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Journal of Molecular Modeling

Mustafa Alhaji Isa, Rita Singh Majumdhar, Shazia Haider
The shikimate pathway is as an attractive target because it is present in bacteria, algae, fungi, and plants but does not occur in mammals. In Mycobacterium tuberculosis (MTB), the shikimate pathway is integral to the biosynthesis of naphthoquinones, menaquinones, and mycobactin. In these study, novel inhibitors of 3-dehydroquinate synthase (DHQS), an enzyme that catalyzes the second step of the shikimate pathway in MTB, were determined. 12,165 compounds were selected from two public databases through virtual screening and molecular docking analysis using PyRx 8...
May 11, 2018: Journal of Molecular Modeling
Rodrigo A Mendes, Shawan K C Almeida, Iuri N Soares, Cristina A Barboza, Renato G Freitas, Alex Brown, Gabriel L C de Souza
In this work, we present a computational study on the antioxidant potential of myricetin 3,4[Formula: see text]-di-O-α-L-rhamnopyranoside (Compound M). A density functional theory (DFT) approach with the B3LYP and LC-ωPBE functionals and with both the 6-311G(d,p) and 6-311+G(d,p) basis sets was used. The focus of the investigation was on the structural and energetic parameters including both bond dissociation enthalpies (BDEs) and ionization potentials (IPs), which provide information on the potential antioxidant activity...
May 11, 2018: Journal of Molecular Modeling
Junjie Song, Yue Su, Yanping Jia, Lusheng Chen, Guiqiu Zhang
Several noble-gas-containing molecules XNgY were observed experimentally. However, the bonding in such systems is still not understood. Using natural bond orbital and natural resonance theory (NBO/NRT) methods, the present work investigated bonding of the title molecules. The results show that each of the studied XNgY molecules should be better described as a resonance hybrid of ω-bonding and [Formula: see text]-type long-bonding structures: X:- Ng+  - Y, X - Ng+ : Y- , and X^ Y. The ω-bonding and long-bonding make competing contributions to the composite resonance hybrid due to the accurately preserved bond order conservation principle...
May 7, 2018: Journal of Molecular Modeling
Shakeel Ahmad Khandy, Ishtihadah Islam, Dinesh C Gupta, Amel Laref
Density functional theory (DFT)-based investigations have been put forward on the elastic, mechanical, and thermo-dynamical properties of BaPaO3 . The pressure dependence of electronic band structure and other physical properties has been carefully analyzed. The increase in Bulk modulus and decrease in lattice constant is seen on going from 0 to 30 GPa. The predicted lattice constants describe this material as anisotropic and ductile in nature at ambient conditions. Post-DFT calculations using quasi-harmonic Debye model are employed to envisage the pressure-dependent thermodynamic properties like Debye temperature, specific heat capacity, Grüneisen parameter, thermal expansion, etc...
May 7, 2018: Journal of Molecular Modeling
Jie Liu, Xiangang Jiang, Yu Cao, Chen Zhang, Guangyao Zhao, Maoshuang Zhao, Li Feng
Graphene oxide with different degrees of oxidation was prepared and selected as a model compound of lignite to study quantitatively, using both experiment and theoretical calculation methods, the effect on water-holding capacity of oxygen-containing functional groups. The experimental results showed that graphite can be oxidized, and forms epoxy groups most easily, followed by hydroxyl and carboxyl groups. The prepared graphene oxide forms a membrane-state as a single layer structure, with an irregular surface...
May 7, 2018: Journal of Molecular Modeling
Lakshmi C S Nair, S Balachandran, D Arul Dhas, I Hubert Joe
Noncentrosymmetric π conjugated systems with suitable electron donor acceptor groups play a crucial role in material NLO activity. The influence of an electron donating mono substituent at the para position of the phenylene ring of chalcone was investigated as a resource for second harmonic generation. The geometrical optimization of 11 electron donating group substituted chalcones were performed using density functional theory at the B3LYP/6-311G(d,p) level and compared with experimental geometrical parameters of five reported chalcones...
May 4, 2018: Journal of Molecular Modeling
I Borges, Alexander M Silva, Lucas Modesto-Costa
Single-sheet nanoclusters of MoS2 , NiMoS or CoMoS are widely used in hydrodesulfurization (HDS) catalysis in the petroleum industry. In HDS reactions under microwave irradiation, experiments indirectly pointed out that for pristine MoS2 reaction rates are accelerated because hot spots are generated on the catalyst bed. In this work, we investigated NiMoS and CoMoS isolated single-sheet substituted catalysts before and after thiophene adsorption focusing on quantifying the effect of microwave irradiation. For that purpose, density functional theory (DFT) molecular charge densities of each system were decomposed according to the distributed multipole analysis (DMA) of Stone...
May 4, 2018: Journal of Molecular Modeling
Alyson C M Oliveira, A C Pavão
Adsorption, absorption and desorption energies and other properties of hydrogen storage in palladium and in the metal hydrides AlH3 , MgH2 , Mg(BH4 )2 , Mg(BH4 )(NH2 ) and LiNH2 were analyzed. The DFT calculations on cluster models show that, at a low concentration, the hydrogen atom remains adsorbed in a stable state near the palladium surface. By increasing the hydrogen concentration, the tetrahedral and the octahedral sites are sequentially occupied. In the α phase the tetrahedral site releases hydrogen more easily than at the octahedral sites, but the opposite occurs in the β phase...
May 4, 2018: Journal of Molecular Modeling
Changjun Zhou, Chuan Sun, Bin Wang, Xiaojun Wang
Protein structure prediction (PSP) is a significant area for biological information research, disease treatment, and drug development and so on. In this paper, three-dimensional structures of proteins are predicted based on the known amino acid sequences, and the structure prediction problem is transformed into a typical NP problem by an AB off-lattice model. This work applies a novel improved Stochastic Fractal Search algorithm (ISFS) to solve the problem. The Stochastic Fractal Search algorithm (SFS) is an effective evolutionary algorithm that performs well in exploring the search space but falls into local minimums sometimes...
May 3, 2018: Journal of Molecular Modeling
Chunfu Shao, Kunpeng Shi, Qingyuan Hua, Liming Zhang, Yujie Dai, Wei You, Yang Liu, Changwen Li, Chaozheng Zhang
The mechanism for the hydroxyl-radical-induced depolymerization of cellulose under alkaline conditions in air was investigated using density functional theory at the B3LYP/6-31+G(d,p) level as well as electron transfer theory. The pathway for the depolymerization of cellulose was obtained theoretically and H abstraction from the C(3) atom of the pyran ring during the cleavage of the glucosidic bond was found to be the rate-limiting step due to its high energy barrier (16.81 kcal/mol) and low reaction rate constant (4...
May 2, 2018: Journal of Molecular Modeling
Ablimit Abdukadir, Aygul Mattursun, Ablikim Kerim, Kamalbek Omar, Lutpulla Hushur
The aromaticity of the rings of thiophene, pyrrole, furan, and benzene annelated cyclooctatetraene (COT) derivatives and of their double charged ions was studied using the graph-theoretical theory of aromaticity. On the basis of topological resonance energy, it was found that the global aromaticity is dependent upon on the arrangement of heteroatoms in the given molecule. Relative stability of these molecules when in different charged states can been explained in terms of the topological charge stabilization rule...
May 2, 2018: Journal of Molecular Modeling
Yuniawan Hidayat, Ria Armunanto, Harno Dwi Pranowo
Rb(I) ion solvation in liquid ammonia has been studied by an ab initio quantum mechanical charge field molecular dynamics simulation, and the first solvation shell structure has been analyzed using natural bond orbital. The simulation was performed for an ion and 593 ammonia molecules in a box with a length of 29.03 Å corresponding to a liquid ammonia density of 0.69 g/mL at 235.16 K. The quantum mechanical calculation was carried out for atomic interactions in the radius of 6.4 Å from the ion using LANL2DZ ECP and DZP (Dunning) basis sets for Rb(I) ion and ammonia respectively...
April 27, 2018: Journal of Molecular Modeling
Qiong Wu, Zewu Zhang, Bo Kou, Weihua Zhu
In this work, six series of new energetic metal complexes were designed. Each complex contained a large, high-energy, high-nitrogen, anionic chelating ligand (either the 5,5'-bistetrazolate anion, the 5,5'-azobistetrazolate anion, or the 5,5'-(hydrazine-1,2-diyl)bis-[1H-tetrazol-1-ide] anion-each of which has a different bridging group), Cu or Ni as the metal atom, and two small complexing agent ligands (NH3 and/or NH2 NO2 ). The molecular and electronic structures, heats of formation, densities, detonation properties, and impact sensitivities of the novel complexes were studied using density functional theory...
April 26, 2018: Journal of Molecular Modeling
Adam K Sieradzan, Magdalena A Mozolewska
Carbon nanotubes (CNTs) have recently received considerable attention because of their possible applications in various branches of nanotechnology. For their cogent application, knowledge of their interactions with biological macromolecules, especially proteins, is essential and computer simulations are very useful for such studies. Classical all-atom force fields limit simulation time scale and size of the systems significantly. Therefore, in this work, we implemented CNTs into the coarse-grained UNited RESidue (UNRES) force field...
April 26, 2018: Journal of Molecular Modeling
Bibek Dash
The present work deals with a density functional theory (DFT) study of porous organic framework materials containing - groups for CO2 capture. In this study, first principle calculations were performed for CO2 adsorption using N-containing covalent organic framework (COFs) models. Ab initio and DFT-based methods were used to characterize the N-containing porous model system based on their interaction energies upon complexing with CO2 and nitrogen gas. Binding energies (BEs) of CO2 and N2 molecules with the polymer framework were calculated with DFT methods...
April 26, 2018: Journal of Molecular Modeling
Semanti Ghosh, Angshuman Bagchi
Sulfur metabolism is one of the oldest known biochemical processes. Chemotrophic or phototrophic proteobacteria, through the dissimilatory pathway, use sulfate, sulfide, sulfite, thiosulfate or elementary sulfur by either reductive or oxidative mechanisms. During anoxygenic photosynthesis, anaerobic sulfur oxidizer Allochromatium vinosum forms sulfur globules that are further oxidized by dsr operon. One of the key redox enzymes in reductive or oxidative sulfur metabolic pathways is the DsrAB protein complex...
April 26, 2018: Journal of Molecular Modeling
Tao Wang, Xiao-Huan Liu, Mian-Bin Wu, Shun Ge
Bacilysin is one of the simplest antimicrobial peptides and has drawn great attention for its excellent performance against Candida albicans. In this study, the antifungal mechanism of bacilysin was investigated. The target enzyme glucosamine-6-phosphate synthase (GFA) was expressed heterologously in Escherichia coli and its inhibition by bacilysin and derivatives was studied. It was concluded that bacilysin could be hydrolyzed by a proteinase of C. albicans, and that the released product, anticapsin, then inhibited the aminotransferase activity of GFA...
April 26, 2018: Journal of Molecular Modeling
George Wang, A K Fazlur Rahman, Bin Wang
Ionic hydrocarbon compounds that contain hypercarbon atoms, which bond to five or more atoms, are important intermediates in chemical synthesis and may also find applications in hydrogen storage. Extensive investigations have identified hydrocarbon compounds that contain a five- or six-coordinated hypercarbon atom, such as the pentagonal-pyramidal hexamethylbenzene, C6 (CH3 )6 2+ , in which a hexacoordinate carbon atom is involved. It remains challenging to search for further higher-coordinated carbon in ionic hydrocarbon compounds, such as seven- and eight-coordinated carbon...
April 25, 2018: Journal of Molecular Modeling
Yushi Wen, Ke Zheng, Xinping Long, Ming Li, Xianggui Xue, Xiaogan Dai, Chuan Deng
In this work, self-assembly mechanism of single-wall carbon nanotube (SWCNT) during the annealing process of hot gaseous carbon is presented using reactive force field (ReaxFF)-based reactive molecular simulations. A series of simulations were performed on the evolution of reactive carbon gas. The simulation results show that the reactive carbon gas can be assembled into regular SWCNT without a catalyst. Five distinct stages of SWCNT self-assembly are proposed. For some initial configurations, the CNT was found to spin at an ultra-high rate after the nucleation...
April 25, 2018: Journal of Molecular Modeling
D Cheshmedzhieva, N Toshev, M Gerova, O Petrov, T Dudev
Hydroxamic acids are regarded as potent inhibitors of histone deacetylases (HDAC), and can therefore be used to reduce malignancy growth and size in affected organisms. Although there is a substantial body of information on the structures, syntheses, and biological activities of HDAC inhibitors, several important questions regarding their physicochemical properties and metal affinities/selectivities remain answered. First, how do the conformation and ionization of the hydroxamic group depend on its chemical composition and the dielectric properties of the medium? Second, how do these factors affect the affinities and selectivities of HDAC inhibitors for essential biogenic metal cations? Third, what is the preferred deprotonation site of the hydroxamic moiety and its mode of binding to the metal cation? The present work addressed these questions by performing density functional calculations combined with polarizable continuum model computations...
April 24, 2018: Journal of Molecular Modeling
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