{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,2]],"date-time":"2026-05-02T05:13:08Z","timestamp":1777698788909,"version":"3.51.4"},"reference-count":46,"publisher":"MDPI AG","issue":"8","license":[{"start":{"date-parts":[[2011,7,28]],"date-time":"2011-07-28T00:00:00Z","timestamp":1311811200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/3.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>In this article we present a model for molecularly imprinted polymers, which considers both complexation processes in the pre-polymerization mixture and adsorption in the imprinted structures within a single consistent framework. As a case study we investigate MAA\/EGDMA polymers imprinted with pyrazine and pyrimidine. A polymer imprinted with pyrazine shows substantial selectivity towards pyrazine over pyrimidine, thus exhibiting molecular recognition, whereas the pyrimidine imprinted structure shows no preferential adsorption of the template. Binding sites responsible for the molecular recognition of pyrazine involve one MAA molecule and one EGDMA molecule, forming associations with the two functional groups of the pyrazine molecule. Presence of these specific sites in the pyrazine imprinted system and lack of the analogous sites in the pyrimidine imprinted system is directly linked to the complexation processes in the pre-polymerization solution. These processes are quite different for pyrazine and pyrimidine as a result of both enthalpic and entropic effects.<\/jats:p>","DOI":"10.3390\/ijms12084781","type":"journal-article","created":{"date-parts":[[2011,7,28]],"date-time":"2011-07-28T11:27:34Z","timestamp":1311852454000},"page":"4781-4804","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":14,"title":["Molecular Recognition Effects in Atomistic Models of Imprinted Polymers"],"prefix":"10.3390","volume":"12","author":[{"given":"Eduardo M. A.","family":"Dourado","sequence":"first","affiliation":[{"name":"Institute for Materials and Processes, School of Engineering, University of Edinburgh, Edinburgh, Midlothian EH9 3JL, UK"}]},{"given":"Carmelo","family":"Herdes","sequence":"additional","affiliation":[{"name":"Centro de Qu\u00edmica de \u00c9vora, Universidade de \u00c9vora, Rua Rom\u00e3o Romalho 59, 7000 \u00c9vora, Portugal"}]},{"given":"Paul R. Van","family":"Tassel","sequence":"additional","affiliation":[{"name":"Department of Chemical and Environmental Engineering, Yale University, New Haven, CT 06520-8286, USA"}]},{"given":"Lev","family":"Sarkisov","sequence":"additional","affiliation":[{"name":"Institute for Materials and Processes, School of Engineering, University of Edinburgh, Edinburgh, Midlothian EH9 3JL, UK"}]}],"member":"1968","published-online":{"date-parts":[[2011,7,28]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"543","DOI":"10.1016\/j.bios.2009.03.038","article-title":"Theoretical and computational strategies for rational molecularly imprinted polymer design","volume":"25","author":"Nicholls","year":"2009","journal-title":"Biosens. Bioelectron"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"106","DOI":"10.1002\/jmr.760","article-title":"Molecular imprinting science and technology: A survey of the literature for the years up to and including 2003","volume":"19","author":"Alexander","year":"2006","journal-title":"J. Mol. Recognit"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"1288","DOI":"10.1021\/ac010840b","article-title":"Rational design of a polymer specific for microcystin-LR using a computational approach","volume":"74","author":"Chianella","year":"2002","journal-title":"Anal. Chem"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"1795","DOI":"10.1016\/j.addr.2005.07.013","article-title":"How to find effective functional monomers for effective molecularly imprinted polymers?","volume":"57","author":"Karim","year":"2005","journal-title":"Adv. Drug Deliv. Rev"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"73","DOI":"10.1016\/j.aca.2005.11.068","article-title":"Computational design and synthesis of molecularly imprinted polymers with high binding capacity for pharmaceutical applications-model case: Adsorbent for abacavir","volume":"559","author":"Chianella","year":"2006","journal-title":"Anal. Chim. Acta"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"1161","DOI":"10.1039\/b706258c","article-title":"Correlated theoretical, spectroscopic and X-ray crystallographic studies of a non-covalent molecularly imprinted polymerisation system","volume":"132","author":"Karlsson","year":"2007","journal-title":"Analyst"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"13297","DOI":"10.1021\/ja902087t","article-title":"Structure and dynamics of monomer-template complexation: An explanation for molecularly imprinted polymer recognition site heterogeneity","volume":"131","author":"Karlsson","year":"2009","journal-title":"J. Am. Chem. Soc"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"657","DOI":"10.1021\/cm050598f","article-title":"Factors contributing to binding-site imperfections in imprinted polymers","volume":"18","author":"Yungerman","year":"2006","journal-title":"Chem. Mater"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"6084","DOI":"10.1021\/ie061369l","article-title":"Molecular simulations of recognitive behavior of molecularly imprinted intelligent polymeric networks","volume":"46","author":"Henthorn","year":"2007","journal-title":"Ind. Eng. Chem. Res"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"5352","DOI":"10.1021\/la804168b","article-title":"Computer simulation of volatile organic compound adsorption in atomistic models of molecularly imprinted polymers","volume":"25","author":"Herdes","year":"2009","journal-title":"Langmuir"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"164706:1","DOI":"10.1063\/1.2049247","article-title":"Replica Ornstein-Zernike theory of adsorption in a templated porous material: Interaction site systems","volume":"123","author":"Sarkisov","year":"2005","journal-title":"J Chem Phys"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"15726","DOI":"10.1021\/jp073536g","article-title":"Integral equation theory of adsorption in templated materials: Influence of molecular attraction","volume":"111","author":"Sarkisov","year":"2007","journal-title":"J. Phys. Chem. C"},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"214701:1","DOI":"10.1063\/1.3140204","article-title":"Emergence of molecular recognition phenomena in a simple model of imprinted porous materials","volume":"130","author":"Dourado","year":"2009","journal-title":"J Chem Phys"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"537","DOI":"10.1007\/BF01028471","article-title":"Distribution-functions for fluids in random-media","volume":"51","author":"Madden","year":"1988","journal-title":"J. Stat. Phys"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"5945","DOI":"10.1063\/1.459505","article-title":"Fluids in equilibrium with disordered porous materials\u2014integral-equation theory","volume":"93","author":"Fanti","year":"1990","journal-title":"J. Chem. Phys"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"816","DOI":"10.1103\/PhysRevA.45.816","article-title":"Liquid-state methods for random-media\u2014Random sequential adsorption","volume":"45","author":"Given","year":"1992","journal-title":"Phys. Rev. A"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"5422","DOI":"10.1063\/1.462726","article-title":"Fluid distributions in random media: Arbitrary matrices","volume":"96","author":"Madden","year":"1992","journal-title":"J. Chem. Phys"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"495","DOI":"10.1016\/0378-4371(94)90200-3","article-title":"The replica Ornstein-Zernike equations and the structure of partly quenched media","volume":"209","author":"Given","year":"1994","journal-title":"Phys. A"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"333101","DOI":"10.1088\/0953-8984\/20\/33\/333101","article-title":"Theories of molecular fluids confined in disordered porous materials","volume":"20","author":"Sarkisov","year":"2008","journal-title":"J. Phys.-Condens. Matter"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"675","DOI":"10.1002\/(SICI)1099-1352(199634\/12)9:5\/6<675::AID-JMR320>3.0.CO;2-C","article-title":"Study of the nature of recognition in molecularly imprinted polymers","volume":"9","author":"Andersson","year":"1996","journal-title":"J. Mol. Recogn"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1016\/0263-7855(96)00018-5","article-title":"VMD: Visual molecular dynamics","volume":"14","author":"Humphrey","year":"1996","journal-title":"J. Mol. Graph"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"4508","DOI":"10.1021\/jp984742e","article-title":"Novel configurational-bias Monte Carlo method for branched molecules. Transferable potentials for phase equilibria. 2. United-atom description of branched alkanes","volume":"103","author":"Martin","year":"1999","journal-title":"J. Phys. Chem. B"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"8008","DOI":"10.1021\/jp001044x","article-title":"Transferable potentials for phase equilibria. 4. United-atom description of linear and branched alkenes and alkylbenzenes","volume":"104","author":"Wick","year":"2000","journal-title":"J. Phys. Chem. B"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"3093","DOI":"10.1021\/jp003882x","article-title":"Monte Carlo calculations for alcohols and their mixtures with alkanes. Transferable potentials for phase equilibria. 5. United-atom description of primary, secondary, and tertiary alcohols","volume":"105","author":"Chen","year":"2001","journal-title":"J. Phys. Chem. B"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"10790","DOI":"10.1021\/jp073586l","article-title":"Transferable potentials for phase equilibria. 9. Explicit hydrogen description of benzene and five-membered and six-membered heterocyclic aromatic compounds","volume":"111","author":"Rai","year":"2007","journal-title":"J. Phys. Chem. B"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"5370","DOI":"10.1021\/jp990822m","article-title":"Transferable potentials for phase equilibria. 3. Explicit-hydrogen description of normal alkanes","volume":"103","author":"Chen","year":"1999","journal-title":"J. Phys. Chem. B"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"24100","DOI":"10.1021\/jp0549125","article-title":"Transferable potentials for phase equilibria. 8. United-atom description for thiols, sulfides, disulfides, and thiophene","volume":"109","author":"Lubna","year":"2005","journal-title":"J. Phys. Chem. B"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"2569","DOI":"10.1021\/jp972543+","article-title":"Transferable potentials for phase equilibria. 1. United-atom description of n-alkanes","volume":"102","author":"Martin","year":"1998","journal-title":"J. Phys. Chem. B"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"17596","DOI":"10.1021\/jp049459w","article-title":"Transferable potentials for phase equilibria. 6. United-atom description for ethers, glycols, ketones, and aldehydes","volume":"108","author":"Stubbs","year":"2004","journal-title":"J. Phys. Chem. B"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"18974","DOI":"10.1021\/jp0504827","article-title":"Transferable potentials for phase equilibria. 7. Primary, secondary, and tertiary amines, nitroalkanes and nitrobenzene, nitriles, amides, pyridine, and pyrimidine","volume":"109","author":"Wick","year":"2005","journal-title":"J. Phys. Chem. B"},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"21938","DOI":"10.1021\/jp0625053","article-title":"Monte carlo simulation of carboxylic acid phase equilibria","volume":"110","author":"Clifford","year":"2006","journal-title":"J. Phys. Chem. B"},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"306","DOI":"10.1007\/s008940100045","article-title":"GROMACS 3.0: A package for molecular simulation and trajectory analysis","volume":"7","author":"Lindahl","year":"2001","journal-title":"J. Mol. Model"},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"3684","DOI":"10.1063\/1.448118","article-title":"Molecular-dynamics with coupling to an external bath","volume":"81","author":"Berendsen","year":"1984","journal-title":"J. Chem. Phys"},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"10089","DOI":"10.1063\/1.464397","article-title":"Particle mesh ewald\u2014An n.log(n) method for Ewald sums in large systems","volume":"98","author":"Darden","year":"1993","journal-title":"J. Chem. Phys"},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"8577","DOI":"10.1063\/1.470117","article-title":"A smooth particle mesh Ewald method","volume":"103","author":"Essmann","year":"1995","journal-title":"J. Chem. Phys"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"29","DOI":"10.1080\/0892702031000065719","article-title":"Object-oriented programming paradigms for molecular modeling","volume":"29","author":"Gupta","year":"2003","journal-title":"Mol. Simul"},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"13742","DOI":"10.1021\/j100153a051","article-title":"Prediction of adsorption of aromatic-hydrocarbons in silicalite from grand-canonical monte-carlo simulations with biased insertions","volume":"97","author":"Snurr","year":"1993","journal-title":"J. Phys. Chem"},{"key":"ref_38","unstructured":"Frenkel, D, and Smit, B (2002). Understanding Molecular Simulation: From Algorithms to Applications, Academic Press. [2nd ed]."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"8254","DOI":"10.1063\/1.478738","article-title":"Exact method for the simulation of Coulombic systems by spherically truncated, pairwise r(-1) summation","volume":"110","author":"Wolf","year":"1999","journal-title":"J. Chem. Phys"},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"234104:1","DOI":"10.1063\/1.2206581","article-title":"Is the Ewald summation still necessary? Pairwise alternatives to the accepted standard for long-range electrostatics","volume":"124","author":"Fennell","year":"2006","journal-title":"J Chem Phys"},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"49","DOI":"10.1007\/s11224-008-9389-5","article-title":"An examination of the vaporization enthalpies and vapor pressures of pyrazine, pyrimidine, pyridazine, and 1,3,5-triazine","volume":"20","author":"Lipkind","year":"2009","journal-title":"Struct. Chem"},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"1035","DOI":"10.1246\/cl.1995.1035","article-title":"Thermodynamic considerations for the design of and ligand recognition by molecularly imprinted polymers","volume":"24","author":"Nicholls","year":"1995","journal-title":"Chem. Lett"},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"79","DOI":"10.1002\/(SICI)1099-1352(199812)11:1\/6<79::AID-JMR394>3.0.CO;2-B","article-title":"Towards the rational design of molecularly imprinted polymers","volume":"11","author":"Nicholls","year":"1998","journal-title":"J. Mol. Recogn"},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"1930","DOI":"10.1063\/1.1678513","article-title":"Optimized cluster expansions for classical fluids. II. Theory of molecular liquids","volume":"57","author":"Chandler","year":"1972","journal-title":"J. Chem. Phys"},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"383","DOI":"10.1080\/00268978200101291","article-title":"Interaction site models for molecular fluids","volume":"46","author":"Cummings","year":"1982","journal-title":"Mol. Phys"},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"141","DOI":"10.1016\/j.jchromb.2004.01.064","article-title":"Characterization of the heterogeneous binding site affinity distributions in molecularly imprinted polymers","volume":"804","author":"Umpleby","year":"2004","journal-title":"J. Chromatogr. B"}],"container-title":["International Journal of Molecular Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1422-0067\/12\/8\/4781\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T21:56:54Z","timestamp":1760219814000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1422-0067\/12\/8\/4781"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2011,7,28]]},"references-count":46,"journal-issue":{"issue":"8","published-online":{"date-parts":[[2011,8]]}},"alternative-id":["ijms12084781"],"URL":"https:\/\/doi.org\/10.3390\/ijms12084781","relation":{},"ISSN":["1422-0067"],"issn-type":[{"value":"1422-0067","type":"electronic"}],"subject":[],"published":{"date-parts":[[2011,7,28]]}}}