title: The resonance Raman spectra of spheroidene revisited with a first-principles approach.
abstract: The resonance Raman (RR) spectra of different configurations of spheroidene are calculated by means of quantum chemical methods to investigate the nature of the cis configuration of this carotenoid molecule in the photosynthetic reaction center (RC) of the purple bacterium Rhodobacter sphaeroides. For validation of our methodology, we also calculate the spectrum of the all-trans structure present in the light-harvesting complexes of this bacterium. While former theoretical resonance Raman studies only considered truncated models of spheroidene, we report on calculations employing the full pigment here. The calculated frequencies for the all-trans configuration are in good agreement with former experimental and simulated data. Among the possible cis structures, the 15,15'-cis configuration shows a RR spectrum that is in best agreement with the experimental spectrum of spheroidene in the RC. In order to assess model truncation effects, we compare calculations for the full spheroidene molecule to those for the truncated model. While the main features can already be found in the latter, the full model leads to considerably different intensities in the region around 1150 cm(-1), which improve the agreement with experiment. A slight mismatch for the vibrational frequencies in the C=C stretch region is investigated by considering a model for spheroidene in the binding pocket comprising more than 500 atoms in total. The results do not lead to improved agreement with experiment, in contrast to the simpler strategy of introducing constraints in the structural optimization of a truncated spheroidene model. The calculated RR spectrum of the 13,14-cis configuration shows additional features which can also be identified in the experimental RR spectrum. This shows that the most likely cis structure is the 15,15'-cis configuration. Besides this, the 13,14-cis configuration remains a candidate for an additional spheroidene structure in the RC of Rhodobacter sphaeroides mutant R26.
authors.affiliation: Gorlaeus Laboratories, Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands.
authors.forename: Jelle M
authors.initials: JM
authors.lastname: Boereboom
authors.forename: Marc C
authors.initials: MC
authors.lastname: van Hemert
authors.forename: Johannes
authors.initials: J
authors.lastname: Neugebauer
mesh_terms: D001665:Binding Sites; D002338:Carotenoids / Q000737:chemistry*; D007536:Isomerism; D008958:Models, Molecular; D009154:Mutation; D045322:Photosynthetic Reaction Center Complex Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D017434:Protein Structure, Tertiary; D012242:Rhodobacter sphaeroides / Q000378:metabolism; D013059:Spectrum Analysis, Raman; D013816:Thermodynamics
chemical_list: D045322:Photosynthetic Reaction Center Complex Proteins; C005637:spheroidene; D002338:Carotenoids