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atomic structure

Florian Albrecht, Felix Bischoff, Wilhelm Auwärter, Johannes V Barth, Jascha Repp
In recent years atomic force microscopy (AFM) at highest resolution was widely applied to mostly planar molecules, while its application towards exploring species with structural flexibility and a distinct 3D-character remains a challenge. Herein, the scope of non-contact AFM is widened by investigating subtle conformational differences occurring in the well-studied reference systems 2H-TPP and Cu-TPP on Cu(111). Different saddle-shape conformations of both species can be recognized in conventional constant-height AFM images...
October 25, 2016: Nano Letters
Ana Martínez
In this investigation, the feasibility of functionalizing fullerene and bismullene with Bi and C as intruders is theoretically explored. The systems analyzed are C60-xBix (with x = 0-10, fullerene-like) and Bi60-yCy (with y = 0-10, bismullene-like). Optimized geometries, reactivity indexes, and highest occupied molecular orbital to lowest unoccupied molecular orbital (HOMO-LUMO) gaps (for analyzing the potential application of these molecules as materials for solar cells) are reported. The most stable structures of bismullene-like systems have cage geometries...
October 25, 2016: Journal of Physical Chemistry. A
Serge Ruccolo, Wesley Sattler, Yi Rong, Gerard Parkin
Bond lengths between pairs of atoms in covalent molecules are generally predicted well by the sum of their respective covalent radii, such that there are usually only small variations in related compounds. It is, therefore, significant that we have demonstrated that the incorporation of appropriately sized linkers between carbon and a metal center provides a means to modulate the length and nature of a metal-carbon interaction. Specifically, X-ray diffraction studies on a series of tris(1-methylimidazol-2-ylthio)methyl zinc complexes, [Titm(Me)]ZnX, demonstrate how the Zn-C bond lengths are highly variable (2...
October 25, 2016: Journal of the American Chemical Society
Soji Shimizu
Subporphyrinato boron (subporphyrin) was elusive until the syntheses of tribenzosubporphine in 2006 and meso-aryl-substituted subporphyrin in 2007. These novel contracted analogues possess a 14π-electron conjugated system embedded in a bowl-shaped structure. They exhibit absorption and fluorescence in the UV/vis region and nonlinear optical properties due to their octupolar structures. The unique coordination geometry around the central boron atom in the structure of subporphyrin enabled investigation of rare boron species, such as borenium cations, boron hydrides, and boron peroxides...
October 25, 2016: Chemical Reviews
Mostafa Fakhraee, Mohammad Reza Gholami
The effects of ester addition on structural and dynamic properties of biodegradable ILs composed of the 1-(alkoxycarbonyl)-3-alkylimidazolium cation ([C1COOCnC1im](+), n = 1, 2, 4) coupled with [Br](-), [NO3](-), [BF4](-), [PF6](-), [TfO](-), and [Tf2N](-) are explored using the molecular dynamics (MD) simulations and quantum theory of atoms in molecules (QTAIM) at 400 K. Formation of the intramolecular H bonds between O atoms of the ester group and H atoms of the imidazolium ring as well as the nearest H atom of the alkyl chain to the ester group are disclosed from reduced density gradient (RDG) results...
October 25, 2016: Journal of Physical Chemistry. B
Z W Wu, F X Li, C W Huo, M Z Li, W H Wang, K X Liu
The temperature evolution of icosahedral medium-range order formed by interpenetrating icosahedra in CuZr metallic glassforming liquids was investigated via molecular dynamics simulations. Scaling analysis based on percolation theory was employed, and it is found that the size distribution of clusters formed by the central atoms of icosahedra at various temperatures follows a very good scaling law with the cluster number density scaled by S(-τ) and the cluster size S scaled by |1 - Tc/T|(-1/σ), respectively...
October 25, 2016: Scientific Reports
S H Chen, T M Yue, C P Tsui, K C Chan
Inheriting amorphous atomic structures without crystalline lattices, bulk metallic glasses (BMGs) are known to have superior mechanical properties, such as high strength approaching the ideal value, but are susceptible to catastrophic failures. Understanding the plastic-flow dynamics of BMGs is important for achieving stable plastic flow in order to avoid catastrophic failures, especially under tension, where almost all BMGs demonstrate limited plastic flow with catastrophic failure. Previous findings have shown that the plastic flow of BMGs displays critical dynamics under compression tests, however, the plastic-flow dynamics under tension are still unknown...
October 25, 2016: Scientific Reports
Sebastian Schneider, Davide Provasi, Marta Filizola
Substantial attention has recently been devoted to G protein-biased agonism of the µ-opioid receptor (MOR) as an ideal new mechanism for the design of analgesics devoid of serious side effects. However, designing opioids with appropriate efficacy and bias is challenging because it requires an understanding of the ligand binding process and of the allosteric modulation of the receptor. Here, we investigated these phenomena for TRV-130, a G protein-biased MOR small-molecule agonist that has been shown to exert analgesia with less respiratory depression and constipation than morphine, and that it is currently being evaluated in human clinical trials for acute pain management...
October 25, 2016: Biochemistry
Mohammad Goli, Shant Shahbazian
Recently, it has been demonstrated that the domain-averaged exchange-correlation energies, V(xc) , are capable of tracing the covalent character of atom-atom interactions unequivocally and thus pave the way for detailed bonding analysis within the context of the quantum theory of atoms in molecules (QTAIM) [M. García-Revilla, E. Francisco, P. L. Popelier, A. Martín Pendás, ChemPhysChem 2013, 14, 1211-1218]. Herein, the concept of V(xc) is extended within the context of the newly developed multicomponent QTAIM (MC-QTAIM)...
October 25, 2016: Chemphyschem: a European Journal of Chemical Physics and Physical Chemistry
Mariete B Moreira, Camila F N Da Silva, Rafaela B P Pesci, Victor M Deflon, Sofia Nikolaou
We synthesized and characterized a series of oxo-centered carbonyl-triruthenium complexes with the general formula [Ru3O(CH3COO)6(L)2(CO)], where L = 2,6-dimethylpyrazine (dmpz) (1), isonicotinamide (adpy) (2), 4-acetylpyridine (acpy) (3), 3-methylpyridine (3-pic) (4), 4-methylpyridine (4-pic) (5), 4-tert-butylpyridine (4-tbpy) (6), 4-(dimethyl)aminopyridine (dmap) (7), or 4-aminopyridine (ampy) (8); we also investigated the photoreactivity of these complexes. Single-crystal X-ray diffraction helped to elucidate the structures of 1·H2O, 7·C2H4Cl2, and 8...
October 25, 2016: Dalton Transactions: An International Journal of Inorganic Chemistry
Yan Peng, Tilmann Bodenstein, Karin Fink, Valeriu Mereacre, Christopher E Anson, Annie K Powell
The single ion magnetic properties of Co(ii) are affected by the details of the coordination geometry of the ion. Here we show that a geometry close to trigonal prismatic which arises when the ligand 6,6'-((1Z)-((piperazine-1,4-diylbis(propane-3,1-diyl))bis(azanylylidene))bis(methanylylidene))bis(2-methoxyphenol) coordinates to Co(ii) does indeed lead to enhanced single-ion behaviour as has previously been predicted. Synthesis of the compound, structural information, and static as well as dynamic magnetic data are presented along with an analysis using quantum chemical ab initio calculations...
October 25, 2016: Physical Chemistry Chemical Physics: PCCP
Cong-Jun Liu, Yan-Ping Liu, Shu-Ling Yu, Xing-Jie Dai, Tao Zhang, Jing-Chao Tao
A series of novel 1,2,3-triazole-linked isosteviol derivatives were designed and synthesized via Huisgen-click reaction. Their cytotoxicities in vitro against HCT-116 and JEKO-1 cells were screened. The preliminary bioassays indicated that most of the title compounds exhibited noteworthy cytotoxic activities. Particularly, the compound 10b revealed the most potent inhibitory activities against HCT-116 cells with IC50 value of 2.987±0.098μM, which was better than that (3.906±0.261μM) of positive control cisplatin...
October 13, 2016: Bioorganic & Medicinal Chemistry Letters
Mohammad T Mazhab-Jafari, Alexis Rohou, Carla Schmidt, Stephanie A Bueler, Samir Benlekbir, Carol V Robinson, John L Rubinstein
Vacuolar-type ATPases (V-ATPases) are ATP-powered proton pumps involved in processes such as endocytosis, lysosomal degradation, secondary transport, TOR signalling, and osteoclast and kidney function. ATP hydrolysis in the soluble catalytic V1 region drives proton translocation through the membrane-embedded VO region via rotation of a rotor subcomplex. Variability in the structure of the intact enzyme has prevented construction of an atomic model for the membrane-embedded motor of any rotary ATPase. We induced dissociation and auto-inhibition of the V1 and VO regions of the V-ATPase by starving the yeast Saccharomyces cerevisiae, allowing us to obtain a ~3...
October 24, 2016: Nature
F Tumino, C S Casari, M Passoni, C E Bottani, A Li Bassi
Two-dimensional (2D) ZnO structures have been deposited on the Au(111) surface by means of the pulsed laser deposition technique. In situ scanning tunneling microscopy and scanning tunneling spectroscopy measurements have been performed to characterize morphological, structural and electronic properties of 2D ZnO at the nanoscale. Starting from a sub-monolayer coverage, we investigated the growth of ZnO, identifying different atomic layers (up to the fifth). At low coverage, we observed single- and bi-layer nanocrystals, characterized by a surface moiré pattern that is associated to a graphene-like ZnO structure...
October 24, 2016: Nanotechnology
Stavros Karakalos, Yun-Fei Xu, Fairoja Cheenicode Kabeer, Wei Chen, Juan Carlos F Rodriguez-Reyes, Alexandre Tkatchenko, Efthimios Kaxiras, Robert J Madix, Cynthia M Friend
Enhancing the selectivity of catalytic processes has potential for substantially increasing the sustainability of chemical production. Herein, we establish relationships between reaction selectivity and molecular structure for a homologous series of key intermediates for oxidative coupling of alcohols on gold using a combination of experiment and theory. We establish a scale of binding for molecules with different alkyl structures and chain lengths and thereby demonstrate the critical nature of non-covalent van der Waals interactions in determining the selectivity by modulating the stability of key reaction intermediates bound to the surface...
October 24, 2016: Journal of the American Chemical Society
David W Shaffer, Indrani Bhowmick, Arnold L Rheingold, Charlene Tsay, Brooke N Livesay, Matthew P Shores, Jenny Y Yang
We describe the structural and electronic impacts of modifying the bridging atom in a family of Co(ii) pincer complexes with the formula Co(t-Bu)2P(E)Py(E)P(t-Bu)2Br2 (Py = pyridine, E = CH2, NH, and O for compounds 1-3, respectively). Structural characterization by single crystal X-ray diffraction indicates that compounds 1 and 3 are 5-coordinate complexes with both bromides bound to the Co(ii) ion, while compound 2 is square planar with one bromide in the outer coordination sphere. The reduction potentials of 1-3, characterized by cyclic voltammetry, are consistent with the increasing electron-withdrawing character of the pincer ligand as the linker (E) between the pyridine and phosphine arms becomes more electronegative...
October 24, 2016: Dalton Transactions: An International Journal of Inorganic Chemistry
Nuria A Illán-Cabeza, Sonia B Jiménez-Pulido, Francisco Hueso-Ureña, Tomás Peña-Ruiz, Miguel Quirós-Olozábal, Miguel N Moreno-Carretero
2,4-Bis(1,3,7-trimethyl-pteridine-2,4(1H,3H)-dione-6-yl)-2,3-dihydro-2-methyl-1H-1,5-benzodiazepine (DLMBZD) has been prepared and its molecular and crystal structures have been determined from spectral and XRD data. The benzodiazepine ligand was reacted with zinc(ii), cadmium(ii) and mercury(ii) chloride, bromide and iodide to give complexes with general formula [M(DLMBZD)X2]. The complexes have been synthesized and characterized by IR, NMR and elemental analysis. The structure of seven complexes has been obtained by single crystal X-ray diffraction...
October 24, 2016: Dalton Transactions: An International Journal of Inorganic Chemistry
Emily S Walker, Seung Ryul Na, Daehwan Jung, Stephen D March, Joon-Seok Kim, Tanuj Trivedi, Wei Li, Li Tao, Minjoo L Lee, Kenneth M Liechti, Deji Akinwande, Seth R Bank
We report the first direct dry transfer of a single-crystalline thin film grown by molecular beam epitaxy. A double cantilever beam fracture technique was used to transfer epitaxial bismuth thin films grown on silicon (111) to silicon strips coated with epoxy. The transferred bismuth films retained electrical, optical, and structural properties comparable to the as-grown epitaxial films. Additionally, we isolated the bismuth thin films on freestanding flexible cured-epoxy post-transfer. The adhesion energy at the bismuth/silicon interface was measured to be ∼1 J/m(2), comparable to that of exfoliated and wet transferred graphene...
October 24, 2016: Nano Letters
Christian Helbing, Robert Stößel, Dominik A Hering, Matthias Michael Lothar Arras, Jörg Bossert, Klaus D Jandt
Nanostructured surfaces have the potential to influence the assembly as well as the orientation of adsorbed proteins and may, thus, strongly influence the biomaterials performance. For the class of polymeric (bio)materials a reproducible and well characterized nanostructure is the ordered chain folded surface of a polyethylene single crystal (PE-SC). We tested the hypothesis that the trinodal-rod shaped protein human plasma fibrinogen (HPF) adsorbs on the (001) surface of PE-SCs along specific crystallographic directions...
October 24, 2016: Langmuir: the ACS Journal of Surfaces and Colloids
Wojciech Pulawski, Michal Jamroz, Michal Kolinski, Andrzej Kolinski, Sebastian Kmiecik
The CABS coarse-grained model is a well-established tool for modeling globular proteins (predicting their structure, dynamics and interactions). Here we introduce an extension of CABS representation and force field (CABS-membrane) to the modeling of the effect of biological membrane environment on the structure of membrane proteins. We validate the CABS-membrane model in folding simulations of 10 short helical membrane proteins not using any knowledge about their structure. The simulations start from random protein conformations placed outside the membrane environment and allow for full flexibility of the modeled proteins during their spontaneous insertion into the membrane...
October 24, 2016: Journal of Chemical Information and Modeling
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