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The consequences of substitution of fluorine for the para hydrogen of a phenylalanine residue in ribonuclease-S were investigated by conformational energy calculations using the AMBER force field. Both the fluorine-containing protein and the corresponding nonfluorinated material were subjected to conformational adjustment through energy minimization and the minimum energy structures so defined were compared. Fluorine substitution leads to small alterations in many atomic positions in the protein, with adjustments at at sites more than 0.5 nm from the fluorine appearing to be somewhat larger than those within the immediate vicinity of the fluorine. Several atoms proximate to the fluorine atom were observed to move toward the fluorine while others in the same vicinity move away. The greater bulk of the fluorine atom and the strongly different electronic properties of fluorine compared to hydrogen thus appear to be insufficient to cause a consistent, unidirectional change in nearest-neighbor interactions upon introduction of a fluorine atom into a protein structure. Virtually all changes in atomic positions that are predicted by these calculations would be barely detectable by a crystallographic study with a resolution of 0.2 nm.

Empirical intermolecular force field parameters for the fluorine atom of the 4-fluorophenyl group have been generated for use in molecular mechanics programs. Partial charges on the ring system were obtained by Mulliken population analysis of wave functions generated by molecular orbital calculations in the STO-3G approximation. Fluorine van der Waals parameters were obtained by non-linear least-squares fitting of crystallographic data following the procedure of Hagler and Lifson. The parameters developed are compared to fluorine parameters reported previously.