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Journal of Molecular Modeling

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https://www.readbyqxmd.com/read/28647872/identification-and-characterization-of-intramolecular-%C3%AE-halo-interaction-in-d-0-complexes-a-theoretical-approach
#1
Tanay Debnath, Tamalika Ash, Subhendu Sarkar, Abhijit K Das
A mechanistic investigation to detect intramolecular M⋯X-C type interactions in d(0) neutral and cationic complexes was carried out through a benchmark study employing different density functional methods. As γ-halogen is involved in M⋯X-C type interactions, it is denoted as a γ-halo interaction and the respective conformers are designated as halo-conformers. By analyzing the geometrical parameters of halo-conformers, it was observed that, irrespective of the nature of the metal and the halogen, the Cγ-X bond distance increases compared to the usual C-X bond, which brings the M and X centers close enough to generate a weak interaction...
July 2017: Journal of Molecular Modeling
https://www.readbyqxmd.com/read/28646429/decoupled-side-chain-and-backbone-dynamics-for-proton-translocation-m2-of-influenza-a
#2
Monoj Mon Kalita, Wolfgang B Fischer
The 97 amino acid bitopic membrane protein M2 of influenza A forms a tetrameric bundle in which two of the monomers are covalently linked via a cysteine bridge. In its tetrameric assembly the protein conducts protons across the viral envelope and within intracellular compartments during the infectivity cycle of the virus. A key residue in the translocation of the protons is His-37 which forms a planar tetrad in the configuration of the bundle accepting and translocating the incoming protons from the N terminal side, exterior of the virus, to the C terminal side, inside the virus...
July 2017: Journal of Molecular Modeling
https://www.readbyqxmd.com/read/28643001/prediction-of-self-assemblies-of-sodium-dodecyl-sulfate-and-fragrance-additives-using-coarse-grained-force-fields
#3
Chunwei Yang, Zhe Shen, Liang Wu, Haiqiu Tang, Lifeng Zhao, FengLei Cao, Huai Sun
Coarse-grained force field (CGFF) methods were applied to study the self-assembly of sodium dodecyl sulfate with fragrance additives. The CGFF parameters were parameterized and validated using experimental and all-atom simulation data. Direct molecular dynamics simulations were carried out to characterize the initial aggregation, partitioning of fragrances, and chemical potentials of the surfactant and fragrance molecules in aggregates of different sizes. The equilibrium critical micelle concentrations (CMCs) and micelle size distributions, which could not be obtained by direct simulation, were predicted using the calculated chemical potentials in combination with a thermodynamic model...
July 2017: Journal of Molecular Modeling
https://www.readbyqxmd.com/read/28643000/interaction-of-the-interleukin-8-protein-with-a-sodium-dodecyl-sulfate-micelle-a-computer-simulation-study
#4
Hector Dominguez
Molecular simulations were carried out to study the sodium dodecyl sulfate (SDS) surfactant with the interleukin 8 (IL8) protein as a model to investigate the influence of amphiphilic molecules on proteins. Simulations for an SDS micelle with an IL8 protein show that both aggregates, which were initially separated, eventually approach each other to form a single complex. The results showed that the protein was attached to the SDS micelle by the charged positive amino acids whereas less contacts were observed for the negatively charged amino acids...
July 2017: Journal of Molecular Modeling
https://www.readbyqxmd.com/read/28638992/a-qm-mm-study-on-the-enzymatic-inactivation-of-cefotaxime
#5
Ignacio Lizana, Eduardo J Delgado
The reaction between the antibiotic cefotaxime and the CTX-M-14 class A serine hydrolase is addressed from a theoretical point of view, by means of hybrid quantum mechanics/molecular mechanical (QM/MM) calculations, adopting a new approach that postulates that the residue Ser70 itself should play the role of the acid-base species required for the cefotaxime acylation. The proposed mechanism differs from earlier proposals existing in literature for other class A β-lactamases. The results confirm the hypothesis, and show that the reaction should occur via a concerted mechanism in which the acylation of the lactam carbonyl carbon, protonation of the N7 lactam atom, and opening of the β-lactam ring occurs simultaneously...
July 2017: Journal of Molecular Modeling
https://www.readbyqxmd.com/read/28634829/potential-inhibitory-effect-of-indolizine-derivatives-on-the-two-enzymes-nicotinamide-phosphoribosyltransferase-and-beta-lactamase-a-molecular-dynamics-study
#6
Beata Szefler, Przemysław Czeleń
Nicotinamide phosphoribosyl-transferases (NAMPT) are enzymes that play a role in targeting cancer metabolism, while beta lactamases are involved in bacterial resistance to beta-lactam antibiotics. Many protein inhibitors exhibit such property which is often correlated with their cellular potency. In order to understand such a phenomenon, the present article conducts an analysis of the dynamic behavior of complexes formed by the inhibitors, that is indolizine derivatives, with the studied enzymes. Both docking and molecular dynamics led to identification of their interactions and showed the mechanism of inhibition of the two studied enzymes...
July 2017: Journal of Molecular Modeling
https://www.readbyqxmd.com/read/28634828/donation-and-back-donation-analyzed-through-a-charge-transfer-model-based-on-density-functional-theory
#7
Ulises Orozco-Valencia, José L Gázquez, Alberto Vela
The net charge transfer process that occurs between two species, A and B, interacting with each other, may be decomposed into two processes: one in which A receives charge from B, which can be identified as the electrophilic channel for A or the nucleophilic channel for B, and a second in which A donates charge to B, which can be identified as the nucleophilic channel for A or the electrophilic channel for B. By determining the amount of charge associated with both processes through the minimization of the interaction energy associated with each case, the expressions for the amount of charge involved in each case can be expressed in terms of the directional chemical potentials and the hardnesses of the interacting species...
July 2017: Journal of Molecular Modeling
https://www.readbyqxmd.com/read/28626846/salt-bridge-networks-within-globular-and-disordered-proteins-characterizing-trends-for-designable-interactions
#8
Sankar Basu, Debasish Mukharjee
There has been considerable debate about the contribution of salt bridges to the stabilization of protein folds, in spite of their participation in crucial protein functions. Salt bridges appear to contribute to the activity-stability trade-off within proteins by bringing high-entropy charged amino acids into close contacts during the course of their functions. The current study analyzes the modes of association of salt bridges (in terms of networks) within globular proteins and at protein-protein interfaces...
July 2017: Journal of Molecular Modeling
https://www.readbyqxmd.com/read/28623601/is-the-hydrophobic-core-a-universal-structural-element-in-proteins
#9
Barbara Kalinowska, Mateusz Banach, Zdzisław Wiśniowski, Leszek Konieczny, Irena Roterman
The hydrophobic core, when subjected to analysis based on the fuzzy oil drop model, appears to be a universal structural component of proteins irrespective of their secondary, supersecondary, and tertiary conformations. A study has been performed on a set of nonhomologous proteins representing a variety of CATH categories. The presence of a well-ordered hydrophobic core has been confirmed in each case, regardless of the protein's biological function, chain length or source organism. In light of fuzzy oil drop (FOD) analysis, various supersecondary forms seem to share a common structural factor in the form of a hydrophobic core, emerging either as part of the whole protein or a specific domain...
July 2017: Journal of Molecular Modeling
https://www.readbyqxmd.com/read/28623600/stability-of-rolled-up-gaas-nanotubes
#10
Júnio C F Silva, José D Dos Santos, Carlton A Taft, João B L Martins, Elson Longo
This work presents a theoretical study of gallium arsenide (GaAs) nanotubes obtained from the (100), (110) and (111) crystal planes of zincblende structure in order to evaluate the electronic properties. The DFT/B3LYP/6-31G method was used to predict structures and stabilities. It was found that nanotubes from the (110) crystal plane tended to be the most stable. The results for average diameter and bond length obtained for optimized nanotube geometries show that nanotubes constructed from the (100) plane have a hyperbolic format, while (110) or (111) nanotubes have a conical format...
July 2017: Journal of Molecular Modeling
https://www.readbyqxmd.com/read/28623599/energetics-and-reactivity-of-small-beryllium-deuterides
#11
Ivan Sukuba, Alexander Kaiser, Stefan E Huber, Jan Urban, Michael Probst
Enthalpies and free energies of reaction for small neutral and charged beryllium deuterides BeD, BeD2, and BeD3 that have been calculated are reported for a temperature range of 0 K to 1000 K. We discuss probable dissociation channels and possible ways of producing BeD by localizing the relevant transition states and by calculating corresponding rate constants. BeD and BeD(+) are found to be the most stable ones among the considered compounds. BeD2 and [Formula: see text] are more likely to decompose into Be(0,+) + D2 than into BeD(0,+) + D...
July 2017: Journal of Molecular Modeling
https://www.readbyqxmd.com/read/28620813/an-in-silico-insight-into-the-substrate-binding-characteristics-of-the-active-site-of-amorpha-4-11-diene-synthase-a-key-enzyme-in-artemisinin-biosynthesis
#12
Habib Eslami, Seyed Kaveh Mohtashami, Maryam Taghavi Basmanj, Maryam Rahati, Hamzeh Rahimi
The enzyme amorphadiene synthase (ADS) conducts the first committed step in the biosynthetic conversion of the substrate farnesyl pyrophosphate (FPP) to artemisinin, which is a highly effective natural product against multidrug-resistant strains of malaria. Due to the either low abundance or low turn-over rate of the enzyme, obtaining artemisinin from both natural and synthetic sources is costly and laborious. In this in silico study, we strived to elucidate the substrate binding site specificities of the ADS, with the rational that unraveling enzyme features paves the way for enzyme engineering to increase synthesis rate...
July 2017: Journal of Molecular Modeling
https://www.readbyqxmd.com/read/28600721/a-novel-way-to-calculate-the-diffusivity-of-water-in-carbon-nanotubes
#13
Lei Li, Hui Zhang, Xiaofeng Yang
Theoretical studies on water diffusion in carbon nanotubes have been challenged because the diffusivities calculated by molecular simulations are much lower than what experiments show. This paper proposes a new way to estimate transport diffusivity in such systems directly by simply inspecting the long term behaviors of the velocity autocorrelation functions of water molecules. The results from simulation of molecular dynamics based on this method show that the new method can generate much higher diffusivities, in accordance with experimental measurements, and of the correct order of magnitude...
July 2017: Journal of Molecular Modeling
https://www.readbyqxmd.com/read/28597191/theoretical-analysis-of-the-binding-of-iron-iii-protoporphyrin-ix-to-4-methoxyacetophenone-thiosemicarbazone-via-dft-d3-mep-qtaim-nci-elf-and-lol-studies
#14
Nyiang Kennet Nkungli, Julius Numbonui Ghogomu
Thiosemicarbazones display diverse pharmacological properties, including antimalarial activities. Their pharmacological activities have been studied in depth, but little of this research has focused on their antimalarial mode of action. To elucidate this antimalarial mechanism, we investigated the nature of the interactions between iron(III) protoporphyrin IX (Fe(III)PPIX) and the thione-thiol tautomers of 4-methoxyacetophenone thiosemicarbazone (MAPTSC). Dispersion-corrected density functional theory (DFT-D3), the quantum theory of atoms in molecules (QTAIM), the noncovalent interaction (NCI) index, the electron localization function (ELF), the localized orbital locator (LOL), and thermodynamic calculations were employed in this work...
July 2017: Journal of Molecular Modeling
https://www.readbyqxmd.com/read/28593344/the-addition-reactions-of-germylenoid-h2gealcl3-with-ethylene-a-theoretical-investigation
#15
Mingxia Zhang, Wenzuo Li, Qingzhong Li, Jianbo Cheng
Theoretical calculations using the M062X and QCISD methods were performed on the addition reactions of the aluminum germylenoid H2GeAlCl3 with ethylene. The most two stable structures of germylenoid H2GeAlCl3, i.e., the p-complex and three-membered ring structures, respectively, were employed as reactants. The calculated results indicate that, for the p-complex, H2GeAlCl3 there are two pathways, I and II, of which path I involves just one transition state, while path II involves two transition states between reactants and products...
July 2017: Journal of Molecular Modeling
https://www.readbyqxmd.com/read/28593343/configurations-and-characteristics-of-boron-and-b36-clusters
#16
REVIEW
Shuhong Xu, Renjie Dong, Changgui Lv, Chunlei Wang, Yiping Cui
Characteristics of the ring and linear structures of the boron cluster B36 and its doped clusters were investigated with DFT/B3LYP/6-31G. The results illustrate that the ring B3 structure is the most stable configuration compared with other rings. Odd and even linear structures have different bonding; there is one different bond in the center of even linear structures, while the remaining bonds have left and right symmetry. The B36 cluster upholds the configuration rule of pure ring and linear molecules. However, the N-doped B36N cluster exhibits obvious distortion compared with the B36 molecule...
July 2017: Journal of Molecular Modeling
https://www.readbyqxmd.com/read/28589464/epsp-synthase-flexibility-is-determinant%C3%A2-to-its-function-computational-molecular-dynamics-and-metadynamics-studies
#17
Luís Fernando Saraiva Macedo Timmers, Antônio M S Neto, Rinaldo W Montalvão, Luiz A Basso, Diógenes S Santos, Osmar Norberto de Souza
Flexibility is involved in a wide range of biological processes, such as protein assembly and binding recognition. EPSP synthase is an enzyme that must undergo a large conformational change to accommodate its ligands into its binding cavity. However, although the structure of EPSP synthase has been determined, its plasticity has not been explored in depth. Therefore, in this work, we extensively examined the influence of the flexibility of Mycobacterium tuberculosis EPSP (MtEPSP) synthase on the function of this protein using classical and replica-exchange metadynamics simulations...
July 2017: Journal of Molecular Modeling
https://www.readbyqxmd.com/read/28589463/experimental-and-theoretical-description-of-the-optical-properties-of-myrcia-sylvatica-essential-oil
#18
Andriele da Silva Prado, Luciano Almeida Leal, Patrick Pascoal de Brito, Antonio Luciano de Almeida Fonseca, Stefan Blawid, Artemis Marti Ceschin, Rosa Helena Veras Mourão, Antônio Quaresma da Silva Júnior, Demétrio Antonio da Silva Filho, Luiz Antonio Ribeiro Junior, Wiliam Ferreira da Cunha
We present an extensive study of the optical properties of Myrcia sylvatica essential oil with the goal of investigating the suitability of its material system for uses in organic photovoltaics. The methods of extraction, experimental analysis, and theoretical modeling are described in detail. The precise composition of the oil in our samples is determined via gas chromatography, mass spectrometry, and X-ray scattering techniques. The measurements indicate that, indeed, the material system of Myrcia sylvatica essential oil may be successfully employed for the design of organic photovoltaic devices...
July 2017: Journal of Molecular Modeling
https://www.readbyqxmd.com/read/28560578/md-simulation-study-of-the-diffusion-and-local-structure-of-n-alkanes-in-liquid-and-supercritical-methanol-at-infinite-dilution
#19
Huajie Feng, Wei Gao, Li Su, Zhenfan Sun, Liuping Chen
The diffusion coefficients of 14 n-alkanes (ranging from methane to n-tetradecane) in liquid and supercritical methanol at infinite dilution (at a pressure of 10.5 MPa and at temperatures of 299 K and 515 K) were deduced via molecular dynamics simulations. Values for the radial distribution function, coordination number, and number of hydrogen bonds were then calculated to explore the local structure of each fluid. The flexibility of the n-alkane (as characterized by the computed dihedral distribution, end-to-end distance, and radius of gyration) was found to be a major influence and hydrogen bonding to be a minor influence on the local structure...
June 2017: Journal of Molecular Modeling
https://www.readbyqxmd.com/read/28550376/development-of-an-amber-compatible-transferable-force-field-for-poly-ethylene-glycol-ethers-glymes
#20
Nathalia S V Barbosa, Yong Zhang, Eduardo R A Lima, Frederico W Tavares, Edward J Maginn
An all-atom force field consistent with the general AMBER force field (GAFF) format for poly(ethylene glycol) dimethyl ether (diglyme or G2) was developed by fitting to experimental liquid densities and dielectric constants. Not surprisingly, the new force field gives excellent agreement with experimental liquid phase densities and dielectric constants over a wide temperature range. Other dynamic and thermodynamic properties of liquid G2 such as its self-diffusion coefficient, shear viscosity, and vaporization enthalpy were also calculated and compared to experimental data...
June 2017: Journal of Molecular Modeling
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