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  • 1.
    Abid, Abdul Rahman
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics. Univ Oulu, Nano & Mol Syst Res Unit, Fac Sci, POB 3000, Oulu 90570, Finland.
    Reinhardt, Maximilian
    Boudjemia, Nacer
    Pelimanni, Eetu
    Milosavljevic, Aleksandar R.
    Saak, Clara-Magdalena
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics.
    Huttula, Marko
    Björneholm, Olle
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics.
    Patanen, Minna
    The effect of relative humidity on CaCl2 nanoparticles studied by soft X-ray absorption spectroscopy2021In: RSC Advances, E-ISSN 2046-2069, Vol. 11, no 4, p. 2103-2111Article in journal (Refereed)
    Abstract [en]

    Ca- and Cl-containing nanoparticles are common in atmosphere, originating for example from desert dust and sea water. The properties and effects on atmospheric processes of these aerosol particles depend onthe relative humidity (RH) as they are often both hygroscopic and deliquescent. We present here a study of surface structure of free-flying CaCl2 nanoparticles (CaCl2-NPs) in the 100 nm size regime prepared at different humidity levels (RH: 11–85%). We also created mixed nanoparticles by aerosolizing a solution ofCaCl2 and phenylalanine (Phe), which is a hydrophobic amino acid present in atmosphere. Information of hydration state of CaCl2-NPs and production of mixed CaCl2 + Phe nanoparticles was obtained using soft X-ray absorption spectroscopy (XAS) at Ca 2p, Cl 2p, C 1s, and O 1s edges. We also report Ca 2p andCl 2p X-ray absorption spectra of an aqueous CaCl2 solution. The O 1s X-ray absorption spectra measured from hydrated CaCl2-NPs resemble liquid-like water spectrum, which is heavily influenced by the presence of ions. Core level spectra of Ca2+ and Cl- ions do not show a clear dependence of % RH, indicating that the first coordination shell remains similar in all measured hydrated CaCl2-NPs, but they differ from aqueous solution and solid CaCl2.

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  • 2.
    Adranno, Brando
    et al.
    Stockholm Univ, Dept Mat & Environm Chem, Svante Arrhenius vag 16C, S-10691 Stockholm, Sweden..
    Renier, Olivier
    Stockholm Univ, Dept Mat & Environm Chem, Svante Arrhenius vag 16C, S-10691 Stockholm, Sweden..
    Bousrez, Guillaume
    Stockholm Univ, Dept Mat & Environm Chem, Svante Arrhenius vag 16C, S-10691 Stockholm, Sweden.;Linköping Univ, Dept Sci & Technol, Lab Organ Elect, S-60174 Norrköping, Sweden..
    Paterlini, Veronica
    Stockholm Univ, Dept Mat & Environm Chem, Svante Arrhenius vag 16C, S-10691 Stockholm, Sweden..
    Baryshnikov, Glib V.
    Smetana, Volodymyr
    Stockholm Univ, Dept Mat & Environm Chem, Svante Arrhenius vag 16C, S-10691 Stockholm, Sweden..
    Tang, Shi
    Umeå Univ, Organ Photon & Elect Grp, S-90187 Umeå, Sweden..
    Ågren, Hans
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics.
    Metlen, Andreas
    Queens Univ Belfast, QUILL Res Ctr, Sch Chem & Chem Engn, Belfast BT95AG, North Ireland..
    Edman, Ludvig
    Umeå Univ, Organ Photon & Elect Grp, S-90187 Umeå, Sweden..
    Anja-Verena, Mudring
    Stockholm Univ, Dept Mat & Environm Chem, Svante Arrhenius vag 16C, S-10691 Stockholm, Sweden.;Aarhus Univ, Dept Biol & Chem Engn & iNANO, Intelligent Adv Mat iAM, DK-8000 Aarhus, Denmark..
    Rogers, Robin D.
    Stockholm Univ, Dept Mat & Environm Chem, Svante Arrhenius vag 16C, S-10691 Stockholm, Sweden.;Queens Univ Belfast, QUILL Res Ctr, Sch Chem & Chem Engn, Belfast BT95AG, North Ireland.;Univ Alabama, Dept Chem & Biochem, Tuscaloosa, AL 35487 USA..
    The 8-Hydroxyquinolinium Cation as a Lead Structure for Efficient Color-Tunable Ionic Small Molecule Emitting Materials2023In: ADVANCED PHOTONICS RESEARCH, ISSN 2699-9293, Vol. 4, no 3, article id 2200279Article in journal (Refereed)
    Abstract [en]

    Albeit tris(8-hydroxyquinolinato) aluminum (Alq(3)) and its derivatives are prominent emitter materials for organic lighting devices, and the optical transitions occur among ligand-centered states, the use of metal-free 8-hydroxyquinoline is impractical as it suffers from strong nonradiative quenching, mainly through fast proton transfer. Herein, it is shown that the problem of rapid proton exchange and vibration quenching of light emission can be overcome not only by complexation, but also by organization of the 8-hydroxyquinolinium cations into a solid rigid network with appropriate counter-anions (here bis(trifluoromethanesulfonyl)imide). The resulting structure is stiffened by secondary bonding interactions such as pi-stacking and hydrogen bonds, which efficiently block rapid proton transfer quenching and reduce vibrational deactivation. Additionally, the optical properties are tuned through methyl substitution from deep blue (455 nm) to blue-green (488 nm). Time-dependent density functional theory (TDFT) calculations reveal the emission to occur from which an unexpectedly long-lived S-1 level, unusual for organic fluorophores. All compounds show comparable, even superior photoluminescence compared to Alq(3) and related materials, both as solids and thin films with quantum yields (QYs) up to 40-50%. In addition, all compounds show appreciable thermal stability with decomposition temperatures above 310 degrees C.

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  • 3.
    Akiyama, Tomoko
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics.
    Ionization Influence on the Dynamics of Simple Organic Molecules2023Licentiate thesis, comprehensive summary (Other academic)
    Abstract [en]

    This licentiate thesis is devoted to the investigation of how bonding in simple organic molecules are affected by X-ray beam irradiation. The investigation targets molecules with three carbons as their main-chain structure. The stability of the bonds under ionization are simulated using the SIESTA package. SIESTA is a simulation package that provides molecular dynamics simulations based on density functional theory within the Born-Oppenheimer approximation. The aim of this study is to understand statistically the damaging process and selectivity among different types of bond. As the first targets, 4 hydrocarbons are investigated. They are propane, propene, propyne and propadiene, which have different combinations of single, double and triple bonds as their main-chain structures. Depending on the combinations, the structures can be either symmetric around the central atom or not. The structure of the symmetric molecules propane and propadiene are  stable until charge +3. In contrast, the asymmetric molecules propene and propyne, the  main-chain bonds show a tendency towards a more similar bond-distance as the level of ionization increases. In addition, hydrogens relocation occurs in propene, leading to a symmetric structure. Secondly, the bond fluctuations are investigated among 4 types of three-carbon molecules which have functional parts. Alcohol and carboxyl groups molecules show the stable bond integrities at charging 0 to +2. On the other hand, the carbon-carbon bonds in molecules with  acetyl and ketone groups are broken by ionization. Comparing the 8 kinds of bond breaking processes in these molecules, this statistical study gives an insight to organic molecules bonding systems.

    List of papers
    1. Influence of Ionization on the Dynamics of Hydrocarbons
    Open this publication in new window or tab >>Influence of Ionization on the Dynamics of Hydrocarbons
    (English)Manuscript (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

    National Category
    Physical Sciences
    Identifiers
    urn:nbn:se:uu:diva-500674 (URN)
    Funder
    Swedish Research Council, 2018-0074
    Available from: 2023-04-20 Created: 2023-04-20 Last updated: 2023-04-24Bibliographically approved
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  • 4.
    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

  • 5.
    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.

  • 6.
    Awel, Salah
    et al.
    Deutsch Elektronen Synchrotron DESY, Ctr Free Electron Laser Sci CFEL, Notkestr 85, D-22607 Hamburg, Germany..
    Bohne, Sven
    Hamburg Univ Technol, Eissendorfer Str 42, D-21073 Hamburg, Germany..
    Ebrahimifard, Reza
    Deutsch Elektronen Synchrotron DESY, Notkestr 85, D-22607 Hamburg, Germany..
    Trieu, Hoc Khiem
    Bajt, Sasa
    Deutsch Elektronen Synchrotron DESY, Notkestr 85, D-22607 Hamburg, Germany.;Hamburg Ctr Ultrafast Imaging, Luruper Chaussee 149, D-22761 Hamburg, Germany..
    Chapman, Henry
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics. Deutsch Elektronen Synchrotron DESY, Ctr Free Electron Laser Sci CFEL, Notkestr 85, D-22607 Hamburg, Germany.;Hamburg Ctr Ultrafast Imaging, Luruper Chaussee 149, D-22761 Hamburg, Germany.;Univ Hamburg, Dept Phys, Luruper Chaussee 149, D-22761 Hamburg, Germany.;Uppsala Univ, Dept Phys & Astron, Mol & Condensed Matter Phys, Uppsala, Sweden..
    Optical bunching of particles in a liquid flow2021In: Optics Express, E-ISSN 1094-4087, Vol. 29, no 21, p. 34394-34410Article in journal (Refereed)
    Abstract [en]

    High-speed liquid micro-jets are used to rapidly and repeatedly deliver protein microcrystals to focused and pulsed X-ray beams in the method of serial femtosecond crystallography. However, the current continuous flow of crystals is mismatched to the arrival of X-ray pulses, wasting vast amounts of an often rare and precious sample. Here, we introduce a method to address this problem by periodically trapping and releasing crystals in the liquid flow, creating locally concentrated crystal bunches, using an optical trap integrated in the microfluidic supply line. We experimentally demonstrate a 30-fold increase of particle concentration into 10 Hz bunches of 6.4 tm diameter polystyrene particles. Furthermore, using particle trajectory simulations, a comprehensive description of the optical bunching process and parameter space is presented. Adding this compact optofluidics device to existing injection systems would thereby dramatically reduce sample consumption and extend the application of serial crystallography to a greater range of protein crystal systems that cannot be produced in high abundance. Our approach is suitable for other microfluidic systems that require synchronous measurements of flowing objects. (C) 2021 Optical Society of America under the terms of the OSA Open Access Publishing Agreement

  • 7.
    Baidya, Anurag T. K.
    et al.
    Indian Inst Technol BHU, Dept Pharmaceut Engn & Technol, Uttar pradesh 221005, India..
    Das, Bhanuranjan
    Indian Inst Technol BHU, Dept Pharmaceut Engn & Technol, Uttar pradesh 221005, India..
    Devi, Bharti
    Indian Inst Technol BHU, Dept Pharmaceut Engn & Technol, Uttar pradesh 221005, India..
    Långström, Bengt
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC.
    Ågren, Hans
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics.
    Darreh-Shori, Taher
    Karolinska Inst, Dept Neurobiol Care Sci & Soc, Div Clin Geriatr, Ctr Alzhe Res imr, S-14152 Stockholm, Sweden..
    Kumar, Rajnish
    Indian Inst Technol BHU, Dept Pharmaceut Engn & Technol, Uttar pradesh 221005, India..
    Mechanistic Insight into the Inhibition of Choline Acetyltransferase by Proton Pump Inhibitors2023In: ACS Chemical Neuroscience, E-ISSN 1948-7193, Vol. 14, no 4, p. 749-765Article in journal (Refereed)
    Abstract [en]

    Various pharmacoepidemiological investigational studies have indicated that Proton Pump Inhibitors (PPIs) may increase the likelihood of developing Alzheimer's disease (AD) and non-AD related dementias. Previously, we have reported the inhibition of the acetylcholine biosynthesizing enzyme choline acetyltransferase (ChAT) by PPIs, for which omeprazole, lansoprazole, and pantoprazole exhibited IC50 values of 0.1, 1.5, and 5.3 mu M, respectively. In this study we utilize a battery of computational tools to perceive a mechanistic insight into the molecular interaction of PPIs with the ChAT binding pocket that may further help in designing novel ChAT ligands. Various in-silico tools make it possible for us to elucidate the binding interaction, conformational stability, and dynamics of the protein-ligand complexes within a 200 ns time frame. Further, the binding free energies for the PPI-ChAT complexes were explored. The results suggest that the PPIs exhibit equal or higher binding affinity toward the ChAT catalytic tunnel and are stable throughout the simulated time and that the pyridine ring of the PPIs interacts primarily with the catalytic residue His324. A free energy landscape analysis showed that the folding process was linear, and the residue interaction network analysis can provide insight into the roles of various amino acid residues in stabilization of the PPIs in the ChAT binding pocket. As a major factor for the onset of Alzheimer's disease is linked to cholinergic dysfunction, our previous and the present findings give clear insight into the PPI interaction with ChAT. The scaffold can be further simplified to develop novel ChAT ligands, which can also be used as ChAT tracer probes for the diagnosis of cholinergic dysfunction and to initiate timely therapeutic interventions to prevent or delay the progression of AD.

  • 8.
    Banerjee, Ambar
    et al.
    Stockholm Univ, AlbaNova Univ Ctr, Dept Phys, SE-10691 Stockholm, Sweden..
    Coates, Michael R.
    Stockholm Univ, AlbaNova Univ Ctr, Dept Phys, SE-10691 Stockholm, Sweden..
    Kowalewski, Markus
    Stockholm Univ, AlbaNova Univ Ctr, Dept Phys, SE-10691 Stockholm, Sweden..
    Wikmark, Hampus
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics.
    Jay, Raphael
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics.
    Wernet, Philippe
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics.
    Odelius, Michael
    Stockholm Univ, AlbaNova Univ Ctr, Dept Phys, SE-10691 Stockholm, Sweden..
    Photoinduced bond oscillations in ironpentacarbonyl give delayed synchronous bursts of carbonmonoxide release2022In: Nature Communications, E-ISSN 2041-1723, Vol. 13, no 1, article id 1337Article in journal (Refereed)
    Abstract [en]

    Early excited state dynamics in the photodissociation of transition metal carbonyls determines the chemical nature of short-lived catalytically active reaction intermediates. However, time-resolved experiments have not yet revealed mechanistic details in the sub-picosecond regime. Hence, in this study the photoexcitation of ironpentacarbonyl Fe(CO)(5) is simulated with semi-classical excited state molecular dynamics. We find that the bright metal-to-ligand charge-transfer (MLCT) transition induces synchronous Fe-C oscillations in the trigonal bipyramidal complex leading to periodically reoccurring release of predominantly axial CO. Metaphorically the photoactivated Fe(CO)(5) acts as a CO geyser, as a result of dynamics in the potential energy landscape of the axial Fe-C distances and non-adiabatic transitions between manifolds of bound MLCT and dissociative metal-centered (MC) excited states. The predominant release of axial CO ligands and delayed release of equatorial CO ligands are explained in a unified mechanism based on the sigma*(Fe-C) anti-bonding character of the receiving orbital in the dissociative MC states. The photodissociation of transition metal carbonyls is involved in catalysis and synthetic processes. Here the authors, using semi-classical excited state molecular dynamics, observe details of the early stage dynamics in the photodissociation of Fe(CO)(5), including synchronous bursts of CO at periodic intervals of 90 femtoseconds.

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  • 9.
    Banerjee, Ambar
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics.
    Jay, Raphael
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics.
    Leitner, Torsten
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy.
    Wang, Ru-Pan
    Center for Free-Electron Laser Science, Department of Physics, University of Hamburg, 22761 Hamburg, Germany.
    Harich, Jessica
    Center for Free-Electron Laser Science, Department of Physics, University of Hamburg, 22761 Hamburg, Germany.
    Stefanuik, Robert
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics.
    Coates, Michael R.
    Department of Physics, Stockholm University, AlbaNova University Center, 106 91 Stockholm, Sweden.
    Beale, Emma V.
    Paul Scherrer Institute, CH-5232 Villigen PSI, Switzerland.
    Kabanova, Victoria
    Paul Scherrer Institute, CH-5232 Villigen PSI, Switzerland.
    Kahraman, Abdullah
    Paul Scherrer Institute, CH-5232 Villigen PSI, Switzerland.
    Wach, Anna
    Paul Scherrer Institute, CH-5232 Villigen PSI, Switzerland;Institute of Nuclear Physics, Polish Academy of Sciences, PL-31342 Krakow, Poland.
    Ozerov, Dmitry
    Paul Scherrer Institute, CH-5232 Villigen PSI, Switzerland.
    Arrell, Christopher
    Paul Scherrer Institute, CH-5232 Villigen PSI, Switzerland.
    Milne, Christopher
    European XFEL GmbH, 22869 Schenefeld, Germany.
    Johnson, Philip J. M.
    Paul Scherrer Institute, CH-5232 Villigen PSI, Switzerland.
    Cirelli, Claudio
    Paul Scherrer Institute, CH-5232 Villigen PSI, Switzerland.
    Bacellar, Camila
    Paul Scherrer Institute, CH-5232 Villigen PSI, Switzerland.
    Huse, Nils
    Center for Free-Electron Laser Science, Department of Physics, University of Hamburg, 22761 Hamburg, Germany.
    Odelius, Michael
    Department of Physics, Stockholm University, AlbaNova University Center, 106 91 Stockholm, Sweden.
    Wernet, Philippe
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics.
    Accessing metal-specific orbital interactions in C–H activation with resonant inelastic X-ray scattering2024In: Chemical Science, ISSN 2041-6520, E-ISSN 2041-6539, Vol. 15, no 7, p. 2398-2409Article in journal (Refereed)
    Abstract [en]

    Photochemically prepared transition-metal complexes are known to be effective at cleaving the strong C–H bonds of organic molecules in room temperature solutions. There is also ample theoretical evidence that the two-way, metal to ligand (MLCT) and ligand to metal (LMCT), charge-transfer between an incoming alkane C–H group and the transition metal is the decisive interaction in the C–H activation reaction. What is missing, however, are experimental methods to directly probe these interactions in order to reveal what determines reactivity of intermediates and the rate of the reaction. Here, using quantum chemical simulations we predict and propose future time-resolved valence-to-core resonant inelastic X-ray scattering (VtC-RIXS) experiments at the transition metal L-edge as a method to provide a full account of the evolution of metal–alkane interactions during transition-metal mediated C–H activation reactions. For the model system cyclopentadienyl rhodium dicarbonyl (CpRh(CO)2), we demonstrate, by simulating the VtC-RIXS signatures of key intermediates in the C–H activation pathway, how the Rh-centered valence-excited states accessible through VtC-RIXS directly reflect changes in donation and back-donation between the alkane C–H group and the transition metal as the reaction proceeds via those intermediates. We benchmark and validate our quantum chemical simulations against experimental steady-state measurements of CpRh(CO)2 and Rh(acac)(CO)2 (where acac is acetylacetonate). Our study constitutes the first step towards establishing VtC-RIXS as a new experimental observable for probing reactivity of C–H activation reactions. More generally, the study further motivates the use of time-resolved VtC-RIXS to follow the valence electronic structure evolution along photochemical, photoinitiated and photocatalytic reactions with transition metal complexes.

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  • 10.
    Banerjee, Ambar
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics. Stockholm Univ, AlbaNova Univ Ctr, Dept Phys, SE-10691 Stockholm, Sweden.
    Vaz da Cruz, Vinicius
    Helmholtz Ctr Berlin Mat & Energy, Inst Methods & Instrumentat Synchrotron Radiat Re, D-12489 Berlin, Germany..
    Ekholm, Victor
    Lund Univ, MAX IV Lab, SE-22100 Lund, Sweden..
    Såthe, Conny
    Lund Univ, MAX IV Lab, SE-22100 Lund, Sweden..
    Rubensson, Jan-Erik
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics.
    Ignatova, Nina
    Royal Inst Technol, Theoret Chem & Biol, S-10691 Stockholm, Sweden..
    Gel'mukhanov, Faris
    Helmholtz Ctr Berlin Mat & Energy, Inst Methods & Instrumentat Synchrotron Radiat Re, D-12489 Berlin, Germany.;Royal Inst Technol, Theoret Chem & Biol, S-10691 Stockholm, Sweden..
    Odelius, Michael
    Stockholm Univ, AlbaNova Univ Ctr, Dept Phys, SE-10691 Stockholm, Sweden..
    Simulating fluorine K-edge resonant inelastic x-ray scattering of sulfur hexafluoride and the effect of dissociative dynamics2023In: Physical Review A: covering atomic, molecular, and optical physics and quantum information, ISSN 2469-9926, E-ISSN 2469-9934, Vol. 108, no 2, article id 023103Article in journal (Refereed)
    Abstract [en]

    We report on a computational study of resonant inelastic x-ray scattering (RIXS), at different fluorine K-edge resonances of the SF6 molecule, and corresponding nonresonant x-ray emission. Previously measured polarization dependence in RIXS is reproduced and traced back to the local σ and π symmetry of the molecular orbitals and corresponding states involved in the RIXS process. Also electron-hole coupling energies are calculated and related to experimentally observed spectator shifts. The role of dissociative S-F bond dynamics is explored to model detuning of RIXS spectra at the |F1s−16a11g⟩ resonance, which shows challenges to accurately reproduce the required steepness for core-excited potential energy surface. We show that the RIXS spectra can only be properly described by considering breaking of the global inversion symmetry of the electronic wave function and core-hole localization, induced by vibronic coupling. Due to the core-hole localization we have symmetry forbidden transitions, which lead to additional resonances and changing width of the RIXS profile.

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  • 11.
    Barillot, T.
    et al.
    Imperial Coll London, Blackett Lab, Quantum Opt & Laser Sci Grp, London SW7 2BW, England..
    Alexander, O.
    Imperial Coll London, Blackett Lab, Quantum Opt & Laser Sci Grp, London SW7 2BW, England..
    Cooper, B.
    Imperial Coll London, Blackett Lab, Quantum Opt & Laser Sci Grp, London SW7 2BW, England.;UCL, Dept Phys & Astron, Atom Mol Opt & Positron Phys Grp, Gower St, London WC1E 6BT, England..
    Driver, T.
    Imperial Coll London, Blackett Lab, Quantum Opt & Laser Sci Grp, London SW7 2BW, England.;SLAC Natl Accelerator Lab, Stanford PULSE Inst, Menlo Pk, CA 94025 USA.;SLAC Natl Accelerator Lab, Linac Coherent Light Source, Menlo Pk, CA 94025 USA..
    Garratt, D.
    Imperial Coll London, Blackett Lab, Quantum Opt & Laser Sci Grp, London SW7 2BW, England..
    Li, S.
    SLAC Natl Accelerator Lab, Accelerator Directorate, Menlo Pk, CA 94025 USA..
    Al Haddad, A.
    Argonne Natl Lab, Chem Sci & Engn Div, Lemont, IL 60439 USA.;Paul Scherrer Inst, CH-5232 Villigen, Switzerland..
    Sanchez-Gonzalez, A.
    Imperial Coll London, Blackett Lab, Quantum Opt & Laser Sci Grp, London SW7 2BW, England..
    Agåker, Marcus
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics. Lund Univ, MAX IV Lab, Box 118, SE-22100 Lund, Sweden..
    Arrell, C.
    Paul Scherrer Inst, CH-5232 Villigen, Switzerland..
    Bearpark, M. J.
    Imperial Coll London, Dept Chem, Mol Sci Res Hub, London W12 0BZ, England..
    Berrah, N.
    Univ Connecticut, Dept Phys, Storrs, CT 06268 USA..
    Bostedt, C.
    Argonne Natl Lab, Chem Sci & Engn Div, Lemont, IL 60439 USA.;Paul Scherrer Inst, CH-5232 Villigen, Switzerland.;Ecole Polytech Fed Lausanne EPFL, LUXS Lab Ultrafast Xray Sci, Inst Chem Sci & Engn, CH-1015 Lausanne, Switzerland..
    Bozek, J.
    Orme Merisiers, Synchrotron SOLEIL, BP 48, F-91192 Gif Sur Yvette, France..
    Brahms, C.
    Imperial Coll London, Blackett Lab, Quantum Opt & Laser Sci Grp, London SW7 2BW, England..
    Bucksbaum, P. H.
    SLAC Natl Accelerator Lab, Stanford PULSE Inst, Menlo Pk, CA 94025 USA..
    Clark, A.
    Ecole Polytech Fed Lausanne, Lab Mol Nanodynam, CH-1015 Lausanne, Switzerland..
    Doumy, G.
    Argonne Natl Lab, Chem Sci & Engn Div, Lemont, IL 60439 USA..
    Feifel, R.
    Univ Gothenburg, Dept Phys, Origovagen 6B, S-41258 Gothenburg, Sweden..
    Frasinski, L. J.
    Imperial Coll London, Blackett Lab, Quantum Opt & Laser Sci Grp, London SW7 2BW, England..
    Jarosch, S.
    Imperial Coll London, Blackett Lab, Quantum Opt & Laser Sci Grp, London SW7 2BW, England..
    Johnson, A. S.
    Imperial Coll London, Blackett Lab, Quantum Opt & Laser Sci Grp, London SW7 2BW, England..
    Kjellsson, Ludvig
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics.
    Kumagai, Y.
    Argonne Natl Lab, Chem Sci & Engn Div, Lemont, IL 60439 USA..
    Larsen, E. W.
    Imperial Coll London, Blackett Lab, Quantum Opt & Laser Sci Grp, London SW7 2BW, England..
    Matia-Hernando, P.
    Imperial Coll London, Blackett Lab, Quantum Opt & Laser Sci Grp, London SW7 2BW, England..
    Robb, M.
    Imperial Coll London, Dept Chem, Mol Sci Res Hub, London W12 0BZ, England..
    Rubensson, Jan-Erik
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics.
    Ruberti, M.
    Imperial Coll London, Blackett Lab, Quantum Opt & Laser Sci Grp, London SW7 2BW, England..
    Sathe, C.
    Lund Univ, MAX IV Lab, Box 118, SE-22100 Lund, Sweden..
    Squibb, R. J.
    Univ Gothenburg, Dept Phys, Origovagen 6B, S-41258 Gothenburg, Sweden..
    Tan, A.
    Imperial Coll London, Blackett Lab, Quantum Opt & Laser Sci Grp, London SW7 2BW, England..
    Tisch, J. W. G.
    Imperial Coll London, Blackett Lab, Quantum Opt & Laser Sci Grp, London SW7 2BW, England..
    Vacher, M.
    Imperial Coll London, Dept Chem, Mol Sci Res Hub, London W12 0BZ, England.;Univ Nantes, CNRS, CEISAM UMR 6230, F-44000 Nantes, France..
    Walke, D. J.
    Imperial Coll London, Blackett Lab, Quantum Opt & Laser Sci Grp, London SW7 2BW, England..
    Wolf, T. J. A.
    SLAC Natl Accelerator Lab, Stanford PULSE Inst, Menlo Pk, CA 94025 USA..
    Wood, D.
    Imperial Coll London, Blackett Lab, Quantum Opt & Laser Sci Grp, London SW7 2BW, England..
    Zhaunerchyk, V
    Univ Gothenburg, Dept Phys, Origovagen 6B, S-41258 Gothenburg, Sweden..
    Walter, P.
    SLAC Natl Accelerator Lab, Linac Coherent Light Source, Menlo Pk, CA 94025 USA..
    Osipov, T.
    SLAC Natl Accelerator Lab, Linac Coherent Light Source, Menlo Pk, CA 94025 USA..
    Marinelli, A.
    SLAC Natl Accelerator Lab, Accelerator Directorate, Menlo Pk, CA 94025 USA..
    Maxwell, T. J.
    SLAC Natl Accelerator Lab, Accelerator Directorate, Menlo Pk, CA 94025 USA..
    Coffee, R.
    SLAC Natl Accelerator Lab, Linac Coherent Light Source, Menlo Pk, CA 94025 USA..
    Lutman, A. A.
    SLAC Natl Accelerator Lab, Accelerator Directorate, Menlo Pk, CA 94025 USA..
    Averbukh, V
    Imperial Coll London, Blackett Lab, Quantum Opt & Laser Sci Grp, London SW7 2BW, England..
    Ueda, K.
    Tohoku Univ, Inst Multidisciplinary Res Adv Mat, Sendai, Miyagi 9808577, Japan.;Tohoku Univ, Dept Chem, Aoba Ku, 6-3 Aramaki Aza Aoba, Sendai, Miyagi 9808578, Japan..
    Cryan, J. P.
    SLAC Natl Accelerator Lab, Stanford PULSE Inst, Menlo Pk, CA 94025 USA.;SLAC Natl Accelerator Lab, Linac Coherent Light Source, Menlo Pk, CA 94025 USA..
    Marangos, J. P.
    Imperial Coll London, Blackett Lab, Quantum Opt & Laser Sci Grp, London SW7 2BW, England..
    Kolorenc, P.
    Charles Univ Prague, Fac Math & Phys, Inst Theoret Phys, V Holesovickach 2, Prague 18000, Czech Republic..
    Correlation-Driven Transient Hole Dynamics Resolved in Space and Time in the Isopropanol Molecule2021In: Physical Review X, E-ISSN 2160-3308, Vol. 11, no 3, article id 031048Article in journal (Refereed)
    Abstract [en]

    The possibility of suddenly ionized molecules undergoing extremely fast electron hole (or hole) dynamics prior to significant structural change was first recognized more than 20 years ago and termed charge migration. The accurate probing of ultrafast electron hole dynamics requires measurements that have both sufficient temporal resolution and can detect the localization of a specific hole within the molecule. We report an investigation of the dynamics of inner valence hole states in isopropanol where we use an x-ray pump-x-ray probe experiment, with site and state-specific probing of a transient hole state localized near the oxygen atom in the molecule, together with an ab initio theoretical treatment. We record the signature of transient hole dynamics and make the first tentative observation of dynamics driven by frustrated Auger-Meitner transitions. We verify that the effective hole lifetime is consistent with our theoretical prediction. This state-specific measurement paves the way to widespread application for observations of transient hole dynamics localized in space and time in molecules and thus to charge transfer phenomena that are fundamental in chemical and material physics.

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  • 12.
    Baryshnikov, Glib V.
    et al.
    Henan Univ, Coll Chem & Chem Engn, Kaifeng 475004, Henan, Peoples R China.;Linköping Univ, Dept Sci & Technol, Lab Organ Elect, SE-60174 Norrköping, Sweden.
    Valiev, Rashid R.
    Univ Helsinki, Dept Chem, Fac Sci, FIN-00014 Helsinki, Finland.
    Valiulina, Lenara I.
    Tomsk State Univ, Dept Opt & Spect, Tomsk 634050, Russia.
    Kurtsevich, Alexandr E.
    Tomsk State Univ, Dept Opt & Spect, Tomsk 634050, Russia.
    Kurten, Theo
    Univ Helsinki, Dept Chem, Fac Sci, FIN-00014 Helsinki, Finland.
    Sundholm, Dage
    Univ Helsinki, Dept Chem, Fac Sci, FIN-00014 Helsinki, Finland.
    Pittelkow, Michael
    Univ Copenhagen, Dept Chem, DK-2100 Copenhagen O, Denmark.
    Zhang, Jinglai
    Henan Univ, Coll Chem & Chem Engn, Kaifeng 475004, Henan, Peoples R China.
    Ågren, Hans
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics. Henan Univ, Coll Chem & Chem Engn, Kaifeng 475004, Henan, Peoples R China.
    Odd-Number Cyclo[n]Carbons Sustaining Alternating Aromaticity2022In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 126, no 16, p. 2445-2452Article in journal (Refereed)
    Abstract [en]

    Cyclo[n]carbons (n = 5, 7, 9,..., 29) composed from an odd number of carbon atoms are studied computationally at density functional theory (DFT) and ab initio complete active space self-consistent field (CASSCF) levels of theory to get insight into their electronic structure and aromaticity. DFT calculations predict a strongly delocalized carbene structure of the cyclo[n]carbons and an aromatic character for all of them. In contrast, calculations at the CASSCF level yield geometrically bent and electronically localized carbene structures leading to an alternating double aromaticity of the odd-number cyclo[n]carbons. CASSCF calculations yield a singlet electronic ground state for the studied cyclo[n]carbons except for C25, whereas at the DFT level the energy difference between the lowest singlet and triplet states depends on the employed functional. The BHandHLYP functional predicts a triplet ground state of the larger odd-number cyclo[n]carbons starting from n = 13. Current-density calculations at the BHandHLYP level using the CASSCFoptimized molecular structures show that there is a through-space delocalization in the cyclo[n]carbons. The current density avoids the carbene carbon atom, leading to an alternating double aromaticity of the oddnumber cyclo[n]carbons satisfying the antiaromatic [4k+1] and aromatic [4k+3] rules. C11, C15, and C19 are aromatic and can be prioritized in future synthesis. We predict a bond-shift phenomenon for the triplet state of the cyclo[n]carbons leading to resonance structures that have different reactivity toward dimerization.

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  • 13.
    Begunovich, Lyudmila V.
    et al.
    Siberian Fed Univ, Int Res Ctr Spect & Quantum Chem IRC SQC, 26 Kirensky St, Krasnoyarsk 660074, Russia..
    Kuklin, Artem, V
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy. Siberian Fed Univ, Int Res Ctr Spect & Quantum Chem IRC SQC, 26 Kirensky St, Krasnoyarsk 660074, Russia.;Uppsala Univ, Dept Phys & Astron, Box 516, SE-75120 Uppsala, Sweden..
    Baryshnikov, Glib, V.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics. Uppsala Univ, Dept Phys & Astron, Box 516, SE-75120 Uppsala, Sweden.;Bohdan Khmelnytsky Natl Univ, Dept Chem & Nanomat Sci, UA-18031 Cherkassy, Ukraine..
    Valiev, Rashid R.
    Natl Res Tomsk Polytech Univ, Res Sch Chem & Appl Biomed Sci, Lenin Ave 30, Tomsk 634050, Russia.;Univ Helsinki, Fac Sci, Dept Chem, FIN-00014 Helsinki, Finland..
    Ågren, Hans
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics. Uppsala Univ, Dept Phys & Astron, Box 516, SE-75120 Uppsala, Sweden.;Henan Univ, Coll Chem & Chem Engn, Kaifeng 475004, Henan, Peoples R China..
    Single-layer polymeric tetraoxa[8]circulene modified by s-block metals: toward stable spin qubits and novel superconductors2021In: Nanoscale, ISSN 2040-3364, E-ISSN 2040-3372, Vol. 13, no 9, p. 4799-4811Article in journal (Refereed)
    Abstract [en]

    Tunable electronic properties of low-dimensional materials have been the object of extensive research, as such properties are highly desirable in order to provide flexibility in the design and optimization of functional devices. In this study, we account for the fact that such properties can be tuned by embedding diverse metal atoms and theoretically study a series of new organometallic porous sheets based on two-dimensional tetraoxa[8]circulene (TOC) polymers doped with alkali or alkaline-earth metals. The results reveal that the metal-decorated sheets change their electronic structure from semiconducting to metallic behaviour due to n-doping. Complete active space self-consistent field (CASSCF) calculations reveal a unique open-shell singlet ground state in the TOC-Ca complex, which is formed by two closed-shell species. Moreover, Ca becomes a doublet state, which is promising for magnetic quantum bit applications due to the long spin coherence time. Ca-doped TOC also demonstrates a high density of states in the vicinity of the Fermi level and induced superconductivity. Using the ab initio Eliashberg formalism, we find that the TOC-Ca polymers are phonon-mediated superconductors with a critical temperature T-C = 14.5 K, which is within the range of typical carbon based superconducting materials. Therefore, combining the proved superconductivity and the long spin lifetime in doublet Ca, such materials could be an ideal platform for the realization of quantum bits.

  • 14.
    Berholts, Marta
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics. Department of Physics, University of Tartu, EST-50411 Tartu, Estonia.
    Knut, Ronny
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy.
    Stefanuik, Robert
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy.
    Wikmark, Hampus
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy.
    Saha, Susmita
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy. Department of Physics, Ashoka University, IN-131029 Sonipat, India.
    Söderström, Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy.
    Quantum watch and its intrinsic proof of accuracy2022In: Physical Review Research, E-ISSN 2643-1564, Vol. 4, no 4, article id 043041Article in journal (Refereed)
    Abstract [en]

    We have investigated the rich dynamics of complex wave packets composed of multiple high-lying Rydbergstates in He. A quantitative agreement is found between theory and time-resolved photoelectron spectroscopyexperiments. We show that the intricate time dependence of such wave packets can be used for investigatingquantum defects and performing artifact-free timekeeping. The latter relies on the unique fingerprint that iscreated by the time-dependent photoionization of these complex wave packets. These fingerprints determinehow much time has passed since the wave packet was formed and provide an assurance that the measured time iscorrect. Unlike any other clock, this quantum watch does not utilize a counter and is fully quantum mechanicalin its nature. The quantum watch has the potential to become an invaluable tool in pump-probe spectroscopy dueto its simplicity, assurance of accuracy, and ability to provide an absolute timestamp, i.e., there is no need to findtime zero.

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  • 15.
    Bijedic, Adi
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics. Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Condensed Matter Physics of Energy Materials. Man.
    Sustaining Orientation of Ubiquitin for Single Particle Imaging Using Electric Fields2021Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    Single-particle imaging, or SPI, is a method used to obtain the three-dimensional structure of particles. Repeatedly aiming X-rays at samples of a particle produces diffraction patterns, which are combined to a best-fit three-dimensional model of the particle. SPI of proteins can be improved by orienting the protein before imaging. Protein dipole orientation makes use of a protein's dipole moment and an external electric field to generate torque, which can orient the protein. A protein subject to an electric field may however result in damage of the protein's geometrical structure, or insufficient protein orientation, depending on the magnitude of the electric field.

    Sufficient protein orientation without substantial protein damage is possible in an interval of electric field strengths. The results in this report reveal that the method of SPI can be further improved. With a protein being fully oriented in an electric field, it is possible to reduce the electric field strength and yet sustain sufficient orientation, with some constraints. Longer times for imaging and less structural damage to the protein are hence possible. This study implements Molecular Dynamics (MD) and the most extensively used open-source MD software, GROMACS, with ubiquitin as a sample protein.

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  • 16.
    Björneholm, Olle
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics.
    Muchova, Eva
    Univ Chem & Technol, Prague, Czech Republic..
    Hot spots of radiation damage from extensive water ionization around metal ions2023In: Nature Chemistry, ISSN 1755-4330, E-ISSN 1755-4349, Vol. 15, no 10, p. 1338-1339Article in journal (Other academic)
    Abstract [en]

    Radiation damage in biological systems by radicals and low-energy electrons formed from water ionization is a consequence of ultrafast processes that follow core-level ionization of hydrated metal ions. More details of the complex pathway are now revealed from the study of aluminium-ion relaxation through sequential electron-transfer-mediated decay.

  • 17.
    Boudjemia, N.
    et al.
    Univ Oulu, Nano & Mol Syst Res Unit, POB 3000, Oulu 90014, Finland..
    Jankala, K.
    Univ Oulu, Nano & Mol Syst Res Unit, POB 3000, Oulu 90014, Finland..
    Gejo, T.
    RIKEN SPring 8 Ctr, 1-1-1 Kouto, Sayo, Hyogo 6795148, Japan.;Univ Hyogo, Grad Sch Mat Sci, Kamigori, Hyogo 6781297, Japan..
    Kohmura, Y.
    RIKEN SPring 8 Ctr, 1-1-1 Kouto, Sayo, Hyogo 6795148, Japan..
    Huttula, M.
    Univ Oulu, Nano & Mol Syst Res Unit, POB 3000, Oulu 90014, Finland..
    Piancastelli, Maria Novella
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics. RIKEN SPring 8 Ctr, 1-1-1 Kouto, Sayo, Hyogo 6795148, Japan.;Sorbonne Univ, CNRS, LCPMR, F-75005 Paris 05, France..
    Simon, M.
    RIKEN SPring 8 Ctr, 1-1-1 Kouto, Sayo, Hyogo 6795148, Japan.;Sorbonne Univ, CNRS, LCPMR, F-75005 Paris 05, France..
    Oura, M.
    RIKEN SPring 8 Ctr, 1-1-1 Kouto, Sayo, Hyogo 6795148, Japan..
    Püttner, R.
    Free Univ Berlin, Fachbereich Phys, Arnimallee 14, D-14195 Berlin, Germany..
    Experimental and theoretical study of the Kr L-shell Auger decay2021In: Physical Review A: covering atomic, molecular, and optical physics and quantum information, ISSN 2469-9926, E-ISSN 2469-9934, Vol. 104, no 1, article id 012804Article in journal (Refereed)
    Abstract [en]

    The LMM Auger spectra of krypton are measured using the photon energies hv = 1709 eV, 1792 eV, 1950 eV, and 13 keV. This approach allows separating the contributions from the various core holes L-1 , L-2., and L-3. Previously unobserved transitions are presented. Complementary theoretical work is performed allowing the assignment of the spectral features. The L2,3Y -MMY (Y = M-4,M-5, N-1,N-2,N-3) Auger transitions of Kr2+ formed via Coster-Kronig Auger decay of the core holes L-1 and L-2. are also investigated. These spectra comprise about 4000 and 13 000 transitions, respectively, so that only general statements on the assignment, such as the configurations involved in the transitions, can be given.

  • 18.
    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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  • 19.
    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
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Biochemistry.
    Collision induced unfolding and molecular dynamics simulations of norovirus capsid dimers reveal strain-specific stability profiles2024In: 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.

  • 20.
    Budnyak, Tetyana M.
    et al.
    Natl Acad Sci Ukraine, Chuiko Inst Surface Chem, UA-03164 Kiev, Ukraine.;Stockholm Univ, Dept Mat & Environm Chem, S-10691 Stockholm, Sweden..
    Vlasova, Nataliya N.
    Natl Acad Sci Ukraine, Chuiko Inst Surface Chem, UA-03164 Kiev, Ukraine..
    Golovkova, Lyudmila P.
    Natl Acad Sci Ukraine, Chuiko Inst Surface Chem, UA-03164 Kiev, Ukraine..
    Markitan, Olga
    Natl Acad Sci Ukraine, Chuiko Inst Surface Chem, UA-03164 Kiev, Ukraine..
    Baryshnikov, Glib
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics. Bohdan Khmelnytsky Natl Univ, Dept Chem & Nanomat Sci, UA-18031 Cherkassy, Ukraine..
    Ågren, Hans
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics. Henan Univ, Coll Chem & Chem Engn, Kaifeng 475004, Henan, Peoples R China..
    Slabon, Adam
    Stockholm Univ, Dept Mat & Environm Chem, S-10691 Stockholm, Sweden..
    Nucleotide Interaction with a Chitosan Layer on a Silica Surface: Establishing the Mechanism at the Molecular Level2021In: Langmuir, ISSN 0743-7463, E-ISSN 1520-5827, Vol. 37, no 4, p. 1511-1520Article in journal (Refereed)
    Abstract [en]

    The growing interest in gene therapy is coupled with the strong need for the development of safe and efficient gene transfection vectors. A composite based on chitosan and fumed silica has been found to be a prospective gene delivery carrier. This study presents an investigation of the nature of the bonds between a series of nucleotides with a chitosan layer deposited on a fumed silica surface. Experimentally measured surface complex formation constants (logK) of the nucleotides were found to be in the range of 2.69-4.02, which is higher than that for the orthophosphate (2.39). Theoretically calculated nucleotide complexation energies for chitosan deposited on the surface range from 11.5 to 23.0 kcal.mol(-)(1), in agreement with experimental data. The adsorption of nucleotides was interpreted using their calculated speciation in an aqueous solution. Based on the structures of all optimized complexes determined from quantum-chemical PM6 calculations, electrostatic interactions between the surface-located NH3- groups and -PO3H--/-PO32- fragments of the nucleotides were identified to play the decisive role in the adsorption mechanism. The saccharide fragment of monophosphates also plays an important role in the binding of the nucleotides to chitosan through the creation of hydrogen bonds.

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  • 21.
    Cao, Fangcheng
    et al.
    Univ South China, Sch Chem & Chem Engn, Lab Optoelect Technol Low Dimens Nanomat, Hengyang 421001, Peoples R China.
    Zhang, Ye
    Univ South China, Sch Chem & Chem Engn, Lab Optoelect Technol Low Dimens Nanomat, Hengyang 421001, Peoples R China.
    Wang, Hongqing
    Univ South China, Sch Chem & Chem Engn, Lab Optoelect Technol Low Dimens Nanomat, Hengyang 421001, Peoples R China.
    Khan, Karim
    Shenzhen Univ, Coll Phyiscs & Optoelect Engn, Shenzhen Engn Lab Phosphorene & Optoelect, Shenzhen 518060, Peoples R China.
    Tareen, Ayesha Khan
    Shenzhen Univ, Coll Phyiscs & Optoelect Engn, Shenzhen Engn Lab Phosphorene & Optoelect, Shenzhen 518060, Peoples R China.
    Qian, Wenjing
    Tongji Univ, Sch Mat Sci & Engn, Shanghai 201804, Peoples R China.
    Zhang, Han
    Shenzhen Univ, Coll Phyiscs & Optoelect Engn, Shenzhen Engn Lab Phosphorene & Optoelect, Shenzhen 518060, Peoples R China.
    Ågren, Hans
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics.
    Recent Advances in Oxidation Stable Chemistry of 2D MXenes2022In: Advanced Materials, ISSN 0935-9648, E-ISSN 1521-4095, Vol. 34, no 13, article id 2107554Article, review/survey (Refereed)
    Abstract [en]

    As an emerging star of 2D nanomaterials, 2D transition metal carbides and nitrides, named MXenes, present a large potential in various research areas owing to their intrinsic multilayer structure and intriguing physico-chemical properties. However, the fabrication and application of functional MXene-based devices still remain challenging as they are prone to oxidative degradation under ambient environment. Within this review, the preparation methods of MXenes focusing on the recent investigations on their thermal structure-stability relationships in inert, oxidizing, and aqueous environments are systematically introduced. Moreover, the key factors that affect the oxidation of MXenes, such as, atmosphere, temperature, composition, microstructure, and aqueous environment, are reviewed. Based on different scenarios, strategies for avoiding or delaying the oxidation of MXenes are proposed to encourage the utilization of MXenes in complicated environments, especially at high temperature. Furthermore, the chemistry of MXene-derived oxides is analyzed, which can offer perspectives on the further design and fabrication of novel 2D composites with the unique structures of MXenes being preserved.

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  • 22.
    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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  • 23.
    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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  • 24.
    Carravetta, Vincenzo
    et al.
    Inst Chem & Phys Proc, CNR IPCF, Via G Moruzzi 1, I-56124 Pisa, Italy..
    de Abreu Gomes, Anderson Herbert
    Campinas Univ, Inst Phys Gleb Wataghin, Dept Appl Phys, BR-13083859 Campinas, SP, Brazil.;Brazilian Ctr Res Energy & Mat CNPEM, Brazilian Synchrotron Light Lab LNLS, POB 6192, BR-13083970 Campinas, SP, Brazil..
    Teixeira Marinho, Ricardo dos Reis
    Univ Fed Bahia, Inst Phys, BR-40170115 Salvador, BA, Brazil.;Brasilia Univ UnB, Inst Phys, BR-70919970 Brasilia, DF, Brazil..
    Ohrwall, Gunnar
    Lund Univ, MAX IV Lab, Box 118, SE-22100 Lund, Sweden..
    Ågren, Hans
    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.
    de Brito, Arnaldo Naves
    Campinas Univ, Inst Phys Gleb Wataghin, Dept Appl Phys, BR-13083859 Campinas, SP, Brazil..
    An atomistic explanation of the ethanol-water azeotrope2022In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 24, no 42, p. 26037-26045Article in journal (Refereed)
    Abstract [en]

    Ethanol and water form an azeotropic mixture at an ethanol molecular percentage of similar to 91% (similar to 96% by volume), which prohibits ethanol from being further purified via distillation. Aqueous solutions at different concentrations in ethanol have been studied both experimentally and theoretically. We performed cylindrical micro-jet photoelectron spectroscopy, excited by synchrotron radiation, 70 eV above C1s ionization threshold, providing optimal atomic-scale surface-probing. Large model systems have been employed to simulate, by molecular dynamics, slabs of the aqueous solutions and obtain an atomistic description of both bulk and surface regions. We show how the azeotropic behaviour results from an unexpected concentration-dependence of the surface composition. While ethanol strongly dominates the surface and water is almost completely depleted from the surface for most mixing ratios, the different intermolecular bonding patterns of the two components cause water to penetrate to the surface region at high ethanol concentrations. The addition of surface water increases its relative vapour pressure, giving rise to the azeotropic behaviour.

  • 25.
    Chapman, Henry
    et al.
    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, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics. Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany.;Univ Hamburg, Hamburg Ctr Ultrafast Imaging, Luruper Chaussee 149, D-22761 Hamburg, Germany.;Univ Hamburg, Dept Phys, Luruper Chaussee 149, D-22761 Hamburg, Germany.;Uppsala Univ, Dept Phys & Astron, Mol & Condensed Matter Phys, Box 516, S-75120 Uppsala, Sweden..
    Bajt, S.
    DESY, Notkestr 85, D-22607 Hamburg, Germany.;Univ Hamburg, Hamburg Ctr Ultrafast Imaging, Luruper Chaussee 149, D-22761 Hamburg, Germany..
    High-resolution achromatic X-ray optical systems for broad-band imaging and for focusing attosecond pulses2021In: Proceedings of the Royal Society. Mathematical, Physical and Engineering Sciences, ISSN 1364-5021, E-ISSN 1471-2946, Vol. 477, no 2251, article id 20210334Article in journal (Refereed)
    Abstract [en]

    Achromatic focusing systems for hard X-rays are examined which consist of a refractive lens paired with a diffractive lens. Compared with previous analyses, we take into account the behaviour of thick refractive lenses, such as compound refractive lenses and waveguide gradient index refractive lenses, in which both the focal length and the position of the principal planes vary with wavelength. Achromatic systems formed by the combination of such a thick refractive lens with a multilayer Laue lens are found that can operate at a focusing resolution of about 3 nm, over a relative bandwidth of about 1%. With the appropriate distance between the refractive and diffractive lenses, apochromatic systems can also be found, which operate over relative bandwidth greater than 10%. These systems can be used to focus short pulses without distorting them in time by more than several attoseconds. Such systems are suitable for high-flux scanning microscopy and for creating high intensities from attosecond X-ray pulses.

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  • 26.
    Chen, Kuan
    et al.
    Peking Univ, Sch Pharmaceut Sci, State Key Lab Nat & Biomimet Drugs, Beijing, Peoples R China.;Capital Med Univ, Beijing Friendship Hosp, Beijing Inst Clin Pharm, Beijing, Peoples R China..
    Zhang, Meng
    Peking Univ, Sch Pharmaceut Sci, State Key Lab Nat & Biomimet Drugs, Beijing, Peoples R China..
    Gao, Baihan
    Peking Univ, Sch Pharmaceut Sci, State Key Lab Nat & Biomimet Drugs, Beijing, Peoples R China..
    Hasan, Aobulikasimu
    Peking Univ, Sch Pharmaceut Sci, State Key Lab Nat & Biomimet Drugs, Beijing, Peoples R China..
    Li, Junhao
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics.
    Bao, Yang'oujie
    Peking Univ, Sch Pharmaceut Sci, State Key Lab Nat & Biomimet Drugs, Beijing, Peoples R China..
    Fan, Jingjing
    Peking Univ, Sch Pharmaceut Sci, State Key Lab Nat & Biomimet Drugs, Beijing, Peoples R China..
    Yu, Rong
    Peking Univ, Sch Pharmaceut Sci, State Key Lab Nat & Biomimet Drugs, Beijing, Peoples R China..
    Yi, Yang
    Peking Univ, Sch Pharmaceut Sci, State Key Lab Nat & Biomimet Drugs, Beijing, Peoples R China..
    Ågren, Hans
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics.
    Wang, Zilong
    Peking Univ, Sch Pharmaceut Sci, State Key Lab Nat & Biomimet Drugs, Beijing, Peoples R China..
    Liu, Haiyang
    Chinese Acad Sci, Kunming Inst Bot, State Key Lab Phytochem & Plant Resources West Ch, Kunming, Yunnan, Peoples R China.;Chinese Acad Sci, Kunming Inst Bot, Yunnan Key Lab Nat Med Chem, Kunming, Yunnan, Peoples R China..
    Ye, Min
    Peking Univ, Sch Pharmaceut Sci, State Key Lab Nat & Biomimet Drugs, Beijing, Peoples R China..
    Qiao, Xue
    Peking Univ, Sch Pharmaceut Sci, State Key Lab Nat & Biomimet Drugs, Beijing, Peoples R China..
    Characterization and protein engineering of glycosyltransferases for the biosynthesis of diverse hepatoprotective cycloartane-type saponins in Astragalus membranaceus2023In: Plant Biotechnology Journal, ISSN 1467-7644, E-ISSN 1467-7652, Vol. 21, no 4, p. 698-710Article in journal (Refereed)
    Abstract [en]

    Although plant secondary metabolites are important source of new drugs, obtaining these compounds is challenging due to their high structural diversity and low abundance. The roots of Astragalus membranaceus are a popular herbal medicine worldwide. It contains a series of cycloartane-type saponins (astragalosides) as hepatoprotective and antivirus components. However, astragalosides exhibit complex sugar substitution patterns which hindered their purification and bioactivity investigation. In this work, glycosyltransferases (GT) from A. membranaceus were studied to synthesize structurally diverse astragalosides. Three new GTs, AmGT1/5 and AmGT9, were characterized as 3-O-glycosyltransferase and 25-O-glycosyltransferase of cycloastragenol respectively. AmGT1(G146V/I) variants were obtained as specific 3-O-xylosyltransferases by sequence alignment, molecular modelling and site-directed mutagenesis. A combinatorial synthesis system was established using AmGT1/5/9, AmGT1(G146V/S) and the reported AmGT8 and AmGT8(A394F). The system allowed the synthesis of 13 astragalosides in Astragalus root with conversion rates from 22.6% to 98.7%, covering most of the sugar-substitution patterns for astragalosides. In addition, AmGT1 exhibited remarkable sugar donor promiscuity to use 10 different donors, and was used to synthesize three novel astragalosides and ginsenosides. Glycosylation remarkably improved the hepatoprotective and SARS-CoV-2 inhibition activities for triterpenoids. This is one of the first attempts to produce a series of herbal constituents via combinatorial synthesis. The results provided new biocatalytic tools for saponin biosynthesis.

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  • 27.
    Coates, Michael R.
    et al.
    Stockholm Univ, Albanova Univ Ctr, Dept Phys, SE-106 91 Stockholm, Sweden..
    Banerjee, Ambar
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics. Stockholm Univ, Albanova Univ Ctr, Dept Phys, SE-106 91 Stockholm, Sweden..
    Odelius, Michael
    Stockholm Univ, Albanova Univ Ctr, Dept Phys, SE-106 91 Stockholm, Sweden..
    Simulations of the Aqueous "Brown-Ring" Complex Reveal Fluctuations in Electronic Character2023In: Inorganic Chemistry, ISSN 0020-1669, E-ISSN 1520-510X, Vol. 62, no 41, p. 16854-16866Article in journal (Refereed)
    Abstract [en]

    Ab initio molecular dynamics (AIMD) simulations of the aqueous [Fe(H2O)(5)(NO)](2+) "brown-ring" complex in different spin states, in combination with multiconfigurational quantum chemical calculations, show a structural dependence on the electronic character of the complex. Sampling in the quartet and sextet ground states show that the multiplicity is correlated with the Fe-N distance. This provides a motivation for a rigid Fe-N scan in the isolated "brown-ring" complex to investigate how the multiconfigurational wave function and the electron density change around the FeNO moiety. Our results show that subtle changes in the Fe-N distance produce a large response in the electronic configurations underlying the quartet wave function. However, while changes in spin density and potential energy are pronounced, variations in charge are negligible. These trends within the FeNO moiety are preserved in structural sampling of the AIMD simulations, despite distortions present in other degrees of freedom in the bulk solution.

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  • 28.
    Couto, Rafael C.
    et al.
    Royal Inst Technol, Sch Chem Biotechnol & Hlth, Dept Theoret Chem & Biol, SE-10691 Stockholm, Sweden.;Stockholm Univ, Albanova Univ Ctr, Dept Phys, SE-10691 Stockholm, Sweden..
    Hua, Weijie
    Nanjing Univ Sci & Technol, Sch Sci, Dept Appl Phys, MIIT Key Lab Semicond Microstruct & Quantum Sensi, Nanjing 210094, Peoples R China..
    Lindblad, Rebecka
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Inorganic Chemistry. Lund Univ, Dept Phys, Box 118, S-22100 Lund, Sweden.;Helmholtz Zentrum Berlin Mat & Energie, Abt Hochempfindliche Rontgenspektroskopie, Albert Einstein Str 15, D-12489 Berlin, Germany..
    Kjellsson, Ludvig
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy. European XFEL GmbH, Holzkoppel 4, D-22869 Schenefeld, Germany..
    Sorensen, Stacey L.
    Lund Univ, Dept Phys, Box 118, S-22100 Lund, Sweden..
    Kubin, Markus
    Helmholtz Zentrum Berlin Mat & Energie, Abt Hochempfindliche Rontgenspektroskopie, Albert Einstein Str 15, D-12489 Berlin, Germany..
    Bülow, Christine
    Helmholtz Zentrum Berlin Mat & Energie, Abt Hochempfindliche Rontgenspektroskopie, Albert Einstein Str 15, D-12489 Berlin, Germany..
    Timm, Martin
    Helmholtz Zentrum Berlin Mat & Energie, Abt Hochempfindliche Rontgenspektroskopie, Albert Einstein Str 15, D-12489 Berlin, Germany..
    Zamudio-Bayer, Vicente
    Helmholtz Zentrum Berlin Mat & Energie, Abt Hochempfindliche Rontgenspektroskopie, Albert Einstein Str 15, D-12489 Berlin, Germany..
    von Issendorff, Bernd
    Albert Ludwigs Univ Freiburg, Phys Inst, Hermann Herder Str 3, D-79104 Freiburg, Germany..
    Söderström, Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics.
    Lau, J. Tobias
    Helmholtz Zentrum Berlin Mat & Energie, Abt Hochempfindliche Rontgenspektroskopie, Albert Einstein Str 15, D-12489 Berlin, Germany.;Albert Ludwigs Univ Freiburg, Phys Inst, Hermann Herder Str 3, D-79104 Freiburg, Germany..
    Rubensson, Jan-Erik
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics.
    Ågren, Hans
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy. Tomsk State Univ, 36 Lenin Ave, Tomsk, Russia..
    Carravetta, Vincenzo
    CNR, IPCF, Via Moruzzi 1, I-56124 Pisa, Italy..
    Breaking inversion symmetry by protonation: experimental and theoretical NEXAFS study of the diazynium ion, N2H+2021In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 23, no 32, p. 17166-17176Article in journal (Refereed)
    Abstract [en]

    As an example of symmetry breaking in NEXAFS spectra of protonated species we present a high resolution NEXAFS spectrum of protonated dinitrogen, the diazynium ion N2H+. By ab initio calculations we show that the spectrum consists of a superposition of two nitrogen 1s absorption spectra, each including a pi* band, and a nitrogen 1s to H+ charge transfer band followed by a weak irregular progression of high energy excitations. Calculations also show that, as an effect of symmetry breaking by protonation, the pi* transitions are separated by 0.23 eV, only slightly exceeding the difference in the corresponding dark (symmetry forbidden) and bright (symmetry allowed) core excitations of neutral N-2. By DFT and calculations and vibrational analysis, the complex pi* excitation band of N2H+ is understood as due to the superposition of the significantly different vibrational progressions of excitations from terminal and central nitrogen atoms, both leading to bent final state geometries. We also show computationally that the electronic structure of the charge transfer excitation smoothly depends on the nitrogen-proton distance and that there is a clear extension of the spectra going from infinity to close nitrogen-proton distance where fine structures show some, although not fully detailed, similarities. An interesting feature of partial localization of the nitrogen core orbitals, with a strong, non-monotonous, variation with nitrogen-proton distance could be highlighted. Specific effects could be unraveled when comparing molecular cation NEXAFS spectra, as represented by recently recorded spectra of N-2(+) and CO+, and spectra of protonated molecules as represented here by the N2H+ ion. Both types containing rich physical effects not represented in NEXAFS of neutral molecules because of the positive charge, whereas protonation also breaks the symmetry. The effect of the protonation on dinitrogen can be separated in charge, which extends the high-energy part of the spectrum, and symmetry-breaking, which is most clearly seen in the low-energy pi* transition.

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  • 29.
    Danyliv, Yan
    et al.
    Lviv Polytech Natl Univ, Stepan Bandera 12, UA-79013 Lvov, Ukraine..
    Ivaniuk, Khrystyna
    Lviv Polytech Natl Univ, Stepan Bandera 12, UA-79013 Lvov, Ukraine..
    Danyliv, Iryna
    Lviv Polytech Natl Univ, Stepan Bandera 12, UA-79013 Lvov, Ukraine..
    Bezvikonnyi, Oleksandr
    Kaunas Univ Technol, Dept Polymer Chem & Technol, Radvilenu Pl 19, LT-50254 Kaunas, Lithuania..
    Volyniuk, Dmytro
    Kaunas Univ Technol, Dept Polymer Chem & Technol, Radvilenu Pl 19, LT-50254 Kaunas, Lithuania..
    Galyna, Sych
    Univ Savoie Mont Blanc, Univ Grenoble Alpes, CNRS, Grenoble INP,LEPMI, F-38000 Grenoble, France..
    Lazauskas, Algirdas
    Kaunas Univ Technol, Inst Mat Sci, K Barsausko St 59, LT-51423 Kaunas, Lithuania..
    Skhirtladze, Levani
    Kaunas Univ Technol, Dept Polymer Chem & Technol, Radvilenu Pl 19, LT-50254 Kaunas, Lithuania..
    Ågren, Hans
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics.
    Stakhira, Pavlo
    Lviv Polytech Natl Univ, Stepan Bandera 12, UA-79013 Lvov, Ukraine..
    Karaush-Karmazin, Nataliya
    Bohdan Khmelnytsky Natl Univ, Dept Chem & Nanomat Sci, UA-18031 Cherkassy, Ukraine..
    Ali, Amjad
    Linköping Univ, Dept Sci & Technol, Lab Organ Elect, SE-60174 Norrköping, Sweden..
    Baryshnikov, Glib
    Bohdan Khmelnytsky Natl Univ, Dept Chem & Nanomat Sci, UA-18031 Cherkassy, Ukraine.;Linköping Univ, Dept Sci & Technol, Lab Organ Elect, SE-60174 Norrköping, Sweden..
    Grazulevicius, Juozas V.
    Kaunas Univ Technol, Dept Polymer Chem & Technol, Radvilenu Pl 19, LT-50254 Kaunas, Lithuania..
    Carbazole-s-sulfobenzimide derivative exhibiting mechanochromic thermally activated delayed fluorescence as emitter for flexible OLEDs: Theoretical and experimental insights2022In: Dyes and pigments, ISSN 0143-7208, E-ISSN 1873-3743, Vol. 208, article id 110841Article in journal (Refereed)
    Abstract [en]

    For the first time exploiting sulfobenzimide moiety as an acceptor unit, the new type of donor-sigma-acceptor emitter exhibiting thermally activated delayed fluorescence (TADF) is demonstrated. In different solutions, the synthesized compound emits light resulting from either locally excited carbazole moiety or trough-space charge transfer (exciplex-like) between carbazole and sulfobenzimide units. In the solid state, this emitter demonstrates aggregation-induced emission enhancement and different emission colours due to its different conformations. The mechanoluminescence of the donor-sigma-acceptor compound was observed and studied in detail by experimental and theoretical approaches including single-crystal and powder X-ray analyses. Electroluminescence of the different colours was observed when the compound was utilized as non-doped TADF emitter in rigid and flexible organic light-emitting diodes fabricated on glass or poly(ethylene terephthalate) substrates. The device fabricated on the rigid substrate exhibited the best performance with maximum current efficiency, power efficiency, and external quantum efficiency of 11.0 cd A(-1), 3.0 lm W-1, and 4.3%, respectively.

  • 30.
    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.

  • 31.
    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.

  • 32.
    Demirbay, Baris
    et al.
    Royal Inst Technol KTH, Albanova Univ Ctr, Dept Appl Phys, Expt Biomol Phys, SE-10691 Stockholm, Sweden..
    Baryshnikov, Glib
    Linköping Univ, Dept Sci & Technol, Lab Organ Elect, SE-60174 Norrköping, Sweden..
    Haraldsson, Martin
    Karolinska Inst, Chem Biol Consortium Sweden, Sci Life Lab, Dept Med Biochem & Biophys, SE-17177 Stockholm, Sweden..
    Piguet, Joachim
    Royal Inst Technol KTH, Albanova Univ Ctr, Dept Appl Phys, Expt Biomol Phys, SE-10691 Stockholm, Sweden..
    Ågren, Hans
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics.
    Widengren, Jerker
    Royal Inst Technol KTH, Albanova Univ Ctr, Dept Appl Phys, Expt Biomol Phys, SE-10691 Stockholm, Sweden..
    Photo-physical characterization of high triplet yield brominated fluoresceins by transient state (TRAST) spectroscopy2023In: METHODS AND APPLICATIONS IN FLUORESCENCE, ISSN 2050-6120, Vol. 11, no 4, article id 045011Article in journal (Refereed)
    Abstract [en]

    Photo-induced dark transient states of fluorophores can pose a problem in fluorescence spectroscopy. However, their typically long lifetimes also make them highly environment sensitive, suggesting fluorophores with prominent dark-state formation yields to be used as microenvironmental sensors in bio-molecular spectroscopy and imaging. In this work, we analyzed the singlet-triplet transitions of fluorescein and three synthesized carboxy-fluorescein derivatives, with one, two or four bromines linked to the anthracence backbone. Using transient state (TRAST) spectroscopy, we found a prominent internal heavy atom (IHA) enhancement of the intersystem crossing (ISC) rates upon bromination, inferred by density functional theory calculations to take place via a higher triplet state, followed by relaxation to the lowest triplet state. A corresponding external heavy atom (EHA) enhancement was found upon adding potassium iodide (KI). Notably, increased KI concentrations still resulted in lowered triplet state buildup in the brominated fluorophores, due to relatively lower enhancements in ISC, than in the triplet decay. Together with an antioxidative effect on the fluorophores, adding KI thus generated a fluorescence enhancement of the brominated fluorophores. By TRAST measurements, analyzing the average fluorescence intensity of fluorescent molecules subject to a systematically varied excitation modulation, dark state transitions within very high triplet yield (>90%) fluorophores can be directly analyzed under biologically relevant conditions. These measurements, not possible by other techniques such as fluorescence correlation spectroscopy, opens for bio-sensing applications based on high triplet yield fluorophores, and for characterization of high triplet yield photodynamic therapy agents, and how they are influenced by IHA and EHA effects.

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  • 33.
    Du, Zhixue
    et al.
    Royal Inst Technol KTH, Expt Biomol Phys, Dept Appl Phys, Albanova Univ Ctr, S-10691 Stockholm, Sweden..
    Piguet, Joachim
    Royal Inst Technol KTH, Expt Biomol Phys, Dept Appl Phys, Albanova Univ Ctr, S-10691 Stockholm, Sweden..
    Baryshnikov, Glib
    Linköping Univ, Dept Sci & Technol, Lab Organ Elect, SE-60174 Norrköping, Sweden..
    Tornmalm, Johan
    Royal Inst Technol KTH, Expt Biomol Phys, Dept Appl Phys, Albanova Univ Ctr, S-10691 Stockholm, Sweden..
    Demirbay, Baris
    Royal Inst Technol KTH, Expt Biomol Phys, Dept Appl Phys, Albanova Univ Ctr, S-10691 Stockholm, Sweden..
    Ågren, Hans
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics.
    Widengren, Jerker
    Royal Inst Technol KTH, Expt Biomol Phys, Dept Appl Phys, Albanova Univ Ctr, S-10691 Stockholm, Sweden..
    Imaging Fluorescence Blinking of a Mitochondrial Localization Probe: Cellular Localization Probes Turned into Multifunctional Sensors br2022In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 126, no 16, p. 3048-3058Article in journal (Refereed)
    Abstract [en]

    Mitochondrial membranes and their microenviron-ments directly influence and reflect cellular metabolic states but aredifficult to probe on site in live cells. Here, we demonstrate astrategy, showing how the widely used mitochondrial membranelocalizationfluorophore 10-nonyl acridine orange (NAO) can betransformed into a multifunctional probe of membrane micro-environments by monitoring its blinking kinetics. By transient state(TRAST) studies of NAO in small unilamellar vesicles (SUVs),together with computational simulations, we found that NAOexhibits prominent reversible singlet-triplet state transitions andcan act as a light-induced Lewis acid forming a red-emissivedoublet radical. The resulting blinking kinetics are highlyenvironment-sensitive, specifically reflecting local membrane oxy-gen concentrations, redox conditions, membrane charge,fluidity, and lipid compositions. Here, not only cardiolipin concentrationbut also the cardiolipin acyl chain composition was found to strongly influence the NAO blinking kinetics. The blinking kinetics alsoreflect hydroxyl ion-dependent transitions to and from thefluorophore doublet radical, closely coupled to the proton-transfer eventsin the membranes, local pH, and two- and three-dimensional buffering properties on and above the membranes. Following the SUVstudies, we show by TRAST imaging that thefluorescence blinking properties of NAO can be imaged in live cells in a spatiallyresolved manner. Generally, the demonstrated blinking imaging strategy can transform existingfluorophore markers intomultiparametric sensors reflecting conditions of large biological relevance, which are difficult to retrieve by other means. This opensadditional possibilities for fundamental membrane studies in lipid vesicles and live cells

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  • 34.
    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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  • 35.
    Eckert, Sebastian
    et al.
    Helmholtz Zentrum Berlin Mat & Energie GmbH, Inst Methods & Instrumentat Synchrotron Radiat Re, D-12489 Berlin, Germany..
    Mascarenhas, Eric J.
    Univ Potsdam, Inst Phys & Astron, D-14476 Potsdam, Germany.;Helmholtz Zentrum Berlin Mat & Energie GmbH, Inst Methods & Instrumentat Synchrotron Radiat Re, D-12489 Berlin, Germany..
    Mitzner, Rolf
    Helmholtz Zentrum Berlin Mat & Energie GmbH, Inst Methods & Instrumentat Synchrotron Radiat Re, D-12489 Berlin, Germany..
    Jay, Raphael
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics. Univ Potsdam, Inst Phys & Astron, D-14476 Potsdam, Germany..
    Pietzsch, Annette
    Helmholtz Zentrum Berlin Mat & Energie GmbH, Inst Methods & Instrumentat Synchrotron Radiat Re, D-12489 Berlin, Germany..
    Fondell, Mattis
    Helmholtz Zentrum Berlin Mat & Energie GmbH, Inst Methods & Instrumentat Synchrotron Radiat Re, D-12489 Berlin, Germany..
    da Cruz, Vinicius Vaz
    Helmholtz Zentrum Berlin Mat & Energie GmbH, Inst Methods & Instrumentat Synchrotron Radiat Re, D-12489 Berlin, Germany..
    Föhlisch, Alexander
    Univ Potsdam, Inst Phys & Astron, D-14476 Potsdam, Germany.;Helmholtz Zentrum Berlin Mat & Energie GmbH, Inst Methods & Instrumentat Synchrotron Radiat Re, D-12489 Berlin, Germany..
    From the Free Ligand to the Transition Metal Complex: FeEDTA- Formation Seen at Ligand K-Edges2022In: Inorganic Chemistry, ISSN 0020-1669, E-ISSN 1520-510X, Vol. 61, no 27, p. 10321-10328Article in journal (Refereed)
    Abstract [en]

    Chelating agents are an integral part of transition metal complex chemistry with broad biological and industrial relevance. The hexadentate chelating agent ethylenediaminetetraacetic acid (EDTA) has the capability to bind to metal ions at its two nitrogen and four of its carboxylate oxygen sites. We use resonant inelastic X-ray scattering at the 1s absorption edge of the aforementioned elements in EDTA and the iron(III)-EDTA complex to investigate the impact of the metal-ligand bond formation on the electronic structure of EDTA. Frontier orbital distortions, occupation changes, and energy shifts through metal- ligand bond formation are probed through distinct spectroscopic signatures.

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  • 36.
    Eckert, Sebastian
    et al.
    Max Born Inst Nichtlineare Opt & Kurzzeitspektros, Max Born Str 2A, D-12489 Berlin, Germany..
    Winghart, Marc-Oliver
    Max Born Inst Nichtlineare Opt & Kurzzeitspektros, Max Born Str 2A, D-12489 Berlin, Germany..
    Kleine, Carlo
    Max Born Inst Nichtlineare Opt & Kurzzeitspektros, Max Born Str 2A, D-12489 Berlin, Germany..
    Banerjee, Ambar
    Stockholm Univ, Alba Nova Univ Ctr, Dept Phys, S-10691 Stockholm, Sweden..
    Ekimova, Maria
    Max Born Inst Nichtlineare Opt & Kurzzeitspektros, Max Born Str 2A, D-12489 Berlin, Germany..
    Ludwig, Jan
    Max Born Inst Nichtlineare Opt & Kurzzeitspektros, Max Born Str 2A, D-12489 Berlin, Germany..
    Harich, Jessica
    Ctr Free Electron Laser Sci, Inst Nanostruct & Solid State Phys, Luruper Chaussee 149, D-22761 Hamburg, Germany..
    Fondell, Mattis
    Helmholtz Zentrum Berlin Mat & Energie GmbH, Inst Methods & Instrumentat Synchrotron Radiat Re, Albert Einstein Str 15, D-12489 Berlin, Germany..
    Mitzner, Rolf
    Helmholtz Zentrum Berlin Mat & Energie GmbH, Inst Methods & Instrumentat Synchrotron Radiat Re, Albert Einstein Str 15, D-12489 Berlin, Germany..
    Pines, Ehud
    Ben Gurion Univ Negev, Dept Chem, POB 653, IL-84105 Beer Sheva, Israel..
    Huse, Nils
    Ctr Free Electron Laser Sci, Inst Nanostruct & Solid State Phys, Luruper Chaussee 149, D-22761 Hamburg, Germany..
    Wernet, Philippe
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics.
    Odelius, Michael
    Stockholm Univ, Alba Nova Univ Ctr, Dept Phys, S-10691 Stockholm, Sweden..
    Nibbering, Erik T. J.
    Max Born Inst Nichtlineare Opt & Kurzzeitspektros, Max Born Str 2A, D-12489 Berlin, Germany..
    Electronic Structure Changes of an Aromatic Amine Photoacid along the Forster Cycle2022In: Angewandte Chemie International Edition, ISSN 1433-7851, E-ISSN 1521-3773, Vol. 61, no 27, article id e202200709Article in journal (Refereed)
    Abstract [en]

    Photoacids show a strong increase in acidity in the first electronic excited state, enabling real-time studies of proton transfer in acid-base reactions, proton transport in energy storage devices and biomolecular sensor protein systems. Several explanations have been proposed for what determines photoacidity, ranging from variations in solvation free energy to changes in electronic structure occurring along the four stages of the Forster cycle. Here we use picosecond nitrogen K-edge spectroscopy to monitor the electronic structure changes of the proton donating group in a protonated aromatic amine photoacid in solution upon photoexcitation and subsequent proton transfer dynamics. Probing core-to-valence transitions locally at the amine functional group and with orbital specificity, we clearly reveal pronounced electronic structure, dipole moment and energetic changes on the conjugate photobase side. This result paves the way for a detailed electronic structural characterization of the photoacidity phenomenon.

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  • 37.
    Ekeberg, Tomas
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Assalauova, Dameli
    Bielecki, Johan
    European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany.
    Boll, Rebecca
    Daurer, Benedikt J.
    Diamond Light Source, Harwell Science & Innovation Campus, Didcot, OX11 0DE, UK.
    Eichacker, Lutz A.
    Franken, Linda E.
    Galli, Davide E.
    Gelisio, Luca
    Gumprecht, Lars
    Gunn, Laura H.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA.
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hartmann, Robert
    Hasse, Dirk
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Ignatenko, Alexandr
    Koliyadu, Jayanath
    Kulyk, Olena
    Kurta, Ruslan
    Kuster, Markus
    Lugmayr, Wolfgang
    Lübke, Jannik
    Mancuso, Adrian P.
    Mazza, Tommaso
    Nettelblad, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Ovcharenko, Yevheniy
    Rivas, Daniel E.
    Rose, Max
    Samanta, Amit K.
    Schmidt, Philipp
    Sobolev, Egor
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics.
    Usenko, Sergey
    Westphal, Daniel
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Wollweber, Tamme
    Worbs, Lena
    Xavier, Paul Lourdu
    Yousef, Hazem
    Ayyer, Kartik
    Chapman, Henry N.
    Sellberg, Jonas A.
    Seuring, Carolin
    Vartanyants, Ivan A.
    Küpper, Jochen
    Meyer, Michael
    Maia, Filipe R. N. C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. NERSC, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
    Observation of a single protein by ultrafast X-ray diffraction2024In: Light: Science & Applications, ISSN 2095-5545, E-ISSN 2047-7538, Vol. 13, no 1, article id 15Article in journal (Refereed)
    Abstract [en]

    The idea of using ultrashort X-ray pulses to obtain images of single proteins frozen in time has fascinated and inspired many. It was one of the arguments for building X-ray free-electron lasers. According to theory, the extremely intense pulses provide sufficient signal to dispense with using crystals as an amplifier, and the ultrashort pulse duration permits capturing the diffraction data before the sample inevitably explodes. This was first demonstrated on biological samples a decade ago on the giant mimivirus. Since then, a large collaboration has been pushing the limit of the smallest sample that can be imaged. The ability to capture snapshots on the timescale of atomic vibrations, while keeping the sample at room temperature, may allow probing the entire conformational phase space of macromolecules. Here we show the first observation of an X-ray diffraction pattern from a single protein, that of Escherichia coli GroEL which at 14 nm in diameter is the smallest biological sample ever imaged by X-rays, and demonstrate that the concept of diffraction before destruction extends to single proteins. From the pattern, it is possible to determine the approximate orientation of the protein. Our experiment demonstrates the feasibility of ultrafast imaging of single proteins, opening the way to single-molecule time-resolved studies on the femtosecond timescale.

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  • 38.
    Ekimova, Maria
    et al.
    Max Born Inst Nichtlineare Opt & Kurzzeitspektros, Max Born Str 2A, D-12489 Berlin, Germany..
    Kleine, Carlo
    Max Born Inst Nichtlineare Opt & Kurzzeitspektros, Max Born Str 2A, D-12489 Berlin, Germany..
    Ludwig, Jan
    Max Born Inst Nichtlineare Opt & Kurzzeitspektros, Max Born Str 2A, D-12489 Berlin, Germany..
    Ochmann, Miguel
    Ctr Free Electron Laser Sci, Inst Nanostruct & Solid State Phys, Luruper Chaussee 149, D-22761 Hamburg, Germany..
    Agrenius, Thomas E. G.
    Stockholm Univ, AlbaNova Univ Ctr, Dept Phys, S-10691 Stockholm, Sweden..
    Kozari, Eve
    Ben Gurion Univ Negev, Dept Chem, POB 653, IL-84105 Beer Sheva, Israel..
    Pines, Dina
    Ben Gurion Univ Negev, Dept Chem, POB 653, IL-84105 Beer Sheva, Israel..
    Pines, Ehud
    Ben Gurion Univ Negev, Dept Chem, POB 653, IL-84105 Beer Sheva, Israel..
    Huse, Nils
    Ctr Free Electron Laser Sci, Inst Nanostruct & Solid State Phys, Luruper Chaussee 149, D-22761 Hamburg, Germany..
    Wernet, Philippe
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics.
    Odelius, Michael
    Stockholm Univ, AlbaNova Univ Ctr, Dept Phys, S-10691 Stockholm, Sweden..
    Nibbering, Erik T. J.
    Max Born Inst Nichtlineare Opt & Kurzzeitspektros, Max Born Str 2A, D-12489 Berlin, Germany..
    From Local Covalent Bonding to Extended Electric Field Interactions in Proton Hydration2022In: Angewandte Chemie International Edition, ISSN 1433-7851, E-ISSN 1521-3773, Vol. 61, no 46Article in journal (Refereed)
    Abstract [en]

    Seemingly simple yet surprisingly difficult to probe, excess protons in water constitute complex quantum objects with strong interactions with the extended and dynamically changing hydrogen-bonding network of the liquid. Proton hydration plays pivotal roles in energy transport in hydrogen fuel cells and signal transduction in transmembrane proteins. While geometries and stoichiometry have been widely addressed in both experiment and theory, the electronic structure of these specific hydrated proton complexes has remained elusive. Here we show, layer by layer, how utilizing novel flatjet technology for accurate x-ray spectroscopic measurements and combining infrared spectral analysis and calculations, we find orbital-specific markers that distinguish two main electronic-structure effects: Local orbital interactions determine covalent bonding between the proton and neigbouring water molecules, while orbital-energy shifts measure the strength of the extended electric field of the proton.

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  • 39.
    Eliah 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.
    Simulations of ultrafast photon-matter interactions for molecular imaging with X-ray lasers2024Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Biological structure determination has had new avenues of investigation opened due to the introduction of X-ray free-electron lasers (XFELs). These X-ray lasers provide an extreme amount of photons on ultrafast timescales used to probe matter, and in particular biomolecules. The high intensity of the X-rays destroys the sample, though not before structural information has been acquired. The unique properties of the probe provide the unprecedented opportunity to study the un-crystallized form of biological macromolecules, small crystals of biomolecules and their dynamics. 

    In this work, we study processes in XFEL imaging experiments that could affect the achievable resolution of the protein structure in a diffraction experiment. Elastic scattering is the process which provides structural information and leaves the sample unperturbed. This interaction occurs far less often compared to damage inducing processes, such as photoabsorption, which leads to rapid ionization of the studied sample. By using density functional theory, we study the effect of ultrahigh charge states in small systems, such as amino acids and peptides, on the subsequent bond breaking and charge dynamics. Reproducible fragmentation patterns are studied in order to find features that could be understood in larger systems, such as proteins. 

    Biomolecules are dynamical systems, and the currently used pulse duration is not short enough to outrun the movement of the atoms. The diffraction patterns acquired in an experiment are therefore an incoherent sum of slightly different conformations of the same system. Water can help to reduce these structural variations, but the water molecules themselves will then be a source of noise. Using classical molecular dynamics, we study the optimal amount of water that should be used to achieve the highest resolution. 

    To simulate ultrafast molecular dynamics of larger systems such as proteins, we develop a hybrid Monte Carlo/molecular dynamics model. We utilize it to simulate the fragmentation dynamics of small proteins and investigate the possibility to extract structural information from the fragmentation patterns. For larger systems exposed to X-ray lasers, such as viruses and crystals, we develop a hybrid collisional-radiative and classical molecular dynamics approach. The method is used in several projects, both in theoretical studies and to support experiments conducted at XFEL facilities. In particular, we simulate the interaction of hexagonal ice with an X-ray laser, and show the structure makes a phase transition from the native crystal state to a plasma, while still partly retaining structural order. Furthermore, we note that the structural changes occur in an anisotropic manner, where different local structural configurations in ice decay on different time-scales. 

    Preliminary experimental results show this anisotropic dynamics in an X-ray pump-probe serial femtosecond X-ray crystallography experiment performed on  I3C crystals. The real space dynamics as a function of probe delay given by our theoretical model and the experiment both show good agreement, where the iodine atoms exhibit correlated motion. The model is also used to calculate the expected atomic displacement and ionization in a hemoglobin crystal, revealing the time and length scales of the dynamics in the protein during the experiment. 

    List of papers
    1. Femtosecond bond breaking and charge dynamics in ultracharged amino acids
    Open this publication in new window or tab >>Femtosecond bond breaking and charge dynamics in ultracharged amino acids
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    2019 (English)In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 151, no 14, article id 144307Article in journal (Refereed) Published
    Abstract [en]

    Historically, structure determination of nanocrystals, proteins, and macromolecules required the growth of high-quality crystals sufficiently large to diffract X-rays efficiently while withstanding radiation damage. The development of the X-ray free-electron laser has opened the path toward high resolution single particle imaging, and the extreme intensity of the X-rays ensures that enough diffraction statistics are collected before the sample is destroyed by radiation damage. Still, recovery of the structure is a challenge, in part due to the partial fragmentation of the sample during the diffraction event. In this study, we use first-principles based methods to study the impact of radiation induced ionization of six amino acids on the reconstruction process. In particular, we study the fragmentation and charge rearrangement to elucidate the time scales involved and the characteristic fragments occurring.

    National Category
    Atom and Molecular Physics and Optics
    Identifiers
    urn:nbn:se:uu:diva-395440 (URN)10.1063/1.5116814 (DOI)000500356200030 ()31615216 (PubMedID)
    Funder
    Swedish National Infrastructure for Computing (SNIC), SNIC 2019/8-30Swedish National Infrastructure for Computing (SNIC), SNIC 2018/3-221Swedish Research Council, 637-2013-7303Swedish Research Council, 2013-3940Swedish Foundation for Strategic Research , ICA16-0037
    Available from: 2019-10-18 Created: 2019-10-18 Last updated: 2024-01-09Bibliographically approved
    2. Imaging of femtosecond bond breaking and charge dynamics in ultracharged peptides
    Open this publication in new window or tab >>Imaging of femtosecond bond breaking and charge dynamics in ultracharged peptides
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    2022 (English)In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 24, no 3, p. 1532-1543Article in journal (Refereed) Published
    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.

    Place, publisher, year, edition, pages
    Royal Society of Chemistry (RSC), 2022
    National Category
    Physical Chemistry
    Identifiers
    urn:nbn:se:uu:diva-468649 (URN)10.1039/d1cp03419g (DOI)000733885500001 ()34939631 (PubMedID)
    Funder
    Swedish Research Council, 2018-05973Swedish Research Council, 2019-03935Swedish Research Council, 2018-00740Swedish Foundation for Strategic Research, ICA16-0037Swedish National Infrastructure for Computing (SNIC)
    Available from: 2022-02-28 Created: 2022-02-28 Last updated: 2024-01-09Bibliographically approved
    3. MolDStruct: modelling the dynamics and structure of matter exposed to ultrafast X-ray lasers with hybrid collisional-radiative/molecular dynamics
    Open this publication in new window or tab >>MolDStruct: modelling the dynamics and structure of matter exposed to ultrafast X-ray lasers with hybrid collisional-radiative/molecular dynamics
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    (English)Manuscript (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.

    National Category
    Atom and Molecular Physics and Optics
    Identifiers
    urn:nbn:se:uu:diva-519450 (URN)
    Projects
    In thesis
    Funder
    Swedish Research Council, 2018- 00740, 2019-03935
    Available from: 2024-01-08 Created: 2024-01-08 Last updated: 2024-01-09
    4. Anisotropic melting of ice induced by ultrafast non-thermal heating
    Open this publication in new window or tab >>Anisotropic melting of ice induced by ultrafast non-thermal heating
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    (English)Manuscript (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.

    National Category
    Atom and Molecular Physics and Optics
    Identifiers
    urn:nbn:se:uu:diva-519477 (URN)
    Projects
    In thesis
    Funder
    Swedish Research Council, 2017-05128, 2018-00740, 2019-03935Carl Tryggers foundation , CTS 18:392The Swedish Foundation for International Cooperation in Research and Higher Education (STINT)
    Available from: 2024-01-08 Created: 2024-01-08 Last updated: 2024-01-09
    5. Radiation damage in a hemoglobin crystal studied with an X-ray free-electron laser
    Open this publication in new window or tab >>Radiation damage in a hemoglobin crystal studied with an X-ray free-electron laser
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    (English)Manuscript (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.

    National Category
    Atom and Molecular Physics and Optics
    Identifiers
    urn:nbn:se:uu:diva-519591 (URN)
    Projects
    In thesis
    Funder
    Swedish Research Council, 2018-00740, 2019-03935
    Available from: 2024-01-08 Created: 2024-01-08 Last updated: 2024-01-18
    6. Macromolecule classification using X-ray laser induced fragmentation simulated with hybrid Monte Carlo/Molecular Dynamics
    Open this publication in new window or tab >>Macromolecule classification using X-ray laser induced fragmentation simulated with hybrid Monte Carlo/Molecular Dynamics
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    (English)Manuscript (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.

    National Category
    Atom and Molecular Physics and Optics
    Identifiers
    urn:nbn:se:uu:diva-519565 (URN)
    Projects
    In thesis
    Funder
    Swedish Research Council, 2018-00740, 2019-03935, 2021-05988
    Available from: 2024-01-08 Created: 2024-01-08 Last updated: 2024-01-09
    7. Structural Heterogeneity in Single Particle Imaging Using X-ray Lasers
    Open this publication in new window or tab >>Structural Heterogeneity in Single Particle Imaging Using X-ray Lasers
    Show others...
    2020 (English)In: Journal of Physical Chemistry Letters, ISSN 1948-7185, E-ISSN 1948-7185, Vol. 11, no 15, p. 6077-6083Article in journal (Refereed) Published
    Abstract [en]

    One of the challenges facing single particle imaging with ultrafast X-ray pulses is the structural heterogeneity of the sample to be imaged. For the method to succeed with weakly scattering samples, the diffracted images from a large number of individual proteins need to be averaged. The more the individual proteins differ in structure, the lower the achievable resolution in the final reconstructed image. We use molecular dynamics to simulate two globular proteins in vacuum, fully desolvated as well as with two different solvation layers, at various temperatures. We calculate the diffraction patterns based on the simulations and evaluate the noise in the averaged patterns arising from the structural differences and the surrounding water. Our simulations show that the presence of a minimal water coverage with an average 3 Å thickness will stabilize the protein, reducing the noise associated with structural heterogeneity, whereas additional water will generate more background noise.

    National Category
    Biophysics Atom and Molecular Physics and Optics
    Identifiers
    urn:nbn:se:uu:diva-416668 (URN)10.1021/acs.jpclett.0c01144 (DOI)000562064500038 ()32578996 (PubMedID)
    Funder
    Swedish National Infrastructure for Computing (SNIC), SNIC 2019/8-30EU, Horizon 2020, 801406Swedish Research Council, 201800740Australian Research Council, DP190103027
    Available from: 2020-07-28 Created: 2020-07-28 Last updated: 2024-01-09Bibliographically approved
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  • 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.
    Fedorov, A. S.
    et al.
    Siberian Fed Univ, Int Res Ctr Spect & Quantum Chem, Krasnoyarsk 660074, Russia.;RAS, Kirensky Inst Phys, Fed Res Ctr, KSC,SB, Krasnoyarsk 660036, Russia..
    Eremkin, E. V.
    Siberian Fed Univ, Int Res Ctr Spect & Quantum Chem, Krasnoyarsk 660074, Russia..
    Krasnov, P. O.
    Siberian Fed Univ, Int Res Ctr Spect & Quantum Chem, Krasnoyarsk 660074, Russia..
    Gerasimov, V. S.
    RAS, Inst Computat Modeling, SB, Krasnoyarsk 660036, Russia..
    Ågren, Hans
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics.
    Polyutov, S. P.
    Siberian Fed Univ, Int Res Ctr Spect & Quantum Chem, Krasnoyarsk 660074, Russia..
    A hybrid quantum-classical theory for predicting terahertz charge-transfer plasmons in metal nanoparticles on graphene2024In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 160, no 4, article id 044117Article in journal (Refereed)
    Abstract [en]

    Metal nanoparticle (NP) complexes lying on a single-layer graphene surface are studied with a developed original hybrid quantum-classical theory using the Finite Element Method (FEM) that is computationally cheap. Our theory is based on the motivated assumption that the carrier charge density in the doped graphene does not vary significantly during the plasmon oscillations. Charge transfer plasmon (CTP) frequencies, eigenvectors, quality factors, energy loss in the NPs and in graphene, and the absorption power are aspects that are theoretically studied and numerically calculated. It is shown the CTP frequencies reside in the terahertz range and can be represented as a product of two factors: the Fermi level of graphene and the geometry of the NP complex. The energy losses in the NPs are predicted to be inversely dependent on the radius R of the nanoparticle, while the loss in graphene is proportional to R and the interparticle distance. The CTP quality factors are predicted to be in the range similar to 10-100. The absorption power under CTP excitation is proportional to the scalar product of the CTP dipole moment and the external electromagnetic field. The developed theory makes it possible to simulate different properties of CTPs 3-4 orders of magnitude faster compared to the original FEM or the finite-difference time domain method, providing possibilities for predicting the plasmonic properties of very large systems for different applications.

  • 42.
    Fedorov, Aleksandr S.
    et al.
    Siberian Fed Univ, Int Res Ctr Spect & Quantum Chem IRC SQC, Krasnoyarsk 660041, Russia.;Fed Res Ctr KSC SB RAS, Kirensky Inst Phys, Krasnoyarsk 660036, Russia..
    Visotin, Maxim A.
    Siberian Fed Univ, Int Res Ctr Spect & Quantum Chem IRC SQC, Krasnoyarsk 660041, Russia.;Fed Res Ctr KSC SB RAS, Kirensky Inst Phys, Krasnoyarsk 660036, Russia..
    Eremkin, Egor, V
    Siberian Fed Univ, Int Res Ctr Spect & Quantum Chem IRC SQC, Krasnoyarsk 660041, Russia..
    Krasnov, Pavel O.
    Siberian Fed Univ, Int Res Ctr Spect & Quantum Chem IRC SQC, Krasnoyarsk 660041, Russia..
    Ågren, Hans
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics.
    Polyutov, Sergey P.
    Siberian Fed Univ, Int Res Ctr Spect & Quantum Chem IRC SQC, Krasnoyarsk 660041, Russia.;Fed Siberian Res Clin Ctr FMBA Russia, Krasnoyarsk 660037, Russia..
    Charge-transfer plasmons of complex nanoparticle arrays connected by conductive molecular bridges2022In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 24, no 32, p. 19531-19540Article in journal (Refereed)
    Abstract [en]

    Charge-transfer plasmons (CTP) in complexes of metal nanoparticles bridged by conductive molecular linkers are theoretically analysed using a statistic approach. The applied model takes into account the kinetic energy of carriers inside the linkers including its dissipation and the Coulomb energy of the charged nanoparticles. The plasmons are statistically investigated for systems containing a large number of complexes of bridged nanoparticles of realistic sizes generated using a simplified molecular dynamics algorithm, where the geometries of the complexes are dependent on the rate of connection of the linkers with the nanoparticles. As illustrated, the distribution of CTP frequencies in the generated nanoparticle complexes is very inhomogeneous. It has a narrow peak, corresponding to CTP plasmons in dimers, and two broad peaks, corresponding mainly to low and high-frequency oscillations in chains of connected nanoparticles. It is found that in general the plasmon frequencies depend inversely on the value of the complex dipole moment of the plasmon oscillation, where the assumption follows that low-frequency plasmons will be more efficiently excited in an external electromagnetic field. To calculate the CTP energy absorption in this field two model modifications are proposed: a system-external electromagnetic field interaction model and a simplified broadening plasmon peak model where the plasmons are calculated at first without damping and where the delta-shaped oscillation peaks are broadened then due to the damping. It is demonstrated that both modifications lead to a wide and almost monotonic absorption in the IR region for all generated systems containing a large number of bridged nanoparticles due to the presence of a large number of CTPs in this region.

  • 43.
    Fuller, Franklin D.
    et al.
    SLAC Natl Accelerator Lab, Menlo Pk, CA 94025 USA..
    Loukianov, Anton
    SLAC Natl Accelerator Lab, Menlo Pk, CA 94025 USA..
    Takanashi, Tsukasa
    Tohoku Univ, Sendai, Miyagi, Japan..
    You, Daehyun
    Tohoku Univ, Sendai, Miyagi, Japan..
    Li, Yiwen
    Tohoku Univ, Sendai, Miyagi, Japan..
    Ueda, Kiyoshi
    Tohoku Univ, Sendai, Miyagi, Japan..
    Fransson, Thomas
    SLAC Natl Accelerator Lab, Menlo Pk, CA 94025 USA..
    Yabashi, Makina
    RIKEN, Spring Ctr 8, Sayo, Hyogo, Japan..
    Katayama, Tetsuo
    RIKEN, Spring Ctr 8, Sayo, Hyogo, Japan.;Japan Synchrotron Radiat Res Inst, Sayo, Hyogo, Japan..
    Weng, Tsu-Chien
    ShanghaiTech Univ, Sch Phys Sci & Technol, Shanghai, Peoples R China..
    Alonso-Mori, Roberto
    SLAC Natl Accelerator Lab, Menlo Pk, CA 94025 USA..
    Bergmann, Uwe
    Univ Wisconsin, Madison, WI USA..
    Kern, Jan
    Lawrence Berkeley Natl Lab, Berkeley, CA USA..
    Yachandra, Vittal K.
    Lawrence Berkeley Natl Lab, Berkeley, CA USA..
    Wernet, Philippe
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics.
    Yano, Junko
    Lawrence Berkeley Natl Lab, Berkeley, CA USA..
    Resonant X-ray emission spectroscopy from broadband stochastic pulses at an X-ray free electron laser2021In: Communications Chemistry, E-ISSN 2399-3669, Vol. 4, no 1, article id 84Article in journal (Refereed)
    Abstract [en]

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

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  • 44.
    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.

  • 45.
    Gao, Lingfeng
    et al.
    Shenzhen Univ, Inst Microscale Optoelect, Collaborat Innovat Ctr Optoelect Sci & Technol, Key Lab Optoelect Devices & Syst, Minist Educ, Shenzhen 518060, Peoples R China; Shenzhen Univ, Guangdong Prov Coll Phys & Optoelect Engn, Shenzhen Key Lab Micronano Photon Informat Techno, Guangdong Lab Artificial Intelligence & Digital E, Shenzhen 518060, Peoples R China.
    Wang, Rui
    Peking Univ, Sch Phys, State Key Lab Mesoscop Phys & Frontiers, Sci Ctr Nanooptoelect, Beijing 100871, Peoples R China.
    Kuklin, Artem V.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy.
    Zhang, Han
    Shenzhen Univ, Inst Microscale Optoelect, Collaborat Innovat Ctr Optoelect Sci & Technol, Key Lab Optoelect Devices & Syst, Minist Educ, Shenzhen 518060, Peoples R China; Shenzhen Univ, Guangdong Prov Coll Phys & Optoelect Engn, Shenzhen Key Lab Micronano Photon Informat Techno, Guangdong Lab Artificial Intelligence & Digital E, Shenzhen 518060, Peoples R China.
    Ågren, Hans
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics. Henan Univ, Coll Chem & Chem Engn, Kaifeng 475004, Henan, Peoples R China.
    PbSe Nanocrystals Produced by Facile Liquid Phase Exfoliation for Efficient UV-Vis Photodetectors2021In: Advanced Functional Materials, ISSN 1616-301X, E-ISSN 1616-3028, Vol. 31, no 17, article id 2010401Article in journal (Refereed)
    Abstract [en]

    Lead selenide (PbSe)-based nanomaterials have been extensively investigated as building blocks for next-generation optoelectronic devices owing to their unique properties. In this work, PbSe nanocrystals (NCs) have been successfully fabricated by a facile liquid phase exfoliation approach and directly applied as active materials for photo-electrochemical (PEC)-type photodetectors (PDs). Taking advantage of broadband absorption and fast carrier dynamics, the PbSe NCs-based PDs exhibit excellent photo-current density (11.88 μA cm−2), photo-responsivity (12.37 mA W−1), response/recovery time (0.12/0.13 s), and long-term cycling stability. The working mechanism of PbSe NCs-based PDs is explored by density functional theory calculations based on their structural and electronic properties under various conditions. It is anticipated that this contribution paves the way to readily fabricate low-dimensional PbSe NCs and extend their practical applications in PEC-type PDs.

  • 46.
    Gao, Lingfeng
    et al.
    Coll Mat Chem & Chem Engn, Key Lab Organosilicon Chem & Mat Technol, Key Lab Organosilicon Mat Technol, Minist Educ, Hangzhou 311121, Zhejiang, Peoples R China..
    Zhao, Yiming
    Zhejiang Univ Technol, Coll Chem Engn, Hangzhou 310014, Peoples R China..
    Chang, Xiaohua
    Coll Mat Chem & Chem Engn, Key Lab Organosilicon Chem & Mat Technol, Key Lab Organosilicon Mat Technol, Minist Educ, Hangzhou 311121, Zhejiang, Peoples R China..
    Zhang, Jian
    Shenzhen Univ, Coll Optoelect Engn, Shenzhen 518060, Peoples R China..
    Li, Ying
    Zhejiang Univ Technol, Coll Chem Engn, Hangzhou 310014, Peoples R China..
    Wageh, Swelm
    King Abdulaziz Univ, Fac Sci, Dept Phys, Jeddah 21589, Saudi Arabia..
    Al-Hartomy, Omar A.
    King Abdulaziz Univ, Fac Sci, Dept Phys, Jeddah 21589, Saudi Arabia..
    Al-Sehemi, Abdullah G.
    King Khalid Univ, Res Ctr Adv Mat Sci RCAMS, POB 9004, Abha 61413, Saudi Arabia..
    Zhang, Han
    Shenzhen Univ, Coll Optoelect Engn, Shenzhen 518060, Peoples R China..
    Ågren, Hans
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics. Henan Univ, Coll Chem & Chem Engn, Kaifeng 475004, Henan, Peoples R China..
    Emerging applications of MXenes for photodetection: Recent advances and future challenges2022In: Materials Today, ISSN 1369-7021, E-ISSN 1873-4103, Vol. 61, p. 169-190Article in journal (Refereed)
    Abstract [en]

    The development and applications of transition metal carbides, nitrides and carbonitrides, commonly denoted as MXenes, have during the last few years rapidly expanded in various technological fields owing to their unique and controllable properties. These materials exhibit competing performance comparing with traditional materials and have created numerous opportunities for technology markets. Taking the advantage of excellent optoelectronic features, MXenes have been utilized for the construction of photodetectors with various structures and unique functionalities. While the appli-cation of MXenes in this area can be traced back to 2016, we have during the recent three years witnessed a dramatic development of MXene-based photodetectors, calling for a timely review to guideline their future direction. In this work, synthetic strategies of pristine MXenes are briefly introduced and their properties are discussed focusing on the optoelectronic aspects that are fundamental for the photoelectric conversion. Recent advances of MXene-based photodetectors are comprehensively summarized based on different types of MXenes and innovative designs of device construction. Finally, we provide perspectives for future challenges and opportunities of MXene-based photodetectors, which may enlighten their further development.

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  • 47.
    Gel'mukhanov, Faris
    et al.
    KTH Royal Inst Technol, Div Theoret Chem & Biol, SE-10691 Stockholm, Sweden.;Siberian Fed Univ, Int Res Ctr Spect & Quantum Chem IRC SQC, Krasnoyarsk 660041, Russia..
    Liu, Ji-Cai
    North China Elect Power Univ, Sch Math & Phys, Beijing 102206, Peoples R China.;North China Elect Power Univ, Hebei Key Lab Phys & Energy Technol, Baoding 071000, Peoples R China..
    Krasnov, Pavel
    Siberian Fed Univ, Int Res Ctr Spect & Quantum Chem IRC SQC, Krasnoyarsk 660041, Russia..
    Ignatova, Nina
    Siberian Fed Univ, Int Res Ctr Spect & Quantum Chem IRC SQC, Krasnoyarsk 660041, Russia..
    Rubensson, Jan-Erik
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics.
    Kimberg, Victor
    KTH Royal Inst Technol, Div Theoret Chem & Biol, SE-10691 Stockholm, Sweden..
    Nonlocal resonant inelastic x-ray scattering2023In: Physical Review A: covering atomic, molecular, and optical physics and quantum information, ISSN 2469-9926, E-ISSN 2469-9934, Vol. 108, no 5, article id 052820Article in journal (Refereed)
    Abstract [en]

    In the description of resonant inelastic x-ray scattering (RIXS) from inversion-symmetric molecules the small core-level splitting is typically neglected. However, the spacing Delta between gerade and ungerade core levels in homonuclear diatomic molecules can be comparable with the lifetime broadening of the intermediate core-excited state Gamma. We show that when Delta similar to Gamma the scattering becomes nonlocal in the sense that x-ray absorption at one atomic site is followed by emission at the other one. This is manifested in an unusual dependence of the RIXS cross section on the sum of the momenta of incoming and outgoing x-ray photons k + k', contrary to the normal k - k' dependence in the conventional local RIXS theory. The nonlocality of the scattering influences strongly the scattering angle and excitation energy dependence of the intensity ratio between parity forbidden and allowed RIXS channels. Numerical simulations for N-2 show that this effect can readily be measured at present-day x-ray radiation facilities.

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  • 48.
    Ghosh, Anirudha
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy. Lund Univ, MAXLab 4, POB 118, S-22100 Lund, Sweden..
    Jönsson, H. Johan M.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy. Asia Pacific Ctr Theoret Phys, Pohang 37673, South Korea..
    Mukkattukavil, D. John
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy.
    Kvashnin, Yaroslav
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Phuyal, Dibya
    KTH Royal Inst Technol, Dept Appl Phys, S-10691 Stockholm, Sweden..
    Thunström, Patrik
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Agåker, Marcus
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics. Lund Univ, MAXLab 4, POB 118, S-22100 Lund, Sweden..
    Nicolaou, Alessandro
    Synchrotron SOLEIL, Orme Merisiers, BP48, F-91192 Gif Sur Yvette, France..
    Jonak, Martin
    Heidelberg Univ, Kirchhoff Inst Phys, D-69120 Heidelberg, Germany..
    Klingeler, Ruediger
    Heidelberg Univ, Kirchhoff Inst Phys, D-69120 Heidelberg, Germany..
    Kamalakar, M. Venkata
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Condensed Matter Physics of Energy Materials.
    Sarkar, Tapati
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Materials Science and Engineering, Solid State Physics.
    Vasiliev, Alexander N.
    Natl Univ Sci & Tech MISS, Moscow 119049, Russia.;Lomonosov Moscow State Univ, Moscow 119991, Russia.;Ural Fed Univ, Ekaterinburg 620002, Russia..
    Butorin, Sergei
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Condensed Matter Physics of Energy Materials.
    Eriksson, Olle
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory. Örebro Univ, Sch Sci & Technol, S-70182 Örebro, Sweden..
    Abdel-Hafiez, Mahmoud
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy. Univ Doha Sci & Technol, POB 24449, Doha, Qatar..
    Magnetic circular dichroism in the dd excitation in the van der Waals magnet CrI3 probed by resonant inelastic x-ray scattering2023In: Physical Review B, ISSN 2469-9950, E-ISSN 2469-9969, Vol. 107, no 11, article id 115148Article in journal (Refereed)
    Abstract [en]

    We report on a combined experimental and theoretical study on CrI3 single crystals by employing the polarization dependence of resonant inelastic x-ray scattering (RIXS). Our investigations reveal multiple Cr 3d orbital splitting (dd excitations) as well as magnetic dichroism (MD) in the RIXS spectra. The dd excitation energies are similar on the two sides of the ferromagnetic transition temperature, T-C similar to 61 K, although MD in RIXS is predominant at 0.4 T magnetic field below TC. This demonstrates that the ferromagnetic superexchange interaction that is responsible for the interatomic exchange field is vanishingly small compared with the local exchange field that comes from exchange and correlation interaction among the interacting Cr 3d orbitals. The recorded RIXS spectra reported here reveal clearly resolved Cr 3d intraorbital dd excitations that represent transitions between electronic levels that are heavily influenced by dynamic correlations and multiconfiguration effects. Our calculations taking into account the Cr 3d hybridization with the ligand valence states and the full multiplet structure due to intra-atomic and crystal field interactions in Oh and D3d symmetry clearly reproduced the dichroic trend in experimental RIXS spectra.

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  • 49.
    Ghosh, Anirudha
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics.
    Singh, Deobrat
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Aramaki, T.
    Kyushu Inst Technol, Grad Sch Engn, Fukuoka 8048550, Japan..
    Mu, Qingge
    Max Planck Inst Chem Phys Solids, D-01187 Dresden, Germany..
    Borisov, Vladislav
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Kvashnin, Yaroslav
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Haider, G.
    Czech Acad Sci, J Heyrovsky Inst Phys Chem, Dolejskova 2155, Prague 18223, Czech Republic..
    Jonak, M.
    Heidelberg Univ, Kirchhoff Inst Phys, D-69120 Heidelberg, Germany..
    Chareev, D.
    Natl Univ Sci & Technol MISiS, Moscow 119049, Russia.;Inst Expt Mineral IEM RAS, Chernogolovka 142432, Moscow Region, Russia.;Ural Fed Univ, Ekaterinburg 620002, Russia..
    Medvedev, S. A.
    Max Planck Inst Chem Phys Solids, D-01187 Dresden, Germany..
    Klingeler, R.
    Heidelberg Univ, Kirchhoff Inst Phys, D-69120 Heidelberg, Germany..
    Mito, M.
    Kyushu Inst Technol, Grad Sch Engn, Fukuoka 8048550, Japan..
    Abdul-Hafidh, E. H.
    Taibah Univ, Fac Sci, Phys Dept, King Khalid Rd, Al Amoedi 46423, Yanbu El Bahr, Saudi Arabia..
    Vejpravova, J.
    Charles Univ Prague, Fac Math & Phys, Dept Condensed Matter Phys, Ke Karlovu 5, Prague 12116 2, Czech Republic..
    Kalbac, M.
    Czech Acad Sci, J Heyrovsky Inst Phys Chem, Dolejskova 2155, Prague 18223, Czech Republic..
    Ahuja, Rajeev
    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 Univ, Dept Phys & Astron, Box 516, SE-75120 Uppsala, Sweden..
    Eriksson, Olle
    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, Materials Physics. Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Materials Science and Engineering, Solid State Physics. Örebro Univ, Sch Sci & Technol, SE-70182 Örebro, Sweden..
    Abdel-Hafiez, Mahmoud
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Condensed Matter Physics of Energy Materials.
    Exotic magnetic and electronic properties of layered CrI3 single crystals under high pressure2022In: Physical Review B, ISSN 2469-9950, E-ISSN 2469-9969, Vol. 105, no 8, article id L081104Article in journal (Refereed)
    Abstract [en]

    Through advanced experimental techniques on CrI3 single crystals, we derive a pressure-temperature phase diagram. We find that T-c increases to similar to 66 K with pressure up to similar to 3 GPa followed by a decrease to similar to 10 K at 21.2 GPa. The experimental results are reproduced by theoretical calculations based on density functional theory where electron-electron interactions are treated by a static on-site Hubbard U on Cr 3d orbitals. The origin of the pressure-induced reduction of the ordering temperature is associated with a decrease in the calculated bond angle, from 95 degrees at ambient pressure to similar to 85 degrees at 25 GPa. Above 22 GPa, experiment and theory jointly point to the idea that the ferromagnetically ordered state is destroyed, giving rise first to a complex, unknown magnetic configuration, and at sufficiently high pressures a pure antiferromagnetic configuration. This sequence of transitions in the magnetism is accompanied by a well-detected pressure-induced semiconductor-to-metal phase transition that is revealed by both high-pressure resistivity measurements and ab initio theory.

  • 50.
    Giangrisostomi, Erika
    et al.
    Helmholtz Zent Berlin, Inst Methods & Instrumentat Synchrotron Radiat Res, Albert Einstein Str 15, D-12489 Berlin, Germany..
    Ovsyannikov, Ruslan
    Helmholtz Zent Berlin, Inst Methods & Instrumentat Synchrotron Radiat Res, Albert Einstein Str 15, D-12489 Berlin, Germany..
    Haverkamp, Robert
    Helmholtz Zent Berlin, Inst Methods & Instrumentat Synchrotron Radiat Res, Albert Einstein Str 15, D-12489 Berlin, Germany.;Univ Potsdam, Inst Phys & Astron, Karl Liebknecht Str 24-25, D-14476 Potsdam, Germany..
    Sorgenfrei, Nomi L. A. N.
    Helmholtz Zent Berlin, Inst Methods & Instrumentat Synchrotron Radiat Res, Albert Einstein Str 15, D-12489 Berlin, Germany.;Univ Potsdam, Inst Phys & Astron, Karl Liebknecht Str 24-25, D-14476 Potsdam, Germany..
    Neppl, Stefan
    Univ Potsdam, Inst Phys & Astron, Karl Liebknecht Str 24-25, D-14476 Potsdam, Germany.;Paul Scherrer Inst, Villigen, Switzerland..
    Sezen, Hikmet
    Helmholtz Zent Berlin, Inst Methods & Instrumentat Synchrotron Radiat Res, Albert Einstein Str 15, D-12489 Berlin, Germany.;Tech Univ Darmstadt, Darmstadt, Germany..
    Johansson, Fredrik O. L.
    Helmholtz Zent Berlin, Inst Methods & Instrumentat Synchrotron Radiat Res, Albert Einstein Str 15, D-12489 Berlin, Germany.;Univ Potsdam, Inst Phys & Astron, Karl Liebknecht Str 24-25, D-14476 Potsdam, Germany.;Sorbonne Univ, Paris, France.;Royal Inst Technol, Stockholm, Sweden..
    Svensson, Svante
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics.
    Föhlisch, Alexander
    Helmholtz Zent Berlin, Inst Methods & Instrumentat Synchrotron Radiat Res, Albert Einstein Str 15, D-12489 Berlin, Germany.;Univ Potsdam, Inst Phys & Astron, Karl Liebknecht Str 24-25, D-14476 Potsdam, Germany..
    Inhomogeneity of Cleaved Bulk MoS2 and Compensation of Its Charge Imbalances by Room-Temperature Hydrogen Treatment2023In: Advanced Materials Interfaces, ISSN 2196-7350, article id 2300392Article in journal (Refereed)
    Abstract [en]

    Synthetic single crystals of bulk molybdenum disulphide cleaved in ultrahigh vacuum are mapped across a large (approximate to 25 mm(2)) area by X-ray photoelectron spectroscopy, both statically and transiently following above-bandgap excitation by an ultrafast laser. This work finds that: I) A cleaved surface typically displays spatially inhomogeneous properties, manifested by large (approximate to 1 eV) variations in binding energy and band bending and variable degrees of stability of those over time as a result of variable gas uptakes from the residual atmosphere. II) Moderate (350 degrees C) annealing and exposure to molecular hydrogen can be cycled to switch between smaller and larger surface band bending, the switch being reversible but strongly sample-position dependent. III) Upon exposure to atomic hydrogen, the binding energy of the entire surface levels out to a common (within <0.05 eV) value corresponding to a Fermi level pinned close to mid-bandgap. Such remarkable effect is attributed to the ability of hydrogen atoms to serve as donors and acceptors alike, thus neutralizing local charge imbalances inevitably present at the surface in consequence of intrinsic and/or cleavage-induced defects. With subsequent moderate annealing, the hydrogenated surface preserves a fairly homogenous electronic state which is however characterized by a lower binding energy and little to no band bending.

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