@article{MegowRoehrBuschetal.2015,
  author    = {Megow, J{\"o}rg and R{\"o}hr, Merle I. S. and Busch, Marcel and Renger, Thomas and Mitric, Roland and Kirstein, Stefan and Rabe, J{\"u}rgen P. and May, Volkhard},
  title     = {Site-dependence of van der Waals interaction explains exciton spectra of double-walled tubular J-aggregates},
  series = {Physical chemistry, chemical physics : a journal of European Chemical Societies},
  volume    = {17},
  journal   = {Physical chemistry, chemical physics : a journal of European Chemical Societies},
  number    = {10},
  publisher = {Royal Society of Chemistry},
  address   = {Cambridge},
  issn      = {1463-9076},
  doi       = {10.1039/c4cp05945j},
  pages     = {6741 -- 6747},
  year      = {2015},
  abstract  = {The simulation of the optical properties of supramolecular aggregates requires the development of methods, which are able to treat a large number of coupled chromophores interacting with the environment. Since it is currently not possible to treat large systems by quantum chemistry, the Frenkel exciton model is a valuable alternative. In this work we show how the Frenkel exciton model can be extended in order to explain the excitonic spectra of a specific double-walled tubular dye aggregate explicitly taking into account dispersive energy shifts of ground and excited states due to van der Waals interaction with all surrounding molecules. The experimentally observed splitting is well explained by the site-dependent energy shift of molecules placed at the inner or outer side of the double-walled tube, respectively. Therefore we can conclude that inclusion of the site-dependent dispersive effect in the theoretical description of optical properties of nanoscaled dye aggregates is mandatory.},
  language  = {en}
}
@article{GoetzeGrecoMitricetal.2012,
  author    = {Goetze, Jan P. and Greco, Claudio and Mitric, Roland and Bonacic-Koutecky, Vlasta and Saalfrank, Peter},
  title     = {BLUF Hydrogen network dynamics and UV/Vis spectra: A combined molecular dynamics and quantum chemical study},
  series = {JOURNAL OF COMPUTATIONAL CHEMISTRY},
  volume    = {33},
  journal   = {JOURNAL OF COMPUTATIONAL CHEMISTRY},
  number    = {28},
  publisher = {WILEY-BLACKWELL},
  address   = {HOBOKEN},
  issn      = {0192-8651},
  doi       = {10.1002/jcc.23056},
  pages     = {2233 -- 2242},
  year      = {2012},
  abstract  = {Blue light sensing using flavin (BLUF) protein photoreceptor domains change their hydrogen bond network after photoexcitation. To explore this phenomenon, BLUF domains from R. sphaeroides were simulated using Amber99 molecular dynamics (MD). Five starting configurations were considered, to study different BLUF proteins (AppA/BlrB), Trp conformations (Win/Wout), structure determination (X-ray/NMR), and finally, His protonation states. We found dependencies of the hydrogen bonds on almost all parameters. Our data show an especially strong correlation of the Trp position and hydrogen bonds involving Gln63. The latter is in some contradiction to earlier results (Obanayama et al., Photochem. Photobiol. 2008, 84 10031010). Possible origins and implications are discussed. Our calculations support conjectures that Gln63 is more flexible with Trp104 in Win position. Using snapshots from MD and time-dependent density functional theory, UV/vis spectra for the chromophore were determined, which account for molecular motion of the protein under ambient conditions. In accord with experiment, it is found that the UV/vis spectra of BLUF bound flavin are red-shifted and thermally broadened for all calculated p ? p* transitions, relative to gas phase flavin at T = 0 K. However, differences in the spectra between the various BLUF configurations cannot be resolved with the present approach. (c) 2012 Wiley Periodicals, Inc.},
  language  = {en}
}