UNCORRECTED PROOF Journal : Large 214 Dispatch : 30-12-2015 Pages : 10 Article No : 1779 ¨ LE ¨ TYPESET MS Code : TCAC-D-15-00278 þ CP þ DISK 1 3 Theor Chem Acc _#####################_ DOI 10.1007/s00214-015-1779-3 REGULAR ARTICLE Radiation damage in X-ray crystallography: a quantum-mechanical study of photoinduced defect formation in beeswax-analogue n-eicosane crystals Leonardo Bernasconi 1 · José Brandao-Neto 2 Received: 15 September 2015 / Accepted: 30 November 2015 © Springer-Verlag Berlin Heidelberg 2015 discuss these findings in the context of radiation damage in organic/biological macromolecules and X-ray diffraction techniques. Keywords TD-DFT · Dynamics · Photoemission · Absorption · X-rays 1 Introduction The damage caused by ionising radiation, such as X-rays and electrons, is one of the most important factors limiting the reliability of structure determination in biomolecules and organic samples in the crystalline state [15]. Highly brilliant third-generation X-ray sources for macromolecu- lar crystallography can potentially yield structural details at virtually an atomic level, and their resolution is currently only limited by the effects of radiation damage. Radiation damage alters the structure and, potentially, ultimately destroys the sample during a measurement. Radiation- induced physical and chemical changes in complex mac- romolecules often lead to incorrect conclusions concerning the structure of the sample, and it is not unlikely that many of the protein structure data sets deposited in the Protein Data Bank (PDB) suffer, at least to some extent, from inac- curacies originating from these effects [36]. In typical energy ranges used in X-ray crystallography, physical and chemical changes in the sample are caused by photoelectric absorption and inelastic scattering [18, 31–33, 40]. Damage can arise from the direct interaction of photons with the sample through photoelectric absorption or Compton scattering, which release a cascade of electrons with energies of a few up to several tens of eV [29, 46]. The result of these processes is usually referred to as primary damage and can be followed by sequences of radiolytic Abstract We study the nuclear dynamics of n-eicosane (C 20 H 42 ) in the crystalline state after photoirradation at room temperature using adiabatic ab initio excited-state dynamics based on hybrid time-dependent density-func- tional theory. We consider the weak perturbation (absorp- tion) limit, in which an excited electron and a hole are simultaneously created in the system, and the strong per- turbation (photoemission) regime, in which one electron is removed. We examine the changes in the carbon chain con- formation 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-func- tional theory. Whereas the system retains its ground-state structure in the photoemission limit, the formation of struc- tural defects, in the form of local distortions of the chain geometry, is observed in the absorption limit. We attrib- ute the formation of these defects to the nuclear screening of the electron–hole pair created by photoexcitation. We Published as part of the special collection of articles “Health and Energy from the Sun”. 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. * Leonardo Bernasconi leonardo.bernasconi@stfc.ac.uk José Brandao-Neto jose.brandao-neto@diamond.ac.uk 1 STFC Rutherford Appleton Laboratory, Harwell Oxford, Didcot OX11 0QX, UK 2 Diamond Light Source Ltd, Harwell Oxford, Didcot OX11 0QX, UK 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 A1 A2 A3 A4 A5 A6 A7 A8 A9 A10 A11 A12 A13 Author Proof