Bio


I'm currently a Lead Scientist within the LCLS Chemical Sciences Department at SLAC and the Group Lead of the Biochemistry and Condensed Phase Chemistry Group composed of >10 scientists, RA’s and students. This group is responsible for experiments on ultrafast photochemical dynamics in condensed phase performed at multiple LCLS instruments. The aforementioned department and group's mission is to perform research and support and ensure the success of such experiments at LCLS by operating, maintaining and upgrading its instrumentation. This also involves supporting (including planning and performing) forefront experiments in ultrafast X-ray science using LCLS.

I joined SLAC in 2009 after obtaining my bachelor degree in Physics from the University of Oviedo in Spain followed by a Master of Science in Physics by the University of Grenoble in France and a PhD in Earth Science from the University of Camerino in Italy, both through research performed at the ESRF (European Synchrotron Radiation Facility) in Grenoble, France. I started my SLAC career as a Research Associate working at both SSRL and LCLS light sources and later held different positions at LCLS until my current role as a Lead Scientist and Group Lead.

Current Role at Stanford


Lead Scientist and Group Lead of the Biochemistry and Condensed Phase Chemistry Group within the Chemical Sciences Department at LCLS (SLAC National Accelerator Laboratory)

Professional Interests


I'm interested in the use of X-ray spectroscopy techniques for the study of the electronic structure in material science, chemical and biological systems. In particular on the development and application of time-resolved based techniques to a variety of projects in different areas of science including :

- the study of electronic and structural dynamics of geochemical systems at high P/T condition at the MEC instrument of LCLS

- the study of ultrafast photochemical dynamics in condensed phase chemical systems.Transition metal complexes have interesting applications in photocatalysis and solar energy conversion. Time-resolved X-ray methods present intriguing opportunities to investigate the photochemical mechanisms at play in such reactions. By combining Hard X-ray scattering measurements with sensitivity to the structural evolution of photoexcited transition metal complexes to X-ray absorption and emission spectroscopy we can gain complementary information about electronic structure changes during photochemical dynamics.

- the use of time resolved hard X-ray diffraction and spectroscopy at XFELs to study the electronic and geometric structure of biological systems like the catalytically sun induced photosynthetic system PSII, and other metalloproteins.

- the development of advanced X-ray emission and absorption spectroscopy instrumentation and optics at synchrotron radiation and X-ray free electron laser sources.

All Publications


  • 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

  • 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)
  • 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
  • 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

  • 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)
  • 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
  • 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
  • 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
  • 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
  • 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

  • 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

  • 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

  • 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