Molecular dynamics of the interaction of L-tryptophan with polypyrrole oligomers

Abstract

There is a current interest in the fabrication of electrochemical sensors based on conducting polymers, such as polypyrrole, (Py)n, for the highly selective sensing of amino acids, for instance, tryptophan, Trp. When (Py)n and other polymers grow in the presence of a target analyte, the material develops cavities that are complementary in size and shape to the analyte. These materials, called molecularly imprinted polymers, MIPs, are very useful for the selective detection of many compounds of biomedical interest. The detailed structure of the MIP complementary cavities is not known. For the design and fabrication of highly selective sensors, information about the structure of such cavities in MIPs is highly desirable. However, this kind of information is not accessible through experimental methods. As a first approach to study the interaction between (Py)n and Trp, in this paper, we use molecular dynamics simulations of Trp and small oligomers of (Py)n (where n = 1, 2, 3, 5) in aqueous solutions. The most significant interactions occur between the indole ring of Trp and the pyrrole pentamer. Attractions occur mainly between the nitrogens of the oligomer chain and the Trp heterocycle, causing the amino acid to walk on the oligomer surface. This process starts with the attraction of Trp by one of the terminal rings in the chain, then, in a concerted way, the nitrogens of the subsequent rings can make a sequence of dipole dipole interactions with the amino acid. Further simulations will address the interaction of Trp with several (Py)n chains simultaneously.