Modeling the extent of conjugation in histochemical dyes and fluorescent probes: clarification in calculating conjugated bond number (CBN) and introduction of a new parameter, resonance energy.

Determining the extent of conjugation in dyes and fluorochromes is a helpful tool for understanding or predicting the behavior of these compounds when used as stains for microscopy. One measure that has been used repeatedly is conjugated bond number (CBN), which is the number of bonds in a conjugated system. CBN can be obtained by inspection of the structure of a compound, but the rules for how to determine what constitutes a conjugated system are not fully established. Using molecular modeling software, we have defined more clearly which groups contribute to conjugation and which do not. We accomplished this by using a new parameter, resonance energy (RE'), which is the energy differential between a conjugated compound and its unconjugated counterpart. Conjugated compounds possess less energy. If a compound contains a questionable atom or group, RE' can be calculated for the compound with and without that group. If RE' is the same for both, the group in question plays no role in the resonance and thus is not part of the conjugated system.