Pub Date : 2023-11-03eCollection Date: 2023-11-01DOI: 10.1063/4.0000204
Christopher J Milne, Natalia Nagornova, Thomas Pope, Hui-Yuan Chen, Thomas Rossi, Jakub Szlachetko, Wojciech Gawelda, Alexander Britz, Tim B van Driel, Leonardo Sala, Simon Ebner, Tetsuo Katayama, Stephen H Southworth, Gilles Doumy, Anne Marie March, C Stefan Lehmann, Melanie Mucke, Denys Iablonskyi, Yoshiaki Kumagai, Gregor Knopp, Koji Motomura, Tadashi Togashi, Shigeki Owada, Makina Yabashi, Martin M Nielsen, Marek Pajek, Kiyoshi Ueda, Rafael Abela, Thomas J Penfold, Majed Chergui
The evolution of charge carriers in photoexcited room temperature ZnO nanoparticles in solution is investigated using ultrafast ultraviolet photoluminescence spectroscopy, ultrafast Zn K-edge absorption spectroscopy, and ab initio molecular dynamics (MD) simulations. The photoluminescence is excited at 4.66 eV, well above the band edge, and shows that electron cooling in the conduction band and exciton formation occur in <500 fs, in excellent agreement with theoretical predictions. The x-ray absorption measurements, obtained upon excitation close to the band edge at 3.49 eV, are sensitive to the migration and trapping of holes. They reveal that the 2 ps transient largely reproduces the previously reported transient obtained at 100 ps time delay in synchrotron studies. In addition, the x-ray absorption signal is found to rise in ∼1.4 ps, which we attribute to the diffusion of holes through the lattice prior to their trapping at singly charged oxygen vacancies. Indeed, the MD simulations show that impulsive trapping of holes induces an ultrafast expansion of the cage of Zn atoms in <200 fs, followed by an oscillatory response at a frequency of ∼100 cm-1, which corresponds to a phonon mode of the system involving the Zn sub-lattice.
{"title":"Disentangling the evolution of electrons and holes in photoexcited ZnO nanoparticles.","authors":"Christopher J Milne, Natalia Nagornova, Thomas Pope, Hui-Yuan Chen, Thomas Rossi, Jakub Szlachetko, Wojciech Gawelda, Alexander Britz, Tim B van Driel, Leonardo Sala, Simon Ebner, Tetsuo Katayama, Stephen H Southworth, Gilles Doumy, Anne Marie March, C Stefan Lehmann, Melanie Mucke, Denys Iablonskyi, Yoshiaki Kumagai, Gregor Knopp, Koji Motomura, Tadashi Togashi, Shigeki Owada, Makina Yabashi, Martin M Nielsen, Marek Pajek, Kiyoshi Ueda, Rafael Abela, Thomas J Penfold, Majed Chergui","doi":"10.1063/4.0000204","DOIUrl":"10.1063/4.0000204","url":null,"abstract":"<p><p>The evolution of charge carriers in photoexcited room temperature ZnO nanoparticles in solution is investigated using ultrafast ultraviolet photoluminescence spectroscopy, ultrafast Zn K-edge absorption spectroscopy, and <i>ab initio</i> molecular dynamics (MD) simulations. The photoluminescence is excited at 4.66 eV, well above the band edge, and shows that electron cooling in the conduction band and exciton formation occur in <500 fs, in excellent agreement with theoretical predictions. The x-ray absorption measurements, obtained upon excitation close to the band edge at 3.49 eV, are sensitive to the migration and trapping of holes. They reveal that the 2 ps transient largely reproduces the previously reported transient obtained at 100 ps time delay in synchrotron studies. In addition, the x-ray absorption signal is found to rise in ∼1.4 ps, which we attribute to the diffusion of holes through the lattice prior to their trapping at singly charged oxygen vacancies. Indeed, the MD simulations show that impulsive trapping of holes induces an ultrafast expansion of the cage of Zn atoms in <200 fs, followed by an oscillatory response at a frequency of ∼100 cm<sup>-1</sup>, which corresponds to a phonon mode of the system involving the Zn sub-lattice.</p>","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":"10 6","pages":"064501"},"PeriodicalIF":2.3,"publicationDate":"2023-11-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10628992/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71522980","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-10-27eCollection Date: 2023-09-01DOI: 10.1063/4.0000193
Philip Heimann, Nicholas J Hartley, Ichiro Inoue, Victor Tkachenko, Andre Antoine, Fabien Dorchies, Roger Falcone, Jérôme Gaudin, Hauke Höppner, Yuichi Inubushi, Konrad J Kapcia, Hae Ja Lee, Vladimir Lipp, Paloma Martinez, Nikita Medvedev, Franz Tavella, Sven Toleikis, Makina Yabashi, Toshinori Yabuuchi, Jumpei Yamada, Beata Ziaja
Intense x-ray pulses can cause the non-thermal structural transformation of diamond. At the SACLA XFEL facility, pump x-ray pulses triggered this phase transition, and probe x-ray pulses produced diffraction patterns. Time delays were observed from 0 to 250 fs, and the x-ray dose varied from 0.9 to 8.0 eV/atom. The intensity of the (111), (220), and (311) diffraction peaks decreased with time, indicating a disordering of the crystal lattice. From a Debye-Waller analysis, the rms atomic displacements perpendicular to the (111) planes were observed to be significantly larger than those perpendicular to the (220) or (311) planes. At a long time delay of 33 ms, graphite (002) diffraction indicates that graphitization did occur above a threshold dose of 1.2 eV/atom. These experimental results are in qualitative agreement with XTANT+ simulations using a hybrid model based on density-functional tight-binding molecular dynamics.
{"title":"Non-thermal structural transformation of diamond driven by x-rays.","authors":"Philip Heimann, Nicholas J Hartley, Ichiro Inoue, Victor Tkachenko, Andre Antoine, Fabien Dorchies, Roger Falcone, Jérôme Gaudin, Hauke Höppner, Yuichi Inubushi, Konrad J Kapcia, Hae Ja Lee, Vladimir Lipp, Paloma Martinez, Nikita Medvedev, Franz Tavella, Sven Toleikis, Makina Yabashi, Toshinori Yabuuchi, Jumpei Yamada, Beata Ziaja","doi":"10.1063/4.0000193","DOIUrl":"https://doi.org/10.1063/4.0000193","url":null,"abstract":"<p><p>Intense x-ray pulses can cause the non-thermal structural transformation of diamond. At the SACLA XFEL facility, pump x-ray pulses triggered this phase transition, and probe x-ray pulses produced diffraction patterns. Time delays were observed from 0 to 250 fs, and the x-ray dose varied from 0.9 to 8.0 eV/atom. The intensity of the (111), (220), and (311) diffraction peaks decreased with time, indicating a disordering of the crystal lattice. From a Debye-Waller analysis, the rms atomic displacements perpendicular to the (111) planes were observed to be significantly larger than those perpendicular to the (220) or (311) planes. At a long time delay of 33 ms, graphite (002) diffraction indicates that graphitization did occur above a threshold dose of 1.2 eV/atom. These experimental results are in qualitative agreement with XTANT+ simulations using a hybrid model based on density-functional tight-binding molecular dynamics.</p>","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":"10 5","pages":"054502"},"PeriodicalIF":2.8,"publicationDate":"2023-10-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10613085/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71414817","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-10-27eCollection Date: 2023-09-01DOI: 10.1063/4.0000207
Marco Reinhard, Dean Skoien, Jacob A Spies, Angel T Garcia-Esparza, Benjamin D Matson, Jeff Corbett, Kai Tian, James Safranek, Eduardo Granados, Matthew Strader, Kelly J Gaffney, Roberto Alonso-Mori, Thomas Kroll, Dimosthenis Sokaras
We present a dedicated end-station for solution phase high repetition rate (MHz) picosecond hard x-ray spectroscopy at beamline 15-2 of the Stanford Synchrotron Radiation Lightsource. A high-power ultrafast ytterbium-doped fiber laser is used to photoexcite the samples at a repetition rate of 640 kHz, while the data acquisition operates at the 1.28 MHz repetition rate of the storage ring recording data in an alternating on-off mode. The time-resolved x-ray measurements are enabled via gating the x-ray detectors with the 20 mA/70 ps camshaft bunch of SPEAR3, a mode available during the routine operations of the Stanford Synchrotron Radiation Lightsource. As a benchmark study, aiming to demonstrate the advantageous capabilities of this end-station, we have conducted picosecond Fe K-edge x-ray absorption spectroscopy on aqueous [FeII(phen)3]2+, a prototypical spin crossover complex that undergoes light-induced excited spin state trapping forming an electronic excited state with a 0.6-0.7 ns lifetime. In addition, we report transient Fe Kβ main line and valence-to-core x-ray emission spectra, showing a unique detection sensitivity and an excellent agreement with model spectra and density functional theory calculations, respectively. Notably, the achieved signal-to-noise ratio, the overall performance, and the routine availability of the developed end-station have enabled a systematic time-resolved science program using the monochromatic beam at the Stanford Synchrotron Radiation Lightsource.
{"title":"Solution phase high repetition rate laser pump x-ray probe picosecond hard x-ray spectroscopy at the Stanford Synchrotron Radiation Lightsource.","authors":"Marco Reinhard, Dean Skoien, Jacob A Spies, Angel T Garcia-Esparza, Benjamin D Matson, Jeff Corbett, Kai Tian, James Safranek, Eduardo Granados, Matthew Strader, Kelly J Gaffney, Roberto Alonso-Mori, Thomas Kroll, Dimosthenis Sokaras","doi":"10.1063/4.0000207","DOIUrl":"10.1063/4.0000207","url":null,"abstract":"<p><p>We present a dedicated end-station for solution phase high repetition rate (MHz) picosecond hard x-ray spectroscopy at beamline 15-2 of the Stanford Synchrotron Radiation Lightsource. A high-power ultrafast ytterbium-doped fiber laser is used to photoexcite the samples at a repetition rate of 640 kHz, while the data acquisition operates at the 1.28 MHz repetition rate of the storage ring recording data in an alternating on-off mode. The time-resolved x-ray measurements are enabled via gating the x-ray detectors with the 20 mA/70 ps camshaft bunch of SPEAR3, a mode available during the routine operations of the Stanford Synchrotron Radiation Lightsource. As a benchmark study, aiming to demonstrate the advantageous capabilities of this end-station, we have conducted picosecond Fe K-edge x-ray absorption spectroscopy on aqueous [Fe<sup>II</sup>(phen)<sub>3</sub>]<sup>2+</sup>, a prototypical spin crossover complex that undergoes light-induced excited spin state trapping forming an electronic excited state with a 0.6-0.7 ns lifetime. In addition, we report transient Fe Kβ main line and valence-to-core x-ray emission spectra, showing a unique detection sensitivity and an excellent agreement with model spectra and density functional theory calculations, respectively. Notably, the achieved signal-to-noise ratio, the overall performance, and the routine availability of the developed end-station have enabled a systematic time-resolved science program using the monochromatic beam at the Stanford Synchrotron Radiation Lightsource.</p>","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":"10 5","pages":"054304"},"PeriodicalIF":2.8,"publicationDate":"2023-10-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10613086/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71414818","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
N. Bach, A. Feist, M. Möller, C. Ropers, S. Schäfer
Optically excited nanostructures provide a versatile platform for the generation of confined nanophononic fields with potential (non-)linear interactions between different degrees of freedom. Control of resonance frequencies and the selective excitation of acoustic modes still remains challenging due to the interplay of nanoscale geometries and interfacial coupling mechanisms. Here, we demonstrate that a semiconductor membrane patterned with a platinum stripe acts as a tailored source for high-frequency strain waves generating a multi-modal distortion wave propagating through the membrane. To locally monitor the ultrafast structural dynamics at a specific distance from the deposited metal stripe, we employ ultrafast convergent beam electron diffraction in a laser-pump/electron-probe scheme. Experimentally observed acoustic deformations are reproduced by numerical simulations in a continuous medium model, revealing a spatiotemporal evolution of the lattice dynamics dominated by local rotations with minor strain and shear contributions.
{"title":"Tailored nanophononic wavefield in a patterned bilayer system probed by ultrafast convergent beam electron diffraction","authors":"N. Bach, A. Feist, M. Möller, C. Ropers, S. Schäfer","doi":"10.1063/4.0000144","DOIUrl":"https://doi.org/10.1063/4.0000144","url":null,"abstract":"Optically excited nanostructures provide a versatile platform for the generation of confined nanophononic fields with potential (non-)linear interactions between different degrees of freedom. Control of resonance frequencies and the selective excitation of acoustic modes still remains challenging due to the interplay of nanoscale geometries and interfacial coupling mechanisms. Here, we demonstrate that a semiconductor membrane patterned with a platinum stripe acts as a tailored source for high-frequency strain waves generating a multi-modal distortion wave propagating through the membrane. To locally monitor the ultrafast structural dynamics at a specific distance from the deposited metal stripe, we employ ultrafast convergent beam electron diffraction in a laser-pump/electron-probe scheme. Experimentally observed acoustic deformations are reproduced by numerical simulations in a continuous medium model, revealing a spatiotemporal evolution of the lattice dynamics dominated by local rotations with minor strain and shear contributions.","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":"1 1","pages":""},"PeriodicalIF":2.8,"publicationDate":"2022-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41437212","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Yi-Ping Chang, Z. Yin, T. Balciunas, H. Wörner, J. Wolf
Sub-μm thin samples are essential for spectroscopic purposes. The development of flat micro-jets enabled novel spectroscopic and scattering methods for investigating molecular systems in the liquid phase. However, the temperature of these ultra-thin liquid sheets in vacuum has not been systematically investigated. Here, we present a comprehensive temperature characterization using optical Raman spectroscopy of sub-micron flatjets produced by two different methods: colliding of two cylindrical jets and a cylindrical jet compressed by a high pressure gas. Our results reveal the dependence of the cooling rate on the material properties and the source characteristics, i.e., nozzle-orifice size, flow rate, and pressure. We show that materials with higher vapor pressures exhibit faster cooling rates, which is illustrated by comparing the temperature profiles of water and ethanol flatjets. In a sub-μm liquid sheet, the temperature of the water sample reaches around 268 K and the ethanol around 253 K close to the flatjet's terminus.
{"title":"Temperature measurements of liquid flat jets in vacuum","authors":"Yi-Ping Chang, Z. Yin, T. Balciunas, H. Wörner, J. Wolf","doi":"10.1063/4.0000139","DOIUrl":"https://doi.org/10.1063/4.0000139","url":null,"abstract":"Sub-μm thin samples are essential for spectroscopic purposes. The development of flat micro-jets enabled novel spectroscopic and scattering methods for investigating molecular systems in the liquid phase. However, the temperature of these ultra-thin liquid sheets in vacuum has not been systematically investigated. Here, we present a comprehensive temperature characterization using optical Raman spectroscopy of sub-micron flatjets produced by two different methods: colliding of two cylindrical jets and a cylindrical jet compressed by a high pressure gas. Our results reveal the dependence of the cooling rate on the material properties and the source characteristics, i.e., nozzle-orifice size, flow rate, and pressure. We show that materials with higher vapor pressures exhibit faster cooling rates, which is illustrated by comparing the temperature profiles of water and ethanol flatjets. In a sub-μm liquid sheet, the temperature of the water sample reaches around 268 K and the ethanol around 253 K close to the flatjet's terminus.","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":"9 1","pages":""},"PeriodicalIF":2.8,"publicationDate":"2021-12-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45476733","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2021-01-01DOI: 10.1007/978-3-030-69674-0_2
M. Mukhopadhyay
{"title":"Free Vibration of Single Degree of Freedom System","authors":"M. Mukhopadhyay","doi":"10.1007/978-3-030-69674-0_2","DOIUrl":"https://doi.org/10.1007/978-3-030-69674-0_2","url":null,"abstract":"","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":"77 6","pages":""},"PeriodicalIF":2.8,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"50973519","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Seongsoo Kang, Christina Kaufmann, Yongseok Hong, Woojae Kim, Agnieszka Nowak‐Król, F. Würthner, Dongho Kim
For H-aggregates of perylene bisimide (PBI), it has been reported that upon photoexcitation, an initially delocalized Frenkel exciton is localized by excimer formation. However, in recent studies, the beforehand exciton dynamics preceding the excimer formation was suggested in larger aggregates consisting of at least more than 10-PBI subunits, which was not observed in small aggregates comprising less than four-PBI subunits. This feature implies that the size of molecular aggregates plays a crucial role in the initial exciton dynamics. In this regard, we have tried to unveil the initial exciton dynamics in PBI H-aggregates by tracking down the transient reorientations of electronic transition dipoles formed by interactions between the PBI subunits in systematically size-controlled PBI H-aggregates. The ultrafast coherent exciton dynamics depending on the molecular aggregate sizes can be distinguished using polarization-dependent femtosecond-transient absorption anisotropy spectroscopic measurements with a time resolution of ∼40 fs. The ultrafast decay profiles of the anisotropy values are unaffected by vibrational relaxation and rotational diffusion processes; hence, the coherent exciton dynamics of the PBI H-aggregates prior to the excimer formation can be directly revealed as the energy migration processes along the PBI H-aggregates.
{"title":"Ultrafast coherent exciton dynamics in size-controlled perylene bisimide aggregates","authors":"Seongsoo Kang, Christina Kaufmann, Yongseok Hong, Woojae Kim, Agnieszka Nowak‐Król, F. Würthner, Dongho Kim","doi":"10.1063/1.5124148","DOIUrl":"https://doi.org/10.1063/1.5124148","url":null,"abstract":"For H-aggregates of perylene bisimide (PBI), it has been reported that upon photoexcitation, an initially delocalized Frenkel exciton is localized by excimer formation. However, in recent studies, the beforehand exciton dynamics preceding the excimer formation was suggested in larger aggregates consisting of at least more than 10-PBI subunits, which was not observed in small aggregates comprising less than four-PBI subunits. This feature implies that the size of molecular aggregates plays a crucial role in the initial exciton dynamics. In this regard, we have tried to unveil the initial exciton dynamics in PBI H-aggregates by tracking down the transient reorientations of electronic transition dipoles formed by interactions between the PBI subunits in systematically size-controlled PBI H-aggregates. The ultrafast coherent exciton dynamics depending on the molecular aggregate sizes can be distinguished using polarization-dependent femtosecond-transient absorption anisotropy spectroscopic measurements with a time resolution of ∼40 fs. The ultrafast decay profiles of the anisotropy values are unaffected by vibrational relaxation and rotational diffusion processes; hence, the coherent exciton dynamics of the PBI H-aggregates prior to the excimer formation can be directly revealed as the energy migration processes along the PBI H-aggregates.","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2019-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1063/1.5124148","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48381977","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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 a time constant of 12 ps. This transient nonequilibrium situation is attributed to the weak coupling between bulk and surface phonon modes which hampers the energy flow between the two subsystems. From the absence of a fast component in the transient diffraction intensity, it is in addition concluded that truncated bulk phonon modes are absent at the surface.
{"title":"Decelerated lattice excitation and absence of bulk phonon modes at surfaces: Ultra-fast electron diffraction from Bi(111) surface upon fs-laser excitation","authors":"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","doi":"10.1063/1.5128275","DOIUrl":"https://doi.org/10.1063/1.5128275","url":null,"abstract":"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 a time constant of 12 ps. This transient nonequilibrium situation is attributed to the weak coupling between bulk and surface phonon modes which hampers the energy flow between the two subsystems. From the absence of a fast component in the transient diffraction intensity, it is in addition concluded that truncated bulk phonon modes are absent at the surface.","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2019-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1063/1.5128275","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45685728","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
M. Dennis, B. J. Morrow, O. Dolezal, A. Cuzzupe, Alexandra E Stupple, J. Newman, J. Bentley, M. Hattarki, S. Nuttall, R. Foitzik, I. Street, P. Stupple, B. Monahan, T. 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 the “WIN” site of WDR5 that cause displacement from chromatin have been additionally implicated to be of broader use in cancer treatment. In this study, a fragment screen with Surface Plasmon Resonance (SPR) was used to identify a highly ligand-efficient imidazole-containing compound that is bound in the WIN site. The subsequent medicinal chemistry campaign—guided by a suite of high-resolution cocrystal structures with WDR5—progressed the initial hit to a low micromolar binder. One outcome from this study is a moiety that substitutes well for the side chain of arginine; a tripeptide containing one such substitution was resolved in a high resolution structure (1.5 Å) with a binding mode analogous to the native tripeptide. SPR furthermore indicates a similar residence time (kd = ∼0.06 s−1) for these two analogs. This novel scaffold therefore represents a possible means to overcome the potential permeability issues of WDR5 ligands that possess highly basic groups like guanidine. The series reported here furthers the understanding of the WDR5 WIN site and functions as a starting point for the development of more potent WDR5 inhibitors that may serve as cancer therapeutics.
{"title":"Fragment screening for a protein-protein interaction inhibitor to WDR5","authors":"M. Dennis, B. J. Morrow, O. Dolezal, A. Cuzzupe, Alexandra E Stupple, J. Newman, J. Bentley, M. Hattarki, S. Nuttall, R. Foitzik, I. Street, P. Stupple, B. Monahan, T. Peat","doi":"10.1063/1.5122849","DOIUrl":"https://doi.org/10.1063/1.5122849","url":null,"abstract":"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 the “WIN” site of WDR5 that cause displacement from chromatin have been additionally implicated to be of broader use in cancer treatment. In this study, a fragment screen with Surface Plasmon Resonance (SPR) was used to identify a highly ligand-efficient imidazole-containing compound that is bound in the WIN site. The subsequent medicinal chemistry campaign—guided by a suite of high-resolution cocrystal structures with WDR5—progressed the initial hit to a low micromolar binder. One outcome from this study is a moiety that substitutes well for the side chain of arginine; a tripeptide containing one such substitution was resolved in a high resolution structure (1.5 Å) with a binding mode analogous to the native tripeptide. SPR furthermore indicates a similar residence time (kd = ∼0.06 s−1) for these two analogs. This novel scaffold therefore represents a possible means to overcome the potential permeability issues of WDR5 ligands that possess highly basic groups like guanidine. The series reported here furthers the understanding of the WDR5 WIN site and functions as a starting point for the development of more potent WDR5 inhibitors that may serve as cancer therapeutics.","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2019-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1063/1.5122849","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44703840","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
M. Grabowski, M. Cymborowski, P. Porebski, T. Osinski, I. Shabalin, D. Cooper, W. 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 dedicated resources created in recent years. Here, we describe our experiences developing the Integrated Resource for Reproducibility in Molecular Crystallography (IRRMC) and describe several examples of a crucial role that diffraction data can play in improving previously determined protein structures. In its first four years, several hundred crystallographers have deposited data from over 5200 diffraction experiments performed at over 60 different synchrotron beamlines or home sources all over the world. In addition to improving the resource and curating submitted data, we have been building a pipeline for extraction or, in some cases, reconstruction of the metadata necessary for seamless automated processing. Preliminary analysis indicates that about 95% of the archived data can be automatically reprocessed. A high rate of reprocessing success shows the feasibility of using the automated metadata extraction and automated processing as a validation step for the deposition of raw diffraction images. The IRRMC is guided by the Findable, Accessible, Interoperable, and Reusable data management principles.
{"title":"The Integrated Resource for Reproducibility in Macromolecular Crystallography: Experiences of the first four years","authors":"M. Grabowski, M. Cymborowski, P. Porebski, T. Osinski, I. Shabalin, D. Cooper, W. Minor","doi":"10.1063/1.5128672","DOIUrl":"https://doi.org/10.1063/1.5128672","url":null,"abstract":"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 dedicated resources created in recent years. Here, we describe our experiences developing the Integrated Resource for Reproducibility in Molecular Crystallography (IRRMC) and describe several examples of a crucial role that diffraction data can play in improving previously determined protein structures. In its first four years, several hundred crystallographers have deposited data from over 5200 diffraction experiments performed at over 60 different synchrotron beamlines or home sources all over the world. In addition to improving the resource and curating submitted data, we have been building a pipeline for extraction or, in some cases, reconstruction of the metadata necessary for seamless automated processing. Preliminary analysis indicates that about 95% of the archived data can be automatically reprocessed. A high rate of reprocessing success shows the feasibility of using the automated metadata extraction and automated processing as a validation step for the deposition of raw diffraction images. The IRRMC is guided by the Findable, Accessible, Interoperable, and Reusable data management principles.","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2019-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1063/1.5128672","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44236757","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}