@article{VillatoroWeberZuehlkeetal.2019,
  author    = {Villatoro, Jos{\´e} Andr{\´e}s and Weber, M. and Z{\"u}hlke, Martin and Lehmann, A. and Zenichowski, Karl and Riebe, Daniel and Beitz, Toralf and L{\"o}hmannsr{\"o}ben, Hans-Gerd and Kreuzer, O.},
  title     = {Structural characterization of synthetic peptides using electrospray ion mobility spectrometry and molecular dynamics simulations},
  series = {International Journal of Mass Spectrometry},
  volume    = {436},
  journal   = {International Journal of Mass Spectrometry},
  publisher = {Elsevier},
  address   = {Amsterdam},
  issn      = {1387-3806},
  doi       = {10.1016/j.ijms.2018.10.036},
  pages     = {108 -- 117},
  year      = {2019},
  abstract  = {Electrospray ionization-ion mobility spectrometry was employed for the determination of collision cross sections (CCS) of 25 synthetically produced peptides in the mass range between 540-3310 Da. The experimental measurement of the CCS is complemented by their calculation applying two different methods. One prediction method is the intrinsic size parameter (ISP) method developed by the Clemmer group. The second new method is based on the evaluation of molecular dynamics (MD) simulation trajectories as a whole, resulting in a single, averaged collision cross-section value for a given peptide in the gas phase. A high temperature MD simulation is run in order to scan through the whole conformational space. The lower temperature conformational distribution is obtained through thermodynamic reweighting. In the first part, various correlations, e.g. CCS vs. mass and inverse mobility vs. m/z correlations, are presented. Differences in CCS between peptides are also discussed in terms of their respective mass and m/z differences, as well as their respective structures. In the second part, measured and calculated CCS are compared. The agreement between the prediction results and the experimental values is in the same range for both calculation methods. While the calculation effort of the ISP method is much lower, the MD method comprises several tools providing deeper insights into the conformations of peptides. Advantages and limitations of both methods are discussed. Based on the separation of two pairs of linear and cyclic peptides of virtually the same mass, the influence of the structure on the cross sections is discussed. The shift in cross section differences and peak shape after transition from the linear to the cyclic peptide can be well understood by applying different MD tools, e.g. the root-mean-square deviation (RMSD) and the root mean square fluctuation (RMSF). (C) 2018 Elsevier B.V. All rights reserved.},
  language  = {en}
}
@article{BeyeWernetSchuesslerLangeheineetal.2013,
  author    = {Beye, Martin and Wernet, Ph. and Sch{\"u}ßler-Langeheine, Christian and F{\"o}hlisch, Alexander},
  title     = {Time resolved resonant inelastic X-ray scattering: a supreme tool to understand dynamics in solids and molecules},
  series = {Journal of electron spectroscopy and related phenomena : the international journal on theoretical and experimental aspects of electron spectroscopy},
  volume    = {188},
  journal   = {Journal of electron spectroscopy and related phenomena : the international journal on theoretical and experimental aspects of electron spectroscopy},
  number    = {3},
  publisher = {Elsevier},
  address   = {Amsterdam},
  issn      = {0368-2048},
  doi       = {10.1016/j.elspec.2013.04.013},
  pages     = {172 -- 182},
  year      = {2013},
  abstract  = {Dynamics in materials typically involve different degrees of freedom, like charge, lattice, orbital and spin in a complex interplay. Time-resolved resonant inelastic X-ray scattering (RIXS) as a highly selective tool can provide unique insight and follow the details of dynamical processes while resolving symmetries, chemical and charge states, momenta, spin configurations, etc. In this paper, we review examples where the intrinsic scattering duration time is used to study femtosecond phenomena. Free-electron lasers access timescales starting in the sub-ps range through pump-probe methods and synchrotrons study the time scales longer than tens of ps. In these examples, time-resolved resonant inelastic X-ray scattering is applied to solids as well as molecular systems.},
  language  = {en}
}