Roberto Alonso-Mori

All Publications

• Structural evolution of liquid silicates under conditions in Super-Earth interiors. Nature communications Morard, G., Hernandez, J. A., Pege, C., Nagy, C., Libon, L., Lacquement, A., Sokaras, D., Lee, H. J., Galtier, E., Heimann, P., Cunningham, E., Glenzer, S. H., Vinci, T., Prescher, C., Boccato, S., Chantel, J., Merkel, S., Zhang, Y., Yang, H., Wei, X., Pandolfi, S., Mao, W. L., Gleason, A. E., Shim, S. H., Alonso-Mori, R., Ravasio, A. 2024; 15 (1): 8483

  Abstract

  Molten silicates at depth are crucial for planetary evolution, yet their local structure and physical properties under extreme conditions remain elusive due to experimental challenges. In this study, we utilize in situ X-ray diffraction (XRD) at the Matter in Extreme Conditions (MEC) end-station of the Linear Coherent Linac Source (LCLS) at SLAC National Accelerator Laboratory to investigate liquid silicates. Using an ultrabright X-ray source and a high-power optical laser, we probed the local atomic arrangement of shock-compressed liquid (Mg,Fe)SiO3 with varying Fe content, at pressures from 81(9) to 385(40) GPa. We compared these findings to ab initio molecular dynamics simulations under similar conditions. Results indicate continuous densification of the O-O and Mg-Si networks beyond Earth's interior pressure range, potentially altering melt properties at extreme conditions. This could have significant implications for early planetary evolution, leading to notable differences in differentiation processes between smaller rocky planets, such as Earth and Venus, and super-Earths, which are exoplanets with masses nearly three times that of Earth.

  View details for DOI 10.1038/s41467-024-51796-7

  View details for PubMedID 39362851

  View details for PubMedCentralID PMC11452200

• Structural Evolution of Photoexcited Methylcobalamin toward a CarH-like Metastable State: Evidence from Time-Resolved X-ray Absorption and X-ray Emission JOURNAL OF PHYSICAL CHEMISTRY B Sension, R. J., McClain, T. P., Michocki, L. B., Miller, N. A., Alonso-Mori, R., Lima, F., Ardana-Lamas, F., Biednov, M., Chung, T., Deb, A., Jiang, Y., Kaneshiro, A. K., Khakhulin, D., Kubarych, K. J., Lamb, R. M., Meadows, J. H., Otte, F., Sofferman, D. L., Song, S., Uemura, Y., van Driel, T. B., Penner-Hahn, J. E. 2024

  Abstract

  CarH is a protein photoreceptor that uses a form of B12, adenosylcobalamin (AdoCbl), to sense light via formation of a metastable excited state. Aside from AdoCbl bound to CarH, methylcobalamin (MeCbl) is the only other example─to date─of photoexcited cobalamins forming metastable excited states with lifetimes of nanoseconds or longer. The UV-visible spectra of the excited states of MeCbl and AdoCbl bound to CarH are similar. We have used transient Co K-edge X-ray absorption and X-ray emission spectroscopies in conjunction with transient absorption spectroscopy in the UV-visible region to characterize the excited states of MeCbl. These data show that the metastable excited state of MeCbl has a slightly expanded corrin ring and increased electron density on the cobalt, but only small changes in the axial bond lengths.

  View details for DOI 10.1021/acs.jpcb.4c03729

  View details for Web of Science ID 001293313300001

  View details for PubMedID 39150518

• Time-Resolved X-ray Emission Spectroscopy and Synthetic High-Spin Model Complexes Resolve Ambiguities in Excited-State Assignments of Transition-Metal Chromophores: A Case Study of Fe-Amido Complexes. Journal of the American Chemical Society Reinhard, M. E., Sidhu, B. K., Lozada, I. B., Powers-Riggs, N., Ortiz, R. J., Lim, H., Nickel, R., Lierop, J. v., Alonso-Mori, R., Chollet, M., Gee, L. B., Kramer, P. L., Kroll, T., Raj, S. L., van Driel, T. B., Cordones, A. A., Sokaras, D., Herbert, D. E., Gaffney, K. J. 2024

  Abstract

  To fully harness the potential of abundant metal coordination complex photosensitizers, a detailed understanding of the molecular properties that dictate and control the electronic excited-state population dynamics initiated by light absorption is critical. In the absence of detectable luminescence, optical transient absorption (TA) spectroscopy is the most widely employed method for interpreting electron redistribution in such excited states, particularly for those with a charge-transfer character. The assignment of excited-state TA spectral features often relies on spectroelectrochemical measurements, where the transient absorption spectrum generated by a metal-to-ligand charge-transfer (MLCT) electronic excited state, for instance, can be approximated using steady-state spectra generated by electrochemical ligand reduction and metal oxidation and accounting for the loss of absorptions by the electronic ground state. However, the reliability of this approach can be clouded when multiple electronic configurations have similar optical signatures. Using a case study of Fe(II) complexes supported by benzannulated diarylamido ligands, we highlight an example of such an ambiguity and show how time-resolved X-ray emission spectroscopy (XES) measurements can reliably assign excited states from the perspective of the metal, particularly in conjunction with accurate synthetic models of ligand-field electronic excited states, leading to a reinterpretation of the long-lived excited state as a ligand-field metal-centered quintet state. A detailed analysis of the XES data on the long-lived excited state is presented, along with a discussion of the ultrafast dynamics following the photoexcitation of low-spin Fe(II)-Namido complexes using a high-spin ground-state analogue as a spectral model for the 5T2 excited state.

  View details for DOI 10.1021/jacs.4c02748

  View details for PubMedID 38889309

• Observation of a Picosecond Light-Induced Spin Transition in Polymeric Nanorods. ACS nano Reinhard, M., Kunnus, K., Ledbetter, K., Biasin, E., Zederkof, D. B., Alonso-Mori, R., van Driel, T. B., Nelson, S., Kozina, M., Borkiewicz, O. J., Lorenc, M., Cammarata, M., Collet, E., Sokaras, D., Cordones, A. A., Gaffney, K. J. 2024

  Abstract

  Spin transition (ST) materials are attractive for developing photoswitchable devices, but their slow material transformations limit device applications. Size reduction could enable faster switching, but the photoinduced dynamics at the nanoscale remains poorly understood. Here, we report a femtosecond optical pump multimodal X-ray probe study of polymeric nanorods. Simultaneously tracking the ST order parameter with X-ray emission spectroscopy and structure with X-ray diffraction, we observe photodoping of the low-spin-lattice within ∼150 fs. Above a ∼16% photodoping threshold, the transition to the high-spin phase occurs following an incubation period assigned to vibrational energy redistribution within the nanorods activating the molecular spin switching. Above ∼60% photodoping, the incubation period disappears, and the transition completes within ∼50 ps, preceded by the elastic nanorod expansion in response to the photodoping. These results support the feasibility of ST material-based GHz optical switching applications.

  View details for DOI 10.1021/acsnano.3c10042

  View details for PubMedID 38833689

• The Liquid Jet Endstation for Hard X-ray Scattering and Spectroscopy at the Linac Coherent Light Source. Molecules (Basel, Switzerland) Antolini, C., Sosa Alfaro, V., Reinhard, M., Chatterjee, G., Ribson, R., Sokaras, D., Gee, L., Sato, T., Kramer, P. L., Raj, S. L., Hayes, B., Schleissner, P., Garcia-Esparza, A. T., Lim, J., Babicz, J. T., Follmer, A. H., Nelson, S., Chollet, M., Alonso-Mori, R., van Driel, T. B. 2024; 29 (10)

  Abstract

  The ability to study chemical dynamics on ultrafast timescales has greatly advanced with the introduction of X-ray free electron lasers (XFELs) providing short pulses of intense X-rays tailored to probe atomic structure and electronic configuration. Fully exploiting the full potential of XFELs requires specialized experimental endstations along with the development of techniques and methods to successfully carry out experiments. The liquid jet endstation (LJE) at the Linac Coherent Light Source (LCLS) has been developed to study photochemistry and biochemistry in solution systems using a combination of X-ray solution scattering (XSS), X-ray absorption spectroscopy (XAS), and X-ray emission spectroscopy (XES). The pump-probe setup utilizes an optical laser to excite the sample, which is subsequently probed by a hard X-ray pulse to resolve structural and electronic dynamics at their intrinsic femtosecond timescales. The LJE ensures reliable sample delivery to the X-ray interaction point via various liquid jets, enabling rapid replenishment of thin samples with millimolar concentrations and low sample volumes at the 120 Hz repetition rate of the LCLS beam. This paper provides a detailed description of the LJE design and of the techniques it enables, with an emphasis on the diagnostics required for real-time monitoring of the liquid jet and on the spatiotemporal overlap methods used to optimize the signal. Additionally, various scientific examples are discussed, highlighting the versatility of the LJE.

  View details for DOI 10.3390/molecules29102323

  View details for PubMedID 38792184

• Ultrafast X-ray Absorption Spectroscopy Reveals Excited-State Dynamics of B12Coenzymes Controlled by the Axial Base. The journal of physical chemistry. B Chung, T., McClain, T. P., Alonso-Mori, R., Chollet, M., Deb, A., Garcia-Esparza, A. T., Huang Ze En, J., Lamb, R. M., Michocki, L. B., Reinhard, M., van Driel, T. B., Penner-Hahn, J. E., Sension, R. J. 2024

  Abstract

  Polarized time-resolved X-ray absorption spectroscopy at the Co K-edge is used to probe the excited-state dynamics and photolysis of base-off methylcobalamin and the excited-state structure of base-off adenosylcobalamin. For both molecules, the final excited-state minimum shows evidence for an expansion of the cavity around the Co ion by ca. 0.04 to 0.05 A. The 5-coordinate base-off cob(II)alamin that is formed following photodissociation has a structure similar to that of the 5-coordinate base-on cob(II)alamin, with a ring expansion of 0.03 to 0.04 A and a contraction of the lower axial bond length relative to that in the 6-coordinate ground state. These data provide insights into the role of the lower axial ligand in modulating the reactivity of B12 coenzymes.

  View details for DOI 10.1021/acs.jpcb.3c07779

  View details for PubMedID 38301132

• Structural evidence for intermediates during O₂ formation in photosystem II( Vol <bold>617</bold>, pg 629, 2023) NATURE Bhowmick, A., Hussein, R., Bogacz, I., Simon, P. S., Ibrahim, M., Chatterjee, R., Doyle, M. D., Cheah, M., Fransson, T., Chernev, P., Kim, I., Makita, H., Dasgupta, M., Kaminsky, C. J., Zhang, M., Gaetcke, J., Haupt, S., Nangca, I. I., Keable, S. M., Aydin, A., Tono, K., Owada, S., Gee, L. B., Fuller, F. D., Batyuk, A., Alonso-Mori, R., Holton, J. M., Paley, D. W., Moriarty, N. W., Mamedov, F., Adams, P. D., Brewster, A. S., Dobbek, H., Sauter, N. K., Bergmann, U., Zouni, A., Messinger, J., Kern, J., Yano, J., Yachandra, V. K. 2024: E12

  View details for DOI 10.1038/s41586-024-07099-4

  View details for Web of Science ID 001179131000001

  View details for PubMedID 38291188

  View details for PubMedCentralID PMC10866699

• Seeded stimulated x-ray emission at 5.9 keV (vol 10, pg 513, 2023) OPTICA Doyle, M. D., Halavanau, A., Zhang, Y., Michine, Y., Everts, J., Fuller, F., Alonso-Mori, R., Yabashi, M., Inoue, I., Osaka, T., Yamada, J., Inubushi, Y., Hara, T., Kern, J., Yano, J., Yachandra, V. K., Rohringer, N., Yoneda, H., Kroll, T., Pellegrini, C., Bergmann, U. 2023; 10 (12): 1602-1604

  View details for DOI 10.1364/OPTICA.510641

  View details for Web of Science ID 001166326400003

• In Situ Structural Observation of a Substrate- and Peroxide-Bound High-Spin Ferric-Hydroperoxo Intermediate in the P450 Enzyme CYP121 JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Nguyen, R. C., Davis, I., Dasgupta, M., Wang, Y., Simon, P. S., Butryn, A., Makita, H., Bogacz, I., Dornevil, K., Aller, P., Bhowmick, A., Chatterjee, R., Kim, I., Zhou, T., Mendez, D., Paley, D. W., Fuller, F., Mori, R., Batyuk, A., Sauter, N. K., Brewster, A. S., Orville, A. M., Yachandra, V. K., Yano, J., Kern, J. F., Liu, A. 2023; 145 (46): 25120-25133

  Abstract

  The P450 enzyme CYP121 from Mycobacterium tuberculosis catalyzes a carbon-carbon (C-C) bond coupling cyclization of the dityrosine substrate containing a diketopiperazine ring, cyclo(l-tyrosine-l-tyrosine) (cYY). An unusual high-spin (S = 5/2) ferric intermediate maximizes its population in less than 5 ms in the rapid freeze-quenching study of CYP121 during the shunt reaction with peracetic acid or hydrogen peroxide in acetic acid solution. We show that this intermediate can also be observed in the crystalline state by EPR spectroscopy. By developing an on-demand-rapid-mixing method for time-resolved serial femtosecond crystallography with X-ray free-electron laser (tr-SFX-XFEL) technology covering the millisecond time domain and without freezing, we structurally monitored the reaction in situ at room temperature. After a 200 ms peracetic acid reaction with the cocrystallized enzyme-substrate microcrystal slurry, a ferric-hydroperoxo intermediate is observed, and its structure is determined at 1.85 Å resolution. The structure shows a hydroperoxyl ligand between the heme and the native substrate, cYY. The oxygen atoms of the hydroperoxo are 2.5 and 3.2 Å from the iron ion. The end-on binding ligand adopts a near-side-on geometry and is weakly associated with the iron ion, causing the unusual high-spin state. This compound 0 intermediate, spectroscopically and structurally observed during the catalytic shunt pathway, reveals a unique binding mode that deviates from the end-on compound 0 intermediates in other heme enzymes. The hydroperoxyl ligand is only 2.9 Å from the bound cYY, suggesting an active oxidant role of the intermediate for direct substrate oxidation in the nonhydroxylation C-C bond coupling chemistry.

  View details for DOI 10.1021/jacs.3c04991

  View details for Web of Science ID 001108496800001

  View details for PubMedID 37939223

• Ultrafast x-ray detection of low-spin iron in molten silicate under deep planetary interior conditions. Science advances Shim, S. H., Ko, B., Sokaras, D., Nagler, B., Lee, H. J., Galtier, E., Glenzer, S., Granados, E., Vinci, T., Fiquet, G., Dolinschi, J., Tappan, J., Kulka, B., Mao, W. L., Morard, G., Ravasio, A., Gleason, A., Alonso-Mori, R. 2023; 9 (42): eadi6153

  Abstract

  The spin state of Fe can alter the key physical properties of silicate melts, affecting the early differentiation and the dynamic stability of the melts in the deep rocky planets. The low-spin state of Fe can increase the affinity of Fe for the melt over the solid phases and the electrical conductivity of melt at high pressures. However, the spin state of Fe has never been measured in dense silicate melts due to experimental challenges. We report detection of dominantly low-spin Fe in dynamically compressed olivine melt at 150 to 256 gigapascals and 3000 to 6000 kelvin using laser-driven shock wave compression combined with femtosecond x-ray diffraction and x-ray emission spectroscopy using an x-ray free electron laser. The observation of dominantly low-spin Fe supports gravitationally stable melt in the deep mantle and generation of a dynamo from the silicate melt portion of rocky planets.

  View details for DOI 10.1126/sciadv.adi6153

  View details for PubMedID 37862409

• Solution phase high repetition rate laser pump x-ray probe picosecond hard x-ray spectroscopy at the Stanford Synchrotron Radiation Lightsource STRUCTURAL DYNAMICS-US Reinhard, M., Skoien, D., Spies, J. A., Garcia-Esparza, A. T., Matson, B. D., Corbett, J., Tian, K., Safranek, J., Granados, E., Strader, M., Gaffney, K. J., Alonso-Mori, R., Kroll, T., Sokaras, D. 2023; 10 (5): 054304

  Abstract

  We present a dedicated end-station for solution phase high repetition rate (MHz) picosecond hard x-ray spectroscopy at beamline 15-2 of the Stanford Synchrotron Radiation Lightsource. A high-power ultrafast ytterbium-doped fiber laser is used to photoexcite the samples at a repetition rate of 640 kHz, while the data acquisition operates at the 1.28 MHz repetition rate of the storage ring recording data in an alternating on-off mode. The time-resolved x-ray measurements are enabled via gating the x-ray detectors with the 20 mA/70 ps camshaft bunch of SPEAR3, a mode available during the routine operations of the Stanford Synchrotron Radiation Lightsource. As a benchmark study, aiming to demonstrate the advantageous capabilities of this end-station, we have conducted picosecond Fe K-edge x-ray absorption spectroscopy on aqueous [FeII(phen)3]2+, a prototypical spin crossover complex that undergoes light-induced excited spin state trapping forming an electronic excited state with a 0.6-0.7 ns lifetime. In addition, we report transient Fe Kβ main line and valence-to-core x-ray emission spectra, showing a unique detection sensitivity and an excellent agreement with model spectra and density functional theory calculations, respectively. Notably, the achieved signal-to-noise ratio, the overall performance, and the routine availability of the developed end-station have enabled a systematic time-resolved science program using the monochromatic beam at the Stanford Synchrotron Radiation Lightsource.

  View details for DOI 10.1063/4.0000207

  View details for Web of Science ID 001094050700002

  View details for PubMedID 37901682

  View details for PubMedCentralID PMC10613086

• Unraveling Metal-Ligand Bonding in an HNO-Evolving {FeNO}6 Complex with a Combined X-ray Spectroscopic Approach. Journal of the American Chemical Society Gee, L. B., Lim, J., Kroll, T., Sokaras, D., Alonso-Mori, R., Lee, C. 2023

  Abstract

  Photolytic delivery of nitric oxide and nitroxide has substantial biomedical and phototherapeutic applications. Here, we utilized hard X-ray spectroscopic methods to identify key geometric and electronic structural features of two photolabile {FeNO}6 complexes where the compounds differ in the presence of a pendant thiol in [Fe(NO)(TMSPS2)(TMSPS2H)] and thioether in [Fe(NO)(TMSPS2)(TMSPS2CH3)] with the former complex being the only transition metal system to photolytically generate HNO. Fe Kbeta XES identifies the photoreactant systems as essentially Fe(II)-NO+, while valence-to-core XES extracts a NO oxidation state of +0.5. Finally, the pre-edge of the Fe high-energy-resolution fluorescence detected (HERFD) XAS spectra is shown to be acutely sensitive to perturbation of the Fe-NO covalency enhanced by the 3d-4p orbital mixing dipole intensity contribution. Collectively, this X-ray spectroscopic approach enables future time-resolved insights in these systems and extensions to other challenging redox noninnocent {FeNO}x systems.

  View details for DOI 10.1021/jacs.3c04479

  View details for PubMedID 37610249

• Watching Excited State Dynamics with Optical and X-ray Probes: The Excited State Dynamics of Aquocobalamin and Hydroxocobalamin JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Sension, R. J., McClain, T. P., Lamb, R. M., Alonso-Mori, R., Lima, F., Ardana-Lamas, F., Biednov, M., Chollet, M., Chung, T., Deb, A., Dewan Jr, P. A., Gee, L. B., En, J., Jiang, Y., Khakhulin, D., Li, J., Michocki, L. B., Miller, N. A., Otte, F., Uemura, Y., van Driel, T. B., Penner-Hahn, J. E. 2023; 145 (25): 14070-14086

  Abstract

  Femtosecond time-resolved X-ray absorption (XANES) at the Co K-edge, X-ray emission (XES) in the Co Kβ and valence-to-core regions, and broadband UV-vis transient absorption are combined to probe the femtosecond to picosecond sequential atomic and electronic dynamics following photoexcitation of two vitamin B12 compounds, hydroxocobalamin and aquocobalamin. Polarized XANES difference spectra allow identification of sequential structural evolution involving first the equatorial and then the axial ligands, with the latter showing rapid coherent bond elongation to the outer turning point of the excited state potential followed by recoil to a relaxed excited state structure. Time-resolved XES, especially in the valence-to-core region, along with polarized optical transient absorption suggests that the recoil results in the formation of a metal-centered excited state with a lifetime of 2-5 ps. This combination of methods provides a uniquely powerful tool to probe the electronic and structural dynamics of photoactive transition-metal complexes and will be applicable to a wide variety of systems.

  View details for DOI 10.1021/jacs.3c04099

  View details for Web of Science ID 001013964500001

  View details for PubMedID 37327324

• Uncovering the 3d and 4d Electronic Interactions in Solvated Ru Complexes with 2p3d Resonant Inelastic X-ray Scattering. Inorganic chemistry Poulter, B. I., Biasin, E., Nowak, S. H., Kroll, T., Alonso-Mori, R., Schoenlein, R. W., Govind, N., Sokaras, D., Khalil, M. 2023

  Abstract

  The electronic structure and dynamics of ruthenium complexes are widely studied given their use in catalytic and light-harvesting materials. Here we investigate three model Ru complexes, [RuIII(NH3)6]3+, [RuII(bpy)3]2+, and [RuII(CN)6]4-, with L3-edge 2p3d resonant inelastic X-ray scattering (RIXS) to probe unoccupied 4d valence orbitals and occupied 3d orbitals and to gain insight into the interactions between these levels. The 2p3d RIXS maps contain a higher level of spectral information than the L3 X-ray absorption near edge structure (XANES). This study provides a direct measure of the 3d spin-orbit splittings of 4.3, 4.0, and 4.1 eV between the 3d5/2 and 3d3/2 orbitals of the [RuIII(NH3)6]3+, [RuII(bpy)3]2+, and [RuII(CN)6]4- complexes, respectively.

  View details for DOI 10.1021/acs.inorgchem.3c00919

  View details for PubMedID 37314410

• Revealing core-valence interactions in solution with femtosecond X-ray pump X-ray probe spectroscopy. Nature communications Weakly, R. B., Liekhus-Schmaltz, C. E., Poulter, B. I., Biasin, E., Alonso-Mori, R., Aquila, A., Boutet, S., Fuller, F. D., Ho, P. J., Kroll, T., Loe, C. M., Lutman, A., Zhu, D., Bergmann, U., Schoenlein, R. W., Govind, N., Khalil, M. 2023; 14 (1): 3384

  Abstract

  Femtosecond pump-probe spectroscopy using ultrafast optical and infrared pulses has become an essential tool to discover and understand complex electronic and structural dynamics in solvated molecular, biological, and material systems. Here we report the experimental realization of anultrafast two-color X-ray pump X-ray probe transient absorption experiment performed in solution. A 10fs X-ray pump pulse creates a localized excitation by removing a 1s electron from an Fe atom in solvated ferro- and ferricyanide complexes. Following the ensuing Auger-Meitner cascade, the second X-ray pulse probes the Fe 1s3p transitions in resultant novel core-excited electronic states. Careful comparison of the experimental spectra with theory, extracts +2eV shifts in transition energies per valence hole, providing insight into correlated interactions of valence 3d with 3p and deeper-lying electrons. Such information is essential for accurate modeling and predictive synthesis of transition metal complexes relevant for applications ranging from catalysis to information storage technology. This study demonstrates the experimental realization of the scientific opportunities possible with the continued development of multicolor multi-pulse X-ray spectroscopy to study electronic correlations in complex condensed phase systems.

  View details for DOI 10.1038/s41467-023-39165-2

  View details for PubMedID 37291130

• Ferricyanide photo-aquation pathway revealed by combined femtosecond Kβ main line and valence-to-core x-ray emission spectroscopy. Nature communications Reinhard, M., Gallo, A., Guo, M., Garcia-Esparza, A. T., Biasin, E., Qureshi, M., Britz, A., Ledbetter, K., Kunnus, K., Weninger, C., van Driel, T., Robinson, J., Glownia, J. M., Gaffney, K. J., Kroll, T., Weng, T. C., Alonso-Mori, R., Sokaras, D. 2023; 14 (1): 2443

  Abstract

  Reliably identifying short-lived chemical reaction intermediates is crucial to elucidate reaction mechanisms but becomes particularly challenging when multiple transient species occur simultaneously. Here, we report a femtosecond x-ray emission spectroscopy and scattering study of the aqueous ferricyanide photochemistry, utilizing the combined Fe Kβ main and valence-to-core emission lines. Following UV-excitation, we observe a ligand-to-metal charge transfer excited state that decays within 0.5 ps. On this timescale, we also detect a hitherto unobserved short-lived species that we assign to a ferric penta-coordinate intermediate of the photo-aquation reaction. We provide evidence that bond photolysis occurs from reactive metal-centered excited states that are populated through relaxation of the charge transfer excited state. Beyond illuminating the elusive ferricyanide photochemistry, these results show how current limitations of Kβ main line analysis in assigning ultrafast reaction intermediates can be circumvented by simultaneously using the valence-to-core spectral range.

  View details for DOI 10.1038/s41467-023-37922-x

  View details for PubMedID 37147295

  View details for PubMedCentralID 16604

• Structural evidence for intermediates during O-2 formation in photosystem II NATURE Bhowmick, A., Hussein, R., Bogacz, I., Simon, P. S., Ibrahim, M., Chatterjee, R., Doyle, M. D., Cheah, M., Fransson, T., Chernev, P., Kim, I., Makita, H., Dasgupta, M., Kaminsky, C. J., Zhang, M., Gaetcke, J., Haupt, S., Nangca, I. I., Keable, S. M., Aydin, A., Tono, K., Owada, S., Gee, L. B., Fuller, F. D., Batyuk, A., Alonso-Mori, R., Holton, J. M., Paley, D. W., Moriarty, N. W., Mamedov, F., Adams, P. D., Brewster, A. S., Dobbek, H., Sauter, N. K., Bergmann, U., Zouni, A., Messinger, J., Kern, J., Yano, J., Yachandra, V. K. 2023: 629-636

  Abstract

  In natural photosynthesis, the light-driven splitting of water into electrons, protons and molecular oxygen forms the first step of the solar-to-chemical energy conversion process. The reaction takes place in photosystem II, where the Mn4CaO5 cluster first stores four oxidizing equivalents, the S0 to S4 intermediate states in the Kok cycle, sequentially generated by photochemical charge separations in the reaction center and then catalyzes the O-O bond formation chemistry1-3. Here, we report room temperature snapshots by serial femtosecond X-ray crystallography to provide structural insights into the final reaction step of Kok's photosynthetic water oxidation cycle, the S3→[S4]→S0 transition where O2 is formed and Kok's water oxidation clock is reset. Our data reveal a complex sequence of events, which occur over micro- to milliseconds, comprising changes at the Mn4CaO5 cluster, its ligands and water pathways as well as controlled proton release through the hydrogen-bonding network of the Cl1 channel. Importantly, the extra O atom Ox, which was introduced as a bridging ligand between Ca and Mn1 during the S2→S3 transition4-6, disappears or relocates in parallel with Yz reduction starting at approximately 700 μs after the third flash. The onset of O2 evolution, as indicated by the shortening of the Mn1-Mn4 distance, occurs at around 1,200 μs, signifying the presence of a reduced intermediate, possibly a bound peroxide.

  View details for DOI 10.1038/s41586-023-06038-z

  View details for Web of Science ID 000991687000024

  View details for PubMedID 37138085

  View details for PubMedCentralID PMC10191843

• Seeded stimulated X-ray emission at 5.9 keV OPTICA Doyle, M. D., Halavanau, A., Zhang, Y., Michine, Y., Everts, J., Fuller, F., Alonso-Mori, R., Yabashi, M., Inoue, I., Osaka, T., Yamada, J., Inubushi, Y., Hara, T., Kern, J., Yano, J., Yachandra, V. K., Rohringer, N., Yoneda, H., Kroll, T., Pellegrini, C., Bergmann, U. 2023; 10 (4): 513-519

  View details for DOI 10.1364/OPTICA.485989

  View details for Web of Science ID 001029173400003

• Room temperature X-ray absorption spectroscopy of metalloenzymes with drop-on-demand sample delivery at XFELs PURE AND APPLIED CHEMISTRY Bogacz, I., Makita, H., Simon, P. S., Zhang, M., Doyle, M. D., Chatterjee, R., Fransson, T., Weninger, C., Fuller, F., Gee, L., Sato, T., Seaberg, M., Alonso-Mori, R., Bergmann, U., Yachandra, V. K., Kern, J., Yano, J. 2023

  View details for DOI 10.1515/pac-2023-0213

  View details for Web of Science ID 000973579500001

• 5f Covalency from X-Ray Resonant Raman Spectroscopy. Journal of physics. Condensed matter : an Institute of Physics journal Tobin, J. G., Nowak, S., Yu, S. W., Alonso Mori, R., Kroll, T., Nordlund, D., Weng, T., Sokaras, D. 2022

  Abstract

  X-Ray Resonant Raman Scattering (XRRS), a variant of Resonant X-ray Inelastic Scattering (RXIS), has been used to investigate the two prototype systems, UF4 and UO2. Both are U5f2 and each is an example of 5f localized, ionic behavior and 5f localized, covalent behavior, respectively. From the M5 XRRR measurements, the 5f band gap in each can be directly determined and, moreover, a clear and powerful sensitivity to 5f covalency emerges.

  View details for DOI 10.1088/1361-648X/ac9bbd

  View details for PubMedID 36261038

• Local Structure of Sulfur Vacancies on the Basal Plane of Monolayer MoS2. ACS nano Garcia-Esparza, A. T., Park, S., Abroshan, H., Paredes Mellone, O. A., Vinson, J., Abraham, B., Kim, T. R., Nordlund, D., Gallo, A., Alonso-Mori, R., Zheng, X., Sokaras, D. 2022

  Abstract

  The nature of the S-vacancy is central to controlling the electronic properties of monolayer MoS2. Understanding the geometric and electronic structures of the S-vacancy on the basal plane of monolayer MoS2 remains elusive. Here, operando S K-edge X-ray absorption spectroscopy shows the formation of clustered S-vacancies on the basal plane of monolayer MoS2 under reaction conditions (H2 atmosphere, 100-600 °C). First-principles calculations predict spectral fingerprints consistent with the experimental results. The Mo K-edge extended X-ray absorption fine structure shows the local structure as coordinatively unsaturated Mo with 4.1 ± 0.4 S atoms as nearest neighbors (above 400 °C in an H2 atmosphere). Conversely, the 6-fold Mo-Mo coordination in the crystal remains unchanged. Electrochemistry confirms similar active sites for hydrogen evolution. The identity of the S-vacancy defect on the basal plane of monolayer MoS2 is herein elucidated for applications in optoelectronics and catalysis.

  View details for DOI 10.1021/acsnano.2c01388

  View details for PubMedID 35380038

• Generation of intense phase-stable femtosecond hard X-ray pulse pairs. Proceedings of the National Academy of Sciences of the United States of America Zhang, Y., Kroll, T., Weninger, C., Michine, Y., Fuller, F. D., Zhu, D., Alonso-Mori, R., Sokaras, D., Lutman, A. A., Halavanau, A., Pellegrini, C., Benediktovitch, A., Yabashi, M., Inoue, I., Inubushi, Y., Osaka, T., Yamada, J., Babu, G., Salpekar, D., Sayed, F. N., Ajayan, P. M., Kern, J., Yano, J., Yachandra, V. K., Yoneda, H., Rohringer, N., Bergmann, U. 2022; 119 (12): e2119616119

  Abstract

  SignificanceThe generation of phase-stable femtosecond X-ray pulse pairs will advance nonlinear spectroscopies and imaging, providing direct insight into the coupled motions of electrons and nuclei with resolution on the electronic length scale and timescale. This paper presents the generation of such pulse pairs in the X-ray domain. The approach uses X-ray free-electron laser pulses to induce highly directional, intense, phase-stable pairs of superfluorescence and seeded stimulated emission at the 5.9 keV manganese Kalpha1 line. The finding is evidenced by strong interference fringes in the superfluorescence and stimulated emission signals.

  View details for DOI 10.1073/pnas.2119616119

  View details for PubMedID 35290124

• Ultrafast structural response of shock-compressed plagioclase METEORITICS & PLANETARY SCIENCE Gleason, A. E., Park, S., Rittman, D. R., Ravasio, A., Langenhorst, F., Bolis, R. M., Granados, E., Hok, S., Kroll, T., Sikorski, M., Weng, T., Lee, H., Nagler, B., Sisson, T., Xing, Z., Zhu, D., Giuli, G., Mao, W. L., Glenzer, S. H., Sokaras, D., Alonso-Mori, R. 2022

  View details for DOI 10.1111/maps.13785

  View details for Web of Science ID 000755921800001

• Femtosecond X-ray Spectroscopy Directly Quantifies Transient Excited-State Mixed Valency. The journal of physical chemistry letters Liekhus-Schmaltz, C., Fox, Z. W., Andersen, A., Kjaer, K. S., Alonso-Mori, R., Biasin, E., Carlstad, J., Chollet, M., Gaynor, J. D., Glownia, J. M., Hong, K., Kroll, T., Lee, J. H., Poulter, B. I., Reinhard, M., Sokaras, D., Zhang, Y., Doumy, G., March, A. M., Southworth, S. H., Mukamel, S., Cordones, A. A., Schoenlein, R. W., Govind, N., Khalil, M. 1800: 378-386

  Abstract

  Quantifying charge delocalization associated with short-lived photoexcited states of molecular complexes in solution remains experimentally challenging, requiring local element specific femtosecond experimental probes of time-evolving electron transfer. In this study, we quantify the evolving valence hole charge distribution in the photoexcited charge transfer state of a prototypical mixed valence bimetallic iron-ruthenium complex, [(CN)5FeIICNRuIII(NH3)5]-, in water by combining femtosecond X-ray spectroscopy measurements with time-dependent density functional theory calculations of the excited-state dynamics. We estimate the valence hole charge that accumulated at the Fe atom to be 0.6 ± 0.2, resulting from excited-state metal-to-metal charge transfer, on an 60 fs time scale. Our combined experimental and computational approach provides a spectroscopic ruler for quantifying excited-state valency in solvated complexes.

  View details for DOI 10.1021/acs.jpclett.1c03613

  View details for PubMedID 34985900

• Effects of x-ray free-electron laser pulse intensity on the Mn K beta(1,3) x-ray emission spectrum in photosystem II-A case study for metalloprotein crystals and solutions STRUCTURAL DYNAMICS-US Fransson, T., Alonso-Mori, R., Chatterjee, R., Cheah, M., Ibrahim, M., Hussein, R., Zhang, M., Fuller, F., Gul, S., Kim, I., Simon, P. S., Bogacz, I., Makita, H., de Lichtenberg, C., Song, S., Batyuk, A., Sokaras, D., Massad, R., Doyle, M., Britz, A., Weninger, C., Zouni, A., Messinger, J., Yachandra, V. K., Yano, J., Kern, J., Bergmann, U. 2021; 8 (6): 064302

  Abstract

  In the last ten years, x-ray free-electron lasers (XFELs) have been successfully employed to characterize metalloproteins at room temperature using various techniques including x-ray diffraction, scattering, and spectroscopy. The approach has been to outrun the radiation damage by using femtosecond (fs) x-ray pulses. An example of an important and damage sensitive active metal center is the Mn4CaO5 cluster in photosystem II (PS II), the catalytic site of photosynthetic water oxidation. The combination of serial femtosecond x-ray crystallography and Kβ x-ray emission spectroscopy (XES) has proven to be a powerful multimodal approach for simultaneously probing the overall protein structure and the electronic state of the Mn4CaO5 cluster throughout the catalytic (Kok) cycle. As the observed spectral changes in the Mn4CaO5 cluster are very subtle, it is critical to consider the potential effects of the intense XFEL pulses on the Kβ XES signal. We report here a systematic study of the effects of XFEL peak power, beam focus, and dose on the Mn Kβ1,3 XES spectra in PS II over a wide range of pulse parameters collected over seven different experimental runs using both microcrystal and solution PS II samples. Our findings show that for beam intensities ranging from ∼5 × 1015 to 5 × 1017 W/cm2 at a pulse length of ∼35 fs, the spectral effects are small compared to those observed between S-states in the Kok cycle. Our results provide a benchmark for other XFEL-based XES studies on metalloproteins, confirming the viability of this approach.

  View details for DOI 10.1063/4.0000130

  View details for Web of Science ID 000723107700001

  View details for PubMedID 34849380

  View details for PubMedCentralID PMC8610604

• X-ray free-electron laser studies reveal correlated motion during isopenicillin N synthase catalysis. Science advances Rabe, P., Kamps, J. J., Sutherlin, K. D., Linyard, J. D., Aller, P., Pham, C. C., Makita, H., Clifton, I., McDonough, M. A., Leissing, T. M., Shutin, D., Lang, P. A., Butryn, A., Brem, J., Gul, S., Fuller, F. D., Kim, I., Cheah, M. H., Fransson, T., Bhowmick, A., Young, I. D., O'Riordan, L., Brewster, A. S., Pettinati, I., Doyle, M., Joti, Y., Owada, S., Tono, K., Batyuk, A., Hunter, M. S., Alonso-Mori, R., Bergmann, U., Owen, R. L., Sauter, N. K., Claridge, T. D., Robinson, C. V., Yachandra, V. K., Yano, J., Kern, J. F., Orville, A. M., Schofield, C. J. 2021; 7 (34)

  Abstract

  Isopenicillin N synthase (IPNS) catalyzes the unique reaction of l-delta-(alpha-aminoadipoyl)-l-cysteinyl-d-valine (ACV) with dioxygen giving isopenicillin N (IPN), the precursor of all natural penicillins and cephalosporins. X-ray free-electron laser studies including time-resolved crystallography and emission spectroscopy reveal how reaction of IPNS:Fe(II):ACV with dioxygen to yield an Fe(III) superoxide causes differences in active site volume and unexpected conformational changes that propagate to structurally remote regions. Combined with solution studies, the results reveal the importance of protein dynamics in regulating intermediate conformations during conversion of ACV to IPN. The results have implications for catalysis by multiple IPNS-related oxygenases, including those involved in the human hypoxic response, and highlight the power of serial femtosecond crystallography to provide insight into long-range enzyme dynamics during reactions presently impossible for nonprotein catalysts.

  View details for DOI 10.1126/sciadv.abh0250

  View details for PubMedID 34417180

• Resonant X-ray Emission spectroscopy from broadband stochastic pulses at an X-ray free electron laser Communications Chemistry Fuller, F. D., Loukianov, A., Takanashi, T., You, D., Li, Y., Ueda, K., Fransson, T., Yabashi, M., Katayama, T., Weng, T., Alonso-Mori, R., Bergmann, U., Kern, J., Yachandra, V. K., Wernet, P., Yano, J., et al 2021; 4 (84): 84

  Abstract

  Hard X-ray spectroscopy is an element specific probe of electronic state, but signals are weak and require intense light to study low concentration samples. Free electron laser facilities offer the highest intensity X-rays of any available light source. The light produced at such facilities is stochastic, with spikey, broadband spectra that change drastically from shot to shot. Here, using aqueous ferrocyanide, we show that the resonant X-ray emission (RXES) spectrum can be inferred by correlating for each shot the fluorescence intensity from the sample with spectra of the fluctuating, self-amplified spontaneous emission (SASE) source. We obtain resolved narrow and chemically rich information in core-to-valence transitions of the pre-edge region at the Fe K-edge. Our approach avoids monochromatization, provides higher photon flux to the sample, and allows non-resonant signals like elastic scattering to be simultaneously recorded. The spectra obtained match well with spectra measured using a monochromator. We also show that inaccurate measurements of the stochastic light spectra reduce the measurement efficiency of our approach.

  View details for DOI 10.1038/s42004-021-00512-3

• Laser-induced transient magnons in Sr3Ir2O7 throughout the Brillouin zone PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Mazzone, D. G., Meyers, D., Cao, Y., Vale, J. G., Dashwood, C. D., Shi, Y., James, A. A., Robinson, N. J., Lin, J., Thampy, V., Tanaka, Y., Johnson, A. S., Miao, H., Wang, R., Assefa, T. A., Kim, J., Casa, D., Mankowsky, R., Zhu, D., Alonso-Mori, R., Song, S., Yavas, H., Katayama, T., Yabashi, M., Kubota, Y., Owada, S., Liu, J., Yang, J., Konik, R. M., Robinson, I. K., Hill, J. P., McMorrow, D. F., Forst, M., Wall, S., Liu, X., Dean, M. M. 2021; 118 (22)

  View details for DOI 10.1073/pnas.2103696118|1of6

  View details for Web of Science ID 000659461200013

• Operando Study of Thermal Oxidation of Monolayer MoS2. Advanced science (Weinheim, Baden-Wurttemberg, Germany) Park, S., Garcia-Esparza, A. T., Abroshan, H., Abraham, B., Vinson, J., Gallo, A., Nordlund, D., Park, J., Kim, T. R., Vallez, L., Alonso-Mori, R., Sokaras, D., Zheng, X. 2021; 8 (9): 2002768

  Abstract

  Monolayer MoS2 is a promising semiconductor to overcome the physical dimension limits of microelectronic devices. Understanding the thermochemical stability of MoS2 is essential since these devices generate heat and are susceptible to oxidative environments. Herein, the promoting effect of molybdenum oxides (MoO x ) particles on the thermal oxidation of MoS2 monolayers is shown by employing operando X-ray absorption spectroscopy, ex situ scanning electron microscopy and X-ray photoelectron spectroscopy. The study demonstrates that chemical vapor deposition-grown MoS2 monolayers contain intrinsic MoO x and are quickly oxidized at 100 °C (3 vol% O2/He), in contrast to previously reported oxidation thresholds (e.g., 250 °C, t ≤ 1 h in the air). Otherwise, removing MoO x increases the thermal oxidation onset temperature of monolayer MoS2 to 300 °C. These results indicate that MoO x promote oxidation. An oxide-free lattice is critical to the long-term stability of monolayer MoS2 in state-of-the-art 2D electronic, optical, and catalytic applications.

  View details for DOI 10.1002/advs.202002768

  View details for PubMedID 33977043

  View details for PubMedCentralID PMC8097340

• Revealing the bonding of solvated Ru complexes with valence-to-core resonant inelastic X-ray scattering CHEMICAL SCIENCE Biasin, E., Nascimento, D. R., Poulter, B. I., Abraham, B., Kunnus, K., Garcia-Esparza, A. T., Nowak, S. H., Kroll, T., Schoenlein, R. W., Alonso-Mori, R., Khalil, M., Govind, N., Sokaras, D. 2021; 12 (10): 3713–25

  View details for DOI 10.1039/d0sc06227h

  View details for Web of Science ID 000630166700031

• Operando Study of Thermal Oxidation of Monolayer MoS2 ADVANCED SCIENCE Park, S., Garcia-Esparza, A. T., Abroshan, H., Abraham, B., Vinson, J., Gallo, A., Nordlund, D., Park, J., Kim, T., Vallez, L., Alonso-Mori, R., Sokaras, D., Zheng, X. 2021

  View details for DOI 10.1002/advs.202002768

  View details for Web of Science ID 000623202400001

• Sulfur K beta X-ray emission spectroscopy: comparison with sulfur K-edge X-ray absorption spectroscopy for speciation of organosulfur compounds PHYSICAL CHEMISTRY CHEMICAL PHYSICS Qureshi, M., Nowak, S. H., Vogt, L. I., Cotelesage, J. H., Dolgova, N. V., Sharifi, S., Kroll, T., Nordlund, D., Alonso-Mori, R., Weng, T., Pickering, I. J., George, G. N., Sokaras, D. 2021; 23 (8): 4500-4508

  Abstract

  Until recently, sulfur was known as a "spectroscopically silent" element because of a paucity of convenient spectroscopic probes suitable for in situ chemical speciation. In recent years the technique of sulfur K-edge X-ray absorption spectroscopy (XAS) has been used extensively in sulfur speciation in a variety of different fields. With an initial focus on reduced forms of organic sulfur, we have explored a complementary X-ray based spectroscopy - sulfur Kβ X-ray emission spectroscopy (XES) - as a potential analytical tool for sulfur speciation in complex samples. We compare and contrast the sensitivity of sulfur Kβ XES with that of sulfur K-edge XAS, and find differing sensitivities for the two techniques. In some cases an approach involving both sulfur K-edge XAS and sulfur Kβ XES may be a powerful combination for deducing sulfur speciation in samples containing complex mixtures.

  View details for DOI 10.1039/d0cp05323f

  View details for Web of Science ID 000625306100057

  View details for PubMedID 33355326

• Author Correction: Direct observation of coherent femtosecond solvent reorganization coupled to intramolecular electron transfer. Nature chemistry Biasin, E., Fox, Z. W., Andersen, A., Ledbetter, K., Kjar, K. S., Alonso-Mori, R., Carlstad, J. M., Chollet, M., Gaynor, J. D., Glownia, J. M., Hong, K., Kroll, T., Lee, J. H., Liekhus-Schmaltz, C., Reinhard, M., Sokaras, D., Zhang, Y., Doumy, G., March, A. M., Southworth, S. H., Mukamel, S., Gaffney, K. J., Schoenlein, R. W., Govind, N., Cordones, A. A., Khalil, M. 2021

  View details for DOI 10.1038/s41557-021-00663-9

  View details for PubMedID 33627886

• Direct observation of coherent femtosecond solvent reorganization coupled to intramolecular electron transfer. Nature chemistry Biasin, E., Fox, Z. W., Andersen, A., Ledbetter, K., Kjar, K. S., Alonso-Mori, R., Carlstad, J. M., Chollet, M., Gaynor, J. D., Glownia, J. M., Hong, K., Kroll, T., Lee, J. H., Liekhus-Schmaltz, C., Reinhard, M., Sokaras, D., Zhang, Y., Doumy, G., March, A. M., Southworth, S. H., Mukamel, S., Gaffney, K. J., Schoenlein, R. W., Govind, N., Cordones, A. A., Khalil, M. 2021

  Abstract

  It is well known that the solvent plays a critical role in ultrafast electron-transfer reactions. However, solvent reorganization occurs on multiple length scales, and selectively measuring short-range solute-solvent interactions at the atomic level with femtosecond time resolution remains a challenge. Here we report femtosecond X-ray scattering and emission measurements following photoinduced charge-transfer excitation in a mixed-valence bimetallic (FeiiRuiii) complex in water, and their interpretation using non-equilibrium molecular dynamics simulations. Combined experimental and computational analysis reveals that the charge-transfer excited state has a lifetime of 62fs and that coherent translational motions of the first solvation shell are coupled to the back electron transfer. Our molecular dynamics simulations identify that the observed coherent translational motions arise from hydrogen bonding changes between the solute and nearby water molecules upon photoexcitation, and have an amplitude of tenths of angstroms, 120-200cm-1 frequency and ~100fs relaxation time. This study provides an atomistic view of coherent solvent reorganization mediating ultrafast intramolecular electron transfer.

  View details for DOI 10.1038/s41557-020-00629-3

  View details for PubMedID 33589787

• Visualization of dynamic polaronic strain fields in hybrid lead halide perovskites. Nature materials Guzelturk, B., Winkler, T., Van de Goor, T. W., Smith, M. D., Bourelle, S. A., Feldmann, S., Trigo, M., Teitelbaum, S. W., Steinruck, H., de la Pena, G. A., Alonso-Mori, R., Zhu, D., Sato, T., Karunadasa, H. I., Toney, M. F., Deschler, F., Lindenberg, A. M. 2021

  Abstract

  Excitation localization involving dynamic nanoscale distortions is a central aspect of photocatalysis1, quantum materials2 and molecular optoelectronics3. Experimental characterization of such distortions requires techniques sensitive to the formation of point-defect-like local structural rearrangements in real time. Here, we visualize excitation-induced strain fields in a prototypical member of the lead halide perovskites4 via femtosecond resolution diffuse X-ray scattering measurements. This enables momentum-resolved phonon spectroscopy of the locally distorted structure and reveals radially expanding nanometre-scale strain fields associated with the formation and relaxation of polarons in photoexcited perovskites. Quantitative estimates of the magnitude and shape of this polaronic distortion are obtained, providing direct insights into the dynamic structural distortions that occur in these materials5-9. Optical pump-probe reflection spectroscopy corroborates these results and shows how these large polaronic distortions transiently modify the carrier effective mass, providing a unified picture of the coupled structural and electronic dynamics that underlie the optoelectronic functionality of the hybrid perovskites.

  View details for DOI 10.1038/s41563-020-00865-5

  View details for PubMedID 33398119

• Short-lived metal-centered excited state initiates iron-methionine photodissociation in ferrous cytochrome c. Nature communications Reinhard, M. E., Mara, M. W., Kroll, T., Lim, H., Hadt, R. G., Alonso-Mori, R., Chollet, M., Glownia, J. M., Nelson, S., Sokaras, D., Kunnus, K., Driel, T. B., Hartsock, R. W., Kjaer, K. S., Weninger, C., Biasin, E., Gee, L. B., Hodgson, K. O., Hedman, B., Bergmann, U., Solomon, E. I., Gaffney, K. J. 2021; 12 (1): 1086

  Abstract

  The dynamics of photodissociation and recombination in heme proteins represent an archetypical photochemical reaction widely used to understand the interplay between chemical dynamics and reaction environment. We report a study of the photodissociation mechanism for the Fe(II)-S bond between the heme iron and methionine sulfur of ferrous cytochrome c. This bond dissociation is an essential step in the conversion of cytochrome c from an electron transfer protein to a peroxidase enzyme. We use ultrafast X-ray solution scattering to follow the dynamics of Fe(II)-S bond dissociation and 1s3p (Kbeta) X-ray emission spectroscopy to follow the dynamics of the iron charge and spin multiplicity during bond dissociation. From these measurements, we conclude that the formation of a triplet metal-centered excited state with anti-bonding Fe(II)-S interactions triggers the bond dissociation and precedes the formation of the metastable Fe high-spin quintet state.

  View details for DOI 10.1038/s41467-021-21423-w

  View details for PubMedID 33597529

• Charge transfer driven by ultrafast spin transition in a CoFe Prussian blue analogue NATURE CHEMISTRY Cammarata, M., Zerdane, S., Balducci, L., Azzolina, G., Mazerat, S., Exertier, C., Trabuco, M., Levantino, M., Alonso-Mori, R., Glownia, J. M., Song, S., Catala, L., Mallah, T., Matar, S. F., Collet, E. 2021; 13 (1): 10-+

  Abstract

  Photoinduced charge-transfer is an important process in nature and technology and is responsible for the emergence of exotic functionalities, such as magnetic order for cyanide-bridged bimetallic coordination networks. Despite its broad interest and intensive developments in chemistry and material sciences, the atomic-scale description of the initial photoinduced process, which couples intermetallic charge-transfer and spin transition, has been debated for decades; it has been beyond reach due to its extreme speed. Here we study this process in a prototype cyanide-bridged CoFe system by femtosecond X-ray and optical absorption spectroscopies, enabling the disentanglement of ultrafast electronic and structural dynamics. Our results demonstrate that it is the spin transition that occurs first on the Co site within ~50 fs, and it is this that drives the subsequent Fe-to-Co charge-transfer within ~200 fs. This study represents a step towards understanding and controlling charge-transfer-based functions using light.

  View details for DOI 10.1038/s41557-020-00597-8

  View details for Web of Science ID 000599012700005

  View details for PubMedID 33288895

• The Photoactive Excited State of the B12-Based Photoreceptor CarH. The journal of physical chemistry. B Miller, N. A., Kaneshiro, A. K., Konar, A., Alonso-Mori, R., Britz, A., Deb, A., Glownia, J. M., Koralek, J. D., Mallik, L., Meadows, J. H., Michocki, L. B., van Driel, T. B., Koutmos, M., Padmanabhan, S., Elias-Arnanz, M., Kubarych, K. J., Marsh, E. N., Penner-Hahn, J. E., Sension, R. J. 2020

  Abstract

  We have used transient absorption spectroscopy in the UV-visible and X-ray regions to characterize the excited state of CarH, a protein photoreceptor that uses a form of B12, adenosylcobalamin (AdoCbl), to sense light. With visible excitation, a nanosecond-lifetime photoactive excited state is formed with unit quantum yield. The time-resolved X-ray absorption near edge structure difference spectrum of this state demonstrates that the excited state of AdoCbl in CarH undergoes only modest structural expansion around the central cobalt, a behavior similar to that observed for methylcobalamin rather than for AdoCbl free in solution. We propose a new mechanism for CarH photoreactivity involving formation of a triplet excited state. This allows the sensor to operate with high quantum efficiency and without formation of potentially dangerous side products. By stabilizing the excited electronic state, CarH controls reactivity of AdoCbl and enables slow reactions that yield nonreactive products and bypass bond homolysis and reactive radical species formation.

  View details for DOI 10.1021/acs.jpcb.0c09428

  View details for PubMedID 33174757

• High-Resolution XFEL Structure of the Soluble Methane Monooxygenase Hydroxylase Complex with its Regulatory Component at Ambient Temperature in Two Oxidation States JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Srinivas, V., Banerjee, R., Lebrette, H., Jones, J. C., Aurelius, O., Kim, I., Pham, C. C., Gul, S., Sutherlin, K. D., Bhowmick, A., John, J., Bozkurt, E., Fransson, T., Aller, P., Butryn, A., Bogacz, I., Simon, P., Keable, S., Britz, A., Tono, K., Kim, K., Park, S., Lee, S., Park, J., Alonso-Mori, R., Fuller, F. D., Batyuk, A., Brewster, A. S., Bergmann, U., Sauter, N. K., Orville, A. M., Yachandra, V. K., Yano, J., Lipscomb, J. D., Kern, J., Hogbom, M. 2020; 142 (33): 14249–66

  Abstract

  Soluble methane monooxygenase (sMMO) is a multicomponent metalloenzyme that catalyzes the conversion of methane to methanol at ambient temperature using a nonheme, oxygen-bridged dinuclear iron cluster in the active site. Structural changes in the hydroxylase component (sMMOH) containing the diiron cluster caused by complex formation with a regulatory component (MMOB) and by iron reduction are important for the regulation of O2 activation and substrate hydroxylation. Structural studies of metalloenzymes using traditional synchrotron-based X-ray crystallography are often complicated by partial X-ray-induced photoreduction of the metal center, thereby obviating determination of the structure of the enzyme in pure oxidation states. Here, microcrystals of the sMMOH:MMOB complex from Methylosinus trichosporium OB3b were serially exposed to X-ray free electron laser (XFEL) pulses, where the ≤35 fs duration of exposure of an individual crystal yields diffraction data before photoreduction-induced structural changes can manifest. Merging diffraction patterns obtained from thousands of crystals generates radiation damage-free, 1.95 Å resolution crystal structures for the fully oxidized and fully reduced states of the sMMOH:MMOB complex for the first time. The results provide new insight into the manner by which the diiron cluster and the active site environment are reorganized by the regulatory protein component in order to enhance the steps of oxygen activation and methane oxidation. This study also emphasizes the value of XFEL and serial femtosecond crystallography (SFX) methods for investigating the structures of metalloenzymes with radiation sensitive metal active sites.

  View details for DOI 10.1021/jacs.0c05613

  View details for Web of Science ID 000563079000029

  View details for PubMedID 32683863

  View details for PubMedCentralID PMC7457426

• Observation of Seeded Mn K beta Stimulated X-Ray Emission Using Two-Color X-Ray Free-Electron Laser Pulses PHYSICAL REVIEW LETTERS Kroll, T., Weninger, C., Fuller, F. D., Guetg, M. W., Benediktovitch, A., Zhang, Y., Marinelli, A., Alonso-Mori, R., Aquila, A., Liang, M., Koglin, J. E., Koralek, J., Sokaras, D., Zhu, D., Kern, J., Yano, J., Yachandra, V. K., Rohringer, N., Lutman, A., Bergmann, U. 2020; 125 (3)

  View details for DOI 10.1103/PhysRevLett.125.037404

  View details for Web of Science ID 000549758200018

• Untangling the sequence of events during the S2 S3 transition in photosystem II and implications for the water oxidation mechanism. Proceedings of the National Academy of Sciences of the United States of America Ibrahim, M., Fransson, T., Chatterjee, R., Cheah, M. H., Hussein, R., Lassalle, L., Sutherlin, K. D., Young, I. D., Fuller, F. D., Gul, S., Kim, I., Simon, P. S., de Lichtenberg, C., Chernev, P., Bogacz, I., Pham, C. C., Orville, A. M., Saichek, N., Northen, T., Batyuk, A., Carbajo, S., Alonso-Mori, R., Tono, K., Owada, S., Bhowmick, A., Bolotovsky, R., Mendez, D., Moriarty, N. W., Holton, J. M., Dobbek, H., Brewster, A. S., Adams, P. D., Sauter, N. K., Bergmann, U., Zouni, A., Messinger, J., Kern, J., Yachandra, V. K., Yano, J. 2020

  Abstract

  In oxygenic photosynthesis, light-driven oxidation of water to molecular oxygen is carried out by the oxygen-evolving complex (OEC) in photosystem II (PS II). Recently, we reported the room-temperature structures of PS II in the four (semi)stable S-states, S1, S2, S3, and S0, showing that a water molecule is inserted during the S2 S3 transition, as a new bridging O(H)-ligand between Mn1 and Ca. To understand the sequence of events leading to the formation of this last stable intermediate state before O2 formation, we recorded diffraction and Mn X-ray emission spectroscopy (XES) data at several time points during the S2 S3 transition. At the electron acceptor site, changes due to the two-electron redox chemistry at the quinones, QA and QB, are observed. At the donor site, tyrosine YZ and His190 H-bonded to it move by 50 s after the second flash, and Glu189 moves away from Ca. This is followed by Mn1 and Mn4 moving apart, and the insertion of OX(H) at the open coordination site of Mn1. This water, possibly a ligand of Ca, could be supplied via a "water wheel"-like arrangement of five waters next to the OEC that is connected by a large channel to the bulk solvent. XES spectra show that Mn oxidation (tau of 350 s) during the S2 S3 transition mirrors the appearance of OX electron density. This indicates that the oxidation state change and the insertion of water as a bridging atom between Mn1 and Ca are highly correlated.

  View details for DOI 10.1073/pnas.2000529117

  View details for PubMedID 32434915

• Vibrational wavepacket dynamics in Fe carbene photosensitizer determined with femtosecond X-ray emission and scattering. Nature communications Kunnus, K., Vacher, M., Harlang, T. C., Kjar, K. S., Haldrup, K., Biasin, E., van Driel, T. B., Papai, M., Chabera, P., Liu, Y., Tatsuno, H., Timm, C., Kallman, E., Delcey, M., Hartsock, R. W., Reinhard, M. E., Koroidov, S., Laursen, M. G., Hansen, F. B., Vester, P., Christensen, M., Sandberg, L., Nemeth, Z., Szemes, D. S., Bajnoczi, E., Alonso-Mori, R., Glownia, J. M., Nelson, S., Sikorski, M., Sokaras, D., Lemke, H. T., Canton, S. E., Moller, K. B., Nielsen, M. M., Vanko, G., Warnmark, K., Sundstrom, V., Persson, P., Lundberg, M., Uhlig, J., Gaffney, K. J. 2020; 11 (1): 634

  Abstract

  The non-equilibrium dynamics of electrons and nuclei govern the function of photoactive materials. Disentangling these dynamics remains a critical goal for understanding photoactive materials. Here we investigate the photoinduced dynamics of the [Fe(bmip)2]2+ photosensitizer, where bmip=2,6-bis(3-methyl-imidazole-1-ylidine)-pyridine, with simultaneous femtosecond-resolution Fe Kalpha and Kbeta X-ray emission spectroscopy (XES) and X-ray solution scattering (XSS). This measurement shows temporal oscillations in the XES and XSS difference signals with the same 278fs period oscillation. These oscillations originate from an Fe-ligand stretching vibrational wavepacket on a triplet metal-centered (3MC) excited state surface. This 3MC state is populated with a 110fs time constant by 40% of the excited molecules while the rest relax to a 3MLCT excited state. The sensitivity of the Kalpha XES to molecular structure results from a 0.7% average Fe-ligand bond length shift between the 1s and 2p core-ionized states surfaces.

  View details for DOI 10.1038/s41467-020-14468-w

  View details for PubMedID 32005815

• Excited state charge distribution and bond expansion of ferrous complexes observed with femtosecond valence-to-core x-ray emission spectroscopy. The Journal of chemical physics Ledbetter, K. n., Reinhard, M. E., Kunnus, K. n., Gallo, A. n., Britz, A. n., Biasin, E. n., Glownia, J. M., Nelson, S. n., Van Driel, T. B., Weninger, C. n., Zederkof, D. B., Haldrup, K. n., Cordones, A. A., Gaffney, K. J., Sokaras, D. n., Alonso-Mori, R. n. 2020; 152 (7): 074203

  Abstract

  Valence-to-core x-ray emission spectroscopy (VtC XES) combines the sample flexibility and element specificity of hard x-rays with the chemical environment sensitivity of valence spectroscopy. We extend this technique to study geometric and electronic structural changes induced by photoexcitation in the femtosecond time domain via laser-pump, x-ray probe experiments using an x-ray free electron laser. The results of time-resolved VtC XES on a series of ferrous complexes [Fe(CN)2n(2, 2'-bipyridine)3-n]-2n+2, n = 1, 2, 3, are presented. Comparisons of spectra obtained from ground state density functional theory calculations reveal signatures of excited state bond length and oxidation state changes. An oxidation state change associated with a metal-to-ligand charge transfer state with a lifetime of less than 100 fs is observed, as well as bond length changes associated with metal-centered excited states with lifetimes of 13 ps and 250 ps.

  View details for DOI 10.1063/1.5139441

  View details for PubMedID 32087640

• Femtosecond electronic structure response to high intensity XFEL pulses probed by iron X-ray emission spectroscopy. Scientific reports Alonso-Mori, R. n., Sokaras, D. n., Cammarata, M. n., Ding, Y. n., Feng, Y. n., Fritz, D. n., Gaffney, K. J., Hastings, J. n., Kao, C. C., Lemke, H. T., Maxwell, T. n., Robert, A. n., Schropp, A. n., Seiboth, F. n., Sikorski, M. n., Song, S. n., Weng, T. C., Zhang, W. n., Glenzer, S. n., Bergmann, U. n., Zhu, D. n. 2020; 10 (1): 16837

  Abstract

  We report the time-resolved femtosecond evolution of the K-shell X-ray emission spectra of iron during high intensity illumination of X-rays in a micron-sized focused hard X-ray free electron laser (XFEL) beam. Detailed pulse length dependent measurements revealed that rapid spectral energy shift and broadening started within the first 10 fs of the X-ray illumination at intensity levels between 1017 and 1018 W cm-2. We attribute these spectral changes to the rapid evolution of high-density photoelectron mediated secondary collisional ionization processes upon the absorption of the incident XFEL radiation. These fast electronic processes, occurring at timescales well within the typical XFEL pulse durations (i.e., tens of fs), set the boundary conditions of the pulse intensity and sample parameters where the widely-accepted 'probe-before-destroy' measurement strategy can be adopted for electronic-structure related XFEL experiments.

  View details for DOI 10.1038/s41598-020-74003-1

  View details for PubMedID 33033373

• Excited state charge distribution and bond expansion of ferrous complexes observed with femtosecond valence-to-core x-ray emission spectroscopy Journal of Chemical Physics Ledbetter, K., Reinhard, M. E., Kunnus, K., Gallo, A., Britz, A., Biasin, E., Glownia, J. M., Nelson, S., Van Driel, T. B., Weninger, C., Zederkof, D. B., Haldrup, K., Cordones, A. A., Gaffney, K. J., Sokaras, D., Alonso-Mori, R. 2020; 152

  View details for DOI 10.1063/1.5139441

• In situ X-ray diffraction of silicate liquids and glasses under dynamic and static compression to megabar pressures. Proceedings of the National Academy of Sciences of the United States of America Morard, G. n., Hernandez, J. A., Guarguaglini, M. n., Bolis, R. n., Benuzzi-Mounaix, A. n., Vinci, T. n., Fiquet, G. n., Baron, M. A., Shim, S. H., Ko, B. n., Gleason, A. E., Mao, W. L., Alonso-Mori, R. n., Lee, H. J., Nagler, B. n., Galtier, E. n., Sokaras, D. n., Glenzer, S. H., Andrault, D. n., Garbarino, G. n., Mezouar, M. n., Schuster, A. K., Ravasio, A. n. 2020

  Abstract

  Properties of liquid silicates under high-pressure and high-temperature conditions are critical for modeling the dynamics and solidification mechanisms of the magma ocean in the early Earth, as well as for constraining entrainment of melts in the mantle and in the present-day core-mantle boundary. Here we present in situ structural measurements by X-ray diffraction of selected amorphous silicates compressed statically in diamond anvil cells (up to 157 GPa at room temperature) or dynamically by laser-generated shock compression (up to 130 GPa and 6,000 K along the MgSiO3 glass Hugoniot). The X-ray diffraction patterns of silicate glasses and liquids reveal similar characteristics over a wide pressure and temperature range. Beyond the increase in Si coordination observed at 20 GPa, we find no evidence for major structural changes occurring in the silicate melts studied up to pressures and temperatures exceeding Earth's core mantle boundary conditions. This result is supported by molecular dynamics calculations. Our findings reinforce the widely used assumption that the silicate glasses studies are appropriate structural analogs for understanding the atomic arrangement of silicate liquids at these high pressures.

  View details for DOI 10.1073/pnas.1920470117

  View details for PubMedID 32414927

• Photoreversible interconversion of a phytochrome photosensory module in the crystalline state. Proceedings of the National Academy of Sciences of the United States of America Burgie, E. S., Clinger, J. A., Miller, M. D., Brewster, A. S., Aller, P., Butryn, A., Fuller, F. D., Gul, S., Young, I. D., Pham, C. C., Kim, I., Bhowmick, A., O'Riordan, L. J., Sutherlin, K. D., Heinemann, J. V., Batyuk, A., Alonso-Mori, R., Hunter, M. S., Koglin, J. E., Yano, J., Yachandra, V. K., Sauter, N. K., Cohen, A. E., Kern, J., Orville, A. M., Phillips, G. N., Vierstra, R. D. 2019

  Abstract

  A major barrier to defining the structural intermediates that arise during the reversible photointerconversion of phytochromes between their biologically inactive and active states has been the lack of crystals that faithfully undergo this transition within the crystal lattice. Here, we describe a crystalline form of the cyclic GMP phosphodiesterases/adenylyl cyclase/FhlA (GAF) domain from the cyanobacteriochrome PixJ in Thermosynechococcus elongatus assembled with phycocyanobilin that permits reversible photoconversion between the blue light-absorbing Pb and green light-absorbing Pg states, as well as thermal reversion of Pg back to Pb. The X-ray crystallographic structure of Pb matches previous models, including autocatalytic conversion of phycocyanobilin to phycoviolobilin upon binding and its tandem thioether linkage to the GAF domain. Cryocrystallography at 150 K, which compared diffraction data from a single crystal as Pb or after irradiation with blue light, detected photoconversion product(s) based on Fobs - Fobs difference maps that were consistent with rotation of the bonds connecting pyrrole rings C and D. Further spectroscopic analyses showed that phycoviolobilin is susceptible to X-ray radiation damage, especially as Pg, during single-crystal X-ray diffraction analyses, which could complicate fine mapping of the various intermediate states. Fortunately, we found that PixJ crystals are amenable to serial femtosecond crystallography (SFX) analyses using X-ray free-electron lasers (XFELs). As proof of principle, we solved by room temperature SFX the GAF domain structure of Pb to 1.55-A resolution, which was strongly congruent with synchrotron-based models. Analysis of these crystals by SFX should now enable structural characterization of the early events that drive phytochrome photoconversion.

  View details for DOI 10.1073/pnas.1912041116

  View details for PubMedID 31852825

• Mix-and-inject XFEL crystallography reveals gated conformational dynamics during enzyme catalysis. Proceedings of the National Academy of Sciences of the United States of America Dasgupta, M., Budday, D., de Oliveira, S. H., Madzelan, P., Marchany-Rivera, D., Seravalli, J., Hayes, B., Sierra, R. G., Boutet, S., Hunter, M. S., Alonso-Mori, R., Batyuk, A., Wierman, J., Lyubimov, A., Brewster, A. S., Sauter, N. K., Applegate, G. A., Tiwari, V. K., Berkowitz, D. B., Thompson, M. C., Cohen, A. E., Fraser, J. S., Wall, M. E., van den Bedem, H., Wilson, M. A. 2019

  Abstract

  How changes in enzyme structure and dynamics facilitate passage along the reaction coordinate is a fundamental unanswered question. Here, we use time-resolved mix-and-inject serial crystallography (MISC) at an X-ray free electron laser (XFEL), ambient-temperature X-ray crystallography, computer simulations, and enzyme kinetics to characterize how covalent catalysis modulates isocyanide hydratase (ICH) conformational dynamics throughout its catalytic cycle. We visualize this previously hypothetical reaction mechanism, directly observing formation of a thioimidate covalent intermediate in ICH microcrystals during catalysis. ICH exhibits a concerted helical displacement upon active-site cysteine modification that is gated by changes in hydrogen bond strength between the cysteine thiolate and the backbone amide of the highly strained Ile152 residue. These catalysis-activated motions permit water entry into the ICH active site for intermediate hydrolysis. Mutations at a Gly residue (Gly150) that modulate helical mobility reduce ICH catalytic turnover and alter its pre-steady-state kinetic behavior, establishing that helical mobility is important for ICH catalytic efficiency. These results demonstrate that MISC can capture otherwise elusive aspects of enzyme mechanism and dynamics in microcrystalline samples, resolving long-standing questions about the connection between nonequilibrium protein motions and enzyme catalysis.

  View details for DOI 10.1073/pnas.1901864116

  View details for PubMedID 31801874

• Antivitamins B12 in a Microdrop: The Excited-State Structure of a Precious Sample Using Transient Polarized X-ray Absorption Near-Edge Structure. The journal of physical chemistry letters Miller, N. A., Michocki, L. B., Alonso-Mori, R., Britz, A., Deb, A., DePonte, D. P., Glownia, J. M., Kaneshiro, A. K., Kieninger, C., Koralek, J., Meadows, J. H., van Driel, T. B., Krautler, B., Kubarych, K. J., Penner-Hahn, J. E., Sension, R. J. 2019: 5484–89

  Abstract

  Polarized transient X-ray absorption near-edge structure (XANES) was used to probe the excited-state structure of a photostable B12 antivitamin (Cobeta-2-(2,4-difluorophenyl)-ethynylcobalamin, F2PhEtyCbl). A drop-on-demand delivery system synchronized to the LCLS X-ray free electron laser pulses was implemented and used to measure the XANES difference spectrum 12 ps following excitation, exposing only 45 muL of sample. Unlike cyanocobalamin (CNCbl), where the Co-C bond expands 15-20%, the excited state of F2PhEtyCbl is characterized by little change in the Co-C bond, suggesting that the acetylide linkage raises the barrier for expansion of the Co-C bond. In contrast, the lower axial Co-NDMB bond is elongated in the excited state of F2PhEtyCbl by ca. 10% or more, comparable to the 10% elongation observed for Co-NDMB in CNCbl.

  View details for DOI 10.1021/acs.jpclett.9b02202

  View details for PubMedID 31483136

• XANES and EXAFS of dilute solutions of transition metals at XFELs. Journal of synchrotron radiation Chatterjee, R., Weninger, C., Loukianov, A., Gul, S., Fuller, F. D., Cheah, M. H., Fransson, T., Pham, C. C., Nelson, S., Song, S., Britz, A., Messinger, J., Bergmann, U., Alonso-Mori, R., Yachandra, V. K., Kern, J., Yano, J. 2019; 26 (Pt 5): 1716–24

  Abstract

  This work has demonstrated that X-ray absorption spectroscopy (XAS), both Mn XANES and EXAFS, of solutions with millimolar concentrations of metal is possible using the femtosecond X-ray pulses from XFELs. Mn XAS data were collected using two different sample delivery methods, a Rayleigh jet and a drop-on-demand setup, with varying concentrations of Mn. Here, a new method for normalization of XAS spectra based on solvent scattering that is compatible with data collection from a highly variable pulsed source is described. The measured XANES and EXAFS spectra of such dilute solution samples are in good agreement with data collected at synchrotron sources using traditional scanning protocols. The procedures described here will enable XFEL-based XAS on dilute biological samples, especially metalloproteins, with low sample consumption. Details of the experimental setup and data analysis methods used in this XANES and EXAFS study are presented. This method will also benefit XAS performed at high-repetition-rate XFELs such as the European XFEL, LCLS-II and LCLS-II-HE.

  View details for DOI 10.1107/S1600577519007550

  View details for PubMedID 31490163

• Diagram, valence-to-core, and hypersatellite K beta X-ray transitions in metallic chromium Zeeshan, F., Hoszowska, J., Dousse, J., Sokaras, D., Weng, T., Alonso-Mori, R., Kavcic, M., Guerra, M., Sampaio, J., Parente, F., Indelicato, P., Marques, J., Santos, J. WILEY. 2019: 351-359

  View details for DOI 10.1002/xrs.3019

  View details for Web of Science ID 000483574400006

• Finding intersections between electronic excited state potential energy surfaces with simultaneous ultrafast X-ray scattering and spectroscopy. Chemical science Kjar, K. S., Van Driel, T. B., Harlang, T. C., Kunnus, K., Biasin, E., Ledbetter, K., Hartsock, R. W., Reinhard, M. E., Koroidov, S., Li, L., Laursen, M. G., Hansen, F. B., Vester, P., Christensen, M., Haldrup, K., Nielsen, M. M., Dohn, A. O., Papai, M. I., Moller, K. B., Chabera, P., Liu, Y., Tatsuno, H., Timm, C., Jarenmark, M., Uhlig, J., Sundstom, V., Warnmark, K., Persson, P., Nemeth, Z., Szemes, D. S., Bajnoczi, E., Vanko, G., Alonso-Mori, R., Glownia, J. M., Nelson, S., Sikorski, M., Sokaras, D., Canton, S. E., Lemke, H. T., Gaffney, K. J. 2019; 10 (22): 5749–60

  Abstract

  Light-driven molecular reactions are dictated by the excited state potential energy landscape, depending critically on the location of conical intersections and intersystem crossing points between potential surfaces where non-adiabatic effects govern transition probabilities between distinct electronic states. While ultrafast studies have provided significant insight into electronic excited state reaction dynamics, experimental approaches for identifying and characterizing intersections and seams between electronic states remain highly system dependent. Here we show that for 3d transition metal systems simultaneously recorded X-ray diffuse scattering and X-ray emission spectroscopy at sub-70 femtosecond time-resolution provide a solid experimental foundation for determining the mechanistic details of excited state reactions. In modeling the mechanistic information retrieved from such experiments, it becomes possible to identify the dominant trajectory followed during the excited state cascade and to determine the relevant loci of intersections between states. We illustrate our approach by explicitly mapping parts of the potential energy landscape dictating the light driven low-to-high spin-state transition (spin crossover) of [Fe(2,2'-bipyridine)3]2+, where the strongly coupled nuclear and electronic dynamics have been a source of interest and controversy. We anticipate that simultaneous X-ray diffuse scattering and X-ray emission spectroscopy will provide a valuable approach for mapping the reactive trajectories of light-triggered molecular systems involving 3d transition metals.

  View details for DOI 10.1039/c8sc04023k

  View details for PubMedID 31293761

• Pheomelanin pigment remnants mapped in fossils of an extinct mammal NATURE COMMUNICATIONS Manning, P. L., Edwards, N. P., Bergmann, U., Anne, J., Sellers, W. I., van Veelen, A., Sokaras, D., Egerton, V. M., Alonso-Mori, R., Ignatyev, K., van Dongen, B. E., Wakamatsu, K., Ito, S., Knoll, F., Wogelius, R. A. 2019; 10: 2250

  Abstract

  Recent progress has been made in paleontology with respect to resolving pigmentation in fossil material. Morphological identification of fossilized melanosomes has been one approach, while a second methodology using chemical imaging and spectroscopy has also provided critical information particularly concerning eumelanin (black pigment) residue. In this work we develop the chemical imaging methodology to show that organosulfur-Zn complexes are indicators of pheomelanin (red pigment) in extant and fossil soft tissue and that the mapping of these residual biochemical compounds can be used to restore melanin pigment distribution in a 3 million year old extinct mammal species (Apodemus atavus). Synchotron Rapid Scanning X-ray Fluorescence imaging showed that the distributions of Zn and organic S are correlated within this fossil fur just as in pheomelanin-rich modern integument. Furthermore, Zn coordination chemistry within this fossil fur is closely comparable to that determined from pheomelanin-rich fur and hair standards. The non-destructive methods presented here provide a protocol for detecting residual pheomelanin in precious specimens.

  View details for DOI 10.1038/s41467-019-10087-2

  View details for Web of Science ID 000468448100007

  View details for PubMedID 31113945

  View details for PubMedCentralID PMC6529433

• A high-throughput energy-dispersive tender X-ray spectrometer for shot-to-shot sulfur measurements. Journal of synchrotron radiation Abraham, B., Nowak, S., Weninger, C., Armenta, R., Defever, J., Day, D., Carini, G., Nakahara, K., Gallo, A., Nelson, S., Nordlund, D., Kroll, T., Hunter, M. S., van Driel, T., Zhu, D., Weng, T. C., Alonso-Mori, R., Sokaras, D. 2019; 26 (Pt 3): 629–34

  Abstract

  An X-ray emission spectrometer that can detect the sulfur Kalpha emission lines with large throughput and a high energy resolution is presented. The instrument is based on a large d-spacing perfect Bragg analyzer that diffracts the sulfur Kalpha emission at close to backscattering angles. This facilitates the application of efficient concepts routinely employed in hard X-ray spectrometers towards the tender X-ray regime. The instrument described in this work is based on an energy-dispersive von Hamos geometry that is well suited for photon-in photon-out spectroscopy at X-ray free-electron laser and synchrotron sources. Comparison of its performance with previously used instrumentation is presented through measurements using sulfur-containing species performed at the LCLS. It is shown that the overall signal intensity is increased by a factor of 15. Implementation of this approach in the design of a tender X-ray spectroscopy endstation for LCLS-II is also discussed.

  View details for DOI 10.1107/S1600577519002431

  View details for PubMedID 31074425

• The Macromolecular Femtosecond Crystallography Instrument at the Linac Coherent Light Source JOURNAL OF SYNCHROTRON RADIATION Sierra, R. G., Batyuk, A., Sun, Z., Aquila, A., Hunter, M. S., Lane, T. J., Liang, M., Yoon, C., Alonso-Mori, R., Armenta, R., Castagna, J., Hollenbeck, M., Osier, T. O., Hayes, M., Aldrich, J., Curtis, R., Koglin, J. E., Rendahl, T., Rodriguez, E., Carbajo, S., Guillet, S., Paul, R., Hart, P., Nakahara, K., Carini, G., DeMirci, H., Dao, E., Hayes, B. M., Rao, Y. P., Chollet, M., Feng, Y., Fuller, F. D., Kupitz, C., Sato, T., Seaberg, M. H., Song, S., van Driel, T. B., Yavas, H., Zhu, D., Cohen, A. E., Wakatsuki, S., Boutet, S. 2019; 26: 346–57

  View details for DOI 10.1107/S1600577519001577

  View details for Web of Science ID 000460859600007

• The Macromolecular Femtosecond Crystallography Instrument at the Linac Coherent Light Source. Journal of synchrotron radiation Sierra, R. G., Batyuk, A. n., Sun, Z. n., Aquila, A. n., Hunter, M. S., Lane, T. J., Liang, M. n., Yoon, C. H., Alonso-Mori, R. n., Armenta, R. n., Castagna, J. C., Hollenbeck, M. n., Osier, T. O., Hayes, M. n., Aldrich, J. n., Curtis, R. n., Koglin, J. E., Rendahl, T. n., Rodriguez, E. n., Carbajo, S. n., Guillet, S. n., Paul, R. n., Hart, P. n., Nakahara, K. n., Carini, G. n., DeMirci, H. n., Dao, E. H., Hayes, B. M., Rao, Y. P., Chollet, M. n., Feng, Y. n., Fuller, F. D., Kupitz, C. n., Sato, T. n., Seaberg, M. H., Song, S. n., van Driel, T. B., Yavas, H. n., Zhu, D. n., Cohen, A. E., Wakatsuki, S. n., Boutet, S. n. 2019; 26 (Pt 2): 346–57

  Abstract

  The Macromolecular Femtosecond Crystallography (MFX) instrument at the Linac Coherent Light Source (LCLS) is the seventh and newest instrument at the world's first hard X-ray free-electron laser. It was designed with a primary focus on structural biology, employing the ultrafast pulses of X-rays from LCLS at atmospheric conditions to overcome radiation damage limitations in biological measurements. It is also capable of performing various time-resolved measurements. The MFX design consists of a versatile base system capable of supporting multiple methods, techniques and experimental endstations. The primary techniques supported are forward scattering and crystallography, with capabilities for various spectroscopic methods and time-resolved measurements. The location of the MFX instrument allows for utilization of multiplexing methods, increasing user access to LCLS by running multiple experiments simultaneously.

  View details for PubMedID 30855242

• Soft X-ray spectroscopy with transition-edge sensors at Stanford Synchrotron Radiation Lightsource beamline 10-1. The Review of scientific instruments Lee, S. J., Titus, C. J., Alonso Mori, R. n., Baker, M. L., Bennett, D. A., Cho, H. M., Doriese, W. B., Fowler, J. W., Gaffney, K. J., Gallo, A. n., Gard, J. D., Hilton, G. C., Jang, H. n., Joe, Y. I., Kenney, C. J., Knight, J. n., Kroll, T. n., Lee, J. S., Li, D. n., Lu, D. n., Marks, R. n., Minitti, M. P., Morgan, K. M., Ogasawara, H. n., O'Neil, G. C., Reintsema, C. D., Schmidt, D. R., Sokaras, D. n., Ullom, J. N., Weng, T. C., Williams, C. n., Young, B. A., Swetz, D. S., Irwin, K. D., Nordlund, D. n. 2019; 90 (11): 113101

  Abstract

  We present results obtained with a new soft X-ray spectrometer based on transition-edge sensors (TESs) composed of Mo/Cu bilayers coupled to bismuth absorbers. This spectrometer simultaneously provides excellent energy resolution, high detection efficiency, and broadband spectral coverage. The new spectrometer is optimized for incident X-ray energies below 2 keV. Each pixel serves as both a highly sensitive calorimeter and an X-ray absorber with near unity quantum efficiency. We have commissioned this 240-pixel TES spectrometer at the Stanford Synchrotron Radiation Lightsource beamline 10-1 (BL 10-1) and used it to probe the local electronic structure of sample materials with unprecedented sensitivity in the soft X-ray regime. As mounted, the TES spectrometer has a maximum detection solid angle of 2 × 10-3 sr. The energy resolution of all pixels combined is 1.5 eV full width at half maximum at 500 eV. We describe the performance of the TES spectrometer in terms of its energy resolution and count-rate capability and demonstrate its utility as a high throughput detector for synchrotron-based X-ray spectroscopy. Results from initial X-ray emission spectroscopy and resonant inelastic X-ray scattering experiments obtained with the spectrometer are presented.

  View details for DOI 10.1063/1.5119155

  View details for PubMedID 31779391

• Hot Branching Dynamics in a Light-Harvesting Iron Carbene Complex Revealed by Ultrafast X-ray Emission Spectroscopy. Angewandte Chemie (International ed. in English) Tatsuno, H. n., Kjaer, K. S., Kunnus, K. n., Harlang, T. C., Timm, C. n., Guo, M. n., Chàbera, P. n., Fredin, L. A., Hartsock, R. W., Reinhard, M. E., Koroidov, S. n., Li, L. n., Cordones, A. A., Gordivska, O. n., Prakash, O. n., Liu, Y. n., Laursen, M. G., Biasin, E. n., Hansen, F. B., Vester, P. n., Christensen, M. n., Haldrup, K. n., Németh, Z. n., Sárosiné Szemes, D. n., Bajnóczi, É. n., Vankó, G. n., Van Driel, T. B., Alonso-Mori, R. n., Glownia, J. M., Nelson, S. n., Sikorski, M. n., Lemke, H. T., Sokaras, D. n., Canton, S. E., Dohn, A. O., Møller, K. B., Nielsen, M. M., Gaffney, K. J., Wärnmark, K. n., Sundström, V. n., Persson, P. n., Uhlig, J. n. 2019

  Abstract

  Iron N-heterocyclic carbene (NHC) complexes have received a great deal of attention recently because of their growing potential as light sensitizers or photocatalysts. We present a sub-ps X-ray spectroscopy study of an FeII NHC complex that identifies and quantifies the states involved in the deactivation cascade after light absorption. Excited molecules relax back to the ground state along two pathways: After population of a hot 3 MLCT state, from the initially excited 1 MLCT state, 30 % of the molecules undergo ultrafast (150 fs) relaxation to the 3 MC state, in competition with vibrational relaxation and cooling to the relaxed 3 MLCT state. The relaxed 3 MLCT state then decays much more slowly (7.6 ps) to the 3 MC state. The 3 MC state is rapidly (2.2 ps) deactivated to the ground state. The 5 MC state is not involved in the deactivation pathway. The ultrafast partial deactivation of the 3 MLCT state constitutes a loss channel from the point of view of photochemical efficiency and highlights the necessity to screen transition-metal complexes for similar ultrafast decays to optimize photochemical performance.

  View details for DOI 10.1002/anie.201908065

  View details for PubMedID 31602726

• Resolving structures of transition metal complex reaction intermediates with femtosecond EXAFS. Physical chemistry chemical physics : PCCP Britz, A. n., Abraham, B. n., Biasin, E. n., van Driel, T. B., Gallo, A. n., Garcia-Esparza, A. T., Glownia, J. n., Loukianov, A. n., Nelson, S. n., Reinhard, M. n., Sokaras, D. n., Alonso-Mori, R. n. 2019

  Abstract

  Femtosecond-resolved Extended X-ray Absorption Fine Structure (EXAFS) measurements of solvated transition metal complexes are successfully implemented at the X-ray Free Electron Laser LCLS. Benchmark experiments on [Fe(terpy)2]2+ in solution show a signal-to-noise ratio on the order of 500, comparable to typical 100 ps-resolution synchrotron measurements. In the few femtoseconds after photoexcitation, we observe the EXAFS fingerprints of a short-lived (∼100 fs) intermediate as well as those of a vibrationally hot long-lived (∼ns) excited state.

  View details for DOI 10.1039/c9cp03483h

  View details for PubMedID 31441480

• Morphological and chemical evidence for cyclic bone growth in a fossil hyaena JOURNAL OF ANALYTICAL ATOMIC SPECTROMETRY Anne, J., Wogelius, R. A., Edwards, N. P., van Veelen, A., Buckley, M., Sellers, W. I., Bergmann, U., Sokaras, D., Alonso-Mori, R., Harvey, V. L., Egerton, V. M., Manning, P. L. 2018; 33 (12): 2062-2069

  View details for DOI 10.1039/c8ja00314a

  View details for Web of Science ID 000451536000002

• Structures of the intermediates of Kok's photosynthetic water oxidation clock. Nature Kern, J., Chatterjee, R., Young, I. D., Fuller, F. D., Lassalle, L., Ibrahim, M., Gul, S., Fransson, T., Brewster, A. S., Alonso-Mori, R., Hussein, R., Zhang, M., Douthit, L., de Lichtenberg, C., Cheah, M. H., Shevela, D., Wersig, J., Seuffert, I., Sokaras, D., Pastor, E., Weninger, C., Kroll, T., Sierra, R. G., Aller, P., Butryn, A., Orville, A. M., Liang, M., Batyuk, A., Koglin, J. E., Carbajo, S., Boutet, S., Moriarty, N. W., Holton, J. M., Dobbek, H., Adams, P. D., Bergmann, U., Sauter, N. K., Zouni, A., Messinger, J., Yano, J., Yachandra, V. K. 2018

  Abstract

  Inspired by the period-four oscillation in flash-induced oxygen evolution of photosystem II discovered by Joliot in 1969, Kok performed additional experiments and proposed a five-state kinetic model for photosynthetic oxygen evolution, known as Kok's S-state clock or cycle1,2. The model comprises four (meta)stable intermediates (S0, S1, S2 and S3) and one transient S4 state, which precedes dioxygen formation occurring in a concerted reaction from two water-derived oxygens bound at an oxo-bridged tetra manganese calcium (Mn4CaO5) cluster in the oxygen-evolving complex3-7. This reaction is coupled to the two-step reduction and protonation of the mobile plastoquinone QB at the acceptor side of PSII. Here, using serial femtosecond X-ray crystallography and simultaneous X-ray emission spectroscopy with multi-flash visible laser excitation at room temperature, we visualize all (meta)stable states of Kok's cycle as high-resolution structures (2.04-2.08A). In addition, we report structures of two transient states at 150 and 400s, revealing notable structural changes including the binding of one additional 'water', Ox, during the S2S3 state transition. Our results suggest that one water ligand to calcium (W3) is directly involved in substrate delivery. The binding of the additional oxygen Ox in the S3 state between Ca and Mn1 supports O-O bond formation mechanisms involving O5 as one substrate, where Ox is either the other substrate oxygen or is perfectly positioned to refill the O5 position during O2 release. Thus, our results exclude peroxo-bond formation in the S3 state, and the nucleophilic attack of W3 onto W2 is unlikely.

  View details for DOI 10.1038/s41586-018-0681-2

  View details for PubMedID 30405241

• Relativistic and resonant effects in the ionization of heavy atoms by ultra-intense hard X-rays NATURE COMMUNICATIONS Rudek, B., Toyota, K., Foucar, L., Erk, B., Boll, R., Bomme, C., Correa, J., Carron, S., Boutet, S., Williams, G. J., Ferguson, K. R., Alonso-Mori, R., Koglin, J. E., Gorkhover, T., Bucher, M., Lehmann, C., Krassig, B., Southworth, S. H., Young, L., Bostedt, C., Ueda, K., Marchenko, T., Simon, M., Jurek, Z., Santra, R., Rudenko, A., Son, S., Rolles, D. 2018; 9: 4200

  Abstract

  An accurate description of the interaction of intense hard X-ray pulses with heavy atoms, which is crucial for many applications of free-electron lasers, represents a hitherto unresolved challenge for theory because of the enormous number of electronic configurations and relativistic effects, which need to be taken into account. Here we report results on multiple ionization of xenon atoms by ultra-intense (about 1019 W/cm2) femtosecond X-ray pulses at photon energies from 5.5 to 8.3 keV and present a theoretical model capable of reproducing the experimental data in the entire energy range. Our analysis shows that the interplay of resonant and relativistic effects results in strongly structured charge state distributions, which reflect resonant positions of relativistically shifted electronic levels of highly charged ions created during the X-ray pulse. The theoretical approach described here provides a basis for accurate modeling of radiation damage in hard X-ray imaging experiments on targets with high-Z constituents.

  View details for DOI 10.1038/s41467-018-06745-6

  View details for Web of Science ID 000446846600019

  View details for PubMedID 30305630

  View details for PubMedCentralID PMC6180123

• X-ray Emission Spectroscopy as an in Situ Diagnostic Tool for X-ray Crystallography of Metalloproteins Using an X-ray Free-Electron Laser. Biochemistry Fransson, T., Chatterjee, R., Fuller, F. D., Gul, S., Weninger, C., Sokaras, D., Kroll, T., Alonso-Mori, R., Bergmann, U., Kern, J., Yachandra, V. K., Yano, J. 2018

  Abstract

  Serial femtosecond crystallography (SFX) using the ultrashort X-ray pulses from a X-ray free-electron laser (XFEL) provides a new way of collecting structural data at room temperature that allows for following the reaction in real time after initiation. XFEL experiments are conducted in a shot-by-shot mode as the sample is destroyed and replenished after each X-ray pulse, and therefore, monitoring and controlling the data quality by using in situ diagnostic tools is critical. To study metalloenzymes, we developed the use of simultaneous collection of X-ray diffraction of crystals along with X-ray emission spectroscopy (XES) data that is used as a diagnostic tool for crystallography, by monitoring the chemical state of the metal catalytic center. We have optimized data analysis methods and sample delivery techniques for fast and active feedback to ensure the quality of each batch of samples and the turnover of the catalytic reaction caused by reaction triggering methods. Here, we describe this active in situ feedback system using Photosystem II as an example that catalyzes the oxidation of H2O to O2 at the Mn4CaO5 active site. We used the first moments of the Mn Kbeta1,3 emission spectra, which are sensitive to the oxidation state of Mn, as the primary diagnostics. This approach is applicable to different metalloproteins to determine the integrity of samples and follow changes in the chemical states of the reaction that can be initiated by light or activated by substrates and offers a metric for determining the diffraction images that are used for the final data sets.

  View details for DOI 10.1021/acs.biochem.8b00325

  View details for PubMedID 29906115

• Stimulated X-Ray Emission Spectroscopy in Transition Metal Complexes PHYSICAL REVIEW LETTERS Kroll, T., Weninger, C., Alonso-Mori, R., Sokaras, D., Zhu, D., Mercadier, L., Majety, V. P., Marinelli, A., Lutman, A., Guetg, M. W., Decker, F., Boutet, S., Aquila, A., Koglin, J., Koralek, J., DePonte, D. P., Kern, J., Fuller, F. D., Pastor, E., Fransson, T., Zhang, Y., Yano, J., Yachandra, V. K., Rohringer, N., Bergmann, U. 2018; 120 (13): 133203

  Abstract

  We report the observation and analysis of the gain curve of amplified Kα x-ray emission from solutions of Mn(II) and Mn(VII) complexes using an x-ray free electron laser to create the 1s core-hole population inversion. We find spectra at amplification levels extending over 4 orders of magnitude until saturation. We observe bandwidths below the Mn 1s core-hole lifetime broadening in the onset of the stimulated emission. In the exponential amplification regime the resolution corrected spectral width of ∼1.7  eV FWHM is constant over 3 orders of magnitude, pointing to the buildup of transform limited pulses of ∼1  fs duration. Driving the amplification into saturation leads to broadening and a shift of the line. Importantly, the chemical sensitivity of the stimulated x-ray emission to the Mn oxidation state is preserved at power densities of ∼10^{20}  W/cm^{2} for the incoming x-ray pulses. Differences in signal sensitivity and spectral information compared to conventional (spontaneous) x-ray emission spectroscopy are discussed. Our findings build a baseline for nonlinear x-ray spectroscopy for a wide range of transition metal complexes in inorganic chemistry, catalysis, and materials science.

  View details for DOI 10.1103/PhysRevLett.120.133203

  View details for Web of Science ID 000428394800008

  View details for PubMedID 29694162

• Solvent control of charge transfer excited state relaxation pathways in [Fe(2,2 '-bipyridine)(CN)(4)](2-) PHYSICAL CHEMISTRY CHEMICAL PHYSICS Kjaer, K. S., Kunnus, K., Harlang, T. B., Van Driel, T. B., Ledbetter, K., Hartsock, R. W., Reinhard, M. E., Koroidov, S., Li, L., Laursen, M. G., Biasin, E., Hansen, F. B., Vester, P., Christensen, M., Haldrup, K., Nielsen, M. M., Chabera, P., Liu, Y., Tatsuno, H., Timm, C., Uhlig, J., Sundstom, V., Nemeth, Z., Szemes, D., Bajnoczi, E., Vanko, G., Alonso-Mori, R., Glownia, J. M., Nelson, S., Sikorski, M., Sokaras, D., Lemke, H. T., Canton, S. E., Warnmark, K., Persson, P., Cordones, A. A., Gaffney, K. J. 2018; 20 (6): 4238–49

  Abstract

  The excited state dynamics of solvated [Fe(bpy)(CN)4]2-, where bpy = 2,2'-bipyridine, show significant sensitivity to the solvent Lewis acidity. Using a combination of optical absorption and X-ray emission transient spectroscopies, we have previously shown that the metal to ligand charge transfer (MLCT) excited state of [Fe(bpy)(CN)4]2- has a 19 picosecond lifetime and no discernable contribution from metal centered (MC) states in weak Lewis acid solvents, such as dimethyl sulfoxide and acetonitrile.1,2 In the present work, we use the same combination of spectroscopic techniques to measure the MLCT excited state relaxation dynamics of [Fe(bpy)(CN)4]2- in water, a strong Lewis acid solvent. The charge-transfer excited state is now found to decay in less than 100 femtoseconds, forming a quasi-stable metal centered excited state with a 13 picosecond lifetime. We find that this MC excited state has triplet (3MC) character, unlike other reported six-coordinate Fe(ii)-centered coordination compounds, which form MC quintet (5MC) states. The solvent dependent changes in excited state non-radiative relaxation for [Fe(bpy)(CN)4]2- allows us to infer the influence of the solvent on the electronic structure of the complex. Furthermore, the robust characterization of the dynamics and optical spectral signatures of the isolated 3MC intermediate provides a strong foundation for identifying 3MC intermediates in the electronic excited state relaxation mechanisms of similar Fe-centered systems being developed for solar applications.

  View details for PubMedID 29364300

• Soft x-ray absorption spectroscopy of metalloproteins and high-valent metal-complexes at room temperature using free-electron lasers STRUCTURAL DYNAMICS Kubin, M., Kern, J., Gul, S., Kroll, T., Chatterjee, R., Loechel, H., Fuller, F. D., Sierra, R. G., Quevedo, W., Weniger, C., Rehanek, J., Firsov, A., Laksmono, H., Weninger, C., Alonso-Mori, R., Nordlund, D. L., Lassalle-Kaiser, B., Glownia, J. M., Krzywinski, J., Moeller, S., Turner, J. J., Minitti, M. P., Dakovski, G. L., Koroidov, S., Kawde, A., Kanady, J. S., Tsui, E. Y., Suseno, S., Han, Z., Hill, E., Taguchi, T., Borovik, A. S., Agapie, T., Messinger, J., Erko, A., Foehlisch, A., Bergmann, U., Mitzner, R., Yachandra, V. K., Yano, J., Wernet, P. 2017; 4 (5): 054307

  Abstract

  X-ray absorption spectroscopy at the L-edge of 3d transition metals provides unique information on the local metal charge and spin states by directly probing 3d-derived molecular orbitals through 2p-3d transitions. However, this soft x-ray technique has been rarely used at synchrotron facilities for mechanistic studies of metalloenzymes due to the difficulties of x-ray-induced sample damage and strong background signals from light elements that can dominate the low metal signal. Here, we combine femtosecond soft x-ray pulses from a free-electron laser with a novel x-ray fluorescence-yield spectrometer to overcome these difficulties. We present L-edge absorption spectra of inorganic high-valent Mn complexes (Mn ∼ 6-15 mmol/l) with no visible effects of radiation damage. We also present the first L-edge absorption spectra of the oxygen evolving complex (Mn4CaO5) in Photosystem II (Mn < 1 mmol/l) at room temperature, measured under similar conditions. Our approach opens new ways to study metalloenzymes under functional conditions.

  View details for PubMedID 28944255

• Insight into the electronic structure of transition metal ion complexes from resonant inelastic X-ray scattering Kroll, T., Hadt, R., Wilson, S., Baker, M., Lundberg, M., Yan, J., Weng, T., Sokaras, D., Alonso-Mori, R., Casa, D., Upton, M., Hedman, B., Hodgson, K., Solomon, E. AMER CHEMICAL SOC. 2017

  View details for Web of Science ID 000429556700220

• Ligand manipulation of charge transfer excited state relaxation and spin crossover in [Fe(2,2 '- bipyridine)(2)(CN)(2)] STRUCTURAL DYNAMICS Kjaer, K. S., Zhang, W., Alonso-Mori, R., Bergmann, U., Chollet, M., Hadt, R. G., Hartsock, R. W., Harlang, T., Kroll, T., Kubicek, K., Lemke, H. T., Liang, H. W., Liu, Y., Nielsen, M. M., Robinson, J. S., Solomon, E. I., Sokaras, D., van Driel, T. B., Weng, T., Zhu, D., Persson, P., Warnmark, K., Sundstrom, V., Gaffney, K. J. 2017; 4 (4): 044030

  Abstract

  We have used femtosecond resolution UV-visible and Kβ x-ray emission spectroscopy to characterize the electronic excited state dynamics of [Fe(bpy)2(CN)2], where bpy=2,2'-bipyridine, initiated by metal-to-ligand charge transfer (MLCT) excitation. The excited-state absorption in the transient UV-visible spectra, associated with the 2,2'-bipyridine radical anion, provides a robust marker for the MLCT excited state, while the transient Kβ x-ray emission spectra provide a clear measure of intermediate and high spin metal-centered excited states. From these measurements, we conclude that the MLCT state of [Fe(bpy)2(CN)2] undergoes ultrafast spin crossover to a metal-centered quintet excited state through a short lived metal-centered triplet transient species. These measurements of [Fe(bpy)2(CN)2] complement prior measurement performed on [Fe(bpy)3]2+ and [Fe(bpy)(CN)4]2- in dimethylsulfoxide solution and help complete the chemical series [Fe(bpy)N(CN)6-2N]2N-4, where N = 1-3. The measurements confirm that simple ligand modifications can significantly change the relaxation pathways and excited state lifetimes and support the further investigation of light harvesting and photocatalytic applications of 3d transition metal complexes.

  View details for PubMedID 28653021

• Metalloprotein entatic control of ligand-metal bonds quantified by ultrafast x-ray spectroscopy SCIENCE Mara, M. W., Hadt, R. G., Reinhard, M., Kroll, T., Lim, H., Hartsock, R. W., Alonso-Mori, R., Chollet, M., Glownia, J. M., Nelson, S., Sokaras, D., Kunnus, K., Hodgson, K. O., Hedman, B., Bergmann, U., Gaffney, K. J., Solomon, E. I. 2017; 356 (6344): 1276-+

  Abstract

  The multifunctional protein cytochrome c (cyt c) plays key roles in electron transport and apoptosis, switching function by modulating bonding between a heme iron and the sulfur in a methionine residue. This Fe-S(Met) bond is too weak to persist in the absence of protein constraints. We ruptured the bond in ferrous cyt c using an optical laser pulse and monitored the bond reformation within the protein active site using ultrafast x-ray pulses from an x-ray free-electron laser, determining that the Fe-S(Met) bond enthalpy is ~4 kcal/mol stronger than in the absence of protein constraints. The 4 kcal/mol is comparable with calculations of stabilization effects in other systems, demonstrating how biological systems use an entatic state for modest yet accessible energetics to modulate chemical function.

  View details for PubMedID 28642436

  View details for PubMedCentralID PMC5706643

• Drop-on-demand sample delivery for studying biocatalysts in action at X-ray free-electron lasers. Nature methods Fuller, F. D., Gul, S., Chatterjee, R., Burgie, E. S., Young, I. D., Lebrette, H., Srinivas, V., Brewster, A. S., Michels-Clark, T., Clinger, J. A., Andi, B., Ibrahim, M., Pastor, E., de Lichtenberg, C., Hussein, R., Pollock, C. J., Zhang, M., Stan, C. A., Kroll, T., Fransson, T., Weninger, C., Kubin, M., Aller, P., Lassalle, L., Bräuer, P., Miller, M. D., Amin, M., Koroidov, S., Roessler, C. G., Allaire, M., Sierra, R. G., Docker, P. T., Glownia, J. M., Nelson, S., Koglin, J. E., Zhu, D., Chollet, M., Song, S., Lemke, H., Liang, M., Sokaras, D., Alonso-Mori, R., Zouni, A., Messinger, J., Bergmann, U., Boal, A. K., Bollinger, J. M., Krebs, C., Högbom, M., Phillips, G. N., Vierstra, R. D., Sauter, N. K., Orville, A. M., Kern, J., Yachandra, V. K., Yano, J. 2017

  Abstract

  X-ray crystallography at X-ray free-electron laser sources is a powerful method for studying macromolecules at biologically relevant temperatures. Moreover, when combined with complementary techniques like X-ray emission spectroscopy, both global structures and chemical properties of metalloenzymes can be obtained concurrently, providing insights into the interplay between the protein structure and dynamics and the chemistry at an active site. The implementation of such a multimodal approach can be compromised by conflicting requirements to optimize each individual method. In particular, the method used for sample delivery greatly affects the data quality. We present here a robust way of delivering controlled sample amounts on demand using acoustic droplet ejection coupled with a conveyor belt drive that is optimized for crystallography and spectroscopy measurements of photochemical and chemical reactions over a wide range of time scales. Studies with photosystem II, the phytochrome photoreceptor, and ribonucleotide reductase R2 illustrate the power and versatility of this method.

  View details for DOI 10.1038/nmeth.4195

  View details for PubMedID 28250468

  View details for PubMedCentralID PMC5376230

• Manipulating charge transfer excited state relaxation and spin crossover in iron coordination complexes with ligand substitution CHEMICAL SCIENCE Zhang, W., Kjaer, K. S., Alonso-Mori, R., Bergmann, U., Chollet, M., Fredin, L. A., Hadt, R. G., Hartsock, R. W., Harlang, T., Kroll, T., Kubicek, K., Lemke, H. T., Liang, H. W., Liu, Y., Nielsen, M. M., Persson, P., Robinson, J. S., Solomon, E. I., Sun, Z., Sokaras, D., van Driel, T. B., Weng, T., Zhu, D., Warnmark, K., Sundstromb, V., Gaffney, K. J. 2017; 8 (1): 515-523

  Abstract

  Developing light-harvesting and photocatalytic molecules made with iron could provide a cost effective, scalable, and environmentally benign path for solar energy conversion. To date these developments have been limited by the sub-picosecond metal-to-ligand charge transfer (MLCT) electronic excited state lifetime of iron based complexes due to spin crossover - the extremely fast intersystem crossing and internal conversion to high spin metal-centered excited states. We revitalize a 30 year old synthetic strategy for extending the MLCT excited state lifetimes of iron complexes by making mixed ligand iron complexes with four cyanide (CN-) ligands and one 2,2'-bipyridine (bpy) ligand. This enables MLCT excited state and metal-centered excited state energies to be manipulated with partial independence and provides a path to suppressing spin crossover. We have combined X-ray Free-Electron Laser (XFEL) Kβ hard X-ray fluorescence spectroscopy with femtosecond time-resolved UV-visible absorption spectroscopy to characterize the electronic excited state dynamics initiated by MLCT excitation of [Fe(CN)4(bpy)]2-. The two experimental techniques are highly complementary; the time-resolved UV-visible measurement probes allowed electronic transitions between valence states making it sensitive to ligand-centered electronic states such as MLCT states, whereas the Kβ fluorescence spectroscopy provides a sensitive measure of changes in the Fe spin state characteristic of metal-centered excited states. We conclude that the MLCT excited state of [Fe(CN)4(bpy)]2- decays with roughly a 20 ps lifetime without undergoing spin crossover, exceeding the MLCT excited state lifetime of [Fe(2,2'-bipyridine)3]2+ by more than two orders of magnitude.

  View details for DOI 10.1039/c6sc03070j

  View details for Web of Science ID 000391454500060

  View details for PubMedCentralID PMC5341207

• Time-resolved structural biology benefits from complementary methods Orville, A., Fuller, F., Gul, S., Kern, J., Brewster, A., Sauter, N., Bergmann, U., Alonso-Mori, R., Yachandra, V., Yano, J. INT UNION CRYSTALLOGRAPHY. 2017: C1128

  View details for DOI 10.1107/S2053273317084467

  View details for Web of Science ID 000481522001131

• Taking Snapshots of Photosynthetic Water Oxidation with an X-ray Laser Yachandra, V., Kern, J., Zouni, A., Messinger, J., Bergmann, U., Alonso-Mori, R., Wernet, P., Sauter, N., Yano, J. INT UNION CRYSTALLOGRAPHY. 2017: C14

  View details for DOI 10.1107/S2053273317095560

  View details for Web of Science ID 000481522000015

• Structure of photosystem II and substrate binding at room temperature NATURE Young, I. D., Ibrahim, M., Chatterjee, R., Gul, S., Fuller, F. D., Koroidov, S., Brewster, A. S., Tran, R., Alonso-Mori, R., Kroll, T., Michels-Clark, T., Laksmono, H., Sierra, R. G., Stan, C. A., Hussein, R., Zhang, M., Douthit, L., Kubin, M., de Lichtenberg, C., Long Vo Pham, L. V., Nilsson, H., Cheah, M. H., Shevela, D., Saracini, C., Bean, M. A., Seuffert, I., Sokaras, D., Weng, T., Pastor, E., Weninger, C., Fransson, T., Lassalle, L., Braeuer, P., Aller, P., Docker, P. T., Andi, B., Orville, A. M., Glownia, J. M., Nelson, S., Sikorski, M., Zhu, D., Hunter, M. S., Lane, T. J., Aquila, A., Koglin, J. E., Robinson, J., Liang, M., Boutet, S., Lyubimov, A. Y., Uervirojnangkoorn, M., Moriarty, N. W., Liebschner, D., Afonine, P. V., Waterman, D. G., Evans, G., Wernet, P., Dobbek, H., Weis, W. I., Brunger, A. T., Zwart, P. H., Adams, P. D., Zouni, A., Messinger, J., Bergmann, U., Sauter, N. K., Kern, J., Yachandra, V. K., Yano, J. 2016; 540 (7633): 453-?

  Abstract

  Light-induced oxidation of water by photosystem II (PS II) in plants, algae and cyanobacteria has generated most of the dioxygen in the atmosphere. PS II, a membrane-bound multi-subunit pigment protein complex, couples the one-electron photochemistry at the reaction centre with the four-electron redox chemistry of water oxidation at the Mn4CaO5 cluster in the oxygen-evolving complex (OEC). Under illumination, the OEC cycles through five intermediate S-states (S0 to S4), in which S1 is the dark-stable state and S3 is the last semi-stable state before O-O bond formation and O2 evolution. A detailed understanding of the O-O bond formation mechanism remains a challenge, and will require elucidation of both the structures of the OEC in the different S-states and the binding of the two substrate waters to the catalytic site. Here we report the use of femtosecond pulses from an X-ray free electron laser (XFEL) to obtain damage-free, room temperature structures of dark-adapted (S1), two-flash illuminated (2F; S3-enriched), and ammonia-bound two-flash illuminated (2F-NH3; S3-enriched) PS II. Although the recent 1.95 Å resolution structure of PS II at cryogenic temperature using an XFEL provided a damage-free view of the S1 state, measurements at room temperature are required to study the structural landscape of proteins under functional conditions, and also for in situ advancement of the S-states. To investigate the water-binding site(s), ammonia, a water analogue, has been used as a marker, as it binds to the Mn4CaO5 cluster in the S2 and S3 states. Since the ammonia-bound OEC is active, the ammonia-binding Mn site is not a substrate water site. This approach, together with a comparison of the native dark and 2F states, is used to discriminate between proposed O-O bond formation mechanisms.

  View details for DOI 10.1038/nature20161

  View details for Web of Science ID 000389716800046

  View details for PubMedID 27871088

  View details for PubMedCentralID PMC5201176

• X-ray absorption spectroscopy using a self-seeded soft X-ray free-electron laser OPTICS EXPRESS Kroll, T., Kern, J., Kubin, M., Ratner, D., Gul, S., Fuller, F. D., Loechel, H., Krzywinski, J., Lutman, A., Ding, Y., Dakovski, G. L., Moeller, S., Turner, J. J., Alonso-Mori, R., Nordlund, D. L., Rehanek, J., Weniger, C., Firsov, A., Brzhezinskaya, M., Chatterjee, R., Lassalle-Kaiser, B., Sierra, R. G., Laksmono, H., Hill, E., Borovik, A., Erko, A., Foehlisch, A., Mitzner, R., Yachandra, V. K., Yano, J., Wernet, P., Bergmann, U. 2016; 24 (20): 22469-22480

  Abstract

  X-ray free electron lasers (XFELs) enable unprecedented new ways to study the electronic structure and dynamics of transition metal systems. L-edge absorption spectroscopy is a powerful technique for such studies and the feasibility of this method at XFELs for solutions and solids has been demonstrated. However, the required x-ray bandwidth is an order of magnitude narrower than that of self-amplified spontaneous emission (SASE), and additional monochromatization is needed. Here we compare L-edge x-ray absorption spectroscopy (XAS) of a prototypical transition metal system based on monochromatizing the SASE radiation of the linac coherent light source (LCLS) with a new technique based on self-seeding of LCLS. We demonstrate how L-edge XAS can be performed using the self-seeding scheme without the need of an additional beam line monochromator. We show how the spectral shape and pulse energy depend on the undulator setup and how this affects the x-ray spectroscopy measurements.

  View details for DOI 10.1364/OE.24.022469

  View details for Web of Science ID 000387543000016

  View details for PubMedID 27828320

  View details for PubMedCentralID PMC5234502

• Elemental characterisation of melanin in feathers via synchrotron X-ray imaging and absorption spectroscopy SCIENTIFIC REPORTS Edwards, N. P., van Veelen, A., Anne, J., Manning, P. L., Bergmann, U., Sellers, W. I., Egerton, V. M., Sokaras, D., Alonso-Mori, R., Wakamatsu, K., Ito, S., Wogelius, R. A. 2016; 6: 34002

  Abstract

  Melanin is a critical component of biological systems, but the exact chemistry of melanin is still imprecisely known. This is partly due to melanin's complex heterogeneous nature and partly because many studies use synthetic analogues and/or pigments extracted from their natural biological setting, which may display important differences from endogenous pigments. Here we demonstrate how synchrotron X-ray analyses can non-destructively characterise the elements associated with melanin pigment in situ within extant feathers. Elemental imaging shows that the distributions of Ca, Cu and Zn are almost exclusively controlled by melanin pigment distribution. X-ray absorption spectroscopy demonstrates that the atomic coordination of zinc and sulfur is different within eumelanised regions compared to pheomelanised regions. This not only impacts our fundamental understanding of pigmentation in extant organisms but also provides a significant contribution to the evidence-based colour palette available for reconstructing the appearance of fossil organisms.

  View details for DOI 10.1038/srep34002

  View details for Web of Science ID 000384068300001

  View details for PubMedID 27658854

  View details for PubMedCentralID PMC5034265

• No observable conformational changes in PSII NATURE Sauter, N. K., Echols, N., Adams, P. D., Zwart, P. H., Kern, J., Brewster, A. S., Koroidov, S., Alonso-Mori, R., Zouni, A., Messinger, J., Bergmann, U., Yano, J., Yachandra, V. K. 2016; 533 (7603): E1-E2

  View details for DOI 10.1038/nature17983

  View details for Web of Science ID 000376004300001

  View details for PubMedID 27193689

  View details for PubMedCentralID PMC6020672

• Acoustic Injectors for Drop-On-Demand Serial Femtosecond Crystallography STRUCTURE Roessler, C. G., Agarwal, R., Allaire, M., Alonso-Mori, R., Andi, B., Bachega, J. F., Bommer, M., Brewster, A. S., Browne, M. C., Chatterjee, R., Cho, E., Cohen, A. E., Cowan, M., Datwani, S., Davidson, V. L., Defever, J., Eaton, B., Ellson, R., Feng, Y., Ghislain, L. P., Glownia, J. M., Han, G., Hattne, J., Hellmich, J., Heroux, A., Ibrahim, M., Kern, J., Kuczewski, A., Lemke, H. T., Liu, P., Majlof, L., McClintock, W. M., Myers, S., Nelsen, S., Olechno, J., Orville, A. M., Sauter, N. K., Soares, A. S., Soltis, S. M., Song, H., Stearns, R. G., Tran, R., Tsai, Y., Uervirojnangkoorn, M., Wilmot, C. M., Yachandra, V., Yano, J., Yukl, E. T., Zhu, D., Zouni, A. 2016; 24 (4): 631-640

  Abstract

  X-ray free-electron lasers (XFELs) provide very intense X-ray pulses suitable for macromolecular crystallography. Each X-ray pulse typically lasts for tens of femtoseconds and the interval between pulses is many orders of magnitude longer. Here we describe two novel acoustic injection systems that use focused sound waves to eject picoliter to nanoliter crystal-containing droplets out of microplates and into the X-ray pulse from which diffraction data are collected. The on-demand droplet delivery is synchronized to the XFEL pulse scheme, resulting in X-ray pulses intersecting up to 88% of the droplets. We tested several types of samples in a range of crystallization conditions, wherein the overall crystal hit ratio (e.g., fraction of images with observable diffraction patterns) is a function of the microcrystal slurry concentration. We report crystal structures from lysozyme, thermolysin, and stachydrine demethylase (Stc2). Additional samples were screened to demonstrate that these methods can be applied to rare samples.

  View details for DOI 10.1016/j.str.2016.02.007

  View details for Web of Science ID 000373568700019

  View details for PubMedID 26996959

• High-density grids for efficient data collection from multiple crystals. Acta crystallographica. Section D, Structural biology Baxter, E. L., Aguila, L., Alonso-Mori, R., Barnes, C. O., Bonagura, C. A., Brehmer, W., Brunger, A. T., Calero, G., Caradoc-Davies, T. T., Chatterjee, R., DeGrado, W. F., Fraser, J. S., Ibrahim, M., Kern, J., Kobilka, B. K., Kruse, A. C., Larsson, K. M., Lemke, H. T., Lyubimov, A. Y., Manglik, A., McPhillips, S. E., Norgren, E., Pang, S. S., Soltis, S. M., Song, J., Thomaston, J., Tsai, Y., Weis, W. I., Woldeyes, R. A., Yachandra, V., Yano, J., Zouni, A., Cohen, A. E. 2016; 72: 2-11

  Abstract

  Higher throughput methods to mount and collect data from multiple small and radiation-sensitive crystals are important to support challenging structural investigations using microfocus synchrotron beamlines. Furthermore, efficient sample-delivery methods are essential to carry out productive femtosecond crystallography experiments at X-ray free-electron laser (XFEL) sources such as the Linac Coherent Light Source (LCLS). To address these needs, a high-density sample grid useful as a scaffold for both crystal growth and diffraction data collection has been developed and utilized for efficient goniometer-based sample delivery at synchrotron and XFEL sources. A single grid contains 75 mounting ports and fits inside an SSRL cassette or uni-puck storage container. The use of grids with an SSRL cassette expands the cassette capacity up to 7200 samples. Grids may also be covered with a polymer film or sleeve for efficient room-temperature data collection from multiple samples. New automated routines have been incorporated into the Blu-Ice/DCSS experimental control system to support grids, including semi-automated grid alignment, fully automated positioning of grid ports, rastering and automated data collection. Specialized tools have been developed to support crystallization experiments on grids, including a universal adaptor, which allows grids to be filled by commercial liquid-handling robots, as well as incubation chambers, which support vapor-diffusion and lipidic cubic phase crystallization experiments. Experiments in which crystals were loaded into grids or grown on grids using liquid-handling robots and incubation chambers are described. Crystals were screened at LCLS-XPP and SSRL BL12-2 at room temperature and cryogenic temperatures.

  View details for DOI 10.1107/S2059798315020847

  View details for PubMedID 26894529

  View details for PubMedCentralID PMC4756618

• Architecture of the synaptotagmin-SNARE machinery for neuronal exocytosis NATURE Zhou, Q., Lai, Y., Bacaj, T., Zhao, M., Lyubimov, A. Y., Uervirojnangkoorn, M., Zeldin, O. B., Brewster, A. S., Sauter, N. K., Cohen, A. E., Soltis, S. M., Alonso-Mori, R., Chollet, M., Lemke, H. T., Pfuetzner, R. A., Choi, U. B., Weis, W. I., Diao, J., Suedhof, T. C., Brunger, A. T. 2015; 525 (7567): 62-?

  Abstract

  Synaptotagmin-1 and neuronal SNARE proteins have central roles in evoked synchronous neurotransmitter release; however, it is unknown how they cooperate to trigger synaptic vesicle fusion. Here we report atomic-resolution crystal structures of Ca(2+)- and Mg(2+)-bound complexes between synaptotagmin-1 and the neuronal SNARE complex, one of which was determined with diffraction data from an X-ray free-electron laser, leading to an atomic-resolution structure with accurate rotamer assignments for many side chains. The structures reveal several interfaces, including a large, specific, Ca(2+)-independent and conserved interface. Tests of this interface by mutagenesis suggest that it is essential for Ca(2+)-triggered neurotransmitter release in mouse hippocampal neuronal synapses and for Ca(2+)-triggered vesicle fusion in a reconstituted system. We propose that this interface forms before Ca(2+) triggering, moves en bloc as Ca(2+) influx promotes the interactions between synaptotagmin-1 and the plasma membrane, and consequently remodels the membrane to promote fusion, possibly in conjunction with other interfaces.

  View details for DOI 10.1038/nature14975

  View details for Web of Science ID 000360594100025

• Goniometer-based femtosecond X-ray diffraction of mutant 30S ribosomal subunit crystals STRUCTURAL DYNAMICS Dao, E. H., Sierra, R. G., Laksmono, H., Lemke, H. T., Alonso-Mori, R., Coey, A., Larsen, K., Baxter, E. L., Cohen, A. E., Soltis, S. M., DeMirci, H. 2015; 2 (4)

  Abstract

  In this work, we collected radiation-damage-free data from a set of cryo-cooled crystals for a novel 30S ribosomal subunit mutant using goniometer-based femtosecond crystallography. Crystal quality assessment for these samples was conducted at the X-ray Pump Probe end-station of the Linac Coherent Light Source (LCLS) using recently introduced goniometer-based instrumentation. These 30S subunit crystals were genetically engineered to omit a 26-residue protein, Thx, which is present in the wild-type Thermus thermophilus 30S ribosomal subunit. We are primarily interested in elucidating the contribution of this ribosomal protein to the overall 30S subunit structure. To assess the viability of this study, femtosecond X-ray diffraction patterns from these crystals were recorded at the LCLS during a protein crystal screening beam time. During our data collection, we successfully observed diffraction from these difficult-to-grow 30S ribosomal subunit crystals. Most of our crystals were found to diffract to low resolution, while one crystal diffracted to 3.2 Å resolution. These data suggest the feasibility of pursuing high-resolution data collection as well as the need to improve sample preparation and handling in order to collect a complete radiation-damage-free data set using an X-ray Free Electron Laser.

  View details for DOI 10.1063/1.4919407

  View details for Web of Science ID 000360649200008

  View details for PubMedCentralID PMC4711619

• Focus characterization at an X-ray free-electron laser by coherent scattering and speckle analysis JOURNAL OF SYNCHROTRON RADIATION Sikorski, M., Song, S., Schropp, A., Seiboth, F., Feng, Y., Alonso-Mori, R., Chollet, M., Lemke, H. T., Sokaras, D., Weng, T., Zhang, W., Robert, A., Zhu, D. 2015; 22: 599-605

  Abstract

  X-ray focus optimization and characterization based on coherent scattering and quantitative speckle size measurements was demonstrated at the Linac Coherent Light Source. Its performance as a single-pulse free-electron laser beam diagnostic was tested for two typical focusing configurations. The results derived from the speckle size/shape analysis show the effectiveness of this technique in finding the focus' location, size and shape. In addition, its single-pulse compatibility enables users to capture pulse-to-pulse fluctuations in focus properties compared with other techniques that require scanning and averaging.

  View details for DOI 10.1107/S1600577515004361

  View details for Web of Science ID 000353920300021

  View details for PubMedID 25931074

  View details for PubMedCentralID PMC4416675

• Photon-in photon-out hard X-ray spectroscopy at the Linac Coherent Light Source JOURNAL OF SYNCHROTRON RADIATION Alonso-Mori, R., Sokaras, D., Zhu, D., Kroll, T., Chollet, M., Feng, Y., Glownia, J. M., Kern, J., Lemke, H. T., Nordlund, D., Robert, A., Sikorski, M., Song, S., Weng, T., Bergmann, U. 2015; 22: 612-620

  Abstract

  X-ray free-electron lasers (FELs) have opened unprecedented possibilities to study the structure and dynamics of matter at an atomic level and ultra-fast timescale. Many of the techniques routinely used at storage ring facilities are being adapted for experiments conducted at FELs. In order to take full advantage of these new sources several challenges have to be overcome. They are related to the very different source characteristics and its resulting impact on sample delivery, X-ray optics, X-ray detection and data acquisition. Here it is described how photon-in photon-out hard X-ray spectroscopy techniques can be applied to study the electronic structure and its dynamics of transition metal systems with ultra-bright and ultra-short FEL X-ray pulses. In particular, some of the experimental details that are different compared with synchrotron-based setups are discussed and illustrated by recent measurements performed at the Linac Coherent Light Source.

  View details for DOI 10.1107/S1600577515004488

  View details for Web of Science ID 000353920300023

  View details for PubMedID 25931076

  View details for PubMedCentralID PMC4416677

• The mapping and differentiation of biological and environmental elemental signatures in the fossil remains of a 50 million year old bird JOURNAL OF ANALYTICAL ATOMIC SPECTROMETRY Egerton, V. M., Wogelius, R. A., Norell, M. A., Edwards, N. P., Sellers, W. I., Bergmann, U., Sokaras, D., Alonso-Mori, R., Ignatyev, K., van Veelen, A., Anne, J., van Dongen, B., Knoll, F., Manning, P. L. 2015; 30 (3): 627-634

  View details for DOI 10.1039/c4ja00395k

  View details for Web of Science ID 000350650800007

• Identification of Highly Active Fe Sites in (Ni,Fe)OOH for Electrocatalytic Water Splitting JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Friebel, D., Louie, M. W., Bajdich, M., Sanwald, K. E., Cai, Y., Wise, A. M., Cheng, M., Sokaras, D., Weng, T., Alonso-Mori, R., Davis, R. C., Bargar, J. R., Norskov, J. K., Nilsson, A., Bell, A. T. 2015; 137 (3): 1305-1313

  Abstract

  Highly active catalysts for the oxygen evolution reaction (OER) are required for the development of photoelectrochemical devices that generate hydrogen efficiently from water using solar energy. Here, we identify the origin of a 500-fold OER activity enhancement that can be achieved with mixed (Ni,Fe)oxyhydroxides (Ni(1-x)Fe(x)OOH) over their pure Ni and Fe parent compounds, resulting in one of the most active currently known OER catalysts in alkaline electrolyte. Operando X-ray absorption spectroscopy (XAS) using high energy resolution fluorescence detection (HERFD) reveals that Fe(3+) in Ni(1-x)Fe(x)OOH occupies octahedral sites with unusually short Fe-O bond distances, induced by edge-sharing with surrounding [NiO6] octahedra. Using computational methods, we establish that this structural motif results in near optimal adsorption energies of OER intermediates and low overpotentials at Fe sites. By contrast, Ni sites in Ni(1-x)Fe(x)OOH are not active sites for the oxidation of water.

  View details for DOI 10.1021/ja511559d

  View details for Web of Science ID 000348690100042

  View details for PubMedID 25562406

• Simultaneous detection of electronic structure changes from two elements of a bifunctional catalyst using wavelength-dispersive X-ray emission spectroscopy and in situ electrochemistry PHYSICAL CHEMISTRY CHEMICAL PHYSICS Gul, S., Ng, J. W., Alonso-Mori, R., Kern, J., Sokaras, D., Anzenberg, E., Lassalle-Kaiser, B., Gorlin, Y., Weng, T., Zwart, P. H., Zhang, J. Z., Bergmann, U., Yachandra, V. K., Jaramillo, T. F., Yano, J. 2015; 17 (14): 8901-8912

  Abstract

  Multielectron catalytic reactions, such as water oxidation, nitrogen reduction, or hydrogen production in enzymes and inorganic catalysts often involve multimetallic clusters. In these systems, the reaction takes place between metals or metals and ligands to facilitate charge transfer, bond formation/breaking, substrate binding, and release of products. In this study, we present a method to detect X-ray emission signals from multiple elements simultaneously, which allows for the study of charge transfer and the sequential chemistry occurring between elements. Kβ X-ray emission spectroscopy (XES) probes charge and spin states of metals as well as their ligand environment. A wavelength-dispersive spectrometer based on the von Hamos geometry was used to disperse Kβ signals of multiple elements onto a position detector, enabling an XES spectrum to be measured in a single-shot mode. This overcomes the scanning needs of the scanning spectrometers, providing data free from temporal and normalization errors and therefore ideal to follow sequential chemistry at multiple sites. We have applied this method to study MnOx-based bifunctional electrocatalysts for the oxygen evolution reaction (OER) and the oxygen reduction reaction (ORR). In particular, we investigated the effects of adding a secondary element, Ni, to form MnNiOx and its impact on the chemical states and catalytic activity, by tracking the redox characteristics of each element upon sweeping the electrode potential. The detection scheme we describe here is general and can be applied to time-resolved studies of materials consisting of multiple elements, to follow the dynamics of catalytic and electron transfer reactions.

  View details for DOI 10.1039/c5cp01023c

  View details for Web of Science ID 000351933600043

  View details for PubMedID 25747045

• Mapping the conformational landscape of a dynamic enzyme by multitemperature and XFEL crystallography. eLife Keedy, D. A., Kenner, L. R., Warkentin, M., Woldeyes, R. A., Hopkins, J. B., Thompson, M. C., Brewster, A. S., Van Benschoten, A. H., Baxter, E. L., Uervirojnangkoorn, M., McPhillips, S. E., Song, J., Alonso-Mori, R., Holton, J. M., Weis, W. I., Brunger, A. T., Soltis, S. M., Lemke, H., Gonzalez, A., Sauter, N. K., Cohen, A. E., van den Bedem, H., Thorne, R. E., Fraser, J. S. 2015; 4

  Abstract

  Determining the interconverting conformations of dynamic proteins in atomic detail is a major challenge for structural biology. Conformational heterogeneity in the active site of the dynamic enzyme cyclophilin A (CypA) has been previously linked to its catalytic function, but the extent to which the different conformations of these residues are correlated is unclear. Here we compare the conformational ensembles of CypA by multitemperature synchrotron crystallography and fixed-target X-ray free-electron laser (XFEL) crystallography. The diffraction-before-destruction nature of XFEL experiments provides a radiation-damage-free view of the functionally important alternative conformations of CypA, confirming earlier synchrotron-based results. We monitored the temperature dependences of these alternative conformations with eight synchrotron datasets spanning 100-310 K. Multiconformer models show that many alternative conformations in CypA are populated only at 240 K and above, yet others remain populated or become populated at 180 K and below. These results point to a complex evolution of conformational heterogeneity between 180--240 K that involves both thermal deactivation and solvent-driven arrest of protein motions in the crystal. The lack of a single shared conformational response to temperature within the dynamic active-site network provides evidence for a conformation shuffling model, in which exchange between rotamer states of a large aromatic ring in the middle of the network shifts the conformational ensemble for the other residues in the network. Together, our multitemperature analyses and XFEL data motivate a new generation of temperature- and time-resolved experiments to structurally characterize the dynamic underpinnings of protein function.

  View details for DOI 10.7554/eLife.07574

  View details for PubMedID 26422513

  View details for PubMedCentralID PMC4721965

• Resonant Inelastic X-ray Scattering on Ferrous and Ferric Bis-imidazole Porphyrin and Cytochrome c: Nature and Role of the Axial Methionine-Fe Bond. Journal of the American Chemical Society Kroll, T., Hadt, R. G., Wilson, S. A., Lundberg, M., Yan, J. J., Weng, T., Sokaras, D., Alonso-Mori, R., Casa, D., Upton, M. H., Hedman, B., Hodgson, K. O., Solomon, E. I. 2014; 136 (52): 18087-18099

  Abstract

  Axial Cu-S(Met) bonds in electron transfer (ET) active sites are generally found to lower their reduction potentials. An axial S(Met) bond is also present in cytochrome c (cyt c) and is generally thought to increase the reduction potential. The highly covalent nature of the porphyrin environment in heme proteins precludes using many spectroscopic approaches to directly study the Fe site to experimentally quantify this bond. Alternatively, L-edge X-ray absorption spectroscopy (XAS) enables one to directly focus on the 3d-orbitals in a highly covalent environment and has previously been successfully applied to porphyrin model complexes. However, this technique cannot be extended to metalloproteins in solution. Here, we use metal K-edge XAS to obtain L-edge like data through 1s2p resonance inelastic X-ray scattering (RIXS). It has been applied here to a bis-imidazole porphyrin model complex and cyt c. The RIXS data on the model complex are directly correlated to L-edge XAS data to develop the complementary nature of these two spectroscopic methods. Comparison between the bis-imidazole model complex and cyt c in ferrous and ferric oxidation states show quantitative differences that reflect differences in axial ligand covalency. The data reveal an increased covalency for the S(Met) relative to N(His) axial ligand and a higher degree of covalency for the ferric states relative to the ferrous states. These results are reproduced by DFT calculations, which are used to evaluate the thermodynamics of the Fe-S(Met) bond and its dependence on redox state. These results provide insight into a number of previous chemical and physical results on cyt c.

  View details for DOI 10.1021/ja5100367

  View details for PubMedID 25475739

  View details for PubMedCentralID PMC4291809

• Goniometer-based femtosecond crystallography with X-ray free electron lasers PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Cohen, A. E., Soltis, S. M., Gonzalez, A., Aguila, L., Alonso-Mori, R., Barnes, C. O., Baxter, E. L., Brehmer, W., Brewster, A. S., Brunger, A. T., Calero, G., Chang, J. F., Chollet, M., Ehrensberger, P., Eriksson, T. L., Feng, Y., Hattne, J., Hedman, B., Hollenbeck, M., Holton, J. M., Keable, S., Kobilka, B. K., Kovaleva, E. G., Kruse, A. C., Lemke, H. T., Lin, G., Lyubimov, A. Y., Manglik, A., Mathews, I. I., McPhillips, S. E., Nelson, S., Peters, J. W., Sauter, N. K., Smith, C. A., Song, J., Stevenson, H. P., Tsai, Y., Uervirojnangkoorn, M., Vinetsky, V., Wakatsuki, S., Weis, W. I., Zadvornyy, O. A., Zeldin, O. B., Zhu, D., Hodgson, K. O. 2014; 111 (48): 17122-17127

  Abstract

  The emerging method of femtosecond crystallography (FX) may extend the diffraction resolution accessible from small radiation-sensitive crystals and provides a means to determine catalytically accurate structures of acutely radiation-sensitive metalloenzymes. Automated goniometer-based instrumentation developed for use at the Linac Coherent Light Source enabled efficient and flexible FX experiments to be performed on a variety of sample types. In the case of rod-shaped Cpl hydrogenase crystals, only five crystals and about 30 min of beam time were used to obtain the 125 still diffraction patterns used to produce a 1.6-Å resolution electron density map. For smaller crystals, high-density grids were used to increase sample throughput; 930 myoglobin crystals mounted at random orientation inside 32 grids were exposed, demonstrating the utility of this approach. Screening results from cryocooled crystals of β2-adrenoreceptor and an RNA polymerase II complex indicate the potential to extend the diffraction resolution obtainable from very radiation-sensitive samples beyond that possible with undulator-based synchrotron sources.

  View details for DOI 10.1073/pnas.1418733111

  View details for Web of Science ID 000345920800042

  View details for PubMedID 25362050

  View details for PubMedCentralID PMC4260607

• Methods development for diffraction and spectroscopy studies of metalloenzymes at X-ray free-electron lasers PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES Kern, J., Hattne, J., Rosalie Tran, R., Alonso-Mori, R., Laksmono, H., Gul, S., Sierra, R. G., Rehanek, J., Erko, A., Mitzner, R., Wernet, P., Bergmann, U., Sauter, N. K., Yachandra, V., Yano, J. 2014; 369 (1647)

  Abstract

  X-ray free-electron lasers (XFELs) open up new possibilities for X-ray crystallographic and spectroscopic studies of radiation-sensitive biological samples under close to physiological conditions. To facilitate these new X-ray sources, tailored experimental methods and data-processing protocols have to be developed. The highly radiation-sensitive photosystem II (PSII) protein complex is a prime target for XFEL experiments aiming to study the mechanism of light-induced water oxidation taking place at a Mn cluster in this complex. We developed a set of tools for the study of PSII at XFELs, including a new liquid jet based on electrofocusing, an energy dispersive von Hamos X-ray emission spectrometer for the hard X-ray range and a high-throughput soft X-ray spectrometer based on a reflection zone plate. While our immediate focus is on PSII, the methods we describe here are applicable to a wide range of metalloenzymes. These experimental developments were complemented by a new software suite, cctbx.xfel. This software suite allows for near-real-time monitoring of the experimental parameters and detector signals and the detailed analysis of the diffraction and spectroscopy data collected by us at the Linac Coherent Light Source, taking into account the specific characteristics of data measured at an XFEL.

  View details for DOI 10.1098/rstb.2013.0590

  View details for Web of Science ID 000337367600026

  View details for PubMedCentralID PMC4052878

• Synchrotron imaging reveals bone healing and remodelling strategies in extinct and extant vertebrates JOURNAL OF THE ROYAL SOCIETY INTERFACE Anne, J., Edwards, N. P., Wogelius, R. A., Tumarkin-Deratzian, A. R., Sellers, W. I., van Veelen, A., Bergmann, U., Sokaras, D., Alonso-Mori, R., Ignatyev, K., Egerton, V. M., Manning, P. L. 2014; 11 (96): 20140277

  Abstract

  Current understanding of bone healing and remodelling strategies in vertebrates has traditionally relied on morphological observations through the histological analysis of thin sections. However, chemical analysis may also be used in such interpretations, as different elements are known to be absorbed and used by bone for different physiological purposes such as growth and healing. These chemical signatures are beyond the detection limit of most laboratory-based analytical techniques (e.g. scanning electron microscopy). However, synchrotron rapid scanning-X-ray fluorescence (SRS-XRF) is an elemental mapping technique that uniquely combines high sensitivity (ppm), excellent sample resolution (20-100 µm) and the ability to scan large specimens (decimetre scale) approximately 3000 times faster than other mapping techniques. Here, we use SRS-XRF combined with microfocus elemental mapping (2-20 µm) to determine the distribution and concentration of trace elements within pathological and normal bone of both extant and extinct archosaurs (Cathartes aura and Allosaurus fragilis). Results reveal discrete chemical inventories within different bone tissue types and preservation modes. Chemical inventories also revealed detail of histological features not observable in thin section, including fine structures within the interface between pathological and normal bone as well as woven texture within pathological tissue.

  View details for DOI 10.1098/rsif.2014.0277

  View details for Web of Science ID 000336159200018

  View details for PubMedID 24806709

  View details for PubMedCentralID PMC4032541

• Tracking excited-state charge and spin dynamics in iron coordination complexes. Nature Zhang, W., Alonso-Mori, R., Bergmann, U., Bressler, C., Chollet, M., Galler, A., Gawelda, W., Hadt, R. G., Hartsock, R. W., Kroll, T., Kjær, K. S., Kubicek, K., Lemke, H. T., Liang, H. W., Meyer, D. A., Nielsen, M. M., Purser, C., Robinson, J. S., Solomon, E. I., Sun, Z., Sokaras, D., van Driel, T. B., Vankó, G., Weng, T., Zhu, D., Gaffney, K. J. 2014; 509 (7500): 345-348

  Abstract

  Crucial to many light-driven processes in transition metal complexes is the absorption and dissipation of energy by 3d electrons. But a detailed understanding of such non-equilibrium excited-state dynamics and their interplay with structural changes is challenging: a multitude of excited states and possible transitions result in phenomena too complex to unravel when faced with the indirect sensitivity of optical spectroscopy to spin dynamics and the flux limitations of ultrafast X-ray sources. Such a situation exists for archetypal polypyridyl iron complexes, such as [Fe(2,2'-bipyridine)3](2+), where the excited-state charge and spin dynamics involved in the transition from a low- to a high-spin state (spin crossover) have long been a source of interest and controversy. Here we demonstrate that femtosecond resolution X-ray fluorescence spectroscopy, with its sensitivity to spin state, can elucidate the spin crossover dynamics of [Fe(2,2'-bipyridine)3](2+) on photoinduced metal-to-ligand charge transfer excitation. We are able to track the charge and spin dynamics, and establish the critical role of intermediate spin states in the crossover mechanism. We anticipate that these capabilities will make our method a valuable tool for mapping in unprecedented detail the fundamental electronic excited-state dynamics that underpin many useful light-triggered molecular phenomena involving 3d transition metal complexes.

  View details for DOI 10.1038/nature13252

  View details for PubMedID 24805234

• Tracking excited-state charge and spin dynamics in iron coordination complexes. Nature Zhang, W., Alonso-Mori, R., Bergmann, U., Bressler, C., Chollet, M., Galler, A., Gawelda, W., Hadt, R. G., Hartsock, R. W., Kroll, T., Kjær, K. S., Kubicek, K., Lemke, H. T., Liang, H. W., Meyer, D. A., Nielsen, M. M., Purser, C., Robinson, J. S., Solomon, E. I., Sun, Z., Sokaras, D., van Driel, T. B., Vankó, G., Weng, T., Zhu, D., Gaffney, K. J. 2014; 509 (7500): 345-348

  Abstract

  Crucial to many light-driven processes in transition metal complexes is the absorption and dissipation of energy by 3d electrons. But a detailed understanding of such non-equilibrium excited-state dynamics and their interplay with structural changes is challenging: a multitude of excited states and possible transitions result in phenomena too complex to unravel when faced with the indirect sensitivity of optical spectroscopy to spin dynamics and the flux limitations of ultrafast X-ray sources. Such a situation exists for archetypal polypyridyl iron complexes, such as [Fe(2,2'-bipyridine)3](2+), where the excited-state charge and spin dynamics involved in the transition from a low- to a high-spin state (spin crossover) have long been a source of interest and controversy. Here we demonstrate that femtosecond resolution X-ray fluorescence spectroscopy, with its sensitivity to spin state, can elucidate the spin crossover dynamics of [Fe(2,2'-bipyridine)3](2+) on photoinduced metal-to-ligand charge transfer excitation. We are able to track the charge and spin dynamics, and establish the critical role of intermediate spin states in the crossover mechanism. We anticipate that these capabilities will make our method a valuable tool for mapping in unprecedented detail the fundamental electronic excited-state dynamics that underpin many useful light-triggered molecular phenomena involving 3d transition metal complexes.

  View details for DOI 10.1038/nature13252

  View details for PubMedID 24805234

• Accurate macromolecular structures using minimal measurements from X-ray free-electron lasers NATURE METHODS Hattne, J., Echols, N., Rosalie Tran, R., Kern, J., Gildea, R. J., Brewster, A. S., Alonso-Mori, R., Gloeckner, C., Hellmich, J., Laksmono, H., Sierra, R. G., Lassalle-Kaiser, B., Lampe, A., Han, G., Gul, S., DiFiore, D., Milathianaki, D., Fry, A. R., Miahnahri, A., White, W. E., Schafer, D. W., Seibert, M. M., Koglin, J. E., Sokaras, D., Weng, T., Sellberg, J., Latimers, M. J., Glatzel, P., Zwart, P. H., Grosse-Kunstleve, R. W., Bogan, M. J., Messerschmidt, M., Williams, G. J., Boutet, S., Messinger, J., Zouni, A., Yano, J., Bergmann, U., Yachandra, V. K., Adams, P. D., Sauter, N. K. 2014; 11 (5): 545-548

  Abstract

  X-ray free-electron laser (XFEL) sources enable the use of crystallography to solve three-dimensional macromolecular structures under native conditions and without radiation damage. Results to date, however, have been limited by the challenge of deriving accurate Bragg intensities from a heterogeneous population of microcrystals, while at the same time modeling the X-ray spectrum and detector geometry. Here we present a computational approach designed to extract meaningful high-resolution signals from fewer diffraction measurements.

  View details for DOI 10.1038/NMETH.2887

  View details for Web of Science ID 000335873400020

  View details for PubMedID 24633409

  View details for PubMedCentralID PMC4008696

• Structure, Redox Chemistry, and Interfacial Alloy Formation in Monolayer and Multilayer Cu/Au(111) Model Catalysts for CO2 Electroreduction JOURNAL OF PHYSICAL CHEMISTRY C Friebel, D., Mbuga, F., Rajasekaran, S., Miller, D. J., Ogasawara, H., Alonso-Mori, R., Sokaras, D., Nordlund, D., Weng, T., Nilsson, A. 2014; 118 (15): 7954-7961

  View details for DOI 10.1021/jp412000j

  View details for Web of Science ID 000334730300023

• L-Edge X-ray Absorption Spectroscopy of Dilute Systems Relevant to Metalloproteins Using an X-ray Free-Electron Laser JOURNAL OF PHYSICAL CHEMISTRY LETTERS Mitzner, R., Rehanek, J., Kern, J., Gul, S., Hattne, J., Taguchi, T., Alonso-Mori, R., Tran, R., Weniger, C., Schroeder, H., Quevedo, W., Laksmono, H., Sierra, R. G., Han, G., Lassalle-Kaiser, B., Koroidov, S., Kubicek, K., Schreck, S., Kunnus, K., Brzhezinskaya, M., Firsov, A., Minitti, M. P., Turner, J. J., Moeller, S., Sauter, N. K., Bogan, M. J., Nordlund, D., Schlotter, W. F., Messinger, J., Borovik, A., Techert, S., de Groot, F. M., Foehlisch, A., Erko, A., Bergmann, U., Yachandra, V. K., Wernet, P., Yano, J. 2013; 4 (21): 3641-3647

  Abstract

  L-edge spectroscopy of 3d transition metals provides important electronic structure information and has been used in many fields. However, the use of this method for studying dilute aqueous systems, such as metalloenzymes, has not been prevalent because of severe radiation damage and the lack of suitable detection systems. Here we present spectra from a dilute Mn aqueous solution using a high-transmission zone-plate spectrometer at the Linac Coherent Light Source (LCLS). The spectrometer has been optimized for discriminating the Mn L-edge signal from the overwhelming O K-edge background that arises from water and protein itself, and the ultrashort LCLS X-ray pulses can outrun X-ray induced damage. We show that the deviations of the partial-fluorescence yield-detected spectra from the true absorption can be well modeled using the state-dependence of the fluorescence yield, and discuss implications for the application of our concept to biological samples.

  View details for DOI 10.1021/jz401837f

  View details for Web of Science ID 000326845200010

  View details for PubMedCentralID PMC3901369

• On the chemical state of Co oxide electrocatalysts during alkaline water splitting. Physical chemistry chemical physics Friebel, D., Bajdich, M., Yeo, B. S., Louie, M. W., Miller, D. J., Sanchez Casalongue, H., Mbuga, F., Weng, T., Nordlund, D., Sokaras, D., Alonso-Mori, R., Bell, A. T., Nilsson, A. 2013; 15 (40): 17460-17467

  Abstract

  Resonant inelastic X-ray scattering and high-resolution X-ray absorption spectroscopy were used to identify the chemical state of a Co electrocatalyst in situ during the oxygen evolution reaction. After anodic electrodeposition onto Au(111) from a Co(2+)-containing electrolyte, the chemical environment of Co can be identified to be almost identical to CoOOH. With increasing potentials, a subtle increase of the Co oxidation state is observed, indicating a non-stoichiometric composition of the working OER catalyst containing a small fraction of Co(4+) sites. In order to confirm this interpretation, we used density functional theory with a Hubbard-U correction approach to compute X-ray absorption spectra of model compounds, which agree well with the experimental spectra. In situ monitoring of catalyst local structure and bonding is essential in the development of structure-activity relationships that can guide the discovery of efficient and earth abundant water splitting catalysts.

  View details for DOI 10.1039/c3cp52981a

  View details for PubMedID 24026021

• A seven-crystal Johann-type hard x-ray spectrometer at the Stanford Synchrotron Radiation Lightsource REVIEW OF SCIENTIFIC INSTRUMENTS Sokaras, D., Weng, T., Nordlund, D., Alonso-Mori, R., Velikov, P., Wenger, D., Garachtchenko, A., George, M., Borzenets, V., Johnson, B., Rabedeau, T., Bergmann, U. 2013; 84 (5): 053102

  Abstract

  We present a multicrystal Johann-type hard x-ray spectrometer (~5-18 keV) recently developed, installed, and operated at the Stanford Synchrotron Radiation Lightsource. The instrument is set at the wiggler beamline 6-2 equipped with two liquid nitrogen cooled monochromators--Si(111) and Si(311)--as well as collimating and focusing optics. The spectrometer consists of seven spherically bent crystal analyzers placed on intersecting vertical Rowland circles of 1 m of diameter. The spectrometer is scanned vertically capturing an extended backscattering Bragg angular range (88°-74°) while maintaining all crystals on the Rowland circle trace. The instrument operates in atmospheric pressure by means of a helium bag and when all the seven crystals are used (100 mm of projected diameter each), has a solid angle of about 0.45% of 4π sr. The typical resolving power is in the order of E/ΔE ~ 10,000. The spectrometer's high detection efficiency combined with the beamline 6-2 characteristics permits routine studies of x-ray emission, high energy resolution fluorescence detected x-ray absorption and resonant inelastic x-ray scattering of very diluted samples as well as implementation of demanding in situ environments.

  View details for DOI 10.1063/1.4803669

  View details for Web of Science ID 000319999300003

  View details for PubMedID 23742527

  View details for PubMedCentralID PMC4108715

• Simultaneous Femtosecond X-ray Spectroscopy and Diffraction of Photosystem II at Room Temperature SCIENCE Kern, J., Alonso-Mori, R., Tran, R., Hattne, J., Gildea, R. J., Echols, N., Gloeckner, C., Hellmich, J., Laksmono, H., Sierra, R. G., Lassalle-Kaiser, B., Koroidov, S., Lampe, A., Han, G., Gul, S., DiFiore, D., Milathianaki, D., Fry, A. R., Miahnahri, A., Schafer, D. W., Messerschmidt, M., Seibert, M. M., Koglin, J. E., Sokaras, D., Weng, T., Sellberg, J., Latimer, M. J., Grosse-Kunstleve, R. W., Zwart, P. H., White, W. E., Glatzel, P., Adams, P. D., Bogan, M. J., Williams, G. J., Boutet, S., Messinger, J., Zouni, A., Sauter, N. K., Yachandra, V. K., Bergmann, U., Yano, J. 2013; 340 (6131): 491-495

  Abstract

  Intense femtosecond x-ray pulses produced at the Linac Coherent Light Source (LCLS) were used for simultaneous x-ray diffraction (XRD) and x-ray emission spectroscopy (XES) of microcrystals of photosystem II (PS II) at room temperature. This method probes the overall protein structure and the electronic structure of the Mn4CaO5 cluster in the oxygen-evolving complex of PS II. XRD data are presented from both the dark state (S1) and the first illuminated state (S2) of PS II. Our simultaneous XRD-XES study shows that the PS II crystals are intact during our measurements at the LCLS, not only with respect to the structure of PS II, but also with regard to the electronic structure of the highly radiation-sensitive Mn4CaO5 cluster, opening new directions for future dynamics studies.

  View details for DOI 10.1126/science.1234273

  View details for Web of Science ID 000318016700046

  View details for PubMedID 23413188

• Energy-dispersive X-ray emission spectroscopy using an X-ray free-electron laser in a shot-by-shot mode PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Alonso-Mori, R., Kern, J., Gildea, R. J., Sokaras, D., Weng, T., Lassalle-Kaiser, B., Rosalie Tran, R., Hattne, J., Laksmono, H., Hellmich, J., Gloeckner, C., Echols, N., Sierra, R. G., Schafer, D. W., Sellberg, J., Kenney, C., Herbst, R., Pines, J., Hart, P., Herrmann, S., Grosse-Kunstleve, R. W., Latimer, M. J., Fry, A. R., Messerschmidt, M. M., Miahnahri, A., Seibert, M. M., Zwart, P. H., White, W. E., Adams, P. D., Bogan, M. J., Boutet, S., Williams, G. J., Zouni, A., Messinger, J., Glatzel, P., Sauter, N. K., Yachandra, V. K., Yano, J., Bergmann, U. 2012; 109 (47): 19103-19107

  Abstract

  The ultrabright femtosecond X-ray pulses provided by X-ray free-electron lasers open capabilities for studying the structure and dynamics of a wide variety of systems beyond what is possible with synchrotron sources. Recently, this "probe-before-destroy" approach has been demonstrated for atomic structure determination by serial X-ray diffraction of microcrystals. There has been the question whether a similar approach can be extended to probe the local electronic structure by X-ray spectroscopy. To address this, we have carried out femtosecond X-ray emission spectroscopy (XES) at the Linac Coherent Light Source using redox-active Mn complexes. XES probes the charge and spin states as well as the ligand environment, critical for understanding the functional role of redox-active metal sites. Kβ(1,3) XES spectra of Mn(II) and Mn(2)(III,IV) complexes at room temperature were collected using a wavelength dispersive spectrometer and femtosecond X-ray pulses with an individual dose of up to >100 MGy. The spectra were found in agreement with undamaged spectra collected at low dose using synchrotron radiation. Our results demonstrate that the intact electronic structure of redox active transition metal compounds in different oxidation states can be characterized with this shot-by-shot method. This opens the door for studying the chemical dynamics of metal catalytic sites by following reactions under functional conditions. The technique can be combined with X-ray diffraction to simultaneously obtain the geometric structure of the overall protein and the local chemistry of active metal sites and is expected to prove valuable for understanding the mechanism of important metalloproteins, such as photosystem II.

  View details for DOI 10.1073/pnas.1211384109

  View details for Web of Science ID 000311997200025

  View details for PubMedID 23129631

  View details for PubMedCentralID PMC3511075

• Nanoflow electrospinning serial femtosecond crystallography ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY Sierra, R. G., Laksmono, H., Kern, J., Rosalie Tran, R., Hattne, J., Alonso-Mori, R., Lassalle-Kaiser, B., Gloeckner, C., Hellmich, J., Schafer, D. W., Echols, N., Gildea, R. J., Grosse-Kunstleve, R. W., Sellberg, J., McQueen, T. A., Fry, A. R., Messerschmidt, M. M., Miahnahri, A., Seibert, M. M., Hampton, C. Y., Starodub, D., Loh, N. D., Sokaras, D., Weng, T., Zwart, P. H., Glatzel, P., Milathianaki, D., White, W. E., Adams, P. D., Williams, G. J., Boutet, S., Zouni, A., Messinger, J., Sauter, N. K., Bergmann, U., Yano, J., Yachandra, V. K., Bogan, M. J. 2012; 68: 1584-1587

  Abstract

  An electrospun liquid microjet has been developed that delivers protein microcrystal suspensions at flow rates of 0.14-3.1 µl min(-1) to perform serial femtosecond crystallography (SFX) studies with X-ray lasers. Thermolysin microcrystals flowed at 0.17 µl min(-1) and diffracted to beyond 4 Å resolution, producing 14,000 indexable diffraction patterns, or four per second, from 140 µg of protein. Nanoflow electrospinning extends SFX to biological samples that necessitate minimal sample consumption.

  View details for DOI 10.1107/S0907444912038152

  View details for Web of Science ID 000310069500017

  View details for PubMedID 23090408

  View details for PubMedCentralID PMC3478121

• Electrochemical Oxidation of Size-Selected Pt Nanoparticles Studied Using in Situ High-Energy-Resolution X-ray Absorption Spectroscopy ACS CATALYSIS Merte, L. R., Behafarid, F., Miller, D. J., Friebel, D., Cho, S., Mbuga, F., Sokaras, D., Alonso-Mori, R., Weng, T., Nordlund, D., Nilsson, A., Cuenya, B. R. 2012; 2 (11): 2371-2376

  View details for DOI 10.1021/cs300494f

  View details for Web of Science ID 000310723900018

• A multi-crystal wavelength dispersive x-ray spectrometer REVIEW OF SCIENTIFIC INSTRUMENTS Alonso-Mori, R., Kern, J., Sokaras, D., Weng, T., Nordlund, D., Tran, R., Montanez, P., Delor, J., Yachandra, V. K., Yano, J., Bergmann, U. 2012; 83 (7): 073114

  Abstract

  A multi-crystal wavelength dispersive hard x-ray spectrometer with high-energy resolution and large solid angle collection is described. The instrument is specifically designed for time-resolved applications of x-ray emission spectroscopy (XES) and x-ray Raman scattering (XRS) at X-ray Free Electron Lasers (XFEL) and synchrotron radiation facilities. It also simplifies resonant inelastic x-ray scattering (RIXS) studies of the whole 2d RIXS plane. The spectrometer is based on the Von Hamos geometry. This dispersive setup enables an XES or XRS spectrum to be measured in a single-shot mode, overcoming the scanning needs of the Rowland circle spectrometers. In conjunction with the XFEL temporal profile and high-flux, it is a powerful tool for studying the dynamics of time-dependent systems. Photo-induced processes and fast catalytic reaction kinetics, ranging from femtoseconds to milliseconds, will be resolvable in a wide array of systems circumventing radiation damage.

  View details for DOI 10.1063/1.4737630

  View details for Web of Science ID 000307527900015

  View details for PubMedID 22852678

  View details for PubMedCentralID PMC3422323

• Room temperature femtosecond X-ray diffraction of photosystem II microcrystals PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Kern, J., Alonso-Mori, R., Hellmich, J., Rosalie Tran, R., Hattne, J., Laksmono, H., Gloeckner, C., Echols, N., Sierra, R. G., Sellberg, J., Lassalle-Kaiser, B., Gildea, R. J., Glatzel, P., Grosse-Kunstleve, R. W., Latimer, M. J., McQueen, T. A., DiFiore, D., Fry, A. R., Messerschmidt, M., Miahnahri, A., Schafer, D. W., Seibert, M. M., Sokaras, D., Weng, T., Zwart, P. H., White, W. E., Adams, P. D., Bogan, M. J., Boutet, S., Williams, G. J., Messinger, J., Sauter, N. K., Zouni, A., Bergmann, U., Yano, J., Yachandra, V. K. 2012; 109 (25): 9721-9726

  Abstract

  Most of the dioxygen on earth is generated by the oxidation of water by photosystem II (PS II) using light from the sun. This light-driven, four-photon reaction is catalyzed by the Mn(4)CaO(5) cluster located at the lumenal side of PS II. Various X-ray studies have been carried out at cryogenic temperatures to understand the intermediate steps involved in the water oxidation mechanism. However, the necessity for collecting data at room temperature, especially for studying the transient steps during the O-O bond formation, requires the development of new methodologies. In this paper we report room temperature X-ray diffraction data of PS II microcrystals obtained using ultrashort (< 50 fs) 9 keV X-ray pulses from a hard X-ray free electron laser, namely the Linac Coherent Light Source. The results presented here demonstrate that the "probe before destroy" approach using an X-ray free electron laser works even for the highly-sensitive Mn(4)CaO(5) cluster in PS II at room temperature. We show that these data are comparable to those obtained in synchrotron radiation studies as seen by the similarities in the overall structure of the helices, the protein subunits and the location of the various cofactors. This work is, therefore, an important step toward future studies for resolving the structure of the Mn(4)CaO(5) cluster without any damage at room temperature, and of the reaction intermediates of PS II during O-O bond formation.

  View details for DOI 10.1073/pnas.1204598109

  View details for Web of Science ID 000306061400021

  View details for PubMedID 22665786

  View details for PubMedCentralID PMC3382516

• A high resolution and large solid angle x-ray Raman spectroscopy end-station at the Stanford Synchrotron Radiation Lightsource REVIEW OF SCIENTIFIC INSTRUMENTS Sokaras, D., Nordlund, D., Weng, T., Mori, R., Velikov, P., Wenger, D., Garachtchenko, A., George, M., Borzenets, V., Johnson, B., Qian, Q., Rabedeau, T., Bergmann, U. 2012; 83 (4): 043112

  Abstract

  We present a new x-ray Raman spectroscopy end-station recently developed, installed, and operated at the Stanford Synchrotron Radiation Lightsource. The end-station is located at wiggler beamline 6-2 equipped with two monochromators-Si(111) and Si(311) as well as collimating and focusing optics. It consists of two multi-crystal Johann type spectrometers arranged on intersecting Rowland circles of 1 m diameter. The first one, positioned at the forward scattering angles (low-q), consists of 40 spherically bent and diced Si(110) crystals with 100 mm diameters providing about 1.9% of 4π sr solid angle of detection. When operated in the (440) order in combination with the Si (311) monochromator, an overall energy resolution of 270 meV is obtained at 6462.20 eV. The second spectrometer, consisting of 14 spherically bent Si(110) crystal analyzers (not diced), is positioned at the backward scattering angles (high-q) enabling the study of non-dipole transitions. The solid angle of this spectrometer is about 0.9% of 4π sr, with a combined energy resolution of 600 meV using the Si (311) monochromator. These features exceed the specifications of currently existing relevant instrumentation, opening new opportunities for the routine application of this photon-in/photon-out hard x-ray technique to emerging research in multidisciplinary scientific fields, such as energy-related sciences, material sciences, physical chemistry, etc.

  View details for DOI 10.1063/1.4704458

  View details for Web of Science ID 000303415300013

  View details for PubMedID 22559520

  View details for PubMedCentralID PMC4108631

• Effect of alkalis on the Fe oxidation state and local environment in peralkaline rhyolitic glasses AMERICAN MINERALOGIST Giuli, G., Alonso-Mori, R., Cicconi, M., Paris, E., Glatzel, P., Eeckhout, S., Scaillet, B. 2012; 97 (2-3): 468-475

  View details for DOI 10.2138/am.2012.3888

  View details for Web of Science ID 000300209500024

• In situ X-ray Raman spectroscopy of LiBH4 PHYSICAL CHEMISTRY CHEMICAL PHYSICS Miedema, P. S., Ngene, P., van der Eerden, A. J., Weng, T., Nordlund, D., Sokaras, D., Alonso-Mori, R., Juhin, A., de Jongh, P. E., de Groot, F. F. 2012; 14 (16): 5581-5587

  Abstract

  X-Ray Raman Spectroscopy (XRS) is used to study the electronic properties of bulk lithium borohydride (LiBH(4)) and LiBH(4) in porous carbon nano-composites (LiBH(4)/C) during dehydrogenation. The lithium (Li), boron (B) and carbon (C) K-edges are studied and compared with calculations of the starting material and intermediate compounds. Comparison of the B and C K-edge XRS spectra of the as-prepared samples with rehydrogenated samples shows that the B and C electronic structure is largely regained after rehydrogenation. Both Li and C K-edge spectra show that during dehydrogenation, part of the Li intercalates into the porous carbon. This study shows that XRS in combination with calculations is a promising tool to study the electronic properties of nano-crystalline light-weight materials for energy storage.

  View details for DOI 10.1039/c2cp24025d

  View details for Web of Science ID 000302062200027

  View details for PubMedID 22428166

• Five-element Johann-type x-ray emission spectrometer with a single-photon-counting pixel detector REVIEW OF SCIENTIFIC INSTRUMENTS Kleymenov, E., van Bokhoven, J. A., David, C., Glatzel, P., Janousch, M., Alonso-Mori, R., Studer, M., Willimann, M., Bergamaschi, A., Henrich, B., Nachtegaal, M. 2011; 82 (6): 065107

  Abstract

  A Johann-type spectrometer with five spherically bent crystals and a pixel detector was constructed for a range of hard x-ray photon-in photon-out synchrotron techniques, covering a Bragg-angle range of 60°-88°. The spectrometer provides a sub emission line width energy resolution from sub-eV to a few eV and precise energy calibration, better than 1.5 eV for the full range of Bragg angles. The use of a pixel detector allows fast and easy optimization of the signal-to-background ratio. A concentration detection limit below 0.4 wt% was reached at the Cu Kα(1) line. The spectrometer is designed as a modular mobile device for easy integration in a multi-purpose hard x-ray synchrotron beamline, such as the SuperXAS beamline at the Swiss Light Source.

  View details for DOI 10.1063/1.3600452

  View details for Web of Science ID 000292334000064

  View details for PubMedID 21721730

• Sulfur-Metal Orbital Hybridization in Sulfur-Bearing Compounds Studied by X-ray Emission Spectroscopy INORGANIC CHEMISTRY Mori, R., Paris, E., Giuli, G., Eeckhout, S. G., Kavcic, M., Zitnik, M., Bucar, K., Pettersson, L. M., Glatzel, P. 2010; 49 (14): 6468-6473

  Abstract

  The electronic structure and ligand environment of sulfur was investigated in various sulfur-containing compounds with different structures and chemical states by using X-ray emission spectroscopy (XES). Calculations were performed using density functional theory (DFT) as implemented in the StoBe code. The sulfur chemical state and atomic environment is discussed in terms of the molecular orbitals and partial charges that are obtained from the calculations. The main spectral features can be modeled using our calculational approach. The sensitivity of the Kbeta emission to the cation and the local symmetry is discussed.

  View details for DOI 10.1021/ic100304z

  View details for Web of Science ID 000279621200032

  View details for PubMedID 20553025

• A multi-spectroscopic investigation of sulphur speciation in silicate glasses and slags GLASS TECHNOLOGY-EUROPEAN JOURNAL OF GLASS SCIENCE AND TECHNOLOGY PART A Bingham, P. A., Connelly, A. J., Hand, R. J., Hyatt, N. C., Northrup, P. A., Mori, R., Glatzel, P., Kavcic, M., Zitnik, M., Bucar, K., Edge, R. 2010; 51 (2): 63-80

  View details for Web of Science ID 000278869400003

• Electronic Structure of Sulfur Studied by X-ray Absorption and Emission Spectroscopy ANALYTICAL CHEMISTRY Mori, R., Paris, E., Giuli, G., Eeckhout, S. G., Kavcic, M., Zitnik, M., Bucar, K., Pettersson, L. M., Glatzel, P. 2009; 81 (15): 6516-6525

  View details for DOI 10.1021/ac900970z

  View details for Web of Science ID 000268455600071

• Separation of Two-Electron Photoexcited Atomic Processes near the Inner-Shell Threshold PHYSICAL REVIEW LETTERS Kavcic, M., Zitnik, M., Bucar, K., Mihelic, A., Stuhec, M., Szlachetko, J., Cao, W., Mori, R., Glatzel, P. 2009; 102 (14): 143001

  Abstract

  By means of a high resolution resonant inelastic x-ray scattering spectroscopy, we have for the first time separated spectral features pertaining to different two-electron atomic processes in the vicinity of an inner-shell threshold. Contributions of shakeoff, shakeup, and resonant 1s3p double excitations were extracted from the Ar KM-M{2,3}M x-ray satellite line intensity measured as a function of photon energy from [1s3p] double excitation threshold to saturation. The isolated [1s3p]nln'l' excitation spectrum is critically compared to the outcome of the multiconfiguration Dirac-Fock model with relaxation.

  View details for DOI 10.1103/PhysRevLett.102.143001

  View details for Web of Science ID 000265082500019

  View details for PubMedID 19392433

• Spatial correlation between Bi atoms in dilute GaAs(1-x)Bi(x): From random distribution to Bi pairing and clustering PHYSICAL REVIEW B Ciatto, G., Young, E. C., Glas, F., Chen, J., Mori, R., Tiedje, T. 2008; 78 (3)

  View details for DOI 10.1103/PhysRevB.78.035325

  View details for Web of Science ID 000258190300101

• Anions relative location in the group-V sublattice of GaAsSbN/GaAs epilayers: XAFS measurements and simulations PHYSICAL REVIEW B Ciatto, G., Harmand, J., Glas, F., Largeau, L., Le Du, M., Boscherini, F., Malvestuto, M., Floreano, L., Glatzel, P., Mori, R. 2007; 75 (24)

  View details for DOI 10.1103/PhysRevB.75.245212

  View details for Web of Science ID 000247625000065