Computer simulation of volatile organic compound adsorption in atomistic models of molecularly imprinted polymers

Molecularly imprinted electrochemical sensor to sensitively detect tetramethylpyrazine in Baijiu

Tetramethylpyrazine (TMP) is a compound known for its natural health benefits, but current detection methods for TMP are overly expensive and time-consuming. In this study, we developed functional materials with TMP molecular recognition properties using molecularly imprinted technology. As TMP does not produce electrochemical signals in the detection potential range, hexacyanoferrate was selected as a redox probe, combined with the highly conductive polymer PEDOT:PSS to enhance electrode conductivity. When coupled with the TMP-specific functional materials prepared through molecular imprinting, an electrochemical sensor specifically recognizing TMP was successfully developed, and this was confirmed through characterization techniques such as ultraviolet spectroscopy and scanning electron microscopy. Additionally, the crucial experimental parameters were optimized for improved performance. Under optimal conditions, the use of differential pulse voltammetry (DPV) to measure the peak currents of hexacyanoferrate showed a linear relationship with TMP concentrations from 0.50 × 10-6 to 5.00 × 10-3 M, achieving a detection limit of 2.1 × 10-7 M. This method proved effective for quantifying TMP in Baijiu samples, demonstrating good precision with relative standard deviations (RSD) ranging from 2.71% to 3.28%, and recovery percentages between 95.77% and 101.88%. These results indicate the potential of the molecularly imprinted polymer (MIP) sensor for accurately measuring TMP in actual samples.

Rational In Silico Design of Molecularly Imprinted Polymers: Current Challenges and Future Potential

The rational design of molecularly imprinted polymers has evolved along with state-of-the-art experimental imprinting strategies taking advantage of sophisticated computational tools. In silico methods enable the screening and simulation of innovative polymerization components and conditions superseding conventional formulations. The combined use of quantum mechanics, molecular mechanics, and molecular dynamics strategies allows for macromolecular modelling to study the systematic translation from the pre- to the post-polymerization stage. However, predictive design and high-performance computing to advance MIP development are neither fully explored nor practiced comprehensively on a routine basis to date. In this review, we focus on different steps along the molecular imprinting process and discuss appropriate computational methods that may assist in optimizing the associated experimental strategies. We discuss the potential, challenges, and limitations of computational approaches including ML/AI and present perspectives that may guide next-generation rational MIP design for accelerating the discovery of innovative molecularly templated materials.

Multifunctional Lanthanide-Based Metal-Organic Frameworks Derived from 3-Amino-4-hydroxybenzoate: Single-Molecule Magnet Behavior, Luminescent Properties for Thermometry, and CO2 Adsorptive Capacity

Herein, we describe and study a new family of isostructural multifunctional metal–organic frameworks (MOFs) with the formula {[Ln₅L₆(OH)₃(DMF)₃]·5H₂O}_n (where (H₂L) is 3-amino-4-hydroxybenzoic acid ligand) for magnetism and photoluminescence. Interestingly, three of the materials (Dy-, Er-, and Yb-based MOFs) present single-molecule magnet (SMM) behavior derived from the magnetic anisotropy of the lanthanide ions as a consequence of the adequate electronic distribution of the coordination environment. Additionally, photoluminescence properties of the ligand in combination with Eu and Tb counterparts were studied, including the heterometallic Eu–Tb mixed MOF that shows potential as ratiometric luminescent thermometers. Finally, the porous nature of the framework allowed showing the CO₂ sorption capacity.

A new family of isostructural multifunctional metal−organic frameworks has been described and studied for magnetism and photoluminescence. Interestingly, some materials present single-molecule magnet behavior, and photoluminescence properties of the ligand in combination with Eu and Tb counterparts were studied, including the heterometallic Eu−Tb mixed MOF that shows potential as ratiometric luminescent thermometers. Finally, the porous nature of the framework allowed showing the CO₂ sorption capacity.

Comparison and recent progress of molecular imprinting technology and dummy template molecular imprinting technology

Molecular imprinting technology for the preparation of polymers with specific molecular recognition function had become one of the current research hotspots. It has been widely applied in chromatographic separation, antibody and receptor mimetics, solid-phase extraction, bio-sensors, and other fields in the last decades. In this study, molecular imprinting technology was summarized from the points of templates and dummy templates, and four typical target analytes were selected to compare the differences between templates and dummy templates. The current status and prospects of molecular imprinting technology were also proposed.

Single-Crystal-to-Single-Crystal Cluster Transformation in a Microporous Molybdoarsenate(V)-Metalorganic Framework

The hybrid compound [Cu(cyclam)(H₂O)₂]_0.5[{Cu(cyclam)}_1.5{B-H₂As₂Mo₆O₂₆(H₂O)}]·9H₂O (1) (cyclam = 1,4,8,11-tetraazacyclotetradecane) was synthesized in aqueous solution by reacting the {Cu(cyclam)}²⁺ complex with a mixture of heptamolybdate and an arsenate(V) source. Crystal packing of 1 exhibits a supramolecular open-framework built of discrete covalent molybdoarsenate/metalorganic units and additional [Cu(cyclam)(H₂O)₂]²⁺ cations, the stacking of which generates squarelike channels parallel to the z axis with an approximate cross section of 10 × 11 Ų where all the hydration water molecules are hosted. Thermal evacuation of solvent molecules yields a new anhydrous crystalline phase, but compound 1 does not preserve its single-crystalline nature upon heating. However, when crystals are dehydrated under vacuum, they undergo a structural transformation that proceeds via a single-crystal-to-single-crystal pathway, leading to the anhydrous phase [{Cu(cyclam)}₂(A-H₂As₂Mo₆O₂₆)] (2). Total dehydration results in important modifications within the inorganic cluster skeleton which reveals an unprecedented solid-state B to A isomerization of the polyoxoanion. This transition also involves changes in the Cu^II bonding scheme that lead to covalent cluster/metalorganic layers by retaining the open-framework nature of 1. Compound 2 adsorbs ambient moisture upon air exposure, but it does not revert back to 1, and the hydrated phase [{Cu(cyclam)}₂(A-H₂As₂Mo₆O₂₆)]·6H₂O (2h) is obtained instead. Structural variations between 1 and 2 are reflected in electron paramagnetic resonance spectroscopy measurements, and the permanent microporosity of 2 provides interesting functionalities to the system such as the selective adsorption of gaseous CO₂ over N₂.

A supramolecular open framework built of copper(II)-complexes of a macrocyclic tetraaza ligand and arsenomolybdate anions undergoes a single-crystal-to-single-crystal transformation upon dehydration that implies an unprecedented solid state cluster isomerization. The permanent porosity of the system allows the selective adsorption of CO₂ over N₂.

Optimization of Cortisol-Selective Molecularly Imprinted Polymers Enabled by Molecular Dynamics Simulations

Today, we heavily rely on technology and increasingly utilize it to monitor our own health. The identification of sensitive, accurate biosensors that are capable of real-time cortisol analysis is one important potential feature for these technologies to aid us in the maintenance of our physical and mental wellbeing. Detection and quantification of cortisol, a well-known stress biomarker present in sweat, offers a noninvasive and potentially real-time method for monitoring anxiety. Molecularly imprinted polymers are attractive candidates for cortisol recognition elements in such devices as they can selectively rebind a targeted template molecule. However, mechanisms of imprinting and subsequent rebinding depend on the choice and composition of the prepolymerization mixture where the molecular interactions between the template, functional monomer, cross-linker, and solvent molecules are not fully understood. Here, we report the synthesis and evaluation of a molecularly imprinted polymer selective for cortisol detection. Molecular dynamics simulations were used to investigate the interactions between all components in the prepolymerization mixture of the as-synthesized molecularly imprinted polymer. Varying the component ratio of the prepolymerization mixture indicates that the number of cross-linker molecules relative to the template impacts the quality of imprinting. It was determined that a component ratio of 1:6:30 of cortisol, methacrylic acid, and ethylene glycol dimethacrylate, respectively, yields the optimal theoretical complexation of cortisol for the polymeric systems investigated. Experimental synthesis and rebinding results demonstrate an imprinting factor of up to 6.45. The trends in cortisol affinity predicted by molecular dynamics simulations of the prepolymerization mixture were also corroborated through experimental analysis of those modeled molecularly imprinted compositions, demonstrating the predictive capabilities of these simulations.

The Use of Computational Methods for the Development of Molecularly Imprinted Polymers

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 Concentration of C(sp3) Atoms and Properties of an Activated Carbon with over 3000 m2/g BET Surface Area

The alkaline activation of a carbonized graphene oxide/dextrin mixture yielded a carbon-based nanoscale material (AC-TR) with a unique highly porous structure. The BET-estimated specific surface area of the material is 3167 m2/g, which is higher than the specific surface area of a graphene layer. The material has a density of 0.34 g/cm3 and electrical resistivity of 0.25 Ω·cm and its properties were studied using the elemental analysis, transmission electron microscopy (TEM), electron diffraction (ED), X-ray diffraction (XRD), Raman spectroscopy, X-ray photoelectron spectroscopy (XPS), X-ray induced Auger electron spectroscopy (XAES), and electron energy loss spectroscopy (EELS) in the plasmon excitation range. From these data, we derive an integral understanding of the structure of this material. The concentration of sp3 carbon atoms was found to be relatively low with an absolute value that depends on the measurement method. It was shown that there is no graphite-like (002) peak in the electron and X-ray diffraction pattern. The characteristic size of a sp2-domain in the basal plane estimated from the Raman spectra was 7 nm. It was also found that plasmon peaks in the EELS spectrum of AC-TR are downshifted compared to those of graphite.

Biomimetic Sensitive Elements for 2,4,6-Trinitrotoluene Tested on Multi-Layered Sensors

In spite of technological progress, most of the current techniques for 2,4,6-trinitrotoluene (TNT) detection are time consuming due to laborious sensor preparation. Thereby, the aim of this work was to enlarge the knowledge for preparing sensitive elements for TNT with the aid of molecular imprinting; a known technique used to deliver biomimetic materials. The study first depicts the auto-assembly mechanism of (TNT) with functional diamino-silanes (i.e., N-(2-aminoethyl)-3-aminopropyl methyl dimethoxysilane), via “double” Meisenheimer complexes. This mechanism is being described herein for the first time and applied further to obtain molecularly imprinted polymer (MIP) films for TNT recognition. For testing the potential application of films as chemical sensor elements, typical rebinding assays of TNT in a liquid state and the rebinding of TNT in a vapor state, using multilayered sensor chips composed of quartz-chromium (Cr)-gold (Au)-titanium oxide (TiO2), were employed. Batch rebinding experiments have shown that thinner films were more efficient on retaining TNT molecules in the first five min, with a specificity of about 1.90. The quartz-Cr-Au-TiO2-MIP capacitive sensors, tested in vapor state, registered short response times (less than 25 s), low sensitivity to humidity and high specificity for TNT.

Virtually imprinted polymers (VIPs): understanding molecularly templated materialsviamolecular dynamics simulations

Theoretical model of molecularly imprinted polymers based on molecular dynamics simulations.

Towards EMIC rational design: setting the molecular simulation toolbox for enantiopure molecularly imprinted catalysts

A critical appraisal of the current strategies for the synthesis of enantiopure drugs is presented, along with a systematic background for the computational design of stereoselective porous polymers. These materials aim to achieve the enantiomeric excess of any chiral drug, avoiding the racemic separation. Particular emphasis is given to link statistical mechanics methods to the description of each one of the experimental stages within the catalyst’s synthesis, setting a framework for the fundamental study of the emerging field of molecularly imprinted catalysts.Graphical abstract

Rational design of molecularly imprinted polymers

Molecular imprinting is the process whereby a polymer matrix is cross-linked in the presence of molecules with surface sites that can bind selectively to certain ligands on the polymer. The cross-linking process endows the polymer matrix with a chemical 'memory', such that the target molecules can subsequently be recognized by the matrix. We present a simple model that accounts for the key features of this molecular recognition. Using a combination of analytical calculations and Monte Carlo simulations, we show that the model can account for the binding of rigid particles to an imprinted polymer matrix with valence-limited interactions. We show how the binding multivalency and the polymer material properties affect the efficiency and selectivity of molecular imprinting. Our calculations allow us to formulate design criteria for optimal molecular imprinting.

Influence of activated carbon porosity and surface oxygen functionalities' presence on adsorption of acetonitrile as a simple polar volatile organic compound

Based on series of porous carbon models, systematic Monte Carlo studies on the adsorption of acetonitrile (as a simple representative of polar volatile organic compounds) were performed. The influence of porosity and chemical composition of the carbon surface on CH3CN adsorption was studied and it was shown that both the factors influenced the adsorption mechanism. A decrease in the pore size and the introduction of oxygen surface groups led to a rise in adsorption energy and to an increase in the filling of accessible volume in the low-pressure part of the isotherm. However, from a practical point of view, it is easier to increase the adsorption by introducing polar groups on the carbon surface than by modifying the porosity.

Tuning the porosity through interpenetration of azobenzene-4,4′-dicarboxylate-based metal–organic frameworks

Pore size is tuned in a series of azobenzene-4,4′-dicarboxylate/3,6-bis(4-pyridyl)-1,2,4,5-tetrazine/Zn or Cd based MOFs through a variable interpenetration degree. These structural features promote subtle shifts in the blue emission of the compounds.

Molecular imprinting science and technology: a survey of the literature for the years 2004-2011

Herein, we present a survey of the literature covering the development of molecular imprinting science and technology over the years 2004-2011. In total, 3779 references to the original papers, reviews, edited volumes and monographs from this period are included, along with recently identified uncited materials from prior to 2004, which were omitted in the first instalment of this series covering the years 1930-2003. In the presentation of the assembled references, a section presenting reviews and monographs covering the area is followed by sections describing fundamental aspects of molecular imprinting including the development of novel polymer formats. Thereafter, literature describing efforts to apply these polymeric materials to a range of application areas is presented. Current trends and areas of rapid development are discussed.

A computational exploration of imprinted polymer affinity based on voriconazole metabolites

The aim of this study was to create a new computational model capable of evaluating the affinity of imprinted materials to the specific target. A 1-(2,4-difluorophenyl)-2-(1H-1,2,4-triazol-1-yl)ethanone (L1), the main metabolite of voriconazole (L2)--a modern antifungal drug, was proposed as a template. In a computational analysis of polymerization systems composed of the template, the monomers and the cross-linker molecules the appropriate porogens were simulated. A non-covalent approach for the formation of a polymer matrix from eight functional monomers was employed in the theoretical and experimental studies. The binding affinities towards the template were measured for eight synthesized polymers. The experimental results confirmed that the proposed theoretical model properly showed isopropenylbenzene 1 as the most suitable monomer to synthesize the polymer with the best affinity to L1. The novel computational protocol was more suitable to predict the properties of polymer systems than the simple analysis of template-monomer interactions. On the basis of the polymerization complex P(MC1) (template-isopropenylbenzene 1-cross-linker), the adsorption cavity was modeled and the intermolecular interactions of the template molecule and the other voriconazole metabolites inside the cavity were analyzed to get an insight into the polymer matrix selectivity.

MD simulation of organics adsorption from aqueous solution in carbon slit-like pores. Foundations of the pore blocking effect

The results of systematic studies of organics adsorption from aqueous solutions (at the neutral pH level) in a system of slit-like carbon pores having different sizes and oxygen groups located at the pore mouth are reported. Using molecular dynamics simulations (GROMACS package) the properties of adsorbent-adsorbate (benzene, phenol or paracetamol) as well as adsorbent-water systems are discussed. After the introduction of surface oxygen functionalities, adsorption of organic compounds decreases (in accordance with experimental data) and this is caused by the accumulation of water molecules at pore entrances. The pore blocking effect decreases with the diameter of slits and practically vanishes for widths larger than approx. 0.68 nm. We observed the increase in phenol adsorption with the rise in temperature. Moreover, adsorbed molecules occupy the external surface of the slit pores (the entrances) in the case of oxidized adsorbents. Among the studied molecules benzene, phenol and paracetamol prefer an almost flat orientation and with the rise in the pore width the number of molecules oriented in parallel decreases. The decrease or increase in temperature (with respect to 298 K) leads to insignificant changes of angular orientation of adsorbed molecules.

Uniform core–shell molecularly imprinted polymers: a correlation study between shell thickness and binding capacity

A model of core–shell MIPs was constructed to evaluate the correlation between shell thickness and binding capacity.

Hg2+ion-imprinted polymers sorbents based on dithizone–Hg2+chelation for mercury speciation analysis in environmental and biological samples

Novel Hg²⁺ion-imprinted polymers were synthesized using the chelate of dithizone and Hg²⁺as template for mercury speciation analysis.

Volatile organic compound adsorption on a nonporous silica surface: how do different probe molecules sense the same surface?

In this work, we compare experimental results to molecular simulation results of volatile organic compound (VOC) adsorption on nonporous silica. We adopted an effective model for the rough solid surface, obtained by a temperature annealing scheme, plus an experimental/simulation nitrogen adsorption tuning process over the silica energetic oxygen parameter. The measurement/prediction of selected VOCs, specifically, n-pentane and methylcyclohexane, is presented in terms of adsorption isotherms, with an emphasis on the angle distribution analysis of the three studied probe molecules with respect to the same modeled surface.

Molecular recognition effects in atomistic models of imprinted polymers

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.

Recent advances in molecular imprinting technology: current status, challenges and highlighted applications

Molecular imprinting technology (MIT) concerns formation of selective sites in a polymer matrix with the memory of a template. Recently, molecularly imprinted polymers (MIPs) have aroused extensive attention and been widely applied in many fields, such as solid-phase extraction, chemical sensors and artificial antibodies owing to their desired selectivity, physical robustness, thermal stability, as well as low cost and easy preparation. With the rapid development of MIT as a research hotspot, it faces a number of challenges, involving biological macromolecule imprinting, heterogeneous binding sites, template leakage, incompatibility with aqueous media, low binding capacity and slow mass transfer, which restricts its applications in various aspects. This critical review briefly reviews the current status of MIT, particular emphasis on significant progresses of novel imprinting methods, some challenges and effective strategies for MIT, and highlighted applications of MIPs. Finally, some significant attempts in further developing MIT are also proposed (236 references).