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      Molecular mechanics force field parameterization of the fluorescent probe rhodamine 6G using automated frequency matching.

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          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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          Author and article information

          Journal
          J Comput Chem
          Journal of computational chemistry
          Wiley
          0192-8651
          0192-8651
          Apr 15 2003
          : 24
          : 5
          Affiliations
          [1 ] IWR-Biocomputing, Universität Heidelberg, Im Neuenheimer Feld 368, D-69120 Heidelberg, Germany.
          Article
          10.1002/jcc.10190
          12632478
          60048ff3-c274-40ce-b36f-3cb82873416f
          Copyright 2003 Wiley Periodicals, Inc. J Comput Chem 24: 632-639, 2003
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