Computational approaches to design a molecular imprinted polymer for high selective extraction of 3,4-methylenedioxymethamphetamine from plasma

In this work, a molecular imprinted polymer (MIP) as a novel selective sorbent for extraction of 3,4-methylenedioxymethamphetamine (MDMA) from plasma samples was prepared. For selecting a more suitable monomer and polymerization solvent a methodology based on density functional theory calculations was developed. This computational design is based on the comparison of stabilization energies of the prepolymerization adducts between the template and different functional monomers. The effect of polymerization solvent was studied using of polarizable continuum model (PCM). The computational results revealed that the best suitable monomer and polymerization solvent for preparation of MIP is methacrylic acid (MAA) and chloroform, respectively. Also, another MIP with methacrylic acid (MAA) as monomer in acetonitrile was prepared to evaluate the validity of polarizable continuum model for selection of polymerization solvent. The performance of each polymer was evaluated by using Langmuir-Freundlich (LF) isotherm. As it is expected, the best results were obtained for the MIP which was prepared in chloroform. This MIP was used as a selective sorbent in solid-phase extraction coupled with high performance liquid chromatography-ultraviolet detector (MISPE-HPLC-UV) for rapid screening of MDMA in human plasma. For the proposed MISPE-HPLC-UV method, the linearity between responses (peak areas) and concentrations was found over the range of 3.6-11500 ng mL(-1) with a linear regression coefficient of 0.998. The limit of detection (LOD) and quantification (LOQ) in plasma were 1.0 and 3.3 ng mL(-1), respectively. The %RSD (n=5) data for five plasma samples containing 15, 25, 50, and 100 ng mL(-1) of MDMA were 1.02, 1.12, 2.05, 2.54, respectively.     

Computational design and synthesis of molecular imprinted polymers with high selectivity for removal of aniline from contaminated water

A computational approach was developed to screening functional monomers and polymerization solvents for rational design of molecularly imprinted polymer (MIP). It was based on the comparison of the binding energy of the complexes between the template and different functional monomers. The effect of the polymerization solvent was included using the polarizable continuum model. According to the theoretical calculation results, the MIP with aniline as template was prepared by emulsion polymerization method using acrylamide (AAM) as functional monomer and divinylbenzene as cross-linker in carbon tetrachloride. The synthesized MIP was then tested by equilibrium-adsorption method, and the MIP demonstrated high removal efficiency to the aniline. The results of this study have indicated the possibility of using computer aided design for rational selection of functional monomers and solvents capable of removal of aniline from contaminated water.     

Rationally designed molecularly imprinted polymers for selective extraction of methocarbamol from human plasma

Molecularly imprinted polymers (MIPs) with high selectivity toward methocarbamol have been computationally designed and synthesized based on the general non-covalent molecular imprinting approach. A virtual library consisting of 18 functional monomers was built and possible interactions between the template and functional monomers were investigated using a semiempirical approach. The monomers with the highest binding scores were then considered for additional calculations using a more accurate quantum mechanical (QM) calculation exploiting the density functional theory (DFT) at B3LYP/6-31G(d,p) level. The cosmo polarizable continuum model (CPCM) was also used to simulate the polymerization solvent. On the basis of computational results, acrylic acid (AA) and tetrahydrofuran (THF) were found to be the best choices of functional monomer and polymerization solvent, respectively. MIPs were then synthesized by the precipitation polymerization method and used as selective adsorbents to develop a molecularly imprinted solid-phase extraction (MISPE) procedure before quantitative analysis. After MISPE the drug could be determined either by differential pulse voltammetry (DPV), on a glassy carbon electrode modified with multiwalled-carbon nanotubes (GC/MWNT), or high performance chromatography (HPLC) with UV detection. A comparative study between MISPE-DPV and MISPE-HPLC-UV was performed. The MISPE-DPV was more sensitive but both techniques showed similar accuracy and precision.     

Selectivity features of molecularly imprinted polymers recognising the carbamate group

The molecular recognition properties of molecular imprinted polymers which bind the carbamate function were studied. Functional monomers potentially able to form non-covalent interactions with the model molecule N,O-dibenzylcarbamate were selected on the basis of a computational approach describing possible interactions between the template and a small library of vinylic monomers. These results were in accordance with N,O-dibenzylcarbamate batch-rebinding measurements performed on several miniMIPs prepared with the same library. From these preliminary results, four polymers were prepared by thermoinduced radical polymerization, using ethylene dimethacrylate as a cross-linker, chloroform (MIP1, MIP3) or acetonitrile (MIP2, MIP4) as porogens and methacrylic acid (MIP1, MIP2) or acrylamide (MIP3, MIP4) as functional monomers. Molecular recognition features of these materials were studied by high-performance liquid chromatography. In this manner selectivity was evaluated by considering the column retention of a library of sixteen structural analogues of dibenzylcarbamate, characterized by the transformation of the carbamate into a related function, or by the alteration of the molecular structure.The experimental results show that methacrylic acid is more efficient than acrylamide as a functional monomer (imprinting factors: MIP1 = 24.1, MIP2 = 25.6, MIP3 = 13.3, MIP4 = 2.44), and that chloroform enhances polymer selectivity. As regards structural motifs which conditionate the selectivity, the carbamate function strictly controls the presence/absence of molecular recognition, while shape and dimension of the substituents modulate the recognition itself. In particular, a marked recognition for analogs which were slightly bigger than the template was observed (N-benzyl-O-phenethylcarbamate: MIP1 α = 1.13, MIP2 α = 1.41, MIP3 α = 0.97; N-phenethyl-N-benzylcarbamate: MIP1 α = 1.61, MIP2 α = 1.17, MIP3 α = 0.81; N,O-diphenethylcarbamate: MIP1 α = 0.89, MIP2 α = 1.20, MIP3 α = 0.55).     

齐墩果酸分子印迹聚合物预组装体系的分子模拟及聚合物制备

以齐墩果酸(OA)为模板分子,三氟甲基丙烯酸(TFMAA)、α-甲基丙烯酸(MAA)、丙烯酰胺(AM)、4-乙烯基吡啶(4-VP)为功能单体,三氯甲烷、四氢呋喃、乙醇、甲醇和丙酮为溶剂,基于量子化学密度泛函理论(DFT)和ONIOM方法,采用Gaussian09软件模拟计算了模板分子与不同功能单体的印迹聚合物预组装体系的构型,探讨了模板分子与功能单体在不同印迹比例时所形成复合物的成键情况以及反应过程中的结合能,并采用自洽反应场极化连续模型(CPCM)计算了功能单体与模板分子在不同溶剂中的溶剂化能。结果表明,TFMAA与模板分子OA以1:1摩尔比形成复合物的结合能ΔE最高(-70.99kJ·mol~(-1)),结构最稳定,模板分子和功能单体在三氯甲烷中的溶剂化能最小。同时,采用实验方法验证模拟结果,并利用扫描电镜、傅里叶红外光谱仪和静态吸附实验对印迹聚合物的形貌、化学基团和吸附性能等进行表征。结果表明,模拟结果与实验结果完全一致,计算机模拟对分子印迹体系的筛选和机理研究提供了理论依据。     

Development of a molecularly imprinted polymer for pyridoxine using an ion-pair as template

One of the main challenges in the molecularly imprinted polymers (MIP) field is the proper MIP design for water-soluble compounds because of appearance of serious drawbacks in polar solvents and insolubility of those compounds in non-polar solvents which are commonly used for MIP synthesis. In this work a novel and simple method for synthesis of molecularly imprinted polymers for a water-soluble compound was introduced. Pyridoxine was chosen as a target molecule and the ion-pair complex formed between pyridoxine ion (Py⁺) and dodecyl sulfate ion (DS⁻) was transferred into the chloroform via liquid-liquid extraction. Then polymerization was carried out in chloroform. The molecular mechanics and density functional theory were proposed to screen proper monomer. Binding energy, ΔE, of a template and a monomer as a measure of their interaction was considered. Ion-pair [Py⁺-DS⁻] was supposed as a template molecule and acrylic acid, methacrylic acid, allyamine, vinylpridine and 2-hydroxy ethyl methacrylate were as tested monomers. The MIP synthesized using acrylic acid showed the highest selectivity to pyridoxine as predicted from the ΔE calculation. The obtained MIP showed very high affinity against vitamin B6 in comparison to non-imprinted polymers (NIP). It was proved that the obtained MIP with introduced method was much better than that prepared in methanol as porogen. It was showed that the MIP prepared by this new method could be used as an adsorber for extraction and determination of pyridoxine in real and synthetic samples.     

An extensible interface for QM/MM molecular dynamics simulations with AMBER

We present an extensible interface between the AMBER molecular dynamics (MD) software package and electronic structure software packages for quantum mechanical (QM) and mixed QM and classical molecular mechanical (MM) MD simulations within both mechanical and electronic embedding schemes. With this interface, ab initio wave function theory and density functional theory methods, as available in the supported electronic structure software packages, become available for QM/MM MD simulations with AMBER. The interface has been written in a modular fashion that allows straight forward extensions to support additional QM software packages and can easily be ported to other MD software. Data exchange between the MD and QM software is implemented by means of files and system calls or the message passing interface standard. Based on extensive tests, default settings for the supported QM packages are provided such that energy is conserved for typical QM/MM MD simulations in the microcanonical ensemble. Results for the free energy of binding of calcium ions to aspartate in aqueous solution comparing semiempirical and density functional Hamiltonians are shown to demonstrate features of this interface. © 2013 Wiley Periodicals, Inc.     

Implementation of the IMOMM methodology for performing combined QM/MM molecular dynamics simulations and frequency calculations

A technique for implementing the integrated molecular orbital and molecular mechanics (IMOMM) methodology developed by Maseras and Morokuma that is used to perform combined quantum mechanics/molecular mechanics (QM/MM) molecular dynamics simulations, frequency calculations and simulations of macromolecules including explicit solvent is presented. Although the IMOMM methodology is generalized to any coordinate system, the implementation first described by Maseras and Morokuma requires that the QM and MM gradients be transformed into internal coordinates before they are added together. This coordinate transformation can be cumbersome for macromolecular systems and can become ill-defined during the course of a molecular dynamics simulation. We describe an implementation of the IMOMM method in which the QM and MM gradients are combined in the cartesian coordinate system, thereby avoiding potential problems associated with using the internal coordinate system. The implementation can be used to perform combined QM/MM molecular dynamics simulations and frequency calculations within the IMOMM framework. Finally, we have examined the applicability of thermochemical data derived from IMOMM framework. Finally, we have examined the applicability of thermochemical data derived from IMOMM frequency calculations. Received: 11 May 1998 / Accepted: 14 August 1998 / Published online: 16 November 1998     

Investigating the mechanisms of 17<Emphasis Type="Italic">β</Emphasis>-estradiol imprinting by computational prediction and spectroscopic analysis

Molecular dynamics simulations combined with spectroscopic analysis were applied to understand the nature of recognition in molecularly imprinted polymers (MIPs), and for optimizing the MIP formulation. The best monomers for synthesizing imprinted materials for 17β-estradiol (BE2) were selected by evaluating the strength of the template–monomer interaction derived from molecular dynamics simulations. A number of potential functional monomers for BE2 were screened for hydrogen-bonding strength in order to analyze template–monomer interactions favorable for synthesizing noncovalent MIPs, with the simulations revealing that methacrylic acid, 2-(diethylamino)ethyl methacrylate, and methacrylamide provided the highest binding affinity to BE2. These theoretical predictions agree with previously reported results on batch rebinding studies using the corresponding functional monomers for synthesizing a series of MIPs. Molecular analysis such as ¹H NMR was used for experimentally confirming the prevalent template–monomer interactions derived from the modeling results. Molecular dynamics simulations indicating monomer dimerization in the prepolymerization solution correlated with the nature of the porogenic solvent, which was confirmed by NMR studies on hydrogen-bonding interactions of methacrylic acid in different solvents. Furthermore, batch rebinding studies revealed that the specific functionalities of the monomers essential to rebinding are retained after polymerization, which proves that the application of computational methods for modeling the prepolymerization solution provides useful information for optimizing real MIP systems.     

Synthesis and Evaluation of Molecularly Imprinted Polymers as Sorbents for Selective Extraction of Coumarins

Coumarin, 7-hydroxycoumarin and dicoumarol molecularly imprinted polymers (MIP) were synthesized by bulk polymerization. Methacrylic acid and 4-vinylpyridine were tested as functional monomers and methanol, ethanol, acetonitrile, toluene and chloroform were tested as porogens. The binding capabilities of the imprinted polymers were assessed by equilibrium binding analysis. Highest binding capacity was obtained for MIP prepared for the template 7-hydroxycoumarin synthesized in methacrylic acid as functional monomer, chloroform as porogen and methanol/water as analyte solvent. Scanning electron microscopy analysis documented its appropriate morphology. ATR-FTIR spectra confirmed successful polymerization of MIP. Coumarin structural analogues were employed to evaluate the polymer selectivity and it was found that polymer prepared for 7-hydroxycoumarin was selective for its template molecule. Kinetic studies showed relatively fast adsorption of analytes to MIPs (1 h). Rebinding properties of MIPs were evaluated by adsorption isotherms. The calculated data fitted well with experimental data showing that Freundlich isotherm is suitable for modelling the adsorption of tested coumarins on prepared MIPs. Applicability of polymer prepared for 7-hydroxycoumarin was tested for the selective extraction of coumarins from the sample of chicory.     

Employment of Molecularly Imprinted Polymers to High‐Throughput Screen nNOS‐PSD‐95 Interruptions: Structure and Dynamics Investigations on Monomer–Template Complexation

Molecularly imprinted polymers (MIPs) are employed to screen nNOS‐PSD‐95 (neuronal nitric oxide synthase post‐synaptic density protein‐95) interruptions. 5‐(3,5‐Dichloro‐2‐hydroxybenzylamino)‐2‐hydroxybenzoic acid (ZL006; a potential drug candidate for the treatment of stroke, depression, and pain) is employed as a template. Four kinds of functional monomers (2‐VP: 2‐vinylpyridine; 4‐VP: 4‐vinylpyridine; MMA: methyl methacrylate; and MAAM: methacrylamide) are designed, and their complexation with ZL006 in various solvents (methanol, acetonitrile, toluene, chloroform) is investigated by molecular dynamics simulations and quantum mechanics calculations. Both 4‐VP and MAAM have stronger interactions with ZL006 than those of 2‐VP and MMA. The appropriate ratio of monomer to template is 3:1. Intermolecular hydrogen bonds play a dominant role in monomer–template complexation. Ideal solvents are toluene and chloroform, and the solvation effect on monomer–template complexation is revealed. Both molecular modeling and adsorption experiments demonstrate that as‐synthesized ZL006‐MIP with 4‐VP as a monomer has better selectivity than that employing MAAM to screen for nNOS‐PSD‐95 interruptions.     

Impact of the solvent on the conformational isomerism of calix[4]arenes: a study based on continuum solvation models

The influence of solvation on the conformational isomerism of calix[4]arene and p-tert-butylcalix[4]arene has been investigated by using the continuum model reported by Miertus, Scrocco, and Tomasi (MST). The quantum mechanical (QM) and semiclassical (SC) formalisms of the MST model have been considered for two different solvents (chloroform and water). The suitability of the QM-MST and SC-MST methods has been examined by comparison with previous results derived from classical molecular dynamics (MD) simulations with explicit solvent molecules. The application of the continuum model to the solute configurations generated by using in vacuo classical MD simulations provides a fast strategy to evaluate the effects of the solvent on the conformational preferences of calixarenes. These encouraging results allow us to propose the use of continuum models to solutes with complex molecular structures, which are traditionally studied by MD simulations.     

Preparation of a PTE simulacrum based on surface molecular imprinting

Firstly,we synthesized N-methacryloyl-histidine monomer and N-methacryloyl-histidine-Cu²⁺ complex(MAH-Cu²⁺).Then the molecular imprinting polymers（MIP） has been prepared by surface grafting on uniform polystyrene（PS） core using reversible addition-fragmentation transfer polymerization（RAFT） with MAH-Cu²⁺ as the functional monomer,methyl paraoxon as the template to simulate phosphodiesterase（PTE）.Finally,we have investigated the catalytic hydrolytic activities of MIP and non-imprinting polymers（NIP） to the template methyl paraoxon and the template analogue ethyl paraoxon respectively by UV spectrophotometry.The results showed that the catalytic hydrolytic activity of MIP to the template methyl paraoxon was highest and the value of k is 8.67×10^-5 mmol L^-1 min^-1,3.89-fold higher than MIP to the template analogue ethyl paraoxon,2.79-fold higher than NIP to the template methyl paraoxon.The K_M,r_m of MSP are also determined,and K_M = 3.95×10^-4mol/L,r_m = 2.12μmol/ min.The MIP can be reused with only lose 7%of catalytic activity for four cycles.     

Rational design and synthesis of water-compatible molecularly imprinted polymers for selective solid phase extraction of amiodarone

Novel water-compatible molecularly imprinted polymers (MIPs) selective for amiodarone (AD) were designed via a new methodology which relies on screening library of non-imprinted polymers (NIPs). The NIP library consisted of eighteen cross-linked co-polymers synthesized from monomers commonly used in molecular imprinting. The binding capacity of each polymer in the library was analyzed in two different solvents. Binding in water was used to assess non-specific (hydrophobic) interactions and binding in an appropriate organic solvent was used to assess specific interactions. A good correlation was found between the screening tests and modeling of monomer–template interactions performed using computational approach. Additionally, analysis of template–monomer interactions was performed using UV–vis spectroscopy. As the result, 4-vinylpyridine (4-VP) was selected as the best monomer for developing MIP for AD. The 4-VP-based polymers demonstrated imprinting factor equal 3.9. The polymers performance in SPE was evaluated using AD and its structural analogues. The recovery of AD was as high as 96% when extracted from spiked phosphate buffer (pH 4.5) solution and 82.1% from spiked serum samples. The developed MIP shown as a material with specific binding to AD, comparing to its structural analogues, 1-(2-diethylaminoethoxy)-2,6-diiodo-4-nitrobenzene and lidocaine, which shown 9.9% and 25.4% of recovery from the buffer solution, correspondingly. We believe that the screening of NIP library could be proposed as an alternative to commonly used computational and combinatorial approaches.     

The dynamo library for molecular simulations using hybrid quantum mechanical and molecular mechanical potentials

The Dynamo module library has been developed for the simulation of molecular systems using hybrid quantum mechanical (QM) and molecular mechanical (MM) potentials. Dynamo is not a program package but is a library of Fortran 90 modules that can be employed by those interested in writing their own programs for performing molecular simulations. The library supports a range of different types of molecular calculation including geometry optimizations, reaction‐path determinations and molecular dynamics and Monte Carlo simulations. This article outlines the general structure and capabilities of the library and describes in detail Dynamo's semiempirical QM/MM hybrid potential. Results are presented to indicate three particular aspects of this implementation—the handling of long‐range nonbonding interactions, the nature of the boundary between the quantum mechanical and molecular mechanical atoms and how to perform path‐integral hybrid‐potential molecular dynamics simulations. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 1088–1100, 2000     

Evaluation of the Polymerization and Recognition Mechanism for Phenol Imprinting SPE

In order to develop more efficient preparation technologies for imprinted polymers (MIPs), the nature of pre-polymerization and molecular recognition in MIP was investigated by molecular dynamics modeling (MD), ¹H NMR, FTIR and some indirect techniques. Phenol was used as the template for the study of mechanism through the analysis of hydrogen bonding, hydrophobic and π–π bonding interaction. The 4-vinylpyridine-based MIP had the highest selectivity to its phenol template. Hydrogen bonding was proved to be present by characterizing the pre-polymerization complex and evaluating the recognition process and the effects of rebinding solvents were also studied. It was found that a good rebinding solvent should have less affinity with both template and polymer, but good solubility. MD modeling and some indirect techniques demonstrated that 4-vinylpyridine-based MIP recognized phenol mainly through hydrophobic interactions when the rebinding medium was water, while hydrogen bonding was present in the recognition process when the rebinding solvent was n-hexane.     

三唑酮分子印迹预组装体系的分子模拟与吸附性能

以三唑酮为模板分子, 以丙烯酰胺(AM)、 丙烯酸(AA)、 甲基丙烯酸(MAA)和三氟甲基丙烯酸(TFMAA)为功能单体预组装了分子印迹聚合物体系, 采用半经验法和从头算法, 利用Hyperchem软件模拟了三唑酮与4种功能单体所组成的分子印迹预组装体系的构型、 能量、 反应配比及复合反应的结合能, 选择复合物结合能最高的功能单体用于分子印迹聚合物的合成. 采用密度泛函方法计算了模板与单体在不同致孔剂中的溶剂化能. 结果表明, 三唑酮与三氟甲基丙烯酸所形成复合物的作用力最强, 在非极性溶剂中溶剂化能最弱. 由预组装体系的差示紫外光谱法研究发现, 一分子三唑酮可与两分子三氟甲基丙烯酸在氯仿中形成氢键复合物, 与分子模拟的结果一致. 在最佳模拟条件下, 合成了三唑酮的印迹聚合物, 利用吸附等温线Langmuir和Freundlich模型研究了印迹聚合物的吸附行为及识别机理. 上述方法对于分子印迹体系的筛选及分子印迹聚合物性能的预测有重要的意义.     

Novel polymer system for molecular imprinting polymer against amino acid derivatives

Molecular imprinting polymers (MIPs) against N-Cbz-L-Tyr were prepared utilizing different polymer systems and evaluated in HPLC mode. It was found that MEP utilizing cocktail functional monomers, acrylamide 2-vinylpyridine showed better molecular recognition and better separation ability for the template molecule than those utilizing other functional monomers. MIP utilizing trimethylolpropane trimethacrylate as cross-linker showed higher load capacity and separation factor than those utilizing ethylene glycol dimethacrylate as cross-linker. Increasing the concentration of competing solvent, acetic acid weakened the ionic interaction and hydrogen bonding between the analyte and the functional monomers, 2-vinylpyridine and acrylamide, when the template enantiomer was separated by HPLC. Therefore increasing of the concentration of acetic acid leads to decreasing of capacity factor, separation factor and resolution.     

Development of massive multilevel molecular dynamics simulation program,platypus (PLATform for dYnamic protein unified simulation), for the elucidation of protein functions

A massively parallel program for quantum mechanical‐molecular mechanical (QM/MM) molecular dynamics simulation, called Platypus (PLATform for dYnamic Protein Unified Simulation), was developed to elucidate protein functions. The speedup and the parallelization ratio of Platypus in the QM and QM/MM calculations were assessed for a bacteriochlorophyll dimer in the photosynthetic reaction center (DIMER) on the K computer, a massively parallel computer achieving 10 PetaFLOPs with 705,024 cores. Platypus exhibited the increase in speedup up to 20,000 core processors at the HF/cc‐pVDZ and B3LYP/cc‐pVDZ, and up to 10,000 core processors by the CASCI(16,16)/6‐31G** calculations. We also performed excited QM/MM‐MD simulations on the chromophore of Sirius (SIRIUS) in water. Sirius is a pH‐insensitive and photo‐stable ultramarine fluorescent protein. Platypus accelerated on‐the‐fly excited‐state QM/MM‐MD simulations for SIRIUS in water, using over 4000 core processors. In addition, it also succeeded in 50‐ps (200,000‐step) on‐the‐fly excited‐state QM/MM‐MD simulations for the SIRIUS in water. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.