Search results for: molecular data

Authors: Ali M. EL-Soll

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Physical properties of Sarir waxy crude oil was investigated, pour-point was determined using ASTM D-79 procedure, paraffin content and carbon number distribution of the paraffin was determined using gas liquid Chromatography(GLC), polymeric additives were prepared and their structures were confirmed using IR spectrophotometer. The molecular weight and molecular weigh distribution of these additives were determined by gel permeation chromatography (GPC). the performance of the synthesized additives as pour-point depressants was evaluated, for the mentioned crude oil.

Keywords: sarir, waxy, crude, pour point, depressants

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Authors: Strahinja Kovačević, Sanja Podunavac-Kuzmanović, Lidija Jevrić, Milica Karadžić

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The present study is based on the quantitative structure-activity relationship (QSAR) analysis of eighteen compounds with anti-prion activity. The structures and anti-prion activities (expressed in response units, RU%) of the analyzed compounds are taken from CHEMBL database. In the first step of analysis 85 molecular descriptors were calculated and based on them the hierarchical cluster analysis (HCA) and principal component analysis (PCA) were carried out in order to detect potential significant similarities or dissimilarities among the studied compounds. The calculated molecular descriptors were physicochemical, lipophilicity and ADMET (absorption, distribution, metabolism, excretion and toxicity) descriptors. The first stage of the QSAR analysis was simple linear regression modeling. It resulted in one acceptable model that correlates Henry's law constant with RU% units. The obtained 2D-QSAR model was validated by cross-validation as an internal validation method. The validation procedure confirmed the model’s quality and therefore it can be used for prediction of anti-prion activity. The next stage of the analysis of anti-prion activity will include 3D-QSAR and molecular docking approaches in order to select the most promising compounds in treatment of prion diseases. These results are the part of the project No. 114-451-268/2016-02 financially supported by the Provincial Secretariat for Science and Technological Development of AP Vojvodina.

Keywords: anti-prion activity, chemometrics, molecular modeling, QSAR

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Authors: M. F. Elzarei, A. M. Alseaf

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Hundred uncorrelated animal and thirty six markers were used in this study to study the molecular characterization of Saudi native Ardi goat (BM18189, ILSTS030, INRA005, OarFCB48, BM2113, ILSTS033, INRA023, RM088, CSRD247, ILSTS034, INRA063, SRCRSP1, ILSTS002, ILSTS044, INRA172, SRCRSP5, ILSTS005, ILSTS049, MAF70, SRCRSP8, ILSTS011, ILSTS058, OarAE54, SRCRSP9, ILSTS019, ILSTS059, OARCP34, TGLA53, ILSTS022, ILSTS082, OARE129, TGLA73, ILSTS029, ILSTS087, OARE193, and RM004). Ardi goat showed high variability. The mean number of alleles per locus ranged from 5 in SRCRSP1 locus to 13.5 in CSRD247 locus. Gene diversities varied within a wide range, from 0.53 in ILSTS002 locus to 0.86 in RM088 locus. Hardy-Weinberg equilibrium was tested in order to evaluate the significance of inbreeding occurring in each locus in Ardi population. Only SRCRSP9, INRA005, ILSTS030 loci showed significance in this way.

Keywords: molecular characterization, microsatellite markers, Ardi goats, Hardy-Weinberg equilibrium

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Authors: Asma Ahmed Aljohani, Mohammed Orif

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The concentration of polycyclic aromatic hydrocarbons (PAH) in clam (A. glabrata) was examined in samples collected from Alseef Beach, 30 km south of Jeddah city. Gas chromatography-mass spectrometry (GC-MS) was used to analyse the 14 PAHs. The concentration of total PAHs was found to range from 11.521 to 40.149 ng/gdw with a mean concentration of 21.857 ng/gdw, which is lower compared to similar studies. The lower molecular weight PAHs with three rings comprised 18.14% of the total PAH concentrations in the clams, while the high molecular weight PAHs with four rings, five rings, and six rings account for 81.86%. Diagnostic ratios for PAH source distinction suggested pyrogenic or anthropogenic sources.

Keywords: bivalves, biomonitoring, hydrocarbons, PAHs

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Authors: A. Douka, S. Vouyiouka, L. M. Papaspyridi, D. Korres, C. Papaspyrides

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A "green" process was studied for the preparation of partially renewable aliphatic polyesters based on 1,4-butanediol and 1,8-octanediol with various diacids and derivatives, namely diethyl succinate, adipic acid, sebacic acid, 1,12-dodecanedioic acid and 1,14-tetradecanedioic acid. A first step of enzymatic prepolymerization was carried out in the presence of two different solvents, toluene and diphenylether, applying molecular sieves and vacuum, respectively, to remove polycondensation by-products. Poly(octylene adipate) (PE 8.6), poly(octylene dodecanate)(PE 8.12) and poly(octylene tetradecanate) (PE 8.14) were firstly enzymatically produced in toluene using molecular sieves giving however, low-molecular-weight products. Thereafter, the synthesis of PE 8.12 and PE 8.14 was examined under optimized conditions using diphenylether as solvent and a more vigorous by-product removal step, such as application of vacuum. Apart from these polyesters, the optimized process was also implemented for the production of another long-chain polyester-poly(octylene sebacate) (PE 8.10) and a short-chain polyester-poly(butylene succinate) (PE 4.4). Subsequently, bulk post-polymerization in the melt or solid state was performed. SSP runs involved absence of biocatalyst and reaction temperatures (T) in the vicinity of the prepolymer melting point (Tm-T varied between 15.5 up to 4oC). Focusing on PE 4.4 and PE 8.12, SSP took place under vacuum or flowing nitrogen leading to increase of the molecular weight and improvement of the end product physical appearance and thermal properties.

Keywords: aliphatic polyester, enzymatic polymerization, solid state polymerization, Novozym 435

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Authors: Masoud Sheidai

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Biologists with a special field of population genetics and phylogeny have different research tasks such as populations’ genetic variability and divergence, species relatedness, the evolution of genetic and morphological characters, and identification of DNA SNPs with adaptive potential. To tackle these problems and reach a concise conclusion, they must use the proper and efficient statistical and bioinformatic methods as well as suitable genetic and morphological characteristics. In recent years application of different bioinformatic and statistical methods, which are based on various well-documented assumptions, are the proper analytical tools in the hands of researchers. The species delineation is usually carried out with the use of different clustering methods like K-means clustering based on proper distance measures according to the studied features of organisms. A well-defined species are assumed to be separated from the other taxa by molecular barcodes. The species relationships are studied by using molecular markers, which are analyzed by different analytical methods like multidimensional scaling (MDS) and principal coordinate analysis (PCoA). The species population structuring and genetic divergence are usually investigated by PCoA and PCA methods and a network diagram. These are based on bootstrapping of data. The Association of different genes and DNA sequences to ecological and geographical variables is determined by LFMM (Latent factor mixed model) and redundancy analysis (RDA), which are based on Bayesian and distance methods. Molecular and morphological differentiating characters in the studied species may be identified by linear discriminant analysis (DA) and discriminant analysis of principal components (DAPC). We shall illustrate these methods and related conclusions by giving examples from different edible and medicinal plant species.

Keywords: GWAS analysis, K-Means clustering, LFMM, multidimensional scaling, redundancy analysis

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Authors: Muhammet Baldan, Emel Timuçin

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Molecular solubility prediction plays a crucial role in various fields, such as drug discovery, environmental science, and material science. In this study, we compare the performance of five machine learning algorithms—linear regression, support vector machines (SVM), random forests, gradient boosting machines (GBM), and neural networks—for predicting molecular solubility using the AqSolDB dataset. The dataset consists of 9981 data points with their corresponding solubility values. MACCS keys (166 bits), RDKit properties (20 properties), and structural properties(3) features are extracted for every smile representation in the dataset. A total of 189 features were used for training and testing for every molecule. Each algorithm is trained on a subset of the dataset and evaluated using metrics accuracy scores. Additionally, computational time for training and testing is recorded to assess the efficiency of each algorithm. Our results demonstrate that random forest model outperformed other algorithms in terms of predictive accuracy, achieving an 0.93 accuracy score. Gradient boosting machines and neural networks also exhibit strong performance, closely followed by support vector machines. Linear regression, while simpler in nature, demonstrates competitive performance but with slightly higher errors compared to ensemble methods. Overall, this study provides valuable insights into the performance of machine learning algorithms for molecular solubility prediction, highlighting the importance of algorithm selection in achieving accurate and efficient predictions in practical applications.

Keywords: random forest, machine learning, comparison, feature extraction

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Authors: Strahinja Kovačević, Sanja Podunavac-Kuzmanović, Lidija Jevrić, Cristina Prandi, Piermichele Kobauri

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The present study is based on molecular modeling of a series of twelve 5-(4-substituent-phenoxy)-3-methylfuran-2(5H)-one derivatives which have potential of strigolactones mimics toward Striga hermonthica. The first step of the analysis included the calculation of molecular descriptors which numerically describe the structures of the analyzed compounds. The descriptors ALOGP (lipophilicity), AClogS (water solubility) and BBB (blood-brain barrier penetration), served as the input variables in multiple linear regression (MLR) modeling of germination activity toward S. hermonthica. Two MLR models were obtained. The first MLR model contains ALOGP and AClogS descriptors, while the second one is based on these two descriptors plus BBB descriptor. Despite the braking Topliss-Costello rule in the second MLR model, it has much better statistical and cross-validation characteristics than the first one. The ALOGP and AClogS descriptors are often very suitable predictors of the biological activity of many compounds. They are very important descriptors of the biological behavior and availability of a compound in any biological system (i.e. the ability to pass through the cell membranes). BBB descriptor defines the ability of a molecule to pass through the blood-brain barrier. Besides the lipophilicity of a compound, this descriptor carries the information of the molecular bulkiness (its value strongly depends on molecular bulkiness). According to the obtained results of MLR modeling, these three descriptors are considered as very good predictors of germination activity of the analyzed compounds toward S. hermonthica seeds. This article is based upon work from COST Action (FA1206), supported by COST (European Cooperation in Science and Technology).

Keywords: chemometrics, germination activity, molecular modeling, QSAR analysis, strigolactones

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Authors: Maria Pintea, Nigel Mason

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Induced chemistry is one of the newest pathways in the nanotechnology field with applications in the focused electron beam induced processes for deposition of nm scale structures. Si(OPr)₄ and Ti(OEt)₄ are two of the precursors that have not been so extensively researched, though highly sought for semiconductor and medical applications fields, the two compounds make good candidates for FEBIP and are the subject of velocity slice map imaging analysis for deposition purposes, offering information on kinetic energies, fragmentation channels, and angular distributions. The velocity slice map imaging technique is a method used for the characterization of molecular dynamics of the molecule and the fragmentation channels as a result of induced chemistry. To support the gas-phase analysis, Meso-Bio-Nano simulations of irradiation dynamics studies are employed with final results on Fe(CO)₅ deposited on various substrates. The software is capable of running large scale simulations for complex biomolecular, nano- and mesoscopic systems with applications to thermos-mechanical DNA damage, complex materials, gases, nanoparticles for cancer research and deposition applications for nanotechnology, using a large library of classical potentials, many-body force fields, molecular force fields involved in the classical molecular dynamics.

Keywords: focused electron beam induced deposition, FEBID, induced chemistry, molecular dynamics, velocity map slice imaging

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Authors: Sundus Mona, Atif Adnan, Babar Ali, Fareeha Arshad, Allah Rakha

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Molecular diversity is the variation in the abundance of species. Forensic entomology is a neglected field in Pakistan. Insects collected from the crime scene should be handled by forensic entomologists who are currently virtually non-existent in Pakistan. Correct identification of insect specimen along with knowledge of their biodiversity can aid in solving many problems related to complicated forensic cases. Inadequate morphological identification and insufficient thermal biological studies limit the entomological utility in Forensic Medicine. Recently molecular identification of entomological evidence has gained attention globally. DNA barcoding is the latest and established method for species identification. Only proper identification can provide a precise estimation of postmortem intervals. Arthropods are known to be the first tourists scavenging on decomposing dead matter. The objective of the proposed study was to identify species by molecular techniques and analyze their phylogenetic importance with barcoded necrophagous insect species of early succession on human cadavers. Based upon this identification, the study outcomes will be the utilization of established DNA bar codes to identify carrion feeding insect species for concordant estimation of post mortem interval. A molecular identification method involving sequencing of a 658bp ‘barcode’ fragment of the mitochondrial cytochrome oxidase subunit 1 (CO1) gene from collected specimens of unknown dipteral species from cadavers of Lahore was evaluated. Nucleotide sequence divergences were calculated using MEGA 7 and Arlequin, and a neighbor-joining phylogenetic tree was generated. Three species were identified, Chrysomya megacephala, Chrysomya saffranea, and Chrysomya rufifacies with low genetic diversity. The fixation index was 0.83992 that suggests a need for further studies to identify and classify forensically relevant insects in Pakistan. There is an exigency demand for further research especially when immature forms of arthropods are recovered from the crime scene.

Keywords: molecular diversity, DNA barcoding, species identification, forensically relevant

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Authors: A. Chouaih, N. Benhalima, N. Boukabcha, R. Rahmani, F. Hamzaoui

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Zwitterionic compounds have received the interest of chemists and physicists due to their applications as nonlinear optical materials. Recently, zwitterionic compounds exhibiting high nonlinear optical activity have been investigated. In this context, the molecular electron charge density distribution of the title compound is described accurately using the multipolar model of Hansen and Coppens. The net atomic charge and the molecular dipole moment have been determined in order to understand the nature of inter- and intramolecular charge transfer. The study reveals the nature of intermolecular interactions including charge transfer and hydrogen bonds in the title compound. In this crystal, the molecules form dimers via intermolecular hydrogen bonds. The dimers are further linked by C–H...O hydrogen bonds into chains along the c crystallographic axis. This study has also allowed us to determine various nonlinear optical properties such as molecular electrostatic potential, polarizability, and hyperpolarizability of the title compound.

Keywords: organic compounds, polarizability, hyperpolarizability, dipole moment

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Authors: Luguang Qi, Chuang Xie

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In recent years, there has been an increase in the number of reports on cocrystal polymorphism and stoichiomorphism. However, the research on the factors that influence these phenomena is limited. Herein, picolinamide (PAM), nicotinamide (NAM), and isonicotinamide (INA) were selected as co-formers to form multicomponent solids with 4-chloro-3-sulfamoylbenzoic acid (CSBA). Six new cocrystal forms of CSBA were discovered, and their crystal structures were determined. It was found that PAM and NAM can only form one cocrystal with CSBA, while INA can form up to four cocrystals, including both cocrystal polymorphism and stoichiomorphism. Molecular electrostatic potential analysis and crystal structure analysis showed that the functional group position of PAM limited the diversity of cocrystal synthons, while the lattice energy limited the diversity of cocrystal synthons when NAM acted as a co-former. Only INA was not subject to these restrictions when forming cocrystals. Finally, the influence of solvents on cocrystals was illustrated by determining the ternary phase diagrams. The mechanism of two similar solvents, ethyl acetate, and acetone, controlling the crystallization of cocrystal polymorphism was analyzed by molecular simulations.

Keywords: cocrystal polymorphism, cocrystal stoichiomorphism, phase diagram, molecular simulation

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Authors: Ruqaiya Khalil, Saman Usmani, Zaheer Ul-Haq

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The accurate characterization of ligand binding affinity is indispensable for designing molecules with optimized binding affinity. Computational tools help in many directions to predict quantitative correlations between protein-ligand structure and their binding affinities. Molecular dynamics (MD) simulation is a modern state-of-the-art technique to evaluate the underlying basis of ligand-protein interactions by characterizing dynamic and energetic properties during the event. Autoimmune diseases arise from an abnormal immune response of the body against own tissues. The current regimen for the described condition is limited to immune-modulators having compromised pharmacodynamics and pharmacokinetics profiles. One of the key player mediating immunity and tolerance, thus invoking autoimmunity is Interleukin-2; a cytokine influencing the growth of T cells. Molecular dynamics simulation techniques are applied to seek insight into the inhibitory mechanisms of newly synthesized compounds that manifested immunosuppressant potentials during in silico pipeline. In addition to estimation of free energies associated with ligand binding, MD simulation yielded us a great deal of information about ligand-macromolecule interactions to evaluate the pattern of interactions and the molecular basis of inhibition. The present study is a continuum of our efforts to identify interleukin-2 inhibitors of both natural and synthetic origin. Herein, we report molecular dynamics simulation studies of Interluekin-2 complexed with different antagonists previously reported by our group. The study of protein-ligand dynamics enabled us to gain a better understanding of the contribution of different active site residues in ligand binding. The results of the study will be used as the guide to rationalize the fragment based synthesis of drug-like interleukin-2 inhibitors as immune-modulators.

Keywords: immuno-modulators, MD simulation, protein-ligand interaction, structure-based drug design

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Authors: Anita Jäger, Andrew Salazar, Jörg von Hagen, Harald Kolmar

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In the treatment of individuals with sensitive and psoriatic skin, several inflammation and itch-related molecular and cellular targets have been identified, but many of these have yet to be characterized. In this study, we present two potential targets in the skin that can be linked to the inflammation and itch cycle. 11ßHSD1 is the enzyme responsible for converting inactive cortisone to active cortisol used to transmit signals downstream. The activation of the receptor NK1R correlates with promoting inflammation and the perception of itch and pain in the skin. In this study, both targets have been investigated based on their involvement in inflammation. The role of both identified targets was characterized based on the secretion of inflammation cytokine- IL6, IL-8, and CCL2, as well as phosphorylation and signaling pathways. It was found that treating skin cells with molecules able to inhibit inflammatory pathways results in the reduction of inflammatory signaling molecules secreted by skin cells and increases their proliferative capacity. Therefore, these molecular targets and their associated pathways show therapeutic potential and can be mitigated via small molecules. This research can be used for further studies in inflammation and itch pathways and can help to treat pathological symptoms.

Keywords: inflammation, itch, signaling pathway, skin

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Authors: A. G. Barua, Uttam Rajkhowa, Pranjal Moni Nath, Nur Abdul Kadir

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Mycobacterium tuberculosis (MTB) is one of the most closely-related intracellular bacterial pathogens, grouped as the M. tuberculosis complex (MTC). MTB, the primary agent of human tuberculosis (TB), can develop clinical TB in animals as 75 percent of canine mycobacterial infection is caused by close contact with an infected human being. In the present study, molecular detection of TB in dogs in three North-eastern states of India, Assam Mizoram, and Nagaland was carried out. So far, there has been a lack of systematic study in these regions, hampered by slow diagnostic methods and poor infrastructure. In an attempt to rectify this situation, molecular epidemiology was carried out for nine months to detect canine TB in a sample of 340 dogs. Isolation of DNA was done with swabs (throat/nasal), nodules of lungs and fluids from 100 suspected dogs and the molecular study were carried out with the help of conventional and real-time PCR. Post-mortem study was also carried out. Our results showed that the prevalence of clinical TB in dogs from a high-risk setting was 1 percent. However, the prevalence of immunological sensitization to M. tuberculosis antigen in dogs living in contact with sputum smeared positive TB cases was almost 50 percent. The latter setting had the maximum impact in terms of TB transmission. During the study period, a survey with a standard questionnaire was carried out in the TB hospitals to study reverse zoonosis. It was observed that an infected human being was one of the major risk factors for dogs to contract the infection. This observation was drawn by examining the probable airborne transmission from humans to their pets or strays. The present study helped to discover the nuances of TB transmission more clearly and systematically as compared to other sporadic tests to detect MTB in canine.

Keywords: Assam and Nagaland, canine TB, India, molecular detection, tuberculosis

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Authors: Gajanan M. Sonwane

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The computational studies on 2-phenazinamines with their protein targets have been carried out to design compounds with potential anticancer activity. This strategy of designing compounds possessing selectivity over specific tyrosine kinase has been achieved through G-QSAR and molecular docking studies. The objective of this research has been to design newer 2-phenazinamine derivatives as Bcr-Abl tyrosine kinase inhibitors by G-QSAR, molecular docking studies followed by wet-lab studies along with evaluation of their anticancer potential. Computational chemistry was done by using VLife MDS 4.3 and Autodock 4.2 followed by wet-lab experiments for synthesizing 2-phenazinamine derivatives. The chemical structures of ligands in 2D were drawn by employing Chemdraw 2D Ultra 8.0 and were converted into 3D. These were optimized by using a semi-empirical method called MOPAC. The protein structure was retrieved from RCSC protein data bank as a PDB file. The binding interactions of protein and ligands were done by using PYMOL. The molecular properties of the designed compounds were predicted in silico by using Osiris property explorer. The parent compound 2-phenazinamine was synthesized by reduction of 2, 4-dinitro-N-phenyl-benzenamine in the presence of tin chloride followed by cyclization in the presence of nitrobenzene and magnesium sulfate. The derivatization at the amino function of 2-phenazinamine was performed by treating parent compound with various aldehydes in the presence of dicyclohexylcarbodiimide (DCC) and urea to afford 2-(2-chlorophenyl)-3-(phenazine-2-yl) thiazolidine-4-one. Synthesized 39 novel derivatives of 2-phenazinamine and performed antioxidant activity, anti antiproliferative on the bulb of onion and anticancer activity on cell line showing significant competition with marked blockbuster drug imatinib.

Keywords: computer-aided drug design, tyrosin kinases, anticancer, docking

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Authors: Sihana Ahmeti Lika, Merita Dauti, Ledjan Malaj

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The objective of this study is to analyze the prophylactic usage of low molecular weight heparine (LMWH) along pregnancy and the correlation between their usage and month/week of pregnancy, in the Department of Gynecology and Obstetrics, at Clinical Hospital in Tetovo. A retrospective study was undertaken during 01 January–31 December 2012. Over of one year, the total number of patients was 4636. Among the 1447 (32.21%) pregnant women, 298 (20.59%) of them were prescribed LMWH. The majority of patients given LMWH, 119 (39.93%) were diagnosed hypercoagulable. The age group with the highest attendance was 25-35, 141 patients (47.32%). For 195 (65.44%) patients, this was their first pregnancy. Earliest stage of using LMWH was the second month of pregnancy 4 (1.34%) cases. The most common patients, were 70 women along the seventh month (23.49%), followed by 68 in the ninth month of pregnancy (22.81%). Women in the 28th gestational week, were found to be the most affected, a total of 55 (78.57%) were in that week. Clexane 2000 and Fraxiparine 0.3 were the most common for which low molecular weight heparine was prescribed. The number of patients which received Clexane 2000 was 84 (28.19%), followed by those with Fraxiparine 0.3 81 (27.18%). The administration of LMWH is associated with long hospitalization (median 14,6 days).

Keywords: hypercoagulable state, low moleculare weight heparine, month of pregnancy, pregnant women

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Authors: Walid Mousa, Mohamed Nayel, Ahmed Zaghawa, Akram Salama, Ahmed El-Sify, Hesham Rashad, Dina El-Shafey

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Mycoplasmosis in small ruminants constitutes a serious contagious problem in smallholders causing severe economic losses worldwide. This study was conducted to determine the clinical, Minimum Inhibitory Concentration (MIC) and molecular characterization of Mycoplasma species associated in sheep breeding herds in Menoufiya governorate, Egypt. Out of the examination of 400 sheep, 104 (26%) showed respiratory manifestations, nasal discharges, cough and conjunctivitis with systemic body reaction. Meanwhile, out of these examined sheep, only 56 (14%) were positive for mycoplasma isolation onto PPLO(Pleuropneumonia-like organisms) specific medium. The MIC for evaluating the efficacy of sensitivity of Mycoplasma isolates against different antibiotics groups revealed that both the Linospectin and Tylosin with 2ug, 0.25ug/ml concentration were the most effective antibiotics for Mycoplasma isolates. The application of PCR was the rapid, specific and sensitive molecular approach for detection of M. ovipneumoniae, and M. arginine at 390 and 326 bp, respectively, in all tested isolates. In conclusion, the diagnosis of Mycoplsamosis in sheep is important to achieve effective control measures and minimizing the disease dissemination among sheep herds.

Keywords: MIC, mycoplasmosis, PCR, sheep

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Authors: Hosam Abdelhady

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Filming the behaviors of individual DNA molecules in their environment when they interact with individual medicinal nano-polymers in a molecular scale has opened the door to understand the effect of the molecular shape, size, and incubation time with nanocarriers on optimizing the design of robust genetic Nano molecules able to resist the enzymatic degradation, enter the cell, reach to the nucleus and kill individual cancer cells in their environment. To this end, we will show how we applied the 4D AFM as a guide to finetune the design of genetic nanoparticles and to film the effects of these nanoparticles on the nanomechanical and morphological profiles of individual cancer cells.

Keywords: AFM, dendrimers, nanoparticles, DNA, gene therapy, imaging

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Authors: Oscar Corredor, Alexander Guzman, Adan Leon

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Density is a bulk physical property that indicates the quality of a petroleum fraction. It is also a useful property to estimate various physicochemical properties of fraction and petroleum fluids; however, the determination of density of extra heavy residual (EHR) fractions by standard methodologies, (ASTM D70) shows limitations for samples with higher densities than 1.0879 g/cm3. For this reason, a dilution methodology was developed in order to determinate density for those particular fractions, 87 (EHR) fractions were obtained as products of the fractionation of Colombian typical Vacuum Distillation Residual Fractions using molecular distillation (MD) and extraction with Solvent N-hexane in Supercritical Conditions (SFEF) pilot plants. The proposed methodology showed reliable results that can be demonstrated with the standard deviation of repeatability and reproducibility values of 0.0031 and 0.0061 g/ml respectively. In the same way, it was possible to determine densities in fractions EHR up to 1.1647g/cm3 and °API values obtained were ten times less than the water reference value.

Keywords: API, density, vacuum residual, molecular distillation, supercritical fluid extraction

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Authors: Mansour Mohammadpour

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Data transformation refers to the modification of any point in a data set by a mathematical function. When applying transformations, the measurement scale of the data is modified. Data transformations are commonly employed to turn data into the appropriate form, which can serve various functions in the quantitative analysis of the data. This study addresses the investigation of the use of data transformations in Data Envelopment Analysis (DEA). Although data transformations are important options for analysis, they do fundamentally alter the nature of the variable, making the interpretation of the results somewhat more complex.

Keywords: data transformation, data envelopment analysis, undesirable data, negative data

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Authors: Md. Fazlul Karim, Ashik Sharfaraz, Aysha Ferdoushi

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Background: Computational medicinal chemistry approaches are used for designing and identifying new drug-like molecules, predicting properties and pharmacological activities, and optimizing lead compounds in drug development. SIRT7, a nicotinamide adenine dinucleotide (NAD+)-dependent deacylase which regulates aging, is an emerging target for cancer therapy with mounting evidence that SIRT7 downregulation plays important roles in reversing cancer phenotypes and suppressing tumor growth. Activation or altered expression of SIRT7 is associated with the progression and invasion of various cancers, including liver, breast, gastric, prostate, and non-small cell lung cancer. Objectives: The goal of this work was to identify potent and selective bioactive candidate inhibitors of SIRT7 by in silico screening of small molecule compounds obtained from Nigella sativa (N. sativa). Methods: SIRT7 structure was retrieved from The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), and its active site was identified using CASTp and metaPocket. Molecular docking simulation was performed with PyRx 0.8 virtual screening software. Drug-likeness properties were tested using SwissADME and pkCSM. In silico toxicity was evaluated by Osiris Property Explorer. Bioactivity was predicted by Molinspiration software. Antitumor activity was screened for Prediction of Activity Spectra for Substances (PASS) using Way2Drug web server. Molecular dynamics (MD) simulation was carried out by Desmond v3.6 package. Results: A total of 159 bioactive compounds from the N. Sativa were screened against the SIRT7 enzyme. Five bioactive compounds: chrysin (CID:5281607), pinocembrin (CID:68071), nigellidine (CID:136828302), nigellicine (CID:11402337), and epicatechin (CID:72276) were identified as potent SIRT7 anti-cancer candidates after docking score evaluation and applying Lipinski's Rule of Five. Finally, MD simulation identified Chrysin as the top SIRT7 anti-cancer candidate molecule. Conclusion: Chrysin, which shows a potential inhibitory effect against SIRT7, can act as a possible anti-cancer drug candidate. This inhibitor warrants further evaluation to check its pharmacokinetics and pharmacodynamics properties both in vitro and in vivo.

Keywords: SIRT7, antitumor, molecular docking, molecular dynamics simulation

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Authors: Shagufta Tabassum

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The study of dielectric properties in a binary mixture of liquids is very useful to understand the liquid structure, molecular interaction, dynamics, and kinematics of the mixture. Time-domain reflectometry (TDR) is a powerful tool for studying the cooperation and molecular dynamics of the H-bonded system. In this paper, we discuss the basic calibration and normalization procedure for time-domain reflectometry measurements. Our approach is to explain the different types of error occur during TDR measurements and how these errors can be eliminated or minimized.

Keywords: time domain reflectometry measurement techinque, cable and connector loss, oscilloscope loss, and normalization technique

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Authors: Nisha Prakash, Kritika Anand, Arun Barvat, Prabir Pal, Sonachand Adhikari, Suraj P. Khanna

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Group-III nitride semiconductors (GaN, AlN, InN and their ternary and quaternary compounds) have attracted a great deal of attention for the development of high-performance Ultraviolet (UV) photodetectors. Any midgap defect states in the epitaxial grown film have a direct influence on the photodetectors responsivity. The proportion of the midgap defect states can be controlled by the growth parameters. To study this we have grown high quality epitaxial GaN films on MOCVD- grown GaN template using plasma-assisted molecular beam epitaxy (PAMBE) with different growth parameters. Optical and electrical properties of the films were characterized by room temperature photoluminescence and photoconductivity measurements, respectively. The observed persistent photoconductivity behaviour is proportional to the yellow luminescence (YL) and the absolute responsivity has been found to decrease with decreasing YL. The results will be discussed in more detail later.

Keywords: gallium nitride, plasma-assisted molecular beam epitaxy, photoluminescence, photoconductivity, persistent photoconductivity, yellow luminescence

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Authors: Archana Gupta, Rajesh Kumar

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The chemistry of chalcones has generated intensive scientific studies throughout the world. Especially, interest has been focused on the synthesis and biodynamic activities of chalcones. The blue light transmittance, excellent crystallizability and the two planar rings connected through a conjugated double bond show that chalcone derivatives are superior nonlinear organic compounds. 3-(2-Chloro-6-fluoro¬phen¬yl)-1-(2-thien¬yl) prop-2-en-1-one, 3-(2, 4- Dichlorophenyl) – 1 - (4-methylphenyl) – prop -2-en-1-one, (2E)-3-[4-(methylsulfanyl) phenyl]-1-(4-nitrophenyl) prop-2-en-1-one are some chalcone derivatives exhibiting non linear optical (NLO) properties. NLO materials have been extensively investigated in recent years as they are the key elements for photonic technologies of optical communication, optical interconnect oscillator, amplifier, frequency converter etc. Due to their high molecular hyperpolarizabilities, organic materials display a number of significant NLO properties. Experimental measurements and theoretical calculations on molecular hyperpolarizability β have become one of the key factors in the design of second order NLO materials. Theoretical determination of hyperpolarizability is quite useful both in understanding the relationship between the molecular structure and NLO properties. It also provides a guideline to experimentalists for the design and synthesis of organic NLO materials. Quantum-chemical calculations have made an important contribution to the understanding of the electronic polarization underlying the molecular NLO processes and the establishment of structure–property relationships. In the present investigation, the detailed vibrational analysis of some chalcone derivatives is taken up to understand the correlation of the charge transfer interaction and the NLO activity of the molecules based on density functional theory calculations. The vibrational modes contributing toward the NLO activity have been identified and analyzed. Rather large hyperpolarizability derived by theoretical calculations suggests the possible future use of these compounds for non-linear optical applications. The study suggests the importance of π - conjugated systems for non-linear optical properties and the possibility of charge transfer interactions. We hope that the results of the present study of chalcone derivatives are of assistance in development of new efficient materials for technological applications.

Keywords: hyperpolarizability, molecular structure, NLO material, quantum chemical calculations

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Authors: Lablali Mohammed, Mes-Adi Hassan, Mazroui M’Hammed

Abstract:

To tackle the complexity of grasping atomic-scale structures and unraveling the factors affecting the development of thin films. In our work, we perform the deposition of Nb atoms on Cu substrates using the molecular dynamics simulation combined with the embedded atom method to describe the interaction between different atoms. We investigated the impact of varying deposition rates and thermal annealing processes on the microstructural, morphological, and mechanical characteristics of the deposited Nb film. Our findings reveal that Nb atom growth on the Cu substrate occurs in island mode, accompanied by the presence of nucleation phenomena during growth. On the other hand, mixing behavior was observed at the interface between the film and the substrate, where Nb penetration is initially limited to the first Cu layer, whereas Cu atoms diffuse until reaching the third layer in the Nb film. Furthermore, Nb exhibits a BCC structure, with a significant concentration observed at a rate of 5 atoms/ps, and annealing further amplifies these percentages. Deposition at different rates leads to distinct levels of compressive normal and biaxial stress.

Keywords: molecular dynamics, Nb thin film, structure and morphology, atomic penetration

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Authors: Diego Liberati

Abstract:

Standard molecular modeling is traditionally done through Schroedinger equations via the help of powerful tools helping to manage them atom by atom, often needing High Performance Computing. Here, a full portfolio of new tools, conjugating statistical inference in the so called eXplainable Artificial Intelligence framework (in the form of Machine Learning of understandable rules) to the more traditional modeling and simulation control theory of mixed dynamic logic hybrid processes, is offered as quite a general purpose even if making an example to a popular chemical physics set of problems.

Keywords: understandable rules ML, k-means, PCA, PieceWise Affine Auto Regression with eXogenous input

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Authors: Virendra Nath, Vipin Kumar

Abstract:

Background: TypeII Diabetes mellitus is a foremost health problem worldwide, predisposing to increased mortality and morbidity. Undesirable effects of the current medications have prompted the researcher to develop more potential drug(s) against the disease. The peroxisome proliferator-activated receptors (PPARs) are members of the nuclear receptors family and take part in a vital role in the regulation of metabolic equilibrium. They can induce or repress genes associated with adipogenesis, lipid, and glucose metabolism. Aims: Investigation of PPARα/γ agonistic hits were screened by hierarchical virtual screening followed by molecular dynamics simulation and knowledge-based structure-activity relation (SAR) analysis using approved PPAR α/γ dual agonist. Methods: The PPARα/γ agonistic activity of compounds was searched by using Maestro through structure-based virtual screening and molecular dynamics (MD) simulation application. Virtual screening of nuclear-receptor ligands was done, and the binding modes with protein-ligand interactions of newer entity(s) were investigated. Further, binding energy prediction, Stability studies using molecular dynamics (MD) simulation of PPARα and γ complex was performed with the most promising hit along with the structural comparative analysis of approved PPARα/γ agonists with screened hit was done for knowledge-based SAR. Results and Discussion: The silicone chip-based approach recognized the most capable nine hits and had better predictive binding energy as compared to the reference drug compound (Tesaglitazar). In this study, the key amino acid residues of binding pockets of both targets PPARα/γ were acknowledged as essential and were found to be associated in the key interactions with the most potential dual hit (ChemDiv-3269-0443). Stability studies using molecular dynamics (MD) simulation of PPARα and γ complex was performed with the most promising hit and found root mean square deviation (RMSD) stabile around 2Å and 2.1Å, respectively. Frequency distribution data also revealed that the key residues of both proteins showed maximum contacts with a potent hit during the MD simulation of 20 nanoseconds (ns). The knowledge-based SAR studies of PPARα/γ agonists were studied using 2D structures of approved drugs like aleglitazar, tesaglitazar, etc. for successful designing and synthesis of compounds PPARγ agonistic candidates with anti-hyperlipidimic potential.

Keywords: computational, diabetes, PPAR, simulation

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Authors: E. G. Zaki, M. A. Migahed, A. M. Al-Sabagh, E. A. Khamis

Abstract:

Inhibition effect of four novel nonionic surfactants based on sulphonamide, of linear alkyl benzene sulphonic acid (LABS), was reacted with 1 mole triethylenetetramine, tetraethylenepentamine then Ethoxylation of amide X 65 type carbon steel in oil wells formation water under H2S environment was investigated by electrochemical measurements. Scanning electron microscopy (SEM) and energy dispersion X-ray (EDX) were used to characterize the steel surface. The results showed that these surfactants act as a corrosion inhibitor in and their inhibition efficiencies depend on the ethylene oxide content in the system. The obtained results showed that the percentage inhibition efficiency (η%) was increased by increasing the inhibitor concentration until the critical micelle concentration (CMC) reached The quantum chemistry calculations were carried out to study the molecular geometry and electronic structure of obtained derivatives. The energy gap between the highest occupied molecular orbital and lowest unoccupied molecular orbital has been calculated using the theoretical computations to reflect the chemical reactivity and kinetic stability of compounds.

Keywords: corrosion, surfactants, steel surface, quantum

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Authors: Nariman Shahhosseini, Sadegh Chinikar

Abstract:

Introduction: Crimean-Congo hemorrhagic fever virus (CCHFV) causes severe disease with fatality rates of 30%. The virus is transmitted to humans through the bite of an infected tick, direct contact with the products of infected livestock and nosocomially. The disease occurs sporadically throughout many of African, Asian, and European countries. Different species of ticks serve either as vector or reservoir for CCHFV. Materials and Methods: A molecular survey was conducted on hard ticks (Ixodidae) in Golestan province, north of Iran during 2014-2015. Samples were sent to National Reference Laboratory of Arboviruses (Pasteur Institute of Iran) and viral RNA was detected by RT-PCR. Results: Result revealed the presence of CCHFV in 5.3% of the selected ticks. The infected ticks belonged to Hy. dromedarii, Hy. anatolicum, Hy. marginatum, and Rh. sanguineus. Conclusions: These data demonstrates that Hyalomma ticks are the main vectors of CCHFV in Golestan province. Thus, preventive strategies such as using acaricides and repellents in order to avoid contact with Hyalomma ticks are proposed. Also, personal protective equipment (PPE) must be utilized at abattoirs.

Keywords: tick, CCHFV, surveillance, vector diversity

Procedia PDF Downloads 365