title: Analytical Harmonic Vibrational Frequencies for the Green Fluorescent Protein Computed with ONIOM: Chromophore Mode Character and Its Response to Environment.
abstract: A systematic comparison of different environmental effects on the vibrational modes of the 4-hydroxybenzylidene-2,3-dimethylimidazolinone (HBDI) chromophore using the ONIOM method allows us to model how the molecule's spectroscopic transitions are modified in the Green Fluorescent Protein (GFP). ONIOM(QM:MM) reduces the expense of normal mode calculations when computing the majority of second derivatives only at the MM level. New developments described here for the efficient solution of the CPHF equations, including contributions from electrostatic interactions with environment charges, mean that QM model systems of ∼100 atoms can be embedded within a much larger MM environment of ∼5000 atoms. The resulting vibrational normal modes, their associated frequencies, and dipole derivative vectors have been used to interpret experimental difference spectra (GFPI2-GFPA), chromophore vibrational Stark shifts, and changes in the difference between electronic and vibrational transition dipoles (mode angles) in the protein environment.
authors.affiliation: Department of Chemistry, Imperial College , London SW7 2AZ, United Kingdom.
authors.forename: Lee M
authors.initials: LM
authors.lastname: Thompson
authors.affiliation: Department of Chemistry, Imperial College , London SW7 2AZ, United Kingdom.|Ecole Normale Supérieure, Département de Chimie, ENS-CNRS-UPMC UMR8640, 75005 Paris, France.
authors.forename: Aurélie
authors.initials: A
authors.lastname: Lasoroski
authors.affiliation: Department of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University , Boston, Massachusetts 02115, United States.
authors.forename: Paul M
authors.initials: PM
authors.lastname: Champion
authors.affiliation: Department of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University , Boston, Massachusetts 02115, United States.
authors.forename: J Timothy
authors.initials: JT
authors.lastname: Sage
authors.affiliation: Gaussian, Inc., 340 Quinnipiac Street, Building 40, Wallingford, Connecticut 06492, United States.
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Frisch
authors.affiliation: Division of Molecular Biosciences, Imperial College , London SW7 2AZ, United Kingdom.
authors.forename: Jasper J
authors.initials: JJ
authors.lastname: van Thor
authors.affiliation: Department of Chemistry, Imperial College , London SW7 2AZ, United Kingdom.
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Bearpark