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# atomic structure

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#1
Duangtip Sudhan, Thamrongjet Puttamuk, Supachai Vuttipongchaikij, Pitak Chuawong
Citrus Huanglongbing (HLB) or citrus greening is one of the most destructive diseases affecting citrus industry worldwide. The causal agent in Asia is a phloem-limited, Gram-negative bacterium, 'Candidatus Liberibacter asiaticus' (CLas). Within the genome of CLas lies prophage regions, classified as Type-A, B, C, and D. In particular, Type-D has been indicated to correlate with the blotchy-mottle symptoms of citrus trees. Here we reported the cloning, overexpression, and purification of the ORF1, an open reading frame from the partial Type-D region of CLas obtained from an infected lime tree (Citrus aurantifolia Swingle)...
May 21, 2018: Protein Expression and Purification
#2
Thiago Sousa, Thales Fernando Damasceno Fernandes, Matheus J S Matos, Eduardo Nery Duarte Araujo, Mario S C Mazzoni, Bernardo R A Neves, Flávio Plentz
The association of organic molecules with 2D materials, creating hybrid systems with mutual influences, constitutes an important testbed for both basic science self-assembly studies and perspective applications. Following this concept, in this work, we show a rich phenomenology that is involved in the interaction of thionine with graphene, leading to a hybrid material formed by well-organized self-assembled structures atop graphene. This composite system is investigated by atomic force microscopy, electric transport measurements, and first principles calculations, which show: 1) an interesting time evolution of thionine self-assembled structures atop graphene; 2) the final molecular assembly is highly oriented (in accordance with the underlying graphene surface symmetry); and 3) thionine introduces a strong n-type doping effect in graphene...
May 24, 2018: Langmuir: the ACS Journal of Surfaces and Colloids
#3
Jun Shang, Ben Hu, Junmei Wang, Feng Zhu, Yu Kang, Dan Li, Huiyong Sun, De-Xin Kong, Tingjun Hou
This is a new golden age for the drug discovery based on natural products derived from both marine and terrestrial sources. Herein, a straightforward but important question is what are the major structural differences between marine natural products (MNPs) and terrestrial natural products (TNPs). To answer this question, we analyzed the important physicochemical properties, structural features and drug-likeness of the two types of natural products and discussed their differences from the perceptive of evolution...
May 24, 2018: Journal of Chemical Information and Modeling
#4
Hidenori Takahashi, Yuji Shimabukuro, Daiki Asakawa, Shosei Yamauchi, Sadanori Sekiya, Shinichi Iwamoto, Motoi Wada, Koichi Tanaka
Gas-phase hydrogen radicals were introduced into a quadrupole ion trap containing singly charged phospholipids to obtain structural fragmentation patterns in tandem mass spectrometry (MS/MS). Saturated and unsaturated phosphatidylcholines were used as a model phospholipid, whose chain-length ranges between 16 and 24. The MS/MS spectrum yielded a continuous series of fragment ions with a mass differencesdifference of 14 Da, representing the saturated fatty acyl chains. The fragment ions corresponding to the double-bond position within a single fatty acyl chain showed thea characteristic mass difference of 12 Da...
May 24, 2018: Analytical Chemistry
#5
Rex T Skodje, Jonathan R Church
A novel double hydrogen atom exchange process, HX+H'O2H'X+HO2 for the halogen series X=F, Cl, Br, and I, is identified using theoretical methods. These concerted reactions are mediated through a stabilized five-member planar ring transition state structure. The transition state barrier for the double exchange process is found to be significantly lower than that for the abstraction reaction of a single hydrogen atom, . Density functional theory employing the M11 exchange functional is used to compute parameters of the potential energy surface and the rate coefficients are obtained using transition state theory with small curvature tunneling...
May 24, 2018: Journal of Physical Chemistry. A
#6
Federica Battistin, Gabriele Balducci, Barbara Milani, Enzo Alessio
As a continuation of our strategy for preparing new Ru(II) precursors with improved water solubility through the introduction of highly water-soluble 1,3,5-triaza-7-phosphoadamantane (PTA) supporting ligands in the coordination sphere, in this work, we address the largely unexplored preparation of Ru(II)-PTA carbonyls. Two complementary synthetic approaches were used: (1) the treatment of a series of neutral Ru(II)-CO-dmso compounds of general formula RuCl2 (CO) n (dmso)4- n ( n = 1-3, 1-5) with PTA; (2) the reaction of Ru(II)-PTA complexes with CO...
May 24, 2018: Inorganic Chemistry
#7
Priscilla L S Boon, Wuan Geok Saw, Xin Xiang Lim, Palur Venkata Raghuvamsi, Roland G Huber, Jan K Marzinek, Daniel A Holdbrook, Ganesh S Anand, Gerhard Grüber, Peter J Bond
The 11 kDa, positively charged dengue capsid protein (C protein) exists stably as a homodimer and co-localizes with the viral genome within mature viral particles. Its core is composed of four alpha helices encompassing a small hydrophobic patch that may interact with lipids, but approximately 20% of the protein at the N-terminus is intrinsically disordered, making it challenging to elucidate its conformational landscape. Here, we combine small-angle X-ray scattering (SAXS), amide hydrogen-deuterium exchange mass spectrometry (HDXMS), and atomic-resolution molecular dynamics (MD) simulations to probe the dynamics of dengue C proteins...
May 24, 2018: ACS Chemical Biology
#8
Bin Yang, Youai Qiu, Jan-E Bäckvall
Oxidation reactions play a central role in organic synthesis, and it is highly desirable that these reactions are mild and occur under catalytic conditions. In Nature, oxidation reactions occur under mild conditions via cascade processes, and furthermore, they often occur in an enantioselective manner with many of them involving molecular oxygen or hydrogen peroxide as the terminal oxidant. Inspired by the reactions in Nature, we have developed a number of Pd(II)-catalyzed cascade reactions under mild oxidative conditions...
May 24, 2018: Accounts of Chemical Research
#9
Qiaofeng Yao, Tiankai Chen, Xun Yuan, Jianping Xie
Total synthesis, where desired organic- and/or biomolecules could be produced from simple precursors at atomic precision and with known step-by-step reactions, has prompted centuries-lasting bloom of organic chemistry since its conceptualization in 1828 (Wöhler synthesis of urea). Such expressive science is also highly desirable in nanoscience, since it represents a decisive step toward atom-by-atom customization of nanomaterials for basic and applied research. Although total synthesis chemistry is less established in nanoscience, recent years have witnessed seminal advances and increasing research efforts devoted into this field...
May 24, 2018: Accounts of Chemical Research
#10
Libin Wang, Le Deng, Jieming Qin, Xiaopeng Jia
It has been discussed for a long time that synthetic pressure can effectively optimize thermoelectric properties. The beneficial effect of synthesis pressures on thermoelectric properties has been discussed for a long time. In this paper, it is theoretically and experimentally demonstrated that appropriate synthesis pressures can increase the figure of merit (ZT) through optimizing thermal transport and electronic transport properties. Indium and barium atoms double-filled CoSb3 samples were prepared use high-pressure and high-temperature technique for half an hour...
May 24, 2018: Inorganic Chemistry
#11
Alexander S Mikherdov, Mikhail A Kinzhalov, Alexander S Novikov, Vadim P Boyarskiy, Irina A Boyarskaya, Margarita S Avdontceva, Vadim Yu Kukushkin
The reaction of cis-[PdCl2 (CNXyl)2 ] (Xyl = 2,6-Me2 C6 H3 ) with the aminoazoles [1 H-imidazol-2-amine (1), 4 H-1,2,4-triazol-3-amine (2), 1 H-tetrazol-5-amine (3), 1 H-benzimidazol-2-amine (4), 1-alkyl-1 H-benzimidazol-2-amines, where alkyl = Me (5), Et (6)] in a 2:1 ratio in the presence of a base in CHCl3 at RT proceeds regioselectively and leads to the binuclear diaminocarbene complexes [(ClPdCNXyl)2 {μ-C(N-azolyl)N(Xyl)C═NXyl}] (7-12; 73-91%). Compounds 7-12 were characterized by C, H, N elemental analyses, high-resolution ESI+ -MS, Fourier transform infrared spectroscopy, 1D (1 H, 13 C) and 2D (1 H,1 H-COSY, 1 H,1 H-NOESY, 1 H,13 C-HSQC, 1 H,13 C-HMBC) NMR spectroscopies, and X-ray diffraction (XRDn)...
May 24, 2018: Inorganic Chemistry
#12
Pengfei Li, Wei Zhang, Dongdong Li, Changhao Liang, Xiao Cheng Zeng
The most stable structures of two-dimensional (2D) GexPy and GexAsy monolayers with different stoichiometry (e.g., GeP, GeP2, GeP3) are explored systematically through the combination of the particle-swarm optimization (PSO) technique and density functional theory optimization. For GeP3, we show that the newly predicted most stable C2/m structure is 0.16 eV/atom lower in energy than the state-of-the-art P-3m1 structure reported previously (Nano Lett.2017, 17, 1833). The computed electronic band structures suggest that all the stable and metastable monolayers of GexPy are semiconductors with highly tunable bandgaps under the biaxial strain, allowing strain engineering of their bandgaps within nearly the whole visible-light range...
May 24, 2018: ACS Applied Materials & Interfaces
#13
Ashish Bhattarai, Andrey Krayev, Alexey Temiryazev, Dmitry Evplov, Kevin Thomas Crampton, Wayne P Hess, Patrick Z El Khoury
Tip-enhanced Raman spectroscopy (TERS) is particularly sensitive to analytes residing at plasmonic tip-sample nanojunctions, where the incident and scattered optical fields may be localized and optimally enhanced. However, the enhanced local electric fields in this so-called gap-mode TERS configuration are nominally orthogonal to the sample plane. As such, any given Raman active vibrational Eigenstate needs to have projections (of its polarizability derivative tensor elements) along the sample normal to be detectable via TERS...
May 23, 2018: Nano Letters
#14
G Vilmart, N Dorval, M Orain, D Lambert, R Devillers, Y Fabignon, B Attal-Tretout, A Bresson
Planar laser-induced fluorescence on atomic iron is investigated in this paper, and a measurement strategy is proposed to monitor the fluorescence of iron atoms with good sensitivity. A model is proposed to fit the experimental fluorescence spectra, and good agreement is found between simulated and experimental spectra. Emission and laser-induced fluorescence measurements are performed in the flames of ammonium perchlorate composite propellants containing iron-based catalysts. A fluorescence signal from iron atoms after excitation at 248 nm is observed for the first time in propellant flames...
May 10, 2018: Applied Optics
#15
Quan-De Wang, Zi-Wu Liu
Alkenes are important ingredients of realistic fuels and are also critical intermediates during the combustion of a series of other fuels including alkanes, cycloalkanes and biofules. To provide insights into the combustion behavior of alkenes, detailed quantum chemical studies for crucial reactions are desired. Hydrogen abstractions of alkenes play a very important role in determining the reactivity of fuel molecules. This work is motivated by previous experimental and modeling evidences that current literature rate coefficients for the abstraction reactions of alkenes are still in need of refinement and/or re-determination...
May 23, 2018: Journal of Physical Chemistry. A
#16
Antonio M Echavarren, Rafal Zuzak, Ruth Dorel, Marek Kolmer, Marek Szymonski, Szymon Godlewski
A unified approach to the synthesis of the series of higher acenes up to previously unreported undecacene has been developed through the on-surface dehydrogenation of partially saturated precursors. These molecules could be converted into the parent acenes by atomic manipulation with the tip of a scanning tunneling and atomic force microscope (STM/AFM) as well as by on-surface annealing. The structure of the generated acenes has been visualized by high resolution non-contact AFM imaging and the evolution of the transport gap with the increase of the number of fused benzene rings has been determined on the basis of scanning tunneling spectroscopy (STS) measurements...
May 23, 2018: Angewandte Chemie
#17
Markus Kratzer, Konrad Szajna, Domink Wrana, Wojciech Belza, Franciszek Krok, Christian Teichert
Control over organic thin film growth is a central issue in the development of organic electronics. The anisotropy and extended size of the molecular building blocks introduce a high degree of complexity within the formation of thin films. This complexity can be even increased for substrates with induced, sophisticated morphology and anisotropy. Thus, targeted structuring like ion beam mediated modification of substrates in order to create ripples, pyramids, or pit structures provides a further degree of freedom in manipulating the growth morphology of organic thin films...
May 23, 2018: Journal of Physics. Condensed Matter: An Institute of Physics Journal
#18
Richard Baochang Wang, Anders Hellman
Hematite ($\alpha$-Fe$_2$O$_3$) is the most stable and abundant iron oxide&#13; in nature, and is used in many important environmental and industrial&#13; technologies, such as waste-water treatment, gas sensors, and&#13; photoelectrocatalysis. A clear understanding of&#13; the structure, composition, and chemistry of the hematite surface &#13; is crucial for improving its function in these technologies. The (0001) &#13; facet is reported to dominate under natural &#13; conditions, while the specific terminations depend strongly on&#13; preparation conditions...
May 23, 2018: Journal of Physics. Condensed Matter: An Institute of Physics Journal
#19
Shi-Hao Zhang, Bang-Gui Liu
Excellent monolayer electrode materials can be used to design high-performance alkali-metal-ion batteries. Here, we propose two-dimensional ReN$_2$ monolayers as superior sodium-ion battery materials. Our total-energy optimization results in a buckled tetragonal structure for ReN$_2$ monolayer, and our phonon spectrum and elastic moduli prove that it is dynamically and mechanically stable. Further investigations show that it is metallic and still keep metallic feature after the adsorption of Na or K atoms, and the absorption of Na (or K) atoms changes the lattice parameters by 3...
May 23, 2018: Nanotechnology
#20
Shoji Matsumoto, Mei Watanabe, Motohiro Akazome
The formation of biimidazoldiium structures by the introduction of methyl substituents on the N atoms at the 3 and 3' positions of 2,2'-biimidazoles led to increments in the Stokes shift of these structures. Based on time-dependent density functional theory (TDDFT) calculations, the imidazolium rings become distorted and the N atoms of the imidazolium rings underwent structural changes through sp2 to sp3 rehybridization in the excited states.
May 23, 2018: Organic Letters
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