Computer-simulation-based selection of optimal monomer for imprinting of tri-O-acetyl adenosine in a polymer matrix: calculations for benzene solution

Abstract

Molecular imprinting is a promising way to create polymer materials that can be used as artificial receptors, and have anticipated use in synthetic imitation of natural antibodies. In case of successful imprinting, the selectivity and affinity of the imprint for the substrate molecules are comparable with those of natural counterparts. Various calculation methods can be used to estimate the effects of a large range of imprinting parameters under different conditions, and to find better ways to improve polymer characteristics. However, one difficulty is that properties such as hydrogen bonding can be modeled only by quantum methods that demand a lot of computational resources. Combined quantum mechanics/molecular mechanics (QM/MM) methods allow the use of MM and QM for different parts of the modeled system. In present study this method was realized in the NWChem package to compare estimations of the stability of tri-O-acetyl adenosine–monomer pre-polymerization complexes in benzene solution with previous results under vacuum. © 2016, Springer-Verlag Berlin Heidelberg.