Search results for: molecular imprinted polymers

Authors: Sakiru Badmos, David R. Cole, Alberto Striolo

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It is known that confinement in nm-size pores affects many structural and transport properties of water and co-existing volatile species. Of particular interest for fluids in sub-surface systems, in catalysis, and in separations are reports that confinement can enhance the solubility of gases in water. Equilibrium molecular dynamics simulations were performed for aqueous H₂S confined in slit-shaped silica pores at 313K. The effect of pore width on the H₂S solubility in water was investigated. Other properties of interest include the molecular distribution of the various fluid molecules within the pores, the hydration structure for solvated H₂S molecules, and the dynamical properties of the confined fluids. The simulation results demonstrate that confinement reduces the H₂S solubility in water and that the solubility increases with pore size. Analysis of spatial distribution functions suggests that these results are due to perturbations on the coordination of water molecules around H₂S due to confinement. Confinement is found to dampen the dynamical properties of aqueous H₂S as well. Comparing the results obtained for aqueous H₂S to those reported elsewhere for aqueous CH₄, it can be concluded that H₂S permeates hydrated slit-shaped silica nano-pores faster than CH₄. In addition to contributing to better understanding the behavior of fluids in subsurface formations, these observations could also have important implications for developing new natural gas sweetening technologies.

Keywords: confinement, interfacial properties, molecular dynamic simulation, sub-surface formations

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Authors: Anukul K. Thakur, Ram Bilash Choudhary, Mandira Majumder

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In this technologically driven world, it is requisite to develop better, faster and smaller electronic devices for various applications to keep pace with fast developing modern life. In addition, it is also required to develop sustainable and clean sources of energy in this era where the environment is being threatened by pollution and its severe consequences. Supercapacitor has gained tremendous attention in the recent years because of its various attractive properties such as it is essentially maintenance-free, high specific power, high power density, excellent pulse charge/discharge characteristics, exhibiting a long cycle-life, require a very simple charging circuit and safe operation. Binary and ternary composites of conducting polymers with carbon and other layered transition metal dichalcogenides have shown tremendous progress in the last few decades. Compared with bulk conducting polymer, these days conducting polymers have gained more attention because of their high electrical conductivity, large surface area, short length for the ion transport and superior electrochemical activity. These properties make them very suitable for several energy storage applications. On the other hand, carbon materials have also been studied intensively, owing to its rich specific surface area, very light weight, excellent chemical-mechanical property and a wide range of the operating temperature. These have been extensively employed in the fabrication of carbon-based energy storage devices and also as an electrode material in supercapacitors. Incorporation of carbon materials into the polymers increases the electrical conductivity of the polymeric composite so formed due to high electrical conductivity, high surface area and interconnectivity of the carbon. Further, polymeric composites based on layered transition metal dichalcogenides such as molybdenum disulfide (MoS2) are also considered important because they are thin indirect band gap semiconductors with a band gap around 1.2 to 1.9eV. Amongst the various 2D materials, MoS2 has received much attention because of its unique structure consisting of a graphene-like hexagonal arrangement of Mo and S atoms stacked layer by layer to give S-Mo-S sandwiches with weak Van-der-Waal forces between them. It shows higher intrinsic fast ionic conductivity than oxides and higher theoretical capacitance than the graphite.

Keywords: supercapacitor, layered transition-metal dichalcogenide, conducting polymer, ternary, carbon

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Authors: Elizabeth O. Odewale, Sachithra T. Wanasinghe, Aaron S. Rury

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Cavity polaritons form when molecular excitons strongly couple to photons in carefully constructed optical cavities. These polaritons, which are hybrid light-matter states possessing a unique combination of photonic and excitonic properties, present the opportunity to manipulate the properties of various semiconductor materials. The systematic manipulation of materials through polariton formation could potentially improve the functionalities of many optoelectronic devices such as lasers, light-emitting diodes, photon-based quantum computers, and solar cells. However, the prospects of leveraging polariton formation for novel devices and device operation depend on more complete connections between the properties of molecular chromophores, and the hybrid light-matter states they form, which remains an outstanding scientific goal. Specifically, for most optoelectronic applications, it is paramount to understand how polariton formation affects the spectra of light absorbed by molecules coupled strongly to cavity photons. An essential feature of a polariton state is its dispersive energy, which occurs due to the enhanced spatial delocalization of the polaritons relative to bare molecules. To leverage the spatial delocalization of cavity polaritons, angle-resolved photoluminescence excitation spectroscopy was employed in characterizing light emission from the polaritonic states. Using lasers of appropriate energies, the polariton branches were resonantly excited to understand how molecular light absorption changes under different strong light-matter coupling conditions. Since an excited state has a finite lifetime, the photon absorbed by the polariton decays non-radiatively into lower-lying molecular states, from which radiative relaxation to the ground state occurs. The resulting fluorescence is collected across several angles of excitation incidence. By modeling the behavior of the light emission observed from the lower-lying molecular state and combining this result with the output of angle-resolved transmission measurements, inferences are drawn about how the behavior of molecules changes when they form polaritons. These results show how the intrinsic properties of molecules, such as the excitonic lifetime, affect the rate at which the polaritonic states relax. While it is true that the lifetime of the photon mediates the rate of relaxation in a cavity, the results from this study provide evidence that the lifetime of the molecular exciton also limits the rate of polariton relaxation.

Keywords: flourescece, molecules in cavityies, optical cavity, photoluminescence excitation, spectroscopy, strong coupling

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Authors: Haleden Chiririwa, Sandile S. Gwebu

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The coatings industry is a million dollar business, and it is easy and inexpensive to set-up but it is growing very slowly in developing countries, and this study developed a paint formulation which gives better quality and good application properties. The effect of rheology modifiers, i.e. non-ionic polymers hydrophobically-modified ethoxylated urethanes (HEUR), anionic polymers hydrophobically-modified alkali soluble emulsions (HASE) and hydroxyl ethyl cellulose (HEC) on the quality and properties of water-based paints have been investigated. HEC provides the in-can viscosity and increases open working time while HASE improves application properties like spatter resistance and brush loading and HEUR provides excellent scrub resistance. Four paint recipes were prepared using four different thickeners HEC, HASE (carbopol) and Cellulose nitrate. The fourth formulation was thickened with a combination of HASE and HEC, this aimed at improving quality and at the same time reducing cost. The four samples were tested for quality tests such viscosity, sag resistance, volatile matter, tinter effect, drying times, hiding power, scrub resistance and stability on storage. Environmental factors were incorporated in the attempt to formulate an economic and green product. Hydroxyl ethyl cellulose and cellulose nitrate gave high quality and good properties of the paint. HEC and Cellulose nitrate showed stability on storage whereas carbopol thickener was very unstable.

Keywords: properties, thickeners, rheology modifiers, water based paints

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Authors: Nasim Abuali Galehdari, Venkat Mani, Ajit D. Kelkar

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Space Radiation has become one of the major factors in successful long duration space exploration. Exposure to space radiation not only can affect the health of astronauts but also can disrupt or damage materials and electronics. Hazards to materials include degradation of properties, such as, modulus, strength, or glass transition temperature. Electronics may experience single event effects, gate rupture, burnout of field effect transistors and noise. Presently aluminum is the major component in most of the space structures due to its lightweight and good structural properties. However, aluminum is ineffective at blocking space radiation. Therefore, most of the past research involved studying at polymers which contain large amounts of hydrogen. Again, these materials are not structural materials and would require large amounts of material to achieve the structural properties needed. One of the materials to alleviate this problem is polymeric composite materials, which has good structural properties and use polymers that contained large amounts of hydrogen. This paper presents steps involved in fabrication of multi-functional hybrid sandwich panels that can provide beneficial radiation shielding as well as structural strength. Multifunctional hybrid sandwich panels were manufactured using vacuum assisted resin transfer molding process and were subjected to radiation treatment. Study indicates that various nanoparticles including Boron Nano powder, Boron Carbide and Gadolinium nanoparticles can be successfully used to block the space radiation without sacrificing the structural integrity.

Keywords: multi-functional, polymer composites, radiation shielding, sandwich composites

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Authors: Akarsh Verma, Avinash Parashar

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The aim of this article is to study the effects of hydroxyl functional group on the mechanical strength and fracture toughness of graphene. This functional group forms the backbone of intrinsic atomic structure of graphene oxide (GO). Molecular dynamics-based simulations were performed in conjunction with reactive force field (ReaxFF) parameters to capture the mode-I fracture toughness of hydroxyl functionalised graphene. Moreover, these simulations helped in concluding that spatial distribution and concentration of hydroxyl functional group significantly affects the fracture morphology of graphene nanosheet. In contrast to literature investigations, atomistic simulations predicted a transition in the failure morphology of hydroxyl functionalised graphene from brittle to ductile as a function of its spatial distribution on graphene sheet.

Keywords: graphene, graphene oxide, ReaxFF, molecular dynamics

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Authors: Titus A. Beu

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Many modern gene-delivery protocols rely on condensed complexes of DNA with polycations to introduce the genetic payload into cells by endocytosis. In particular, polyethyleneimine (PEI) stands out by a high buffering capacity (enabling the efficient condensation of DNA) and relatively simple fabrication. Realistic computational studies can offer essential insights into the formation process of DNA-PEI polyplexes, providing hints on efficient designs and engineering routes. We present comprehensive computational investigations of solvated PEI and DNA-PEI polyplexes involving calculations at three levels: ab initio, all-atom (AA), and coarse-grained (CG) molecular mechanics. In the first stage, we developed a rigorous AA CHARMM (Chemistry at Harvard Macromolecular Mechanics) force field (FF) for PEI on the basis of accurate ab initio calculations on protonated model pentamers. We validated this atomistic FF by matching the results of extensive molecular dynamics (MD) simulations of structural and dynamical properties of PEI with experimental data. In a second stage, we developed a CG MARTINI FF for PEI by Boltzmann inversion techniques from bead-based probability distributions obtained from AA simulations and ensuring an optimal match between the AA and CG structural and dynamical properties. In a third stage, we combined the developed CG FF for PEI with the standard MARTINI FF for DNA and performed comprehensive CG simulations of DNA-PEI complex formation and condensation. Various technical aspects which are crucial for the realistic modeling of DNA-PEI polyplexes, such as options of treating electrostatics and the relevance of polarizable water models, are discussed in detail. Massive CG simulations (with up to 500 000 beads) shed light on the mechanism and provide time scales for DNA polyplex formation independence of PEI chain size and protonation pattern. The DNA-PEI condensation mechanism is shown to primarily rely on the formation of DNA bundles, rather than by changes of the DNA-strand curvature. The gained insights are expected to be of significant help for designing effective gene-delivery applications.

Keywords: DNA condensation, gene-delivery, polyethylene-imine, molecular dynamics.

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Authors: Ebraheem Al-Jouri, Youssef Abu-Ahmad, Ramasamy Srinivasan

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The parasitoid, Diadegma semiclausum (Hymenoptera: Ichneumonidae) is one of the most effective exotic parasitoids of diamondback moth (DBM), Plutella xylostella in the lowland areas of Homs, Syria. Molecular evolution studies are useful tools to shed light on the molecular bases of insect geographical spread and adaptation to new hosts and environment and for designing better control strategies. In this study, molecular evolution analysis was performed based on the 42 nuclear internal transcribed spacer-2 (ITS2) sequences representing the D. semiclausum and eight other Diadegma spp. from Syria and worldwide. Possible recombination events were identified by RDP4 program. Four potential recombinants of the American D. insulare and D. fenestrale (Jeju) were detected. After detecting and removing recombinant sequences, the ratio of non-synonymous (dN) to synonymous (dS) substitutions per site (dN/dS=ɷ) has been used to identify codon positions involved in adaptive processes. Bayesian techniques were applied to detect selective pressures at a codon level by using five different approaches including: fixed effects likelihood (FEL), internal fixed effects likelihood (IFEL), random effects method (REL), mixed effects model of evolution (MEME) and Program analysis of maximum liklehood (PAML). Among the 40 positively selected amino acids (aa) that differed significantly between clades of Diadegma species, three aa under positive selection were only identified in D. semiclausum. Additionally, all D. semiclausum branches tree were highly found under episodic diversifying selection (EDS) at p≤0.05. Our study provide evidence that both recombination and positive selection have contributed to the molecular diversity of Diadegma spp. and highlights the significant contribution of D. semiclausum in adaptive evolution and influence the fitness in the DBM parasitoid.

Keywords: diadegma sp, DBM, ITS2, phylogeny, recombination, dN/dS, evolution, positive selection

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Authors: Zain Ul Abdin, Mirza Aizaz Asim, Rao Sohail Ahmad Khan, Luqman Amrao, Fiaz Hussain, Hasooba Hira, Saqi Kosar Abbas

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The success of Integrated vector management programmes mainly depends on the correct identification of insect vector species involved in vector borne diseases. Based on molecular data the most important insect species involved as vectors for Zoonotic diseases in Pakistan were identified. The precise and accurate identification of such type of organism is only possible through molecular based techniques like “DNA barcoding”. Morphological species identification in insects at any life stage, is very challenging, therefore, DNA barcoding was used as a tool for rapid and accurate species identification in a wide variety of taxa across the globe and parallel studies revealed that DNA barcoding data can be effectively used in resolving taxonomic ambiguities, detection of cryptic diversity, invasion biology, description of new species etc. A comprehensive survey was carried out for the collection of insects (both adult and immature stages) in district Faisalabad, Pakistan and their DNA was extracted and mitochondrial cytochrome oxidase subunit I (COI-59) barcode sequences was used for molecular identification of immature and adult life stage.This preliminary research work opens new frontiers for developing sustainable insect vectors management programmes for saving lives of mankind from fatal diseases.

Keywords: zoonotic diseases, cytochrome oxidase, and insect vectors, CO1

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Authors: Hanaa M. Abu El Einin, Ahmed T. Sharaf El- Din

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Biomphalaria snails play an integral role in the transmission of Schistosoma mansoni, the causative agent for human schistosomiasis. Two species of Biomphalaria were reported from Egypt, Biomphalaria alexandrina and Biomphalaria glabrata, and later on a hybrid of B. alexandrina and B. glabrata was reported in streams at Nile Delta. All were known to be excellent hosts of S. mansoni. Host-parasite relationship can be viewed in terms of snail susceptibility and parasite infectivity. The objective of this study will highlight the progress that has been made in using molecular approaches to describe the correct identification of snail species that participating in transmission of schistosomiasis, rapid diagnose of infection in addition to susceptibility and resistance type. Snails were identified using of molecular methods involving Randomly Amplified Polymorphic DNA (RAPD), Polymerase Chain Reaction, Restriction Fragment Length Polymorphisms (PCR-RFLP) and Species - specific- PCR. Molecular approaches to diagnose parasite in snails from Egypt: Nested PCR assay and small subunit (SSU) rRNA gene. Also RAPD PCR for study susceptible and resistance phenotype. The results showed that RAPD- PCR, PCR-RFLP and species-specific-PCR techniques were confirmed that: no evidence for the presence of B. glabrata in Egypt, All Biomphalaria snails collected identified as B. alexandrina snail i-e B alexandrinia is a common and no evidence for hybridization with B. glabrata. The adopted specific nested PCR assay revealed much higher sensitivity which enables the detection of S. mansoni infected snails down to 3 days post infection. Nested PCR method for detection of infected snails using S. mansoni fructose -1,6- bisphosphate aldolase (SMALDO) primer, these primers are specific only for S. mansoni and not cross reactive with other schistosomes or molluscan aldolases Nested PCR for such gene is sensitive enough to detect one cercariae. Genetic variations between B. alexandrina strains that are susceptible and resistant to Schistosoma infec¬tion using a RAPD-PCR showed that 39.8% of the examined snails collected from the field were resistant, while 60.2% of these snails showed high infection rates. In conclusion the genetics of the intermediate host plays a more important role in the epidemiological control of schistosomiasis.

Keywords: biomphalaria, molecular differentiation, parasite detection, schistosomiasis

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Authors: Somayeh Akrami, Habib Onsori, Elham Tahmassebian

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Species of Anemone narcissiflora is belonged to Anemone genus of Ranunculaceae family. This species has two subspecies named narcissiflora and willdenowii which the latest is recorded in Iran in 2010. Some samples of A. narcissiflora is gathered from kuhkamar-zonouz region of East -Azerbaijan province, Iran to study the genetic diversity of the species by using RAPD molecular markers, and estimation of genetic diversity were evaluated with the using 10mer RAPD primers by PCR-RAPD method. 39 polymorphic bands were produced from the six primers used in this technique that the maximum band is related to the RP1 primer, the lowest band is related to the RP7 and the average band for all primers were 6.5 polymorphic bands. Cluster analysis of samples in done by UPGMA method in NTSYSpc 2.02 software. Dendrogram resulting from migrating bands showed that the studied samples can be divided into two groups. The first group includes samples with 1-2 flowers and the second group consists of two sub-groups which the first subgroup consists of samples with 3-5 flowers, and the second subgroup consists of samples with 6-7 flowers. The results of the comparison and analysis of the data obtained from RAPD technique and similarity matrix represents the genetic variation between collected samples. This study shows that RAPD markers can determine the polymorphisms between different genotypes of A. narcissiflora and their hybrids. So RAPD technique can serve as a suitable molecular method to determine the genetic diversity of samples.

Keywords: Anemone narcissiflora, genetic diversity, RAPD-PCR

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Authors: Richa Mardianingrum, Srie R. N. Endah

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In this research, we have designed four isoniazid derivatives i.e., isonicotinohydrazide (1-isonicotinoyl semicarbazide, 1-thiosemi isonicotinoyl carbazide, N '-(1,3-dimethyl-1 h-pyrazole-5-carbonyl) isonicotino hydrazide, and N '-(1,2,3- 4-thiadiazole-carbonyl) isonicotinohydrazide. The docking and molecular dynamic have performed to them in order to study its interaction with Mycobacterium tuberculosis Enoyl-Acyl Carrier Protein Reductase (InhA). Based on this research, all of the compounds were predicted to have a stable interaction with Mycobacterium tuberculosis Enoyl-Acyl Carrier Protein Reductase (INHA) receptor, so they could be used as an anti-tuberculosis drug candidate.

Keywords: anti-tuberculosis, docking, Inhibin alpha subunit, InhA, inhibition, synthesis, isonicotinohydrazide

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Authors: Khabat Barkhordari

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Hepatitis delta virus (HDV) is a RNA virus that needs the function of hepatitis B virus (HBV) for its propagation and assembly. Infection by HDV can occur spontaneously with HBV infection and cause acute hepatitis or develop as secondary infection in HBV suffering patients. Based on genome sequence analysis, HDV has several genotypes which show broad geographic and diverse clinical features. The aim of current study is determine the molecular epidemiology of hepatitis delta virus genotype in patients with positive HBsAg among different ethnic groups of Iran. This systematic review study reviews the results of different studies which examined 2000 Iranian patients with HBV infection from 2010 to 2015. Among 2000 patients in this study, 16.75 % were containing anti-HDV antibody and HDV RNA was found in just 1.75% cases. All of positive cases also have genotype I.

Keywords: HDV, genotype, epidemiology, distribution

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Authors: Tahani H. Alluhaybi, Leila Mejrissi

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In the present theoretical study, we investigated adiabatically the electronic structure of the (BaNa)+ by the use of the ab initio calculation. We optimized a large atomic GTO basis set for Na and Ba atoms. The (BaNa)+ molecular ion is considered a two-electron thank to a non-empirical pseudo-potentials approach applied to Ba and Na cores with the Core Polarization Potentials operator (CPP). Then, we performed the Full Configuration Interaction (FCI) method. Accordingly, we calculated the adiabatic Potential Energy Curves (PECs) and their spectroscopic constants (well depth De, transition energies Te, the equilibrium distances Re, vibrational constant ⍵e, and anharmonic constant ⍵exe) for 10 electronic states in Σ+ symmetry. Then we determined the vibrational level energies and their spacing, and the electric Permanent Dipole Moments (PDM).

Keywords: Ab initio, dipole moment, non-empirical pseudo-potential, potential energy curves, spectroscopic constants, vibrational energy

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Authors: M. Nazim, S. Ameen, H. K. Seo, H. S. Shin

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Energy is the basis of life and strong attention has been growing for the cost-effective energy production. Recently, solution-processed small molecule organic solar cells (SMOSCs) have grown much attention due to the wages such as well-defined molecular structures, definite molecular weight, easy synthesis and easy purification techniques. In particular, the size of donor (D) and acceptor (A) unit is a crucial factor for the exciton-diffusion towards D-A interface and then charge-separation for the effective charge-transport to the electrodes. Furan-bridged materials are more electron-rich, high fluorescence, with better molecular-packing, and greater rigidity and greater solubility than their thiophene-counterparts In this work, a furan-bridged thiazolo[5,4-d]thiazole based organic small molecule (RFTzR) was formulated and applied for BHJ organic solar cells (OSCs). The introduction of furan spacer with two terminal alkyl units improved its absorption and solubility in the common organic solvents, significantly. RFTzR exhibited a HOMO and LUMO energy levels of -5.36 eV and -3.14 eV, respectively. The fabricated solar cell devices of RFTzR (donor) with PC60BM (acceptor) as photoactive materials showed high performance of 2.72% (RFTzR:PC60BM, 2:1, w/w) ratio with open-circuit voltage of 0.756 V and high photocurrent density of 10.13 mA/cm².

Keywords: chromophore, organic solar cells, photoactive materials, small molecule

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Authors: Christina Eleftheria Tzeliou, Demeter Tzeli

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Introduction: Molecular Logic Gates (MLGs) are molecular machines that can perform complex work, such as solving logic operations. Molecular switches, which are molecules that can experience chemical changes are examples of successful types of MLGs. Recently, Quintana-Romero and Ariza-Castolo studied experimentally six stable pseudo-hemi-indigo-derived MLGs capable of solving complex logic operations. The MLG design relies on a molecular switch that experiences Z and E isomerism, thus the molecular switch's axis has to be a double bond. The hemi-indigo structure was preferred for the assembly of molecular switches due to its interaction with visible light. Z and E pseudo-hemi-indigo isomers can also be utilized for selective isomerization as they have distinct absorption spectra. Methodology: Here, the photophysical properties of pseudo-hemi-indigo derivatives are examined, i.e., derivatives of molecule 1 with anthracene, naphthalene, phenanthrene, pyrene, and pyrrole. In conjunction with some trials that were conducted, the level of theory mentioned subsequently was determined. The structures under study were optimized in both cis and trans conformations at the PBE0/6-31G(d,p) level of theory. The absorption spectra of the structures were calculated at PBE0/DEF2TZVP. In all cases, the absorption spectra of the studied systems were calculated including up to 50 singlet- and triplet-spin excited electronic states. Transition states (cis → cis, cis → trans, and trans → trans) were obtained in cases where it was possible, with PBE0/6-31G(d,p) for the optimization of the transition states and PBE0/DEF2TZVP for the respective absorption spectra. Emission spectra were obtained for the first singlet state of each molecule in cis both and trans conformations in PBE0/DEF2TZVP as well. All studies were performed in chloroform solvent that was added as a dielectric constant and the polarizable continuum model was also employed. Findings: Shifts of up to 25 nm are observed in the absorption spectra due to cis-trans isomerization, while the transition state is shifted up to about 150 nm. The electron density distribution is also examined, where charge transfer and electron transfer phenomena are observed regarding the three excitations of interest, i.e., H-1 → L, H → L and H → L+1. Emission spectra calculations were also carried out at PBE0/DEF2TZVP for the complete investigation of these molecules. Using protonation as input, selected molecules act as MLGs. Conclusion: Theoretical data so far indicate that both cis-trans isomerization, and cis-cis and trans-trans conformer isomerization affect the UV-visible absorption and emission spectra. Specifically, shifts of up to 30 nm are observed, while the transition state is shifted up to about 150 nm in cis-cis isomerization. The computational data obtained are in agreement with available experimental data, which have predicted that the pyrrole derivative is a MLG at 445 nm and 400 nm using protonation as input, while the anthracene derivative is a MLG that operates at 445 nm using protonation as input. Finally, it was found that selected molecules are candidates as MLG using protonation and light as inputs. These MLGs could be used as chemical sensors or as particular intracellular indicators, among several other applications. Acknowledgements: The author acknowledges the Hellenic Foundation for Research and Innovation for the financial support of this project (Fellowship Number: 21006).

Keywords: absorption spectra, DFT calculations, isomerization, molecular logic gates

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Authors: Ambrish Singh

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The corrosion inhibition performance of pyran (AP) and benzimidazole (BI) derivatives on J55 steel in 3.5% NaCl solution saturated with CO₂ was investigated by electrochemical, weight loss, surface characterization, and theoretical studies. The electrochemical studies included electrochemical impedance spectroscopy (EIS), potentiodynamic polarization (PDP), electrochemical frequency modulation (EFM), and electrochemical frequency modulation trend (EFMT). Surface characterization was done using contact angle, scanning electron microscopy (SEM), and atomic force microscopy (AFM) techniques. DFT and molecular dynamics (MD) studies were done using Gaussian and Materials Studio softwares. All the studies suggested the good inhibition by the synthesized inhibitors on J55 steel in 3.5% NaCl solution saturated with CO₂ due to the formation of a protective film on the surface. 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.

Keywords: corrosion, inhibitor, EFM, AFM, DFT, MD

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Authors: Majid Farsadrooh, Mehran Feizi-Dehnayebi

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Serum albumin is the most abundant protein that is present in the circulatory system of a wide variety of organisms. Although it is a significant macromolecule, it can contribute to osmotic blood pressure and also, plays a superior role in drug disposition and efficiency. Molecular docking simulation can improve in silico drug design and discovery procedures to propound a lead compound and develop it from the discovery step to the clinic. In this study, the molecular docking simulation was applied to select a lead molecule through an investigation of the interaction of the two anticancer drugs (Alitretinoin and Abemaciclib) with Human Serum Albumin (HSA). Then, a series of new compounds (a-e) were suggested using lead molecule modification. Density functional theory (DFT) including MEP map and HOMO-LUMO analysis were used for the newly proposed compounds to predict the reactivity zones on the molecules, stability, and chemical reactivity. DFT calculation illustrated that these new compounds were stable. The estimated binding free energy (ΔG) values for a-e compounds were obtained as -5.78, -5.81, -5.95, -5,98, and -6.11 kcal/mol, respectively. Finally, the pharmaceutical properties and toxicity of these new compounds were estimated through OSIRIS DataWarrior software. The results indicated no risk of tumorigenic, irritant, or reproductive effects and mutagenicity for compounds d and e. As a result, compounds d and e, could be selected for further study as potential therapeutic candidates. Moreover, employing molecular docking simulation with the prediction of pharmaceutical properties helps to discover new potential drug compounds.

Keywords: drug design, anticancer, computational studies, DFT analysis

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Authors: Eric Chabrol, Sidonia B.G. Eckle, Renate de Boer, James McCluskey, Jamie Rossjohn, Mirjam H.M. Heemskerk, Stephanie Gras

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αβ and γδ T-cells are disparate T-cell lineages that, via their use of either αβ or γδ T-cell antigen receptors (TCRs) respectively, can respond to distinct antigens. Here we characterise a new population of human T-cells, term δβ T-cells, that express TCRs comprising a TCR-δ variable gene fused to a Joining-α/Constant-α domain, paired with an array of TCR-β chains. We characterised the cellular, functional, biophysical and structural characteristic feature of this new T-cells population that reveal some new insight into TCR diversity. We provide molecular bases of how δβ T-cells can recognise viral peptide presented by Human Leukocyte Antigen (HLA) molecule. Our findings highlight how components from αβ and γδTCR gene loci can recombine to confer antigen specificity thus expanding our understanding of T-cell biology and TCR diversity.

Keywords: new delta-beta TCR, HLA, viral peptide, structural immunology

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Authors: Roohallah Yousefi

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Introduction: Voxelotor, also known as GBT 440, binds to the alpha cleft in HbS tetramers and promotes the stability of the relaxed or oxygenated state of HbS. This process hinders the conformational change of the HbS tetramers into the deoxygenated state. Voxelotor prevents interactions between HbS tetramers in the deoxygenated state, ultimately inhibiting the polymerization of HbS tetramers and resulting in significant clinical improvements, particularly in raising hemoglobin levels in patients. In this study, we have explored the use of herbal compound models, such as rosmarinic acid and compounds with similar structures that exhibit high binding affinity to Voxelotor's hemoglobin binding site. Materials and methods: The molecular model of hemoglobin (PDB: 5E83) was initially obtained from the RCSB PDB database. In addition, we collected 453 ligand models with structural similarity to rosmarinic acid from the PubChem database. To prepare these models for molecular docking, we utilized the Molegro Virtual Docker tool. Subsequently, we used the SwissADME web tool to predict the physicochemical properties and pharmacokinetics of these compounds. Results: We investigated the affinity and binding site of 453 compounds similar to rosmarinic acid on the hemoglobin model (PDB: 5E83). Our focus was on the alpha cleft between two alpha chains of the hemoglobin model (PDB: 5E83). The results showed that most compounds had molecular weights above 500 daltons, and some exhibited acceptable hydrophobicity. Furthermore, their solubility in aqueous solutions was good. None of the compounds were able to cross the blood-brain barrier or have gastrointestinal absorption. However, they did have varying inhibitory effects on CYP2C9 cytochromes. The skin penetration rate was generally low. Conclusion: Through our study, we identified three compounds (CID: 162739375, CID: 141386569, and CID: 24015539) with promising potential for further research. These compounds demonstrated high binding affinity to the hemoglobin model, favorable dissolution and digestive absorption rates, as well as suitable hydrophobicity, making them ideal candidates for continued laboratory investigation.

Keywords: voxelotor, binding site, hemoglobin, rosmarinic acid

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Authors: Reyhan Özdoğan, Mithat Çelebi, Özgür Ceylan, Mehmet Arif Kaya

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Super absorbent polymers (SAPs) are defined as materials that can absorb huge amount of water or aqueous solution in comparison to their own mass and retain in their lightly cross-linked structure. SAPs were produced from water soluble monomers via polymerization subsequently controlled crosslinking. SAPs are generally used for water absorbing applications such as baby diapers, patient or elder pads and other hygienic product industries. Crosslinking density (CD) of SAP structure is an essential factor for water absortion capacity (WAC). Low internal CD leads to high WAC values and vice versa. However, SAPs have low CD and high swelling capacities and tend to disintegrate when pressure is applied upon them, so SAPs under load cannot absorb liquids effectively. In order to prevent this undesired situation and to obtain suitable SAP structures having high swelling capacity and ability to work under load, surface crosslinking can be the answer. In industry, these superabsorbent gels are mostly produced via solution polymerization and then they need to be dried, grinded, sized, post polymerized and finally surface croslinked (involves spraying of a crosslinking solution onto dried and grinded SAP particles, and then curing by heat). It can easily be seen that these steps are time consuming and should be handled carefully for the desired final product. If we could synthesize desired final SAPs using less processes it will help reducing time and production costs which are very important for any industries. In this study, synthesis of SAPs were achieved successfully by inverse suspension (Pickering type) polymerization and subsequently in-situ surface cross-linking via using proper surfactants in high boiling point solvents. Our one-pot synthesis of surface cross-linked SAPs invovles only one-step for preparation, thus it can be said that this technique exhibits more preferable characteristic for the industry in comparison to conventional methods due to its one-step easy process. Effects of different surface crosslinking agents onto properties of poly(acrylic acid-co-sodium acrylate) based SAPs are investigated. Surface crosslink degrees are evaluated by swelling under load (SUL) test. It was determined water absorption capacities of obtained SAPs decrease with the increasing surface crosslink density while their mechanic properties are improved.

Keywords: inverse suspension polymerization, polyacrylic acid, super absorbent polymers (SAPs), surface crosslinking, sodium polyacrylate

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Authors: Gadiri Sabiha

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Introduction: Current allergy diagnostic tools using Multiplex technology have made it possible to increase the efficiency of the search for specific IgE. This opportunity is provided by the newly developed “Alex Biochip”, consisting of a panel of 282 allergens in native and molecular form, a CCD inhibitor, and the potential for detecting cross-reactive allergens. We evaluated the performance of this technology in detecting cross-reactivity in previously explored patients. Material/Method: The sera of 39 patients presenting sensitization and polysensitization profiles were explored. The search for specific IgE is carried out by the Alex ® IgE Biochip, and the results are analyzed by nature and by molecular family of allergens using specific software. Results/Discussion: The analysis gave a particular profile of cross-reactivity allergens: 33% for the Ole e1 family, 31% for NPC2, 26% for storage proteins, 20% for Tropomyosin, 10% for LTPs, 10% for Arginine Kinase and 10% for Uteroglobin CCDs were absent in all patients. The “Ole e1” allergen is responsible for a pollen-pollen cross allergy. The storage proteins found and LTP are not species-specific, causing cross-pollen-food allergy. The nDer p2 of the NPC2 family is responsible for cross-reactivity between mite species. Conclusion: The cross-reactivities responsible for mixed syndromes at diagnosis in our patients were dominated by pollen-pollen and pollen-food syndromes. They allow the identification of severity factors linked to the prognosis and the best-adapted immunotherapy.

Keywords: specific IgE, allergy, cross reactivity, molecular allergens

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Authors: Temnov D., Volgina E., Gerasimov D.

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Relaxation processes in polyvinylidene fluoride (PVDF) films were studied by the method of thermally stimulated fractional polarization currents (TSTF). The films were obtained by extrusion of a polymer melt followed by isometric annealing. PVDF granules of the Kynar-720 brand (Atofina Chemicals, USA) with a molecular weight of Mw=190,000 g•mol-1 were used for the manufacture of films. The annealing temperature was varied in the range from 120 °C to 170 °C in increments of 10 °C. The dependences of the degree of crystallinity of films (χ) and the intensity of thermally stimulated depolarization currents on the annealing temperature (Toc) are investigated. The TSTF spectra were obtained at the TSC II facility (Setaram, France). Measurements were carried out in a helium atmosphere, and the values of currents were determined by a Keithley electrometer. The annealed PVDF films were polarized at an electric field strength of 100 V/mm at a temperature of 31°C, after which they were cooled to 26°C, at which they were kept for 1 minute. During depolarization, the external field was removed, and the short-circuit sample was cooled to 0°C. The thermally stimulated short-circuit current was recorded during linear heating. Relaxation processes in PVDF films were studied in the temperature range from 0 – 70 °C. It is shown that the intensity curve of the peaks of TST FP has a course that is the reverse of the dependence of the degree of crystallinity on the annealing temperature. This allows us to conclude that the relaxation processes occurring in PVDF in the 35°C region are associated with the amorphous part of the structure of PVDF films between the layers of the spherulite crystalline phase.

Keywords: molecular and supramolecular structure, thermally stimulated currents, polyvinylidene fluoride films, relaxation processes

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Authors: Amr A. EL Hanafy, Yasir Anwar, Saleh A. Mohamed, Saleh Mohamed Saleh Al-Garni, Jamal S. M. Sabir , Osama A. H. Abu Zinadah, Mohamed Morsi Ahmed

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In the vicinity of the red sea about 15 fungi species were isolated from oil contaminated sites. On the basis of aptitude to degrade the crude oil and DCPIP assay, two fungal isolates were selected amongst 15 oil degrading strains. Analysis of ITS-1, ITS-2 and amplicon pyrosequencing studies of fungal diversity revealed that these strains belong to Penicillium and Aspergillus species. Two strains that proved to be the most efficient in degrading crude oil was Aspergillus niger (54 %) and Penicillium commune (48 %) Subsequent to two weeks of cultivation in BHS medium the degradation rate were recorded by using spectrophotometer and GC-MS. Hence, it is cleared that these fungal strains has the capability of degradation and can be utilized for cleaning the Saudi Arabian environment.

Keywords: fungal strains, hydrocarbon contaminants, molecular identification, biodegradation, GC-MS

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Authors: Amit Tribedi

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Genuine Quantumness present in Quantum Systems is the resource for implementing Quantum Information and Computation Protocols which can outperform the classical counterparts. These Quantumness measures encompass non-local ones known as quantum entanglement (QE) and quantum information theoretic (QIT) ones, e.g. Quantum Discord (QD). In this paper, some well-known measures of QE and QD in some wheel-like frustrated molecular magnetic systems have been studied. One of the systems has already been synthesized using coordination chemistry, and the other is hypothetical, where the dominant interaction is the spin-spin exchange interaction. Exact analytical methods and exact numerical diagonalization methods have been used. Some counter-intuitive non-trivial features, like non-monotonicity of quantum correlations with temperature, persistence of multipartite entanglement over bipartite ones etc. indicated by the behaviour of the correlations and the QIT measures have been found. The measures, being operational ones, can be used to realize the resource of Quantumness in experiments.

Keywords: 0D Magnets, discord, entanglement, frustration

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Authors: Dimitra Das, Anuradha Mitra, Kalyan Kumar Chattopadhyay

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Organic polymers, constructed from light elements like carbon, hydrogen, nitrogen, oxygen, sulphur, and boron atoms, are the emergent class of non-toxic, metal-free, environmental benign advanced materials. Covalent triazine-based polymers with a functional triazine group are significant class of organic materials due to their remarkable stability arising out of strong covalent bonds. They can conventionally form hydrogen bonds, favour π–π contacts, and they were recently revealed to be involved in interesting anion–π interactions. The present work mainly focuses upon the development of a single-crystalline, highly cross-linked triazine-based nitrogen-rich organic polymer with nanodendritic morphology and significant thermal stability. The polymer has been synthesized through hydrothermal treatment of melamine and ethylene glycol resulting in cross-polymerization via condensation-polymerization reaction. The crystal structure of the polymer has been evaluated by employing Rietveld whole profile fitting method. The polymer has been found to be composed of monoclinic melamine having space group P21/a. A detailed insight into the chemical structure of the as synthesized polymer has been elucidated by Fourier Transform Infrared Spectroscopy (FTIR) and Raman spectroscopic analysis. X-Ray Photoelectron Spectroscopic (XPS) analysis has also been carried out for further understanding of the different types of linkages required to create the backbone of the polymer. The unique rod-like morphology of the triazine based polymer has been revealed from the images obtained from Field Emission Scanning Electron Microscopy (FESEM) and Transmission Electron Microscopy (TEM). Interestingly, this polymer has been found to selectively detect mercury (Hg²⁺) ions at an extremely low concentration through fluorescent quenching with detection limit as low as 0.03 ppb. The high toxicity of mercury ions (Hg²⁺) arise from its strong affinity towards the sulphur atoms of biological building blocks. Even a trace quantity of this metal is dangerous for human health. Furthermore, owing to its small ionic radius and high solvation energy, Hg²⁺ ions remain encapsulated by water molecules making its detection a challenging task. There are some existing reports on fluorescent-based heavy metal ion sensors using covalent organic frameworks (COFs) but reports on mercury sensing using triazine based polymers are rather undeveloped. Thus, the importance of ultra-trace detection of Hg²⁺ ions with high level of selectivity and sensitivity has contemporary significance. A plausible sensing phenomenon by the polymer has been proposed to understand the applicability of the material as a potential sensor. The impressive sensitivity of the polymer sample towards Hg²⁺ is the very first report in the field of highly crystalline triazine based polymers (without the introduction of any sulphur groups or functionalization) towards mercury ion detection through photoluminescence quenching technique. This crystalline metal-free organic polymer being cheap, non-toxic and scalable has current relevance and could be a promising candidate for Hg²⁺ ion sensing at commercial level.

Keywords: fluorescence quenching , mercury ion sensing, single-crystalline, triazine-based polymer

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Authors: Sanja O. Podunavac-Kuzmanović, Strahinja Z. Kovačević, Lidija R. Jevrić, Stela Jokić

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The subject of this paper is to correlate antibacterial behavior of benzimidazole derivatives with their molecular characteristics using chemometric QSAR (Quantitative Structure–Activity Relationships) approach. QSAR analysis has been carried out on the inhibitory activity of benzimidazole derivatives against Staphylococcus aureus. The data were processed by linear least squares (LLS) and artificial neural network (ANN) procedures. The LLS mathematical models have been developed as a calibration models for prediction of the inhibitory activity. The quality of the models was validated by leave one out (LOO) technique and by using external data set. High agreement between experimental and predicted inhibitory acivities indicated the good quality of the derived models. These results are part of the CMST COST Action No. CM1306 "Understanding Movement and Mechanism in Molecular Machines".

Keywords: Antibacterial, benzimidazoles, chemometric, QSAR.

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Authors: Babak Safaei, A. M. Fattahi

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Polymer/carbon nanotube nanocomposites have a wide range of promising applications Due to their enhanced properties. In this work, free vibration analysis of single-walled carbon nanotube-reinforced composite plates is conducted in which carbon nanotubes are embedded in an amorphous polyethylene. The rule of mixture based on various types of plate model namely classical plate theory (CLPT), first-order shear deformation theory (FSDT), and higher-order shear deformation theory (HSDT) was employed to obtain fundamental frequencies of the nanocomposite plates. Generalized differential quadrature (GDQ) method was used to discretize the governing differential equations along with the simply supported and clamped boundary conditions. The material properties of the nanocomposite plates were evaluated using molecular dynamic (MD) simulation corresponding to both short-(10,10) SWCNT and long-(10,10) SWCNT composites. Then the results obtained directly from MD simulations were fitted with those calculated by the rule of mixture to extract appropriate values of carbon nanotube efficiency parameters accounting for the scale-dependent material properties. The selected numerical results are presented to address the influences of nanotube volume fraction and edge supports on the value of fundamental frequency of carbon nanotube-reinforced composite plates corresponding to both long- and short-nanotube composites.

Keywords: nanocomposites, molecular dynamics simulation, free vibration, generalized, differential quadrature (GDQ) method

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Authors: Binder Hans

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Cancer is no longer seen as solely a genetic disease where genetic defects such as mutations and copy number variations affect gene regulation and eventually lead to aberrant cell functioning which can be monitored by transcriptome analysis. It has become obvious that epigenetic alterations represent a further important layer of (de-)regulation of gene activity. For example, aberrant DNA methylation is a hallmark of many cancer types, and methylation patterns were successfully used to subtype cancer heterogeneity. Hence, unraveling the interplay between different omics levels such as genome, transcriptome and epigenome is inevitable for a mechanistic understanding of molecular deregulation causing complex diseases such as cancer. This objective requires powerful downstream integrative bioinformatics methods as an essential prerequisite to discover the whole genome mutational, transcriptome and epigenome landscapes of cancer specimen and to discover cancer genesis, progression and heterogeneity. Basic challenges and tasks arise ‘beyond sequencing’ because of the big size of the data, their complexity, the need to search for hidden structures in the data, for knowledge mining to discover biological function and also systems biology conceptual models to deduce developmental interrelations between different cancer states. These tasks are tightly related to cancer biology as an (epi-)genetic disease giving rise to aberrant genomic regulation under micro-environmental control and clonal evolution which leads to heterogeneous cellular states. Machine learning algorithms such as self organizing maps (SOM) represent one interesting option to tackle these bioinformatics tasks. The SOMmethod enables recognizing complex patterns in large-scale data generated by highthroughput omics technologies. It portrays molecular phenotypes by generating individualized, easy to interpret images of the data landscape in combination with comprehensive analysis options. Our image-based, reductionist machine learning methods provide one interesting perspective how to deal with massive data in the discovery of complex diseases, gliomas, melanomas and colon cancer on molecular level. As an important new challenge, we address the combined portrayal of different omics data such as genome-wide genomic, transcriptomic and methylomic ones. The integrative-omics portrayal approach is based on the joint training of the data and it provides separate personalized data portraits for each patient and data type which can be analyzed by visual inspection as one option. The new method enables an integrative genome-wide view on the omics data types and the underlying regulatory modes. It is applied to high and low-grade gliomas and to melanomas where it disentangles transversal and longitudinal molecular heterogeneity in terms of distinct molecular subtypes and progression paths with prognostic impact.

Keywords: integrative bioinformatics, machine learning, molecular mechanisms of cancer, gliomas and melanomas

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Authors: Muhammad Zahid, Ilker S. Bayer, Athanassia Athanassiou

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Fluorinated polymers having C8 chemistry (chemicals with 8 fluorinated carbon atoms) are well renowned for their excellent low surface tension and water repelling properties. However, these polymers degrade into highly toxic heavy perfluoro acids in the environment. When the C8 chemistry is reduced to C6 chemistry, this environmental concern is eliminated at the expense of reduced liquid repellent performance. In order to circumvent this, in this study, we demonstrate pre-treatment of woven cotton fabrics with a fluorinated acrylic copolymer with C6 chemistry and subsequently with a silicone polymer to render them hydrophobic. A commercial fluorinated acrylic copolymer was blended with silica nanoparticles to form hydrophobic nano-roughness on cotton fibers and a second coating layer of polydimethylsiloxane (PDMS) was applied on the fabric. A static water contact angle (for 5µl) and rolling angle (for 12.5µl) of 147°±2° and 31° were observed, respectively. Hydrostatic head measurements were also performed to better understand the performance with 26±1 cm and 2.56kPa column height and static pressure respectively. Fabrication methods (with rod coater etc.) were kept simple, reproducible, and scalable and cost efficient. Moreover, the robustness of applied coatings was also evaluated by sonication cleaning and abrasion methods. Water contact angle (WCA), water shedding angle (WSA), hydrostatic head, droplet bouncing-rolling off and prolonged staining tests were used to characterize hydrophobicity of materials. For chemical and morphological analysis, various characterization methods were used such as attenuated total reflectance-Fourier transform infrared spectroscopy (ATR-FTIR), atomic force microscopy (AFM) and scanning electron microscopy (SEM).

Keywords: fluorinated polymer, hydrophobic, polydimethylsiloxane, water contact angle

Procedia PDF Downloads 325