Molecular Dynamics Simulation and DFT Study to Predict the Refractive Index of Intermediates in the Paal-Knorr Pyrrole Synthesis

Background: Refractive index is an important optical property which can be used to identify substances such as intermediates in organic reactions. Objective: To predict this property we used molecular dynamics simulations and density functional theory. We have calculated refractive indices of intermediates in the Paal-Knorr reaction for 200nm ≤ λ ≤ 800nm. Method: The molecular dynamics simulation with the generalized Amber force field (GAFF) was used to obtain equilibrium densities of intermediates. Molecular polarizabilities were derived from quantum calculations at the B3LYP level. Results: The data obtained show that values of densities, polarizabilites and susceptibility depend on substituent groups. Also, we have found a meaningful ordering for refractive indices of studied intermediates at wavelengths of more than 400 nm. Conclusion: Our calculated refractive indices can be used for detection of intermediate molecules.