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  • Title: Molecular mechanics force field parameterization of the fluorescent probe rhodamine 6G using automated frequency matching.
    Author: Vaiana AC, Schulz A, Wolfrum J, Sauer M, Smith JC.
    Journal: J Comput Chem; 2003 Apr 15; 24(5):632-9. PubMed ID: 12632478.
    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.
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