Algorithm for generation and assessment of probability of possible reaction pathways for multiple-channel bimolecular interactions is presented. The proposed algorithm comprises a combination of few steps. They include conformational search for reaction intermediate using the molecular mechanics (MMX) approach, based on the obtained conformation construction of structures of transition states and pre-reaction complexes, and calculation activation energies to further determine the probable reaction pathways. The proposed algorithm could be adopted for investigation of chemical and biochemical reactions of different types. Here, we have considered the reaction of bicyclo[2.2.1]hept-5-en-endo-2-ylmethylamine (1) with glycidyl ether (2) in a neutral environment that proceeds through SN2-like mechanism forming bipolar ion (3) which is a good starting point for identification of the reaction channels. Conformational properties of intermediate (3) have been investigated using stochastic conformational search. From the 95 localized conformations within 10 kcal/mol of global minimum that have been obtained, 63 unique transition state conformations were generated and optimized by using the PM7 and M062X/6-31G(d) methods for accurate estimation of overall rate constant of reaction. The most energetically favorable pathways have been investigated at the M062X/6-31G(d) level of theory taking into account the influence of solvent.