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Radiation damage in X-ray crystallography: a quantum-mechanical study of photoinduced defect formation in beeswax-analogue n-eicosane crystals

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Abstract

We study the nuclear dynamics of n-eicosane (\(\hbox {C}_{20}\hbox {H}_{42}\)) in the crystalline state after photoirradation at room temperature using adiabatic ab initio excited-state dynamics based on hybrid time-dependent density-functional theory. We consider the weak perturbation (absorption) limit, in which an excited electron and a hole are simultaneously created in the system, and the strong perturbation (photoemission) regime, in which one electron is removed. We examine the changes in the carbon chain conformation occurring over timescales of the order of ca. 5 ps relative to the unperturbed (ground state) crystal structure at room temperature, which we simulate using standard ab initio molecular dynamics based on hybrid density-functional theory. Whereas the system retains its ground-state structure in the photoemission limit, the formation of structural defects, in the form of local distortions of the chain geometry, is observed in the absorption limit. We attribute the formation of these defects to the nuclear screening of the electron–hole pair created by photoexcitation. We discuss these findings in the context of radiation damage in organic/biological macromolecules and X-ray diffraction techniques.

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Notes

  1. We used a locally modified version of CPMD V3.9, Copyright IBM Corp 1990–2008, Copyright MPI fuer Festkoerperforschung Stuttgart 1997–2001; http://www.cpmd.org.

  2. We used the program IGoR, version 2015.1, by L. Bernasconi.

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Acknowledgments

This work was supported by EPSRC through a Service Level Agreement with STFC Scientific Computing Department. Computing resources were provided by the UK Materials Chemistry Consortium (Grant EP/L000202) and by STFC Scientific Computing Department.

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Correspondence to Leonardo Bernasconi.

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Paper dedicated to the UNESCO International Year of Light and Light-based Technologies (IYL 2015). TCA special Issue on Health and Energy from the Sun: a Computational Perspective.

Published as part of the special collection of articles “Health and Energy from the Sun”.

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Bernasconi, L., Brandao-Neto, J. Radiation damage in X-ray crystallography: a quantum-mechanical study of photoinduced defect formation in beeswax-analogue n-eicosane crystals. Theor Chem Acc 135, 28 (2016). https://doi.org/10.1007/s00214-015-1779-3

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