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Freibert A, Mendive-Tapia D, Huse N, Vendrell O. Time-Dependent Resonant Inelastic X-ray Scattering of Pyrazine at the Nitrogen K-Edge: A Quantum Dynamics Approach. J Chem Theory Comput 2024; 20:2167-2180. [PMID: 38315564 PMCID: PMC10938531 DOI: 10.1021/acs.jctc.3c01259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 12/31/2023] [Accepted: 01/03/2024] [Indexed: 02/07/2024]
Abstract
We calculate resonant inelastic X-ray scattering spectra of pyrazine at the nitrogen K-edge in the time domain including wavepacket dynamics in both the valence and core-excited state manifolds. Upon resonant excitation, we observe ultrafast non-adiabatic population transfer between core-excited states within the core-hole lifetime, leading to molecular symmetry distortions. Importantly, our time-domain approach inherently contains the ability to manipulate the dynamics of this process by detuning the excitation energy, which effectively shortens the scattering duration. We also explore the impact of pulsed incident X-ray radiation, which provides a foundation for state-of-the-art time-resolved experiments with coherent pulsed light sources.
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Affiliation(s)
- Antonia Freibert
- Department
of Physics, University of Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
- Theoretical
Chemistry, Institute of Physical Chemistry, Heidelberg University, Im Neuenheimer Feld 229, 69120 Heidelberg, Germany
| | - David Mendive-Tapia
- Theoretical
Chemistry, Institute of Physical Chemistry, Heidelberg University, Im Neuenheimer Feld 229, 69120 Heidelberg, Germany
| | - Nils Huse
- Department
of Physics, University of Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Oriol Vendrell
- Theoretical
Chemistry, Institute of Physical Chemistry, Heidelberg University, Im Neuenheimer Feld 229, 69120 Heidelberg, Germany
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Ochmann M, Vaz da Cruz V, Eckert S, Huse N, Föhlisch A. R-Group stabilization in methylated formamides observed by resonant inelastic X-ray scattering. Chem Commun (Camb) 2022; 58:8834-8837. [PMID: 35848855 PMCID: PMC9350990 DOI: 10.1039/d2cc00053a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 07/07/2022] [Indexed: 11/21/2022]
Abstract
The inherent stability of methylated formamides is traced to a stabilization of the deep-lying σ-framework by resonant inelastic X-ray scattering at the nitrogen K-edge. Charge transfer from the amide nitrogen to the methyl groups underlie this stabilization mechanism that leaves the aldehyde group essentially unaltered and explains the stability of secondary and tertiary amides.
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Affiliation(s)
- Miguel Ochmann
- Department of Physics, University of Hamburg and Center for Free-Electron Laser Science, Luruper Chaussee 149, 22761 Hamburg, Germany.
| | - Vinícius Vaz da Cruz
- Institute for Methods and Instrumentation in Synchrotron Radiation Research G-ISRR, Helmholtz-Zentrum Berlin für Materialien und Energie, Albert-Einstein-Strasse 15, 12489 Berlin, Germany.
| | - Sebastian Eckert
- Institute for Methods and Instrumentation in Synchrotron Radiation Research G-ISRR, Helmholtz-Zentrum Berlin für Materialien und Energie, Albert-Einstein-Strasse 15, 12489 Berlin, Germany.
| | - Nils Huse
- Department of Physics, University of Hamburg and Center for Free-Electron Laser Science, Luruper Chaussee 149, 22761 Hamburg, Germany.
| | - Alexander Föhlisch
- Institute for Methods and Instrumentation in Synchrotron Radiation Research G-ISRR, Helmholtz-Zentrum Berlin für Materialien und Energie, Albert-Einstein-Strasse 15, 12489 Berlin, Germany.
- Institut für Physik and Astronomie, Universität Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany
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Ruppert M, Creon A, Tidow H, Huse N. Population Dynamics of Stretching Excitations of p-Azido-phenylalanine Incorporated in Calmodulin-Peptide Complexes. J Phys Chem B 2022; 126:368-375. [PMID: 34990136 DOI: 10.1021/acs.jpcb.1c06775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We genetically incorporated the unnatural amino acid p-azido-phenylalanine (AzF) into the ubiquitous Ca2+ sensor protein calmodulin (CaM) in complex with different peptides to explore the response of the azido stretching line shape to varying binding motifs with femtosecond infrared spectroscopy. The dynamic response of the azido stretching mode varies in different CaM-peptide complexes. We model these dynamics as coherent excitations of Fermi resonances and extract a lifetime of the azido stretching vibration of about 1 ps. The resulting model parameters are commensurate with the linear infrared absorption lineshapes which suggests that the conformation-sensitive vibrational lineshape could be composed of Fermi resonances that differ between the protein-peptide complexes.
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Affiliation(s)
- Matthias Ruppert
- Hamburg Advanced Research Centre for Bioorganic Chemistry, Institute for Nanostructure and Solid-State Physics, Department of Physics, and Center for Free-Electron Laser Science, University of Hamburg, Luruper Chaussee 149, D-22761 Hamburg, Germany
| | - Anne Creon
- Hamburg Advanced Research Centre for Bioorganic Chemistry, Institute for Nanostructure and Solid-State Physics, Department of Physics, and Center for Free-Electron Laser Science, University of Hamburg, Luruper Chaussee 149, D-22761 Hamburg, Germany.,Hamburg Advanced Research Centre for Bioorganic Chemistry, Institute for Biochemistry and Molecular Biology, Department of Chemistry, University of Hamburg, Martin-Luther-King-Platz 6, D-20146 Hamburg, Germany
| | - Henning Tidow
- Hamburg Advanced Research Centre for Bioorganic Chemistry, Institute for Biochemistry and Molecular Biology, Department of Chemistry, University of Hamburg, Martin-Luther-King-Platz 6, D-20146 Hamburg, Germany.,The Hamburg Centre for Ultrafast Imaging, University of Hamburg, Luruper Chaussee, 149, D-22761 Hamburg, Germany
| | - Nils Huse
- Hamburg Advanced Research Centre for Bioorganic Chemistry, Institute for Nanostructure and Solid-State Physics, Department of Physics, and Center for Free-Electron Laser Science, University of Hamburg, Luruper Chaussee 149, D-22761 Hamburg, Germany.,The Hamburg Centre for Ultrafast Imaging, University of Hamburg, Luruper Chaussee, 149, D-22761 Hamburg, Germany
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Jay RM, Vaz da Cruz V, Eckert S, Fondell M, Mitzner R, Föhlisch A. Probing Solute-Solvent Interactions of Transition Metal Complexes Using L-Edge Absorption Spectroscopy. J Phys Chem B 2020; 124:5636-5645. [PMID: 32532156 PMCID: PMC7357850 DOI: 10.1021/acs.jpcb.0c00638] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
In order to tailor solution-phase chemical reactions involving transition metal complexes, it is critical to understand how their valence electronic charge distributions are affected by the solution environment. Here, solute-solvent interactions of a solvatochromic mixed-ligand iron complex were investigated using X-ray absorption spectroscopy at the transition metal L2,3-edge. Due to the selectivity of the corresponding core excitations to the iron 3d orbitals, the method grants direct access to the valence electronic structure around the iron center and its response to interactions with the solvent environment. A linear increase of the total L2,3-edge absorption cross section as a function of the solvent Lewis acidity is revealed. The effect is caused by relative changes in different metal-ligand-bonding channels, which preserve local charge densities while increasing the density of unoccupied states around the iron center. These conclusions are corroborated by a combination of molecular dynamics and spectrum simulations based on time-dependent density functional theory. The simulations reproduce the spectral trends observed in the X-ray but also optical absorption experiments. Our results underscore the importance of solute-solvent interactions when aiming for an accurate description of the valence electronic structure of solvated transition metal complexes and demonstrate how L2,3-edge absorption spectroscopy can aid in understanding the impact of the solution environment on intramolecular covalency and the electronic charge distribution.
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Affiliation(s)
- Raphael M Jay
- Universität Potsdam, Institut für Physik und Astronomie, Karl-Liebknecht-Straße 24/25, 14476 Potsdam, Germany
| | - Vinícius Vaz da Cruz
- Universität Potsdam, Institut für Physik und Astronomie, Karl-Liebknecht-Straße 24/25, 14476 Potsdam, Germany
| | - Sebastian Eckert
- Universität Potsdam, Institut für Physik und Astronomie, Karl-Liebknecht-Straße 24/25, 14476 Potsdam, Germany
| | - Mattis Fondell
- Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, Institute for Methods and Instrumentation for Synchrotron Radiation Research, Albert-Einstein-Straße 15, 12489 Berlin, Germany
| | - Rolf Mitzner
- Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, Institute for Methods and Instrumentation for Synchrotron Radiation Research, Albert-Einstein-Straße 15, 12489 Berlin, Germany
| | - Alexander Föhlisch
- Universität Potsdam, Institut für Physik und Astronomie, Karl-Liebknecht-Straße 24/25, 14476 Potsdam, Germany.,Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, Institute for Methods and Instrumentation for Synchrotron Radiation Research, Albert-Einstein-Straße 15, 12489 Berlin, Germany
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Creon A, Josts I, Niebling S, Huse N, Tidow H. Conformation-specific detection of calmodulin binding using the unnatural amino acid p-azido-phenylalanine (AzF) as an IR-sensor. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2018; 5:064701. [PMID: 30474048 PMCID: PMC6224318 DOI: 10.1063/1.5053466] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 10/22/2018] [Indexed: 05/13/2023]
Abstract
Calmodulin (CaM) is a very conserved, ubiquitous, eukaryotic protein that binds four Ca2+ ions with high affinity. It acts as a calcium sensor by translating Ca2+ signals into cellular processes such as metabolism, inflammation, immune response, memory, and muscle contraction. Calcium binding to CaM leads to conformational changes that enable Ca2+/CaM to recognize and bind various target proteins with high affinity. The binding mode and binding partners of CaM are very diverse, and a consensus binding sequence is lacking. Here, we describe an elegant system that allows conformation-specific detection of CaM-binding to its binding partners. We incorporate the unnatural amino acid p-azido-phenylalanine (AzF) in different positions of CaM and follow its unique spectral signature by infrared (IR)-spectroscopy of the azido stretching vibration. Our results suggest that the AzF vibrational probe is sensitive to the chemical environment in different CaM/CaM-binding domain (CaMBD) complexes, which allows differentiating between different binding motifs according to the spectral characteristics of the azido stretching mode. We corroborate our results with a crystal structure of AzF-labelled CaM (CaM108AzF) in complex with a binding peptide from calmodulin-dependent protein kinase IIα identifying the structural basis for the observed IR frequency shifts.
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Affiliation(s)
| | | | | | | | - Henning Tidow
- Authors to whom correspondence should be addressed: , Tel.: +49 40428381599 and , Tel.: +49 40428388984
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Ochmann M, Hussain A, von Ahnen I, Cordones AA, Hong K, Lee JH, Ma R, Adamczyk K, Kim TK, Schoenlein RW, Vendrell O, Huse N. UV-Photochemistry of the Disulfide Bond: Evolution of Early Photoproducts from Picosecond X-ray Absorption Spectroscopy at the Sulfur K-Edge. J Am Chem Soc 2018; 140:6554-6561. [PMID: 29771112 DOI: 10.1021/jacs.7b13455] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
We have investigated dimethyl disulfide as the basic moiety for understanding the photochemistry of disulfide bonds, which are central to a broad range of biochemical processes. Picosecond time-resolved X-ray absorption spectroscopy at the sulfur K-edge provides unique element-specific insight into the photochemistry of the disulfide bond initiated by 267 nm femtosecond pulses. We observe a broad but distinct transient induced absorption spectrum which recovers on at least two time scales in the nanosecond range. We employed RASSCF electronic structure calculations to simulate the sulfur-1s transitions of multiple possible chemical species, and identified the methylthiyl and methylperthiyl radicals as the primary reaction products. In addition, we identify disulfur and the CH2S thione as the secondary reaction products of the perthiyl radical that are most likely to explain the observed spectral and kinetic signatures of our experiment. Our study underscores the importance of elemental specificity and the potential of time-resolved X-ray spectroscopy to identify short-lived reaction products in complex reaction schemes that underlie the rich photochemistry of disulfide systems.
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Affiliation(s)
- Miguel Ochmann
- Department of Physics , University of Hamburg and Max Planck Institute for the Structure and Dynamics of Matter, Center for Free Electron Laser Science , 22761 Hamburg , Germany
| | - Abid Hussain
- Department of Physics , University of Hamburg and Max Planck Institute for the Structure and Dynamics of Matter, Center for Free Electron Laser Science , 22761 Hamburg , Germany
| | - Inga von Ahnen
- Department of Physics , University of Hamburg and Max Planck Institute for the Structure and Dynamics of Matter, Center for Free Electron Laser Science , 22761 Hamburg , Germany
| | - Amy A Cordones
- Ultrafast X-ray Science Lab, Chemical Sciences Division , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States
| | - Kiryong Hong
- Department of Chemistry and Chemistry Institute of Functional Materials , Pusan National University , Busan 46241 , South Korea
| | - Jae Hyuk Lee
- Ultrafast X-ray Science Lab, Chemical Sciences Division , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States
| | - Rory Ma
- Department of Chemistry and Chemistry Institute of Functional Materials , Pusan National University , Busan 46241 , South Korea
| | - Katrin Adamczyk
- Department of Physics , University of Hamburg and Max Planck Institute for the Structure and Dynamics of Matter, Center for Free Electron Laser Science , 22761 Hamburg , Germany
| | - Tae Kyu Kim
- Department of Chemistry and Chemistry Institute of Functional Materials , Pusan National University , Busan 46241 , South Korea
| | - Robert W Schoenlein
- Ultrafast X-ray Science Lab, Chemical Sciences Division , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States
| | - Oriol Vendrell
- Center for Free-Electron Laser Science , DESY and The Hamburg Centre for Ultrafast Imaging , 22607 Hamburg , Germany
| | - Nils Huse
- Department of Physics , University of Hamburg and Max Planck Institute for the Structure and Dynamics of Matter, Center for Free Electron Laser Science , 22761 Hamburg , Germany
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