title: Molecular mechanics force field parameterization of the fluorescent probe rhodamine 6G using automated frequency matching.
abstract: Novel single-molecule fluorescence experimental techniques have prompted a growing need to develop refined computational models of dye-tagged biomolecules. As a necessary first step towards useful molecular simulations of fluorescence-labeled biomolecules, we have derived a force field for the commonly used dye, rhodamine 6G (R6G). A novel automated method is used that includes fitting the molecular mechanics potential to both vibrational frequencies and eigenvector projections derived from quantum chemical calculations. The method is benchmarked on a series of aromatic molecules then applied to derive new parameters for R6G. The force field derived reproduces well the crystal structure of R6G.
authors.affiliation: IWR-Biocomputing, Universität Heidelberg, Im Neuenheimer Feld 368, D-69120 Heidelberg, Germany.
authors.forename: Andrea C
authors.initials: AC
authors.lastname: Vaiana
authors.forename: Andreas
authors.initials: A
authors.lastname: Schulz
authors.forename: Jürgen
authors.initials: J
authors.lastname: Wolfrum
authors.forename: Markus
authors.initials: M
authors.lastname: Sauer
authors.forename: Jeremy C
authors.initials: JC
authors.lastname: Smith
mesh_terms: D000465:Algorithms; D003198:Computer Simulation; D018360:Crystallography, X-Ray; D005456:Fluorescent Dyes; D008958:Models, Molecular; D008968:Molecular Conformation; D015394:Molecular Structure; D012235:Rhodamines
chemical_list: D005456:Fluorescent Dyes; D012235:Rhodamines; C026188:rhodamine 6G