scholarly journals Extraction of Fast Changes in the Structure of a Disordered Ensemble of Photoexcited Biomolecules

2013 ◽  
Vol 2013 ◽  
pp. 1-5 ◽  
Author(s):  
H.-C. Poon ◽  
M. Schmidt ◽  
D. K. Saldin
Keyword(s):  
Structural Changes ◽  
Ultrashort Pulses ◽  
Fast Time ◽  
X Rays ◽  
Multiple Diffraction ◽  
Time Resolved ◽  
Pump Probe ◽  
Pump And Probe ◽  
Time Variations ◽  
Diffraction Patterns

Using pump-probe experiments of varying time intervals between pump and probe, the method of time-resolved crystallography has given many insights into the fast time variations of crystallized molecules as a result of photoexcitation. We show here that quantities extractable from multiple diffraction patterns of dissolved molecules in random orientations, as measured using powerful ultrashort pulses of X-rays, also contain information about structural changes of a molecule on photoexcitation.

scholarly journals Deducing fast electron density changes in randomly orientated uncrystallized biomolecules in a pump–probe experiment

2014 ◽  
Vol 369 (1647) ◽  
pp. 20130332 ◽  
Author(s):  
K. Pande ◽  
P. Schwander ◽  
M. Schmidt ◽  
D. K. Saldin
Keyword(s):  
Electron Density ◽  
Correlation Functions ◽  
Structural Changes ◽  
Direct Calculation ◽  
Difference Electron Density ◽  
Time Resolved ◽  
Pump Probe ◽  
The Difference ◽  
Diffraction Patterns ◽  
Pump Probe Experiment

We propose a method for deducing time-resolved structural changes in uncrystallized biomolecules in solution. The method relies on measuring the angular correlations of the intensities, when averaged over a large number of diffraction patterns from randomly oriented biomolecules in solution in a liquid solvent. The experiment is somewhat like a pump–probe version of an experiment on small angle X-ray scattering, except that the data expected by the algorithm are not just the radial variation of the averaged intensities. The differences of these correlation functions as measured from a photoexcited and dark structure enable the direct calculation of the difference electron density with a knowledge of only the dark structure. We exploit a linear relation we derive between the difference in these correlation functions and the difference electron density, applicable for small structural changes.

scholarly journals Laue diffraction and time-resolved crystallography: a personal history

2019 ◽  
Vol 377 (2147) ◽  
pp. 20180243 ◽  
Author(s):  
Keith Moffat
Keyword(s):  
Storage Ring ◽  
Structural Changes ◽  
X Ray Diffraction ◽  
Laue Diffraction ◽  
Time Resolved ◽  
Pump Probe ◽  
X Ray ◽  
Historical View ◽  
Laser Sources ◽  
Diffraction Patterns

A personal, historical view is presented of Laue X-ray diffraction and its application to time-resolved studies of dynamic processes, largely in light-sensitive biological systems. In Laue diffraction, a stationary crystal is illuminated by a polychromatic X-ray source. Laue diffraction has inherent complications largely absent in monochromatic diffraction, and consequently fell into disuse for quantitative structure determination. However, the advent of naturally polychromatic, intense, pulsed storage ring X-ray sources in the 1970s led to re-examination at Daresbury and elsewhere of its underlying principles. Laue diffraction has been successfully applied at storage ring sources to time-resolved, pump–probe crystallographic studies, whose exposure time and time resolution were progressively reduced from minutes to seconds, milliseconds, nanoseconds and 100 ps. Most recently, hard X-ray free electron laser sources have been used to generate narrow bandpass Laue diffraction patterns. The femtosecond X-ray pulses from such sources are completely destructive, generate only one diffraction pattern per tiny crystal and have unusual properties. However, they too are being applied to time-resolved crystallography to explore, for example, isomerization and rapid tertiary structural changes on the chemical, femtosecond timescale. This article is part of the theme issue ‘Fifty years of synchrotron science: achievements and opportunities’.

First-, second- and third-order correlation function in time-resolved X-ray diffraction experiments

2004 ◽  
Vol 37 (3) ◽  
pp. 445-450 ◽  
Author(s):  
Simone Techert
Keyword(s):  
Structural Changes ◽  
X Rays ◽  
X Ray Diffraction ◽  
Structural Reorganization ◽  
Third Order ◽  
Time Resolved ◽  
Pump Probe ◽  
X Ray ◽  
Laser Systems ◽  
Laser Sources

In the past decade, sustained progress has been made in the field of time-resolved X-ray diffraction and photocrystallography. Laser systems have been developed rapidly, and the combination of pulsed laser sources with pulsed X-ray sources, particularly by using synchrotron X-ray radiation and X-rays generated by plasma sources, has made the application of pump-probe schemes routine. So far, however, most studies have been focused on two questions: (i) the refinement of structural changes during the course of a reaction, and (ii) possible relations between transient structural changes and the intermediates found by optical spectroscopy. In this work, a kinetic description for different time laws in time-resolved X-ray diffraction experiments is derived in the framework of time-dependent correlation functions. The derived time laws were applied to time-resolved studies on a [2+2] photodimerization and a reversible reaction undergoing structural reorganization.

scholarly journals Capturing structural changes of the S1 to S2 transition of photosystem II using time-resolved serial femtosecond crystallography

IUCrJ ◽  
2021 ◽  
Vol 8 (3) ◽  
pp. 431-443
Author(s):  
Hongjie Li ◽  
Yoshiki Nakajima ◽  
Takashi Nomura ◽  
Michihiro Sugahara ◽  
Shinichiro Yonekura ◽  
...  
Keyword(s):  
Photosystem Ii ◽  
Water Oxidation ◽  
Structural Changes ◽  
Short Delay ◽  
Time Resolved ◽  
Pump Probe ◽  
Sample Flow Rate ◽  
Excitation Region ◽  
Pump And Probe ◽  
Serial Femtosecond Crystallography

Photosystem II (PSII) catalyzes light-induced water oxidation through an S i -state cycle, leading to the generation of di-oxygen, protons and electrons. Pump–probe time-resolved serial femtosecond crystallography (TR-SFX) has been used to capture structural dynamics of light-sensitive proteins. In this approach, it is crucial to avoid light contamination in the samples when analyzing a particular reaction intermediate. Here, a method for determining a condition that avoids light contamination of the PSII microcrystals while minimizing sample consumption in TR-SFX is described. By swapping the pump and probe pulses with a very short delay between them, the structural changes that occur during the S1-to-S2 transition were examined and a boundary of the excitation region was accurately determined. With the sample flow rate and concomitant illumination conditions determined, the S2-state structure of PSII could be analyzed at room temperature, revealing the structural changes that occur during the S1-to-S2 transition at ambient temperature. Though the structure of the manganese cluster was similar to previous studies, the behaviors of the water molecules in the two channels (O1 and O4 channels) were found to be different. By comparing with the previous studies performed at low temperature or with a different delay time, the possible channels for water inlet and structural changes important for the water-splitting reaction were revealed.

scholarly journals Selective time-dependent changes of Cu(DPPE)(DMP)·PF6on photoexcitation

2014 ◽  
Vol 70 (a1) ◽  
pp. C776-C776 ◽  
Author(s):  
Elzbieta Trzop ◽  
Bertrand Fournier ◽  
Katarzyna Jarzembska ◽  
Jesse Sokolow ◽  
Radoslaw Kaminski ◽  
...  
Keyword(s):  
Structural Changes ◽  
Dye Sensitized Solar Cells ◽  
Department Of Energy ◽  
Data Sets ◽  
Monoclinic System ◽  
Time Resolved ◽  
Pump Probe ◽  
Light Emitting Devices ◽  
Potential Applications ◽  
Photon Source

Thanks to their potential applications as light-emitting devices, chemical sensors and dye-sensitized solar cells, heteroleptic copper (I) complexes have been extensively studied. Cu(DPPE)(DMP)·PF6(dppe= 1,2-bis(diphenylphosphino)ethane; dmp = 2,9-dimethyl-1,10-phenanthroline) crystallizes in the monoclinic system, P21/c, with two independent molecules in the asymmetric unit. Previous studies on this system [1,2] show strong temperature-dependent emission. The complex was studied at 90K under 355nm laser excitation. At this temperature, the luminescence decay for Cu(DPPE)(DMP)·PF6is biexponential with lifetimes of ~3μs and ~28μs. Two time-resolved X-ray diffraction techniques were applied for studies: (1) a Laue technique at BioCARS ID-14 beamline at the Advanced Photon Source, and (2) monochromatic diffraction at a newly constructed in-house pump-probe monochromatic facility at the University at Buffalo. Structural changes determined with the two methods are in qualitative agreement; discrepancies in position of the Cu and P atoms were observed. The molecular distortions were smaller than those determined at 16K in the earlier synchrotron study by Vorontsov et al. [2]. Photodeformation maps (see Figure below), in which the increase in temperature on photoexcitation has been eliminated, clearly illustrate the photoinduced atomic shifts for both data sets. Results will be compared with those obtained for other studied heteroleptic copper (I) complexes, for instance Cu[(1,10-phenanthroline-N,N′) bis(triphenylphosphine)]·BF4[3]. The in-house pump-probe facility is discussed by Radoslaw Kaminski at this meeting. Research funded by the National Science Foundation (CHE1213223). BioCARS Sector 14 at APS is supported by NIH (RR007707). The Advanced Photon Source is funded by the Office of Basic Energy Sciences, U.S. Department of Energy, (W-31-109-ENG-38). KNJ is supported by the Polish Ministry of Science and Higher Education through the "Mobility Plus" program.

scholarly journals Time-resolved pair distribution function analysis of disordered materials on beamlines BL04B2 and BL08W at SPring-8

2018 ◽  
Vol 25 (6) ◽  
pp. 1627-1633 ◽  
Author(s):  
Koji Ohara ◽  
Satoshi Tominaka ◽  
Hiroki Yamada ◽  
Masakuni Takahashi ◽  
Hiroshi Yamaguchi ◽  
...  
Keyword(s):  
Distribution Function ◽  
Pair Distribution Function ◽  
Structural Changes ◽  
Function Analysis ◽  
Image Data ◽  
High Energy ◽  
Disordered Materials ◽  
X Rays ◽  
Two Dimensional ◽  
Time Resolved

A dedicated apparatus has been developed for studying structural changes in amorphous and disordered crystalline materials substantially in real time. The apparatus, which can be set up on beamlines BL04B2 and BL08W at SPring-8, mainly consists of a large two-dimensional flat-panel detector and high-energy X-rays, enabling total scattering measurements to be carried out for time-resolved pair distribution function (PDF) analysis in the temperature range from room temperature to 873 K at pressures of up to 20 bar. For successful time-resolved analysis, a newly developed program was used that can monitor and process two-dimensional image data simultaneously with the data collection. The use of time-resolved hardware and software is of great importance for obtaining a detailed understanding of the structural changes in disordered materials, as exemplified by the results of commissioned measurements carried out on both beamlines. Benchmark results obtained using amorphous silica and demonstration results for the observation of sulfide glass crystallization upon annealing are introduced.

scholarly journals Exploring the structural changes on excitation of a luminescent organic bromine-substituted complex by in-house time-resolved pump-probe diffraction

2017 ◽  
Vol 4 (2) ◽  
pp. 024501 ◽  
Author(s):  
Krishnayan Basuroy ◽  
Yang Chen ◽  
Sounak Sarkar ◽  
Jason Benedict ◽  
Philip Coppens
Keyword(s):  
Structural Changes ◽  
Time Resolved ◽  
Pump Probe

scholarly journals On the assessment of time-resolved diffraction results

2014 ◽  
Vol 70 (3) ◽  
pp. 291-299 ◽  
Author(s):  
Bertrand Fournier ◽  
Philip Coppens
Keyword(s):  
Relative Intensity ◽  
Structural Changes ◽  
External Perturbation ◽  
Dynamic Structure ◽  
Intensity Change ◽  
Data Sets ◽  
Time Resolved ◽  
Pump Probe ◽  
Final Model ◽  
R Factors

Data collected during dynamic structure pump–probe crystallography experiments require appropriate indicators of agreement and tools to visualize the electron-density distribution changes. Agreement factors based on the ratio of intensitiesRwith and without the external perturbation are shown to be analogous to the {\cal R}1andw{\cal R}2{\cal R} factors widely used in standard crystallographic refinements. The η-based {\cal R} factors, normalized by the average relative intensity change, are significantly larger thanR-based values. It is shown that the relative intensity change η-based {\cal R} factors are not suitable for comparing different data sets. Fourier photodifference maps allow the visualization of the externally induced structural changes in the crystal, but also can be used during refinement to observe residual peaks not yet accounted for by the model and thus monitor the progress of the refinement. The photodeformation maps are a complementary tool to confirm the validity of the final model. Photodeformation maps with equalized laser-on and laser-off thermal motion are used to highlight the structural changes.

scholarly journals Time-resolved crystallography and protein design: signalling photoreceptors and optogenetics

2014 ◽  
Vol 369 (1647) ◽  
pp. 20130568 ◽  
Author(s):  
Keith Moffat
Keyword(s):  
Protein Design ◽  
Structural Changes ◽  
Fast Time ◽  
Free Electron Lasers ◽  
Time Resolved ◽  
X Ray ◽  
Biological Targets ◽  
X Ray Crystallography ◽  
X Ray Scattering ◽  
Exciting Possibility

Time-resolved X-ray crystallography and solution scattering have been successfully conducted on proteins on time-scales down to around 100 ps, set by the duration of the hard X-ray pulses emitted by synchrotron sources. The advent of hard X-ray free-electron lasers (FELs), which emit extremely intense, very brief, coherent X-ray pulses, opens the exciting possibility of time-resolved experiments with femtosecond time resolution on macromolecular structure, in both single crystals and solution. The X-ray pulses emitted by an FEL differ greatly in many properties from those emitted by a synchrotron, in ways that at first glance make time-resolved measurements of X-ray scattering with the required accuracy extremely challenging. This opens up several questions which I consider in this brief overview. Are there likely to be chemically and biologically interesting structural changes to be revealed on the femtosecond time-scale? How shall time-resolved experiments best be designed and conducted to exploit the properties of FELs and overcome challenges that they pose? To date, fast time-resolved reactions have been initiated by a brief laser pulse, which obviously requires that the system under study be light-sensitive. Although this is true for proteins of the visual system and for signalling photoreceptors, it is not naturally the case for most interesting biological systems. To generate more biological targets for time-resolved study, can this limitation be overcome by optogenetic, chemical or other means?

Sign in / Sign up

Export Citation Format

Share Document