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atomic structure

K Nejati, A Hosseinian, A Bekhradnia, E Vessally, L Edjlali
It has been recently indicated that the Li-ion batteries may be replaced by Na-ion batteries because of their low safety, high cost, and low-temperature performance, and lack of the Li mineral reserves. Here, using density functional theory calculations, we studied the potential application of B12N12 nanoclusters as anode in Na-ion batteries. Our calculations indicate that the adsorption energy of Na(+) and Na are about -23.4 and -1.4kcal/mol, respectively, and the pristine BN cage to improve suffers from a low cell voltage (∼0...
March 6, 2017: Journal of Molecular Graphics & Modelling
Timur R Galimzyanov, Anna S Lyushnyak, Veronika V Aleksandrova, Liudmila A Shilova, Ilya I Mikhalyov, Irina M Molotkovskaya, Sergey A Akimov, Oleg V Batishchev
Liquid-ordered lipid domains, also called rafts, are assumed to be important players in different cellular processes, mainly signal transduction and membrane trafficking. They are thicker than the disordered part of the membrane and are thought to form for compensating the hydrophobic mismatch between transmembrane proteins and lipid environment. Despite the existence of such structures in vivo is still an open question, they are observed in model systems of multicomponent lipid bilayers. Moreover, the predictions obtained from model experiments allow explaining different physiological processes possibly involving rafts...
March 21, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
Jing Huang, Christopher J Bley, Dustin P Rand, Julian J L Chen, Ming Lei
Telomerase is a unique reverse transcriptase that replicates the telomeric DNA at most eukaryotic chromosomal ends. The telomerase consists of the catalytic protein subunit TERT and the RNA component TR that provides the template for telomeric DNA synthesis. In vitro reconstitution of telomerase core components in large quantity is the prerequisite to studying the catalytic mechanisms of telomerase at the structural level; however, large-scale preparation of recombinant telomerase, especially that of higher eukaryotes, has been a big challenge for a long time...
2017: Methods in Molecular Biology
Lin Cheng, Xiaojuan Yu, Kun Zhao, Hua Hou, Baoshan Wang
Electronic structures of Trifluoromethyl imionosulfur difluoride (CF3NSF2) and degradation mechanisms by hydroxyl radical have been investigated using density functional theory (M06-2X), the complete basis set quadratic CBS-Q, and the explicitly correlated coupled-cluster methods [CCSD(T)-F12]. The d-function augmented Correlation-consistent basis sets including triple- and quadruple- were employed for the sulfur-containing species. It was found that CF3NSF2 exists as two conformations connected by the internal rotation of CF3 around the central NS bond...
March 21, 2017: Journal of Physical Chemistry. A
Aine Devlin-Mullin, Naomi M Todd, Zahra Golrokhi, Hua Geng, Moritz A Konerding, Nigel G Ternan, John A Hunt, Richard J Potter, Chris Sutcliffe, Eric Jones, Peter D Lee, Christopher A Mitchell
Joint replacement surgery is associated with significant morbidity and mortality following infection with either methicillin-resistant Staphylococcus aureus (MRSA) or Staphylococcus epidermidis. These organisms have strong biofilm-forming capability in deep wounds and on prosthetic surfaces, with 10(3) -10(4) microbes resulting in clinically significant infections. To inhibit biofilm formation, we developed 3D titanium structures using selective laser melting and then coated them with a silver nanolayer using atomic layer deposition...
March 21, 2017: Advanced Healthcare Materials
Song Liu, Adri C T van Duin, Diana M van Duin, Bin Liu, James H Edgar
Atomistic-scale insights into the growth of a continuous, atomically thin hexagonal boron nitride (hBN) lattice from elemental boron and nitrogen on Ni substrates were obtained from multi-scale modeling combining density functional theory (DFT) and reactive molecular dynamics (rMD). The quantum mechanical calculations focused on the adsorption and reaction energetics for the hBN building-block species, i.e., atomic B, N, BxNy (x, y = 1-2), on Ni(111) and Ni(211), and the diffusion pathways of elemental B and N on these slab model surfaces and in the sublayer...
March 20, 2017: ACS Nano
Liew Weng Tack, Mohd Asyadi Azam, Raja Noor Amalina Raja Seman
Single-walled carbon nanotubes (SWCNTs) and metal oxides (MOs), such as manganese (IV) oxide (MnO2), cobalt (II, III) oxide (Co3O4), and nickel (II) oxide (NiO) hybrid structures, have received great attention because of their promising application in lithium-ion batteries (LIBs). As electrode materials for LIBs, the structure of SWCNT/MOs provides high power density, good electrical conductivity, and excellent cyclic stability. In this work, first-principles calculations were used to investigate the structural and electronic properties of MOs attached to (5, 5) SWCNT and Li-ion adsorption to SWCNT/ metal oxide composites as electrode materials in LIBs...
March 20, 2017: Journal of Physical Chemistry. A
Alvaro Muñoz-Castro, Wilson Caimanque-Aguilar, Cesar Morales-Verdejo
Corannulene, C20H10, exhibits a concave surface in the ground state which is able to experience a bowl-to-bowl inversion through a planar conformation. Such structure is the smaller example resembling an isolated-pentagon motif, as a relevant fragment in Fullerene chemistry. Here, we explored the differences between bowl and planar conformations involving both energetic and 13C-NMR properties, for the neutral and tetraanionic species by using DFT methods. This allows to understand the variation of the chemical environment at the carbon atoms upon planarization of this representive motif...
March 20, 2017: Journal of Physical Chemistry. A
Ya-Sen Sun, Chien-Fu Lin, Shih-Ting Luo, Ching-Yuan Su
The self-assembly of a block copolymer offers access to micellar nanodomains with tunable dimensions and structural diversity through control of such molecular parameters as the volume fraction and molecular mass. We fabricated hierarchical porous carbon (HPC) nanostructures with bundles of aggregated nanospheres and with nitrogen-rich functional groups through pyrolysis of diblock copolymer micelles in multiple layers. The resultant HPC nanostructures with a considerable specific surface area serve as an excellent substrate for surface-enhanced Raman spectroscopy (SERS), coupled with fluorescence quenching, for molecular sensing of physically adsorbed Rhodamine 6G...
March 20, 2017: ACS Applied Materials & Interfaces
Albert J Erives
Polyglutamine (polyQ) tracts in regulatory proteins are extremely polymorphic. As functional elements under selection for length, triplet repeats are prone to DNA replication slippage and indel mutations. Many polyQ tracts are also embedded within intrinsically disordered domains, which are less constrained, fast evolving, and difficult to characterize. To identify structural principles underlying polyQ tracts in disordered regulatory domains, here I analyze deep evolution of metazoan Notch polyQ tracts, which can generate alleles causing developmental and neurogenic defects...
2017: PloS One
Chung-Chuan Lai, Cecilia Goyenola, Esteban Broitman, Lars-Åke Näslund, Hans Hogberg, Lars Hultman, Gueorgui Gueorguiev, Johanna Rosen
A theoretical and experimental study on the growth and properties of a ternary carbon-based material, CS<sub><i>x</i></sub>F<sub><i>y</i></sub>, synthesized from SF<sub>6</sub> and C as primary precursors is reported. The synthetic growth concept was applied to model the possible species resulting from the fragmentation of SF<sub>6</sub> molecules and the recombination of S-F fragments with atomic C. The possible species were further evaluated for their contribution to the film growth...
March 20, 2017: Journal of Physics. Condensed Matter: An Institute of Physics Journal
Masoud Rashidi, Hans-Olof Andrén, Fang Liu
In creep resistant Z-phase strengthened 12% Cr steels, MX (M=Nb, Ta, or V, and X=C and/or N) to Z-phase (CrMN, M=Ta, Nb, or V) transformation plays an important role in achieving a fine distribution of Z-phase precipitates for creep strengthening. Atom probe tomography was employed to investigate the phase transformation in a Nb-based Z-phase strengthened trial steel. Using iso-concentration surfaces with different concentration values, and subtracting the matrix contribution enabled us to reveal the core-shell structure of the transient precipitates between MX and Z-phase...
March 20, 2017: Microscopy and Microanalysis
Bo Wei, Weizhang Li, Zujin Zhao, Anjun Qin, Rongrong Hu, Ben Zhong Tang
Sequence-controlled polymers, including biopolymers such as DNA, RNA and proteins, have attracted much attention recently because of their sequence-dependent functionalities. The development of efficient synthetic approach for non-natural sequence-controlled polymers are hence of great importance. Multicomponent polymerizations (MCPs) as a powerful and popular synthetic approach for functional polymers with great structural diversity have been demonstrated to be a promising tool for the synthesis of sequence-controlled polymers...
March 20, 2017: Journal of the American Chemical Society
Tianyu Li, Zongchang Zhao, Xiaodong Zhang, Xican Sun
1-ethyl-3-methylimidazolium dimethylphosphate ([Emim][Dmp])-water binary solution is one of the promising new working-pairs for absorption heat pump and absorption chillers, which are widely used to recover industrial waste heat. In the absorption process, the mass and heat transfer at the interface greatly depend on interface microscopes structure. Therefore, in order to understand the absorption process, it is very important to study the interface microscopes structure. The liquid-vapor interface properties, as well as the orientation of [Emim]+, [Dmp]-, water at the interface and its aqueous solution with different water mole fraction, were studied using classical all-atom force field by molecular dynamic simulations...
March 20, 2017: Journal of Physical Chemistry. B
Juan Pablo Arcon, Lucas A Alfredo Defelipe, Carlos Pablo Modenutti, Elias Daniel Lopez, Daniel Alvarez-Garcia, Xavier Barril, Adrian Gustavo Turjanski, Marcelo A Marti
One of the most important biological processes at the molecular level is the formation of protein-ligand complexes. Therefore, determining their structure and underlying key interactions is of paramount relevance and has direct applications in drug development. Due to its low cost relative to its experimental sibling, Molecular Dynamics (MD) simulations in the presence of different solvent probes mimicking specific type of interactions have been increasingly used to analyze protein binding sites and reveal protein-ligand interaction hot spots...
March 20, 2017: Journal of Chemical Information and Modeling
Tiffany M Smith Pellizzeri, Colin D McMillen, Yimei Wen, George Chumanov, Joseph W Kolis
Three new barium manganese vanadates, all containing hexagonal barium chloride layers interpenetrated by [V2O7](4-) groups, were synthesized using a high-temperature (580 °C) hydrothermal method. Two of the compounds were prepared from a mixed BaCl2/Ba(OH)2 mineralizer, and the third compound was prepared from BaCl2 mineralizer. An interesting structural similarity exists between two of the compounds, Ba2Mn(V2O7)(OH)Cl and Ba4Mn2(V2O7)(VO4)2O(OH)Cl. These two compounds crystallize in the orthorhombic space group Pnma, Z = 4, and are structurally related by a nearly doubled a axis...
March 20, 2017: Inorganic Chemistry
Jonathan Dickerhoff, Linn Haase, Walter Langel, Klaus Weisz
A human telomere sequence that folds into an intramolecular (3+1)-hybrid G-quadruplex was modified by the incorporation of 2'-fluoro-2'-deoxyriboguanosines ((F)G) into syn positions of its outer tetrad. A circular dichroism and NMR spectral analysis reveals a nearly quantitative switch of the G-tetrad polarity with concerted syn↔anti transitions of all four G residues. These observations follow findings on a (F)G-substituted (3+1)-hybrid quadruplex with a different fold, suggesting a more general propensity of hybrid-type quadruplexes to undergo a tetrad polarity reversal...
March 20, 2017: ACS Chemical Biology
Changhao Wang, Li Xiao, Ray Luo
Continuum solvent models, particularly those based on the Poisson-Boltzmann equation (PBE), are widely used in the studies of biomolecular structures and functions. Existing PBE developments have been mainly focused on how to obtain more accurate and/or more efficient numerical potentials and energies. However to adopt the PBE models for molecular dynamics simulations, a difficulty is how to interpret dielectric boundary forces accurately and efficiently for robust dynamics simulations. This study documents the implementation and analysis of a range of standard fitting schemes, including both one-sided and two-sided methods with both first-order and second-order Taylor expansions, to calculate molecular surface electric fields to facilitate the numerical calculation of dielectric boundary forces...
March 20, 2017: Journal of Computational Chemistry
Andrea Bazzoli, John Karanicolas
Water engages in two important types of interactions near biomolecules: it forms ordered "cages" around exposed hydrophobic regions, and it participates in hydrogen bonds with surface polar groups. Both types of interaction are critical to biomolecular structure and function, but explicitly including an appropriate number of solvent molecules makes many applications computationally intractable. A number of implicit solvent models have been developed to address this problem, many of which treat these two solvation effects separately...
March 20, 2017: Journal of Computational Chemistry
Chenyi Liao, Xiaochuan Zhao, Jiyuan Liu, Severin T Schneebeli, John C Shelley, Jianing Li
The structures and dynamics of protein complexes are often challenging to model in heterogeneous environments such as biological membranes. Herein, we meet this fundamental challenge at attainable cost with all-atom, mixed-resolution, and coarse-grained models of vital membrane proteins. We systematically simulated five complex models formed by two distinct G protein-coupled receptors (GPCRs) in the lipid-bilayer membrane on the ns-to-μs timescales. These models, which suggest the swinging motion of an intracellular loop, for the first time, provide the molecular details for the regulatory role of such a loop...
March 20, 2017: Physical Chemistry Chemical Physics: PCCP
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