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Journal of Molecular Graphics & Modelling

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https://www.readbyqxmd.com/read/28531817/electronic-properties-and-gas-adsorption-behaviour-of-pristine-silicon-and-boron-doped-8-0-single-walled-carbon-nanotube-a-first-principles-study
#1
Mohd Asyadi Azam, Farizul Muiz Alias, Liew Weng Tack, Raja Noor Amalina Raja Seman, Mohamad Fariz Mohamad Taib
Carbon nanotubes (CNTs) have received enormous attention due to their fascinating properties to be used in various applications including electronics, sensing, energy storage and conversion. The first principles calculations within density functional theory (DFT) have been carried out in order to investigate the structural, electronic and optical properties of un-doped and doped CNT nanostructures. O2, CO2, and CH3OH have been chosen as gas molecules to study the adsorption properties based on zigzag (8,0) SWCNTs...
May 5, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28505566/conformational-study-of-the-structure-of-dibenzo-18-crown-6-comparison-with-18-crown-6
#2
Nada A Al-Jallal, Adel A El-Azhary
We report for the first time the conformational analysis of dibenzo-18-crown-6, db18c6. The conformational search was carried out using the CONFLEX conformational search method of cyclic molecules. Energies were calculated for the low-lying predicted conformations at different levels of theory up to the G3MP2 level. At the G3MP2 level, the predicted ground state (GS) conformation was more stable than the experimental conformation by only 1.60kcal/mol. Strong similarity was found between the GS structure and experimental conformations of db18c6 and 18-crown-6, 18c6...
April 28, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28501530/adsorption-of-plasma-proteins-onto-pegylated-single-walled-carbon-nanotubes-the-effects-of-protein-shape-peg-size-and-grafting-density
#3
Hwankyu Lee
Single-walled carbon nanotubes (SWCNTs) covalently functionalized or noncovalently coated with polyethylene glycol (PEG) of different sizes (Mw=2000 and 5000) and grafting densities (5-16 PEGs per SWCNT) are simulated with human fibrinogen (HFG) and serum albumin (HSA). Proteins migrate toward the SWCNT, but their adsorption extents differ. The extent of the HFG-SWCNT binding decreases with increasing PEG size and grafting density because PEGs more completely cover SWCNTs and thus block hydrophobic interactions between HFGs and SWCNTs, which occurs on PEG-functionalized SWCNTs but not on PEG-coated ones...
April 28, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28521282/the-possibility-of-using-c20-fullerene-and-graphene-as-semiconductor-segments-for-detection-and-destruction-of-cyanogen-chloride-chemical-agent
#4
Parvaneh Pakravan, Seyyed Amir Siadati
Detection of hazardous chemical species by changing the electrical conductivity of a semiconductor matter is a proposed and applied way for decreasing their subsequent unpleasant effects. Recently, many examples of using inorganic or organic materials, polymeric, and also nano-sized species as sensors were reported in which, in some cases, those matters were strongly affective and suitable. In this project, we have made an assessment on whether the graphene segment or C20 fullerene, able to sense the existence of cyanogen chloride NCCl? In order to gain trustable results, the possible reaction pathways along with the adsorption kinetics were investigated...
April 27, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28505567/one-step-versus-two-step-mechanism-of-diels-alder-reaction-of-1-chloro-1-nitroethene-with-cyclopentadiene-and-furan
#5
Radomir Jasiński
DFT computational study shows that Diels-Alder (DA) reactions of 1-chloro-1-nitroethene with cyclopentadiene and furan have polar nature. However, their mechanism is substantially different. In particular, 1-chloro-1-nitroethene react with cyclopentadiene according to one-step mechanism. In the same time, more favourable channel associated with the P-DA reaction between furan and 1-chloro-1-nitroethene is a domino process, that comprises an initial hetero-Diels-Alder reaction yielding a [2+4] cycloadduct, which experiences a subsequent [3,3] sigmatropic shift to yield the expected formal [4+2] cycloadduct...
April 27, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28505565/dft-and-td-dft-theoretical-studies-on-photo-induced-electron-transfer-process-on-cefamandole-c60-nano-complex
#6
Avat Arman Taherpour, Morteza Jamshidi, Omid Rezaei
The C60 fullerene displays a considerable electronegativity. It has a unique photophysical and electrochemical behavior that can be used as a suitable drug carrier. In the present study, the interaction of C60 fullerene as an electron recipient with the Cefamandole antibiotic was investigated in both ground and excited states using DFT and TD-DFT methods. The study of the interaction of C60 and Cefamandole via electron localization function (ELF) and reduced density gradient (RDG) revealed that the complex formation is of van der Waals type...
April 27, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28501532/targeted-inhibition-of-klotho-binding-to-fibroblast-growth-factor-23-prevents-hypophosphetemia
#7
Muhammad Fakhar, Sajid Rashid
Klotho is a transmembrane protein which plays significant role in the pathogenesis of phosphate ion (Pi)-related disorders. Pi accumulation in human kidney tissues results in the major metabolic disorders due to malfunctioning of Klotho-FGFR1-FGF23 trimeric complex. The potential role of Klotho in Pi metabolism was elaborated through modeling and interaction analysis of glycosyl hydrolase (GS1 and GS2) domains with Fibroblast growth factor 23 (FGF23). In order to inhibit the association of Klotho and FGF23, binding patterns of three reported hits (N-(2-chlorophenyl)-1H-indole-3-carboxamide, N-[2-(1-cyclohexen-1-yl)ethyl]-6,7,8,9-tetrahydropyrido[1,2-e]purin-4-amine and 2-(1-propyl)amino-11-chlorothiazolo[5,4-a]acridine) were evaluated through molecular docking analysis...
April 27, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28477574/functional-and-structural-characterization-of-the-pentapeptide-insertion-of-theileria-annulata-lactate-dehydrogenase-by-site-directed-mutagenesis-comparative-modeling-and-molecular-dynamics-simulations
#8
Aysegul Erdemir, Ozal Mutlu
Lactate dehydrogenase (LDH) is an important metabolic enzyme in glycolysis and it has been considered as the main energy source in many organisms including apicomplexan parasites. Differences at the active site loop of the host and parasite LDH's makes this enzyme an attractive target for drug inhibitors. In this study, five amino acid insertions in the active site pocket of Theileria annulata LDH (TaLDH) were deleted by PCR-based site-directed mutagenesis, expression and activity analysis of mutant and wild type TaLDH enzymes were performed...
April 26, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28506671/modeling-of-flux-binding-and-substitution-of-urea-molecules-in-the-urea-transporter-dvut
#9
Hai-Tian Zhang, Zhe Wang, Tao Yu, Jian-Ping Sang, Xian-Wu Zou, Xiaoqin Zou
Urea transporters (UTs) are transmembrane proteins that transport urea molecules across cell membranes and play a crucial role in urea excretion and water balance. Modeling the functional characteristics of UTs helps us understand how their structures accomplish the functions at the atomic level, and facilitates future therapeutic design targeting the UTs. This study was based on the crystal structure of Desulfovibrio vulgaris urea transporter (dvUT). To model the binding behavior of urea molecules in dvUT, we constructed a cooperative binding model...
April 25, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28456097/structure-guided-cancer-blockade-between-bioactive-bursehernin-and-proteins-molecular-docking-and-molecular-dynamics-study
#10
Aman Tedasen, Saowapak Choomwattana, Potchanapond Graidist, Varomyalin Tipmanee
Bursehernin (5'-desmethoxyyatein) is a natural lignan, which has anti-tumor activity in vitro. In this study, the binding-inhibitory effects of bursehernin were screening on selected 80 proteins associated with cancer pathway. The computational analysis suggested inhibitory effect due to bursehernin towards proteins related to cancer proliferation, including FMS kinase receptor, heat shock protein 90-α (Hsp90-α), adenylate cyclase 10 (ADCY10), mitogen-activated protein kinase kinase (MEK1), and α-tubulin...
April 24, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28475967/a-comparative-study-on-the-experimental-and-calculated-results-of-mid-infrared-and-raman-vibrational-modes-of-nucleic-acid-bases
#11
Fang Wang, Dongbo Zhao, Ling Jiang, Li Xu, Haijun Sun, Yunfei Liu
The MIR (mid-infrared) and Raman spectra of the nucleic acid base powders were tested by Fourier transform infrared spectroscopy and laser Raman spectroscopy. The vibrational modes of nucleic acid base crystals were simulated by the generalized energy-based fragmentation approach under periodic boundary conditions (hereinafter referred as PBC-GEBF) together with Guassian09 software. Taking into account the intermolecular hydrogen bonds in the unit cell and the weak interactions between the unit cells, the PBC-GEBF method adopted by our group was for the first time used for calculating nucleic acid base crystals in the 400-2000cm(-1) band...
April 22, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28482272/screening-of-commercial-cyclic-peptide-conjugated-to-hiv-1-tat-peptide-as-inhibitor-of-n-terminal-heptad-repeat-glycoprotein-2-ectodomain-ebola-virus-through-in-silico-analysis
#12
Usman Sumo Friend Tambunan, Ahmad Husein Alkaff, Mochammad Arfin Fardiansyah Nasution, Arli Aditya Parikesit, Djati Kerami
Ebola Hemorrhagic Fever (EHF) is a disease caused by viruses from genus Ebolavirus. Zaire ebolavirus (EBOV) is the deadliest species which has 76% case fatality rate. Up until now, there is no U.S. Food and Drug Administration (FDA) approved drugs to treat EHF. Antiviral drug based on EBOV N-terminal heptad repeat glycoprotein-2 (NHR GP2) Ectodomain inhibitor is one kind of treatment that has not well developed. NHR GP2 Ectodomain has an important role in the process of EBOV entry into the cell through endocytosis mechanism...
April 21, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28458007/probing-the-inhibitory-activity-of-epigallocatechin-gallate-on-toxic-aggregates-of-mutant-l84f-sod1-protein-through-geometry-based-sampling-and-steered-molecular-dynamics
#13
E Srinivasan, R Rajasekaran
Amyloid formation and protein aggregation are considered to be at the core of the disease pathology for the various neurodegenerative disorders such as Amyotrophic lateral sclerosis (ALS). Considerable experimental reports have suggested that epigallocatechin-gallate (EGCG), a natural polyphenol from the green tea inhibits the amyloid formation in multiple neurodegenerative disease. Mutations in SOD1 protein are considered to a key factor that contributes towards the rapid disease progression and the pathogenesis in both, the sporadic and familial form...
April 20, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28458003/molecular-dynamics-simulation-of-gas-phase-ozone-reactions-with-sabinene-and-benzene
#14
H F Ridgway, B Mohan, X Cui, K J Chua, M R Islam
Gas-phase reactions of ozone (O3) with volatile organic compounds were investigated both by experiment and molecular simulations. From our experiments, it was found ozone readily reacts with VOC pure components and reduces it effectively. By introducing ozone intermittently, the reaction between VOC and ozone is markedly enhanced. In order to understand the relationship between intermediate reactions and end products, ozone reaction with benzene and alicyclic monoterpene sabinene were simulated via a novel hybrid quantum mechanical/molecular mechanics (QM/MM) algorithm that forced repeated bimolecular collisions...
April 20, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28475968/the-effect-of-%C3%AE-glucan-and-its-potential-analog-on-the-structure-of-dectin-1-receptor
#15
Navaneet Chaturvedi, Brijesh Singh Yadav, Paras Nath Pandey, Vijay Tripathi
Dectin-1 is a recently discovered pattern-recognition receptor that plays an important role in antifungal innate immunity, which acts a specific receptor for β-glucan (BG). The present study, aimed at clarifying effect of BG and a new analog, maltotriose (MT) on Dectin-1 receptor. We implemented molecular docking of MT on Dectin-1 along with model-independent all-atom-molecular dynamics simulations. Simulations were carried out at three levels of complexity: (1) Apo-Dectin-1; (2) BG:Dectin-1; (3) MT:Dectin-1...
April 19, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28472734/comparative-in-silico-analyses-of-cannabis-sativa-prunella-vulgaris-and-withania-somnifera-compounds-elucidating-the-medicinal-properties-against-rheumatoid-arthritis
#16
Mehreen Zaka, Sheikh Arslan Sehgal, Shagufta Shafique, Bilal Haider Abbasi
From last decade, there has been progressive improvement in computational drug designing. Several diseases are being cured from different plant extracts and products. Rheumatoid arthritis (RA) is the most shared disease among auto-inflammatory diseases. Tumor necrosis factor (TNF)-α is associated with RA pathway and has adverse effects. Extensive literature review showed that plant species under study (Cannabis sativa, Prunella vulgaris and Withania somnifera) possess anti-inflammatory, anti-arthritic and anti-rheumatic properties...
April 19, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28458005/the-solvent-water-and-metal-effects-on-homo-lumo-gaps-of-guanine-base-pair-a-computational-study
#17
Ayhan Üngördü, Nurten Tezer
The most stable structures of guanine dimer and metal-mediated guanine base pair complexes were determined both in vacuum and solvent (water). Density functional theory (DFT) method is generally used in the calculations. The calculations of systems containing C, H, N, O is described by 6-311++G(d,p) basis set and LANL2DZ basis set is used for transition metals. Some geometrical parameters, the LUMO, HOMO energy levels and energy gaps of compounds are calculated. Hydrogen bond stabilization energies in dimer and charge transfer in metal complexes are also determined using NBO analysis...
April 19, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28499270/simulation-studies-on-structural-and-thermal-properties-of-alkane-thiol-capped-gold-nanoparticles
#18
J Meena Devi
The structural and thermal properties of the passivated gold nanoparticles were explored employing molecular dynamics simulation for the different surface coverage densities of the self-assembled monolayer (SAM) of alkane thiol. The structural properties of the monolayer protected gold nanoparticles such us overall shape, organization and conformation of the capping alkane thiol chains were found to be influenced by the capping density. The structural order of the thiol capped gold nanoparticles enhances with the increase in the surface coverage density...
April 18, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28501531/symmetry-in-normal-modes-and-its-strong-dependence-on-symmetry-in-structure
#19
Guang Song
In this work, we look at the symmetry of normal modes in symmetric structures, particularly structures with cyclic symmetry. We show that normal modes of symmetric structures have different levels of symmetry, or symmetricity. One novel theoretical result of this work is that, for a ring structure with m subunits, the symmetricity of the normal modes falls into m groups of equal size, with normal modes in each group having the same symmetricity. The normal modes in each group can be computed separately, using a much smaller amount of memory and time (up to m(3) less)...
April 14, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28477575/conformational-heterogeneity-in-ccr7-undergoes-transitions-to-specific-states-upon-ligand-binding
#20
Zied Gaieb, Dimitrios Morikis
Ligand-binding to G protein-coupled receptors (GPCRs) acts as the local driving force that initiates signal transduction through the receptor and mediates its conformational transitions and interactions with various intracellular effectors. In a recent study, We have shown that the binding of ligands CCL19 and CCL21 to CCR7 induces biased triggering of side chain-based molecular switches, which coordinate concerted transmembrane helical domain motions and transitioning of the receptor to distinct conformational states (Gaieb, Z...
April 13, 2017: Journal of Molecular Graphics & Modelling
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