner
- Helmholtz-Zentrum
Hereon, Institute of Surface
Science, Geesthacht, DE 21502, Germany
- Hamburg
University of Technology, Institute of Polymers
and Composites, Hamburg, DE 21073, Germany
| | - Annika Bande
- Helmholtz-Zentrum
Berlin für Materialien und Energie GmbH, Berlin, DE 10409, Germany
- Leibniz
University Hannover, Institute of Inorganic
Chemistry, Hannover, DE 30167, Germany
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Leroux J, Kotobi A, Hirsch K, Lau T, Ortiz-Mahecha C, Maksimov D, Meißner R, Oostenrijk B, Rossi M, Schubert K, Timm M, Trinter F, Unger I, Zamudio-Bayer V, Schwob L, Bari S. Mapping the electronic transitions of protonation sites in peptides using soft X-ray action spectroscopy. Phys Chem Chem Phys 2023; 25:25603-25618. [PMID: 37721108 DOI: 10.1039/d3cp02524a] [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: 09/19/2023]
Abstract
Near-edge X-ray absorption mass spectrometry (NEXAMS) around the nitrogen and oxygen K-edges was employed on gas-phase peptides to probe the electronic transitions related to their protonation sites, namely at basic side chains, the N-terminus and the amide oxygen. The experimental results are supported by replica exchange molecular dynamics and density-functional theory and restricted open-shell configuration with single calculations to attribute the transitions responsible for the experimentally observed resonances. We studied five tailor-made glycine-based pentapeptides, where we identified the signature of the protonation site of N-terminal proline, histidine, lysine and arginine, at 406 eV, corresponding to N 1s → σ*(NHx+) (x = 2 or 3) transitions, depending on the peptides. We compared the spectra of pentaglycine and triglycine to evaluate the sensitivity of NEXAMS to protomers. Separate resonances have been identified to distinguish two protomers in triglycine, the protonation site at the N-terminus at 406 eV and the protonation site at the amide oxygen characterized by a transition at 403.1 eV.
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Affiliation(s)
- Juliette Leroux
- CIMAP, CEA/CNRS/ENSICAEN/Université de Caen Normandie, 14050 Caen, France
- Deutsches Elektronen-Synchrotron DESY, Germany.
| | - Amir Kotobi
- Deutsches Elektronen-Synchrotron DESY, Germany.
- Helmholtz-Zentrum Hereon, Institute of Surface Science, 21502 Geesthacht, Germany
| | - Konstantin Hirsch
- Abteilung Hochempfindliche Röntgenspektroskopie, Helmholtz-Zentrum Berlin für Materialien und Energie, 12489 Berlin, Germany
| | - Tobias Lau
- Abteilung Hochempfindliche Röntgenspektroskopie, Helmholtz-Zentrum Berlin für Materialien und Energie, 12489 Berlin, Germany
| | - Carlos Ortiz-Mahecha
- Hamburg University of Technology, Institute of Polymers and Composites, 21073 Hamburg, Germany
| | - Dmitrii Maksimov
- Max Planck Institute for the Structure and Dynamics of Matter, 22761 Hamburg, Germany
| | - Robert Meißner
- Helmholtz-Zentrum Hereon, Institute of Surface Science, 21502 Geesthacht, Germany
- Hamburg University of Technology, Institute of Polymers and Composites, 21073 Hamburg, Germany
| | | | - Mariana Rossi
- Max Planck Institute for the Structure and Dynamics of Matter, 22761 Hamburg, Germany
| | | | - Martin Timm
- Abteilung Hochempfindliche Röntgenspektroskopie, Helmholtz-Zentrum Berlin für Materialien und Energie, 12489 Berlin, Germany
| | - Florian Trinter
- Institut für Kernphysik, Goethe-Universität Frankfurt am Main, 60438 Frankfurt am Main, Germany
- Molecular Physics, Fritz-Haber-Institut der Max-Planck-Gesellschaft, 14195 Berlin, Germany
| | - Isaak Unger
- Department of Physics and Astronomy, Uppsala University, 75120 Uppsala, Sweden
| | - Vicente Zamudio-Bayer
- Abteilung Hochempfindliche Röntgenspektroskopie, Helmholtz-Zentrum Berlin für Materialien und Energie, 12489 Berlin, Germany
| | | | - Sadia Bari
- Deutsches Elektronen-Synchrotron DESY, Germany.
- The Hamburg Centre for Ultrafast Imaging, Hamburg, Germany
- Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, The Netherlands
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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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