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Using Molecular Dynamics in the Study of Molecularly Imprinted Polymers

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Molecularly Imprinted Polymers

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2359))

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Abstract

Molecular dynamics (MD) simulations of prepolymerization mixtures can provide detailed insights concerning the molecular-level mechanisms underlying the performance of molecularly imprinted polymers (MIPs) and can be used for the in silico screening of candidate polymer systems. Here, we describe the use of MD simulations of all-atom, all-component MIP prepolymerization mixtures and procedures for the evaluation of the simulation data using the Amber simulation software suite.

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References

  1. Nicholls IA, Olsson GD, Karlsson BCG, Suriyanarayanan S, Wiklander JG (2018) Theoretical and computational strategies in molecularly imprinted polymer development. In: Kutner W, Sharma PS (eds) Molecularly imprinted polymers for analytical chemistry applications, Polymer chemistry series, vol 28. The Royal Society of Chemistry, Cambridge, pp 197–226

    Chapter  Google Scholar 

  2. Cowen T, Busato M, Karim K, Piletsky SA (2016) In silico synthesis of synthetic receptors: a polymerization algorithm. Macromol Rapid Commun 37:2011–2016. https://doi.org/10.1002/marc.201600515

    Article  CAS  Google Scholar 

  3. Bates F, Busato M, Piletska E, Whitcombe MJ, Karim K, Guerreiro A, del Valle M, Giorgetti A, Piletsky S (2017) Computational design of molecularly imprinted polymer for direct detection of melamine in milk. Sep Sci Technol 52:1441–1453. https://doi.org/10.1080/01496395.2017.1287197

    Article  CAS  Google Scholar 

  4. Viveiros R, Karim K, Piletsky SA, Heggie W, Casimiro T (2017) Development of a molecularly imprinted polymer for a pharmaceutical impurity in supercritical CO2: rational design using computational approach. J Clean Prod 168:1025–1031. https://doi.org/10.1016/j.jclepro.2017.09.026

    Article  CAS  Google Scholar 

  5. O'Mahony J, Karlsson BCG, Mizaikoff B, Nicholls IA (2007) Correlated theoretical, spectroscopic and X-ray crystallographic studies of a non-covalent molecularly imprinted polymerisation system. Analyst 132:1161–1168. https://doi.org/10.1039/b706258c

    Article  CAS  Google Scholar 

  6. O’Mahony J, Moloney M, McCormack M, Nicholls IA, Mizaikoff B, Danaher M (2013) Design and implementation of an imprinted material for the extraction of the endocrine disruptor bisphenol A from milk. J Chromatogr B 931:164–169. https://doi.org/10.1016/j.jchromb.2013.05.025

    Article  CAS  Google Scholar 

  7. Yañez F, Chianella I, Piletsky SA, Concheiro A, Alvarez-Lorenzo C (2010) Computational modeling and molecular imprinting for the development of acrylic polymers with high affinity for bile salts. Anal Chim Acta 659:178–185. https://doi.org/10.1016/j.aca.2009.11.054

    Article  CAS  Google Scholar 

  8. Tsyrulneva I, Zaporozhets O, Piletska E, Piletsky S (2014) Molecular modelling and synthesis of a polymer for the extraction of amiloride and triamterene from human urine. Anal Methods 6:3429–3435. https://doi.org/10.1039/c4ay00318g

    Article  CAS  Google Scholar 

  9. Wren SP, Piletsky SA, Karim K, Gascoine P, Lacey R, Sun T, Grattan KTV (2015) Computational design and fabrication of optical fibre fluorescent chemical probes for the detection of cocaine. J Lightwave Technol 33:2572–2579. https://doi.org/10.1109/Jlt.2015.2389036

    Article  CAS  Google Scholar 

  10. Golker K, Olsson GD, Nicholls IA (2017) The influence of a methyl substituent on molecularly imprinted polymer morphology and recognition - acrylic acid versus methacrylic acid. Eur Polym J 92:137–149. https://doi.org/10.1016/j.eurpolymj.2017.04.043

    Article  CAS  Google Scholar 

  11. Shoravi S, Olsson GD, Karlsson BCG, Bexborn F, Abghoui Y, Hussain J, Wiklander JG, Nicholls IA (2016) In silico screening of molecular imprinting prepolymerization systems: oseltamivir selective polymers through full-system molecular dynamics-based studies. Org Biomol Chem 14:4210–4219. https://doi.org/10.1039/c6ob00305b

    Article  CAS  Google Scholar 

  12. Golker K, Nicholls IA (2016) The effect of crosslinking density on molecularly imprinted polymer morphology and recognition. Eur Polym J 75:423–430. https://doi.org/10.1016/j.eurpolymj.2016.01.008

    Article  CAS  Google Scholar 

  13. Olsson GD, Niedergall K, Bach M, Karlsson BCG, Tovar G, Nicholls IA (2015) Simulation of imprinted emulsion prepolymerization mixtures. Polym J 47:827–830. https://doi.org/10.1038/pj.2015.63

    Article  CAS  Google Scholar 

  14. Golker K, Karlsson BCG, Wiklander JG, Rosengren AM, Nicholls IA (2015) Hydrogen bond diversity in the pre-polymerization stage contributes to morphology and MIP-template recognition - MAA versus MMA. Eur Polym J 66:558–568. https://doi.org/10.1016/j.eurpolymj.2015.03.018

    Article  CAS  Google Scholar 

  15. Shoravi S, Olsson GD, Karlsson BCG, Nicholls IA (2014) On the influence of crosslinker on template complexation in molecularly imprinted polymers: a computational study of prepolymerization mixture events with correlations to template-polymer recognition behavior and NMR spectroscopic studies. Int J Mol Sci 15:10622–10634. https://doi.org/10.3390/ijms150610622

    Article  CAS  Google Scholar 

  16. Golker K, Karlsson BCG, Rosengren AM, Nicholls IA (2014) A functional monomer is not enough: principal component analysis of the influence of template complexation in pre-polymerization mixtures on imprinted polymer recognition and morphology. Int J Mol Sci 15:20572–20584. https://doi.org/10.3390/ijms151120572

    Article  CAS  Google Scholar 

  17. Cleland D, Olsson GD, Karlsson BCG, Nicholls IA, McCluskey A (2014) Molecular dynamics approaches to the design and synthesis of PCB targeting molecularly imprinted polymers: interference to monomer–template interactions in imprinting of 1,2,3-trichlorobenzene. Org Biomol Chem 12:844–853. https://doi.org/10.1039/c3ob42399a

    Article  CAS  Google Scholar 

  18. Olsson GD, Karlsson BCG, Schillinger E, Sellergren B, Nicholls IA (2013) Theoretical studies of 17-β-estradiol-imprinted Prepolymerization mixtures: insights concerning the roles of cross-linking and functional monomers in template complexation and polymerization. Ind Eng Chem Res 52:13965–13970. https://doi.org/10.1021/ie401115f

    Article  CAS  Google Scholar 

  19. Golker K, Karlsson BCG, Olsson GD, Rosengren AM, Nicholls IA (2013) Influence of composition and morphology on template recognition in molecularly imprinted polymers. Macromolecules 46:1408–1414. https://doi.org/10.1021/ma3024238

    Article  CAS  Google Scholar 

  20. Schillinger E, Möder M, Olsson GD, Nicholls IA, Sellergren B (2012) An artificial estrogen receptor through combinatorial imprinting. Chem Eur J 18:14773–14783. https://doi.org/10.1002/chem.201201428

    Article  CAS  Google Scholar 

  21. Olsson GD, Karlsson BCG, Shoravi S, Wiklander JG, Nicholls IA (2012) Mechanisms underlying molecularly imprinted polymer molecular memory and the role of crosslinker: resolving debate on the nature of template recognition in phenylalanine anilide imprinted polymers. J Mol Recognit 25:69–73. https://doi.org/10.1002/jmr.2147

    Article  CAS  Google Scholar 

  22. Karlsson BCG, O’Mahony J, Karlsson JG, Bengtsson H, Eriksson LA, Nicholls IA (2009) Structure and dynamics of monomer−template complexation: an explanation for molecularly imprinted polymer recognition site heterogeneity. J Am Chem Soc 131:13297–13304. https://doi.org/10.1021/ja902087t

    Article  CAS  Google Scholar 

  23. Case DA, Belfon K, Ben-Shalom IY, Brozell SR, Cerutti DS, Cheatham TE III, Cruzeiro VWD, Darden TA, Duke RE, Giambasu G, Gilson MK, Gohlke H, Goetz AW, Harris R, Izadi S, Izmailov SA, Kasavajhala K, Kovalenko A, Krasny R, Kurtzman T, Lee TS, LeGrand S, Li P, Lin C, Liu J, Luchko T, Luo R, Man V, Merz KM, Miao Y, Mikhailovskii O, Monard G, Nguyen H, Onufriev A, Pan F, Pantano S, Qi R, Roe DR, Roitberg A, Sagui C, Schott-Verdugo S, Shen J, Simmerling CL, Skrynnikov NR, Smith J, Swails J, Walker RC, Wang J, Wilson L, Wolf RM, Wu X, Xiong Y, Xue Y, York DM, Kollman PA (2020) AMBER 2020. University of California, San Francisco

    Google Scholar 

  24. Hanwell MD, Curtis DE, Lonie DC, Vandermeersch T, Zurek E, Hutchison GR (2012) Avogadro: an advanced semantic chemical editor, visualization, and analysis platform. J Cheminform 4:17. https://doi.org/10.1186/1758-2946-4-17

    Article  CAS  Google Scholar 

  25. Wang J, Wolf RM, Caldwell JW, Kollman PA, Case DA (2004) Development and testing of a general amber force field. J Comput Chem 25:1157–1174. https://doi.org/10.1002/jcc.20035

    Article  CAS  Google Scholar 

  26. Martinez L, Andrade R, Birgin EG, Martinez JM (2009) PACKMOL: a package for building initial configurations for molecular dynamics simulations. J Comput Chem 30:2157–2164. https://doi.org/10.1002/jcc.21224

    Article  CAS  Google Scholar 

  27. Roe DR, Brooks BR (2020) A protocol for preparing explicitly solvated systems for stable molecular dynamics simulations. J Chem Phys 153:054123. https://doi.org/10.1063/5.0013849

    Article  CAS  Google Scholar 

  28. Roe DR, Cheatham TE 3rd (2018) Parallelization of CPPTRAJ enables large scale analysis of molecular dynamics trajectory data. J Comput Chem 39:2110–2117. https://doi.org/10.1002/jcc.25382

    Article  CAS  Google Scholar 

  29. Roe DR, Cheatham TE 3rd (2013) PTRAJ and CPPTRAJ: software for processing and analysis of molecular dynamics trajectory data. J Chem Theory Comput 9:3084–3095. https://doi.org/10.1021/ct400341p

    Article  CAS  Google Scholar 

  30. Humphrey W, Dalke A, Schulten K (1996) VMD: visual molecular dynamics. J Mol Graph 14:33–38. https://doi.org/10.1016/0263-7855(96)00018-5

    Article  CAS  Google Scholar 

  31. Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE (2004) UCSF chimera—a visualization system for exploratory research and analysis. J Comput Chem 25:1605–1612. https://doi.org/10.1002/jcc.20084

    Article  CAS  Google Scholar 

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Correspondence to Ian A. Nicholls .

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Olsson, G.D., Wiklander, J.G., Nicholls, I.A. (2021). Using Molecular Dynamics in the Study of Molecularly Imprinted Polymers. In: Martín-Esteban, A. (eds) Molecularly Imprinted Polymers. Methods in Molecular Biology, vol 2359. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1629-1_21

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  • DOI: https://doi.org/10.1007/978-1-0716-1629-1_21

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-1628-4

  • Online ISBN: 978-1-0716-1629-1

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