期刊
JOURNAL OF COMPUTATIONAL CHEMISTRY
卷 24, 期 5, 页码 632-639出版社
JOHN WILEY & SONS INC
DOI: 10.1002/jcc.10190
关键词
computer simulation; molecular modeling; force field parameters; fluorescent dyes; normal modes
Novel sin le-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. (C) 2003 Wiley Periodicals, Inc.
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