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  • 1.
    Akiyama, Tomoko
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics.
    Björneholm, Olle
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics.
    Caleman, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics. Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany.
    Grånäs, Oscar
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Influence of Ionization on the Dynamics of HydrocarbonsManuscript (preprint) (Other academic)
    Abstract [en]

    The structural changes of four hydrocarbons induced by ionization was investigated using molecular dynamics simulations based on density functional theory within the Born-Oppenheimer approximation. Bond lengths, bond breaking and proton rearrangement was analysed for propane, propene, propyne and propadiene at charges ranging from 0 to +3.   Similar to the case of amino acids, the back-bone of linear hydrocarbons is stabilized by reducing theeffectiv elevel of ionization through dropping protons. Subsequent iniozations, up the the level of 3+, do not break thelinear carbon chain within 250 fs, however the bond-orderis reduced, and bond-distances approach that of a single-bond

  • 2.
    Andreasson, Jakob
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Iwan, Bianca Stella
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Andrejczuk, A.
    Abreu, E.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Bergh, M.
    Caleman, Carl
    Nelson, A. J.
    Bajt, S.
    Chalupsky, J.
    Chapman, H. N.
    Faeustlin, R. R.
    Hajkova, V.
    Heimann, P. A.
    Hjörvarsson, Björgvin
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Physics.
    Juha, L.
    Klinger, D.
    Krzywinski, J.
    Nagler, B.
    Pålsson, Gunnar Karl
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Physics.
    Singer, W.
    Seibert, Marvin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Sobicrajski, R.
    Tolcikis, S.
    Tschentscher, T.
    Vinko, S. M.
    Lee, R. W.
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Saturated ablation in metal hydrides and acceleration of protons and deuterons to keV energies with a soft-x-ray laser2011In: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics, ISSN 1539-3755, E-ISSN 1550-2376, Vol. 83, no 1, p. 016403-Article in journal (Refereed)
    Abstract [en]

    Studies of materials under extreme conditions have relevance to a broad area of research, including planetary physics, fusion research, materials science, and structural biology with x-ray lasers. We study such extreme conditions and experimentally probe the interaction between ultrashort soft x-ray pulses and solid targets (metals and their deuterides) at the FLASH free-electron laser where power densities exceeding 1017 W/cm2 were reached. Time-of-flight ion spectrometry and crater analysis were used to characterize the interaction. The results show the onset of saturation in the ablation process at power densities above 1016 W/cm2. This effect can be linked to a transiently induced x-ray transparency in the solid by the femtosecond x-ray pulse at high power densities. The measured kinetic energies of protons and deuterons ejected from the surface reach several keV and concur with predictions from plasma-expansion models. Simulations of the interactions were performed with a nonlocal thermodynamic equilibrium code with radiation transfer. These calculations return critical depths similar to the observed crater depths and capture the transient surface transparency at higher power densities.

  • 3.
    André, Tomas
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics.
    Dawod, Ibrahim
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics. European XFEL, Holzkoppel 4, DE-22869 Schenefeld, Germany.
    Cardoch, Sebastian
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics.
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics.
    Caleman, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics. Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Notkestraße 85 DE-22607 Hamburg, Germany.
    Macromolecule classification using X-ray laser induced fragmentation simulated with hybrid Monte Carlo/Molecular DynamicsManuscript (preprint) (Other academic)
    Abstract [en]

    We have developed a hybrid Monte Carlo and classical molecular dynamics code to follow the ultrafast atomic dynamics in biological macromolecules induced by a femtosecond X-ray laser. Our model for fragmentation shows good qualitative agreement with ab-initio simulations of small molecules, while being computationally faster.  We applied the code for macromolecules and simulated the Coulomb explosion dynamics due to the fast ionization in six proteins with different physical properties. The trajectories of the ions are followed and projected onto a detector, where the particular pattern depends on the protein, providing a unique footprint. We utilize algorithms such as principal component analysis  and t-distributed stochastic neighbor embedding to classify the fragmentation pattern. The results show that the classification algorithms are able to separate the explosion patterns into distinct groups. We envision that this method could be used to provide additional class information, like particle mass or shape, in structural determination experiments using X-ray lasers.

  • 4. Aquila, Andrew
    et al.
    Hunter, Mark S.
    Doak, R. Bruce
    Kirian, Richard A.
    Fromme, Petra
    White, Thomas A.
    Andreasson, Jakob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Arnlund, David
    Bajt, Saša
    Barends, Thomas R. M.
    Barthelmess, Miriam
    Bogan, Michael J.
    Bostedt, Christoph
    Bottin, Hervé
    Bozek, John D.
    Caleman, Carl
    Coppola, Nicola
    Davidsson, Jan
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Physical Chemistry.
    DePonte, Daniel P.
    Elser, Veit
    Epp, Sascha W.
    Erk, Benjamin
    Fleckenstein, Holger
    Foucar, Lutz
    Frank, Matthias
    Fromme, Raimund
    Graafsma, Heinz
    Grotjohann, Ingo
    Gumprecht, Lars
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hampton, Christina Y.
    Hartmann, Andreas
    Hartmann, Robert
    Hau-Riege, Stefan
    Hauser, Günter
    Hirsemann, Helmut
    Holl, Peter
    Holton, James M.
    Hömke, André
    Johansson, Linda
    Kimmel, Nils
    Kassemeyer, Stephan
    Krasniqi, Faton
    Kühnel, Kai-Uwe
    Liang, Mengning
    Lomb, Lukas
    Malmerberg, Erik
    Marchesini, Stefano
    Martin, Andrew V.
    Maia, Filipe R.N.C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Messerschmidt, Marc
    Nass, Karol
    Reich, Christian
    Neutze, Richard
    Rolles, Daniel
    Rudek, Benedikt
    Rudenko, Artem
    Schlichting, Ilme
    Schmidt, Carlo
    Schmidt, Kevin E.
    Schulz, Joachim
    Seibert, M. Marvin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Soltau, Heike
    Shoeman, Robert L.
    Sierra, Raymond
    Starodub, Dmitri
    Stellato, Francesco
    Stern, Stephan
    Strüder, Lothar
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Ullrich, Joachim
    Wang, Xiaoyu
    Williams, Garth J.
    Weidenspointner, Georg
    Weierstall, Uwe
    Wunderer, Cornelia
    Barty, Anton
    Spence, John C. H.
    Chapman, Henry N.
    Time-resolved protein nanocrystallography using an X-ray free-electron laser2012In: Optics Express, E-ISSN 1094-4087, Vol. 20, no 3, p. 2706-2716Article in journal (Refereed)
    Abstract [en]

    We demonstrate the use of an X-ray free electron laser synchronized with an optical pump laser to obtain X-ray diffraction snapshots from the photoactivated states of large membrane protein complexes in the form of nanocrystals flowing in a liquid jet. Light-induced changes of Photosystem I-Ferredoxin co-crystals were observed at time delays of 5 to 10 µs after excitation. The result correlates with the microsecond kinetics of electron transfer from Photosystem I to ferredoxin. The undocking process that follows the electron transfer leads to large rearrangements in the crystals that will terminally lead to the disintegration of the crystals. We describe the experimental setup and obtain the first time-resolved femtosecond serial X-ray crystallography results from an irreversible photo-chemical reaction at the Linac Coherent Light Source. This technique opens the door to time-resolved structural studies of reaction dynamics in biological systems.

  • 5. Barty, Anton
    et al.
    Caleman, Carl
    Aquila, Andrew
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Lomb, Lukas
    White, Thomas A.
    Andreasson, Jakob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Arnlund, David
    Bajt, Sasa
    Barends, Thomas R. M.
    Barthelmess, Miriam
    Bogan, Michael J.
    Bostedt, Christoph
    Bozek, John D.
    Coffee, Ryan
    Coppola, Nicola
    Davidsson, Jan
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Physical Chemistry.
    DePonte, Daniel P.
    Doak, R. Bruce
    Ekeberg, Tomas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Elser, Veit
    Epp, Sascha W.
    Erk, Benjamin
    Fleckenstein, Holger
    Foucar, Lutz
    Fromme, Petra
    Graafsma, Heinz
    Gumprecht, Lars
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hampton, Christina Y.
    Hartmann, Robert
    Hartmann, Andreas
    Hauser, Guenter
    Hirsemann, Helmut
    Holl, Peter
    Hunter, Mark S.
    Johansson, Linda
    Kassemeyer, Stephan
    Kimmel, Nils
    Kirian, Richard A.
    Liang, Mengning
    Maia, Filipe R. N. C.
    Malmerberg, Erik
    Marchesini, Stefano
    Martin, Andrew V.
    Nass, Karol
    Neutze, Richard
    Reich, Christian
    Rolles, Daniel
    Rudek, Benedikt
    Rudenko, Artem
    Scott, Howard
    Schlichting, Ilme
    Schulz, Joachim
    Seibert, M. Marvin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Shoeman, Robert L.
    Sierra, Raymond G.
    Soltau, Heike
    Spence, John C. H.
    Stellato, Francesco
    Stern, Stephan
    Strueder, Lothar
    Ullrich, Joachim
    Wang, X.
    Weidenspointner, Georg
    Weierstall, Uwe
    Wunderer, Cornelia B.
    Chapman, Henry N.
    Self-terminating diffraction gates femtosecond X-ray nanocrystallography measurements2012In: Nature Photonics, ISSN 1749-4885, E-ISSN 1749-4893, Vol. 6, no 1, p. 35-40Article in journal (Refereed)
    Abstract [en]

    X-ray free-electron lasers have enabled new approaches to the structural determination of protein crystals that are too small or radiation-sensitive for conventional analysis(1). For sufficiently short pulses, diffraction is collected before significant changes occur to the sample, and it has been predicted that pulses as short as 10 fs may be required to acquire atomic-resolution structural information(1-4). Here, we describe a mechanism unique to ultrafast, ultra-intense X-ray experiments that allows structural information to be collected from crystalline samples using high radiation doses without the requirement for the pulse to terminate before the onset of sample damage. Instead, the diffracted X-rays are gated by a rapid loss of crystalline periodicity, producing apparent pulse lengths significantly shorter than the duration of the incident pulse. The shortest apparent pulse lengths occur at the highest resolution, and our measurements indicate that current X-ray free-electron laser technology(5) should enable structural determination from submicrometre protein crystals with atomic resolution.

  • 6.
    Bergh, Magnus
    et al.
    Swedish Def Res Agcy, S-16490 Stockholm, Sweden..
    Caleman, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and condensed matter physics. DESY, Ctr Free Electron Laser Sci, Hamburg, Germany..
    A Validation Study of the General Amber Force Field Applied to Energetic Molecular Crystals2016In: Journal of Energetic Materials, ISSN 0737-0652, E-ISSN 1545-8822, Vol. 34, no 1, p. 62-75Article in journal (Refereed)
    Abstract [en]

    Molecula dynamics is a well-established tool to computationally study molecules. However, to reach predictive capability at the level required for applied research and design, extensive validation of the available force fields is pertinent. Here we present a study of density, isothermal compressibility and coefficients of thermal expansion of four energetic materials (FOX-7, RDX, CL-20 and HMX) based on molecular dynamics simulations with the General Amber Force Field (GAFF), and compare the results to experimental measurements from the literature. Furthermore, we quantify the accuracy of the calculated properties through hydrocode simulation of a typical impact scenario. We find that molecular dynamics simulations with generic and computationally efficient force fields may be used to understand and estimate important physical properties of nitramine-like energetic materials.

  • 7.
    Beyerlein, Kenneth
    et al.
    Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Hamburg, Germany.
    Jönsson, Olof
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Alonso-Mori, Roberto
    SLAC National Accelerator Laboratory, USA.
    Aquila, Andrew
    SLAC National Accelerator Laboratory, USA.
    Bajt, Sasa
    Photon Science, DESY, Hamburg, Germany.
    Barty, Anton
    Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Hamburg, Germany.
    Bean, Richard
    Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Hamburg, Germany.
    Koglin, Jason E.
    SLAC National Accelerator Laboratory, USA.
    Messerschmidt, Marc
    SLAC National Accelerator Laboratory, USA.
    Ragazzon, Davide
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Soklaras, Dimosthenis
    SLAC National Accelerator Laboratory, USA.
    Williams, Garth J.
    SLAC National Accelerator Laboratory, USA.
    Hau-Riege, Stefan
    Lawrence Livermore National Laboratory, USA.
    Boutet, Sebastien
    SLAC National Accelerator Laboratory, USA.
    Chapman, Henry N.
    Center for Free-Electron Laser Science,Deutsches Elektronen-Synchrotron, Hamburg, Germany; Department of Physics, University of Hamburg, Hamburg, Germany; Centre for Ultrafast Imaging, University of Hamburg, Hamburg, Germany .
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Caleman, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics. Center for Free-Electron Laser Science,Deutsches Elektronen-Synchrotron, Hamburg, Germany.
    Ultrafast non-thermal heating of water initiated by an X-ray laser2018In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 115, no 22, p. 5652-5657Article in journal (Refereed)
    Abstract [en]

    X-ray Free-Electron Lasers have opened the door to a new era in structural biology, enabling imaging of biomolecules and dynamics that were impossible to access with conventional methods. A vast majority of imaging experiments, including Serial Femtosecond Crystallography, use a liquid jet to deliver the sample into the interaction region. We have observed structural changes in the carrying water during X-ray exposure, showing how it transforms from the liquid phase to a plasma. This ultrafast phase transition observed in water provides evidence that any biological structure exposed to these X-ray pulses is destroyed during the X-ray exposure.The bright ultrafast pulses of X-ray Free-Electron Lasers allow investigation into the structure of matter under extreme conditions. We have used single pulses to ionize and probe water as it undergoes a phase transition from liquid to plasma. We report changes in the structure of liquid water on a femtosecond time scale when irradiated by single 6.86 keV X-ray pulses of more than 106 J/cm2. These observations are supported by simulations based on molecular dynamics and plasma dynamics of a water system that is rapidly ionized and driven out of equilibrium. This exotic ionic and disordered state with the density of a liquid is suggested to be structurally different from a neutral thermally disordered state.

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  • 8. Boutet, Sébastien
    et al.
    Lomb, Lukas
    Williams, Garth J
    Barends, Thomas R M
    Aquila, Andrew
    Doak, R Bruce
    Weierstall, Uwe
    DePonte, Daniel P
    Steinbrener, Jan
    Shoeman, Robert L
    Messerschmidt, Marc
    Barty, Anton
    White, Thomas A
    Kassemeyer, Stephan
    Kirian, Richard A
    Seibert, M Marvin
    Montanez, Paul A
    Kenney, Chris
    Herbst, Ryan
    Hart, Philip
    Pines, Jack
    Haller, Gunther
    Gruner, Sol M
    Philipp, Hugh T
    Tate, Mark W
    Hromalik, Marianne
    Koerner, Lucas J
    van Bakel, Niels
    Morse, John
    Ghonsalves, Wilfred
    Arnlund, David
    Bogan, Michael J
    Caleman, Carl
    Fromme, Raimund
    Hampton, Christina Y
    Hunter, Mark S
    Johansson, Linda C
    Katona, Gergely
    Kupitz, Christopher
    Liang, Mengning
    Martin, Andrew V
    Nass, Karol
    Redecke, Lars
    Stellato, Francesco
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Wang, Dingjie
    Zatsepin, Nadia A
    Schafer, Donald
    Defever, James
    Neutze, Richard
    Fromme, Petra
    Spence, John C H
    Chapman, Henry N
    Schlichting, Ilme
    High-resolution protein structure determination by serial femtosecond crystallography2012In: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 337, no 6092, p. 362-364Article in journal (Refereed)
    Abstract [en]

    Structure determination of proteins and other macromolecules has historically required the growth of high-quality crystals sufficiently large to diffract x-rays efficiently while withstanding radiation damage. We applied serial femtosecond crystallography (SFX) using an x-ray free-electron laser (XFEL) to obtain high-resolution structural information from microcrystals (less than 1 micrometer by 1 micrometer by 3 micrometers) of the well-characterized model protein lysozyme. The agreement with synchrotron data demonstrates the immediate relevance of SFX for analyzing the structure of the large group of difficult-to-crystallize molecules.

  • 9.
    Brodmerkel, Maxim N.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Biochemistry.
    De Santis, Emiliano
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Biochemistry. Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy.
    Caleman, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics. Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607, Hamburg, Germany.
    Marklund, Erik
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Biochemistry.
    Rehydration Post-orientation: Investigating Field-Induced Structural Changes via Computational Rehydration2023In: The Protein Journal, ISSN 1572-3887, E-ISSN 1875-8355, Vol. 42, no 3, p. 205-218Article in journal (Refereed)
    Abstract [en]

    Proteins can be oriented in the gas phase using strong electric fields, which brings advantages for structure determination using X-ray free electron lasers. Both the vacuum conditions and the electric-field exposure risk damaging the protein structures. Here, we employ molecular dynamics simulations to rehydrate and relax vacuum and electric-field exposed proteins in aqueous solution, which simulates a refinement of structure models derived from oriented gas-phase proteins. We find that the impact of the strong electric fields on the protein structures is of minor importance after rehydration, compared to that of vacuum exposure and ionization in electrospraying. The structures did not fully relax back to their native structure in solution on the simulated timescales of 200 ns, but they recover several features, including native-like intra-protein contacts, which suggests that the structures remain in a state from which the fully native structure is accessible. Our fndings imply that the electric fields used in native mass spectrometry are well below a destructive level, and suggest that structures inferred from X-ray difraction from gas-phase proteins are relevant for solution and in vivo conditions, at least after in silico rehydration.

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  • 10.
    Brodmerkel, Maxim N.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Biochemistry.
    De Santis, Emiliano
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Biochemistry. Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy.
    Uetrecht, Charlotte
    Caleman, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy. Center for Free-Electron Laser Science, DESY, Notkestrasse 85, Hamburg, 22607, Germany.
    Marklund, Erik
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Biochemistry.
    Stability and conformational memory of electrosprayed and rehydrated bacteriophage MS2 virus coat proteins2022In: Current Research in Structural Biology, E-ISSN 2665-928X, Vol. 4, p. 338-348Article in journal (Refereed)
    Abstract [en]

    Proteins are innately dynamic, which is important for their functions, but which also poses significant challenges when studying their structures. Gas-phase techniques can utilise separation and a range of sample manipulations to transcend some of the limitations of conventional techniques for structural biology in crystalline or solution phase, and isolate different states for separate interrogation. However, the transfer from solution to the gas phase risks affecting the structures, and it is unclear to what extent different conformations remain distinct in the gas phase, and if resolution in silico can recover the native conformations and their differences. Here, we use extensive molecular dynamics simulations to study the two distinct conformations of dimeric capsid protein of the MS2 bacteriophage. The protein undergoes notable restructuring of its peripheral parts in the gas phase, but subsequent simulation in solvent largely recovers the native structure. Our results suggest that despite some structural loss due to the experimental conditions, gas-phase structural biology techniques provide meaningful data that inform not only about the structures but also conformational dynamics of proteins.

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  • 11.
    Brodmerkel, Maxim N.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Biochemistry.
    De Santis, Emiliano
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Biochemistry. Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy.
    Uetrecht, Charlotte
    Caleman, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics. Deutsches Elektronen-Synchrotron, DESY, Notkestrasse 85, 22607 Hamburg, Germany.
    Marklund, Erik G.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Biochemistry.
    Simulated collision induced unfolding of norovirus capsid dimers reveal strain-specific stability profilesIn: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084Article in journal (Refereed)
    Abstract [en]

    Collision induced unfolding is method used with ion mobility mass spectrometry to examine protein structures and their stability. Such experiments yield information about higher order protein structures, yet are unable to provide details about the underlying processes. That information can however be provided using molecular dynamics simulations. Here, we investigate the collision induced unfolding of norovirus capsid dimers from the Norwalk and Kawasaki strains by employing molecular dynamics simulations over a range of temperatures, representing different levels of activation. The dimers have highly similar structures, but the activation reveals differences in the dynamics that arises in response to the activation.

  • 12. Caleman, Carl
    et al.
    Bergh, Magnus
    Scott, Howard A.
    Spence, John C. H.
    Chapman, Henry N.
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Simulations of radiation damage in biomolecular nanocrystals induced by femtosecond X-ray pulses2011In: Journal of Modern Optics, ISSN 0950-0340, E-ISSN 1362-3044, Vol. 58, no 16, p. 1486-1497Article in journal (Refereed)
    Abstract [en]

    The Linac Coherent Light Source (LCLS) is the first X-ray free electron laser to achieve lasing at subnanometer wavelengths (6 angstrom). LCLS is poised to reach even shorter wavelengths (1.5 angstrom) and thus holds the promise of single molecular imaging at atomic resolution. The initial operation at a photon energy of 2 keV provides the possibility to perform the first experiments on damage to biological particles, and to assess the limitations to coherent imaging of biological samples, which are directly relevant at atomic resolution. In this paper we theoretically investigate the damage formation and detection possibilities for a biological crystal, by employing and comparing two different damage models with complementary strengths. Molecular dynamics provides a discrete approach which investigates structural details at the atomic level by tracking all atoms in the real space. Our continuum model is based on a non-local thermodynamics equilibrium code with atomic kinetics and radiation transfer and can treat hydrodynamic expansion of the entire system. The latter approach captures the essential features of atomic displacements, without taking into account structural information and intrinsic atomic movements. This proves to be a powerful computational tool for many samples, including biological crystals, which will be studied with X-ray free electron lasers.

  • 13. Caleman, Carl
    et al.
    Hub, Jochen S.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology.
    van Maaren, Paul J.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    van der Spoel, David
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology.
    Atomistic simulation of ion solvation in water explains surface preference of halides2011In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 108, no 17, p. 6838-6842Article in journal (Refereed)
    Abstract [en]

    Water is a demanding partner. It strongly attracts ions, yet some halide anions-chloride, bromide, and iodide-are expelled to the air/water interface. This has important implications for chemistry in the atmosphere, including the ozone cycle. We present a quantitative analysis of the energetics of ion solvation based on molecular simulations of all stable alkali and halide ions in water droplets. The potentials of mean force for Cl-, Br-, and I-have shallow minima near the surface. We demonstrate that these minima derive from more favorable water-water interaction energy when the ions are partially desolvated. Alkali cations are on the inside because of the favorable ion-water energy, whereas F-is driven inside by entropy. Models attempting to explain the surface preference based on one or more ion properties such as polarizability or size are shown to lead to qualitative and quantitative errors, prompting a paradigm shift in chemistry away from such simplifications.

  • 14. Caleman, Carl
    et al.
    Huldt, Gösta
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Maia, Filipe R. N. C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Ortiz, Carlos
    Parak, Fritz G.
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    van der Spoel, David
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology.
    Chapman, Henry N.
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    On the Feasibility of Nanocrystal Imaging Using Intense and Ultrashort X-ray Pulses2011In: ACS Nano, ISSN 1936-0851, Vol. 5, no 1, p. 139-146Article in journal (Refereed)
    Abstract [en]

    Structural studies of biological macromolecules are severely limited by radiation damage. Traditional crystallography curbs the effects of damage by spreading damage over many copies of the molecule of interest in the crystal. X-ray lasers offer an additional opportunity for limiting damage by out-running damage processes with ultrashort and very intense X-ray pulses Such pulses may allow the imaging of single molecules, clusters; Or nanoparticles: Coherent flash Imaging Will also open up new avenues for structural studies on nano- and microcrystalline substances. This paper addresses the theoretical potentials and limitations of nanocrystallography with extremely intense coherent X-ray pulses. We use urea nanocrystals as a model for generic biological substances and simulate the primary and secondary ionization dynamics in the crystalline sample. The results establish conditions for ultrafast single shot nanocrystallography diffraction experiments as a function of X-ray fluence, pulse duration, and the size of nanocrystals. Nanocrystallography using ultrafast X-ray pulses has the potential to open up a new route in protein crystallography to solve atomic structures of many systems that remain Inaccessible using conventional X-ray sources.

  • 15.
    Caleman, Carl
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Huldt, Gösta
    Ortiz, Carlos
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Materials Science, Materials Theory.
    Maia, Filipe R. N. C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Marklund, Erik G.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Parak, Fritz G.
    van der Spool, David
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Nanocrystal imaging using intense and ultrashort X-ray pulsesManuscript (preprint) (Other (popular science, discussion, etc.))
    Abstract [en]

    Structural studies of biological macromolecules are severely limited by radiation damage. Traditional crystallography curbs the effects of damage by spreading damage over many copies of the molecule of interest in the crystal. X-ray lasers offer an additional opportunity for limiting damage by out-running damage processes with ultrashort and very intense X-ray pulses. Such pulses may allow the imaging of single molecules, clusters or nanoparticles, but coherent flash imaging will also open up new avenues for structural studies on nano- and micro-crystalline substances. This paper addresses the potentials and limitations of nanocrystallography with extremely intense coherent X-ray pulses. We use urea nanocrystals as a model for generic biological substances, and simulate the primary and secondary ionization dynamics in the crystalline sample. The results establish conditions for diffraction experiments as a function of X-ray fluence, pulse duration, and the size of nanocrystals.

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  • 16.
    Caleman, Carl
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy. Ctr Free Electron Laser Sci, Notkestr 85, DE-22607 Hamburg, Germany..
    Junior, Francisco Jares
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy.
    Grånäs, Oscar
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Martin, Andrew, V
    RMIT Univ, Sch Sci, Melbourne, Vic 3000, Australia..
    A Perspective on Molecular Structure and Bond-Breaking in Radiation Damage in Serial Femtosecond Crystallography2020In: Crystals, ISSN 2073-4352, Vol. 10, no 7, article id 585Article in journal (Refereed)
    Abstract [en]

    X-ray free-electron lasers (XFELs) have a unique capability for time-resolved studies of protein dynamics and conformational changes on femto- and pico-second time scales. The extreme intensity of X-ray pulses can potentially cause significant modifications to the sample structure during exposure. Successful time-resolved XFEL crystallography depends on the unambiguous interpretation of the protein dynamics of interest from the effects of radiation damage. Proteins containing relatively heavy elements, such as sulfur or metals, have a higher risk for radiation damage. In metaloenzymes, for example, the dynamics of interest usually occur at the metal centers, which are also hotspots for damage due to the higher atomic number of the elements they contain. An ongoing challenge with such local damage is to understand the residual bonding in these locally ionized systems and bond-breaking dynamics. Here, we present a perspective on radiation damage in XFEL experiments with a particular focus on the impacts for time-resolved protein crystallography. We discuss recent experimental and modelling results of bond-breaking and ion motion at disulfide bonding sites in protein crystals.

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  • 17.
    Caleman, Carl
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics. DESY, Ctr Free Electron Laser Sci, Notkestr 85, Hamburg, Germany.
    Jönsson, Olof
    KTH Royal Inst Technol, Dept Appl Phys, S-10691 Stockholm, Sweden.
    Östlin, Christofer
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics. Uppsala Univ, Dept Phys & Astron, Box 516, Uppsala, Sweden.
    Ultrafast dynamics of water exposed to XFEL pulses2019In: Optics Damage and Materials Processing by EUV/X-ray Radiation VII / [ed] Juha, L Bajt, S Guizard, S, SPIE - International Society for Optical Engineering, 2019, article id 1103507Conference paper (Refereed)
    Abstract [en]

    These proceedings investigate the ionization and temperature dynamics of water samples exposed to intense ultrashort X-ray free-electron laser pulses ranging from 10(4) - 10(7) J/cm(2), based on simulations using a non-local thermodynamic plasma code. In comparison to earlier work combining simulations and experiments, a regime where a hybrid simulations approach should be applicable is presented.

  • 18.
    Caleman, Carl
    et al.
    Physik Department E17, Technische Universität München.
    Ortiz, Carlos
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Materials Science, Materials Theory.
    Marklund, Erik
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Bultmark, Fredrik
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Materials Science, Materials Theory.
    Gabrysch, Markus
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Electricity.
    Parak, F. G.
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Klintenberg, Mattias
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Materials Science, Materials Theory.
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Radiation damage in biological material: electronic properties and electron impact ionization in urea2009In: Europhysics letters, ISSN 0295-5075, E-ISSN 1286-4854, Vol. 85, no 1, p. 18005-Article in journal (Refereed)
    Abstract [en]

    Radiation damage is an unavoidable process when performing structural investigations of biological macromolecules with X-rays. In crystallography this process can be limited through damage distribution in a crystal, while for single molecular imaging it can be outrun by employing short intense pulses. Secondary electron generation is crucial during damage formation and we present a study of urea, as model for biomaterial. From first principles we calculate the band structure and energy loss function, and subsequently the inelastic electron cross-section in urea. Using Molecular Dynamics simulations, we quantify the damage and study the magnitude and spatial extent of the electron cloud coming from an incident electron, as well as the dependence with initial energy.

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  • 19.
    Caleman, Carl
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and condensed matter physics.
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and condensed matter physics. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Martin, Andrew V.
    Jönsson, H. Olof
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and condensed matter physics.
    Aquila, Andrew
    Barty, Anton
    Scott, Howard A.
    White, Thomas A.
    Chapman, Henry N.
    Ultrafast self-gating Bragg diffraction of exploding nanocrystals in an X-ray laser2015In: Optics Express, E-ISSN 1094-4087, Vol. 23, no 2, p. 1213-1231Article in journal (Refereed)
    Abstract [en]

    In structural determination of crystalline proteins using intense femtosecond X-ray lasers, damage processes lead to loss of structural coherence during the exposure. We use a nonthermal description for the damage dynamics to calculate the ultrafast ionization and the subsequent atomic displacement. These effects degrade the Bragg diffraction on femtosecond time scales and gate the ultrafast imaging. This process is intensity and resolution dependent. At high intensities the signal is gated by the ionization affecting low resolution information first. At lower intensities, atomic displacement dominates the loss of coherence affecting high-resolution information. We find that pulse length is not a limiting factor as long as there is a high enough X-ray flux to measure a diffracted signal.

  • 20.
    Caleman, Carl
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and condensed matter physics.
    Tîmneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Martin, A. V.
    White, T. A.
    Scott, H. A.
    Barty, A.
    Aquila, A.
    Chapman, H. N.
    Modeling of XFEL induced ionization and atomic displacement in protein nanocrystals2012In: Proceedings of SPIE: The International Society for Optical Engineering, 2012, p. 85040H-Conference paper (Refereed)
    Abstract [en]

    X-ray free-electron lasers enable high-resolution imaging of biological materials by using short enough pulses to outrun many of the effects of radiation damage. Experiments conducted at the LCLS have obtained diffraction data from single particles and protein nanocrystals at doses to the sample over 3 GGy. The details of the interaction of the X-ray FEL pulse with the sample determine the limits of this new paradigm for imaging. Recent studies suggest that in the case of crystalline samples, such as protein nanocrystals, the atomic displacements and loss of bound electrons in the crystal (due to the high X- ray intensity) has the effect of gating the diffraction signal, and hence making the experiment less radiation sensitive. Only the incident photon intensity in the first part of the pulse, before the Bragg diffraction has died out, is relevant to acquiring signal and the rest of the pulse will mainly contribute to a diffuse background. In this work we use a plasma based non-local thermodynamic equilibrium code to explore the displacement and the ionization of a protein nanocrystal at various X-ray wavelengths and intensities.

  • 21.
    Caleman, Carl
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    van der Spoel, David
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Evaporation from water clusters containing singly charged ions2007In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 9, no 37, p. 5105-5111Article in journal (Refereed)
    Abstract [en]

    Molecular dynamics simulations were used to study the evaporation from water clusterscontaining either ClÀ, H2PO4À, Na+ or NH4+ ions. The simulations ranged between 10 and500 ns, and were performed in vacuum starting at 275 K. A number of different models were usedincluding polarizable models. The clusters contain 216 or 512 molecules, 0, 4 or 8 of which wereions. The ions with hydrogen bonding properties do not affect evaporation, even though thephosphate ions have a pronounced ion–ion structure and tend to be inside the cluster whereasammonium shows little ion–ion structure and has a distribution within the cluster similar to thatof the water molecules. Since the individual ion–water interactions are much stronger in the caseof Na+–water and ClÀ–water clusters, evaporation is somewhat slower for clusters containingthese ions. It seems therefore that the main determinant of the evaporation rate in ion–waterclusters is the strength of the interaction. Fission of droplets that contain more ions than allowedaccording to the Rayleigh limit seems to occur more rapidly in clusters containing ammoniumand sodium ions.

  • 22.
    Caleman, Carl
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    van der Spoel, David
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Picosecond Melting of Ice by an Infrared Laser Pulse2008In: Angewandte Chemie International Edition, ISSN 1433-7851, E-ISSN 1521-3773, Vol. 47, no 8, p. 1417-1420Article in journal (Refereed)
    Abstract [en]

    Cold as ice: Molecular dynamics simulation provides snapshots of a melting ice crystal (see picture). The laser pulse heats up the system, and the energy is absorbed in the OH bonds. After a few picoseconds, the energy is transferred to rotational and translational energy, causing the crystal to melt. The melting starts as a nucleation process, and even long after the first melting is initialized, pockets of crystalline structures can be found.

  • 23.
    Caleman, Carl
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    van der Spoel, David
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Temperature and structural changes of water clusters in vacuum due to evaporation2006In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 125, no 15, p. 154508-Article in journal (Refereed)
    Abstract [en]

    This paper presents a study on evaporation of pure water clusters. Molecular dynamics simulations between 20 ns and 3 mu s of clusters ranging from 125 to 4096 molecules in vacuum were performed. Three different models (SPC, TIP4P, and TIP5P) were used to simulate water, starting at temperatures of 250, 275, and 300 K. We monitored the temperature, the number of hydrogen bonds, the tetrahedral order, the evaporation, the radial distribution functions, and the diffusion coefficients. The three models behave very similarly as far as temperature and evaporation are concerned. Clusters starting at a higher temperature show a higher initial evaporation rate and therefore reach the point where evaporation stop (around 240 K) sooner. The radius of the clusters is decreased by 0.16-0.22 nm after 0.5 mu s (larger clusters tend to decrease their radius slightly more), which corresponds to around one evaporated molecule per nm(2). The cluster temperature seems to converge towards 215 K independent of cluster size, when starting at 275 K. We observe only small structural changes, but the clusters modeled by TIP5P show a larger percentage of molecules with low diffusion coefficient as t ->infinity, than those using the two other water models. TIP4P seems to be more structured and more hydrogen bonds are formed than in the other models as the temperature falls. The cooling rates are in good agreement with experimental results, and evaporation rates agree well with a phenomenological expression based on experimental observations.

  • 24. Caleman, Carl
    et al.
    van Maaren, Paul J.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Hong, Minyan
    Hub, Jochen S.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Costa, Luciano T.
    van der Spoer, David
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology.
    Force Field Benchmark of Organic Liquids: Density, Enthalpy of Vaporization, Heat Capacities, Surface Tension, Isothermal Compressibility, Volumetric Expansion Coefficient, and Dielectric Constant2012In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 8, no 1, p. 61-74Article in journal (Refereed)
    Abstract [en]

    The chemical composition of small organic molecules is often very similar to amino acid side chains or the bases in nucleic acids, and hence there is no a priori reason why a molecular mechanics force field could not describe both organic liquids and biomolecules with a single parameter set. Here, we devise a benchmark for force fields in order to test the ability of existing force fields to reproduce some key properties of organic liquids, namely, the density, enthalpy of vaporization, the surface tension, the heat capacity at constant volume and pressure, the isothermal compressibility, the volumetric expansion coefficient, and the static dielectric constant. Well over 1200 experimental measurements were used for comparison to the simulations of 146 organic liquids. Novel polynomial interpolations of the dielectric constant (32 molecules), heat capacity at constant pressure (three molecules), and the isothermal compressibility (53 molecules) as a function of the temperature have been made, based on experimental data, in order to be able to compare simulation results to them. To compute the heat capacities, we applied the two phase thermodynamics method (Lin et al. J. Chem. Phys. 2003, 119, 11792), which allows one to compute thermodynamic properties on the basis of the density of states as derived from the velocity autocorrelation function. The method is implemented in a new utility within the GROMACS molecular simulation package, named g_dos, and a detailed expose of the underlying equations is presented. The purpose of this work is to establish the state of the art of two popular force fields, OPLS/AA (all-atom optimized potential for liquid simulation) and GAFF (generalized Amber force field), to find common bottlenecks, i.e., particularly difficult molecules, and to serve as a reference point for future force field development. To make for a fair playing field, all molecules were evaluated with the same parameter settings, such as thermostats and barostats, treatment of electrostatic interactions, and system size (1000 molecules). The densities and enthalpy of vaporization from an independent data set based on simulations using the CHARMM General Force Field (CGenFF) presented by Vanommeslaeghe et al. (J. Comput. Chem. 2010, 31, 671) are included for comparison. We find that, overall, the OPLS/AA force field performs somewhat better than GAFF, but there are significant issues with reproduction of the surface tension and dielectric constants for both force fields.

  • 25.
    Candanedo, J.
    et al.
    Arizona State Univ, Dept Phys, Tempe, AZ 85282 USA..
    Caleman, C
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics. DESY, Ctr Free Electron Laser Sci, Notkestr 85, Hamburg, Germany..
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Beckstein, O.
    Arizona State Univ, Dept Phys, Tempe, AZ 85282 USA.;Arizona State Univ, Ctr Biol Phys, Tempe, AZ 85282 USA..
    Spence, J. C. H.
    Arizona State Univ, Dept Phys, Tempe, AZ 85282 USA..
    Dynamics of rare gas solids irradiated by electron beams2020In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 152, no 14, article id 144303Article in journal (Refereed)
    Abstract [en]

    The remarkable success of x-ray free-electron lasers and their ability to image biological macromolecules while outrunning secondary radiation damage due to photoelectrons, by using femtosecond pulses, raise the question of whether this can be done using pulsed high-energy electron beams. In this paper, we use excited state molecular dynamics simulations, with tabulated potentials, for rare gas solids to investigate the effect of radiation damage due to inelastic scattering (by plasmons, excitons, and heat) on the pair distribution function. We use electron energy loss spectra to characterize the electronic excitations responsible for radiation damage.

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  • 26.
    Cardoch, Sebastian
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics.
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics.
    Caleman, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics. Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany.
    Scheicher, Ralph H.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Distinguishing between Similar Miniproteins with Single-Molecule Nanopore Sensing: A Computational Study2022In: ACS Nanoscience Au, E-ISSN 2694-2496, Vol. 2, no 2, p. 119-127Article in journal (Refereed)
    Abstract [en]

    A nanopore is a tool in single-molecule sensing biotechnology that offers label-free identification with high throughput. Nanopores have been successfully applied to sequence DNA and show potential in the study of proteins. Nevertheless, the task remains challenging due to the large variability in size, charges, and folds of proteins. Miniproteins have a small number of residues, limited secondary structure, and stable tertiary structure, which can offer a systematic way to reduce complexity. In this computational work, we theoretically evaluated sensing two miniproteins found in the human body using a silicon nitride nanopore. We employed molecular dynamics methods to compute occupied-pore ionic current magnitudes and electronic structure calculations to obtain interaction strengths between pore wall and miniprotein. From the interaction strength, we derived dwell times using a mix of combinatorics and numerical solutions. This latter approach circumvents typical computational demands needed to simulate translocation events using molecular dynamics. We focused on two miniproteins potentially difficult to distinguish owing to their isotropic geometry, similar number of residues, and overall comparable structure. We found that the occupied-pore current magnitudes not to vary significantly, but their dwell times differ by 1 order of magnitude. Together, these results suggest a successful identification protocol for similar miniproteins.

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  • 27.
    Cardoch, Sebastian
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics.
    Trost, Fabian
    Scott, Howard A.
    Chapman, Henry N.
    Caleman, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics.
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics.
    Decreasing ultrafast x-ray pulse durations with saturable absorption and resonant transitions2023In: Physical review. E, ISSN 2470-0045, E-ISSN 2470-0053, Vol. 107, no 1, article id 015205Article in journal (Refereed)
    Abstract [en]

    Saturable absorption is a nonlinear effect where a material's ability to absorb light is frustrated due to a high influx of photons and the creation of electron vacancies. Experimentally induced saturable absorption in copper revealed a reduction in the temporal duration of transmitted x-ray laser pulses, but a detailed account of changes in opacity and emergence of resonances is still missing. In this computational work, we employ nonlocal thermodynamic equilibrium plasma simulations to study the interaction of femtosecond x rays and copper. Following the onset of frustrated absorption, we find that a K–M resonant transition occurring at highly charged states turns copper opaque again. The changes in absorption generate a transient transparent window responsible for the shortened transmission signal. We also propose using fluorescence induced by the incident beam as an alternative source to achieve shorter x-ray pulses. Intense femtosecond x rays are valuable to probe the structure and dynamics of biological samples or to reach extreme states of matter. Shortened pulses could be relevant for emerging imaging techniques.

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  • 28. Cavalieri, A L
    et al.
    Fritz, D M
    Lee, S H
    Bucksbaum, P H
    Reis, D A
    Rudati, J
    Mills, D M
    Fuoss, P H
    Stephenson, G B
    Kao, C C
    Siddons, D P
    Lowney, D P
    Macphee, A G
    Weinstein, D
    Falcone, R W
    Pahl, R
    Als-Nielsen, J
    Blome, C
    Düsterer, S
    Ischebeck, R
    Schlarb, H
    Schulte-Schrepping, H
    Tschentscher, Th
    Schneider, J
    Hignette, O
    Sette, F
    Sokolowski-Tinten, K
    Chapman, H N
    Lee, R W
    Hansen, T N
    Synnergren, O
    Larsson, J
    Techert, S
    Sheppard, J
    Wark, J S
    Bergh, M
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Cell and Molecular Biology. Molekylär biofysik.
    Caleman, C
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Cell and Molecular Biology. Molekylär biofysik.
    Huldt, G
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Cell and Molecular Biology. Molekylär biofysik.
    van der Spoel, D
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Cell and Molecular Biology. Molekylär biofysik.
    Timneanu, N
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Cell and Molecular Biology. Molekylär biofysik.
    Hajdu, J
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Cell and Molecular Biology. Molekylär biofysik.
    Akre, R A
    Bong, E
    Emma, P
    Krejcik, P
    Arthur, J
    Brennan, S
    Gaffney, K J
    Lindenberg, A M
    Luening, K
    Hastings, J B
    Clocking femtosecond X rays.2005In: Phys Rev Lett, ISSN 0031-9007, Vol. 94, no 11, p. 114801-Article in journal (Refereed)
    Abstract [en]

    Linear-accelerator-based sources will revolutionize ultrafast x-ray science due to their unprecedented brightness and short pulse duration. However, time-resolved studies at the resolution of the x-ray pulse duration are hampered by the inability to precisely synchronize an external laser to the accelerator. At the Sub-Picosecond Pulse Source at the Stanford Linear-Accelerator Center we solved this problem by measuring the arrival time of each high energy electron bunch with electro-optic sampling. This measurement indirectly determined the arrival time of each x-ray pulse relative to an external pump laser pulse with a time resolution of better than 60 fs rms.

  • 29. Chalupsky, J.
    et al.
    Juha, L.
    Kuba, J.
    Cihelka, J.
    Hajkova, V.
    Koptyaev, S.
    Krasa, J.
    Velyhan, A.
    Bergh, Magnus
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Caleman, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Bionta, R. M.
    Chapman, H.
    Hau-Riege, S. P.
    London, R. A.
    Jurek, M.
    Krzywinski, J.
    Nietubyc, R.
    Pelka, J. B.
    Sobierajski, R.
    Meyer-ter-Vehn, J.
    Tronnier, A.
    Sokolowski-Tinten, K.
    Stojanovic, N.
    Tiedtke, K.
    Toleikis, S.
    Tschentscher, T.
    Wabnitz, H.
    Zastrau, U.
    Characteristics of focused soft X-ray free-electron laser beam determined by ablation of organic molecular solids2007In: Optics Express, E-ISSN 1094-4087, Vol. 15, no 10, p. 6036-6043Article in journal (Refereed)
    Abstract [en]

    A linear accelerator based source of coherent radiation, FLASH (Free-electron LASer in Hamburg) provides ultra-intense femtosecond radiation pulses at wavelengths from the extreme ultraviolet (XUV; lambda< 100nm) to the soft X-ray (SXR; lambda<30nm) spectral regions. 25-fs pulses of 32-nm FLASH radiation were used to determine the ablation parameters of PMMA - poly ( methyl methacrylate). Under these irradiation conditions the attenuation length and ablation threshold were found to be (56.9 +/- 7.5) nm and similar to 2 mJ center dot cm(-2), respectively. For a second wavelength of 21.7 nm, the PMMA ablation was utilized to image the transverse intensity distribution within the focused beam at mu m resolution by a method developed here.

  • 30. Chapman, Henry N.
    et al.
    Barty, Anton
    Bogan, Michael J.
    Boutet, Sebastien
    Frank, Matthias
    Hau-Riege, Stefan P.
    Marchesini, Stefano
    Woods, Bruce W.
    Bajt, Sasa
    Benner, Henry
    London, Richard A.
    Ploenjes, Elke
    Kuhlmann, Marion
    Treusch, Rolf
    Duesterer, Stefan
    Tschentscher, Thomas
    Schneider, Jochen R.
    Spiller, Eberhard
    Moeller, Thomas
    Bostedt, Christoph
    Hoener, Matthias
    Shapiro, David A.
    Hodgson, Keith O.
    van der Spoel, David
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Bergh, Magnus
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Caleman, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Huldt, Gösta
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Seibert, Marvin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Maia, Filipe
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Lee, Richard W.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Szöke, Abraham
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology. Molekylär Biofysik.
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology. Molekylär Biofysik.
    Femtosecond diffractive imaging with a soft-X-ray free-electron laser2006In: Nature Physics, ISSN 1745-2473, E-ISSN 1745-2481, Vol. 2, no 12, p. 839-843Article in journal (Refereed)
    Abstract [en]

    Theory predicts(1-4) that, with an ultrashort and extremely bright coherent X-ray pulse, a single diffraction pattern may be recorded from a large macromolecule, a virus or a cell before the sample explodes and turns into a plasma. Here we report the first experimental demonstration of this principle using the FLASH soft-X-ray free-electron laser. An intense 25 fs, 4 x 10(13) W cm(-2) pulse, containing 10(12) photons at 32 nm wavelength, produced a coherent diffraction pattern from a nanostructured non-periodic object, before destroying it at 60,000 K. A novel X-ray camera assured single-photon detection sensitivity by filtering out parasitic scattering and plasma radiation. The reconstructed image, obtained directly from the coherent pattern by phase retrieval through oversampling(5-9), shows no measurable damage, and is reconstructed at the diffraction-limited resolution. A three-dimensional data set may be assembled from such images when copies of a reproducible sample are exposed to the beam one by one(10).

  • 31. Chapman, Henry N.
    et al.
    Caleman, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and condensed matter physics.
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and condensed matter physics. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Diffraction before destruction2014In: Philosophical Transactions of the Royal Society of London. Biological Sciences, ISSN 0962-8436, E-ISSN 1471-2970, Vol. 369, no 1647, p. 20130313-Article in journal (Refereed)
    Abstract [en]

    X-ray free-electron lasers have opened up the possibility of structure determination of protein crystals at room temperature, free of radiation damage. The femtosecond-duration pulses of these sources enable diffraction signals to be collected from samples at doses of 1000 MGy or higher. The sample is vaporized by the intense pulse, but not before the scattering that gives rise to the diffraction pattern takes place. Consequently, only a single flash diffraction pattern can be recorded from a crystal, giving rise to the method of serial crystallography where tens of thousands of patterns are collected from individual crystals that flow across the beam and the patterns are indexed and aggregated into a set of structure factors. The high-dose tolerance and the many-crystal averaging approach allow data to be collected from much smaller crystals than have been examined at synchrotron radiation facilities, even from radiation-sensitive samples. Here, we review the interaction of intense femtosecond X-ray pulses with materials and discuss the implications for structure determination. We identify various dose regimes and conclude that the strongest achievable signals for a given sample are attained at the highest possible dose rates, from highest possible pulse intensities.

  • 32. Chapman, Henry N.
    et al.
    Fromme, Petra
    Barty, Anton
    White, Thomas A.
    Kirian, Richard A.
    Aquila, Andrew
    Hunter, Mark S.
    Schulz, Joachim
    DePonte, Daniel P.
    Weierstall, Uwe
    Doak, R. Bruce
    Maia, Filipe R. N. C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Martin, Andrew V.
    Schlichting, Ilme
    Lomb, Lukas
    Coppola, Nicola
    Shoeman, Robert L.
    Epp, Sascha W.
    Hartmann, Robert
    Rolles, Daniel
    Rudenko, Artem
    Foucar, Lutz
    Kimmel, Nils
    Weidenspointner, Georg
    Holl, Peter
    Liang, Mengning
    Barthelmess, Miriam
    Caleman, Carl
    Boutet, Sebastien
    Bogan, Michael J.
    Krzywinski, Jacek
    Bostedt, Christoph
    Bajt, Sasa
    Gumprecht, Lars
    Rudek, Benedikt
    Erk, Benjamin
    Schmidt, Carlo
    Hoemke, Andre
    Reich, Christian
    Pietschner, Daniel
    Strueder, Lothar
    Hauser, Guenter
    Gorke, Hubert
    Ullrich, Joachim
    Herrmann, Sven
    Schaller, Gerhard
    Schopper, Florian
    Soltau, Heike
    Kuehnel, Kai-Uwe
    Messerschmidt, Marc
    Bozek, John D.
    Hau-Riege, Stefan P.
    Frank, Matthias
    Hampton, Christina Y.
    Sierra, Raymond G.
    Starodub, Dmitri
    Williams, Garth J.
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Seibert, M. Marvin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Andreasson, Jakob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Rocker, Andrea
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Jönsson, Olof
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Svenda, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Stern, Stephan
    Nass, Karol
    Andritschke, Robert
    Schroeter, Claus-Dieter
    Krasniqi, Faton
    Bott, Mario
    Schmidt, Kevin E.
    Wang, Xiaoyu
    Grotjohann, Ingo
    Holton, James M.
    Barends, Thomas R. M.
    Neutze, Richard
    Marchesini, Stefano
    Fromme, Raimund
    Schorb, Sebastian
    Rupp, Daniela
    Adolph, Marcus
    Gorkhover, Tais
    Andersson, Inger
    SLU.
    Hirsemann, Helmut
    Potdevin, Guillaume
    Graafsma, Heinz
    Nilsson, Björn
    Spence, John C. H.
    Femtosecond X-ray protein nanocrystallography2011In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 470, no 7332, p. 73-77Article in journal (Refereed)
    Abstract [en]

    X-ray crystallography provides the vast majority of macromolecular structures, but the success of the method relies on growing crystals of sufficient size. In conventional measurements, the necessary increase in X-ray dose to record data from crystals that are too small leads to extensive damage before a diffraction signal can be recorded(1-3). It is particularly challenging to obtain large, well-diffracting crystals of membrane proteins, for which fewer than 300 unique structures have been determined despite their importance in all living cells. Here we present a method for structure determination where single-crystal X-ray diffraction 'snapshots' are collected from a fully hydrated stream of nanocrystals using femtosecond pulses from a hard-X-ray free-electron laser, the Linac Coherent Light Source(4). We prove this concept with nanocrystals of photosystem I, one of the largest membrane protein complexes(5). More than 3,000,000 diffraction patterns were collected in this study, and a three-dimensional data set was assembled from individual photosystem I nanocrystals (similar to 200 nm to 2 mm in size). We mitigate the problem of radiation damage in crystallography by using pulses briefer than the timescale of most damage processes(6). This offers a new approach to structure determination of macromolecules that do not yield crystals of sufficient size for studies using conventional radiation sources or are particularly sensitive to radiation damage.

  • 33. Chapman, Henry N
    et al.
    Hau-Riege, Stefan P
    Bogan, Michael J
    Bajt, Sasa
    Barty, Anton
    Boutet, Sébastien
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Marchesini, Stefano
    Frank, Matthias
    Woods, Bruce W
    Benner, W Henry
    London, Richard A
    Rohner, Urs
    Szöke, Abraham
    Spiller, Eberhard
    Möller, Thomas
    Bostedt, Christoph
    Shapiro, David A
    Kuhlmann, Marion
    Treusch, Rolf
    Plönjes, Elke
    Burmeister, Florian
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Bergh, Magnus
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Caleman, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Huldt, Gösta
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Seibert, M. Marvin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Femtosecond time-delay X-ray holography2007In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 448, no 7154, p. 676-679Article in journal (Refereed)
    Abstract [en]

    Extremely intense and ultrafast X-ray pulses from free-electron lasers offer unique opportunities to study fundamental aspects of complex transient phenomena in materials. Ultrafast time-resolved methods usually require highly synchronized pulses to initiate a transition and then probe it after a precisely defined time delay. In the X-ray regime, these methods are challenging because they require complex optical systems and diagnostics. Here we propose and apply a simple holographic measurement scheme, inspired by Newton's 'dusty mirror' experiment1, to monitor the X-ray-induced explosion of microscopic objects. The sample is placed near an X-ray mirror; after the pulse traverses the sample, triggering the reaction, it is reflected back onto the sample by the mirror to probe this reaction. The delay is encoded in the resulting diffraction pattern to an accuracy of one femtosecond, and the structural change is holographically recorded with high resolution. We apply the technique to monitor the dynamics of polystyrene spheres in intense free-electron-laser pulses, and observe an explosion occurring well after the initial pulse. Our results support the notion that X-ray flash imaging2, 3 can be used to achieve high resolution, beyond radiation damage limits for biological samples4. With upcoming ultrafast X-ray sources we will be able to explore the three-dimensional dynamics of materials at the timescale of atomic motion.

  • 34.
    Dawod, Ibrahim
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics. European XFEL, Holzkoppel 4, DE-22869 Schenefeld, Germany.
    Cardoch, Sebastian
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics.
    André, Tomas
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics.
    De Santis, Emiliano
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Biochemistry.
    E, Juncheng
    European XFEL, Holzkoppel 4, DE-22869 Schenefeld, Germany.
    Mancuso, Adrian P.
    European XFEL, Holzkoppel 4, DE-22869 Schenefeld, Germany. Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia. Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK.
    Caleman, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics. Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Notkestraße 85 DE-22607 Hamburg, Germany.
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics.
    MolDStruct: modelling the dynamics and structure of matter exposed to ultrafast X-ray lasers with hybrid collisional-radiative/molecular dynamicsManuscript (preprint) (Other academic)
    Abstract [en]

    We describe a method to compute photon-matter interaction and atomic dynamics with X-ray lasers using a hybrid code based on classical molecular dynamics and collisional-radiative calculations. The forces between the atoms are dynamically computed based on changes to their electronic occupations and the free electron cloud created due to the irradiation of photons in the X-ray spectrum. The rapid transition from neutral solid matter to dense plasma phase allows the use of screened potentials, which reduces the number of non-bonded interactions required to compute. In combination with parallelization through domain decomposition, large-scale molecular dynamics and ionization induced by X-ray lasers can be followed. This method is applicable for large enough samples (solids, liquids, proteins, viruses, atomic clusters and crystals) that when exposed to an X-ray laser pulse turn into a plasma in the first few femtoseconds of the interaction. We show several examples of the applicability of the method and we quantify the sizes that the method is suitable for. For large systems, we investigate non-thermal heating and scattering of bulk water, which we compare to previous experiments. We simulate molecular dynamics of a protein crystal induced by an X-ray pump, X-ray probe scheme, and find good agreement of the damage dynamics with experiments. For single particle imaging, we simulate ultrafast dynamics of a methane cluster exposed to a femtosecond X-ray laser. In the context of coherent diffractive imaging we study the fragmentation as given by an X-ray pump X-ray probe setup to understand the evolution of radiation damage.

  • 35.
    Dawod, Ibrahim
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics. European XFEL, Holzkoppel 4, DE-22869 Schenefeld, Germany.
    Patra Kumar, Kajwal
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics.
    Cardoch, Sebastian
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics.
    Jönsson, H. Olof
    Department of Applied physics, KTH Royal Institute of Technology, SE-106 91, Stockholm, Sweden.
    Sellberg, Jonas A.
    Department of Applied physics, KTH Royal Institute of Technology, SE-106 91, Stockholm, Sweden.
    Martin, Andrew V.
    School of Science, RMIT University, Melbourne, Victoria 3000, Australia.
    Binns, Jack
    School of Science, RMIT University, Melbourne, Victoria 3000, Australia.
    Grånäs, Oscar
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Mancuso, Adrian P.
    European XFEL, Holzkoppel 4, DE-22869 Schenefeld, Germany. Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia. Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK .
    Caleman, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics. Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Notkestraße 85 DE-22607 Hamburg, Germany.
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics.
    Anisotropic melting of ice induced by ultrafast non-thermal heatingManuscript (preprint) (Other academic)
    Abstract [en]

    Water and ice are routinely studied with X-rays to reveal their diverse structures and anomalous properties. We employ a hybrid collisional-radiative/molecular dynamics method to explore how femtosecond X-ray pulses interact with hexagonal ice. We find that ice makes a phase transition into a crystalline plasma where its initial structure is maintained up to tens of femtoseconds. The ultrafast melting process occurs anisotropically, where different geometric configurations of the structure melt on different time scales. The transient state and anisotropic melting of crystals can be captured by X-ray diffraction, which impacts any study of crystalline structures probed by femtosecond X-ray lasers.

  • 36.
    Duelfer, Jasmin
    et al.
    Leibniz Inst Expt Virol, Heinrich Pette Inst, D-20251 Hamburg, Germany.
    Yan, Hao
    Leibniz Inst Expt Virol, Heinrich Pette Inst, D-20251 Hamburg, Germany.
    Brodmerkel, Maxim N.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Biochemistry.
    Creutznacher, Robert
    Univ Lubeck, Inst Chem & Metabol, D-23562 Lübeck, Germany.
    Mallagaray, Alvaro
    Univ Lubeck, Inst Chem & Metabol, D-23562 Lübeck, Germany.
    Peters, Thomas
    Univ Lubeck, Inst Chem & Metabol, D-23562 Lübeck, Germany.
    Caleman, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics. DESY, Ctr Free Electron Laser Sci, D-22607 Hamburg, Germany.
    Marklund, Erik G.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Biochemistry.
    Uetrecht, Charlotte
    Leibniz Inst Expt Virol, Heinrich Pette Inst, D-20251 Hamburg, Germany; European XFEL GmbH, D-22869 Schenefeld, Germany.
    Glycan-Induced Protein Dynamics in Human Norovirus P Dimers Depend on Virus Strain and Deamidation Status2021In: Molecules, ISSN 1431-5157, E-ISSN 1420-3049, Vol. 26, no 8, article id 2125Article in journal (Refereed)
    Abstract [en]

    Noroviruses are the major cause of viral gastroenteritis and re-emerge worldwide every year, with GII.4 currently being the most frequent human genotype. The norovirus capsid protein VP1 is essential for host immune response. The P domain mediates cell attachment via histo blood-group antigens (HBGAs) in a strain-dependent manner but how these glycan-interactions actually relate to cell entry remains unclear. Here, hydrogen/deuterium exchange mass spectrometry (HDX-MS) is used to investigate glycan-induced protein dynamics in P dimers of different strains, which exhibit high structural similarity but different prevalence in humans. While the almost identical strains GII.4 Saga and GII.4 MI001 share glycan-induced dynamics, the dynamics differ in the emerging GII.17 Kawasaki 308 and rare GII.10 Vietnam 026 strain. The structural aspects of glycan binding to fully deamidated GII.4 P dimers have been investigated before. However, considering the high specificity and half-life of N373D under physiological conditions, large fractions of partially deamidated virions with potentially altered dynamics in their P domains are likely to occur. Therefore, we also examined glycan binding to partially deamidated GII.4 Saga and GII.4 MI001 P dimers. Such mixed species exhibit increased exposure to solvent in the P dimer upon glycan binding as opposed to pure wildtype. Furthermore, deamidated P dimers display increased flexibility and a monomeric subpopulation. Our results indicate that glycan binding induces strain-dependent structural dynamics, which are further altered by N373 deamidation, and hence hint at a complex role of deamidation in modulating glycan-mediated cell attachment in GII.4 strains.

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  • 37.
    Ekholm, Victor
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Caleman, C
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Walz, Marie-Madeleine
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational Biology and Bioinformatics.
    Werner, Josephina
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Öhrwall, Gunnar
    Rubensson, Jan-Erik
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Björneholm, Olle
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Surface propensity of atmospherically relevant carboxylates and alkyl ammonium ions studied by XPS: towards a building-block model of surface propensity based on Langmuir adsorptionManuscript (preprint) (Other academic)
  • 38.
    Ekholm, Victor
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Caleman, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics. DESY, Ctr Free Elec Laser Sci, Notkestr 85, DE-22607 Hamburg, Germany.
    Bjärnhall Prytz, Nicklas
    Royal Inst Tech, Dept App Phys, Roslagstullsbacken 21, SE-11421 Stockholm, Sweden.
    Walz, Marie-Madeleine
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational Biology and Bioinformatics.
    Werner, Josephina
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Öhrwall, Gunnar
    Lund Univ, MAX Lab 4, Box 118, SE-22100 Lund, Sweden.
    Rubensson, Jan-Erik
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Björneholm, Olle
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Strong Enrichment of Atmospherically Relevant Organic Ions at the Aqueous Interface: The Role of Ion Pairing and Cooperative Effects2018In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 20, no 42, p. 27185-27191Article in journal (Refereed)
    Abstract [en]

    Surface affinity, orientation and ion pairing are investigated in mixed and single solute systems of aqueous sodium hexanoate and hexylammonium chloride. The surface sensitive X-ray photoelectron spectroscopy technique has been used to acquire the experimental results, while the computational data have been calculated using molecular dynamics simulations. By comparing the single solute solutions with the mixed one, we observe a non-linear surface enrichment and reorientation of the organic ions with their alkyl chains pointing out of the aqueous surface. We ascribe this effect to ion paring between the charged functional groups on the respective organic ion and hydrophobic expulsion of the alkyl chains from the surface in combination with van der Waals interactions between the alkyl chains. These cooperative effects lead to a substantial surface enrichment of organic ions, with consequences for aerosol surface properties.

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  • 39.
    Ekholm, Victor
    et al.
    Max IV Laboratory, Box 118, SE-221 00 Lund, Sweden.
    Caleman, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy. Center for Free-Electron Laser Science, DESY, Notkestraß e 85, DE-22607 Hamburg, Germany.
    Hub, Jochen S.
    Theoretical Physics and Center for Biophysics, Saarland University, DE-66123 Saarbrücken, Germany.
    Wohlert, Malin
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Materials Science and Engineering, Applied Mechanics.
    Propensity, free energy contributions and conformation of primary n-alcohols at a water surface2021In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 23, no 34, p. 18823-18829Article in journal (Refereed)
  • 40.
    Eliah Dawod, Ibrahim
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics. European XFEL, Holzkoppel 4, DE-22869 Schenefeld, Germany.
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics.
    Mancuso, Adrian P.
    European XFEL, Holzkoppel 4, DE-22869 Schenefeld, Germany.;La Trobe Univ, La Trobe Inst Mol Sci, Dept Chem & Phys, Melbourne, Vic 3086, Australia..
    Caleman, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics. DESY, Ctr Free Electron Laser Sci, Notkestr 85, DE-22607 Hamburg, Germany.
    Grånäs, Oscar
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Imaging of femtosecond bond breaking and charge dynamics in ultracharged peptides2022In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 24, no 3, p. 1532-1543Article in journal (Refereed)
    Abstract [en]

    X-ray free-electrons lasers have revolutionized the method of imaging biological macromolecules such as proteins, viruses and cells by opening the door to structural determination of both single particles and crystals at room temperature. By utilizing high intensity X-ray pulses on femtosecond timescales, the effects of radiation damage can be reduced. Achieving high resolution structures will likely require knowledge of how radiation damage affects the structure on an atomic scale, since the experimentally obtained electron densities will be reconstructed in the presence of radiation damage. Detailed understanding of the expected damage scenarios provides further information, in addition to guiding possible corrections that may need to be made to obtain a damage free reconstruction. In this work, we have quantified the effects of ionizing photon-matter interactions using first principles molecular dynamics. We utilize density functional theory to calculate bond breaking and charge dynamics in three ultracharged molecules and two different structural conformations that are important to the structural integrity of biological macromolecules, comparing to our previous studies on amino acids. The effects of the ultracharged states and subsequent bond breaking in real space are studied in reciprocal space using coherent diffractive imaging of an ensemble of aligned biomolecules in the gas phase.

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  • 41.
    Gabrysch, Markus
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Electricity.
    Marklund, Erik
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Twitchen, D. J.
    Element Six Ltd, Ascot SL5 8BP, Berks, England.
    Rudati, J.
    Stanford Linear Accelerator Ctr, PULSE Ctr, Menlo Pk, CA 94025 USA.
    Lindenberg, A. M.
    Department of Materials Science and Engineering, Stanford University, Stanford, California 94305, USA; PULSE Center, Stanford Linear Accelerator Center, Menlo Park, California 94025, USA.
    Caleman, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Falcone, R. W.
    Department of Physics, University of California, Berkeley, California 94720, USA.
    Tschentscher, T.
    Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany.
    Moffat, K.
    Consortium for Advanced Radiation Sources, The University of Chicago, Chicago, Illinois 60637, USA.
    Bucksbaum, P. H.
    PULSE Center, Stanford Linear Accelerator Center, Menlo Park, California 94025, USA.
    Als-Nielsen, J.
    Niels Bohr Institute, Copenhagen University, 2100 Copenhagen Ø, Denmark.
    Nelson, A. J.
    Lawrence Livermore National Laboratory, Livermore, California 94550, USA.
    Siddons, D. P.
    National Synchrotron Light Source, Brookhaven National Laboratory, Upton, New York 11973, USA.
    Emma, P. J.
    Stanford Linear Accelerator Ctr, PULSE Ctr, Menlo Pk, CA 94025 USA.
    Krejcik, P.
    Stanford Linear Accelerator Ctr, PULSE Ctr, Menlo Pk, CA 94025 USA.
    Schlarb, H.
    Stanford Linear Accelerator Ctr, PULSE Ctr, Menlo Pk, CA 94025 USA.
    Arthur, J.
    Stanford Linear Accelerator Ctr, PULSE Ctr, Menlo Pk, CA 94025 USA.
    Brennan, S.
    Stanford Linear Accelerator Ctr, PULSE Ctr, Menlo Pk, CA 94025 USA.
    Hastings, J.
    Stanford Linear Accelerator Ctr, PULSE Ctr, Menlo Pk, CA 94025 USA.
    Isberg, Jan
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Electricity.
    Formation of secondary electron cascades in single-crystalline plasma-deposited diamond upon exposure to femtosecond x-ray pulses2008In: Journal of Applied Physics, ISSN 0021-8979, E-ISSN 1089-7550, Vol. 103, no 6, article id 064909Article in journal (Refereed)
    Abstract [en]

    Secondary electron cascades were measured in high purity single-crystalline chemical vapor deposition (CVD) diamond, following exposure to ultrashort hard x-ray pulses (140 fs full width at half maximum, 8.9 keV energy) from the Sub-Picosecond Pulse Source at the Stanford Linear Accelerator Center. We report measurements of the pair creation energy and of drift mobility of carriers in two CVD diamond crystals. This was done for the first time using femtosecond x-ray excitation. Values for the average pair creation energy were found to be 12.17 +/- 0.57 and 11.81 +/- 0.59 eV for the two crystals, respectively. These values are in good agreement with recent theoretical predictions. The average drift mobility of carriers, obtained by the best fit to device simulations, was mu(h)= 2750 cm(2)/V s for holes and was mu(e)= 2760 cm(2) / V s for electrons. These mobility values represent lower bounds for charge mobilities due to possible polarization of the samples. The results demonstrate outstanding electric properties and the enormous potential of diamond in ultrafast x-ray detectors.

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  • 42. Gaffney, K J
    et al.
    Lindenberg, A M
    Larsson, J
    Sokolowski-Tinten, K
    Blome, C
    Synnergren, O
    Sheppard, J
    Caleman, C
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Cell and Molecular Biology. Molecular Biophysics.
    MacPhee, A G
    Weinstein, D
    Lowney, D P
    Allison, T
    Matthews, T
    Falcone, R W
    Cavalieri, A L
    Fritz, D M
    Lee, S H
    Bucksbaum, P H
    Reis, D A
    Rudati, J
    Macrander, A T
    Fuoss, P H
    Kao, C C
    Siddons, D P
    Pahl, R
    Moffat, K
    Als-Nielsen, J
    Duesterer, S
    Ischebeck, R
    Schlarb, H
    Schulte-Schrepping, H
    Schneider, J
    von der Linde, D
    Hignette, O
    Sette, F
    Chapman, H N
    Lee, R W
    Hansen, T N
    Wark, J S
    Bergh, M
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Cell and Molecular Biology. Molecular Biophysics.
    Huldt, G
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Cell and Molecular Biology. Molecular Biophysics.
    van der Spoel, D
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Cell and Molecular Biology. Molecular Biophysics.
    Timneanu, N
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Cell and Molecular Biology. Molecular Biophysics.
    Hajdu, J
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Cell and Molecular Biology. Molecular Biophysics.
    Akre, R A
    Bong, E
    Krejcik, P
    Arthur, J
    Brennan, S
    Luening, K
    Hastings, J B
    Observation of structural anisotropy and the onset of liquidlike motion during the nonthermal melting of InSb.2005In: Phys Rev Lett, ISSN 0031-9007, Vol. 95, no 12, p. 125701-Article in journal (Other scientific)
  • 43.
    Galchenkova, Marina
    et al.
    Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Notkestraße 85, DE-22607 Hamburg, Germany.
    Dawod, Ibrahim
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics. European XFEL, Holzkoppel 4, DE-22869 Schenefeld, Germany.
    Sprenger, Janina
    Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Notkestraße 85, DE-22607 Hamburg, Germany.
    Oberthur, Dominik
    Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Notkestraße 85, DE-22607 Hamburg, Germany.
    Cardoch, Sebastian
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics.
    De Santis, Emiliano
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Biochemistry.
    Grånäs, Oscar
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics.
    Chapman, Henry N.
    Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Notkestraße 85, DE-22607 Hamburg, Germany. Centre for Ultrafast Imaging, Universität Hamburg, 22761 Hamburg, Germany. Department of Physics, Universität Hamburg, 22761 Hamburg, Germany .
    Caleman, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics. Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Notkestraße 85, DE-22607 Hamburg, Germany.
    Yefanov, Oleksandr
    Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Notkestraße 85, DE-22607 Hamburg, Germany.
    Radiation damage in a hemoglobin crystal studied with an X-ray free-electron laserManuscript (preprint) (Other academic)
    Abstract [en]

    Radiation damage is a topic since the dawn of X-ray crystallography, and has gained new importance in the era of X-ray free-electron lasers (XFELs), due to their unprecedented brilliance and pulse duration. One of the driving questions has been how short the XFEL pulse has to be for the structural information to be ”damage free”. Here we compare data from Serial Femtosecond Crystallography (SFX) experiments conducted with a 3 fs and a 10 fs X-ray pulse. We conclude that even if the estimated displacement of atoms in the sample is an order of magnitude larger in the case of the 10 fs experiment, the displacement is still too small to affect the experimental data at a resolution relevant for structural determination.

  • 44.
    Galli, L.
    et al.
    Deutsch Elektronen Synchrotron DESY, Ctr Free Electron Laser Sci, D-22607 Hamburg, Germany.;Univ Hamburg, Dept Phys, D-20355 Hamburg, Germany..
    Son, S. -K
    Klinge, M.
    Univ Hamburg, Inst Biochem & Mol Biol, Joint Lab Struct Biol Infect & Inflammat, D-22607 Hamburg, Germany.;Univ Lubeck, Inst Biochem, DESY, D-22607 Hamburg, Germany..
    Bajt, S.
    Deutsch Elektronen Synchrotron DESY, Photon Sci, D-22607 Hamburg, Germany..
    Barty, A.
    Deutsch Elektronen Synchrotron DESY, Ctr Free Electron Laser Sci, D-22607 Hamburg, Germany..
    Bean, R.
    Deutsch Elektronen Synchrotron DESY, Ctr Free Electron Laser Sci, D-22607 Hamburg, Germany..
    Betzel, C.
    Univ Hamburg, DESY, Inst Biochem & Mol Biol, Dept Chem, D-22607 Hamburg, Germany..
    Beyerlein, K. R.
    Deutsch Elektronen Synchrotron DESY, Ctr Free Electron Laser Sci, D-22607 Hamburg, Germany..
    Caleman, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics. Deutsch Elektronen Synchrotron DESY, Ctr Free Electron Laser Sci, D-22607 Hamburg, Germany..
    Doak, R. B.
    Max Planck Inst Med Res, Dept Biomol Mech, D-69120 Heidelberg, Germany..
    Duszenko, M.
    Univ Tubingen, Interfac Inst Biochem, D-72076 Tubingen, Germany..
    Fleckenstein, H.
    Deutsch Elektronen Synchrotron DESY, Ctr Free Electron Laser Sci, D-22607 Hamburg, Germany..
    Gati, C.
    Deutsch Elektronen Synchrotron DESY, Ctr Free Electron Laser Sci, D-22607 Hamburg, Germany..
    Hunt, B.
    Brigham Young Univ, Dept Phys & Astron, Provo, UT 84602 USA..
    Kirian, R. A.
    Deutsch Elektronen Synchrotron DESY, Ctr Free Electron Laser Sci, D-22607 Hamburg, Germany..
    Liang, M.
    Deutsch Elektronen Synchrotron DESY, Ctr Free Electron Laser Sci, D-22607 Hamburg, Germany..
    Nanao, M. H.
    EMBL, Grenoble Outstn, F-38042 Grenoble, France..
    Nass, K.
    Max Planck Inst Med Res, Dept Biomol Mech, D-69120 Heidelberg, Germany..
    Oberthuer, D.
    Deutsch Elektronen Synchrotron DESY, Ctr Free Electron Laser Sci, D-22607 Hamburg, Germany..
    Redecke, L.
    Univ Hamburg, Inst Biochem & Mol Biol, Joint Lab Struct Biol Infect & Inflammat, D-22607 Hamburg, Germany.;Univ Lubeck, Inst Biochem, DESY, D-22607 Hamburg, Germany..
    Shoeman, R.
    Max Planck Inst Med Res, Dept Biomol Mech, D-69120 Heidelberg, Germany..
    Stellato, F.
    Deutsch Elektronen Synchrotron DESY, Ctr Free Electron Laser Sci, D-22607 Hamburg, Germany..
    Yoon, C. H.
    Deutsch Elektronen Synchrotron DESY, Ctr Free Electron Laser Sci, D-22607 Hamburg, Germany.;European XFEL GmbH, D-22761 Hamburg, Germany..
    White, T. A.
    Deutsch Elektronen Synchrotron DESY, Ctr Free Electron Laser Sci, D-22607 Hamburg, Germany..
    Yefanov, O.
    Deutsch Elektronen Synchrotron DESY, Ctr Free Electron Laser Sci, D-22607 Hamburg, Germany..
    Spence, J.
    Arizona State Univ, Dept Phys, Tempe, AZ 85287 USA..
    Chapman, H. N.
    Deutsch Elektronen Synchrotron DESY, Ctr Free Electron Laser Sci, D-22607 Hamburg, Germany.;Univ Hamburg, Dept Phys, D-20355 Hamburg, Germany.;Hamburg Ctr Ultrafast Imaging, D-22761 Hamburg, Germany..
    Electronic damage in S atoms in a native protein crystal induced by an intense X-ray free-electron laser pulse2015In: Structural Dynamics, E-ISSN 2329-7778, Vol. 2, no 4, article id 041703Article in journal (Refereed)
    Abstract [en]

    Current hard X-ray free-electron laser (XFEL) sources can deliver doses to biological macromolecules well exceeding 1 GGy, in timescales of a few tens of femtoseconds. During the pulse, photoionization can reach the point of saturation in which certain atomic species in the sample lose most of their electrons. This electronic radiation damage causes the atomic scattering factors to change, affecting, in particular, the heavy atoms, due to their higher photoabsorption cross sections. Here, it is shown that experimental serial femtosecond crystallography data collected with an extremely bright XFEL source exhibit a reduction of the effective scattering power of the sulfur atoms in a native protein. Quantitative methods are developed to retrieve information on the effective ionization of the damaged atomic species from experimental data, and the implications of utilizing new phasing methods which can take advantage of this localized radiation damage are discussed.

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  • 45. Galli, Lorenzo
    et al.
    Son, Sang-Kil
    Barends, Thomas R. M.
    White, Thomas A.
    Barty, Anton
    Botha, Sabine
    Boutet, Sébastien
    Caleman, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Doak, R. Bruce
    Nanao, Max H.
    Nass, Karol
    Shoeman, Robert L.
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Santra, Robin
    Schlichting, Ilme
    Chapman, Henry N.
    Towards phasing using high X-ray intensity2015In: IUCrJ, E-ISSN 2052-2525, Vol. 2, p. 627-634Article in journal (Refereed)
    Abstract [en]

    X-ray free-electron lasers (XFELs) show great promise for macromolecular structure determination from sub-micrometre-sized crystals, using the emerging method of serial femtosecond crystallography. The extreme brightness of the XFEL radiation can multiply ionize most, if not all, atoms in a protein, causing their scattering factors to change during the pulse, with a preferential ‘bleaching’ of heavy atoms. This paper investigates the effects of electronic damage on experimental data collected from a Gd derivative of lysozyme microcrystals at different X-ray intensities, and the degree of ionization of Gd atoms is quantified from phased difference Fourier maps. A pattern sorting scheme is proposed to maximize the ionization contrast and the way in which the local electronic damage can be used for a new experimental phasing method is discussed.

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  • 46.
    Ghahremanpour, Mohammad Mehdi
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    van Maaren, Paul J.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Caleman, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Hutchison, Geoffrey R.
    Van der Spoel, David
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Polarizable Drude Model with s‑Type Gaussian or Slater Charge Density for General Molecular Mechanics Force Fields2018In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 14, no 11, p. 5553-5566Article in journal (Refereed)
    Abstract [en]

    Gas-phase electric properties of molecules can be computed routinely using wave function methods or density functional theory (DFT). However, these methods remain computationally expensive for high-throughput screening of the vast chemical space of virtual compounds. Therefore, empirical force fields are a more practical choice in many cases, particularly since force field methods allow one to routinely predict the physicochemical properties in the condensed phases. This work presents Drude polarizable models, to increase the physical realism in empirical force fields, where the core particle is treated as a point charge and the Drude particle is treated either as a 1s-Gaussian or a ns-Slater (n = 1, 2, 3) charge density. Systematic parametrization to large high-quality quantum chemistry data obtained from the open access Alexandria Library (https://doi.org/10.5281/zenodo.1004711) ensures the transferability of these parameters. The dipole moments and isotropic polarizabilities of the isolated molecules predicted by the proposed Drude models are in agreement with experiment with accuracy similar to DFT calculations at the B3LYP/aug-cc-pVTZ level of theory. The results show that the inclusion of explicit polarization into the models reduces the root-mean-square deviation with respect to DFT calculations of the predicted dipole moments of 152 dimers and clusters by more than 50%. Finally, we show that the accuracy of the electrostatic interaction energy of the water dimers can be improved systematically by the introduction of polarizable smeared charges as a model for charge penetration.

  • 47.
    Gopakumar, Geethanjali
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics.
    Muchova, E
    Department of Physical Chemistry, University of Chemistry and Technology, Technick ́a 5, Prague 6, 166 28, Czech Republic.
    Unger, Isaak
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy. Center for Free-Electron Laser Science, DESY, Notkestrasse 85, DE-22607 Hamburg, Germany.
    Malerz, S
    Molecular Physics Department, Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany.
    Trinter, F
    Molecular Physics Department, Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany.
    Öhrwall, G
    MAX IV Laboratory, Lund University, Box 118, SE-22100 Lund, Sweden.
    Lipparini, F
    Department of Chemistry and Industrial Chemistry, University of Pisa, Via Giuseppe Moruzzi 13, 56124 Pisa, Italy.
    Menucci, B
    Department of Chemistry and Industrial Chemistry, University of Pisa, Via Giuseppe Moruzzi 13, 56124 Pisa, Italy.
    Ceolin, D
    Synchrotron SOLEIL, L’Orme des Merisiers Saint-Aubin, BP 48 91192 Gif-sur-Yvette Cedex, Paris, France.
    Caleman, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy. Center for Free-Electron Laser Science, DESY, Notkestrasse 85, DE-22607 Hamburg, Germany.
    Wilkinson, I
    Department of Locally-Sensitive Time-Resolved Spectroscopy, Helmholtz-Zentrum Berlin fur Materialien und Energie, 14109 Berlin, Germany.
    Winter, B
    Molecular Physics Department, Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany.
    Slavicek, P
    Department of Physical Chemistry, University of Chemistry and Technology, Technick ́a 5, Prague 6, 166 28, Czech Republic.
    Hergenhahn, U
    Molecular Physics Department, Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany.
    Björneholm, Olle
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics.
    Probing Aqueous Ions with Non-local Auger Relaxation2022In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 24, no 15, p. 8661-8671Article in journal (Refereed)
    Abstract [en]

    The decay of core holes is often regarded as a local process, but in some systems, it involves the autoionization of neighbouring atoms or molecules. Here, we explore such non-local autoionization (Intermolecular Coulombic Decay, ICD) of surrounding molecules upon 1s ionization of aqueous-phase Na+, Mg2+ and Al3+ ions. The three ions are isoelectronic but differ in the strength of the ion-water interactions which is manifested in experimental Auger electron spectra by varying intensities. While for strongly interacting Mg2+ and Al3+ the non-local decay is observed, for weakly bound Na+ no signal was measured. Combined with theoretical simulations we provide a microscopic understanding of the non-local decay processes. We assigned the ICD to decay processes ending with two-hole states delocalized between the central ion and neighbouring water. The ICD process is also shown to be highly selective with respect to water molecular orbitals. The ICD lifetime was estimated to be around 40 fs for Mg and 20 fs for Al. Auger spectroscopy thus represents a novel tool for exploring molecules in the liquid phase, providing simultaneously structural and electronic information.   

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  • 48.
    Gopakumar, Geethanjali
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics.
    Svensson, Pamela
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics.
    Grånäs, Oscar
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Brena, Barbara
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory. Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Theoretical Physics. Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Physics.
    Schwob, Lucas
    Deutsch Elektronen Synchrotron DESY, DE-22607 Hamburg, Germany..
    Unger, Isaak
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics.
    Saak, Clara-Magdalena
    Univ Vienna, Dept Phys Chem, A-1090 Vienna, Austria..
    Timm, Martin
    Helmholtz Zentrum Berlin Mat & Energie, Abt Hochempfindl Rontgenspektroskopie, DE-12489 Berlin, Germany.;Tech Univ Berlin, Inst Opt & Atomare Phys, DE-10623 Berlin, Germany..
    Buelow, Christine
    Helmholtz Zentrum Berlin Mat & Energie, Abt Hochempfindl Rontgenspektroskopie, DE-12489 Berlin, Germany.;Albert Ludwigs Univ Freiburg, Phys Inst, DE-79104 Freiburg, Germany..
    Kubin, Markus
    Helmholtz Zentrum Berlin Mat & Energie, Abt Hochempfindl Rontgenspektroskopie, DE-12489 Berlin, Germany..
    Zamudio-Bayer, Vicente
    Helmholtz Zentrum Berlin Mat & Energie, Abt Hochempfindl Rontgenspektroskopie, DE-12489 Berlin, Germany..
    Lau, J. Tobias
    Helmholtz Zentrum Berlin Mat & Energie, Abt Hochempfindl Rontgenspektroskopie, DE-12489 Berlin, Germany.;Albert Ludwigs Univ Freiburg, Phys Inst, DE-79104 Freiburg, Germany..
    von Issendorff, Bernd
    Albert Ludwigs Univ Freiburg, Phys Inst, DE-79104 Freiburg, Germany..
    Abid, Abdul Rahman
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy. Univ Oulu, Fac Sci, Nano & Mol Syst Res Unit, Oulu 90570, Finland..
    Lindblad, Andreas
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy.
    Danielsson, Emma
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy.
    Koerfer, Ebba
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy.
    Caleman, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy. Deutsch Elektronen Synchrotron DESY, Ctr Free Electron Laser Sci, DE-22607 Hamburg, Germany..
    Björneholm, Olle
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy.
    Lindblad, Rebecka
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy. Helmholtz Zentrum Berlin Mat & Energie, Abt Hochempfindl Rontgenspektroskopie, DE-12489 Berlin, Germany.;Lund Univ, Dept Phys, SE-22100 Lund, Sweden.;Uppsala Univ, Dept Chem, Angstrom Lab, SE-75121 Uppsala, Sweden..
    X-ray Induced Fragmentation of Protonated Cystine2022In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 126, no 9, p. 1496-1503Article in journal (Refereed)
    Abstract [en]

    We demonstrate site-specific X-ray induced fragmentation across the sulfur L-edge of protonated cystine, the dimer of the amino acid cysteine. Ion yield NEXAFS were performed in the gas phase using electrospray ionization (ESI) in combination with an ion trap. The interpretation of the sulfur Ledge NEXAFS spectrum is supported by Restricted Open-Shell Configuration Interaction (ROCIS) calculations. The fragmentation pathway of triply charged cystine ions was modeled by Molecular Dynamics (MD) simulations. We have deduced a possible pathway of fragmentation upon excitation and ionization of S 2p electrons. The disulfide bridge breaks for resonant excitation at lower photon energies but remains intact upon higher energy resonant excitation and upon ionization of S 2p. The larger fragments initially formed subsequently break into smaller fragments.

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  • 49.
    Gopakumar, Geethanjali
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics.
    Svensson, Pamela H.W.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics.
    Grånäs, Oscar
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Brena, Barbara
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Schwob, L
    Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, DE-22607 Hamburg, Germany.
    Unger, Isaak
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics.
    Saak, Clara-Magdalena
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics.
    Timm, M
    Abteilung für Hochempfindliche Röntgenspektroskopie, Helmholtz-Zentrum Berlin für Materialien und Energie, Albert-Einstein-Strasse 15, DE-12489 Berlin, Germany; nstitut für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstrasse 36, DE-10623 Berlin, Germany.
    Bülow, C
    Abteilung für Hochempfindliche Röntgenspektroskopie, Helmholtz-Zentrum Berlin für Materialien und Energie, Albert-Einstein-Strasse 15, DE-12489 Berlin, Germany; Physikalisches Institut, Albert-Ludwigs-Universität Freiburg, Hermann-Herder-Strasse 3, DE-79104 Freiburg, Germany.
    Kubin, M
    Abteilung für Hochempfindliche Röntgenspektroskopie, Helmholtz-Zentrum Berlin für Materialien und Energie, Albert-Einstein-Strasse 15, DE-12489 Berlin, Germany.
    Zamudio-Bayer, V
    Abteilung für Hochempfindliche Röntgenspektroskopie, Helmholtz-Zentrum Berlin für Materialien und Energie, Albert-Einstein-Strasse 15, DE-12489 Berlin, Germany.
    Lau, J-T
    Abteilung für Hochempfindliche Röntgenspektroskopie, Helmholtz-Zentrum Berlin für Materialien und Energie, Albert-Einstein-Strasse 15, DE-12489 Berlin, Germany; Physikalisches Institut, Albert-Ludwigs-Universität Freiburg, Hermann-Herder-Strasse 3, DE-79104 Freiburg, Germany.
    von Issendorff, B
    Physikalisches Institut, Albert-Ludwigs-Universität Freiburg, Hermann-Herder-Strasse 3, DE-79104 Freiburg, Germany.
    Abid, Abdul Rahman
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics. Nano and Molecular Systems Research Unit, Faculty of Science, University of Oulu, P. O. Box 3000, Finland.
    Lindblad, Andreas
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy.
    Danielsson, E
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy.
    Koerfer, E
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy.
    Caleman, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics. Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, DE-22607 Hamburg, Germany.
    Björneholm, Olle
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics.
    Lindblad, Rebecka
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Inorganic Chemistry. Department of Physics, Lund University, Box 118, SE-22100 Lund, Sweden; Abteilung für Hochempfindliche Röntgenspektroskopie, Helmholtz-Zentrum Berlin für Materialien und Energie, Albert-Einstein-Strasse 15, DE-12489 Berlin, Germany.
    X-ray Induced Fragmentation of Protonated CystineManuscript (preprint) (Other academic)
    Abstract [en]

    Protein structure determination using high-intensity X-ray sources induces damage in the protein. Disulfide bridges, formed between two cysteine amino acid residues stabilize the protein structure. Owing to the higher absorption cross-section of sulfur for X-ray photons, and a large number of electrons released from sulfur atoms, these disulfide bridges are hot spots for a higher level of noise in structural studies. But it is yet to be understood how exactly the damage occurs through the interaction of the disulfide bridges with photons. Here we study the fragmentation of protonated cystine in the gas phase, which is the dimer of cysteine, by irradiation with X-rays across the sulfur L-edge using an electrospray ionization source (ESI) in combination with an ion trap. This is complemented with the calculation of the sulfur NEXAFS spectrum on the level of Restricted Open-Shell Configuration Interaction (ROCIS) and Density Functional Theory (DFT) calculations for molecular orbital visualization as well as Molecular Dynamics (MD) simulations for the fragmentation of triply charged cystine ions. We have deduced a possible pathway of fragmentation upon excitation and ionization of S 2p electrons by combining the experiments and simulations. The disulfide bridge breaks for resonant excitation at lower energies but remains intact upon higher energy resonant excitation and upon ionization of S 2p. The larger fragments formed subsequently break into smaller fragments. 

  • 50.
    Gopakumar, Geethanjali
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics.
    Unger, Isaak
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics.
    Saak, Clara-Magdalena
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics.
    Öhrwall, Gunnar
    MAX IV Laboratory, Lund University, PO Box 118, SE-22100 Lund, Sweden.
    Naves de Brito, Arnaldo
    University of Campinas, Campinas, SP, Brazil.
    Costa Rizuti da Rocha, Tulio
    Brazilian Synchrotron Light Laboratory (LNLS), Brazilian Center for Research in Energy and Materials (CNPEM), Sao Paulo, Brazil.
    Nicolas, Christophe
    Synchrotron SOLEIL, Gif-sur-Yvette, France.
    Caleman, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics. Center for Free-Electron Laser Science, DESY, Notkestrasse 85, DE-22607 Hamburg, Germany.
    Björneholm, Olle
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics.
    The Surface Composition of Amino Acid - Halide Salt Solutions is pH-Dependent2022In: Environmental Science: Atmospheres, no 3Article in journal (Refereed)
    Abstract [en]

    In atmospheric aerosol particles, the chemical surface composition governs both heterogeneous chemical reactions with gas-phase species and the ability to act as nuclei for cloud droplets. The pH in aerosol droplets is expected to affect these properties, but it is very challenging to measure the pH in individual droplets, precluding the investigation of its influence on the particle's surface composition. In this work, we use photoelectron spectroscopy to explore how the surface composition of aqueous solutions containing inorganic salt and amino acids changes as a function of pH. We observe a change by a factor of 4-5 of the relative distribution of inorganic ions at the surface of a liquid water jet, as a function of solution pH and type of amino acid in the solution. The driving forces for the surface enhancement or depletion are ion pairing and the formation of charged layers close to the aqueous surface. Our findings apply to any aqueous interface at which organic species with charged functional groups are present.

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