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Title: Radiation Damage in XFEL: Case study from the oxygen-evolving complex of Photosystem II

Abstract

Structural changes induced by radiation damage in X-ray crystallography hinder the ability to understand the structure/function relationship in chemical reactions. Serial femtosecond crystallography overcomes this problem by exposing the sample to very short and intense laser pulse leading to measurement before destruction. Here we use molecular modeling to map the radiation damage during the 10–50 fs to the intensity, the energy and the time duration of the laser pulse on the oxygen-evolving complex (OEC) of photosystem II. In the model, the nuclei move classically in a fully quantum potential created by electron density under the effect of strong laser pulse in the Ehrenfest dynamics regime. The results show that the Mn-Mn and Mn-Ca distances are less affected by radiation damage due to the their heavy masses, while one μ-oxo bridge (O5) moves significantly. The radiation damage may induce conformational changes of the water ligands but only bond elongation for the amino acids ligands. These effects are relatively intensity independent from 1016 to 1017 W/cm2, but changes increase dramatically if the beam intensity is increased to 1018 W/cm2. Finally, in addition, the self amplified spontaneous emission (SASE) nature of the laser beam does not affect the dynamics of the ions.

Authors:
 [1];  [2];  [2]
  1. City College of New York, NY (United States). Dept. of Physics; Zewail City of Science and Technology, Giza (Egypt). Center for Photonics and Smart Materials
  2. Zewail City of Science and Technology, Giza (Egypt). Center for Photonics and Smart Materials
Publication Date:
Research Org.:
City College of New York, NY (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22)
OSTI Identifier:
1426476
Grant/Contract Number:  
SC0001423
Resource Type:
Accepted Manuscript
Journal Name:
Scientific Reports
Additional Journal Information:
Journal Volume: 6; Journal Issue: 1; Journal ID: ISSN 2045-2322
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English
Subject:
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY

Citation Formats

Amin, Muhamed, Badawi, Ashraf, and Obayya, S. S. Radiation Damage in XFEL: Case study from the oxygen-evolving complex of Photosystem II. United States: N. p., 2016. Web. doi:10.1038/srep36492.
Amin, Muhamed, Badawi, Ashraf, & Obayya, S. S. Radiation Damage in XFEL: Case study from the oxygen-evolving complex of Photosystem II. United States. doi:10.1038/srep36492.
Amin, Muhamed, Badawi, Ashraf, and Obayya, S. S. Wed . "Radiation Damage in XFEL: Case study from the oxygen-evolving complex of Photosystem II". United States. doi:10.1038/srep36492. https://www.osti.gov/servlets/purl/1426476.
@article{osti_1426476,
title = {Radiation Damage in XFEL: Case study from the oxygen-evolving complex of Photosystem II},
author = {Amin, Muhamed and Badawi, Ashraf and Obayya, S. S.},
abstractNote = {Structural changes induced by radiation damage in X-ray crystallography hinder the ability to understand the structure/function relationship in chemical reactions. Serial femtosecond crystallography overcomes this problem by exposing the sample to very short and intense laser pulse leading to measurement before destruction. Here we use molecular modeling to map the radiation damage during the 10–50 fs to the intensity, the energy and the time duration of the laser pulse on the oxygen-evolving complex (OEC) of photosystem II. In the model, the nuclei move classically in a fully quantum potential created by electron density under the effect of strong laser pulse in the Ehrenfest dynamics regime. The results show that the Mn-Mn and Mn-Ca distances are less affected by radiation damage due to the their heavy masses, while one μ-oxo bridge (O5) moves significantly. The radiation damage may induce conformational changes of the water ligands but only bond elongation for the amino acids ligands. These effects are relatively intensity independent from 1016 to 1017 W/cm2, but changes increase dramatically if the beam intensity is increased to 1018 W/cm2. Finally, in addition, the self amplified spontaneous emission (SASE) nature of the laser beam does not affect the dynamics of the ions.},
doi = {10.1038/srep36492},
journal = {Scientific Reports},
number = 1,
volume = 6,
place = {United States},
year = {2016},
month = {11}
}

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