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  • Water structure near the surface of Weyl semimetals as catalysts in photocatalytic proton reduction
    Struct. Dyn. (IF 3.216) Pub Date : 2020-05-12
    Jure Gujt; Peter Zimmer; Frederik Zysk; Vicky Süß; Claudia Felser; Matthias Bauer; Thomas D. Kühne

    In this work, second-generation Car–Parrinello-based mixed quantum-classical mechanics molecular dynamics simulations of small nanoparticles of NbP, NbAs, TaAs, and 1T-TaS2 in water are presented. The first three materials are topological Weyl semimetals, which were recently discovered to be active catalysts in photocatalytic water splitting. The aim of this research was to correlate potential differences

    更新日期:2020-06-30
  • Ultrafast x-ray and electron scattering of free molecules: A comparative evaluation
    Struct. Dyn. (IF 3.216) Pub Date : 2020-06-23
    Lingyu Ma; Haiwang Yong; Joseph D. Geiser; Andrés Moreno Carrascosa; Nathan Goff; Peter M. Weber

    Resolving gas phase molecular motions with simultaneous spatial and temporal resolution is rapidly coming within the reach of x-ray Free Electron Lasers (XFELs) and Mega-electron-Volt (MeV) electron beams. These two methods enable scattering experiments that have yielded fascinating new results, and while both are important methods for determining transient molecular structures in photochemical reactions

    更新日期:2020-06-30
  • Method for developing a sub-10 fs ultrafast electron diffraction technology
    Struct. Dyn. (IF 3.216) Pub Date : 2020-06-09
    Hyun Woo Kim; In Hyung Baek; Junho Shin; Sunjeong Park; Hyeon Sang Bark; Key Young Oang; Kyu-Ha Jang; Kitae Lee; Nikolay Vinokurov; Young Uk Jeong

    The experimental observation of femtosecond dynamics in atoms and molecules by stroboscopic technologies utilizing x ray or electron flashes has attracted much attention and has rapidly developed. We propose a feasible ultrafast electron diffraction (UED) technology with high brightness and a sub-10 fs temporal resolution. We previously demonstrated a UED system with an overall temporal resolution

    更新日期:2020-06-30
  • Fluctuation suppression in microgels by polymer electrolytes
    Struct. Dyn. (IF 3.216) Pub Date : 2020-06-15
    S. Pasini; S. Maccarrone; N. K. Székely; L. R. Stingaciu; A. P. H. Gelissen; W. Richtering; M. Monkenbusch; O. Holderer

    Structural details of thermoresponsive, cationically poly(N-iso-propylacrylamide-co-methacrylamido propyl trimethyl ammonium chloride) microgels and the influence of the anionic electrolyte polystyrene sulfonate (PSS) on the internal structure and dynamics of the cationic microgels have been studied with a combination of small angle neutron scattering (SANS) and neutron spin echo (NSE) spectroscopy

    更新日期:2020-06-30
  • Imaging plasma formation in isolated nanoparticles with ultrafast resonant scattering
    Struct. Dyn. (IF 3.216) Pub Date : 2020-06-18
    Daniela Rupp; Leonie Flückiger; Marcus Adolph; Alessandro Colombo; Tais Gorkhover; Marion Harmand; Maria Krikunova; Jan Philippe Müller; Tim Oelze; Yevheniy Ovcharenko; Maria Richter; Mario Sauppe; Sebastian Schorb; Rolf Treusch; David Wolter; Christoph Bostedt; Thomas Möller

    We have recorded the diffraction patterns from individual xenon clusters irradiated with intense extreme ultraviolet pulses to investigate the influence of light-induced electronic changes on the scattering response. The clusters were irradiated with short wavelength pulses in the wavelength regime of different 4d inner-shell resonances of neutral and ionic xenon, resulting in distinctly different

    更新日期:2020-06-30
  • Structural dynamics of incommensurate charge-density waves tracked by ultrafast low-energy electron diffraction
    Struct. Dyn. (IF 3.216) Pub Date : 2020-06-22
    G. Storeck; J. G. Horstmann; T. Diekmann; S. Vogelgesang; G. von Witte; S. V. Yalunin; K. Rossnagel; C. Ropers

    We study the non-equilibrium structural dynamics of the incommensurate and nearly commensurate charge-density wave (CDW) phases in 1T- TaS 2. Employing ultrafast low-energy electron diffraction with 1 ps temporal resolution, we investigate the ultrafast quench and recovery of the CDW-coupled periodic lattice distortion (PLD). Sequential structural relaxation processes are observed by tracking the intensities

    更新日期:2020-06-30
  • Determination of the dehydration pathway in a flexible metal–organic framework by dynamicin situx-ray diffraction
    Struct. Dyn. (IF 3.216) Pub Date : 2020-06-23
    Ian M. Walton; Jordan M. Cox; Shea D. Myers; Cassidy A. Benson; Travis B. Mitchell; Gage S. Bateman; Eric D. Sylvester; Yu-Sheng Chen; Jason B. Benedict

    Understanding guest exchange processes in metal–organic frameworks is an important step toward the rational design of functional materials with tailor-made properties. The dehydration of the flexible metal-organic framework [Co(AIP)(bpy)0.5(H2O)]•2H2O was studied by novel in situ dynamic x-ray diffraction techniques. The complex mechanism of dehydration, along with the as-yet unreported metastable

    更新日期:2020-06-30
  • Imaging phonon dynamics with ultrafast electron microscopy: Kinematical and dynamical simulations.
    Struct. Dyn. (IF 3.216) Pub Date : 2020-04-17
    Daniel X Du,David J Flannigan

    Ultrafast x-ray and electron scattering techniques have proven to be useful for probing the transient elastic lattice deformations associated with photoexcited coherent acoustic phonons. Indeed, femtosecond electron imaging using an ultrafast electron microscope (UEM) has been used to directly image the influence of nanoscale structural and morphological discontinuities on the emergence, propagation

    更新日期:2020-04-17
  • Controlled beams of shock-frozen, isolated, biological and artificial nanoparticles.
    Struct. Dyn. (IF 3.216) Pub Date : 2020-04-17
    Amit K Samanta,Muhamed Amin,Armando D Estillore,Nils Roth,Lena Worbs,Daniel A Horke,Jochen Küpper

    X-ray free-electron lasers promise diffractive imaging of single molecules and nanoparticles with atomic spatial resolution. This relies on the averaging of millions of diffraction patterns of identical particles, which should ideally be isolated in the gas phase and preserved in their native structure. Here, we demonstrated that polystyrene nanospheres and Cydia pomonella granulovirus can be transferred

    更新日期:2020-04-17
  • A tool for visualizing protein motions in time-resolved crystallography
    Struct. Dyn. (IF 3.216) Pub Date : 2020-04-01
    Cecilia Wickstrand, Gergely Katona, Takanori Nakane, Przemyslaw Nogly, Joerg Standfuss, Eriko Nango, Richard Neutze

    Time-resolved serial femtosecond crystallography (TR-SFX) at an x-ray free electron laser enables protein structural changes to be imaged on time-scales from femtoseconds to seconds. It can, however, be difficult to grasp the nature and timescale of global protein motions when structural changes are not isolated near a single active site. New tools are, therefore, needed to represent the global nature

    更新日期:2020-04-01
  • Ultrafast electron imaging of surface charge carrier dynamics at low voltage
    Struct. Dyn. (IF 3.216) Pub Date : 2020-03-30
    Jianfeng Zhao, Osman M. Bakr, Omar F. Mohammed

    The performance of optoelectronic devices strongly depends on charge carrier dynamics on top of surfaces of the absorber layers. Unfortunately, this information cannot be selectively probed using conventional ultrafast laser spectroscopic methods, due to the large penetration depth (tens of nm to μm) of the photon pulses in the pump-probe configurations. Therefore, ultrafast time-resolved approaches

    更新日期:2020-03-30
  • Unconventional picosecond strain pulses resulting from the saturation of magnetic stress within a photoexcited rare earth layer
    Struct. Dyn. (IF 3.216) Pub Date : 2020-03-27
    A. von Reppert, M. Mattern, J.-E. Pudell, S. P. Zeuschner, K. Dumesnil, M. Bargheer

    Optical excitation of spin-ordered rare earth metals triggers a complex response of the crystal lattice since expansive stresses from electron and phonon excitations compete with a contractive stress induced by spin disorder. Using ultrafast x-ray diffraction experiments, we study the layer specific strain response of a dysprosium film within a metallic heterostructure upon femtosecond laser-excitation

    更新日期:2020-03-27
  • Single-particle imaging by x-ray free-electron lasers—How many snapshots are needed?
    Struct. Dyn. (IF 3.216) Pub Date : 2020-03-20
    I. Poudyal, M. Schmidt, P. Schwander

    X-ray free-electron lasers (XFELs) open the possibility of obtaining diffraction information from a single biological macromolecule. This is because XFELs can generate extremely intense x-ray pulses that are so short that diffraction data can be collected before the sample is destroyed. By collecting a sufficient number of single-particle diffraction patterns, the three-dimensional electron density

    更新日期:2020-03-20
  • Ultrafast dynamics of photo-excited 2-thiopyridone: Theoretical insights into triplet state population and proton transfer pathways
    Struct. Dyn. (IF 3.216) Pub Date : 2020-03-17
    Jesper Norell, Michael Odelius, Morgane Vacher

    Ultrafast non-adiabatic dynamics of the small heteroaromatic compound 2-thiopyridone has been studied with surface hopping simulations based on multi-configurational quantum chemistry. Initial excitation of the bright S 2 ( π , π * ) state is found to promptly relax to S 1 ( n ,   π *) through in-plane motion. The subsequent dynamics are oppositely driven by out-of-plane motion, which results in both

    更新日期:2020-03-17
  • Secondary structure effects on internal proton transfer in poly-peptides
    Struct. Dyn. (IF 3.216) Pub Date : 2020-03-17
    M. Bouakil, F. Chirot, M. Girod, P. Dugourd, L. MacAleese

    A pump–probe approach was designed to determine the internal proton transfer (PT) rate in a series of poly-peptide radical cations containing both histidine and tryptophan. The proton transfer is driven by the gas-phase basicity difference between residues. The fragmentation scheme indicates that the gas-phase basicity of histidine is lower than that of radical tryptophan so that histidine is always

    更新日期:2020-03-17
  • Nanoscale thermal transport across an GaAs/AlGaAs heterostructure interface
    Struct. Dyn. (IF 3.216) Pub Date : 2020-03-17
    Matthew Gorfien, Hailong Wang, Long Chen, Hamidreza Rahmani, Junxiao Yu, Pengfei Zhu, Jie Chen, Xuan Wang, Jianhua Zhao, Jianming Cao

    We studied the thermal transport across a GaAs/AlGaAs interface using time-resolved Reflection High Energy Electron Diffraction. The lattice temperature change of the GaAs nanofilm was directly monitored and numerically simulated using diffusive heat equations based on Fourier's Law. The extracted thermal boundary resistances (TBRs) were found to decrease with increasing lattice temperature imbalance

    更新日期:2020-03-17
  • Liquid-phase mega-electron-volt ultrafast electron diffraction
    Struct. Dyn. (IF 3.216) Pub Date : 2020-03-09
    J. P. F. Nunes, K. Ledbetter, M. Lin, M. Kozina, D. P. DePonte, E. Biasin, M. Centurion, C. J. Crissman, M. Dunning, S. Guillet, K. Jobe, Y. Liu, M. Mo, X. Shen, R. Sublett, S. Weathersby, C. Yoneda, T. J. A. Wolf, J. Yang, A. A. Cordones, X. J. Wang

    The conversion of light into usable chemical and mechanical energy is pivotal to several biological and chemical processes, many of which occur in solution. To understand the structure–function relationships mediating these processes, a technique with high spatial and temporal resolutions is required. Here, we report on the design and commissioning of a liquid-phase mega-electron-volt (MeV) ultrafast

    更新日期:2020-03-09
  • Discovering a rotational barrier within a charge-transfer state of a photoexcited chromophore in solution
    Struct. Dyn. (IF 3.216) Pub Date : 2020-03-04
    Taylor D. Krueger, Sean A. Boulanger, Liangdong Zhu, Longteng Tang, Chong Fang

    Methylation occurs in a myriad of systems with protective and regulatory functions. 8-methoxypyrene-1,3,6-trisulfonate (MPTS), a methoxy derivative of a photoacid, serves as a model system to study effects of methylation on the excited state potential energy landscape. A suite of spectroscopic techniques including transient absorption, wavelength-tunable femtosecond stimulated Raman spectroscopy (FSRS)

    更新日期:2020-03-04
  • JUNGFRAU detector for brighter x-ray sources: Solutions for IT and data science challenges in macromolecular crystallography.
    Struct. Dyn. (IF 3.216) Pub Date : 2020-02-26
    Filip Leonarski,Aldo Mozzanica,Martin Brückner,Carlos Lopez-Cuenca,Sophie Redford,Leonardo Sala,Andrej Babic,Heinrich Billich,Oliver Bunk,Bernd Schmitt,Meitian Wang

    In this paper, we present a data workflow developed to operate the adJUstiNg Gain detector FoR the Aramis User station (JUNGFRAU) adaptive gain charge integrating pixel-array detectors at macromolecular crystallography beamlines. We summarize current achievements for operating at 9 GB/s data-rate a JUNGFRAU with 4 Mpixel at 1.1 kHz frame-rate and preparations to operate at 46 GB/s data-rate a JUNGFRAU

    更新日期:2020-02-26
  • Conformational sampling and kinetics changes across a non-Arrhenius break point in the enzyme thermolysin.
    Struct. Dyn. (IF 3.216) Pub Date : 2020-02-14
    Ming Dong,Mackenzie L Lauro,Timothy J Koblish,Brian J Bahnson

    Numerous studies have suggested a significant role that protein dynamics play in optimizing enzyme catalysis, and changes in conformational sampling offer a window to explore this role. Thermolysin from Bacillus thermoproteolyticus rokko, which is a heat-stable zinc metalloproteinase, serves here as a model system to study changes of protein function and conformational sampling across a temperature

    更新日期:2020-02-14
  • MicroED methodology and development.
    Struct. Dyn. (IF 3.216) Pub Date : 2020-02-13
    Brent L Nannenga

    Microcrystal electron diffraction, or MicroED, is a method that is capable of determining structure from very small and thin 3D crystals using a transmission electron microscope. MicroED has been successfully used on microcrystalline samples, including proteins, peptides, and small organic molecules, in many cases to very high resolutions. In this work, the MicroED workflow will be briefly described

    更新日期:2020-02-13
  • Coherent narrowband light source for ultrafast photoelectron spectroscopy in the 17-31 eV photon energy range.
    Struct. Dyn. (IF 3.216) Pub Date : 2020-01-31
    Riccardo Cucini,Tommaso Pincelli,Giancarlo Panaccione,Damir Kopic,Fabio Frassetto,Paolo Miotti,Gian Marco Pierantozzi,Simone Peli,Andrea Fondacaro,Aleksander De Luisa,Alessandro De Vita,Pietro Carrara,Damjan Krizmancic,Daniel T Payne,Federico Salvador,Andrea Sterzi,Luca Poletto,Fulvio Parmigiani,Giorgio Rossi,Federico Cilento

    Here, we report on a novel narrowband High Harmonic Generation (HHG) light source designed for ultrafast photoelectron spectroscopy (PES) on solids. Notably, at 16.9 eV photon energy, the harmonics bandwidth equals 19 meV. This result has been obtained by seeding the HHG process with 230 fs pulses at 515 nm. The ultimate energy resolution achieved on a polycrystalline Au sample at 40 K is ∼22 meV at

    更新日期:2020-01-31
  • Evolving data standards for cryo-EM structures.
    Struct. Dyn. (IF 3.216) Pub Date : 2020-01-24
    Catherine L Lawson,Helen M Berman,Wah Chiu

    Electron cryo-microscopy (cryo-EM) is increasingly being used to determine 3D structures of a broad spectrum of biological specimens from molecules to cells. Anticipating this progress in the early 2000s, an international collaboration of scientists with expertise in both cryo-EM and structure data archiving was established (EMDataResource, previously known as EMDataBank). The major goals of the collaboration

    更新日期:2020-01-24
  • Real-time observation of jumping and spinning nanodroplets.
    Struct. Dyn. (IF 3.216) Pub Date : 2020-01-14
    Pavel K Olshin,Jonathan M Voss,Marcel Drabbels,Ulrich J Lorenz

    The manipulation of liquids at nanoscale dimensions is a central goal of the emergent nanofluidics field. Such endeavors extend to nanodroplets, which are ubiquitous objects involved in many technological applications. Here, we employ time-resolved electron microscopy to elucidate the formation of so-called jumping nanodroplets on a graphene surface. We flash-melt a thin gold nanostructure with a laser

    更新日期:2020-01-14
  • Best practices for high data-rate macromolecular crystallography (HDRMX).
    Struct. Dyn. (IF 3.216) Pub Date : 2020-01-09
    Herbert J Bernstein,Lawrence C Andrews,Jorge A Diaz,Jean Jakoncic,Thu Nguyen,Nicholas K Sauter,Alexei S Soares,Justin Y Wei,Maciej R Wlodek,Mario A Xerri

    In macromolecular crystallography, higher flux, smaller beams, and faster detectors open the door to experiments with very large numbers of very small samples that can reveal polymorphs and dynamics but require re-engineering of approaches to the clustering of images both at synchrotrons and XFELs (X-ray free electron lasers). The need for the management of orders of magnitude more images and limitations

    更新日期:2020-01-09
  • Time-resolved diffraction with an optimized short pulse laser plasma X-ray source.
    Struct. Dyn. (IF 3.216) Pub Date : 2020-01-02
    M Afshari,P Krumey,D Menn,M Nicoul,F Brinks,A Tarasevitch,K Sokolowski-Tinten

    We present a setup for time-resolved X-ray diffraction based on a short pulse, laser-driven plasma X-ray source. The employed modular design provides high flexibility to adapt the setup to the specific requirements (e.g., X-ray optics and sample environment) of particular applications. The configuration discussed here has been optimized toward high angular/momentum resolution and uses K α -radiation

    更新日期:2020-01-02
  • Toward time-resolved laser T-jump/X-ray probe spectroscopy in aqueous solutions.
    Struct. Dyn. (IF 3.216) Pub Date : 2019-12-11
    O Cannelli,C Bacellar,R A Ingle,R Bohinc,D Kinschel,B Bauer,D S Ferreira,D Grolimund,G F Mancini,M Chergui

    Most chemical and biochemical reactions in nature and in industrial processes are driven by thermal effects that bring the reactants above the energy barrier for reaction. In aqueous solutions, this process can also be triggered by the laser driven temperature jump (T-jump) method, in which the water vibrational (stretch, bend, or combination) modes are excited by a short laser pulse, leading to a

    更新日期:2019-12-11
  • Evaluation of serial crystallographic structure determination within megahertz pulse trains.
    Struct. Dyn. (IF 3.216) Pub Date : 2019-12-04
    Oleksandr Yefanov,Dominik Oberthür,Richard Bean,Max O Wiedorn,Juraj Knoska,Gisel Pena,Salah Awel,Lars Gumprecht,Martin Domaracky,Iosifina Sarrou,P Lourdu Xavier,Markus Metz,Saša Bajt,Valerio Mariani,Yaroslav Gevorkov,Thomas A White,Aleksandra Tolstikova,Pablo Villanueva-Perez,Carolin Seuring,Steve Aplin,Armando D Estillore,Jochen Küpper,Alexander Klyuev,Manuela Kuhn,Torsten Laurus,Heinz Graafsma,Diana

    The new European X-ray Free-Electron Laser (European XFEL) is the first X-ray free-electron laser capable of delivering intense X-ray pulses with a megahertz interpulse spacing in a wavelength range suitable for atomic resolution structure determination. An outstanding but crucial question is whether the use of a pulse repetition rate nearly four orders of magnitude higher than previously possible

    更新日期:2019-12-04
  • A shared vision for macromolecular crystallography over the next five years.
    Struct. Dyn. (IF 3.216) Pub Date : 2019-12-04
    Andreas Förster,Clemens Schulze-Briese

    Macromolecular crystallography (MX) is the dominant means of determining the three-dimensional structures of biological macromolecules, but the method has reached a critical juncture. New diffraction-limited storage rings and upgrades to the existing sources will provide beamlines with higher flux and brilliance, and even the largest detectors can collect at rates of several hundred hertz. Electron

    更新日期:2019-12-04
  • The Integrated Resource for Reproducibility in Macromolecular Crystallography: Experiences of the first four years.
    Struct. Dyn. (IF 3.216) Pub Date : 2019-11-27
    Marek Grabowski,Marcin Cymborowski,Przemyslaw J Porebski,Tomasz Osinski,Ivan G Shabalin,David R Cooper,Wladek Minor

    It has been increasingly recognized that preservation and public accessibility of primary experimental data are cornerstones necessary for the reproducibility of empirical sciences. In the field of molecular crystallography, many journals now recommend that authors of manuscripts presenting a new crystal structure should deposit their primary experimental data (X-ray diffraction images) to one of the

    更新日期:2019-11-01
  • Fragment screening for a protein-protein interaction inhibitor to WDR5.
    Struct. Dyn. (IF 3.216) Pub Date : 2019-11-27
    Matthew L Dennis,Benjamin J Morrow,Olan Dolezal,Anthony N Cuzzupe,Alexandra E Stupple,Janet Newman,John Bentley,Meghan Hattarki,Stewart D Nuttall,Richard C Foitzik,Ian P Street,Paul A Stupple,Brendon J Monahan,Thomas S Peat

    The WD40-repeat protein WDR5 scaffolds various epigenetic writers and is a critical component of the mammalian SET/MLL histone methyltransferase complex. Dysregulation of the MLL1 catalytic function is associated with mixed-lineage leukemia, and antagonism of the WDR5-MLL1 interaction by small molecules has been proposed as a therapeutic strategy for MLL-rearranged cancers. Small molecule binders of

    更新日期:2019-11-01
  • Decelerated lattice excitation and absence of bulk phonon modes at surfaces: Ultra-fast electron diffraction from Bi(111) surface upon fs-laser excitation.
    Struct. Dyn. (IF 3.216) Pub Date : 2019-11-09
    V Tinnemann,C Streubühr,B Hafke,T Witte,A Kalus,A Hanisch-Blicharski,M Ligges,P Zhou,D von der Linde,U Bovensiepen,M Horn-von Hoegen

    Ultrafast reflection high-energy electron diffraction is employed to follow the lattice excitation of a Bi(111) surface upon irradiation with a femtosecond laser pulse. The thermal motion of the atoms is analyzed through the Debye-Waller effect. While the Bi bulk is heated on time scales of 2 to 4 ps, we observe that the excitation of vibrational motion of the surface atoms occurs much slower with

    更新日期:2019-11-01
  • Time resolved transient circular dichroism spectroscopy using synchrotron natural polarization.
    Struct. Dyn. (IF 3.216) Pub Date : 2019-11-09
    François Auvray,David Dennetiere,Alexandre Giuliani,Frédéric Jamme,Frank Wien,Bastien Nay,Séverine Zirah,François Polack,Claude Menneglier,Bruno Lagarde,Jonathan D Hirst,Matthieu Réfrégiers

    Ultraviolet (UV) synchrotron radiation circular dichroism (SRCD) spectroscopy has made an important contribution to the determination and understanding of the structure of bio-molecules. In this paper, we report an innovative approach that we term time-resolved SRCD (tr-SRCD), which overcomes the limitations of current broadband UV SRCD setups. This technique allows accessing ultrafast time scales

    更新日期:2019-11-01
  • FACT and FAIR with Big Data allows objectivity in science: The view of crystallography.
    Struct. Dyn. (IF 3.216) Pub Date : 2019-11-02
    John R Helliwell

    A publication is an important narrative of the work done and interpretations made by researchers securing a scientific discovery. As The Royal Society neatly states though, "Nullius in verba" ("Take nobody's word for it"), whereby the role of the underpinning data is paramount. Therefore, the objectivity that preserving that data within the article provides is due to readers being able to check the

    更新日期:2019-11-01
  • Effect of a bound anion on the structure and dynamics of halorhodopsin from Natronomonas pharaonis.
    Struct. Dyn. (IF 3.216) Pub Date : 2019-11-02
    Misao Mizuno,Yumi Shimoo,Hideki Kandori,Yasuhisa Mizutani

    Active ion transport across membranes is vital to maintaining the electrochemical gradients of ions in cells and is mediated by transmembrane proteins. Halorhodopsin (HR) functions as a light-driven inward pump for chloride ions. The protein contains all-trans-retinal bound to a specific lysine residue through a protonated Schiff base. Interaction between the bound chloride ion and the protonated Schiff

    更新日期:2019-11-01
  • Femtosecond gas-phase mega-electron-volt ultrafast electron diffraction.
    Struct. Dyn. (IF 3.216) Pub Date : 2019-10-28
    X Shen,J P F Nunes,J Yang,R K Jobe,R K Li,Ming-Fu Lin,B Moore,M Niebuhr,S P Weathersby,T J A Wolf,C Yoneda,Markus Guehr,Martin Centurion,X J Wang

    The development of ultrafast gas electron diffraction with nonrelativistic electrons has enabled the determination of molecular structures with atomic spatial resolution. It has, however, been challenging to break the picosecond temporal resolution barrier and achieve the goal that has long been envisioned-making space- and-time resolved molecular movies of chemical reaction in the gas-phase. Recently

    更新日期:2019-11-01
  • Make the right measurement: Discovery of an allosteric inhibition site for p300-HAT.
    Struct. Dyn. (IF 3.216) Pub Date : 2019-10-28
    Anna S Gardberg,Annissa J Huhn,Richard Cummings,Archana Bommi-Reddy,Florence Poy,Jeremy Setser,Valerie Vivat,Francois Brucelle,Jonathan Wilson

    Histone acetyltransferases (HATs) and histone deacetylases (HDACs) catalyze the dynamic and reversible acetylation of proteins, an epigenetic regulatory mechanism associated with multiple cancers. Indeed, HDAC inhibitors are already approved in the clinic. The HAT paralogs p300 and CREB-binding protein (CBP) have been implicated in human pathological conditions including several hematological malignancies

    更新日期:2019-11-01
  • Probing ultrafast C-Br bond fission in the UV photochemistry of bromoform with core-to-valence transient absorption spectroscopy.
    Struct. Dyn. (IF 3.216) Pub Date : 2019-10-28
    Benjamin W Toulson,Mario Borgwardt,Han Wang,Florian Lackner,Adam S Chatterley,C D Pemmaraju,Daniel M Neumark,Stephen R Leone,David Prendergast,Oliver Gessner

    UV pump-extreme UV (XUV) probe femtosecond transient absorption spectroscopy is used to study the 268 nm induced photodissociation dynamics of bromoform (CHBr3). Core-to-valence transitions at the Br(3d) absorption edge (∼70 eV) provide an atomic scale perspective of the reaction, sensitive to changes in the local valence electronic structure, with ultrafast time resolution. The XUV spectra track how

    更新日期:2019-11-01
  • The role of transition dipole phase in atomic attosecond transient absorption from the multi-level model.
    Struct. Dyn. (IF 3.216) Pub Date : 2019-10-28
    Guanglu Yuan,Shicheng Jiang,Ziwen Wang,Weijie Hua,Chao Yu,Cheng Jin,Ruifeng Lu

    Based on a multilevel model considering enough bound electronic states of atoms, we theoretically study the role of the transition dipole phase (TDP) in the attosecond transient absorption (ATA) spectrum of helium in intense laser fields. By solving the stationary Schrödinger equation with B-spline basis sets, we first calculate the transition dipole moments with well-defined phases between the bound

    更新日期:2019-11-01
  • Photoemission sources and beam blankers for ultrafast electron microscopy.
    Struct. Dyn. (IF 3.216) Pub Date : 2019-10-09
    Lixin Zhang,Jacob P Hoogenboom,Ben Cook,Pieter Kruit

    Observing atomic motions as they occur is the dream goal of ultrafast electron microscopy (UEM). Great progress has been made so far thanks to the efforts of many scientists in developing the photoemission sources and beam blankers needed to create short pulses of electrons for the UEM experiments. While details on these setups have typically been reported, a systematic overview of methods used to

    更新日期:2019-11-01
  • High-resolution crystal structures of a myxobacterial phytochrome at cryo and room temperatures.
    Struct. Dyn. (IF 3.216) Pub Date : 2019-09-29
    Juan C Sanchez,Melissa Carrillo,Suraj Pandey,Moraima Noda,Luis Aldama,Denisse Feliz,Elin Claesson,Weixiao Yuan Wahlgren,Gregory Tracy,Phu Duong,Angela C Nugent,Andrew Field,Vukica Šrajer,Christopher Kupitz,So Iwata,Eriko Nango,Rie Tanaka,Tomoyuki Tanaka,Luo Fangjia,Kensuke Tono,Shigeki Owada,Sebastian Westenhoff,Marius Schmidt,Emina A Stojković

    Phytochromes (PHYs) are photoreceptor proteins first discovered in plants, where they control a variety of photomorphogenesis events. PHYs as photochromic proteins can reversibly switch between two distinct states: a red light (Pr) and a far-red light (Pfr) absorbing form. The discovery of Bacteriophytochromes (BphPs) in nonphotosynthetic bacteria has opened new frontiers in our understanding of the

    更新日期:2019-11-01
  • Electrostatic subframing and compressive-sensing video in transmission electron microscopy.
    Struct. Dyn. (IF 3.216) Pub Date : 2019-09-29
    B W Reed,A A Moghadam,R S Bloom,S T Park,A M Monterrosa,P M Price,C M Barr,S A Briggs,K Hattar,J T McKeown,D J Masiel

    We present kilohertz-scale video capture rates in a transmission electron microscope, using a camera normally limited to hertz-scale acquisition. An electrostatic deflector rasters a discrete array of images over a large camera, decoupling the acquisition time per subframe from the camera readout time. Total-variation regularization allows features in overlapping subframes to be correctly placed in

    更新日期:2019-11-01
  • Advances and opportunities in ultrafast X-ray crystallography and ultrafast structural optical crystallography of nuclear and electronic protein dynamics.
    Struct. Dyn. (IF 3.216) Pub Date : 2019-09-29
    Jasper J van Thor

    Both nuclear and electronic dynamics contribute to protein function and need multiple and complementary techniques to reveal their ultrafast structural dynamics response. Real-space information obtained from the measurement of electron density dynamics by X-ray crystallography provides aspects of both, while the molecular physics of coherence parameters and frequency-frequency correlation needs spectroscopy

    更新日期:2019-11-01
  • A versatile experimental system for tracking ultrafast chemical reactions with X-ray free-electron lasers.
    Struct. Dyn. (IF 3.216) Pub Date : 2019-09-19
    Tetsuo Katayama,Shunsuke Nozawa,Yasufumi Umena,SungHee Lee,Tadashi Togashi,Shigeki Owada,Makina Yabashi

    An experimental system, SPINETT (SACLA Pump-probe INstrumEnt for Tracking Transient dynamics), dedicated for ultrafast pump-probe experiments using X-ray free-electron lasers has been developed. SPINETT consists of a chamber operated under 1 atm helium pressure, two Von Hamos spectrometers, and a large two-dimensional detector having a short work distance. This platform covers complementary X-ray techniques;

    更新日期:2019-11-01
  • Full-dimensional theoretical description of vibrationally resolved valence-shell photoionization of H2O.
    Struct. Dyn. (IF 3.216) Pub Date : 2019-09-19
    Selma Engin,Jesús González-Vázquez,Gianluigi Grimaldi Maliyar,Aleksandar R Milosavljević,Taishi Ono,Saikat Nandi,Denys Iablonskyi,Kuno Kooser,John D Bozek,Piero Decleva,Edwin Kukk,Kiyoshi Ueda,Fernando Martín

    We have performed a full-dimensional theoretical study of vibrationally resolved photoelectron emission from the valence shell of the water molecule by using an extension of the static-exchange density functional theory that accounts for ionization as well as for vibrational motion in the symmetric stretching, antisymmetric stretching, and bending modes. At variance with previous studies performed

    更新日期:2019-11-01
  • New insights and innovation from a million crystal structures in the Cambridge Structural Database.
    Struct. Dyn. (IF 3.216) Pub Date : 2019-09-07
    Jason C Cole,Seth Wiggin,Francesca Stanzione

    The Cambridge Structural Database (CSD) is the world's largest and most comprehensive collection of organic, organometallic, and metal-organic crystal structure information. Analyses using the data have wide impact across the chemical sciences in allowing understanding of structural preferences. In this short review, we illustrate the more common methods by which CSD data influence molecular design

    更新日期:2019-11-01
  • Structure determination of the tetracene dimer in helium nanodroplets using femtosecond strong-field ionization.
    Struct. Dyn. (IF 3.216) Pub Date : 2019-08-30
    Constant Schouder,Adam S Chatterley,Florent Calvo,Lars Christiansen,Henrik Stapelfeldt

    Dimers of tetracene molecules are formed inside helium nanodroplets and identified through covariance analysis of the emission directions of kinetic tetracene cations stemming from femtosecond laser-induced Coulomb explosion. Next, the dimers are aligned in either one or three dimensions under field-free conditions by a nonresonant, moderately intense laser pulse. The experimental angular covariance

    更新日期:2019-11-01
  • Is radiation damage the limiting factor in high-resolution single particle imaging with X-ray free-electron lasers?
    Struct. Dyn. (IF 3.216) Pub Date : 2019-08-30
    C Östlin,N Timneanu,C Caleman,A V Martin

    The prospect of single particle imaging with atomic resolution is one of the scientific drivers for the development of X-ray free-electron lasers. The assumption since the beginning has been that damage to the sample caused by intense X-ray pulses is one of the limiting factors for achieving subnanometer X-ray imaging of single particles and that X-ray pulses need to be as short as possible. Based

    更新日期:2019-11-01
  • Condensation of ground state from a supercooled phase in the Si(111)-(4 × 1) → (8 × 2)-indium atomic wire system.
    Struct. Dyn. (IF 3.216) Pub Date : 2019-08-14
    B Hafke,T Witte,D Janoschka,P Dreher,F-J Meyer Zu Heringdorf,M Horn-von Hoegen

    Strong optical irradiation of indium atomic wires on a Si(111) surface causes the nonthermal structural transition from the (8 × 2) reconstructed ground state to an excited (4 × 1) state. The immediate recovery of the system to the ground state is hindered by an energy barrier for the collective motion of the indium atoms along the reaction coordinate from the (4 × 1) to the (8 × 2) state. This metastable

    更新日期:2019-11-01
  • Hole dynamics in a photovoltaic donor-acceptor couple revealed by simulated time-resolved X-ray absorption spectroscopy.
    Struct. Dyn. (IF 3.216) Pub Date : 2019-08-03
    Khadijeh Khalili,Ludger Inhester,Caroline Arnold,Ralph Welsch,Jens Wenzel Andreasen,Robin Santra

    Theoretical and experimental methodologies that can characterize electronic and nuclear dynamics, and the coupling between the two, are needed to understand photoinduced charge transfer in molecular building blocks used in organic photovoltaics. Ongoing developments in ultrafast pump-probe techniques such as time-resolved X-ray absorption spectroscopy, using an X-ray free electron laser in combination

    更新日期:2019-11-01
  • Exploring the multiparameter nature of EUV-visible wave mixing at the FERMI FEL.
    Struct. Dyn. (IF 3.216) Pub Date : 2019-08-03
    L Foglia,F Capotondi,H Höppner,A Gessini,L Giannessi,G Kurdi,I Lopez Quintas,C Masciovecchio,M Kiskinova,R Mincigrucci,D Naumenko,I P Nikolov,E Pedersoli,G M Rossi,A Simoncig,F Bencivenga

    The rapid development of extreme ultraviolet (EUV) and x-ray ultrafast coherent light sources such as free electron lasers (FELs) has triggered the extension of wave-mixing techniques to short wavelengths. This class of experiments, based on the interaction of matter with multiple light pulses through the Nth order susceptibility, holds the promise of combining intrinsic ultrafast time resolution and

    更新日期:2019-11-01
  • High-harmonic spectroscopy of transient two-center interference calculated with time-dependent density-functional theory.
    Struct. Dyn. (IF 3.216) Pub Date : 2019-07-26
    François Mauger,Paul M Abanador,Timothy D Scarborough,Timothy T Gorman,Pierre Agostini,Louis F DiMauro,Kenneth Lopata,Kenneth J Schafer,Mette B Gaarde

    We demonstrate high-harmonic spectroscopy in many-electron molecules using time-dependent density-functional theory. We show that a weak attosecond-pulse-train ionization seed that is properly synchronized with the strong driving mid-infrared laser field can produce experimentally relevant high-harmonic generation (HHG) signals, from which we extract both the spectral amplitude and the target-specific

    更新日期:2019-11-01
  • Arguments for an additional long-lived intermediate in the photocycle of the full-length aureochrome 1c receptor: A time-resolved small-angle X-ray scattering study.
    Struct. Dyn. (IF 3.216) Pub Date : 2019-07-03
    Saskia Bannister,Elena Böhm,Thomas Zinn,Thomas Hellweg,Tilman Kottke

    Aureochromes (AUREO) act as blue-light photoreceptors in algae. They consist of a light-, oxygen-, voltage-sensitive (LOV) domain and a DNA-binding basic region/leucine zipper. Illumination of the flavin cofactor in LOV leads to the formation of an adduct, followed by global structural changes. Here, we first applied UV/vis spectroscopy to characterize the photocycle of full-length aureochrome 1c (PtAUREO1c)

    更新日期:2019-11-01
  • Revealing the competing contributions of charge carriers, excitons, and defects to the non-equilibrium optical properties of ZnO.
    Struct. Dyn. (IF 3.216) Pub Date : 2019-05-28
    Laura Foglia,Sesha Vempati,Boubacar Tanda Bonkano,Lukas Gierster,Martin Wolf,Sergey Sadofev,Julia Stähler

    Due to its wide band gap and high carrier mobility, ZnO is, among other transparent conductive oxides, an attractive material for light-harvesting and optoelectronic applications. Its functional efficiency, however, is strongly affected by defect-related in-gap states that open up extrinsic decay channels and modify relaxation timescales. As a consequence, almost every sample behaves differently, leading

    更新日期:2019-11-01
  • Electronic decay of core-excited HCl molecules probed by THz streaking.
    Struct. Dyn. (IF 3.216) Pub Date : 2019-05-28
    K Wenig,M Wieland,A Baumann,S Walther,A Dimitriou,M J Prandolini,O Schepp,I Bermúdez Macias,M Sumfleth,N Stojanovic,S Düsterer,J Rönsch-Schulenburg,E Zapolnova,R Pan,M Drescher,U Frühling

    The ultrafast electronic decay of HCl molecules in the time domain after resonant core excitation was measured. Here, a Cl-2p core electron was promoted to the antibonding σ* orbital initiating molecular dissociation, and simultaneously, the electronic excitation relaxes via an Auger decay. For HCl, both processes compete on similar ultrashort femtosecond time scales. In order to measure the lifetime

    更新日期:2019-11-01
  • Ultrafast electron diffraction from a Bi(111) surface: Impulsive lattice excitation and Debye-Waller analysis at large momentum transfer.
    Struct. Dyn. (IF 3.216) Pub Date : 2019-05-22
    V Tinnemann,C Streubühr,B Hafke,A Kalus,A Hanisch-Blicharski,M Ligges,P Zhou,D von der Linde,U Bovensiepen,M Horn-von Hoegen

    The lattice response of a Bi(111) surface upon impulsive femtosecond laser excitation is studied with time-resolved reflection high-energy electron diffraction. We employ a Debye-Waller analysis at large momentum transfer of 9.3 Å-1 ≤ Δ k ≤ 21.8 Å-1 in order to study the lattice excitation dynamics of the Bi surface under conditions of weak optical excitation up to 2 mJ/cm2 incident pump fluence. The

    更新日期:2019-11-01
  • Structural and mutational analyses of psychrophilic and mesophilic adenylate kinases highlight the role of hydrophobic interactions in protein thermal stability.
    Struct. Dyn. (IF 3.216) Pub Date : 2019-05-22
    Sojin Moon,Junhyung Kim,Jasung Koo,Euiyoung Bae

    Protein thermal stability is an important field since thermally stable proteins are desirable in many academic and industrial settings. Information on protein thermal stabilization can be obtained by comparing homologous proteins from organisms living at distinct temperatures. Here, we report structural and mutational analyses of adenylate kinases (AKs) from psychrophilic Bacillus globisporus (AKp)

    更新日期:2019-11-01
  • Pulse length, energy spread, and temporal evolution of electron pulses generated with an ultrafast beam blanker.
    Struct. Dyn. (IF 3.216) Pub Date : 2019-05-09
    I G C Weppelman,R J Moerland,L Zhang,E Kieft,P Kruit,J P Hoogenboom

    Crucial for the field of ultrafast electron microscopy is the creation of sub-picosecond, high brightness electron pulses. The use of a blanker to chop the beam that originates from a high brightness Schottky source may provide an attractive alternative to direct pulsed laser illumination of the source. We have recently presented the concept of a laser-triggered ultrafast beam blanker and argued that

    更新日期:2019-11-01
  • Structural and dynamical description of the enzymatic reaction of a phosphohexomutase.
    Struct. Dyn. (IF 3.216) Pub Date : 2019-05-02
    Kyle M Stiers,Abigail C Graham,Jian-She Zhu,David L Jakeman,Jay C Nix,Lesa J Beamer

    Enzymes are known to adopt various conformations at different points along their catalytic cycles. Here, we present a comprehensive analysis of 15 isomorphous, high resolution crystal structures of the enzyme phosphoglucomutase from the bacterium Xanthomonas citri. The protein was captured in distinct states critical to function, including enzyme-substrate, enzyme-product, and enzyme-intermediate complexes

    更新日期:2019-11-01
  • Inception of electronic damage of matter by photon-driven post-ionization mechanisms.
    Struct. Dyn. (IF 3.216) Pub Date : 2019-05-02
    W Błachucki,Y Kayser,J Czapla-Masztafiak,M Guo,P Juranić,M Kavčič,E Källman,G Knopp,M Lundberg,C Milne,J Rehanek,J Sá,J Szlachetko

    "Probe-before-destroy" methodology permitted diffraction and imaging measurements of intact specimens using ultrabright but highly destructive X-ray free-electron laser (XFEL) pulses. The methodology takes advantage of XFEL pulses ultrashort duration to outrun the destructive nature of the X-rays. Atomic movement, generally on the order of >50 fs, regulates the maximum pulse duration for intact specimen

    更新日期:2019-11-01
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