15 research outputs found

    Structural dynamics probed by X-ray pulses from synchrotrons and XFELs

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    This review focuses on how short X-ray pulses from synchrotrons and XFELs can be used to track light-induced structural changes in molecular complexes and proteins via the pump–probe method. The upgrade of the European Synchrotron Radiation Facility to a diffraction-limited storage ring, based on the seven-bend achromat lattice, and how it might boost future pump–probe experiments are described. We discuss some of the first X-ray experiments to achieve 100 ps time resolution, including the dissociation and in-cage recombination of diatomic molecules, as probed by wide-angle X-ray scattering, and the 3D filming of ligand transport in myoglobin, as probed by Laue diffraction. Finally, the use of femtosecond XFEL pulses to investigate primary chemical reactions, bond breakage and bond formation, isomerisation and electron transfer are discussed

    Ultrafast structural changes direct the first molecular events of vision

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    èŠ–èŠšă«é–ąă‚ă‚‹ă‚żăƒłăƒ‘ă‚ŻèłȘăźè¶…é«˜é€Ÿćˆ†ć­ć‹•ç”» --è–„æš—ă„ăšă“ă‚ă§ć…‰ă‚’æ„Ÿă˜ă‚‹ä»•ç”„ăż--. äșŹéƒœć€§ć­Šăƒ—ăƒŹă‚čăƒȘăƒȘăƒŒă‚č. 2023-03-23.Vision is initiated by the rhodopsin family of light-sensitive G protein-coupled receptors (GPCRs). A photon is absorbed by the 11-cis retinal chromophore of rhodopsin, which isomerizes within 200 femtoseconds to the all-trans conformation, thereby initiating the cellular signal transduction processes that ultimately lead to vision. However, the intramolecular mechanism by which the photoactivated retinal induces the activation events inside rhodopsin remains experimentally unclear. Here we use ultrafast time-resolved crystallography at room temperature to determine how an isomerized twisted all-trans retinal stores the photon energy that is required to initiate the protein conformational changes associated with the formation of the G protein-binding signalling state. The distorted retinal at a 1-ps time delay after photoactivation has pulled away from half of its numerous interactions with its binding pocket, and the excess of the photon energy is released through an anisotropic protein breathing motion in the direction of the extracellular space. Notably, the very early structural motions in the protein side chains of rhodopsin appear in regions that are involved in later stages of the conserved class A GPCR activation mechanism. Our study sheds light on the earliest stages of vision in vertebrates and points to fundamental aspects of the molecular mechanisms of agonist-mediated GPCR activation

    The Glycan Shield of HIV Is Predominantly Oligomannose Independently of Production System or Viral Clade

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    The N-linked oligomannose glycans of HIV gp120 are a target for both microbicide and vaccine design. The extent of cross-clade conservation of HIV oligomannose glycans is therefore a critical consideration for the development of HIV prophylaxes. We measured the oligomannose content of virion-associated gp120 from primary virus from PBMCs for a range of viral isolates and showed cross-clade elevation (62–79%) of these glycans relative to recombinant, monomeric gp120 (∌30%). We also confirmed that pseudoviral production systems can give rise to notably elevated gp120 oligomannose levels (∌98%), compared to gp120 derived from a single-plasmid viral system using the HIVLAI backbone (56%). This study highlights differences in glycosylation between virion-associated and recombinant gp120

    Structure et dynamique de spin d'un complexe métallique étudié par rayonnement synchrotron

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    The thesis “Structure and Spin Dynamics of a Metal Complex Studied by Synchrotron Radiation” describes an experimental study of the metal complex [FeII(phen)3]2+ in solution by time-resolved X-ray scattering and emission spectroscopy aimed at monitoring changes in structure and spin during its photocycle. In the photoexcited state, a 3d electron is transferred to the ligand for a fraction of a picosecond. From this so-called metal-to-ligand charge transfer state (MLCT), the electron returns to the metal in an excited high spin state (HS) that in turn decays to the low spin (LS) ground state in 725 ps. The structure and spin of the HS state were measured by X-ray scattering (WAXS) and X-ray emission spectroscopy (XES) respectively with 100 picosecond resolution using single X-ray pulses from the synchrotron.Chapter 1 describes the importance of visualising atoms in chemical reactions and transformations. The use of X-rays to gain structural sensitivity is now allowing to visualise photoinduced reactions with 100 picosecond resolution at synchrotrons and lately at 100 femtosecond resolution at XFELs.In chapter two “Probing Molecular Structure in Solution with X-rays”, the theory of X-ray scattering is presented stressing that when the structure is known, the molecular scattering pattern is readily calculated. Compton scattering dominates the scattering at high q and has to be included in the scaling. The intensity of the scattering from a 0.36 mm water sheet is calculated for a 1E+9 photon pulse at 18 keV.When a solute is dissolved in a solvent, the atomic positions are described by statistical atom-atom functions g_ab(r) that can be calculated by MD. The scattering function S(q) is then calculated from g_ab(r) for Fe(phen)3 in water using the TIP4P model with LS and HS structures from DFT.Liquid X-ray scattering probes all atom-atom pairs in the sample including that of the solvent. In the hydrodynamic scattering theory, the liquid is assumed to be in local thermal equilibrium. The theory for the cooling of hot points is presented and the calculation shows that a solution with 2 mM excited Fe(phen)3 attains local thermal equilibrium in 100 ps.The end of chapter 2 gives a summary of X-ray emission spectroscopy (XES). Ka, Kb and valence-to-core (VtC) emission is discussed including their intensity, spin and ligand sensitivity. Kb is the most sensitive probe of the spin state.In chapter 3 the ESRF and ID09 are shortly described. The details of the Johann (JS) and Von Hamos (VH) spectrometers for XES are described with emphasis on the VH since it was used for the first time in this project. The count rate from Kb is extremely low, 0.01 ph/pulse/analyser and the sample has to be exposed for about 1 hour per time delay to get a Kb spectrum with a good S/N ratio.The WAXS and XES experiments are described in Chapter 4. After photoexcitation to the MLCT state, the electron returns to a metal centred HS state in < 100 fs for then to return to the GS in 725 ps. dS(q,t) are 100 ps snapshots of the average structural change for all pairs of atoms at time t. On short time scales t < 10 ns, the solvent is heated adiabatically at constant volume. The thermal response of water was measured in a dye/water mixture. The solvent corrected WAXS data show that the Fe-N distance increases by 0.19 Å in the HS state and that the HS population returns to the LS in 725 ps. The change in the water cage radius is inferred from the low-q data. It is found to contract by 0.3 Å in the HS state in spite of the 0.19 Å expansion of the Fe-N distance.The XES line shapes of the Kb lines were measured with the VH spectrometer and compared with Crispy simulations. The simulations confirm that the 725 ps state is the HS S=2 quintet. Very weak VtC emission, 100 times weaker than Kb, was also observed.Cette thĂšse intitulĂ© «structure et dynamique de spin d’un complexe mĂ©tallique Ă©tudiĂ© par rayonnement synchrotron» dĂ©crit une Ă©tude expĂ©rimentale du complexe mĂ©tallique [FeII(phen)3]]2+ en solution par la diffusion des rayons X rĂ©solue en temps et la spectroscopie d’émission, dont l’objectif est de surveiller les changements structurels et de spin au cours du photocycle du complexe. Dans l’état photo-excitĂ© du complexe, un Ă©lectron de l'orbitale 3d est transfĂ©rĂ© au ligand pour une fraction de picoseconde. AprĂšs ce “transfert de charge mĂ©tal - ligand” (MLCT), l’électron revient au mĂ©tal dans un Ă©tat haut spin (HS) quasi-stable. Le photocycle se termine par un retour Ă  l’état bas spin (BS), l’état fondamental, qui s’effectue en 725 ps. La structure et la rotation de l’état HS ont Ă©tĂ© mesurĂ©es avec une rĂ©solution temporelle de 100 ps.Le 1er chapitre commence par dĂ©crire l’importance de visualiser Ă  l’aide de courtes impulsions de rayons X la façon dont les atomes se dĂ©placent au cours de rĂ©actions chimiques et transformations. L’utilisation de rayons X pour des Ă©tudes structurelles a permis de visualiser les rĂ©actions induites par photons avec une rĂ©solution de 100 ps.Dans le chapitre 2 «Sonder la structure molĂ©culaire en solution avec des rayons X», la thĂ©orie de la diffusion des rayons X est mentionnĂ©e. La diffusion de Debye Ă  partir de molĂ©cules orientĂ©es au hasard est prĂ©sentĂ©e. Lorsque la structure molĂ©culaire est connue, le modĂšle de diffusion est facilement calculĂ©. La diffusion inĂ©lastique domine la diffusion totale Ă  grands q et doit Ă©galement ĂȘtre prise en compte.La position des atomes dans une solution est dĂ©crite par des fonctions inter-atomiques g_ab(r) qui peuvent ĂȘtre simulĂ©es par la dynamique molĂ©culaire. S(q) est calculĂ© pour l’eau basĂ©es sur le modĂšle TIP4P. La diffusion d’un film d’eau de 0,36 mm d’épaisseur est calculĂ©e pour une impulsion de rayons X avec 1E+9 ph/pulse Ă  18 keV.Les modĂšles DFT des structures Ă  bas et haut spins de Fe(phen)3 ont Ă©tĂ© gĂ©nĂ©rĂ©s et les fonctions S(q) ont ensuite Ă©tĂ© calculĂ©es par la fonction de Debye. La conclusion est que les liaisons Fe-N dans l’état HS s’allongent de 0,19 Å.La diffusion des rayons X par les liquides sonde toutes les distributions atome-atome dans l’échantillon, y compris celle du solvant ‘bulk’. Dans la thĂ©orie hydrodynamique, le liquide est supposĂ© ĂȘtre en Ă©quilibre thermique local. L’expression pour le refroidissement des points chauds est examinĂ©e. Pour une concentration de 2 mM de Fe(phen)3 excitĂ© l’équilibre est atteint en 100 ps.La derniĂšre section prĂ©sente l’émission Ka, Kb; et valence-Ă -noyau (VtC, Valence-to-Core). Les spectromĂštres Johann (JS) et Von Hamos (VH) sont prĂ©sentĂ©s. Le taux de comptage de Kb; est faible, 0,01 ph/pulse/analyseur, et l’échantillon a Ă©tĂ© exposĂ© pendant 1 heure par dĂ©lai pour obtenir un bon rapport signal-sur-bruit.Les expĂ©riences WAXS et XES sont dĂ©crites au chapitre 4. AprĂšs la photo-excitation en MLCT, l'Ă©lectron transfĂ©rĂ© retourne Ă  l'Ă©tat HS centrĂ© sur le mĂ©tal en environ 320 fs pour ensuite revenir Ă  l'Ă©tat BS par dĂ©sintĂ©gration non radiative en 725 ps. Le changement de structure dans la transition BS-HS a Ă©tĂ© mesurĂ© par diffusion de rayons X aux grands angles (WAXS) avec une rĂ©solution temporelle de 100 ps. L’échantillon Ă©tait excitĂ© avec des impulsions de 1,2 ps Ă  400 nm et sondĂ© par des impulsions de rayons X Ă  18 keV. Les courbes dS(q,t) sont des instantanĂ©s de 100 ps du changement structurel moyen pour toutes les paires d’atomes dans l’échantillon au moment t. Les donnĂ©es WAXS sont compatibles avec les structures BS et HS simulĂ©es par DFT avec une durĂ©e de vie HS de 725 ps. Le changement du rayon de la cage est dĂ©duit des donnĂ©es Ă  petits q. La cage se contracte de 0,3 Å dans l’état HS.La ligne spectrale Kb a Ă©tĂ© mesurĂ©e avec le spectromĂštre von Hamos et comparĂ©e aux simulations Crispy. Les simulations confirment que l’état 725 ps est le quintet HS

    Structure and spin dynamics of a metal complex studied by synchrotron radiation

    No full text
    Cette thĂšse intitulĂ© «structure et dynamique de spin d’un complexe mĂ©tallique Ă©tudiĂ© par rayonnement synchrotron» dĂ©crit une Ă©tude expĂ©rimentale du complexe mĂ©tallique [FeII(phen)3]]2+ en solution par la diffusion des rayons X rĂ©solue en temps et la spectroscopie d’émission, dont l’objectif est de surveiller les changements structurels et de spin au cours du photocycle du complexe. Dans l’état photo-excitĂ© du complexe, un Ă©lectron de l'orbitale 3d est transfĂ©rĂ© au ligand pour une fraction de picoseconde. AprĂšs ce “transfert de charge mĂ©tal - ligand” (MLCT), l’électron revient au mĂ©tal dans un Ă©tat haut spin (HS) quasi-stable. Le photocycle se termine par un retour Ă  l’état bas spin (BS), l’état fondamental, qui s’effectue en 725 ps. La structure et la rotation de l’état HS ont Ă©tĂ© mesurĂ©es avec une rĂ©solution temporelle de 100 ps.Le 1er chapitre commence par dĂ©crire l’importance de visualiser Ă  l’aide de courtes impulsions de rayons X la façon dont les atomes se dĂ©placent au cours de rĂ©actions chimiques et transformations. L’utilisation de rayons X pour des Ă©tudes structurelles a permis de visualiser les rĂ©actions induites par photons avec une rĂ©solution de 100 ps.Dans le chapitre 2 «Sonder la structure molĂ©culaire en solution avec des rayons X», la thĂ©orie de la diffusion des rayons X est mentionnĂ©e. La diffusion de Debye Ă  partir de molĂ©cules orientĂ©es au hasard est prĂ©sentĂ©e. Lorsque la structure molĂ©culaire est connue, le modĂšle de diffusion est facilement calculĂ©. La diffusion inĂ©lastique domine la diffusion totale Ă  grands q et doit Ă©galement ĂȘtre prise en compte.La position des atomes dans une solution est dĂ©crite par des fonctions inter-atomiques g_ab(r) qui peuvent ĂȘtre simulĂ©es par la dynamique molĂ©culaire. S(q) est calculĂ© pour l’eau basĂ©es sur le modĂšle TIP4P. La diffusion d’un film d’eau de 0,36 mm d’épaisseur est calculĂ©e pour une impulsion de rayons X avec 1E+9 ph/pulse Ă  18 keV.Les modĂšles DFT des structures Ă  bas et haut spins de Fe(phen)3 ont Ă©tĂ© gĂ©nĂ©rĂ©s et les fonctions S(q) ont ensuite Ă©tĂ© calculĂ©es par la fonction de Debye. La conclusion est que les liaisons Fe-N dans l’état HS s’allongent de 0,19 Å.La diffusion des rayons X par les liquides sonde toutes les distributions atome-atome dans l’échantillon, y compris celle du solvant ‘bulk’. Dans la thĂ©orie hydrodynamique, le liquide est supposĂ© ĂȘtre en Ă©quilibre thermique local. L’expression pour le refroidissement des points chauds est examinĂ©e. Pour une concentration de 2 mM de Fe(phen)3 excitĂ© l’équilibre est atteint en 100 ps.La derniĂšre section prĂ©sente l’émission Ka, Kb; et valence-Ă -noyau (VtC, Valence-to-Core). Les spectromĂštres Johann (JS) et Von Hamos (VH) sont prĂ©sentĂ©s. Le taux de comptage de Kb; est faible, 0,01 ph/pulse/analyseur, et l’échantillon a Ă©tĂ© exposĂ© pendant 1 heure par dĂ©lai pour obtenir un bon rapport signal-sur-bruit.Les expĂ©riences WAXS et XES sont dĂ©crites au chapitre 4. AprĂšs la photo-excitation en MLCT, l'Ă©lectron transfĂ©rĂ© retourne Ă  l'Ă©tat HS centrĂ© sur le mĂ©tal en environ 320 fs pour ensuite revenir Ă  l'Ă©tat BS par dĂ©sintĂ©gration non radiative en 725 ps. Le changement de structure dans la transition BS-HS a Ă©tĂ© mesurĂ© par diffusion de rayons X aux grands angles (WAXS) avec une rĂ©solution temporelle de 100 ps. L’échantillon Ă©tait excitĂ© avec des impulsions de 1,2 ps Ă  400 nm et sondĂ© par des impulsions de rayons X Ă  18 keV. Les courbes dS(q,t) sont des instantanĂ©s de 100 ps du changement structurel moyen pour toutes les paires d’atomes dans l’échantillon au moment t. Les donnĂ©es WAXS sont compatibles avec les structures BS et HS simulĂ©es par DFT avec une durĂ©e de vie HS de 725 ps. Le changement du rayon de la cage est dĂ©duit des donnĂ©es Ă  petits q. La cage se contracte de 0,3 Å dans l’état HS.La ligne spectrale Kb a Ă©tĂ© mesurĂ©e avec le spectromĂštre von Hamos et comparĂ©e aux simulations Crispy. Les simulations confirment que l’état 725 ps est le quintet HS.The thesis “Structure and Spin Dynamics of a Metal Complex Studied by Synchrotron Radiation” describes an experimental study of the metal complex [FeII(phen)3]2+ in solution by time-resolved X-ray scattering and emission spectroscopy aimed at monitoring changes in structure and spin during its photocycle. In the photoexcited state, a 3d electron is transferred to the ligand for a fraction of a picosecond. From this so-called metal-to-ligand charge transfer state (MLCT), the electron returns to the metal in an excited high spin state (HS) that in turn decays to the low spin (LS) ground state in 725 ps. The structure and spin of the HS state were measured by X-ray scattering (WAXS) and X-ray emission spectroscopy (XES) respectively with 100 picosecond resolution using single X-ray pulses from the synchrotron.Chapter 1 describes the importance of visualising atoms in chemical reactions and transformations. The use of X-rays to gain structural sensitivity is now allowing to visualise photoinduced reactions with 100 picosecond resolution at synchrotrons and lately at 100 femtosecond resolution at XFELs.In chapter two “Probing Molecular Structure in Solution with X-rays”, the theory of X-ray scattering is presented stressing that when the structure is known, the molecular scattering pattern is readily calculated. Compton scattering dominates the scattering at high q and has to be included in the scaling. The intensity of the scattering from a 0.36 mm water sheet is calculated for a 1E+9 photon pulse at 18 keV.When a solute is dissolved in a solvent, the atomic positions are described by statistical atom-atom functions g_ab(r) that can be calculated by MD. The scattering function S(q) is then calculated from g_ab(r) for Fe(phen)3 in water using the TIP4P model with LS and HS structures from DFT.Liquid X-ray scattering probes all atom-atom pairs in the sample including that of the solvent. In the hydrodynamic scattering theory, the liquid is assumed to be in local thermal equilibrium. The theory for the cooling of hot points is presented and the calculation shows that a solution with 2 mM excited Fe(phen)3 attains local thermal equilibrium in 100 ps.The end of chapter 2 gives a summary of X-ray emission spectroscopy (XES). Ka, Kb and valence-to-core (VtC) emission is discussed including their intensity, spin and ligand sensitivity. Kb is the most sensitive probe of the spin state.In chapter 3 the ESRF and ID09 are shortly described. The details of the Johann (JS) and Von Hamos (VH) spectrometers for XES are described with emphasis on the VH since it was used for the first time in this project. The count rate from Kb is extremely low, 0.01 ph/pulse/analyser and the sample has to be exposed for about 1 hour per time delay to get a Kb spectrum with a good S/N ratio.The WAXS and XES experiments are described in Chapter 4. After photoexcitation to the MLCT state, the electron returns to a metal centred HS state in < 100 fs for then to return to the GS in 725 ps. dS(q,t) are 100 ps snapshots of the average structural change for all pairs of atoms at time t. On short time scales t < 10 ns, the solvent is heated adiabatically at constant volume. The thermal response of water was measured in a dye/water mixture. The solvent corrected WAXS data show that the Fe-N distance increases by 0.19 Å in the HS state and that the HS population returns to the LS in 725 ps. The change in the water cage radius is inferred from the low-q data. It is found to contract by 0.3 Å in the HS state in spite of the 0.19 Å expansion of the Fe-N distance.The XES line shapes of the Kb lines were measured with the VH spectrometer and compared with Crispy simulations. The simulations confirm that the 725 ps state is the HS S=2 quintet. Very weak VtC emission, 100 times weaker than Kb, was also observed

    Tailoring p-Type Behavior in ZnO Quantum Dots through Enhanced Sol-Gel Synthesis: Mechanistic Insights into Zinc Vacancies.

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    The synthesis and control of properties of p-type ZnO is crucial for a variety of optoelectronic and spintronic applications; however, it remains challenging due to the control of intrinsic midgap (defect) states. In this study, we demonstrate a synthetic route to yield colloidal ZnO quantum dots (QD) via an enhanced sol-gel process that effectively eliminates the residual intermediate reaction molecules, which would otherwise weaken the excitonic emission. This process supports the creation of ZnO with p-type properties or compensation of inherited n-type defects, primarily due to zinc vacancies under oxygen-rich conditions. The in-depth analysis of carrier recombination in the midgap across several time scales reveals microsecond carrier lifetimes at room temperature which are expected to occur via zinc vacancy defects, supporting the promoted p-type character of the synthesized ZnO QDs

    High local disorder in Tb2Hf2O7\mathrm{Tb_{2}Hf_{2}O_{7}} pyrochlore oxide nanocrystals

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    The process of Tb2_{2}Hf2_{2}O7_{7} nanocrystals formation upon annealing to 1600°C was investigated by means of X-ray absorption fine structure (XAFS) spectroscopy combined with X-ray diffraction (XRD) and pair distribution function (PDF) analysis. The structure ordering and the growth of nanocrystals upon annealing were estimated independently from XRD patterns and PDF. The probable content of Tb4+^{4+} ions in Tb2_{2}Hf2_{2}O7_{7} was estimated from XANES. All studies indicate a high disorder and a large number of local structure defects in Tb2_{2}Hf2_{2}O7_{7} pyrochlore oxide

    Tailoring p-type behavior in ZnO quantum dots through enhanced sol-gel synthesis: mechanistic insights into zinc vacancies

    No full text
    The synthesis and control of properties of p-type ZnO is crucial for a variety of optoelectronic and spintronic applications; however, it remains challenging due to the control of intrinsic midgap (defect) states. In this study, we demonstrate a synthetic route to yield colloidal ZnO quantum dots (QD) via an enhanced sol-gel process that effectively eliminates the residual intermediate reaction molecules, which would otherwise weaken the excitonic emission. This process supports the creation of ZnO with p-type properties or compensation of inherited n-type defects, primarily due to zinc vacancies under oxygen-rich conditions. The in-depth analysis of carrier recombination in the midgap across several time scales reveals microsecond carrier lifetimes at room temperature which are expected to occur via zinc vacancy defects, supporting the promoted p-type character of the synthesized ZnO QDs

    Tailoring p‑Type Behavior in ZnO Quantum Dots through Enhanced Sol–Gel Synthesis: Mechanistic Insights into Zinc Vacancies

    No full text
    The synthesis and control of properties of p-type ZnO is crucial for a variety of optoelectronic and spintronic applications; however, it remains challenging due to the control of intrinsic midgap (defect) states. In this study, we demonstrate a synthetic route to yield colloidal ZnO quantum dots (QD) via an enhanced sol–gel process that effectively eliminates the residual intermediate reaction molecules, which would otherwise weaken the excitonic emission. This process supports the creation of ZnO with p-type properties or compensation of inherited n-type defects, primarily due to zinc vacancies under oxygen-rich conditions. The in-depth analysis of carrier recombination in the midgap across several time scales reveals microsecond carrier lifetimes at room temperature which are expected to occur via zinc vacancy defects, supporting the promoted p-type character of the synthesized ZnO QDs
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