The interactions between each component of the pre-polymerisation mixtures used in the synthesis of molecularly imprinted polymers (MIP) specific for 1,2,3,4,5-pentachlorobenzene (1) and 1,2,3-trichlorobenzene (2) were examined in four molecular dynamics simulations. These simulations revealed that the relative frequency of functional monomer template (FM T) interactions was consistent with results obtained by the synthesis and evaluation of the actual MIPs. The higher frequency of 1 interaction with tri-methylstyrene (TMS; 54.7%) than 1 interaction with pentafluorostyrene (PFS; 44.7%) correlated with a higher imprinting factor (IF) of 2.1 vs. 1.7 for each functional monomer respectively. The higher frequency of PFS interactions with 2 (29.6%) than TMS interactions with 2 (1.9%) also correlated well with the observed differences in IF (3.7) of 2 MIPs imprinted using PFS as the FM than the IF (2,8) of 2 MIPs imprinted using TMS as the FM. The TMS-1 interaction dominated the molecular simulation due to high interaction energies, but the weaker TMS-2 resulted in low interaction maintenance, and thus lower IF values. Examination of the other pre-polymerisation mixture components revealed that the low levels of TMS-2 interaction was, in part, due to interference caused by the cross linker (CL) ethyleneglycol dimethylacrylate (EGDMA) interactions with TMS. The main reason was, however, attributed to MeOH interactions with TMS in both a hydrogen bond and perpendicular configuration. This positioned a MeOH directly above the it-orbital of all TMS for an average of 63.8% of MD2 creating significant interference to pi-pi stacking interactions between 2 and TMS. These findings are consistent with the deviation from the 'normal' molecularly imprinted polymer synthesis ratio of 1 : 4 : 20 (T : FM : CL) of 20 : 1 : 29 and 15 : 6 : 29 observed with 2 and TMS and PFS respectively. Our molecular dynamics simulations correctly predicted the high level of interference from other MIP synthesis components. The effect on PFS-1 interaction by MeOH was significantly lower and thus this system was not adversely affected.

Molecular imprinting is a technique used to design polymeric recognition materials with selectivity for a predetermined structure. The molecular imprinting process generates cavities in the polymer matrix that are complementary in size, shape and functionality to the template-structure. The recognition properties of molecularly imprinted polymers (MIPs) are comparable to those of antibodies and enzymes, which make MIPs utilizable in a wide range of application areas including biomimetic assays and biosensors [1]. Previous studies have shown that the prepolymerization step is central for the establishment of high affinity binding sites in MIPs [2]. However, our understanding of the physical mechanisms underlying MIP formation and template recognition is still limited. With the rapid increase of computational power and the development of suitable software molecular dynamics (MD) simulation methods have become a valuable theoretical tool to aid our understanding of the molecular imprinting process, and even in the development of rational design strategies [2]. Recently the first simulation of a complete prepolymerization mixture was presented [3].

Here we present 10 ns MD simulations of a series of all-component prepolymerization mixtures. The simulated systems were assembled with different molar ratios using the local anaesthetic bupivacaine as the template, methacrylic acid (MAA) as the functional monomer, ethylene glycol dimethacrylate (EGDMA) as the crosslinker, 2,2’-azobis-(2-methylpropionitrile) (AIBN) as the initiator and toluene as the solvent. The simulations were performed using the AMBER (v. 10.0 UCSF, San Francisco, CA) suite of programs (4) and the GAFF [6] force field. Molecular trajectories were evaluated with radial distribution functions and hydrogen bond analysis.

References

1. Alexander, C.; Andersson, H. S.; Andersson, L. I.; Ansell, R. J.; Kirsch, N.; Nicholls, I. A.; O´Mahony, J.; Whitcombe, J., J. Mol. Recognit. (2006), 19, 106-180
2. Nicholls, I. A.; Andersson, H. S.; Charlton, C.; Henschel, H.; Karlsson, B. C. G.; Karlsson, J. G.; O´Mahony, J.; Rosengren, A. M.; Rosengren, K. J.; Wikman, S. Biosens. Bioelectron. (2009), 25, 543-552
3. Karlsson, B. C. G.; O´Mahony, J.; Karlsson, J. G.; Bengtsson, H.; Eriksson, L. A.; Nicholls, I. A. J. Am. Chem. Soc. (2009), 131, 13297-13304
4. Case, D. A.; Cheatham, T. E.; Darden, T.; Gohlke, H.; Luo, R.; Merz, K. M.; Onufriev, A.; Simmerling, C.; Wang, B.; Woods, R. J. Comput. Chem. (2009), 26, 1668-1688
5. Wang, J.; Wolf, R. M.; Caldwell, J. W.; Kollman, P. A.; Case, D. A. J. Comput. Chem. (2004), 25, 1157-1174

Molecularly imprinted polymers (MIPs) are polymeric receptors with selectivity for a predetermined structure. The molecular imprinting process generates cavities in a synthetic polymer matrix that are complementary in size, shape and functionality to the template. MIPs exhibit recognition properties analogous to their biological counterparts, such as antibodies, and can be utilized in a wide range of application areas [1]. Nonetheless, the physical mechanisms underlying MIP formation and template recognition are still poorly understood. Molecular dynamics (MD) based computer simulations are a valuable theoretical tool which may be used to aid our understanding of the molecular imprinting process, and even for the development of rational design strategies [2]. Recently the first MD simulation of a complete prepolymerization mixture was presented [3].

In the present work, MD simulations of a series of all-component prepolymerization mixtures were performed, using the local anaesthetic bupivacaine as the template, methacrylic acid (MAA) as the functional monomer, ethylene glycol dimethacrylate (EGDMA) as the crosslinker, 2,2’-azobis-(2-methylpropionitrile) (AIBN) as the initiator and toluene as the solvent. The simulated systems differed in the molar fraction of MAA. Systems were evaluated with radial distribution functions and hydrogen bond analyses. By correlating the results with the rebinding behaviour of a series of synthesized MIPs the importance of the stoichiometry between template, functional monomer and crosslinker was highlighted. The analysis of the MD simulations revealed strong competition for hydrogen bonding between the carbonyl oxygen’s of MAA and EGDMA and the amide proton of bupivacaine. Moreover, the hydrogen bonding contact between EGDMA and bupivacaine remained nearly unaffected by the varied molar fraction MAA in the different systems demonstrating the role of the crosslinker being more important as generally accepted.

References

[1]             Alexander, C.; Andersson, H. S.; Andersson, L. I.; Ansell, R. J.; Kirsch, N.; Nicholls, I. A.; O´Mahony, J.; Whitcombe, J., J. Mol. Recognit., 19, 106-180 (2006)

[2]            Nicholls, I. A.; Andersson, H. S.; Charlton, C.; Henschel, H.; Karlsson, B. C. G.; Karlsson, J. G.; O´Mahony, J.; Rosengren, A. M.; Rosengren, K. J.; Wikman, S. Biosens. Bioelectron., 25, 543-552 (2009)

[3]            Karlsson, B. C. G.; O´Mahony, J.; Karlsson, J. G.; Bengtsson, H.; Eriksson, L. A.; Nicholls, I. A. J. Am. Chem. Soc., 131, 13297-13304 (2009)

Through the rapid increase in computational power and the development of suitable software, molecular dynamics (MD) has become a promising tool for use in the development of molecularly imprinted polymers (MIPs).¹ MD is a computational method based on Newtonian mechanics, which enables the simultaneous simulation of thousands of discrete molecules, and can be used to establish the states of the molecular species present in MIP-prepolymerization mixtures. As detailed understanding of the molecular basis for formation of high affinity MIP sites is still lacking and the physical mechanism underlying specific recognition is still a matter of debate, the use of MD as a tool to investigate MIP-prepolymerization mixtures is highly motivated.¹ Recently the first MD simulation of an all-component prepolymerization mixture was presented, which gave a detailed picture of the underlying monomer-template interactions important for the “molecular memory” in MIPs.²

Here, we present results obtained from a series of MD simulations representing all-component MIP/REF prepolymerization mixtures assembled with differences in stoichiometries of functional and crosslinking monomer. In these mixtures, the local anaesthetic drug bupivacaine was used as a template, methacrylic acid as the functional monomer, ethylene dimethacrylate as crosslinking monomer, 2,2’-azobis-(2-methylpropionitrile) as the initiator and toluene as the solvent. Bupivacaine complexation in each system was evaluated with radial distribution functions and hydrogen bond analyses. By correlating the results with the rebinding behaviour of a series of synthesized bupivacaine-MIPs, the relationship between the degree of crosslinking and MIP-performance was highlighted.

[1] Nicholls, I. A.; Andersson, H. S.; Charlton, C.; Henschel, H.; Karlsson, B. C. G.; Karlsson, J. G.; O´Mahony, J.; Rosengren, A. M.; Rosengren, K. J.; Wikman, S. Biosens. Bioelectron., 25, 543-552 (2009)

[2] Karlsson, B. C. G.; O´Mahony, J.; Karlsson, J. G.; Bengtsson, H.; Eriksson, L. A.; Nicholls, I. A. J. Am. Chem. Soc., 131, 13297-13304 (2009)

A combination of theoretical and experimental studies has provided correlations between molecularly imprinted polymer composition, morphology, and recognition behavior obtained using a series of bupivacaine-imprinted methacrylic acid (MAA)–ethylene glycol dimethacrylate copolymers differing in molar ratios of the respective monomers. Results extracted from analysis of molecular dynamics (MD) trajectory data demonstrated that stability and frequency of interactions between bupivacaine and the monomers in the prepolymerization phase were strongly affected by minor changes in polymer composition, which in turn affected binding site affinity and heterogeneity of the imprinted polymers. Moreover, through the characterization of polymer morphology, we show that higher molar fractions of MAA resulted in polymeric materials with increased pore size, a feature that enhanced the binding capacity of the polymers. Furthermore, the results presented point at the strength of MD for predicting MIP-template binding capacity and affinity.

In this report, we have investigated factors contributing to the morphology and template recognition of bupivacaine-imprinted copolymers of methacrylic acid (MAA) and ethyleneglycol dimethacrylate (EGDMA). To this end, MAA, the most commonly used functional monomer in non-covalent molecular imprinting protocols, was compared and contrasted with the closely related acrylic acid (AA) in terms of polymer morphologies, recognition characteristics, and molecular level events in the corresponding pre-polymerization mixtures. Two series of analogous bupivacaine-imprinted EGDMA-copolymers containing increasing fractions of either AA or MAA were studied through all-component MD simulations in the pre-polymerization phase, equilibrium binding experiments on corresponding synthesized polymers and morphology characterization by N2-sorption measurements. A higher degree of hydrogen bonding frequency between respective functional monomer and bupivacaine was recorded for the mixtures containing AA compared to those containing MAA. In contrast, results from binding experiments demonstrated higher binding capacities for the polymers prepared with MAA than for those prepared with AA, which is explained by differences in polymer morphology. The surface areas and pore volumes of the AA-polymers were higher than for the MAA-polymers and the overall pore structure in the AA-polymers was ink-bottle shaped while the pores in the MAA-polymers were slit-shaped. We suggest that the methyl substituent of MAA contributes to differences in the reaction kinetics for AA and MAA during polymerization and resulted in different morphologies, in particular pore shape, which affected mass-transfer and consequently the binding qualities of the materials. © 2017 Elsevier Ltd

The role of the structural diversity of the widely used anticoagulant drug warfarin on its distribution in 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) bilayer membranes was investigated using a series of both restrained (umbrella sampling) and unrestrained molecular dynamics simulations. Data collected from unrestrained simulations revealed favorable positions for neutral isomers of warfarin, the open side chain form (OCO), and the cyclic hemiketal (CCO), along the bilayer normal close to the polar headgroup region and even in the relatively distant nonpolar lipid tails. The deprotonated open side chain form (DCO) was found to have lower affinity for the DOPC bilayer membrane relative to the neutral forms, with only a small fraction interacting with the membrane, typically within the polar headgroup region. The conformation of OCO inside the lipid bilayer was found to be stabilized by intramolecular hydrogen bonding thereby mimicking the structure of CCO. Differences in free energies, for positions of OCO and CCO inside the bilayer membrane, as compared to positions in the aqueous phase, were −97 and −146 kJ·mol^–1. Kinetic analysis based on the computed free energy barriers reveal that warfarin will diffuse through the membranes within hours, in agreement with experimental results on warfarin’s accumulation in the plasma, thus suggesting a passive diffusion mechanism. We propose that this membrane transport may be an isomerization-driven process where warfarin adapts to the various local molecular environments encountered under its journey through the membrane. Collectively, these results improve our understanding of the influence of warfarin’s structural diversity on the drug’s distribution and bioavailability, which in turn may provide insights for developing new formulations of this important pharmaceutical to better address its narrow therapeutic window.

Warfarin is an oral anticoagulant drug used to prevent thrombolic disorders such as myocardial infarction and stroke by inhibiting the active site of vitamin-K dependent epoxide reductase (VKOR) [1]. Despite being in widespread use and having a narrow therapeutic window, its mechanisms of action are not yet fully understood and incorrect warfarin dosage often leads to severe side effects. A factor limiting our understanding of warfarin’s bioavailability is warfarin’s structural diversity, which has been shown to be strongly affected by the nature of molecular environment e.g. solvent polarity and pH [2-7]. One of the major factors contributing to a drug’s biological effect is membrane transport, a process involving exposure of warfarin to environments of quite different character. Since a drug’s transport across membrane may include both active transport by carriers as well as diffusion-controlled processes, it may be envisaged that in order to fully predict warfarin’s anticoagulant effect these mechanisms must be carefully elucidated.

Molecular dynamics (MD) simulations have previously been performed in order to obtain detailed information on static equilibrium as well as dynamic properties of small organic drugs in biomembranes. One of the most studied lipids in cell membrane simulations has been dipalmitoylphosphatidylcholine (DPPC) which is the most abundant phospholipid in cell membranes. Here we present lipid bilayer membrane transport properties for a series of warfarin structures previously reported in the literature using a fully solvated DPPC membrane model. Data extracted from simulations shed light on differences in membrane partioning as well as mobilities of warfarin isomers studied and a mechanism by which warfarin permeates through membranes in vivo is presented.

References

1. Landefeld, C.; Beyth, R. Am. J. Med. 1993, 95, 315-328.
2. Karlsson, B. C. G.; Rosengren, A. M.; Andersson, P. O.; Nicholls, I. A. J. Phys. Chem. B 2007, 111, 10520-10528.
3. Karlsson, B. C. G.; Rosengren, A. M.; Andersson, P. O.; Nicholls, I. A. J. Phys. Chem. B 2009, 113, 7945-7949.
4. Karlsson, B. C. G.; Rosengren, A. M.; Näslund, I.; Andersson, P. O.; Nicholls, I. A. Submitted 2010.
5. Rosengren, A. M.; Karlsson, B. C. G.; Näslund, I.; Andersson, P. O.; Nicholls, I. A. Submitted 2010.
6. Nicholls, I. A.; Karlsson, B. C. G.; Rosengren, A. M.; Henschel, H. J. Mol. Recognit. 2010, In press.
7. Henschel, H.; Karlsson, B. C. G.; Rosengren, A. M.; Nicholls, I. A. Submitted 2010.

Oxytocin imprinted polymer nanoparticles were synthesized by glass bead supported solid phase synthesis, with NMR and molecular dynamics studies used to investigate monomer-template interactions. The nanoparticles were characterized by dynamic light scattering, scanning- and transmission electron microscopy and X-ray photoelectron spectroscopy. Investigation of nanoparticle-template recognition using quartz crystal microbalance-based studies revealed sub-nanomolar affinity, k(d) approximate to 0.3 +/- 0.02 nM (standard error of the mean), comparable to that of commercial polyclonal antibodies, k(d) approximate to 0.02-0.2 nM.

In principle, molecularly imprinted polymer science and technology provides a means for ready access to nano-structured polymeric materials of predetermined selectivity. The versatility of the technique has brought it to the attention of many working with the development of nanomaterials with biological or biomimetic properties for use as therapeutics or in medical devices. Nonetheless, the further evolution of the field necessitates the development of robust predictive tools capable of handling the complexity of molecular imprinting systems. The rapid growth in computer power and software over the past decade has opened new possibilities for simulating aspects of the complex molecular imprinting process. We present here a survey of the current status of the use of in silico-based approaches to aspects of molecular imprinting. Finally, we highlight areas where ongoing and future efforts should yield information critical to our understanding of the underlying mechanisms sufficient to permit the rational design of molecularly imprinted polymers.

The development of in silico strategies for the study of the molecular imprinting process and the properties of molecularly imprinted materials has been driven by a growing awareness of the inherent complexity of these systems and even by an increased awareness of the potential of these materials for use in a range of application areas. Here we highlight the development of theoretical and computational strategies that are contributing to an improved understanding of the mechanisms underlying molecularly imprinted material synthesis and performance, and even their rational design.

Recent years have witnessed a dramatic increase in the use of theoretical and computational approaches in the study and development of molecular imprinting systems. These tools are being used to either improve understanding of the mechanisms underlying the function of molecular imprinting systems or for the design of new systems. Here, we present an overview of the literature describing the application of theoretical and computational techniques to the different stages of the molecular imprinting process (pre-polymerization mixture, polymerization process and ligand-molecularly imprinted polymer rebinding), along with an analysis of trends within and the current status of this aspect of the molecular imprinting field.

The need for materials with predetermined ligand-selectivities for use in sensing and separation technologies, e.g. membranes and chromatography, has driven the development of molecularly imprinted polymer science and technology. Over recent years, the need to develop robust predictive tools capable of handling the complexity of molecular imprinting systems has become apparent The current status of the use of in silica techniques in molecular imprinting is here presented, and we highlight areas where new developments are contributing to improvements in the rational design of molecularly imprinted polymers.

Theoretical and computational studies of molecular imprinting have helped provide valuable insights concerning the nature of the molecular-level events underlying the recognition characteristics of molecularly imprinted materials. Here, we first present an overview of a thermodynamic treatment of factors governing the behaviour of these functional materials, and then a summary of the development and current status of the use of computational strategies for studying aspects of molecular imprinting and the resulting material properties.

The risks to society associated with the spread of new strains of influenza with human pathogenicity, or with impact on agricultureare significant. Our capacity to challenge the threat of the virus is dependent upon our ability to develop new vaccines, and upon ouraccess to effective virus-targeted small molecule pharmaceuticals. The current primary small molecule weapons oseltamivir(Tamiflu) and zanamivir (Relenza) currently form our last line of defence against this virus. More recently, the identification ofstrains resistant to (in particular) drugs targeting neuraminidase has awoken serious concern. Equally as worrying is the clearevidence of the presence of these substances in the World’s water systems which has now come forth. Collectively, this makes thedevelopment of techniques giving us better insight into the virus and antiviral agents a priority. Robust methods for the rapid andsensitive determination of these substances are required, especially as the monitoring methods should be able to withstand therigours of environments not normally conducive to biomacromolecules (temperature, toxic substances etc) e.g. antibodies.Advanced materials fulfilling these requirements can be obtained by Molecular Imprinting, which is a technique forproducing highly selective synthetic receptors for biochemical and chemical structures in synthetic polymers. The polymerscontain nano-structured cavities that are of complementary functional and structural character to predetermined target.The technique entails the judicious selection of a monomer or monomer mixture with chemical functionality comple-mentary to that of the imprint species (template). The complementary interacting functionalities (reversible covalent ornon-covalent) form predictable solution structures, which after polymerisation in the presence of a suitable cross linkingagent and removal of the template lead to the defining of recognition sites of complementary steric and functionaltopography to the template molecule. These sites give selective recognition of the template. Furthermore, by analogy tocatalytic antibody production, using transition state analogues as templates yields synthetic enzymes.Synthetic polymers with neuraminidase-like behaviour have been designed through the screening of candidate polymersystems using a combination of molecular dynamics and NMR studies. The characterisation of the resulting materials hasdemonstrated systems with selectivity for the targeted antiviral agents. Our studies illustrate the potential of these uniquenanostructured materials for the monitoring of these antiviral agents in the environment, which is an important aspect inefforts aimed at limiting the development of resistant strains, and as a tool for policy makers.

In this study, computational methods were employed in efforts to elucidate physical mechanisms underlying the ligand selectivity of polymeric sorbents produced through the molecular imprinting of 17-beta-estradiol. Previous computational and experimental studies had identified candidate systems applicable to the development of synthetic polymeric receptors for the detection and possible removal of pollutants with endocrine-disrupting properties. Here we present a series of comprehensive molecular dynamics studies of candidate molecular imprinting prepolymerization systems. The results from the studies highlight the role of the cross-linker and the importance of the interplay between functionalities of the various monomers employed in template complexation. The significance of these results for future studies is discussed.

A series of molecular dynamics simulations of prepolymerization mixtures for phenylalanine anilide imprinted co-(ethylene glycol dimethacrylate-methacrylic acid) molecularly imprinted polymers have been employed to investigate the mechanistic basis for template selective recognition in these systems. This has provided new insights on the mechanisms underlying template recognition, in particular the significant role played by the crosslinking agent. Importantly, the study supports the occurrence of template self-association events that allows us to resolve debate between the two previously proposed models used to explain this system's underlying recognition mechanisms. Moreover, the complexity of the molecular level events underlying template complexation is highlighted by this study, a factor that should be considered in rational molecularly imprinted polymer design, especially with respect to recognition site heterogeneity.

It is now widely accepted that the recognition properties of a MIP are derived from molecular level events present during the prepolymerization stage.¹ Studies regarding the nature and extent of template complexation during this stage should therefore yield valuable information regarding the template recognition properties of the final MIP. One method of great potential for illuminating molecular level details in this area of MIP research is molecular dynamics (MD).² MD simulations enable studies of molecular-level events in MIP prepolymerization mixtures.

Phenylalanine anilide (PA) is a molecule that has been extensively used as a template in a series of seminal molecular imprinting studies.^3-5 In an effort to elucidate the origin to the imprinting effect, Sellergren, Lepistö and Mosbach proposed that selective high-affinity sites in the PA-MIP were based on functional monomer-template complexation of a 2:1 stoichiometry.³ In a follow-up study, Katz and Davis presented results that revealed further information regarding the origin of recognition in PA-MIPs.⁵ It was suggested that the template recognition sites were based on functional monomer-template complexes of 1:1 stoichiometry, and also that the formation of higher order template-template complexes has important effects on the final PA-MIP recognition properties. In light of this conjecture and several more recent studies highlighting the diversity of template complexation mechanisms in prepolymerization mixtures, have pointed at the complexity and diversity in the ensemble of complexes leading to the final “molecular memory”.

Here we present the novel insights into the molecular basis for PA-MIP template recognition derived from a series of MD simulations of the PA-MIP prepolymerisation systems. Data support the presence of PA-PA complexes and that the most statistically prevalent stoichiometry functional monomer-PA complexes was 1:1. The role of cross-linker is also discussed. This study highlights the potential of all component MD studies for rational MIP design.

(1)      Alexander, C.; Andersson, H.S.; Andersson, L.I.; Ansell, R.J.; Kirsch, N.; Nicholls, I.A.; O'Mahony, J.; Whitcombe, M.J.  Molecular imprinting science and technology: A survey of the literature for the years up to and including 2003. Journal of Molecular Recognition 2006, 19, 106-180.

(2)      Nicholls, I.A.; Andersson, H.S.; Charlton, C; Henschel, H.; Karlsson, B.C.G.; Karlsson, J.G.; O’Mahony, J.; Rosengren, A.M.; Rosengren, J.K.; Wikman, S. Theoretical and computational stratgies for rational molecularly imprinted polymer design. Biosensors and Bioelectronics 2009, 25, 543-552

(3)      Sellergren, B.; Lepistoe, M.; Mosbach, K.. Highly enantioselective and substrate-selective polymers obtained by molecular imprinting utilizing noncovalent interactions. NMR and chromatographic studies on the nature of recognition. Journal of American Chemical Society 1988, 110, 5853-5860

(4)      Sellergren, B.. Molecular imprinting by noncovalent interactions: Tailor-made chiral stationary phases of high selectivity and sample load capacity. Chirality 1989, 1, 63-68

(5)      Katz, A.; Davis, M.E. Investigations into the mechanism of molecular recognition with imprinted polymers. Macromolecules 1999, 32, 4113-4121

In this work, classical molecular dynamics (MD) simulations have been used to provide unique insights on the nature and extent of intermolecular interactions present in a phenylalanine anilide (PA) molecularly imprinted polymers (MIP) prepolymerization mixture.

Molecular Imprinting is a technique for producing highly selective synthetic receptors for a predetermined molecular structure, and involves the formation of cavities in a synthetic polymer matrix that are of complementary functional and structural character to a template molecule.¹ It is generally accepted that the recognition properties of a MIP is a product of the interactions between monomers and template during the prepolymerization stage. Accordingly, studies of the nature and extent of the interactions present in prepolymerization mixtures, in patricular those involving template, should yield information which can be related to the observed recognition properties of the final MIP.

Phenylalanine anilide MIPs have been the subject of a significant number of studies aimed at producing an understanding of the mechanisms underlying the recognition processes. Interestingly, two different models have been proposed to explain the behaviour of PA-MIPs. Studies by Sellergren et al. proposed that template selectivity, was a consequence of  the presence of a functional monomer-template complexes of 2:1 stoichiometry.² Later, however, Katz and Davis proposed an alternative model,³ where the template (PA) recognition sites in the MIP were suggested to arise from functional monomer-template complexes of 1:1 stoichiometry in combination with the presence of higher order template-template complexes.

To resolve this conjecture, we performed a series of MD studies, the results of which demonstrated both the presence of PA-PA self association complexes, and that the most statistically prevalent monomer-PA complex stoichiometry was of a 1:1 nature, though differetn in character from that proposed by Katz and Davis.  Moreover, the role of cross-linker in forming recognition sites was apparnet in these studies, a fact not previously considered.

References

1. Alexander C, Andersson HS, Andersson LI, Ansell RJ, Kirsh N, Nicholls IA, O’Mahony J, Whitcombe MJ. Molecular imprinting science and technology: A survey of the literature for the years up to and including 2003. Journal of Molecular Recognition 2006;19:106-180
2. Sellergren B, Lepistö M, Mosbach K. Highly enantioselective and substrate selective polymers obtained by molecular imprinting utilizing noncovalent interactions. NMR and chromatographic studies on the nature of recognition. Journal of the American Chemical Society 1988;110:5853-5860
3. Katz A, Davis ME. Investigations into the mechanisms of molecular recognition with imprinted polymers. Macromolecules 1999;32:4113-4121

The molecular imprinting technique has received significant attention due to its utility in the production of synthetic polymeric materials with predetermined ligand recognition properties [1].

It is generally accepted that the recognition properties of a molecularly imprinted polymer (MIP) is established during the prepolymerization stage. Previous investigations on the nature and extent of template prepolymerization complexation in a phenylalanine anilide (PA) MIP pointed at the complexity and diversity in the ensemble of complexes leading to the final “molecular memory”. In particular, conflicting models have been used to explain the observed molecular memory. Sellergren, Lepistö and Mosbach [2] proposed that selective, high-affinity sites in the final MIP were based on functional monomer-PA complexation of a 2:1 stoichiometry. Later, Katz and Davis [3] proposed that the template recognition sites arose due to a 1:1 functional monomer-template complex stoichiometry and that the effect of template dimerization is critical for the observed PA-MIP recognition properties.

In this study, we have attempted to shed new light on this as yet unresolved conflict using a series of molecular dynamics (MD) simulations. Results demonstrated the presence of PA-PA complexes and that the most statistically prevalent stoichiometry of functional monomer-PA complexes was of 1:1.

[1]             Alexander C, Andersson HS, Andersson LI, Ansell R, Kirsch N, Nicholls IA et al. Molecular imprinting science and technology: a survey of the literature for the years up to and including 2003, Journal of Molecular Recognition, 19, 106-180 (2006).

[2]            Sellergren B, Lepistö M, Mosbach K. Highly enantioselective and substrate selective polymers obtained by molecular imprinting utilizing noncovalent interactions. NMR and chromatographic studies on the nature of recognition, Journal of the American Chemical Society, 110, 5853-5860 (1988).

[3]             Katz A, Davis ME. Investigations into the mechanisms of molecular recognition with imprinted polymers, Macromolecules, 32, 4113-4121 (1999).

The aim of this study was to develop protocols for and evaluate the use of all-atom full system molecular dynamic (MD) simulations of emulsion systems in the development of molecularly imprinted polymers (MIPs). Here, we report on the first, to the best of our knowledge, use of all-component MD studies to simulate and evaluate MIP miniemulsion prepolymerization mixtures; in this case, the mixtures used in the synthesis of a series of MIP-nanoparticles (MIP-NPs).

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.

Polymeric sorbents targeting endocrine-disrupting estrogen active compounds (EAC) were prepared by terpolymer imprinting using 17 beta-estradiol (E2) as template. From a group of eight functional monomers representing Bronsted acids, bases, hydrogen-bond donors and acceptors, as well as pi-interacting monomers, a terpolymer library that comprises all possible binary combinations of the functional monomers was prepared. Binding tests revealed that imprinted polymers exhibit a markedly higher affinity for E2 compared to nonimprinted polymers (NIPs) or polymers prepared by using single functional monomers. A combination of methacrylic acid (MAA) and p-vinylbenzoic acid offered a particularly promising lead polymer, displaying an imprinting factor of 17 versus 2.4 for a benchmark polymer prepared by using only MAA as functional monomer. The saturation capacities ascribed to imprinted sites were four to five times higher for this polymer compared to previously reported imprinted polymers. NMR titrations and molecular dynamics simulations corroborated these results, indicating an orthogonal preference of the two functional monomers with respect to the E2 3-OH and 17-OH groups. The optimized polymer exhibited a retentivity for EACs that correlates with their inhibitory effect on the natural receptor. By using the optimized molecularly imprinted polymers (MIPs) in a model water-purification system, they were capable of completely removing ppb levels of a small group of EACs from water. This is in contrast to the performance of nonimprinted polymers and well-established sorbents for water purification (e.g., active carbon), which still contained detectable amounts of the compounds after treatment.

The design of artificial oxyanion receptors with switchable ion preference is a challenging goal in host-guest chemistry. We here report on molecularly imprinted polymers (MIPs) with an external phospho-sulpho switch driven by small molecule modifiers. The polymers were prepared by hydrogen bond-mediated imprinting of the mono- or dianions of phenyl phosphonic acid (PPA), phenyl sulfonic acid (PSA), and benzoic acid (BA) using N-3,5-bis-(trifluoromethyl)-phenyl-N-4-vinyl-phenyl urea (1) as the functional host monomer. The interaction mode between the functional monomer and the monoanions was elucidated by H-1 NMR titrations and H-1-H-1 NMR NOESY supported by molecular dynamic simulation, which confirmed the presence of high-order complexes. PPA imprinted polymers bound PPA with an equilibrium constant K-eq = 1.8 x 10(5) M-1 in acetonitrile (0.1% 1,2,2,6,6-pentamethylpiperidine) and inorganic HPO42- and SO42- with K-eq = 2.9 X 10(3) M-1 and 4.5 X 10(3) M-1, respectively, in aqueous buffer. Moreover, the chromatographic retentivity of phosphonate versus sulfonate was shown to be completely switched on this polymer when changing from a basic to an acidic modifier. Mechanistic insights into this system were obtained from kinetic investigations and DSC-, MALDI-TOF-MS-, H-1 NMR-studies of linear polymers prepared in the presence of template. The results suggest the formation of template induced 1-1 diad repeats in the polymer main chain shedding unique light on the relative contributions of configurational and conformational imprinting.

Fundamental studies of molecularly imprinted polymer¹ (MIP) systems are necessary in order to facilitate the development of the field in general, in particular through the development of rational MIP design strategies.² Recent efforts using molecular dynamics studies of all-component molecular imprinting systems have demonstrated the unique insights that can be obtained regarding the massive diversity of interactions present in a given system.³

One of the most widely used templates in molecular imprinting is the beta-blocker propranolol.^4-8 Its use in fundamental studies and for providing proof-of-principle cases has been motivated by a number of factors including its clinical relevance, its inherent chirality, and availability in enantiomerically pure and radio-labelled forms. Significant efforts have been made to map the molecular basis for propranolol-MIP ligand recognition, though never through the simultaneous study of all components present during polymerization.

Here we present the first all component MD study of this system which has provided unique insights concerning, in particular the role of cross-linking agent on template complexation. Through correlations with recognition data, consequences for MIP design are proposed.

(1)      Alexander, C.; Andersson, H.S.; Andersson, L.I.; Ansell, R.J.; Kirsch, N.; Nicholls, I.A.; O'Mahony, J.; Whitcombe, M.J. J. Mol. Recognit. 2006, 19, 106-180.

(2)      Nicholls, I. A.; Andersson, H. S.; Charlton, C.; Henschel, H.; Karlsson, B. C. G.; Karlsson, J. G.; O´Mahony, J.; Rosengren, A. M.; Rosengren, K. J.; Wikman, S. Biosens. Bioelectron. 2009, 25, 543-552.

(3)      Karlsson, B. C. G.; O´Mahony, J.; Karlsson, J. G.; Bengtsson, H.; Eriksson, L. A.; Nicholls, I. A. J. Am. Chem. Soc., 2009, 131, 13297-13304.

(4)      Andersson, L.I. Anal. Chem. 1996, 68, 111-117.

(5)      Schweitz, L.; Andersson, L.I.; Nilsson, S. Anal. Chem. 1997, 69, 1179-1183.

(6)      Haupt, K.; Noworyta, K.; Kutner, W. Anal. Commun. 1999, 36, 391-393.

(7)      Philip, J.Y.N.; Buchweishaija, J.; Mkayula, L.L.; Ye, L. J. Agric Food Sci. 2007, 55, 8870-8876.

(8)      Nguyen, T.H.; Ansell, R.J. Org. Biomol. Chem. 2009, 7, 1211-1220.

All-component molecular dynamics studies were used to probe a library of oseltamivir molecularly imprinted polymer prepolymerization mixtures. Polymers included one of five functional monomers (acrylamide, hydroxyethylmethacrylate, methacrylic acid, 2-(triflouromethyl)acrylic acid, 4-vinylpyridine) and one of three porogens (acetonitrile, chloroform, methanol) combined with the crosslinking agent ethylene glycol dimethacrylate and initiator 2,2'-azobis(2-methylpropionitrile). Polymers were characterized by nitrogen gas sorption measurements and SEM, and affinity studies performed using radioligand binding in various media. In agreement with the predictions made from the simulations, polymers prepared in acetonitrile using either methacrylic or trifluoromethacrylic acid demonstrated the highest affinities for oseltamivir. Further, the ensemble of interactions observed in the methanol system provided an explanation for the morphology of polymers prepared in this solvent. The materials developed here offer potential for use in solid-phase extraction or for catalysis. The results illustrate the strength of this in silico strategy as a potential prognostic tool in molecularly imprinted polymer design.

Aspects of the molecular-level basis for the function of ethylene glycol dimethacrylate and trimethylolproprane trimethacrylate crosslinked methacrylic acid copolymers molecularly imprinted with (S)-propranolol have been studied using a series of all-component and all-atom molecular dynamics studies of the corresponding prepolymerization systems. The crosslinking agents were observed to contribute to template complexation, and the results were contrasted with previously reported template-recognition behavior of the corresponding polymers. Differences in the extent to which the two crosslinkers interacted with the functional monomer were identified, and correlations were made to polymer-ligand recognition behavior and the results of nuclear magnetic resonance spectroscopic studies studies. This study demonstrates the importance of considering the functional monomer-crosslinker interaction when designing molecularly imprinted polymers, and highlights the often neglected general contribution of crosslinker to determining the nature of molecularly imprinted polymer-template selectivity.

A family of non-ionic deep eutectic liquids has been developed based upon mixtures of solid N-alkyl derivatives of urea and acetamide that in some cases have melting points below room temperature. The eutectic behaviour and physical characteristics of a series of eleven eutectic mixtures are presented, along with a molecular dynamics study-supported hypothesis for the origin of the non-ideal mixing of these substances. Their use as solvents in applications ranging from natural product extraction to organic and polymer synthesis are demonstrated.

Controlled on-surface synthesis of polymer films using amide-based, environmentally friendly, nonionic deep eutectic solvents (ni-DESs) has been developed to regulate the porous features of the films. An appropriate combination of acetamide (A), urea (U), and their methyl derivatives (N-methylacetamide (NMA) and N-methylurea (NMU)) was used to prepare ni-DES. Polymer films were electrosynthesized using 4-aminobenzoic acid (4-ABA) and pyrrole as monomers in ni-DESs. We presumed that the flickering-cluster-like complexes and the extended H-bond networks in ni-DESs enhance the porosity of the polymer films, thus improving permeability features, as reflected in sensor performance. Electrosynthesized polymer films, imprinted with biotin templates (MIPs), have been tested as receptors for biotinylated targets. Molecular dynamics simulations of the prepolymerization mixture revealed the formed complexes between 4-ABA and biotin comprising high-frequency H-bonds. X-ray photoelectron spectroscopy (XPS) and reflection absorption infrared spectroscopy (RAIRS) studies revealed the structural integrity in the polymer films irrespective of the medium. Scanning electron microscopy (SEM) and electrochemical impedance spectroscopy (EIS) measurements showed a highly corrugated and porous nature for MIPA-U and MIPNMU-U when prepared in A-U and NMU-U ni-DESs. Atomic force microscope (AFM) studies support these observations, displaying an enhancement in the surface roughness from 1.44 nm (MIPaqueous) to 23.6 nm (MIPNMU-U). QCM analysis demonstrated a remarkable improvement in sensitivity of MIPA-U (17.99 +/- 0.72 Hz/mM) and MIPNMU-U (18.40 +/- 0.81 Hz/mM) films toward the biotin methyl ester (BtOMe, biotin derivative) than the MIPaqueous film. The chemosensor devised with the above MIP recognition films selectively recognized BtOMe (LOD = 12.5 ng/mL) and biotinylated biomolecules, as shown by the stability constant K-s values (MIPA-U = 1442 and MIPNMU-U = 1502 M-1). The porous network generated in the polymer films by the flickering-cluster-like complexes present in the ni-DES facilitates the analyte diffusion and recognition. We propose this ni-DES as an economically advantageous and environmentally friendly alternative to conventional ionic liquids and organic solvents in polymer synthesis and to influence polymer morphology for developing hierarchical materials.