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      An Update on Molecularly Imprinted Polymer Design through a Computational Approach to Produce Molecular Recognition Material with Enhanced Analytical Performance

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          Abstract

          Molecularly imprinted polymer (MIP) computational design is expected to become a routine technique prior to synthesis to produce polymers with high affinity and selectivity towards target molecules. Furthermore, using these simulations reduces the cost of optimizing polymerization composition. There are several computational methods used in MIP fabrication and each requires a comprehensive study in order to select a process with results that are most similar to properties exhibited by polymers synthesized through laboratory experiments. Until now, no review has linked computational strategies with experimental results, which are needed to determine the method that is most appropriate for use in designing MIP with high molecular recognition. This review will present an update of the computational approaches started from 2016 until now on quantum mechanics, molecular mechanics and molecular dynamics that have been widely used. It will also discuss the linear correlation between computational results and the polymer performance tests through laboratory experiments to examine to what extent these methods can be relied upon to obtain polymers with high molecular recognition. Based on the literature search, density functional theory (DFT) with various hybrid functions and basis sets is most often used as a theoretical method to provide a shorter MIP manufacturing process as well as good analytical performance as recognition material.

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          Molecular dynamics simulations: advances and applications

          Molecular dynamics simulations have evolved into a mature technique that can be used effectively to understand macromolecular structure-to-function relationships. Present simulation times are close to biologically relevant ones. Information gathered about the dynamic properties of macromolecules is rich enough to shift the usual paradigm of structural bioinformatics from studying single structures to analyze conformational ensembles. Here, we describe the foundations of molecular dynamics and the improvements made in the direction of getting such ensemble. Specific application of the technique to three main issues (allosteric regulation, docking, and structure refinement) is discussed.
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            Performance of M06, M06-2X, and M06-HF density functionals for conformationally flexible anionic clusters: M06 functionals perform better than B3LYP for a model system with dispersion and ionic hydrogen-bonding interactions.

            We present a comparative assessment of the performance of the M06 suite of density functionals (M06, M06-2X, and M06-HF) against an MP2 benchmark for calculating the relative energies and geometric structures of the Cl(-)·arginine and Br(-)·arginine halide ion-amino acid clusters. Additional results are presented for the popular B3LYP density functional. The Cl(-)·arginine and Br(-)·arginine complexes are important prototypes for the phenomenon of anion-induced zwitterion formation. Results are presented for the canonical (noncharge separated) and zwitterionic (charge separated) tautomers of the clusters, as well as the numerous conformational isomers of the clusters. We find that all of the M06 functions perform well in terms of predicting the general trends in the conformer relative energies and identifying the global minimum conformer. This is in contrast to the B3LYP functional, which performed significantly less well for the canonical tautomers of the clusters where dispersion interactions contribute more significantly to the conformer energetics. We find that the M06 functional gave the lowest mean unsigned error for the relative energies of the canonical conformers (2.10 and 2.36 kJ/mol for Br(-)·arginine and Cl(-)·arginine), while M06-2X gave the lowest mean unsigned error for the zwitterionic conformers (0.85 and 1.23 kJ/mol for Br(-)·arginine and Cl(-)·arginine), thus providing insight into the types of physical systems where each of these functionals should perform best.
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              Dispersion interactions in density-functional theory

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                Author and article information

                Contributors
                Role: Academic Editor
                Journal
                Molecules
                Molecules
                molecules
                Molecules
                MDPI
                1420-3049
                26 March 2021
                April 2021
                : 26
                : 7
                : 1891
                Affiliations
                [1 ]Department of Pharmaceutical Analysis and Medicinal Chemistry, Faculty of Pharmacy, Padjadjaran University, Jl. Raya Bandung Sumedang KM 21, Sumedang 45363, Indonesia; shendi@ 123456uniga.ac.id (S.S.); mutakin@ 123456unpad.ac.id (M.)
                [2 ]Pharmacy Department, Faculty of Mathematics and Natural Sciences, Garut University, Jl. Jati No.42B, Tarogong, Garut 44151, Indonesia
                [3 ]Geophysic Department, Faculty of Mathematics and Natural Sciences, Padjadjaran University, Jl. Raya Bandung Sumedang KM 21, Sumedang 45363, Indonesia; rosandi@ 123456geophys.unpad.ac.id
                [4 ]Drug Development Study Center, Faculty of Pharmacy, Padjadjaran University, Jl. Raya Bandung Sumedang KM 21, Sumedang 45363, Indonesia
                Author notes
                [* ]Correspondence: aliya.n.hasanah@ 123456unpad.ac.id ; Tel.: +62-812-2346-382
                Author information
                https://orcid.org/0000-0003-2387-1338
                https://orcid.org/0000-0002-4085-7872
                Article
                molecules-26-01891
                10.3390/molecules26071891
                8036856
                33810542
                756aa18e-be40-4ad7-8a9c-d2d161cee8c8
                © 2021 by the authors.

                Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license ( http://creativecommons.org/licenses/by/4.0/).

                History
                : 26 February 2021
                : 23 March 2021
                Categories
                Review

                molecularly imprinted polymer,computational method,dft

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