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Imaging of femtosecond bond breaking and charge dynamics in ultracharged peptides

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journal contribution
posted on 2022-05-17, 04:45 authored by I Eliah Dawod, N Tîmneanu, Adrian MancusoAdrian Mancuso, C Caleman, O Grånäs
X-ray free-electrons lasers have revolutionized the method of imaging biological macromolecules such as proteins, viruses and cells by opening the door to structural determination of both single particles and crystals at room temperature. By utilizing high intensity X-ray pulses on femtosecond timescales, the effects of radiation damage can be reduced. Achieving high resolution structures will likely require knowledge of how radiation damage affects the structure on an atomic scale, since the experimentally obtained electron densities will be reconstructed in the presence of radiation damage. Detailed understanding of the expected damage scenarios provides further information, in addition to guiding possible corrections that may need to be made to obtain a damage free reconstruction. In this work, we have quantified the effects of ionizing photon-matter interactions using first principles molecular dynamics. We utilize density functional theory to calculate bond breaking and charge dynamics in three ultracharged molecules and two different structural conformations that are important to the structural integrity of biological macromolecules, comparing to our previous studies on amino acids. The effects of the ultracharged states and subsequent bond breaking in real space are studied in reciprocal space using coherent diffractive imaging of an ensemble of aligned biomolecules in the gas phase. This journal is


We thank the developers of CONDOR for helpful discussions and access to the Davinci computer cluster provided by the Laboratory of Molecular Biophysics, Uppsala University. We thank the biophysics network at Uppsala University for fruitful discussions. The main computations were enabled by resources provided by the Swedish National Infrastructure for Computing (SNIC) at UPPMAX partially funded by the Swedish Research Council through grant agreement no. 2018-05973. N. T. thanks the Swedish Research Council for financial support (2019-03935). C. C. acknowledges the Swedish Research Council (grant 2018-00740) and the Helmholtz Association through the Center for Free-Electron Laser Science at DESY. O. G. acknowledges the Strategic Research Foundation (SSF) for funding through Grant No. ICA16-0037.


Publication Date



Physical Chemistry Chemical Physics






(p. 1532-1543)


Royal Society of Chemistry (RSC)



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