title: An ab initio force field for the cofactors of bacterial photosynthesis.
abstract: This article presents a new ab initio force field for the cofactors of bacterial photosynthesis, namely quinones and bacteriochlorophylls. The parameters has been designed to be suitable for molecular dynamics simulations of photosynthetic proteins by being compatible with the AMBER force field. To our knowledge, this is the first force field for photosynthetic cofactors based on a reliable set of ab initio density functional reference data for methyl bacteriochlorophyll a, methyl bacteriopheophytin a, and of a derivative of ubiquinone. Indeed, the new molecular mechanics force field is able to reproduce very well not only the experimental and ab initio structural properties and the vibrational spectra of the molecules, but also the eigenvectors of the molecular normal modes. For this reason it might also be helpful to understand vibrational spectroscopy results obtained on reaction center proteins.
authors.affiliation: CECAM, Centre Européen de Calcul Atomique et Moleculaire, Ecole Normale Superieure de Lyon, 46 Allée d'Italie, 69364 Lyon, France. mcecca@cscs.ch
authors.forename: Matteo
authors.initials: M
authors.lastname: Ceccarelli
authors.forename: Piero
authors.initials: P
authors.lastname: Procacci
authors.forename: Massimo
authors.initials: M
authors.lastname: Marchi
mesh_terms: D001429:Bacteriochlorophylls; D045342:Light-Harvesting Protein Complexes; D008432:Mathematical Computing; D008956:Models, Chemical; D010788:Photosynthesis; D045322:Photosynthetic Reaction Center Complex Proteins; D011487:Protein Conformation; D011809:Quinones / Q000737:chemistry
chemical_list: D001429:Bacteriochlorophylls; D045342:Light-Harvesting Protein Complexes; D045322:Photosynthetic Reaction Center Complex Proteins; D011809:Quinones