title: Revised force-field parameters for chlorophyll-a, pheophytin-a and plastoquinone-9.
abstract: Biological photosynthetic machineries, such as photosystem I, photosystem II, or the bacterial reaction center, use cofactor molecules that absorb light or directly participate in chemical reactions. Accurate description of the structure of the cofactors, and of their interactions with protein groups, is an important step toward understanding how photosynthetic machineries work. Here we revisit the classical force field parameters for chlorophyll-a, pheophytin-a and plastoquinone-9. We present systematic quantum mechanical and classical mechanical computations that lead to a good description of the structure and non-bonded interactions of these cofactors.
authors.affiliation: Theoretical Molecular Biophysics, Department of Physics, Freie Universitaet Berlin, Arnimallee 14, D-14195 Berlin, Germany.
authors.forename: Federico
authors.initials: F
authors.lastname: Guerra
authors.affiliation: Theoretical Molecular Biophysics, Department of Physics, Freie Universitaet Berlin, Arnimallee 14, D-14195 Berlin, Germany.
authors.forename: Suliman
authors.initials: S
authors.lastname: Adam
authors.affiliation: Theoretical Molecular Biophysics, Department of Physics, Freie Universitaet Berlin, Arnimallee 14, D-14195 Berlin, Germany. Electronic address: nbondar@zedat.fu-berlin.de.
authors.forename: Ana-Nicoleta
authors.initials: AN
authors.lastname: Bondar
mesh_terms: D002734:Chlorophyll / Q000031:analogs & derivatives* / Q000737:chemistry; D008958:Models, Molecular; D015394:Molecular Structure; D010674:Pheophytins / Q000737:chemistry*; D045332:Photosystem II Protein Complex / Q000737:chemistry; D010971:Plastoquinone / Q000737:chemistry*; D011789:Quantum Theory
chemical_list: D010674:Pheophytins; D045332:Photosystem II Protein Complex; D002734:Chlorophyll; C085815:chlorophyll a'; C061694:pheophytin a; D010971:Plastoquinone
keywords: CHARMM force field parameters; CHARMM potential energy function; Chlorophyll-a; Pheophytin-a; Photosystem II; Plastoquinone-9