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https://www.readbyqxmd.com/read/28088325/molecular-dynamics-simulations-of-ternary-lipid-bilayers-containing-plant-sterol-and-glucosylceramide
#1
Shiva Emami, Sodeif Azadmard-Damirchi, Seyed Hadi Peighambardoust, Javad Hesari, Hadi Valizadeh, Roland Faller
An atomic-level molecular dynamics simulation was carried out to study the effects of a plant sterol (sitosterol) and glucosylceramide (GlcCer) on a 1,2-dilinoleoylposphocholine (DLiPC) membrane. Initially, a membrane containing 50mol % sitosterol was compared with that containing the same ratio of cholesterol. These simulations showed differential condensing and ordering effects of sitosterol and cholesterol, with cholesterol being slightly more efficient than sitosterol in packing the membrane more tightly to a liquid ordered phase...
January 11, 2017: Chemistry and Physics of Lipids
https://www.readbyqxmd.com/read/28088140/ring-polymer-molecular-dynamics-studies-on-the-rate-coefficient-of-the-abstraction-channel-of-hydrogen-plus-ethane-propane-and-dimethyl-ether
#2
Qingyong Meng, Jun Chen
To accurately compute the rates of the abstraction channels of hydrogen plus ethane (Et), propane (Pr), and dimethyl ether (DME), ring-polymer molecular dynamics (RPMD) method is used in conjunction with the recently constructed local permutation invariant polynomial neural-networks potential energy surface of the parent H + CH4 system [Q. Meng et al., J. Chem. Phys. 144, 154312 (2016)]. For H + Et, one of the H atoms in CH4 of the parent system is replaced by a methyl group, while for the H + DME reaction, it is replaced by the methoxyl group...
January 14, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28081015/the-prospects-of-phosphorene-as-an-anode-material-for-high-performance-lithium-ion-batteries-a-fundamental-study
#3
Congyan Zhang, Ming Yu, George Anderson, Ruchira Ravinath Dharmasena, Gamini Sumanasekera
To completely understand lithium adsorption, diffusion, and capacity on the surface of phosphorene and, therefore, the prospects of phosphorene as an anode material for high-performance lithium-ion batteries (LIBs), we carried out density-functional-theory calculations and studied the lithium adsorption energy landscape, the lithium diffusion mobility, the lithium intercalation, and the lithium capacity of phosphorene. We also carried out, for the very first time, experimental measurement of the lithium capacity of phosphorene...
January 12, 2017: Nanotechnology
https://www.readbyqxmd.com/read/28080057/identification-of-binding-modes-for-amino-naphthalene-2-cyanoacrylate-anca-probes-to-amyloid-fibrils-from-molecular-dynamics-simulations
#4
Huan He, Juan Xu, Dan-Yang Cheng, Li Fu, Yu-Shu Ge, Feng-Lei Jiang, Yi Liu
Amino naphthalene 2-Cyanoacrylate (ANCA) probe is a kind of fluorescent amyloid binding probe that can report a different fluorescence emission when bound to different types of amyloid deposits in tissue, while their interactions with amyloid fibrils remain unclear due to the insoluble nature of amyloid fibrils. Here, all atom molecular dynamics simulations were used to investigate the interaction between ANCA probes with three different amyloid fibrils. Two common binding modes of ANCA probes on Aβ40 amyloid fibrils were identified by cluster analysis of multiple simulations...
January 12, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28080051/prediction-of-bond-dissociation-energies-heat-of-formation-for-diatomic-transition-metal-compounds-ccsd-t-works
#5
Zongtang Fang, Monica Vasiliu, Kirk A Peterson, David A Dixon
It was recently reported (J. Chem. Theory Comput. 2015, 11, 2036-2052) that the coupled cluster singles and doubles with perturbative triples method, CCSD(T), should not be used as a benchmark tool for the prediction of dissociation energies (heats of formation) for the 1st row transition metal diatomics based on a comparison with the experimental thermodynamic values for a set of 20 diatomics. In the present work the bond dissociation energies as well as the heats of formation for those diatomics have been calculated by the Feller-Peterson-Dixon approach at the CCSD(T)/complete basis set (CBS) level of theory including scalar relativistic corrections and correlation of the outer shell of core electrons in addition to the valence electrons...
January 12, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28080032/heteroprotein-complex-formation-of-bovine-lactoferrin-and-pea-protein-isolate-a-multiscale-structural-analysis
#6
Eda Adal, Amin Sadeghpour, Simon D A Connell, Michael Rappolt, Esra Ibanoglu, Anwesha Sarkar
Associative electrostatic interactions between two oppositely charged globular proteins, lactoferrin (LF) and pea protein isolate (PPI), the latter being a mixture of vicilin, legumin and convicilin, was studied with a specific PPI/ LF molar ratio at room temperature. Structural aspects of the electrostatic complexes probed at different length scales were investigated as a function of pH by means of different complementary techniques, namely with dynamic light scattering, small angle X-ray scattering (SAXS), turbidity measurements and atomic force microscopy (AFM)...
January 12, 2017: Biomacromolecules
https://www.readbyqxmd.com/read/28080028/a-grand-avenue-to-au-nanocluster-electrochemiluminescence
#7
Mahdi Hesari, Zhifeng Ding
In most cases of semiconductor quantum dot nanocrystals, the inherent optical and electrochemical properties of these interesting nanomaterials do not translate into expected efficient electrochemiluminescence or electrogenerated chemiluminescence (ECL) because of the surface-state induction effect. Thus, their low ECL efficiencies, while very interesting to explore, limit their applications. As their electrochemistry is not well-defined, insight into their ECL mechanistic details is also limited. Alternatively, gold nanoclusters possess monodispersed sizes with atomic precision, low and well defined HOMO-LUMO energy gaps, and stable optical and electrochemical properties that make them suitable for potential ECL applications...
January 12, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28079303/mononuclear-clusterfullerene-single-molecule-magnet-containing-strained-fused-pentagons-stabilized-by-a-nearly-linear-metal-cyanide-cluster
#8
Fupin Liu, Song Wang, Cong-Li Gao, Qingming Deng, Xianjun Zhu, Aram Kostanyan, Rasmus Westerström, Fei Jin, Su-Yuan Xie, Alexey A Popov, Thomas Greber, Shangfeng Yang
Fused-pentagons results in an increase of local steric strain according to the isolated pentagon rule (IPR), and for all reported non-IPR clusterfullerenes multiple (two or three) metals are required to stabilize the strained fused-pentagons, making it difficult to access the single-atom properties. Herein, we report the syntheses and isolations of novel non-IPR mononuclear clusterfullerenes MNC@C76 (M=Tb, Y), in which one pair of strained fused-pentagon is stabilized by a mononuclear cluster. The molecular structures of MNC@C76 (M=Tb, Y) were determined unambiguously by single-crystal X-ray diffraction, featuring a non-IPR C2v (19138)-C76 cage entrapping a nearly linear MNC cluster, which is remarkably different from the triangular MNC cluster within the reported analogous clusterfullerenes based on IPR-obeying C82 cages...
January 12, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28079191/enhanced-radiation-tolerant-oxide-dispersion-strengthened-steel-and-its-microstructure-evolution-under-helium-implantation-and-heavy-ion-irradiation
#9
Chenyang Lu, Zheng Lu, Xu Wang, Rui Xie, Zhengyuan Li, Michael Higgins, Chunming Liu, Fei Gao, Lumin Wang
The world eagerly needs cleanly-generated electricity in the future. Fusion reactor is one of the most ideal energy resources to defeat the environmental degradation caused by the consumption of traditional fossil energy. To meet the design requirements of fusion reactor, the development of the structural materials which can sustain the elevated temperature, high helium concentration and extreme radiation environments is the biggest challenge for the entire material society. Oxide dispersion strengthened steel is one of the most popular candidate materials for the first wall/blanket applications in fusion reactor...
January 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28075585/acidity-of-m-vi-o2-oh-2-for-m-group-6-16-and-u-as-central-atoms
#10
Rulin Feng, Monica Vasiliu, Kirk A Peterson, David A Dixon
Gas phase acidities and aqueous solution pKa's are predicted for MO2(OH)2 where center atom M is a main group 6, 16 and U atom using the Feller-Peterson-Dixon approach based on coupled cluster CCSD(T) calculations with additional corrections. The gas phase acidities of the MO2(OH)2 compounds are essentially the same for elements (M) of the same group, 304 - 310 kcal/mol at 298 K. All of the Group 6 compounds are 5 to 6 kcal/mol less acidic in the gas phase than H2SO4. The gas phase acidity of UO2(OH)2 is calculated to be up to 338...
January 11, 2017: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/28075577/reversible-unfolding-and-folding-of-the-metalloprotein-ferredoxin-revealed-by-single-molecule-atomic-force-microscopy
#11
Hai Lei, Yabin Guo, Xiaodong Hu, Chunguang Hu, Xiaotang Hu, Hongbin Li
Plant type [2Fe-2S] ferredoxins function primarily as electron transfer proteins in photosynthesis. Studying the unfolding-folding of ferredoxins in vitro is challenging, since the unfolding of ferredoxin is often irreversible due to the loss or disintegration of the iron-sulfur cluster. Additionally, the in vivo folding of holo-ferredoxin requires ferredoxin biogenesis proteins. Here we employed atomic force microscopy-based single molecule force microscopy and protein engineering techniques to directly study the mechanical unfolding and refolding of a plant type [2Fe-2S] ferredoxin from cyanobacteria Anabaena...
January 11, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28075549/solvent-morphology-property-relationship-of-ptb7-pc71bm-polymer-solar-cells
#12
Shuai Guo, Weijia Wang, Eva M Herzig, Anna Naumann, Gregory Tainter, Jan Perlich, Peter Muller-Buschbaum
The influence of three different solvents and a solvent additive on the morphology and photovoltaic performance of bulk heterojunction films made of the copolymer based on thieno[3,4-b]thiophene-alt-benzodithiophene unit PTB7-F40 blended with [6,6]-phenyl-C71-butyric acid methyl ester (PC71BM) is investigated. Optical microscopy and atomic force microscopy (AFM) are combined with X-ray reflectivity (XRR) and grazing incidence small and wide angle X-ray scattering (GISAXS and GIWAXS) enabling the characterization of the morphology of the whole photoactive film...
January 11, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28071910/direct-measurement-of-the-effect-of-cholesterol-and-6-ketocholestanol-on-membrane-dipole-field-using-vibrational-stark-effect-spectroscopy-coupled-with-molecular-dynamics-simulations
#13
Rebika Shrestha, Cari M Anderson, Alfredo E Cardenas, Ron Elber, Lauren J Webb
Biological membranes are heterogeneous structures with complex electrostatic profiles arising from lipids, sterols, membrane proteins, and water molecules. We investigated the effect of cholesterol and its derivative 6-ketocholestanol (6-kc) on membrane electrostatics by directly measuring the dipole electric field (F ) within lipid bilayers containing cholesterol or 6-kc at concentrations of 0-40 mol% through the vibrational Stark effect (VSE). We found that adding low concentrations of cholesterol, up to ~10 mol%, increases F, while adding more cholesterol up to 40 mol% lowers F...
January 10, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28071903/revisiting-the-m%C3%A3-ssbauer-isomer-shifts-of-the-femoco-cluster-of-nitrogenase-and-the-cofactor-charge
#14
Ragnar Bjornsson, Frank Neese, Serena DeBeer
Despite decades of research, the structure-activity relationship of nitrogenase is still not understood. Only recently was the full molecular structure of the FeMo cofactor (FeMoco) revealed, but the charge and metal oxidation states of FeMoco have been controversial. With the recent identification of the interstitial atom as a carbide and the more recent revised oxidation-state assignment of the molybdenum atom as Mo(III), here we revisit the Mössbauer properties of FeMoco. By a detailed error analysis of density functional theory-computed isomer shifts and computing isomer shifts relative to the P-cluster, we find that only the charge of [MoFe7S9C](1-) fits the experimental data...
January 10, 2017: Inorganic Chemistry
https://www.readbyqxmd.com/read/28071901/accurate-theoretical-thermochemistry-for-fluoroethyl-radicals
#15
Adam Ganyecz, Mihaly Kallay, Jozsef Csontos
An accurate coupled-cluster (CC) based model chemistry was applied to calculate reliable thermochemical quantities for hydrofluorocarbon hydrofluorocarbon derivatives including radicals 1-fluoroethyl (CH3 -CHF), 1,1-difluoroethyl (CH3-CF2), 2-fluoroethyl (CH2F-CH2), 1,2-difluoroethyl (CH2F-CHF), 2,2-difluoroethyl (CHF2-CH2), 2,2,2-trifluoroethyl (CF3-CH2), 1,2,2,2-tetrafluoroethyl (CF3-CHF), and pentafluoroethyl (CF3-CF2). The model chemistry used contains iterative triple and perturbative quadruple excitations in CC theory, as well as scalar relativistic and diagonal Born-Oppenheimer corrections...
January 10, 2017: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/28071896/fe-on-sb-111-potential-two-dimensional-ferromagnetic-superstructures
#16
Yinghui Yu, Huixia Fu, Limin She, Shuangzan Lu, Qinmin Guo, Hui Li, Sheng Meng, Gengyu Cao
It is highly desirable to fabricate two-dimensional ferromagnetic membranes on basis of orthodox magnetic elements due to their inherent magnetic properties. In this work, we report on two superstructures including a honeycomb-like lattice and identical nanocluster arrays formed by depositing Fe on Sb(111). Combined with first-principles calculations, both detailed atomic structures have been clarified. The honeycomb structure consists of a single layered Fe-Sb phase and the cluster phase is assigned as a (3×3) Fe3Sb7 superlattice...
January 10, 2017: ACS Nano
https://www.readbyqxmd.com/read/28071694/structures-stabilities-and-spectral-properties-of-borospherene-b44-and-metalloborospherenes-mb44-0-m%C3%A2-%C3%A2-li-na-and-k
#17
Shixiong Li, Zhengping Zhang, Zhengwen Long, Shuijie Qin
Density functional theory (DFT) and time-dependent density functional theory (TD-DFT) calculations are carried out to study the stabilities, photoelectron, infrared, Raman and electronic absorption spectra of borospherene B44(-) and metalloborospherenes MB44(0/-) (M = Li, Na, and K). It is found that all atoms can form stable exohedral metalloborospherenes M&B44(0/-), whereas only Na and K atoms can be stably encapsulated inside B44(0/-) cage. In addition, relative energies of these metalloborospherenes suggest that Na and K atoms favor exohedral configuration...
January 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28068775/decomposition-of-proteins-into-dynamic-units-from-atomic-cross-correlation-functions
#18
Paolo Calligari, Marco Gerolin, Daniel Abergel, Antonino Polimeno
In this article, we present a clustering method of atoms in proteins based on the analysis of the correlation times of interatomic distance correlation functions computed from MD simulations. The goal is to provide a coarse-grained description of the protein in terms of fewer elements that can be treated as dynamically independent subunits. Importantly, this domain decomposition method does not take into account structural properties of the protein. Instead, the clustering of protein residues in terms of networks of dynamically correlated domains is defined on the basis of the effective correlation times of the pair distance correlation functions...
January 10, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28068082/gold-nanoclusters-promote-electrocatalytic-water-oxidation-at-the-nanocluster-cose2-interface
#19
Shuo Zhao, Renxi Jin, Hadi Abroshan, Chenjie Zeng, Hui Zhang, Stephen D House, Eric Gottlieb, Hyung J Kim, Judith C Yang, Rongchao Jin
Electrocatalytic water splitting to produce hydrogen comprises the hydrogen and oxygen evolution half reactions (HER and OER), with the latter as the bottleneck process. Thus, enhancing the OER performance and understanding the mechanism are critically important. Herein, we report a strategy for OER enhancement by utilizing gold nanoclusters to form cluster/CoSe2 composites; the latter exhibit largely enhanced OER activity in alkaline solutions. The Au25/CoSe2 composite affords a current density of 10 mA cm-2 at small overpotential of ~0...
January 9, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28067516/elucidating-the-bacterial-membrane-disruption-mechanism-of-human-%C3%AE-defensin-5-a-theoretical-study
#20
Sang Won Jung, Juho Lee, Art E Cho
Human α-defensin 5 (HD5) is a broad-spectrum antibacterial peptide produced by small intestinal Paneth cells. Despite considerable experimental evidence for the correlation between bacterial membrane destruction and the antibacterial activity of HD5, its membrane disruption mechanism remains unclear. Using all-atom molecular dynamics (MD) simulations and molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) analysis, we demonstrate the membrane disruption mechanism of HD5 based on the intrinsic binding of HD5 to Gram-negative (GN) bacterial inner-membrane...
January 9, 2017: Journal of Physical Chemistry. B
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