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From All Atom to Coarse Grain: Molecular Dynamic Simulation of Imprinting Process on a Silica Xerogel
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1  REQUIMTE, Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 687, 4169-007 Porto, Portugal.


Molecular imprinted polymers (MIP) are used in very different fields such as solid-phase extraction, enantiomer separations, drug delivery, drug discovery, and so on. Due to this, different techniques have been investigated in the past few years. In this contest, sol-gel polycondensation technique is an interesting alternative since MIP produced with this technique has been proved to present several advantages such as physical robustness, long shelf life, simple preparation, great selectivity, etc. The most widely used precursors for preparing sol−gel materials have been silicon alkoxides, such as tetramethoxysilane (TMOS) or tetraethoxysilane (TEOS). In a recent paper for the first time, we simulated a complex sol-gel system aimed at preparing the (S)-naproxen-imprinted xerogel with an explicit representation of all the ionic species at pH 91. With that simulation we were able to undercover the molecular mechanism behind the imprinting process. However, the simulation ran for only 100ns and we were unable to simulate other important process such as the polymer formation. One possible solution is to move on to a coarse-grain (CG) simulation based on the Martini force field2. The model uses a four-to-one mapping, i.e. on average four heavy atoms and associated hydrogens are represented by a single interaction center. One of the main advantages of this approach is that larger systems may be simulated for longer time. Due to this, the main aim of this study is the simulation of the molecular imprinting process using the Martini force field, in order to simulate all the relevant aspects occurring during the imprinting and polycondensation process.

  1. Concu, R.; Perez, M.; Cordeiro, M. N.; Azenha, M., Molecular dynamics simulations of complex mixtures aimed at the preparation of naproxen-imprinted xerogels. J Chem Inf Model 2014, 54 (12), 3330-43.
  2. Marrink, S. J.; Risselada, H. J.; Yefimov, S.; Tieleman, D. P.; de Vries, A. H., The MARTINI Force Field:  Coarse Grained Model for Biomolecular Simulations. The Journal of Physical Chemistry B 2007, 111 (27), 7812-7824.

Keywords: Molecular Dynamic; Coarse Grain; Martini Force Field; Molecular Imprinting; Xerogel; Sol-Gel; Naproxen; Gromacs