John W. McLeod, Daniel J. Peters
Defence Research and Development Canada
We propose an extension to SMILES syntax that specifies conformation using bond dihedral angles. In the spirit of local configuration codes, the SMILES-local atom order fixes each angle's start and finish direction. Continuous (real valued) and discrete (integer valued) codes are offered. For example, hydrogen peroxide with central dihedral angle 300 degrees has continuous code [H]O[-@300.0]O[H] and discrete duodecimal valued code [H]O[-@A]O[H].
Variants on duodecimal numbers are natural here; think "ten o'clock". Multiple codes are quite expressive. "Boat" cyclo-hexane with C1 and C4 "up" codes discretely as C[-@2]1[-@A]C[-@0]C[-@2]C[-@A]C[-@0]C1 .
We believe a SMILES with these codes comes close to expressing the full geometry of a valence molecular model. Strain issues are also discussed.