Search results for: inorganic molecular crystals

Authors: Mohammed Al-Bloushi, Sanghyun Jeong, Torove Leiknes

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Biofouling in the open recirculating cooling water systems may cause biological corrosion, which can reduce the performance, increase the energy consummation and lower heat exchange efficiencies of the cooling tower. Seawater cooling towers are prone to biofouling due to the presences of organic and inorganic compounds in the seawater. The availability of organic and inorganic nutrients, along with sunlight and continuous aeration of the cooling tower contributes to an environment that is ideal for microbial growth. Various microorganisms (algae, fungi, and bacteria) can grow in a cooling tower system under certain environmental conditions. The most commonly being used method to control the biofouling in the cooling tower is the addition of biocides such as chlorination. In this study, algae containing diatom and green algae were added to the cooling tower basin, and its viability was monitored in the recirculating cooling seawater loop as well as in the cooling tower basin. Continuous addition of biocides was employed in pilot-scale seawater cooling towers, and it was operated continuously for 2 months. Three different types of oxidizing biocides, namely chlorine, chlorine dioxide and ozone, were tested. The results showed that all biocides were effective in keeping the biological growth to the minimum regardless of algal addition. Amongst the biocides, ozone could reduce 99% of total live cells of bacteria and algae, followed by chlorine dioxide at 97%, while the conventional chlorine showed only 89% reduction in the bioactivities.

Keywords: algae, biocide, biofouling, seawater cooling tower

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Authors: Zuxinsun, Samuel Eyley, Yongjian Guo, Reeta Salminen, Wim Thielemans

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Polypyrrole(PPy), as one of the most promising pseudocapacitor electrode materials, has attracted large research interest due to its low cost, high electrical conductivity and easy fabrication, limited capacitance, and cycling stability of PPy films hinder their practical applications. In this study, through adding different amounts of KCl into the pyrrole and CNC-COO⁻ system, three-dimensional, porous, and reticular PPy films were electropolymerized at last without the assistance of any template or substrate. Replacing KCl with NaCl, KBr, and NaClO4, the porous PPy films were still obtained rather than relatively dense PPy films which were deposited with pyrrole and CNC-COO⁻ or pyrrole and KCl. The nucleation and growth mechanisms of PPy films were studied in the deposited electrolyte with or without salts to illustrate the evolution of morphology from relatively dense to porous structure. The capacitance of PPy/CNC-COO⁻-Cl-(ClO4-)_0.5 films increased from 160.6 to 183.4 F g⁻¹ at 0.2 A g⁻¹. More importantly, at a high current density of 2.0 A g⁻¹ (20 mA cm⁻²), the PPy/CNC-COO⁻-Cl-(ClO4-)_0.5 films exhibited an excellent capacitance of 125.0 F g⁻¹ (1.19 F cm⁻²), increasing about 203.7 % over PPy/CNC-COO- films. 103.3 % of its initial capacitance was retained after 5000 cycles at 2 A g⁻¹ (20 mA cm⁻²) for the PPy/CNC-COO⁻-Cl-(ClO4-)_0.5 supercapacitor. The analyses reveal that the porous and reticular PPy/CNC-COO⁻-salts films open up more active reaction areas to store charges. The stiff and ribbonlike CNC-COO⁻ as the permanent dopants improve strength and stability of PPy/CNC-COO⁻-salts films. Our demonstration provides a simple and practical way to deposit PPy-based supercapacitors with high capacitance and cycling ability.

Keywords: polypyrrole, supercapacitors, cellulose nanocrystals, porous and reticular structure, inorganic salts

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Authors: Hyery Kang, Dong-Yeun Koh, Yun-Ho Ahn, Huen Lee

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Terahertz time-domain spectroscopy (THz-TDS) was used to observe the THF clathrate hydrate system with dosage of polyvinylpyrrolidone (PVP) with three different average molecular weights (10,000 g/mol, 40,000 g/mol, 360,000 g/mol). Distinct footprints of phase transition in the THz region (0.4 - 2.2 THz) were analyzed and absorption coefficients and complex refractive indices are obtained and compared in the temperature range of 253 K to 288 K. Along with the optical properties, ring breathing and stretching modes for different molecular weights of PVP in THF hydrate are analyzed by Raman spectroscopy.

Keywords: clathrate hydrate, terahertz, polyvinylpyrrolidone (PVP), THz-TDS, inhibitor

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Authors: R. Pilafkan, M. Kaffash Irzarahimi, S. F. Asbaghian Namin

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The biaxial buckling behavior of single-layered graphene sheets (SLGSs) is studied in the present work. To consider the size-effects in the analysis, Eringen’s nonlocal elasticity equations are incorporated into classical plate theory (CLPT). A Generalized Differential Quadrature Method (GDQM) approach is utilized and numerical solutions for the critical buckling loads are obtained. Then, molecular dynamics (MD) simulations are performed for a series of zigzag SLGSs with different side-lengths and with various boundary conditions, the results of which are matched with those obtained by the nonlocal plate model to numerical the appropriate values of nonlocal parameter relevant to each type of boundary conditions.

Keywords: biaxial buckling, single-layered graphene sheets, nonlocal elasticity, molecular dynamics simulation, classical plate theory

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Authors: Anjana Sagar

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Arsenic poisoned ground water is a major concern in South Asia. The arsenic enters the food chain not only through drinking but also by using arsenic polluted water for irrigation. Arsenic is highly toxic in its inorganic forms; however, organic forms of arsenic are comparatively less toxic. In terrestrial plants, inorganic form of arsenic is predominantly found; however, we found that significant proportion of organic arsenic was present in root and shoot of a staple legume, chickpea (Cicer arientinum L) plants. Chickpea plants were raised in pot culture on soils spiked with arsenic ranging from 0-70 mg arsenate per Kg soil. Total arsenic concentrations of chickpea shoots and roots were determined by inductively coupled plasma-mass-spectrometry (ICP-MS) ranging from 0.76 to 20.26, and 2.09 to 16.43 µg g⁻¹ dry weight, respectively. Information on arsenic species was acquired by methanol/water extraction method, with arsenic species being analyzed by high-performance liquid chromatography (HPLC) coupled with ICP-MS. Dimethylarsinic acid (DMA) was the only organic arsenic species found in amount from 0.02 to 3.16 % of total arsenic shoot concentration and 0 to 6.93 % of total arsenic root concentration, respectively. To investigate the source of the organic arsenic in chickpea plants, arsenic species in the rhizosphere of soils of plants were also examined. The absence of organic arsenic in soils would suggest the possibility of formation of DMA in plants. The present investigation provides useful information for better understanding of distribution of arsenic species in terrestrial legume plants.

Keywords: arsenic, arsenic speciation, dimethylarsinic acid, organoarsenic

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Authors: Mahdi Golriz

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The aim of this work is to estimate the change in molecular structure of linear low-density polyethylene (LLDPE) during peroxide modification can be detected by a simple rheological method. For this purpose a commercial grade LLDPE (Exxon MobileTM LL4004EL) was reacted with different doses of dicumyl peroxide (DCP). The samples were analyzed by size-exclusion chromatography coupled with a light scattering detector. The dynamic shear oscillatory measurements showed a deviation of the δ-׀G ׀٭curve from that of the linear LLDPE, which can be attributed to the presence of long-chain branching (LCB). By the use of a simple rheological method that utilizes melt rheology, transformations in molecular architecture induced on an originally linear low density polyethylene during the early stages of reactive modification were indicated. Reasonable and consistent estimates are obtained, concerning the degree of LCB, the volume fraction of the various molecular species produced in peroxide modification of LLDPE.

Keywords: linear low-density polyethylene, peroxide modification, long-chain branching, rheological method

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Authors: Soraya Abtouche, Zeyneb Ghoualem, Syrine Daoudi, Lina Ouldmohamed, Xavier Assfeld

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This work reports density functional theory calculations of the optimized geometries, molecular reactivity, energy gap,and thermodynamic properties of the free base (H2P) and their Zn (II) metallated (ZnP), bearing one, two, or three carboxylic acid groups using the hybrid functional B3LYP, Cam-B3lYP, wb97xd with 6-31G(d,p) basis sets. When donating groups are attached to the molecular dye, the bond lengths are slightly decreased, which is important for the easy transfer of an electron from donating to the accepting group. For all dyes, the highest occupied molecular orbital/lowest occupied molecular orbital analysis results in positive outcomes upon electron injection to the semiconductor and subsequent dye regeneration by the electrolyte. The ionization potential increases with increasing conjugation; therefore, the compound dye attached to one carboxylic acid group has the highest ionization potential. The results show higher efficiencies of those sensitized with ZnP. These results have been explained, taking into account the electronic character of the metal ion, which acts as a mediator in the injection step, and, on the other hand, considering the number of anchoring groups to which it binds to the surface of TiO2.

Keywords: DSSC, porphyrin, TD-DFT, electronic properties, donor-acceptor groups

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Authors: Mohamed Moussaoui, Mouna Baassi, Soukayna Baammi, Hatim Soufi, Mohammed Salah, Rachid Daoud, Achraf EL Allali, Mohammed Elalaoui Belghiti, Said Belaaouad

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The present study aims to investigate the quantitative structure-activity relationship (QSAR) of a series of Thiazole derivatives reported as anticancer agents (hepatocellular carcinoma), using principally the electronic descriptors calculated by the density functional theory (DFT) method and by applying the multiple linear regression method. The developed model showed good statistical parameters (R²= 0.725, R²ₐ𝒹ⱼ= 0.653, MSE = 0.060, R²ₜₑₛₜ= 0.827, Q²𝒸ᵥ = 0.536). The energy of the highest occupied molecular orbital (EHOMO) orbital, electronic energy (TE), shape coefficient (I), number of rotatable bonds (NROT), and index of refraction (n) were revealed to be the main descriptors influencing the anti-cancer activity. Additional Thiazole derivatives were then designed and their activities and pharmacokinetic properties were predicted using the validated QSAR model. These designed molecules underwent evaluation through molecular docking (MD) and molecular dynamic (MD) simulations, with binding affinity calculated using the MMPBSA script according to a 100 ns simulation trajectory. This process aimed to study both their affinity and stability towards Cyclin-Dependent Kinase 2 (CDK2), a target protein for cancer disease treatment. The research concluded by identifying four CDK2 inhibitors - A1, A3, A5, and A6 - displaying satisfactory pharmacokinetic properties. MDs results indicated that the designed compound A5 remained stable in the active center of the CDK2 protein, suggesting its potential as an effective inhibitor for the treatment of hepatocellular carcinoma. The findings of this study could contribute significantly to the development of effective CDK2 inhibitors.

Keywords: QSAR, ADMET, Thiazole, anticancer, molecular docking, molecular dynamic simulations, MMPBSA calculation

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Authors: Mannar R. Maurya, Bhawna Uprety, Fernando Avecilla, Pedro Adão, J. Costa Pessoa

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The reaction of the tripodal tetradentate dibasic ligand 6,6'–(2–(pyridin–2–yl)ethylazanediyl)bis(methylene)bis(2,4–di–tert–butylphenol), H2L1 I, with [VIVO(acac)2] in CH3CN gives the VVO–complex, [VVO(acac)(L1)] 1. Crystallization of 1 in CH3CN at ~0 ºC, gives dark blue crystals of 1, while at room temperature it affords dark green crystals of [{VVO(L1)}2µ–O] 3. Upon prolonged treatment of 1 in MeOH [VVO(OMe)(MeOH)(L1)] 2 is obtained. All three complexes are analyzed by single–crystal X–ray diffraction, depicting distorted octahedral geometry around vanadium. In the reaction of H2L1 with VIVOSO4 partial hydrolysis of the tripodal ligand results in elimination of the pyridyl fragment of L1 and the formation of H[VVO2(L2)] 4, containing the ONO tridentate ligand 6,6'–azanediylbis(methylene)bis(2,4–di–tert–butylphenol), H2L2 II. Compound 4, which was not fully characterized, undergoes dimerization in acetone yielding the hydroxido–bridged [{VVO(L2)}2µ–(HO)2] 5, having distorted octahedral geometry around each vanadium. In contrast, from a solution of 4 in acetonitrile, the dinuclear compound [{VVO(L2)}2µ–O] 6 is obtained, with trigonal bipyramidal geometry around each vanadium. The methoxido complex 2 is successfully employed as a functional catechol–oxidase mimic in the oxidation of catechol to o–quinone under air. The process is confirmed to follow a Michaelis–Menten type kinetics with respect to catechol, the Vmax and KM values obtained being 7.66×10–6 M min -1 and 0.0557 M, respectively, and the turnover frequency is 0.0541 min–1. Complex 2 is also used as a catalyst precursor for the oxidative bromination of thymol in aqueous medium. The selectivity shows quite interesting trends, namely when not using excess of primary oxidizing agent, H2O2 the para mono–brominated product corresponds to ~93 % of the products and no dibromo derivative is formed.

Keywords: oxidovanadium (V) complexes, tripodal ligand, crystal structure, catechol oxidase mimetic activity

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Authors: Saleh Gorji, Sahil Gulati, Ana Pakzad

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Continuous electron diffraction tomography, also known as microcrystal electron diffraction (MicroED) or three-dimensional electron diffraction (3DED), is a powerful technique, which in combination with cryo-electron microscopy (cryo-ED), can provide atomic-scale 3D information about the crystal structure and composition of different classes of crystalline materials such as proteins, peptides, and small molecules. Unlike the well-established X-ray crystallography method, 3DED does not require large single crystals and can collect accurate electron diffraction data from crystals as small as 50 – 100 nm. This is a critical advantage as growing larger crystals, as required by X-ray crystallography methods, is often very difficult, time-consuming, and expensive. In most cases, specimens studied via 3DED method are electron beam sensitive, which means there is a limitation on the maximum amount of electron dose one can use to collect the required data for a high-resolution structure determination. Therefore, collecting data using a conventional scintillator-based fiber coupled camera brings additional challenges. This is because of the inherent noise introduced during the electron-to-photon conversion in the scintillator and transfer of light via the fibers to the sensor, which results in a poor signal-to-noise ratio and requires a relatively higher and commonly specimen-damaging electron dose rates, especially for protein crystals. As in other cryo-EM techniques, damage to the specimen can be mitigated if a direct detection camera is used which provides a high signal-to-noise ratio at low electron doses. In this work, we have used two classes of such detectors from Gatan, namely the K3® camera (a monolithic active pixel sensor) and Stela™ (that utilizes DECTRIS hybrid-pixel technology), to address this problem. The K3 is an electron counting detector optimized for low-dose applications (like structural biology cryo-EM), and Stela is also a counting electron detector but optimized for diffraction applications with high speed and high dynamic range. Lastly, data collection workflows, including crystal screening, microscope optics setup (for imaging and diffraction), stage height adjustment at each crystal position, and tomogram acquisition, can be one of the other challenges of the 3DED technique. Traditionally this has been all done manually or in a partly automated fashion using open-source software and scripting, requiring long hours on the microscope (extra cost) and extensive user interaction with the system. We have recently introduced Latitude® D in DigitalMicrograph® software, which is compatible with all pre- and post-energy-filter Gatan cameras and enables 3DED data acquisition in an automated and optimized fashion. Higher quality 3DED data enables structure determination with higher confidence, while automated workflows allow these to be completed considerably faster than before. Using multiple examples, this work will demonstrate how to direct detection electron counting cameras enhance 3DED results (3 to better than 1 Angstrom) for protein and small molecule structure determination. We will also show how Latitude D software facilitates collecting such data in an integrated and fully automated user interface.

Keywords: continuous electron diffraction tomography, direct detection, diffraction, Latitude D, Digitalmicrograph, proteins, small molecules

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Authors: Amir Doustgani

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Melt electrospinning is a safe and simple technique for the production of micro and nanofibers which can be an alternative to conventional solvent electrospinning. The effects of various melt-electrospinning parameters, including molecular weight, electric field strength, flow rate and temperature on the morphology and fiber diameter of polylactic acid were studied. It was shown that molecular weight was the predominant factor in determining the obtainable fiber diameter of the collected fibers. An orthogonal design was used to examine process parameters. Results showed that molecular weight is the most effective parameter on the average fiber diameter of melt electrospun PLA nanofibers and the flow rate has the less important impact. Mean fiber diameter increased by increasing MW and flow rate, but decreased by increasing electric field strength and temperature. MFD of optimized fibers was below 100 nm and the result of software was in good agreement with the experimental condition.

Keywords: fiber formation, processing, spinning, melt blowing

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Authors: Mouna Baassi, Mohamed Moussaoui, Sanchaita Rajkhowa, Hatim Soufi, Said Belaaouad

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The objective of this paper is to address the challenging task of targeting Human Immunodeficiency Virus type 1 Reverse Transcriptase (HIV-1 RT) in the treatment of AIDS. Reverse Transcriptase inhibitors (RTIs) have limitations due to the development of Reverse Transcriptase mutations that lead to treatment resistance. In this study, a combination of statistical analysis and bioinformatics tools was adopted to develop a mathematical model that relates the structure of compounds to their inhibitory activities against HIV-1 Reverse Transcriptase. Our approach was based on a series of compounds recognized for their HIV-1 RT enzymatic inhibitory activities. These compounds were designed via software, with their descriptors computed using multiple tools. The most statistically promising model was chosen, and its domain of application was ascertained. Furthermore, compounds exhibiting comparable biological activity to existing drugs were identified as potential inhibitors of HIV-1 RT. The compounds underwent evaluation based on their chemical absorption, distribution, metabolism, excretion, toxicity properties, and adherence to Lipinski's rule. Molecular docking techniques were employed to examine the interaction between the Reverse Transcriptase (Wild Type and Mutant Type) and the ligands, including a known drug available in the market. Molecular dynamics simulations were also conducted to assess the stability of the RT-ligand complexes. Our results reveal some of the new compounds as promising candidates for effectively inhibiting HIV-1 Reverse Transcriptase, matching the potency of the established drug. This necessitates further experimental validation. This study, beyond its immediate results, provides a methodological foundation for future endeavors aiming to discover and design new inhibitors targeting HIV-1 Reverse Transcriptase.

Keywords: QSAR, ADMET properties, molecular docking, molecular dynamics simulation, reverse transcriptase inhibitors, HIV type 1

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Authors: Mohammad Hossein Modarressi, Mozhgan Mondeali, Khabat Barkhordari, Ali Etemadi

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The COVID-19 pandemic, caused by SARS-CoV-2, has led to significant concerns worldwide due to its catastrophic effects on public health. The SARS-CoV-2 infection is initiated with the binding of the receptor-binding domain (RBD) in its spike protein to the ACE2 receptor in the host cell membrane. Due to the error-prone entity of the viral RNA-dependent polymerase complex, the virus genome, including the coding region for the RBD, acquires new mutations, leading to the appearance of multiple variants. These variants can potentially impact transmission, virulence, antigenicity and evasive immune properties. S477N mutation located in the RBD has been observed in the SARS-CoV-2 omicron (B.1.1. 529) variant. In this study, we investigated the consequences of S477N mutation at the molecular level using computational approaches such as molecular dynamics simulation, protein-protein interaction analysis, immunoinformatics and free energy computation. We showed that displacement of Ser with Asn increases the stability of the spike protein and its affinity to ACE2 and thus increases the transmission potential of the virus. This mutation changes the folding and secondary structure of the spike protein. Also, it reduces antibody neutralization, raising concern about re-infection, vaccine breakthrough and therapeutic values.

Keywords: S477N, COVID-19, molecular dynamic, SARS-COV2 mutations

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Authors: R. Kerbachi , Y. Medkour, F. Sahnoune

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The integrated waste management is an important aspect in the implementation of sustainable development. Leachate generated by sanitary landfills is a high-strength wastewater that is likely to contain large amounts of organic and inorganic matter, with humic substances, as well as ammonia nitrogen, heavy metals, chlorinated organic and inorganic salts. Untreated leachates create a great potential for harm to the environment, they can permeate ground water or mix with surface water and contribute to the pollution of soil, ground water, and surface water. In Algeria, the treatment of landfill leachate is the weakest link in the solid waste management. This study focuses on the evaluation of the pollution load carried by leachate produced in a former sanitary landfill located to the west of Algiers and the implementation of advanced oxidation treatment (advanced oxidation process, AOP), Fenton, electro-Fenton etc. The characterization of these leachates shows that they have a high organic load, mineral and nitrogen. Measured COD reaches very high values of the order of 5000 to 20,000 mg O2 / L. On this non-biodegradable leachate, treatment tests have been carried out by the methods of coagulation-flocculation, Fenton oxidation, electrocoagulation and electro-Fenton. The removal efficiencies of pollution obtained for each of these modes of treatment are respectively 69, 80, 84 and 97%. The study shows that advanced oxidation processes are very suitable for the treatment of poorly biodegradable leachate.

Keywords: advanced oxidation processes, electrocoagulation, electro-Fenton, leachates treatment, sanitary landfill

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Authors: Neha Kanodia, M. Kamil

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Properties of mono layers of Pluronic F127 at air/water interface have been investigated by using Langmuir trough method. Pluronic F127 is a triblock copolymer of poly (ethyleneoxide) (PEO groups)– poly (propylene oxide) (PO groups)–poly(ethylene oxide) (PEO groups). Surface pressure versus mean molecular area isotherms is studied. The isotherm of the mono layer showed the characteristics of a pancake-to-brush transition upon compression of the mono layer. The effect of adding surfactant (SDS) to polymer and the effect of increasing loading on polymer was also studied. The effect of repeated compression and expansion cycle (or hysteresis curve) is investigated to know about stability of the film formed. Static elasticity of mono layer gives information about molecular arrangement, phase structure and phase transition.

Keywords: surface-pressure, mean molecular area isotherms, hysteresis, static elasticity

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Authors: T. M. Agbede, A. O. Adekiya

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Field experiments were conducted during 2013, 2014 and 2015 cropping seasons at Rufus Giwa Polytechnic, Owo, Ondo State, southwest Nigeria. The objective of the investigation was to determine the effect of Cocoa Pod Ash (CPA) and Poultry Manure (PM) applied solely and their combined form, as sources of fertilizers on soil properties, leaf nutrient composition, growth and yield of yam. Three soil amendments: CPA, PM (sole forms), CPA and PM (mixture), were applied at 20 t ha^-1 with an inorganic fertilizer (NPK 15-15-15) at 400 kg ha^-1 as a reference and a natural soil fertility, NSF (control). The five treatments were arranged in a randomized complete block design with three replications. The test soil was slightly acidic, low in organic carbon (OC), N, P, K, Ca and Mg. Results showed that soil amendments significantly increased (p = 0.05) tuber weights and growth of yam, soil and leaf N, P, K, Ca and Mg, soil pH and OC concentrations compared with the NSF (control). The mixture of CPA+PM treatment increased tuber weights of yam by 36%, compared with inorganic fertilizer (NPK) and 19%, compared with PM alone. Sole PM increased tuber weight of yam by 15%, compared with NPK. Sole or mixed forms of soil amendments showed remarkable improvement in soil physical properties, nutrient availability, compared with NPK and the NSF (control). Integrated application of CPA at 10 t ha^-1 + PM at 10 t ha^-1 was the most effective treatment in improving soil physical properties, increasing nutrient availability and yam performance than sole application of any of the fertilizer materials.

Keywords: cocoa pod ash, leaf nutrient composition, poultry manure, soil properties, yam

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Authors: Hassan Nour, Nouh Mounadi, Oussama Abchir, Belaidi Salah, Samir Chtita

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Cholinesterase enzymes are biological catalysts essential for the transformation of acetylcholine, which is a neurotransmitter implicated in memory and learning, into acetic acid and choline, altering the neurotransmission process in Alzheimer’s disease patients. Therefore, inhibition of cholinesterase enzymes is a relevant strategy for the symptomatic treatment of Alzheimer’s disease. The current investigation aims to explore potential cholinesterase (ChE) inhibitors through a comprehensive computational approach. Forty-nine phytoconstituents extracted from Cannabis sativa L. were in-silico screened using molecular docking and pharmacokinetic and toxicological analysis to evaluate their possible inhibitory effect on the cholinesterase enzymes. Two phytoconstituents belonging to cannabinoid derivatives were revealed to be promising candidates for Alzheimer's therapy by acting as cholinesterase inhibitors. They have exhibited high binding affinities towards the cholinesterase enzymes and showed their ability to interact with key residues involved in cholinesterase enzymatic activity. In addition, they presented good ADMET profiles allowing them to be promising oral drug candidates. Furthermore, molecular dynamics (MD) simulations were executed to explore their interaction stability under mimetic biological conditions and thus support our findings. To corroborate the docking results, the binding free energy corresponding to the more stable ligand-ChE complexes was re-estimated by applying the MM-PBSA method. MD and MM-PBSA studies affirmed that the ligand-ChE recognition is a spontaneous reaction leading to stable complexes. The conducted investigations have led to great findings that would strongly guide the pharmaceutical industries toward the rational development of potent anti-Alzheimer agents.

Keywords: Alzheimer’s disease, molecular docking, Cannabis sativa L., cholinesterase inhibitors, molecular dynamics, ADMET, MM-PBSA

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Authors: W. P. Hu, J. V. Kumar, Jeffrey J. P. Tsai

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The inhibition of SH2 domain regulated protein-protein interactions is an attractive target for developing an effective chemotherapeutic approach in the treatment of disease. Molecular simulation is a useful tool for developing new drugs and for studying molecular recognition. In this study, we searched potential drug compounds for the inhibition of SH2 domain by performing structural similarity search in PubChem Compound Database. A total of 37 compounds were screened from the database, and then we used the LibDock docking program to evaluate the inhibition effect. The best three compounds (AP22408, CID 71463546 and CID 9917321) were chosen for MD simulations after the LibDock docking. Our results show that the compound CID 9917321 can produce a more stable protein-ligand complex compared to other two currently known inhibitors of Src SH2 domain. The compound CID 9917321 may be useful for the inhibition of SH2 domain based on these computational results. Subsequently experiments are needed to verify the effect of compound CID 9917321 on the SH2 domain in the future studies.

Keywords: nonpeptide inhibitor, Src SH2 domain, LibDock, molecular dynamics simulation

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Authors: Rozhgar A. Khailany, Mehri Igci, Emine Bayraktar, Sakip Erturhan, Metin Karakok, Ahmet Arslan

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Kidney cancer is the most lethal urological cancer accounting for 3% of adult malignancies. VHL, a tumor-suppressor gene, is best known to be associated with renal cell carcinoma (RCC). The VHL functions as negative regulator of hypoxia inducible factors. Recent sequencing efforts have identified several novel frequent mutations of histone modifying and chromatin remodeling genes in ccRCC (clear cell RCC) including PBRM1 and SETD2. The PBRM1 gene encodes the BAF180 protein, which involved in transcriptional activation and repression of selected genes. SETD2 encodes a histone methyltransferase, which may play a role in suppressing tumor development. In this study, RNAs of 30 paired tumor and normal samples that were grouped according to the types of kidney cancer and clinical characteristics of patients, including gender and average age were examined by RT-PCR, SSCP and sequencing techniques. VHL, PBRM1 and SETD2 expressions were relatively down-regulated. However, statistically no significance was found (Wilcoxon signed rank test, p > 0.05). Interestingly, no mutation was observed on the contrary of previous studies. Understanding the molecular mechanisms involved in the pathogenesis of RCC has aided the development of molecular-targeted drugs for kidney cancer. Further analysis is required to identify the responsible genes rather than VHL, PBRM1 and SETD2 in kidney cancer.

Keywords: kidney cancer, molecular biomarker, expression analysis, mutation screening

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Authors: Irati Barandiaran, Xabier Velasco-Iza, Galder Kortaberria

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Hybrid inorganic/organic nanostructured materials based on block copolymers are of considerable interest in the field of Nanotechnology, taking into account that these nanocomposites combine the properties of polymer matrix and the unique properties of the added nanoparticles. The use of block copolymers as templates offers the opportunity to control the size and the distribution of inorganic nanoparticles. This research is focused on the surface modification of inorganic nanoparticles to reach a good interface between nanoparticles and polymer matrices which hinders the nanoparticle aggregation. The aim of this work is to obtain a good and selective dispersion of Fe3O4 magnetic nanoparticles into different types of block copolymers such us, poly(styrene-b-methyl methacrylate) (PS-b-PMMA), poly(styrene-b-ε-caprolactone) (PS-b-PCL) poly(isoprene-b-methyl methacrylate) (PI-b-PMMA) or poly(styrene-b-butadiene-b-methyl methacrylate) (SBM) by using different grafting strategies. Fe3O4 magnetic nanoparticles have been surface-modified with polymer or block copolymer brushes following different grafting methods (grafting to, grafting from and grafting through) to achieve a selective location of nanoparticles into desired domains of the block copolymers. Morphology of fabricated hybrid nanocomposites was studied by means of atomic force microscopy (AFM) and with the aim to reach well-ordered nanostructured composites different annealing methods were used. Additionally, nanoparticle amount has been also varied in order to investigate the effect of the nanoparticle content in the morphology of the block copolymer. Nowadays different characterization methods were using in order to investigate magnetic properties of nanometer-scale electronic devices. Particularly, two different techniques have been used with the aim of characterizing synthesized nanocomposites. First, magnetic force microscopy (MFM) was used to investigate qualitatively the magnetic properties taking into account that this technique allows distinguishing magnetic domains on the sample surface. On the other hand, magnetic characterization by vibrating sample magnetometer and superconducting quantum interference device. This technique demonstrated that magnetic properties of nanoparticles have been transferred to the nanocomposites, exhibiting superparamagnetic behavior similar to that of the maghemite nanoparticles at room temperature. Obtained advanced nanostructured materials could found possible applications in the field of dye-sensitized solar cells and electronic nanodevices.

Keywords: atomic force microscopy, block copolymers, grafting techniques, iron oxide nanoparticles

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Authors: Alok Shiomurti Tripathi, Ajay Kumar Timiri, Papiya Mitra Mazumder, Anil Chandewar

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The present study evaluates the possible drug interaction between glimepiride (GLIM) and sildenafil citrate (SIL) in streptozotocin (STZ) induced in diabetic nephropathic (DN) animals and also postulates the possible mechanism of interaction by molecular modeling studies. Diabetic nephropathy was induced by single dose of STZ (60 mg/kg, ip) and confirms it by assessing the blood and urine biochemical parameters on 28th day of its induction. Selected DN animals were used for the drug interaction between GLIM (0.5mg/kg, p.o.) and SIL (2.5 mg/kg, p.o.) after 29th and 70th day of protocol. Drug interaction were assessed by evaluating the plasma drug concentration using HPLC-UV and also determine the change in the biochemical parameter in blood and urine. Mechanism of the interaction was postulated by molecular modeling study using Maestro module of Schrodinger software. DN was confirmed as there was significant alteration in the blood and urine biochemical parameter in STZ treated groups. The concentration of SIL increased significantly (p<0.001) in rat plasma when co administered with GLIM after 70th day of protocol. Molecular modelling study revealed few important interactions with rat serum albumin and CYP2C9.GLIM has strong hydrophobic interaction with binding site residues of rat serum albumin compared to SIL. Whereas, for CYP2C9, GLIM has strong hydrogen bond with polar contacts and hydrophobic interactions than SIL. Present study concludes that bioavailability of SIL increases when co-administered chronically with GLIM in the management of DN animals and mechanism has been supported by molecular modeling studies.

Keywords: diabetic nephropathy, glimepiride, sildenafil citrate, pharmacokinetics, homology modeling, schrodinger

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Authors: Nahush Modak, Meena Pangarkar, Anand Pathak, Ankita Tamhane

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Background: Breast cancer is the prominent cause of cancer and mortality among women. This study was done to show the statistical analysis of a cohort of over 250 patients detected with breast cancer diagnosed by oncologists using Immunohistochemistry (IHC). IHC was performed by using ER; PR; HER2; Ki-67 antibodies. Materials and methods: Formalin fixed Paraffin embedded tissue samples were obtained by surgical manner and standard protocol was followed for fixation, grossing, tissue processing, embedding, cutting and IHC. The Ventana Benchmark XT machine was used for automated IHC of the samples. Antibodies used were supplied by F. Hoffmann-La Roche Ltd. Statistical analysis was performed by using SPSS for windows. Statistical tests performed were chi-squared test and Correlation tests with p<.01. The raw data was collected and provided by National Cancer Insitute, Jamtha, India. Result: Luminal B was the most prevailing molecular subtype of Breast cancer at our institute. Chi squared test of homogeneity was performed to find equality in distribution and Luminal B was the most prevalent molecular subtype. The worse prognostic indicator for breast cancer depends upon expression of Ki-67 and her2 protein in cancerous cells. Our study was done at p <.01 and significant dependence was observed. There exists no dependence of age on molecular subtype of breast cancer. Similarly, age is an independent variable while considering Ki-67 expression. Chi square test performed on Human epidermal growth factor receptor 2 (HER2) statuses of patients and strong dependence was observed in percentage of Ki-67 expression and Her2 (+/-) character which shows that, value of Ki depends upon Her2 expression in cancerous cells (p<.01). Surprisingly, dependence was observed in case of Ki-67 and Pr, at p <.01. This shows that Progesterone receptor proteins (PR) are over-expressed when there is an elevation in expression of Ki-67 protein. Conclusion: We conclude from that Luminal B is the most prevalent molecular subtype at National Cancer Institute, Jamtha, India. There was found no significant correlation between age and Ki-67 expression in any molecular subtype. And no dependence or correlation exists between patients’ age and molecular subtype. We also found that, when the diagnosis is Luminal A, out of the cohort of 257 patients, no patient shows >14% Ki-67 value. Statistically, extremely significant values were observed for dependence of PR+Her2- and PR-Her2+ scores on Ki-67 expression. (p<.01). Her2 is an important prognostic factor in breast cancer. Chi squared test for Her2 and Ki-67 shows that the expression of Ki depends upon Her2 statuses. Moreover, Ki-67 cannot be used as a standalone prognostic factor for determining breast cancer.

Keywords: breast cancer molecular subtypes , correlation, immunohistochemistry, Ki-67 and HR, statistical analysis

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Authors: Rizwan H. Khan, Saima Nusrat

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Despite the fact that amyloid associated neurodegenerative diseases and non-neuropathic systemic amyloidosis have allured the research endeavors, as no curative drugs have been proclaimed up till now except for symptomatic cure. Therapeutic compounds which can diminish or disaggregate such toxic oligomers and fibrillar species have been examined and more are on its way. In the present study, we had reported an extensive biophysical, microscopic and computational study, revealing that L-3, 4-dihydroxyphenylalanine (L-Dopa) possess undeniable potency to inhibit heat induced human lysozyme (HL) amyloid fibrillation and also retain the fibril disaggregating potential. L-Dopa interferes in the amyloid fibrillogenesis process by interacting hydrophobically and also by forming hydrogen bonds with the amino acid residues found in amyloid fibril forming prone region of HL as elucidated by molecular docking results. L-Dopa also disaggregates the mature amyloid fibrils into some unorganised species. Thus, L-Dopa and related compounds can work as a promising inhibitor for the therapeutic advancement prospective against systemic amyloidosis.

Keywords: amyloids, disaggregation, human lysozyme, molecular docking

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Authors: Kwan-Ho Kim, Jin-Hong Park

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The multi-valued logic (MVL) circuits, which can handle more than two logic states, are one of the promising solutions to overcome the bit density limitations of conventional binary logic systems. Recently, tunneling devices such as Esaki diode and resonant tunneling diode (RTD) have been extensively explored to construct the MVL circuits. These tunneling devices present a negative differential resistance (NDR) phenomenon in which a current decreases as a voltage increases in a specific applied voltage region. Due to this non-monotonic current behavior, the tunneling devices have more than two threshold voltages, consequently enabling construction of MVL circuits. Recently, the emergence of two dimensional (2D) van der Waals (vdW) crystals has opened up the possibility to fabricate such tunneling devices easily. Owing to the defect-free surface of the 2D crystals, a very abrupt junction interface could be formed through a simple stacking process, which subsequently allowed the implementation of a high-performance tunneling device. Here, we report a vdW heterostructure based tunneling device with multiple threshold voltages, which was fabricated with black phosphorus (BP) and hafnium diselenide (HfSe₂). First, we exfoliated BP on the SiO₂ substrate and then transferred HfSe₂ on BP using dry transfer method. The BP and HfSe₂ form type-Ⅲ heterojunction so that the highly doped n+/p+ interface can be easily implemented without additional electrical or chemical doping process. Owing to high natural doping at the junction, record high peak to valley ratio (PVCR) of 16 was observed to the best our knowledge in 2D materials based NDR device. Furthermore, based on this, we first demonstrate the feasibility of the ternary latch by connecting two multi-threshold voltage devices in series.

Keywords: two dimensional van der Waals crystal, multi-valued logic, negative differential resistnace, tunneling device

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Authors: Junkal Gutierrez, Hernane S. Barud, Sidney J. L. Ribeiro, Agnieszka Tercjak

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Nowadays the interest on green nanocomposites and on the development of more environmental friendly products has been increased. Bacterial cellulose has been recently investigated as an attractive environmentally friendly material for the preparation of low-cost nanocomposites. The formation of cellulose by laboratory bacterial cultures is an interesting and attractive biomimetic access to obtain pure cellulose with excellent properties. Additionally, properties as molar mass, molar mass distribution, and the supramolecular structure could be control using different bacterial strain, culture mediums and conditions, including the incorporation of different additives. This kind of cellulose is a natural nanomaterial, and therefore, it has a high surface-to-volume ratio which is highly advantageous in composites production. Such property combined with good biocompatibility, high tensile strength, and high crystallinity makes bacterial cellulose a potential material for applications in different fields. The aim of this investigation work was the fabrication of novel hybrid inorganic-organic composites based on bacterial cellulose, cultivated in our laboratory, as a template. This kind of biohybrid nanocomposites gathers together excellent properties of bacterial cellulose with the ones displayed by typical inorganic nanoparticles like optical, magnetic and electrical properties, luminescence, ionic conductivity and selectivity, as well as chemical or biochemical activity. In addition, the functionalization of cellulose with inorganic materials opens new pathways for the fabrication of novel multifunctional hybrid materials with promising properties for a wide range of applications namely electronic paper, flexible displays, solar cells, sensors, among others. In this work, different pathways for fabrication of multifunctional biohybrid nanopapers with tunable properties based on BC modified with amphiphilic poly(ethylene oxide-b-propylene oxide-b-ethylene oxide) (EPE) block copolymer, sol-gel synthesized nanoparticles (titanium, vanadium and a mixture of both oxides) and functionalized iron oxide nanoparticles will be presented. In situ (biosynthesized) and ex situ (at post-production level) approaches were successfully used to modify BC membranes. Bacterial cellulose based biocomposites modified with different EPE block copolymer contents were developed by in situ technique. Thus, BC growth conditions were manipulated to fabricate EPE/BC nanocomposite during the biosynthesis. Additionally, hybrid inorganic/organic nanocomposites based on BC membranes and inorganic nanoparticles were designed via ex-situ method, by immersion of never-dried BC membranes into different nanoparticle solutions. On the one hand, sol-gel synthesized nanoparticles (titanium, vanadium and a mixture of both oxides) and on the other hand superparamagnetic iron oxide nanoparticles (SPION), Fe2O3-PEO solution. The morphology of designed novel bionanocomposites hybrid materials was investigated by atomic force microscopy (AFM) and scanning electron microscopy (SEM). In order to characterized obtained materials from the point of view of future applications different techniques were employed. On the one hand, optical properties were analyzed by UV-vis spectroscopy and spectrofluorimetry and on the other hand electrical properties were studied at nano and macroscale using electric force microscopy (EFM), tunneling atomic force microscopy (TUNA) and Keithley semiconductor analyzer, respectively. Magnetic properties were measured by means of magnetic force microscopy (MFM). Additionally, mechanical properties were also analyzed.

Keywords: bacterial cellulose, block copolymer, advanced characterization techniques, nanoparticles

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Authors: Rabindranath Jana, Plabani Basu, Keka Rana

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Nucleating agents are widely used to modify the properties of various polymers. The rate of crystallization and the size of the crystals have a strong impact on mechanical and optical properties of a polymer. The addition of nucleating agents to the semi-crystalline polymers provides a surface on which the crystal growth can start easily. As a consequence, fast crystal formation will result in many small crystal domains so that the cycle times for injection molding may be reduced. Moreover, the mechanical properties e.g., modulus, tensile strength, heat distortion temperature and hardness may increase. In the present work, multi-walled carbon nanotubes (MWNTs) as nucleating agents for the crystallization of poly (e-caprolactone)diol (PCL). Thus nanocomposites of PCL filled with MWNTs were prepared by solution blending. Differential scanning calorimetry (DSC) tests were carried out to study the effect of CNTs on on-isothermal crystallization of PCL. The polarizing optical microscopy (POM), and wide-angle X-ray diffraction (WAXD) were used to study the morphology and crystal structure of PCL and its nanocomposites. It is found that MWNTs act as effective nucleating agents that significantly shorten the induction period of crystallization and however, decrease the crystallization rate of PCL, exhibiting a remarkable decrease in the Avrami exponent n, surface folding energy σe and crystallization activation energy ΔE. The carbon-based fillers act as templates for hard block chains of PCL to form an ordered structure on the surface of nanoparticles during the induction period, bringing about some increase in equilibrium temperature. The melting process of PCL and its nanocomposites are also studied; the nanocomposites exhibit two melting peaks at higher crystallization temperature which mainly refer to the melting of the crystals with different crystal sizes however, PCL shows only one melting temperature.

Keywords: poly(e-caprolactone)diol, multiwalled carbon nanotubes, composite materials, nonisothermal crystallization, crystal structure, nucleation

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Authors: Shokofeh Ebrtahimi

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Let G be the chemical graph of a molecule. The matrix D = [dij ] is called the detour matrix of G, if dij is the length of longest path between atoms i and j. The sum of all entries above the main diagonal of D is called the detour index of G.Chemical graph theory is the topology branch of mathematical chemistry which applies graph theory to mathematical modelling of chemical phenomena.[1] The pioneers of the chemical graph theory are Alexandru Balaban, Ante Graovac, Ivan Gutman, Haruo Hosoya, Milan Randić and Nenad TrinajstićLet G be the chemical graph of a molecule. The matrix D = [dij ] is called the detour matrix of G, if dij is the length of longest path between atoms i and j. The sum of all entries above the main diagonal of D is called the detour index of G. In this paper, a new program for computing the detour index of molecular graphs of nanotubes by heptagons is determineded. Some Conjectures about detour index of Molecular graphs of nanotubes is included.

Keywords: chemical graph, detour matrix, Detour index, carbon nanotube

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Authors: A. Didaoui, N. Benhalima, M. Elkeurti, A. Chouaih, F. Hamzaoui

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The monomer and dimer structures of the title molecule have been obtained from density functional theory (DFT) B3LYP method with 6-31G (d,p) as basis set calculations. The optimized geometrical parameters obtained by B3LYP/6-31G (d,p) method show good agreement with xperimental X-ray data. The polarizability and first order hyperpolarizabilty of the title molecule were calculated and interpreted. the intermolecular N–H•••O hydrogen bonds are discussed in dimer structure of the molecule. The vibrational wave numbers and their assignments were examined theoretically using the Gaussian 03 set of quantum chemistry codes. The predicted frontier molecular orbital energies at B3LYP/6-31G(d,p) method set show that charge transfer occurs within the molecule. The frontier molecular orbital calculations clearly show the inverse relationship of HOMO–LUMO gap with the total static hyperpolarizability. The results also show that N-(2-Methylphenyl)-2-nitrobenzenesulfonamide molecule may have nonlinear optical (NLO) comportment with non-zero values.

Keywords: DFT, Gaussian 03, NLO, N-(2-Methylphenyl)-2-nitrobenzenesulfonamide

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Authors: N. Khelloul, N. Benhalima, A. Chouaih, F. Hamzaoui

Abstract:

The monomer and dimer structures of the title molecule have been obtained from density functional theory (DFT) B3LYP method with 6-31G (d,p) as basis set calculations. The optimized geometrical parameters obtained by B3LYP/6-31G (d,p) method shows good agreement with experimental X-ray data. The polarizability and first order hyperpolarizabilty of the title molecule were calculated and interpreted. The intermolecular N–H•••O hydrogen bonds are discussed in dimer structure of the molecule. The vibrational wave numbers and their assignments were examined theoretically using the Gaussian 09 set of quantum chemistry codes. The predicted frontier molecular orbital energies at B3LYP/6-31G(d,p) method set show that charge transfer occurs within the molecule. The frontier molecular orbital calculations clearly show the inverse relationship of HOMO–LUMO gap with the total static hyperpolarizability. The results also show that 2-Chloro-N-(2-methylphenyl) benzamide 2 molecule may have nonlinear optical (NLO) comportment with non-zero values.

Keywords: DFT, HOMO, LUMO, NLO

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Authors: Martynova Alina, Lyubov Buzoleva

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Streptococcus pneumoniae is the causative agent of pneumonias and meningitids throught all the world. Having high genetic diversity, this microorganism can cause different clinical forms of pneumococcal infections and microbiologically it is really difficult diagnosed by routine methods. Also, epidemiological surveillance requires more developed methods of molecular typing because the recent method of serotyping doesn't allow to distinguish invasive and non-invasive isolates properly. Non-coding genome of bacteria seems to be the interesting source for seeking of highly distinguishable markers to discriminate the subspecies of such a variable bacteria as Streptococcus pneumoniae. Technically, we proposed scheme of discrimination of S.pneumoniae strains with amplification of non-coding region (SP_1932) with the following restriction with 2 types of enzymes of Alu1 and Mn1. Aim: This research aimed to compare different methods of typing and their application for molecular epidemiology purposes. Methods: we analyzed population of 100 strains of S.pneumoniae isolated from different patients by different molecular epidemiology methods such as pulse-field gel electophoresis (PFGE), restriction polymorphism analysis (RFLP) and multilolocus sequence typing (MLST), and all of them were compared with classic typing method as serotyping. The discriminative power was estimated with Simpson Index (SI). Results: We revealed that the most discriminative typing method is RFLP (SI=0,97, there were distinguished 42 genotypes).PFGE was slightly less discriminative (SI=0,95, we identified 35 genotypes). MLST is still the best reference method (SI=1.0). Classic method of serotyping showed quite weak discriminative power (SI=0,93, 24 genotypes). In addition, sensivity of RFLP was 100%, specificity was 97,09%. Conclusion: the most appropriate method for routine epidemiology surveillance is RFLP with non-coding region of Streptococcsu pneumoniae, then PFGE, though in some cases these results should be obligatory confirmed by MLST.

Keywords: molecular epidemiology typing, non-coding genome, Streptococcus pneumoniae, MLST

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