Molecular mechanics force field parameterization of the fluorescent probe rhodamine 6G using automated frequency matching
✍ Scribed by Andrea C. Vaiana; Andreas Schulz; Jürgen Wolfrum; Markus Sauer; Jeremy C. Smith
- Publisher
- John Wiley and Sons
- Year
- 2003
- Tongue
- English
- Weight
- 191 KB
- Volume
- 24
- Category
- Article
- ISSN
- 0192-8651
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✦ Synopsis
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. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 632–639, 2003