@article{OstromObergXinetal.2015, author = {Ostrom, H. and Oberg, H. and Xin, H. and Larue, J. and Beye, Martin and Gladh, J. and Ng, M. L. and Sellberg, J. A. and Kaya, S. and Mercurio, G. and Nordlund, D. and Hantschmann, Markus and Hieke, F. and Kuehn, D. and Schlotter, W. F. and Dakovski, G. L. and Turner, J. J. and Minitti, M. P. and Mitra, A. and Moeller, S. P. and F{\"o}hlisch, Alexander and Wolf, M. and Wurth, W. and Persson, Mats and Norskov, J. K. and Abild-Pedersen, Frank and Ogasawara, Hirohito and Pettersson, Lars G. M. and Nilsson, A.}, title = {Probing the transition state region in catalytic CO oxidation on Ru}, series = {Science}, volume = {347}, journal = {Science}, number = {6225}, publisher = {American Assoc. for the Advancement of Science}, address = {Washington}, issn = {0036-8075}, doi = {10.1126/science.1261747}, pages = {978 -- 982}, year = {2015}, abstract = {Femtosecond x-ray laser pulses are used to probe the carbon monoxide (CO) oxidation reaction on ruthenium (Ru) initiated by an optical laser pulse. On a time scale of a few hundred femtoseconds, the optical laser pulse excites motions of CO and oxygen (O) on the surface, allowing the reactants to collide, and, with a transient close to a picosecond (ps), new electronic states appear in the OK-edge x-ray absorption spectrum. Density functional theory calculations indicate that these result from changes in the adsorption site and bond formation between CO and O with a distribution of OC-O bond lengths close to the transition state (TS). After 1 ps, 10\% of the CO populate the TS region, which is consistent with predictions based on a quantum oscillator model.}, language = {en} } @article{KunnusJosefssonRajkovicetal.2016, author = {Kunnus, Kristjan and Josefsson, I. and Rajkovic, Ivan and Schreck, Simon and Quevedo, Wilson and Beye, Martin and Weniger, C. and Gruebel, S. and Scholz, M. and Nordlund, D. and Zhang, W. and Hartsock, R. W. and Gaffney, K. J. and Schlotter, W. F. and Turner, J. J. and Kennedy, B. and Hennies, F. and de Groot, F. M. F. and Techert, S. and Odelius, Michael and Wernet, Ph. and F{\"o}hlisch, Alexander}, title = {Identification of the dominant photochemical pathways and mechanistic insights to the ultrafast ligand exchange of Fe(CO)(5) to Fe(CO)(4)EtOH}, series = {Structural dynamics}, volume = {3}, journal = {Structural dynamics}, publisher = {American Institute of Physics}, address = {Washington}, issn = {2329-7778}, doi = {10.1063/1.4941602}, pages = {16}, year = {2016}, abstract = {We utilized femtosecond time-resolved resonant inelastic X-ray scattering and ab initio theory to study the transient electronic structure and the photoinduced molecular dynamics of a model metal carbonyl photocatalyst Fe(CO)(5) in ethanol solution. We propose mechanistic explanation for the parallel ultrafast intra-molecular spin crossover and ligation of the Fe(CO)(4) which are observed following a charge transfer photoexcitation of Fe(CO)(5) as reported in our previous study [ Wernet et al., Nature 520, 78 (2015)]. We find that branching of the reaction pathway likely happens in the (1)A(1) state of Fe(CO)(4). A sub-picosecond time constant of the spin crossover from B-1(2) to B-3(2) is rationalized by the proposed B-1(2) -> (1)A(1) -> B-3(2) mechanism. Ultrafast ligation of the B-1(2) Fe(CO)(4) state is significantly faster than the spin-forbidden and diffusion limited ligation process occurring from the B-3(2) Fe(CO)(4) ground state that has been observed in the previous studies. We propose that the ultrafast ligation occurs via B-1(2) -> (1)A(1) -> (1)A'Fe(CO)(4)EtOH pathway and the time scale of the (1)A(1) Fe(CO)(4) state ligation is governed by the solute-solvent collision frequency. Our study emphasizes the importance of understanding the interaction of molecular excited states with the surrounding environment to explain the relaxation pathways of photoexcited metal carbonyls in solution. (C) 2016 Author(s).}, language = {en} } @article{KubinKernGuletal.2017, author = {Kubin, Markus and Kern, Jan and Gul, Sheraz and Kroll, Thomas and Chatterjee, Ruchira and Loechel, Heike and Fuller, Franklin D. and Sierra, Raymond G. and Quevedo, Wilson and Weniger, Christian and Rehanek, Jens and Firsov, Anatoly and Laksmono, Hartawan and Weninger, Clemens and Alonso-Mori, Roberto and Nordlund, Dennis L. and Lassalle-Kaiser, Benedikt and Glownia, James M. and Krzywinski, Jacek and Moeller, Stefan and Turner, Joshua J. and Minitti, Michael P. and Dakovski, Georgi L. and Koroidov, Sergey and Kawde, Anurag and Kanady, Jacob S. and Tsui, Emily Y. and Suseno, Sandy and Han, Zhiji and Hill, Ethan and Taguchi, Taketo and Borovik, Andrew S. and Agapie, Theodor and Messinger, Johannes and Erko, Alexei and F{\"o}hlisch, Alexander and Bergmann, Uwe and Mitzner, Rolf and Yachandra, Vittal K. and Yano, Junko and Wernet, Philippe}, title = {Soft x-ray absorption spectroscopy of metalloproteins and high-valent metal-complexes at room temperature using free-electron lasers}, series = {Structural dynamics}, volume = {4}, journal = {Structural dynamics}, publisher = {American Institute of Physics}, address = {Melville}, issn = {2329-7778}, doi = {10.1063/1.4986627}, pages = {16}, year = {2017}, 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 similar to 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. (C) 2017 Author(s).}, language = {en} } @article{KrollKernKubinetal.2016, author = {Kroll, Thomas and Kern, Jan and Kubin, Markus and Ratner, Daniel and Gul, Sheraz and Fuller, Franklin D. and L{\"o}chel, Heike and Krzywinski, Jacek and Lutman, Alberto and Ding, Yuantao and Dakovski, Georgi L. and Moeller, Stefan and Turner, Joshua J. and Alonso-Mori, Roberto and Nordlund, Dennis L. and Rehanek, Jens and Weniger, Christian and Firsov, Alexander and Brzhezinskaya, Maria and Chatterjee, Ruchira and Lassalle-Kaiser, Benedikt and Sierra, Raymond G. and Laksmono, Hartawan and Hill, Ethan and Borovik, Andrew S. and Erko, Alexei and F{\"o}hlisch, Alexander and Mitzner, Rolf and Yachandra, Vittal K. and Yano, Junko and Wernet, Philippe and Bergmann, Uwe}, title = {X-ray absorption spectroscopy using a self-seeded soft X-ray free-electron laser}, series = {Optics express : the international electronic journal of optics}, volume = {24}, journal = {Optics express : the international electronic journal of optics}, publisher = {Optical Society of America}, address = {Washington}, issn = {1094-4087}, doi = {10.1364/OE.24.022469}, pages = {22469 -- 22480}, year = {2016}, 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. (C) 2016 Optical Society of America}, language = {en} } @article{NishikawaHardeeZhangetal.2013, author = {Nishikawa, Ken-Ichi and Hardee, P. and Zhang, B. and Dutan, I. and Medvedev, M. and Choi, E. J. and Min, K. W. and Niemiec, J. and Mizuno, Y. and Nordlund, Ake and Frederiksen, Jacob Trier and Sol, H. and Pohl, Martin and Hartmann, D. H.}, title = {Magnetic field generation in a jet-sheath plasma via the kinetic Kelvin-Helmholtz instability}, series = {Annales geophysicae}, volume = {31}, journal = {Annales geophysicae}, number = {9}, publisher = {Copernicus}, address = {G{\"o}ttingen}, issn = {0992-7689}, doi = {10.5194/angeo-31-1535-2013}, pages = {1535 -- 1541}, year = {2013}, abstract = {We have investigated the generation of magnetic fields associated with velocity shear between an unmagnetized relativistic jet and an unmagnetized sheath plasma. We have examined the strong magnetic fields generated by kinetic shear (Kelvin-Helmholtz) instabilities. Compared to the previous studies using counter-streaming performed by Alves et al. (2012), the structure of the kinetic Kelvin-Helmholtz instability (KKHI) of our jet-sheath configuration is slightly different, even for the global evolution of the strong transverse magnetic field. In our simulations the major components of growing modes are the electric field E-z, perpendicular to the flow boundary, and the magnetic field B-y, transverse to the flow direction. After the B-y component is excited, an induced electric field E-x, parallel to the flow direction, becomes significant. However, other field components remain small. We find that the structure and growth rate of KKHI with mass ratios m(i)/m(e) = 1836 and m(i)/m(e) = 20 are similar. In our simulations in the nonlinear stage is not as clear as in counter-streaming cases. The growth rate for a mildly-relativistic jet case (gamma(j) = 1.5) is larger than for a relativistic jet case (gamma(j) = 15).}, language = {en} } @article{NishikawaFrederiksenNordlundetal.2016, author = {Nishikawa, Ken-Ichi and Frederiksen, J. T. and Nordlund, A. and Mizuno, Y. and Hardee, P. E. and Niemiec, J. and Gomez, J. L. and Dutan, I. and Meli, A. and Sol, H. and Pohl, Martin and Hartmann, D. H.}, title = {EVOLUTION OF GLOBAL RELATIVISTIC JETS: COLLIMATIONS AND EXPANSION WITH kKHI AND THE WEIBEL INSTABILITY}, series = {The astrophysical journal : an international review of spectroscopy and astronomical physics}, volume = {820}, journal = {The astrophysical journal : an international review of spectroscopy and astronomical physics}, publisher = {IOP Publ. Ltd.}, address = {Bristol}, issn = {0004-637X}, doi = {10.3847/0004-637X/820/2/94}, pages = {14}, year = {2016}, abstract = {In the study of relativistic jets one of the key open questions is their interaction with the environment. Here. we study the initial evolution of both electron-proton (e(-) - p(+)) and electron-positron (e(+/-)) relativistic jets, focusing on their lateral interaction with ambient plasma. We follow the evolution of toroidal magnetic fields generated by both the kinetic Kelvin-Helmholtz and Mushroom instabilities. For an e(-) - p(+) jet, the induced magnetic field collimates the jet and electrons are perpendicularly accelerated. As the instabilities saturate and subsequently weaken, the magnetic polarity switches from clockwise to counterclockwise in the middle of the jet. For an e(+/-) jet, we find strong mixing of electrons and positrons with the ambient plasma, resulting in the creation of a bow shock. The merging of current filaments generates density inhomogeneities that. initiate a forward shock. Strong jet-ambient plasma mixing prevents a full development of the jet (on the scale studied), revealing evidence for both jet collimation and particle acceleration in the forming bow shock. Differences in the magnetic field structure generated by e(-) - p(+) and e(+/-) jets may contribute to the polarization properties of the observed emission in AGN jets and gamma-ray bursts.}, language = {en} } @misc{NishikawaZhangChoietal.2012, author = {Nishikawa, K.-I. and Zhang, B. and Choi, E. J. and Min, K. W. and Niemiec, J. and Medvedev, M. and Hardee, P. and Mizuno, Y. and Nordlund, A. and Frederiksen, J. and Sol, H. and Pohl, Martin and Hartmann, D. H. and Fishman, G.J.}, title = {Radiation from accelerated particles in shocks}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe}, number = {600}, issn = {1866-8372}, doi = {10.25932/publishup-41312}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-413128}, pages = {371 -- 372}, year = {2012}, abstract = {Recent PIC simulations of relativistic electron-positron (electron-ion) jets injected into a stationary medium show that particle acceleration occurs in the shocked regions. Simulations show that the Weibel instability is responsible for generating and amplifying highly nonuniform, small-scale magnetic fields and for particle acceleration. These magnetic fields contribute to the electron's transverse eflection behind the shock. The "jitter" radiation from deflected electrons in turbulent magnetic fields has properties different from synchrotron radiation calculated in a uniform magnetic field. This jitter radiation may be important for understanding the complex time evolution and/or spectral structure of gamma-ray bursts, relativistic jets in general, and supernova remnants. In order to calculate radiation from first principles and go beyond the standard synchrotron model, we have used PIC simulations. We present synthetic spectra to compare with the spectra obtained from Fermi observations.}, language = {en} } @article{KatayamaAnniyevBeyeetal.2013, author = {Katayama, T. and Anniyev, Toyli and Beye, Martin and Coffee, Ryan and Dell'Angela, M. and F{\"o}hlisch, Alexander and Gladh, J. and Kaya, S. and Krupin, O. and Nilsson, A. and Nordlund, D. and Schlotter, W. F. and Sellberg, J. A. and Sorgenfrei, Nomi and Turner, J. J. and Wurth, W. and {\"O}str{\"o}m, H. and Ogasawara, H.}, title = {Ultrafast soft X-ray emission spectroscopy of surface adsorbates using an X-ray free electron laser}, series = {Journal of electron spectroscopy and related phenomena : the international journal on theoretical and experimental aspects of electron spectroscopy}, volume = {187}, journal = {Journal of electron spectroscopy and related phenomena : the international journal on theoretical and experimental aspects of electron spectroscopy}, number = {1}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0368-2048}, doi = {10.1016/j.elspec.2013.03.006}, pages = {9 -- 14}, year = {2013}, abstract = {We report on an experimental system designed to probe chemical reactions on solid surfaces on a sub-picosecond timescale using soft X-ray emission spectroscopy at the Linac Coherent Light Source (LCLS) free electron laser (FEL) at the SLAC National Accelerator Laboratory. We analyzed the O 1s X-ray emission spectra recorded from atomic oxygen adsorbed on a Ru(0001) surface at a synchrotron beamline (SSRL, BL13-2) and an FEL beamline (LCLS, SXR). We have demonstrated conditions that provide negligible amount of FEL induced damage of the sample. In addition we show that the setup is capable of tracking the temporal evolution of electronic structure during a surface reaction of submonolayer quantities of CO molecules desorbing from the surface.}, language = {en} } @article{Dell'AngelaAnniyevBeyeetal.2013, author = {Dell'Angela, M. and Anniyev, Toyli and Beye, Martin and Coffee, Ryan and F{\"o}hlisch, Alexander and Gladh, J. and Katayama, T. and Kaya, S. and Krupin, O. and LaRue, J. and Mogelhoj, A. and Nordlund, D. and Norskov, J. K. and Oberg, H. and Ogasawara, H. and Ostrom, H. and Pettersson, Lars G. M. and Schlotter, W. F. and Sellberg, J. A. and Sorgenfrei, Nomi and Turner, J. J. and Wolf, M. and Wurth, W. and Nilsson, A.}, title = {Real-time observation of surface bond breaking with an X-ray Laser}, series = {Science}, volume = {339}, journal = {Science}, number = {6125}, publisher = {American Assoc. for the Advancement of Science}, address = {Washington}, issn = {0036-8075}, doi = {10.1126/science.1231711}, pages = {1302 -- 1305}, year = {2013}, abstract = {We used the Linac Coherent Light Source free-electron x-ray laser to probe the electronic structure of CO molecules as their chemisorption state on Ru(0001) changes upon exciting the substrate by using a femtosecond optical laser pulse. We observed electronic structure changes that are consistent with a weakening of the CO interaction with the substrate but without notable desorption. A large fraction of the molecules (30\%) was trapped in a transient precursor state that would precede desorption. We calculated the free energy of the molecule as a function of the desorption reaction coordinate using density functional theory, including van der Waals interactions. Two distinct adsorption wells-chemisorbed and precursor state separated by an entropy barrier-explain the anomalously high prefactors often observed in desorption of molecules from metals.}, language = {en} } @article{BeyeAnniyevCoffeeetal.2013, author = {Beye, Martin and Anniyev, Toyli and Coffee, Ryan and Dell'Angela, Martina and F{\"o}hlisch, Alexander and Gladh, J. and Katayama, T. and Kaya, S. and Krupin, O. and Mogelhoj, A. and Nilsson, A. and Nordlund, D. and Norskov, J. K. and Oberg, H. and Ogasawara, H. and Pettersson, Lars G. M. and Schlotter, W. F. and Sellberg, J. A. and Sorgenfrei, Nomi and Turner, J. J. and Wolf, M. and Wurth, Wilfried and Ostrom, H.}, title = {Selective ultrafast probing of transient hot chemisorbed and precursor States of CO on Ru(0001)}, series = {Physical review letters}, volume = {110}, journal = {Physical review letters}, number = {18}, publisher = {American Physical Society}, address = {College Park}, issn = {0031-9007}, doi = {10.1103/PhysRevLett.110.186101}, pages = {6}, year = {2013}, abstract = {We have studied the femtosecond dynamics following optical laser excitation of CO adsorbed on a Ru surface by monitoring changes in the occupied and unoccupied electronic structure using ultrafast soft x-ray absorption and emission. We recently reported [M. Dell'Angela et al. Science 339, 1302 (2013)] a phonon-mediated transition into a weakly adsorbed precursor state occurring on a time scale of >2 ps prior to desorption. Here we focus on processes within the first picosecond after laser excitation and show that the metal-adsorbate coordination is initially increased due to hot-electron-driven vibrational excitations. This process is faster than, but occurs in parallel with, the transition into the precursor state. With resonant x-ray emission spectroscopy, we probe each of these states selectively and determine the respective transient populations depending on optical laser fluence. Ab initio molecular dynamics simulations of CO adsorbed on Ru(0001) were performed at 1500 and 3000 K providing insight into the desorption process.}, language = {en} }