Determination of the Structures of Molecularly Imprinted Polymers and Xerogels Using an Automated Stochastic Approach

Abstract

An automated stochastic docking program with a graphical user interface, RANDOMDOCK (RD), has been developed to aid the development of molecularly imprinted polymers and xerogels. RD supports computations with ab initio and semiempirical quantum chemistry programs. The RD algorithms have been tested by searching for the most stable geometries of a varying number of methacrylic acid molecules interacting with nicotinamide. The optimal structures found are either as stable or more stable than those previously proposed for this molecularly imprinted polymer, illustrating that RD is capable of identifying the lowest-energy structures out of a potentially vast number of possible configurations. RD was subsequently applied to determine the most favorable binding sites between silane molecules and tetracycline (TC) as well as TC analogues. Hydrogen bonding between the templates and a silane is an important determinant of stability. Dispersion interactions are also sizable, sometimes dominant, especially between the largest silane and TC analogues not possessing a site readily available for hydrogen bonding. We highlight the importance of exploring the full intermolecular potential energy landscape when studying systems which may not afford highly specific interactions.

Charge-Transfer-Induced Magic Cluster Formation of Azaborine Heterocycles on Noble Metal Surfaces

“…In order to investigate the potential energy landscape for trimers and tetramers of 1,2-azaborine in the gas phase, an automated stochastic docking program, RandomDock, was used. RandomDock has previously been employed successfully to predict the structures of planar trimers of 4-fluorostyrene, croconic acid, and 3-hydroxyphenalenone .…”

Extended Hückel Calculations on Solids Using the Avogadro Molecular Editor and Visualizer

“…However, the visualization program accompanying YAeHMOP (called viewkel) does not run natively on non-Unix systems, and it requires the use of a terminal window, which is not familiar to students. The user-friendly multiplatform open-source molecular builder, editor, and visualizer Avogadro , and its extensions − have recently emerged as a popular choice for research and education. Avogadro’s ease of use and its advanced visualization capabilities render it an ideal graphical platform for YAeHMOP calculations.…”

Computational Modeling and Theoretical Calculations on the Interactions between Spermidine and Functional Monomer (Methacrylic Acid) in a Molecularly Imprinted Polymer

“…Therefore, a computational study prior to MIP synthesis would always be helpful for choosing a suitable pair of template and functional monomer. With the rapid development of computational chemistry, 2 quantum chemical computation has become an effective technique to understand interactions between a template and a functional monomer prior to synthesizing an MIP, thus ensuring suitable match between template-functional monomer pair to yield maximum specificity and selectivity [18,19]. In this regard, density functional theory (DFT) calculation can provide in-depth information with higher accuracy and reliability [20][21][22]; hence, DFT has been applied on this research.…”