Search results for: molecular imprinted polymers

Authors: Salem El-Tohami Ashoor

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A novel new vanadium (IV) complexes incorporating the chelating diamido cyclopentadienyl {ArN(CH2)3NAr)}2-((ηn-Cp)Cp)} (Ar = 2,6-Pri2C6H3)(Cp = C5H5 and n = 1,2,3,4 and 5) have been studied with calculation of the properties of species involved in various of cyclopentadienyl reaction. These were carried out under investigation of density functional theory (DFT) calculation, and comparing together. Other methods, explicitly including electron correlation, are necessary for more accurate calculations; MB3LYP (Becke) (Lee–Yang–Parr) level of theory often being used to obtain more exact results. These complexes were estimated of electronic energy for molecular system, because it accounts for all electron correlation interactions. The optimised of [V(ArN(CH2)3NAr)2Cl(η5-Cp)] (Ar = 2,6-Pri2C6H3 and Cp= C5H5) was found to be thermally more stable than others of vanadium cyclopentadienyl. In the meantime the complex [V(ArN(CH2)3NAr)2Cl(η1-Cp)] (Ar = 2,6-Pri2C6H3 and Cp= C5H5) which is showed a low thermal stability in case of the just one carbon of cyclopentadienyl can be insertion with vanadium metal centre. By using Dewar-Chatt-Duncanson model, as a basis of the molecular orbital (MO) analysis and showed the highest occupied molecular orbital (HOMO) and lowest occupied molecular orbital LUMO.

Keywords: vanadium (IV) cyclopentadienyl complexes, DFT, MO, HOMO, LUMO

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Authors: Said Belaaouad

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This study aimed to explore the quantitative structure-activity relationship (QSAR) of 1,2,4-Triazine-3(2H)-one derivative as a potential anticancer agent against breast cancer. The electronic descriptors were obtained using the Density Functional Theory (DFT) method, and a multiple linear regression techniques was employed to construct the QSAR model. The model exhibited favorable statistical parameters, including R2=0.849, R2adj=0.656, MSE=0.056, R2test=0.710, and Q2cv=0.542, indicating its reliability. Among the descriptors analyzed, absolute electronegativity (χ), total energy (TE), number of hydrogen bond donors (NHD), water solubility (LogS), and shape coefficient (I) were identified as influential factors. Furthermore, leveraging the validated QSAR model, new derivatives of 1,2,4-Triazine-3(2H)-one were designed, and their activity and pharmacokinetic properties were estimated. Subsequently, molecular docking (MD) and molecular dynamics (MD) simulations were employed to assess the binding affinity of the designed molecules. The Tubulin colchicine binding site, which plays a crucial role in cancer treatment, was chosen as the target protein. Through the simulation trajectory spanning 100 ns, the binding affinity was calculated using the MMPBSA script. As a result, fourteen novel Tubulin-colchicine inhibitors with promising pharmacokinetic characteristics were identified. Overall, this study provides valuable insights into the QSAR of 1,2,4-Triazine-3(2H)-one derivative as potential anticancer agent, along with the design of new compounds and their assessment through molecular docking and dynamics simulations targeting the Tubulin-colchicine binding site.

Keywords: QSAR, molecular docking, ADMET, 1, 2, 4-triazin-3(2H)-ones, breast cancer, anticancer, molecular dynamic simulations, MMPBSA calculation

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Authors: Adam Abate, Elham Rasti, Philip Romero

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Beta-glucosidase is the key enzyme component present in cellulase and completes the final step during cellulose hydrolysis by converting the cellobiose to glucose. The regulatory properties of beta-glucosidases are most commonly found for the retaining and inverting enzymes. Hydrolysis of a glycoside typically occurs with general acid and general base assistance from two amino acid side chains, normally glutamic or aspartic acids. In order to obtain more detailed information on the dynamic events origination from the interaction with enzyme active site, we carried out molecular dynamics simulations of beta-glycosidase in protonated state (Glu-H178) and deprotonated state (Glu178). The theoretical models generated from our molecular dynamics simulations complement and advance the structural information currently available, leading to a more detailed understanding of Beta-glycosidase structure and function. This article presents the important role of Asn307 in enzyme activity of beta-glucosidase

Keywords: Beta-glucosidase, GROMACS, molecular dynamics simulation, structural parameters

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Authors: Eunae Lee, Oh-Kuen Kwon, Ki-Sub Kim, Jeong Won Kang

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We investigated the dynamic properties of graphene-nanoribbon (GNR) memory encapsulating graphene-nanoflake (GNF) shuttle in the potential to be applicable as a non-volatile random access memory via molecular dynamics simulations. This work explicitly demonstrates that the GNR encapsulating the GNF shuttle can be applied to nonvolatile memory. The potential well was originated by the increase of the attractive vdW energy between the GNRs when the GNF approached the edges of the GNRs. So the bistable positions were located near the edges of the GNRs. Such a nanoelectromechanical non-volatile memory based on graphene is also applicable to the development of switches, sensors, and quantum computing.

Keywords: graphene nanoribbon, graphene nanoflake, shuttle memory, molecular dynamics

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Authors: Archana Sharma, Vijayashree Nayak, Ashok Kumar

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Three-dimensional matrices were fabricated from blend of natural-natural polymers like carrageenan-gelatin and synthetic -natural polymers such as PEG- gelatin (PEG of different molecular weights (2,000 and 6,000) using two different crosslinkers; glutaraldehyde and EDC-NHS by cryogelation technique. Blends represented a feasible approach to design 3-D scaffolds with controllable mechanical, physical and biochemical properties without compromising biocompatibility and biodegradability. These matrices possessed interconnected porous structure, good mechanical strength, biodegradable nature, constant swelling kinetics, ability to withstand high temperature and visco-elastic behavior. Hemocompatibility of cryogel matrices was determined by coagulation assays and hemolytic activity assay which demonstrated that these cryogels have negligible effects on coagulation time and have excellent blood compatibility. In vitro biocompatibility (cell-matrix interaction) inferred good cell adhesion, proliferation, and secretion of ECM on matrices. These matrices provide a microenvironment for the growth, proliferation, differentiation and secretion of ECM of different cell types such as IMR-32, C2C12, Cos-7, rat bone marrow derived MSCs and human bone marrow MSCs. Hoechst 33342 and PI staining also confirmed that the cells were uniformly distributed, adhered and proliferated properly on the cryogel matrix. An ideal scaffold used for tissue engineering application should allow the cells to adhere, proliferate and maintain their functionality. Neurotransmitter analysis has been done which indicated that IMR-32 cells adhered, proliferated and secreted neurotransmitters when they interacted with these matrices which showed restoration of their functionality. The cell-matrix interaction up to molecular level was also evaluated so to check genotoxicity and protein expression profile which indicated that these cryogel matrices are non-genotoxic and maintained biofunctionality of cells growing on these matrices. All these cryogels, when implanted subcutaneously in balb/c mice, showed no adverse systemic or local toxicity effects at implantation site. There was no significant increase in inflammatory cell count has otherwise been observed after scaffold implantation. These cryogels are supermacroporous and this porous structure allows cell infiltration and proliferation of host cells. This showed the integration and presence of infiltrated cells into the cryogel implants. Histological analysis confirmed that the implanted cryogels do not have any adverse effect in spite of host immune system recognition at the site of implantation, on its surrounding tissues and other vital host organs. In vivo biocompatibility study after in vitro biocompatibility analysis has also concluded that these synthesized cryogels act as important biological substitutes, more adaptable and appropriate for transplantation. Thus, these cryogels showed their potential for soft tissue engineering applications.

Keywords: cryogelation, hemocompatibility, in vitro biocompatibility, in vivo biocompatibility, soft tissue engineering applications

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Authors: Salvana P. M. Costa, Tarcyla A. Gomes, Giovanna C. R. M. Schver, Leslie R. M. Ferraz, Cristovão R. Silva, Magaly A. M. Lyra, Danilo A. F. Fonte, Larissa A. Rolim, Amanda C. Q. M. Vieira, Miracy M. Albuquerque, Pedro J. Rolim-neto

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Efavirenz (EFV) is considered one of the most widely used anti-HIV drugs. However, it is classified as a drug class II (poorly soluble, highly permeable) according to the biopharmaceutical classification system, presenting problems of absorption in the gastrointestinal tract and thereby inadequate bioavailability for its therapeutic action. This study aimed to overcome these barriers by developing and obtaining solid dispersions (SD) in order to increase the EFZ bioavailability. For the development of SD with EFV, theoretical and practical studies were initially performed. Thus, there was a choice of a carrier to be used. For this, it was analyzed the various criteria such as glass transition temperature of the polymer, intra- and intermolecular interactions of hydrogen bonds between drug and polymer, the miscibility between the polymer and EFV. The choice of the obtainment method of the SD came from the analysis of which method is the most consolidated in both industry and literature. Subsequently, the choice of drug and carrier concentrations in the dispersions was carried out. In order to obtain DS to present the drug in its amorphous form, as the DS were obtained, they were analyzed by X-ray diffraction (XRD). SD are more stable the higher the amount of polymer present in the formulation. With this assumption, a SD containing 10% of drug was initially prepared and then this proportion was increased until the XRD showed the presence of EFV in its crystalline form. From this point, it was not produced SD with a higher concentration of drug. Thus, it was allowed to select PVP-K30, PVPVA 64 and the SOLUPLUS formulation as carriers, once it was possible the formation of hydrogen bond between EFV and polymers since these have hydrogen acceptor groups capable of interacting with the donor group of the drug hydrogen. It is worth mentioning also that the films obtained, independent of concentration used, were presented homogeneous and transparent. Thus, it can be said that the EFV is miscible in the three polymers used in the study. The SD and Physical Mixtures (PM) with these polymers were prepared by the solvent method. The EFV diffraction profile showed main peaks at around 2θ of 6,24°, in addition to other minor peaks at 14,34°, 17,08°, 20,3°, 21,36° and 25,06°, evidencing its crystalline character. Furthermore, the polymers showed amorphous nature, as evidenced by the absence of peaks in their XRD patterns. The XRD patterns showed the PM overlapping profile of the drug with the polymer, indicating the presence of EFV in its crystalline form. Regardless the proportion of drug used in SD, all the samples showed the same characteristics with no diffraction peaks EFV, demonstrating the behavior amorphous products. Thus, the polymers enabled, effectively, the formation of amorphous SD, probably due to the potential hydrogen bonds between them and the drug. Moreover, the XRD analysis showed that the polymers were able to maintain its amorphous form in a concentration of up to 80% drug.

Keywords: amorphous form, Efavirenz, solid dispersions, solubility

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Authors: T. Rajamäki

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In clean room environment molecular contamination in very small concentrations can cause significant harm for the components and processes. This is commonly referred as airborne molecular contamination (AMC). There is a shortage of high sensitivity continuous measurement data for existence and behavior of several of these contaminants. Accordingly, in most cases correlation between concentration of harmful molecules and their effect on processes is not known. In addition, the formation and distribution of contaminating molecules are unclear. In this work sensitive optical techniques are applied in clean room facilities for investigation of concentrations, forming mechanisms and effects of contaminating molecules. Special emphasis is on reactive acid and base gases ammonia (NH3) and hydrogen fluoride (HF). They are the key chemicals in several operations taking place in clean room processes.

Keywords: AMC, clean room, concentration, reactive gas

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Authors: Mosaab A. Omara, Layla O. Elmajdoubb, Mohammad Saleh Al-Aboodyc, Ahmed ElSifyd, Ahmed O. Elkhtamd

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The aim of this study is to present the molecular characterization of cysticercus tenuicolis of Taenia hydatigena from livestock isolates in Egypt, using the amplification of sequencing of the mt-CO1 gene. We introduce a detailed image of the Cysticercus tenuicolis infection in ruminant animals in Upper Egypt. Cysticercus tenuicolis inhabits such organs in ruminants as the omentum, viscera, and liver. In the present study, the infection rate of Cysticercus tenuicolis was found to be 16% and 19% in sheep and goat sample respectively. Firstly we report one larval stage of Taenia hydatigena detected in the camel liver in Egypt. Cysticercus tenuicolis infection manifested a higher prevalence in females than in males. Those above 2 years of age manifested a higher infection rate than younger animals. The preferred site for the infection was the omentum: a 70% preference in sheep and a 68% preference in goat samples. The molecular characterization using the mitochondrial cytochrome c oxidase subunit 1 (CO1) gene of isolates from sheep, goats and camels corresponded to T. hydatigena. For this study, molecular characterizations of T. hydatigena were done for the first time in Egypt. Molecular tools are of great assistance in characterizing the Cysticercus tenuicolis parasite especially when the morphological character cannot be detected because the metacestodes are frequently confused with infection by the Hydatid cyst, especially when these occur in the visceral organs. In the present study, Cysticercus tenuicolis manifested high identity in the goat and sheep samples, while differences were found more frequently in the camel samples (10 pairbase). Clearly molecular diagnosis for Cysticercus tenuicolis infection significantly helps to differentiate it from such other metacestodes.

Keywords: cysticercus tenuicolis, its2, genetic, qena, molecular and taenia hydatigena

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Authors: Sophio Kobauri, Vladimir P. Torchilin, David Tugushi, Ramaz Katsarava

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Nanotherapy is an actual newest mode of treatment numerous diseases using nanoparticles (NPs) loading with different pharmaceuticals. NPs of biodegradable polymeric micelles (PMs) are gaining increased attention for their numerous and attractive abilities to be used in a variety of applications in the various fields of medicine. The present paper deals with the synthesis of a class of biodegradable micelle-forming polymers, namely ABA triblock-copolymer in which A-blocks represent amino-poly(ethylene glycol) (H₂N-PEG) and B-block is biodegradable amino acid-based poly(ester amide) constituted of α-amino acid – L-phenylalanine. The obtained copolymer formed micelles of 70±4 nm size at 10 mg/mL concentration.

Keywords: amino acids, biodegradable poly (ester amide), amphiphilic triblock-copolymer, micelles

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Authors: Somayeh Akrami, Vali-Allah Mozaffarian, Habib Onsori

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The studied region in this research, watershed Kuhkamar river, is about 112.66 square kilometers, it is located between 45º 48' 9" to 45º 2' 20" N and 38º 34' 15" to 38º 40' 28" E. The gained results of the studies on flora combinations, proved 287 plant species in 190 genera and 51 families. Asteracea with 49 and Lamiaceae with 27 plant species are the major plant families. Among collected species one interesting plant was found and determined as a new record Anemone narcissiflora L. for flora of Iran. This plant is known as a complex species that shows intraspecific speciation and is classified into about 12 subspecies and 10 varieties in world. To identify the infraspecies taxons of this species, in addition to morphological characteristics, the use of appropriate molecular markers for the better isolation of the individuals were needed.

Keywords: Anemone narcissiflora, floristic Study, kuhkamar, molecular marker

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Authors: Dafna Knani, Sarit S. Sivan

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Aggrecan, one of the main components of the intervertebral disc (IVD), belongs to the family of proteoglycans (PGs) that are composed of glycosaminoglycan (GAG) chains covalently attached to a core protein. Its primary function is to maintain tissue hydration and hence disc height under the high loads imposed by muscle activity and body weight. Significant PG loss is one of the first indications of disc degeneration. A possible solution to recover disc functions is by injecting a synthetic hydrogel into the joint cavity, hence mimicking the role of PGs. One of the hydrogels proposed is GAG-analogues, based on sulfate-containing polymers, which are responsible for hydration in disc tissue. In the present work, we used molecular dynamics (MD) to study the effect of the hydrogel crosslinking (type and degree) on the swelling behavior of the suggested GAG-analogue biomimetics by calculation of cohesive energy density (CED), solubility parameter, enthalpy of mixing (ΔEmix) and the interactions between the molecules at the pure form and as a mixture with water. The simulation results showed that hydrophobicity plays an important role in the swelling of the hydrogel, as indicated by the linear correlation observed between solubility parameter values of the copolymers and crosslinker weight ratio (w/w); this correlation was found useful in predicting the amount of PEGDA needed for the desirable hydration behavior of (CS)₄-peptide. Enthalpy of mixing calculations showed that all the GAG analogs, (CS)₄ and (CS)₄-peptide are water-soluble; radial distribution function analysis revealed that they form interactions with water molecules, which is important for the hydration process. To conclude, our simulation results, beyond supporting the experimental data, can be used as a useful predictive tool in the future development of biomaterials, such as disc replacement.

Keywords: molecular dynamics, proteoglycans, enthalpy of mixing, swelling

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Authors: H. Zouaoui, D. Abdi, B. Nessark, F. Habelhames, A. Bahloul

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Among the conjugated organic polymers, the polythiophenes constitute a particularly important class of conjugated polymers, which has been extensively studied for the relation between the geometrical structure and the optic and electronic properties, while the polythiophene is an intractable material. They are, furthermore, chemically and thermally stable materials, and are very attractive for exploitation of their physical properties. The polythiophenes are extensively studied due to the possibility of synthesizing low band gap materials by using substituted thiophenes as precursors. Low band gap polymers may convert visible light into electricity and some photoelectrochemical cells based on these materials have been prepared. Polythiophenes (PThs) are good candidates for polymer optoelectronic devices such as polymer solar cells (PSCs) polymer light-emitting diodes (PLEDs) field-effect transistors (FETs) electrochromics and biosensors. In this work, MnO2 has been synthesized by hydrothermal method and analyzed by infrared spectroscopy. The polybithiophene+MnO2 composite films were electrochemically prepared by cyclic voltammetry technic on a conductor glass substrate ITO (indium–tin-oxide). The composite films are characterized by cyclic voltammetry, impedance spectroscopy and photoelectrochemical analyses. The results confirmed the presence of manganese dioxide nanoparticles in the polymer layer. An application has been made by using these deposits as an electrode in a photoelectrochemical cell for measuring photocurrent tests. The composite films show a significant photocurrent intensity 80 μA.cm-2.

Keywords: polybithiophene, MnO2, photoelectrochemical cells, composite films

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Authors: Charmi Chande, Ravindra Phadke

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Microfluidics devices are fabricated by using multiple fabrication methods. Photolithography is one of the common methods wherein SU8 is widely used for making master which in turn is used for making working chip by the process of soft lithography. The high-aspect ratio features of SU-8 makes it suitable to be used as micro moulds for injection moulding, hot embossing, and moulds to form polydimethylsiloxane (PDMS) structures for bioMEMS (Microelectromechanical systems) applications. But due to high cost, difficulty in procuring and need for clean room, restricts the use of this polymer especially in developing countries and small research labs. ‘Bisphenol –A’ based polymers in mixture with curing agent are used in various industries like Paints and coatings, Adhesives, Electrical systems and electronics, Industrial tooling and composites. We present the novel use of ‘Bisphenol – A’ based polymer in fabricating micro channels for Lab On Chip(LOC) devices. The present paper describes the prototype for production of microfluidics chips using range of ‘Bisphenol-A’ based polymers viz. GY 250, ATUL B11, DER 331, DER 330 in mixture with cationic photo initiators. All the steps of chip production were carried out using an inexpensive approach that uses low cost chemicals and equipment. This even excludes the need of clean room. The produced chips using all above mentioned polymers were validated with respect to height and the chip giving least height was selected for further experimentation. The lowest height achieved was 7 micrometers by GY250. The cost of the master fabricated was $ 0.20 and working chip was $. 0.22. The best working chip was used for morphological identification and profiling of microorganisms from environmental samples like soil, marine water and salt water pan sites. The current chip can be adapted for various microbiological screening experiments like biochemical based microbial identification, studying uncultivable microorganisms at single cell/community level.

Keywords: bisphenol–A based epoxy, cationic photoinitiators, microfabrication, photolithography

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Authors: Son Nguyen, Thanh Van, Ly Le

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Ca2+ - dependent calmodulin kinase IIa (CaMKIIa) has recently been found to associate with protein tau missorting and polymerization in Alzheimer’s Disease (AD). However, there has yet inhibitors targeting CaMKIIa to investigate the correlation between CaMKIIa activity and protein tau polymer formation. Combining virtual screening and our statistics in binding contribution scoring function (BCSF), we rationally identified potential compounds that bind to specific CaMKIIa active site and specificity-affinity distribution of the ligand within the active site. Using molecular dynamics simulation, we identified structural stability of CaMKIIa and potent inhibitors, and site-directed bonding, separating non-specific and specific molecular interaction features. Despite of variation in confirmation of simulation time, interactions of the potent inhibitors were found to be strongly associated with the unique chemical features extracted from molecular binding poses. In addition, competitive inhibitors within CaMKIIa showed an important molecular recognition pattern toward specific ligand features. Our approach combining virtual screening with BCSF may provide an universally applicable method for precise identification in the discovery of compounds.

Keywords: Alzheimer’s disease, Ca 2+ -dependent calmodulin kinase IIa, protein tau, molecular docking

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Authors: Fathi Soliman

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With the ultimate goal of developing the separation of n-paraffin as phase change material (PCM) by means of molecular dynamic simulations, we attempt to predict the solubility of aromatic n-paraffin in two organic solvents: Butyl Acetate (BA) and Methyl Iso Butyl Ketone (MIBK). A simple model of aromatic paraffin: 2-hexadecylantharacene with amorphous molecular structure and periodic boundary conditions was constructed. The results showed that MIBK is the best solvent to separate ultra-pure phase change materials and this data was compatible with experimental data done to separate ultra-pure n-paraffin from waste petroleum aromatic paraffin wax, the separated n-paraffin was characterized by XRD, TGA, GC and DSC, moreover; data revealed that the n-paraffin separated by using MIBK is better as PCM than that separated using BA.

Keywords: molecular dynamics simulation, n-paraffin, organic solvents, phase change materials, solvent extraction

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Authors: Anis A. Ansari, Aftab A. Ansari

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Electronic waste is inundating the traditional solid-waste-disposal facilities, which are inadequately designed to handle and manage such type of new wastes. Since electronic waste contains mostly hazardous and even toxic materials, the seriousness of its effects on human health and the environment cannot be ignored in present scenario. Waste from the electronic industry is increasing exponentially day by day. From the last 20 years, we are continuously generating huge quantities of e-waste such as obsolete computers and other discarded electronic components, mainly due to evolution of newer technologies as a result of constant efforts in research and development in this sector. Polymers, one of the major constituents in almost every electronic waste, such as computers, printers, electronic equipment, entertainment devices, mobile phones, television sets etc., are if properly recycled can create a new business opportunity. This would not only create potential market for polymers to improve economy but also the priceless land used as dumping sites of electronic waste, can be utilized for other productive purposes.

Keywords: polymer recycling, electronic waste, hazardous materials, electronic components

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Authors: Muchun Yu, Xue Gao, Qian Chen

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As a novel passive vibration isolation technology, molecular spring isolator (MSI) is investigated in this paper. An MSI consists of water and hydrophobic zeolites as working medium. Under periodic excitation, water molecules intrude into hydrophobic pores of zeolites when the pressure rises and water molecules extrude from hydrophobic pores when pressure drops. At the same time, energy is stored, released and dissipated. An MSI of piston-cylinder structure was designed in this work. Experiments were conducted to investigate the stiffness properties of MSI. The results show that MSI exhibits high-static-low dynamic (HSLD) stiffness. Furthermore, factors such as the quantity of zeolites, temperature, and ions in water are proved to have an influence on the stiffness properties of MSI.

Keywords: hydrophobic zeolites, molecular spring, stiffness, vibration isolation

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Authors: Milica Karadžić, Lidija Jevrić, Sanja Podunavac-Kuzmanović, Strahinja Kovačević, Anamarija Mandić, Aleksandar Oklješa, Andrea Nikolić, Marija Sakač, Katarina Penov Gaši

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Using chemometric approach, the relationships between the chromatographic lipophilicity and in silico molecular descriptors for twenty-nine selected steroid derivatives were studied. The chromatographic lipophilicity was predicted using artificial neural networks (ANNs) method. The most important in silico molecular descriptors were selected applying stepwise selection (SS) paired with partial least squares (PLS) method. Molecular descriptors with satisfactory variable importance in projection (VIP) values were selected for ANN modeling. The usefulness of generated models was confirmed by detailed statistical validation. High agreement between experimental and predicted values indicated that obtained models have good quality and high predictive ability. Global sensitivity analysis (GSA) confirmed the importance of each molecular descriptor used as an input variable. High-quality networks indicate a strong non-linear relationship between chromatographic lipophilicity and used in silico molecular descriptors. Applying selected molecular descriptors and generated ANNs the good prediction of chromatographic lipophilicity of the studied steroid derivatives can be obtained. This article is based upon work from COST Actions (CM1306 and CA15222), supported by COST (European Cooperation and Science and Technology).

Keywords: artificial neural networks, chemometrics, global sensitivity analysis, liquid chromatography, steroids

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Authors: M. Masroor Akhtar Khan, Moin Uddin, Lalit Varshney

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Recently, there has been a rapidly expanding interest in finding applications of natural polymers in view of value addition to agriculture. It is now being realized that radiation processing of natural polysaccharides can be beneficially utilized either to improve the existing methodologies used for processing the natural polymers or to impart value addition to agriculture by converting them into more useful form. Gamma-ray irradiation is employed to degrade and lower the molecular weight of some of the natural polysaccharides like alginates, chitosan and carrageenan into small sized oligomers. When these oligomers are applied to plants as foliar sprays, they elicit various kinds of biological and physiological activities, including promotion of plant growth, seed germination, shoot elongation, root growth, flower production, suppression of heavy metal stress, etc. Furthermore, application of these oligomers can shorten the harvesting period of various crops and help in reducing the use of insecticides and chemical fertilizers. In recent years, the oligomers of sodium alginate obtained by irradiating the latter with gamma-rays at 520 kGy dose are being employed. It was noticed that the oligomers derived from the natural polysaccharides could induce growth, photosynthetic efficiency, enzyme activities and most importantly the production of secondary metabolite in the plants like Artemisia annua, Beta vulgaris, Catharanthus roseus, Chrysopogon zizanioides, Cymbopogon flexuosus, Eucalyptus citriodora, Foeniculum vulgare, Geranium sp., Mentha arvensis, Mentha citrata, Mentha piperita, Mentha virdis, Papaver somniferum and Trigonella foenum-graecum. As a result of the application of these oligomers, the yield and/or contents of the active constituents of the aforesaid plants were significantly enhanced. The productivity, as well as quality of medicinal and aromatic plants, may be ameliorated by this novel technique in an economical way as a very little quantity of these irradiated (depolymerised) polysaccharides is needed. Further, this is a very safe technique, as we did not expose the plants directly to radiation. The radiation was used to depolymerize the polysaccharides into oligomers.

Keywords: essential oil, medicinal and aromatic plants, plant production, radiation processed polysaccharides, active constituents

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Authors: S. M. Chabane sari S. Zargou, A.R. Senoudi, F. Benmouna

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Immobilization of nano particles (NPs) is the subject of numerous studies pertaining to the design of polymer nano composites, supported catalysts, bioactive colloidal crystals, inverse opals for novel optical materials, latex templated-hollow inorganic capsules, immunodiagnostic assays; “Pickering” emulsion polymerization for making latex particles and film-forming composites or Janus particles; chemo- and biosensors, tunable plasmonic nano structures, hybrid porous monoliths for separation science and technology, biocidal polymer/metal nano particle composite coatings, and so on. Particularly, in the recent years, the literature has witnessed an impressive progress of investigations on polymer coatings, grafts and particles as supports for anchoring nano particles. This is actually due to several factors: polymer chains are flexible and may contain a variety of functional groups that are able to efficiently immobilize nano particles and their precursors by dispersive or van der Waals, electrostatic, hydrogen or covalent bonds. We review methods to prepare polymer-immobilized nano particles through a plethora of strategies in view of developing systems for separation, sensing, extraction and catalysis. The emphasis is on methods to provide (i) polymer brushes and grafts; (ii) monoliths and porous polymer systems; (iii) natural polymers and (iv) conjugated polymers as platforms for anchoring nano particles. The latter range from soft bio macromolecular species (proteins, DNA) to metallic, C60, semiconductor and oxide nano particles; they can be attached through electrostatic interactions or covalent bonding. It is very clear that physicochemical properties of polymers (e.g. sensing and separation) are enhanced by anchored nano particles, while polymers provide excellent platforms for dispersing nano particles for e.g. high catalytic performances. We thus anticipate that the synergetic role of polymeric supports and anchored particles will increasingly be exploited in view of designing unique hybrid systems with unprecedented properties.

Keywords: gold, layer, polymer, macromolecular

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Authors: M. R. Ghasemi, R. Ghiasi, H. Varaee

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Model updating method has received increasing attention in damage detection structures based on measured modal parameters. Therefore, a probability-based damage detection (PBDD) procedure based on a model updating procedure is presented in this paper, in which a one-stage model-based damage identification technique based on the dynamic features of a structure is investigated. The presented framework uses a finite element updating method with a Monte Carlo simulation that considers the uncertainty caused by measurement noise. Enhanced ideal gas molecular movement (EIGMM) is used as the main algorithm for model updating. Ideal gas molecular movement (IGMM) is a multiagent algorithm based on the ideal gas molecular movement. Ideal gas molecules disperse rapidly in different directions and cover all the space inside. This is embedded in the high speed of molecules, collisions between them and with the surrounding barriers. In IGMM algorithm to accomplish the optimal solutions, the initial population of gas molecules is randomly generated and the governing equations related to the velocity of gas molecules and collisions between those are utilized. In this paper, an enhanced version of IGMM, which removes unchanged variables after specified iterations, is developed. The proposed method is implemented on two numerical examples in the field of structural damage detection. The results show that the proposed method can perform well and competitive in PBDD of structures.

Keywords: enhanced ideal gas molecular movement (EIGMM), ideal gas molecular movement (IGMM), model updating method, probability-based damage detection (PBDD), uncertainty quantification

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Authors: Christy Rosaline, Rathankar Roa, Waheeta Hopper

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Persistence of tuberculosis, emergence of multidrug-resistance and extensively drug-resistant forms of the disease, has increased the interest in developing new antitubercular drugs. Developing inhibitors for 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase from Mycobacterium tuberculosis (MtbDAH7Ps), an enzyme involved in shikimate pathway, gives a selective target for antitubercular agents. MtbDAH7Ps was screened against ZINC database, and shortlisted compounds were subjected to induce fit docking. Prime/Molecular Mechanics Generalized Born Surface Area calculation was used to validate the binding energy of ligand-protein complex. Molecular Dynamics analysis for of the lead compounds–MtbDAH7Ps complexes showed that the backbone of MtbDAH7Ps in their complexes were stable. These results suggest that the shortlisted lead compounds ZINC04097114, ZINC15163225, ZINC16857013, ZINC06275603, and ZINC05331260 could be developed into novel drug leads to inhibit DAH7Ps in Mycobacterium tuberculosis.

Keywords: MtbDAH7Ps, Mycobacterium tuberculosis, HTVS, molecular dynamics

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Authors: Micheale Yifter Weldemichael, Stefaan Werbrouck, Hailay Mehari Gebremedhn

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Sesame (Sesamum indicum L.) is among the most important oilseed crops for its high edible oil quality and quantity. Sesame is grown for food, medicinal, pharmaceutical, and industrial uses. Sesame is also cultivated as a main cash crop in Asia and Africa by smallholder farmers. Despite the global exponential increase in sesame cultivation area, its production and productivity remain low, mainly due to biotic and abiotic constraints. Notwithstanding the efforts to solve these problems, a low level of genetic variation and inadequate genomic resources hinder the progress of sesame improvement. The objective of this paper is, therefore, to review recent advances in the area of molecular breeding and transformation to overcome major production constraints and could result in enhanced and sustained sesame production. This paper reviews various researches conducted to date on molecular breeding and genetic transformation in sesame focusing on molecular markers used in assessing the available online database resources, genes responsible for key agronomic traits as well as transgenic technology and genome editing. The review concentrates on quantitative and semi-quantitative studies on molecular breeding for key agronomic traits such as improvement of yield components, oil and oil-related traits, disease and insect/pest resistance, and drought, waterlogging and salt tolerance, as well as sesame genetic transformation and genome editing techniques. Pitfalls and limitations of existing studies and methodologies used so far are identified and some priorities for future research directions in sesame genetic improvement are identified in this review.

Keywords: molecular breeding, oil, sesame, shattering

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Authors: Nikhil Agrawal, Adam A. Skelton

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Alzheimer’s disease (AD) is one of the most common forms of dementia, which is caused by misfolding and aggregation of amyloid beta (Aβ) peptides into amyloid-β fibrils (Aβ fibrils). To disrupt the remodeling of Aβ fibrils, a number of candidate molecules have been proposed. To study the molecular mechanisms of Aβ fibrils remodeling we performed a series of all-atom molecular dynamics simulations, a total time of 3µs, in explicit solvent. Several previously undiscovered candidate molecule-Aβ fibrils binding modes are unraveled; one of which shows the direct conformational change of the Aβ fibril by understanding the physicochemical factors responsible for binding and subsequent remodeling of Aβ fibrils by the candidate molecule, open avenues into structure-based drug design for AD can be opened.

Keywords: alzheimer’s disease, amyloid, MD simulations, misfolded protein

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Authors: Pallab Datta, Jyotirmoy Chatterjee, Santanu Dhara

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Over the past few years, phosphorous containing polymers have received widespread attention for applications such as high performance optical fibers, flame retardant materials, drug delivery and tissue engineering. Being pentavalent, phosphorous can exist in different chemical environments in these polymers which increase their versatility. In human biochemistry, phosphorous based compounds exert their functions both in soluble and insoluble form occurring as inorganic or as organophosphorous compounds. Specifically in case of biomacromolecules, phosphates are critical for functions of DNA, ATP, phosphoproteins, phospholipids, phosphoglycans and several coenzymes. Inspired by the role of phosphorous in functional biomacromolecules, design and synthesis of biomimetic materials are thus carried out by several authors to study macromolecular function or as substitutes in clinical tissue regeneration conditions. In addition, many regulatory signals of the body are controlled by phoshphorylation of key proteins present either in form of growth factors or matrix-bound scaffold proteins. This inspires works on synthesis of phospho-peptidomimetic amino acids for understanding key signaling pathways and this is extended to obtain molecules with potentially useful biological properties. Apart from above applications, phosphate groups bound to polymer backbones have also been demonstrated to improve function of osteoblast cells and augment performance of bone grafts. Despite the advantages of phosphate grafting, however, there is limited understanding on effect of degree of phosphorylation on macromolecular physicochemical and/or biological properties. Such investigations are necessary to effectively translate knowledge of macromolecular biochemistry into relevant clinical products since they directly influence processability of these polymers into suitable scaffold structures and control subsequent biological response. Amongst various techniques for fabrication of biomimetic scaffolds, nanofibrous scaffolds fabricated by electrospinning technique offer some special advantages in resembling the attributes of natural extracellular matrix. Understanding changes in physico-chemical properties of polymers as function of phosphorylation is therefore going to be crucial in development of nanofiber scaffolds based on phosphorylated polymers. The aim of the present work is to investigate the effect of phosphorous grafting on the electrospinning behavior of polymers with aim to obtain biomaterials for bone regeneration applications. For this purpose, phosphorylated derivatives of two polymers of widely different electrospinning behaviors were selected as starting materials. Poly(vinyl alcohol) is a conveniently electrospinnable polymer at different conditions and concentrations. On the other hand, electrospinning of chitosan backbone based polymers have been viewed as a critical challenge. The phosphorylated derivatives of these polymers were synthesized, characterized and electrospinning behavior of various solutions containing these derivatives was compared with electrospinning of pure poly (vinyl alcohol). In PVA, phosphorylation adversely impacted electrospinnability while in NMPC, higher phosphate content widened concentration range for nanofiber formation. Culture of MG-63 cells on electrospun nanofibers, revealed that degree of phosphate modification of a polymer significantly improves cell adhesion or osteoblast function of cultured cells. It is concluded that improvement of cell response parameters of nanofiber scaffolds can be attained as a function of controlled degree of phosphate grafting in polymeric biomaterials with implications for bone tissue engineering applications.

Keywords: bone regeneration, chitosan, electrospinning, phosphorylation

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Authors: Polina Prokopovich

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Disease-modifying osteoarthritis drugs (DMOADs) are a new therapeutic class for OA, preventing or inhibiting OA development. Unfortunately, none of the DMOADs have been clinically approved due to their poor therapeutic effects in clinical trials. The joint environment has played a role in the poor clinical performance of these drugs by limiting the amount of drug effectively delivered as well as the time that the drug spends within the joint space. The current study aims to enhance the cartilage uptake and retention time of the DMOADs-model (licofelone), which showed a significant therapeutic effect against OA progression and is currently in phase III. Licofelone will be covalently conjugated to the hydrolysable, cytocompatible, and cationic poly beta-amino ester polymers (PBAE). The cationic polymers (A16 and A87) can be electrostatically attached to the negatively charged cartilage component (glycosaminoglycan), which will increase the drug penetration through the cartilage and extend the drug time within the cartilage. In the cartilage uptake and retention time studies, an increase of 18 to 37 times of the total conjugated licofelone to A87 and A16 was observed when compared to the free licofelone. Furthermore, the conjugated licofelone to A87 was detectable within the cartilage at 120 minutes, while the free licofelone was not detectable after 60 minutes. Additionally, the A87-licofelone conjugate showed no effect on the chondrocyte viability. In conclusion, the cationic A87 and A16 polymers increased the percentage of licofelone within the cartilage, which could potentially enhance the therapeutic effect and pharmacokinetic performance of licofelone or other DMOADs clinically.

Keywords: PBAE, cartilage., osteoarthritis, injectable biomaterials, drug delivery

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Authors: Milica Ž. Karadžić, Lidija R. Jevrić, Sanja Podunavac-Kuzmanović, Strahinja Z. Kovačević, Anamarija I. Mandić, Katarina Penov-Gaši, Andrea R. Nikolić, Aleksandar M. Oklješa

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This study considered selection of the in silico molecular descriptors and the models for newly synthesized steroid derivatives description and their characterization using chemometric techniques. Multiple linear regression (MLR) models were established and gave the best molecular descriptors for quantitative structure-retention relationship (QSRR) modeling of the retention of the investigated molecules. MLR models were without multicollinearity among the selected molecular descriptors according to the variance inflation factor (VIF) values. Used molecular descriptors were ranked using generalized pair correlation method (GPCM). In this method, the significant difference between independent variables can be noticed regardless almost equal correlation between dependent variable. Generated MLR models were statistically and cross-validated and the best models were kept. Models were ranked using sum of ranking differences (SRD) method. According to this method, the most consistent QSRR model can be found and similarity or dissimilarity between the models could be noticed. In this study, SRD was performed using average values of experimentally observed data as a golden standard. Chemometric analysis was conducted in order to characterize newly synthesized steroid derivatives for further investigation regarding their potential biological activity and further synthesis. This article is based upon work from COST Action (CM1105), supported by COST (European Cooperation in Science and Technology).

Keywords: generalized pair correlation method, molecular descriptors, regression analysis, steroids, sum of ranking differences

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Authors: Shimaa A. Higazy, Olfat E. El-Azabawy, Ahmed M. Al-Sabagh, Notaila M. Nasser, Eman A. Khamis

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In this work, two novel Schiff base polymers (PSB1 and PSB₂) with extra-high protective barrier features were facilely prepared via Polycondensation reactions. They were applied for the first time as effective corrosion inhibitors in the sour corrosive media of petroleum environments containing hydrogen sulfide (H₂S) gas. For studying the polymers' inhibitive action on the carbon steel, numerous corrosion testing methods including potentiodynamic polarization (PDP), open circuit potential, and electrochemical impedance spectroscopy (EIS) have been employed at various temperatures (298-328 K) in the oil wells formation water with H₂S concentrations of 100, 400, and 700 ppm as aggressive media. The activation energy (Ea) and other thermodynamic parameters were computed to describe the mechanism of adsorption. The corrosion morphological traits and steel samples' surfaces composition were analyzed by field emission scanning electron microscope and energy dispersive X-ray analysis. The PSB2 inhibited sour corrosion more effectively than PSB1 when subjected to electrochemical testing. The 100 ppm concentration of PSB2 exhibited 82.18 % and 81.14 % inhibition efficiencies at 298 K in PDP and EIS measurements, respectively. While at 328 K, the inhibition efficiencies were 61.85 % and 67.4 % at the same dosage and measurements. These poly Schiff bases exhibited fascinating performance as corrosion inhibitors in sour environment. They provide a great corrosion inhibition platform for the sustainable future environment.

Keywords: schiff base polymers, corrosion inhibitors, sour corrosive media, potentiodynamic polarization, H₂S concentrations

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Authors: Jiajun Duan, Yang Li, Jianan Gao, Runzi Cao, Enxiang Shang, Wen Zhang

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Reactive oxygen species (ROS) generation is considered as an important photoaging mechanism of microplastics (MPs) and nanoplastics (NPs). To elucidate the ROS-induced MP/NP aging processes in water under UV365 irradiation, we examined the effects of surface coatings, polymer types, and grain sizes on ROS generation and photoaging intermediates. Bare polystyrene (PS) NPs generated hydroxyl radicals (•OH) and singlet oxygen (¹O₂), while coated PS NPs (carboxyl-modified PS (PS-COOH), amino-modified PS (PS-NH₂)) and PS MPs generated fewer ROS due to coating scavenging or size effects. Polypropylene, polyethylene, polyvinyl chloride, polyethylene terephthalate, and polycarbonate MPs only generated •OH. For aromatic polymers, •OH addition preferentially occurred at benzene rings to form monohydroxy polymers. Excess •OH resulted in H abstraction, C-C scission, and phenyl ring opening to generate aliphatic ketones, esters, aldehydes, and aromatic ketones. For coated PS NPs, •OH preferentially attacked the surface coatings to result in decarboxylation and deamination reactions. For aliphatic polymers, •OH attack resulted in the formation of carbonyl groups from peracid, aldehyde, or ketone via H abstraction and C-C scission. Moreover, ¹O₂ might participate in phenyl ring opening for PS NPs and coating degradation for coated PS NPs. This study facilitates understanding the ROS-induced weathering process of NPs/MPs in water under UV irradiation.

Keywords: microplastics, nanoplastics, photoaging, reactive oxygen species, surface coating

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Authors: Ambrish Singh

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The corrosion inhibition performance of pyran derivatives (AP) on mild steel in 15% HCl was investigated by electrochemical impedance spectroscopy (EIS), potentiodynamic polarization, weight loss, contact angle, and scanning electron microscopy (SEM) measurements, DFT and molecular dynamic simulation. The adsorption of APs on the surface of mild steel obeyed Langmuir isotherm. The potentiodynamic polarization study confirmed that inhibitors are mixed type with cathodic predominance. Molecular dynamic simulation was applied to search for the most stable configuration and adsorption energies for the interaction of the inhibitors with Fe (110) surface. The theoretical data obtained are, in most cases, in agreement with experimental results.

Keywords: acidizing inhibitor, pyran derivatives, DFT, molecular simulation, mild steel, EIS

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