2.0 Computational Methods

Twenty two molecules with the potential to react as Schiff bases (Scheme 1) were taken from data reported by ICCVAM (Interagency Coordinating Committee on the Validation of Alternative Methods)[57] and Kern et al. [58] as described previously.[54] All SB compounds with non-zero EC3 values were chosen, covering a different chemical substructures (Table 1). Some of the substrates contained chemical functionality associated with other chemical domains (SNAr, SN2 and Acyl) or had more than one position capable of forming a SB product. The compounds can be sub-classified as aliphatic and aromatic aldehydes, ketones, 1,2 diones and 1,3 diones. In the case of 1,2 and 1,3 diones, each molecule contains two carbonyl groups leading to two plausible points for nucleophilic attack.
Calculations were performed using a model consisting of the substrate, two water molecules and two methylamine molecules to approximate the biological reaction. The simulated reaction leading to the imine product (Schiff base) involves three distinct steps as shown in Scheme 2. The first step involves nucleophilic attack of the substrate by methylamine giving rise to a carbinolamine or hemiacetal-like intermediate (INT1). Proton transfer from the protonated intermediate, via water, leads to the elimination of water and the formation of the protonated imine product (INT2). The final step involves the deprotonation of INT2 to give the deprotonated imine (PROD).