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# Atomic clusters

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#1
Yong-Chao Liang, Rang-Su Liu, Quan Xie, Ze-An Tian, Yun-Fei Mo, Hai-Tao Zhang, Hai-Rong Liu, Zhao-Yang Hou, Li-Li Zhou, Ping Peng
To investigate the structural evolution and hereditary mechanism of icosahedral nano-clusters formed during rapid solidification, a molecular dynamics (MD) simulation study has been performed for a system consisting of 10(7) atoms of liquid Mg70Zn30 alloy. Adopting Honeycutt-Anderson (HA) bond-type index method and cluster type index method (CTIM-3) to analyse the microstructures in the system it is found that for all the nano-clusters including 2~8 icosahedral clusters in the system, there are 62 kinds of geometrical structures, and those can be classified, by the configurations of the central atoms of basic clusters they contained, into four types: chain-like, triangle-tailed, quadrilateral-tailed and pyramidal-tailed...
February 23, 2017: Scientific Reports
#2
David L Cortie, Yury Khaydukov, Thomas Keller, David John Sprouster, Jacob S Hughes, James P Sullivan, Xiaolin Wang, Anton P Le Brun, Joel Bertinshaw, Sara J Callori, Robert D Aughterson, Michael James, Peter J Evans, Gerry Triani, Frank Klose
High magnetizations are desirable for spintronic devices that operate by manipulating electronic states using built-in magnetic fields. However, the magnetic moment in promising dilute magnetic oxide nanocomposites is very low, typically corresponding to only fractions of a Bohr magneton for each dopant atom. In this study we report a large magnetization formed by ion implantation of Co into amorphous TiO2-δ films producing an inhomogenous magnetic moment, with certain regions producing over 2.5 µB per Co, depending on the local dopant concentration...
February 23, 2017: ACS Applied Materials & Interfaces
#3
Esther M Johnston, Cíntia Carreira, Simone Dell'Acqua, Somdatta Ghosh Dey, Sofia R Pauleta, Isabel Moura, Edward I Solomon
Spectroscopic methods and density functional theory (DFT) calculations are used to determine the geometric and electronic structure of CuZ(o), an intermediate form of the Cu4S active site of nitrous oxide reductase (N2OR) that is observed in single turnover of fully reduced N2OR with N2O. Electron paramagnetic resonance (EPR), absorption, and magnetic circular dichroism (MCD) spectroscopies show that CuZ(o) is a 1-hole (i.e. 3Cu(I)Cu(II)) state with spin density delocalized evenly over CuI and CuIV. Resonance Raman spectroscopy shows two Cu-S vibrations at 425 and 413 cm(-1), the latter with a -3 cm(-1) O(18) solvent isotope shift...
February 22, 2017: Journal of the American Chemical Society
#4
Feiyun Long, Haitao Liu, Dafang Li, Jun Yan
With the help of density functional theory, a series of matryoshka superatoms $\rm{X@Y_{12}@X_{20}}$ (X=Ge, Y=Zn; X=Sn, Y=Mg, Mn, Zn or Cd; X=Pb, Y= Mg, Mn, Cd or Hg) with icosahedral symmetry has been extensively studied, to focus on the influence of the spin-orbit coupling on geometries, stabilities, electronic structures and magnetic moments for these clusters. Generally speaking, the effect of spin-orbit coupling is highly correlated with composition elements of these clusters. $\rm{Ge@Zn_{12}@Ge_{20}}$ is little affected by the spin-orbit coupling, while clusters containing Sn atom will generally undergo a moderate influence on their atomization energy, HOMO-LUMO gap and projected density of states...
February 22, 2017: Journal of Physical Chemistry. A
#5
Alexandros A Kitos, Constantina Papatriantafyllopoulou, Anastasios J Tasiopoulos, Spyros P Perlepes, Albert Escuer, Vassilios Nastopoulos
The initial use of ligands 2'-hydroxyacetophenone (HL(1)), 2-hydroxybenzophenone (HL(2)) and 2,2'-dihydroxybenzophenone (H2L(3)) in iron(iii) chemistry is described. The syntheses and crystal structures are reported for five iron(iii) clusters: [Fe10O4(OMe)14(L(1))6(MeOH)2](NO3)2·3MeOH (1·3MeOH), [Fe12O4(OH)(OMe)17(L(1))8](ClO4)2·2H2O (2·2H2O), [Fe10O4(OMe)14Cl4(L(2))4(MeOH)2] (3), [Fe10O4(OMe)14(L(2))6(py)2](ClO4)2·MeOH (4·MeOH), where py = pyridine, and [Fe6O2(OEt)6(O2CMe)2(L(3))2(HL(3))2] (5). The molecular structures of the decanuclear clusters 1, 3 and 4 are organized around a {Fe10(μ4-O)4(μ3-OMe)2(μ-OMe)12}(8+) core consisting of ten {Fe3O4} face-sharing defective cubane units...
February 22, 2017: Dalton Transactions: An International Journal of Inorganic Chemistry
#6
Joshua D Howe, Yang Liu, Luis Flores, David A Dixon, David S Sholl
To establish a model of metal-organic framework (MOF) surfaces and build an understanding of surface-specific ligand adsorption phenomena in MOFs, we present a computational study exploring multiple models of a series of MOF-2 nanosheet materials, "M-BDCs", with M = Zn, Cu, and Co and BDC = benzene-1,4-dicarboxylate. We study and assess the appropriateness of a series of models ranging from small clusters (18 atoms) to fully periodic sheet models. We additionally study the interactions of these models with acid gases and energy-relevant small molecules (CO, CO2, H2O, SO2, NO2, and H2S)...
February 21, 2017: Journal of Chemical Theory and Computation
#7
Ahibur Rahaman, Carolina Gimbert-Suriñach, Arne Ficks, Graham E Ball, Mohan Bhadbhade, Matti Haukka, Lee Higham, Ebbe Nordlander, Stephen B Colbran
The influence of the substitution, orientation and structure of the phosphido bridges in [Fe2(CO)6(μ-PR2)2] electrocatalysts of proton reduction has been studied. The isomers e,a-[Fe2(CO)6{μ-P(Ar)H}2] (1a(Ar): Ar = Ph, 2'-methoxy-1,1'-binaphthyl (bn')), e,e-[Fe2(CO)6{μ-P(Ar)H}2] (1b(Ar): Ar = Ph, bn') were isolated from reactions of iron pentacarbonyl and the corresponding primary phosphine, syntheses that also afforded the phosphinidene-capped tri-iron clusters, [Fe3(CO)9(μ-CO)(μ3-Pbn')] (2) and [Fe3(CO)9(μ3-PAr)2] (3(Ar), Ar = Ph, bn')...
February 21, 2017: Dalton Transactions: An International Journal of Inorganic Chemistry
#8
Yunteng He, Jie Zhang, Lei Lei, Wei Kong
We present evidence of halogen bond in iodine clusters formed in superfluid helium droplets based on results from electron diffraction. Iodine crystals are known to form layered structures with intralayer halogen bonds, with interatomic distances shorter than the sum of the van der Waals radii of the two neighboring atoms. The diffraction profile of dimer dominated clusters embedded in helium droplets reveals an interatomic distance of 3.65 Å, much closer to the value of 3.5 Å in iodine crystals than to the van der Waals distance of 4...
February 21, 2017: Angewandte Chemie
#9
Sai Zhang, Jing Li, Zhaoming Xia, Chao Wu, Zhiyun Zhang, Yuanyuan Ma, Yongquan Qu
Extensive applications of noble metals as heterogeneous catalysts are limited by their global reserve scarcity and exorbitant price. Identifying the intrinsic active nature of a catalyst benefits the designing of catalysts with trace amounts of noble metals; these catalysts display better or comparable overall catalytic efficiency than their heavily loaded counterparts. Herein, systematic studies on Pd dispersion and surface properties of a series of Pd/CeO2 catalysts for styrene hydrogenation showed that high Pd dispersion and surface abundant defects of the catalysts are essential to realize superior activity...
February 21, 2017: Nanoscale
#10
Michihiro Suga, Fusamichi Akita, Michihiro Sugahara, Minoru Kubo, Yoshiki Nakajima, Takanori Nakane, Keitaro Yamashita, Yasufumi Umena, Makoto Nakabayashi, Takahiro Yamane, Takamitsu Nakano, Mamoru Suzuki, Tetsuya Masuda, Shigeyuki Inoue, Tetsunari Kimura, Takashi Nomura, Shinichiro Yonekura, Long-Jiang Yu, Tomohiro Sakamoto, Taiki Motomura, Jing-Hua Chen, Yuki Kato, Takumi Noguchi, Kensuke Tono, Yasumasa Joti, Takashi Kameshima, Takaki Hatsui, Eriko Nango, Rie Tanaka, Hisashi Naitow, Yoshinori Matsuura, Ayumi Yamashita, Masaki Yamamoto, Osamu Nureki, Makina Yabashi, Tetsuya Ishikawa, So Iwata, Jian-Ren Shen
Photosystem II (PSII) is a huge membrane-protein complex consisting of 20 different subunits with a total molecular mass of 350 kDa for a monomer. It catalyses light-driven water oxidation at its catalytic centre, the oxygen-evolving complex (OEC). The structure of PSII has been analysed at 1.9 Å resolution by synchrotron radiation X-rays, which revealed that the OEC is a Mn4CaO5 cluster organized in an asymmetric, 'distorted-chair' form. This structure was further analysed with femtosecond X-ray free electron lasers (XFEL), providing the 'radiation damage-free' structure...
February 20, 2017: Nature
#11
Douglas R Nevers, Curtis B Williamson, Tobias Hanrath, Richard D Robinson
Optoelectronic properties of nanoparticles are intimately coupled to the complex physiochemical interplay between the inorganic core and the organic ligand shell. Magic-sized clusters, which are predominately surface atoms, provide a promising avenue to clarify these critical surface interactions. Whereas these interactions impact the surface of both nanoparticles and magic-sized clusters, we show here that only clusters manifest a shift in the excitonic peak by up to 0.4 eV upon solvent or ligand treatment...
February 20, 2017: Chemical Communications: Chem Comm
#12
Vincenzo Piccialli, Nicola Borbone, Giorgia Oliviero, Gennaro Piccialli, Stefano D'Errico, Roberto Centore
The title compound, C12H20N4O5, crystallizes in the monoclinic space group P21, with four crystallographically independent mol-ecules in the asymmetric unit. The four mol-ecules have a very similar conformation that is basically determined by the formation of two intra-molecular hydrogen bonds between the amino NH2 donors and the carbonyl and ring O-atom acceptors, forming, respectively, R(6) and R(7) ring motifs.. In the crystal, inter-molecular hydrogen bonding leads to the formation of R2(2)(10) ring patterns, involving one amide CONH2 donor and an imidazole N-atom acceptor...
February 1, 2017: Acta Crystallographica. Section E, Crystallographic Communications
#13
Marcus Johansson, Valera Veryazov
Automatic detection of point groups as well as symmetrisation of molecular geometry and wavefunctions are useful tools in computational quantum chemistry. Algorithms for developing these tools as well as an implementation are presented. The symmetry detection algorithm is a clustering algorithm for symmetry invariant properties, combined with logical deduction of possible symmetry elements using the geometry of sets of symmetrically equivalent atoms. An algorithm for determining the symmetry adapted linear combinations (SALCs) of atomic orbitals is also presented...
2017: Journal of Cheminformatics
#14
Andreas Breitwieser, Jagoba Iturri, Jose-Luis Toca-Herrera, Uwe B Sleytr, Dietmar Pum
The recombinant bacterial surface layer (S-layer) protein rSbpA of Lysinibacillus sphaericus CCM 2177 is an ideal model system to study non-classical nucleation and growth of protein crystals at surfaces since the recrystallization process may be separated into two distinct steps: (i) adsorption of S-layer protein monomers on silicon surfaces is completed within 5 min and the amount of bound S-layer protein sufficient for the subsequent formation of a closed crystalline monolayer; (ii) the recrystallization process is triggered-after washing away the unbound S-layer protein-by the addition of a CaCl₂ containing buffer solution, and completed after approximately 2 h...
February 14, 2017: International Journal of Molecular Sciences
#15
Masoomeh Omidi, Hamid Reza Shamlouei, Motahareh Noormohammadbeigi
Density functional theory (DFT) calculations were used to study the effect of scandium doping on the structural, energetic, electronic, linear and nonlinear optical (NLO) properties of Be12O12, Mg12O12 and Ca12O12 nanoclusters. Scandium (Sc) doping on nanoclusters leads to narrowing of their E g, which enhances their conductance greatly. Also, the polarizability (α) and first hyperpolarizability (β0) of nanoclusters were dramatically increased as Be, Mg or Ca atoms are substituted with a Sc atom. Among all clusters, α and β0 values for Sc-doped Ca12O12 were the largest...
March 2017: Journal of Molecular Modeling
#16
Denis A Rychkov, Jernej Stare, Elena V Boldyreva
The present study delivers a computational approach for the understanding of the mechanism of phase transitions between polymorphs of small organic molecules. By using state of the art periodic DFT calculations augmented with dispersion corrections and an external stress tensor together with gas-phase cluster calculations, we thoroughly explained the reversible phase transitions of three polymorphs of the model system, namely crystalline l-serine in the pressure range up to 8 GPa. This study has shown that at the macroscopic level the main driving force of the phase transitions is the decrease in the volume of the crystal unit cell, which contributes to the enthalpy difference between the two forms, but not to the difference in their internal crystal energies...
February 17, 2017: Physical Chemistry Chemical Physics: PCCP
#17
Víctor Rojas-Cervellera, Lluís Raich, Jaakko Akola, Carme Rovira
The labeling of proteins with heavy atom clusters is of paramount importance in biomedical research, but its detailed molecular mechanism remains unknown. Here we uncover it for the particular case of the anti-influenza N9 neuraminidase NC10 antibody against a glutathione-coated gold cluster by means of ab initio QM/MM calculations. We show that the labeling reaction follows an associative double SN2-like reaction mechanism, involving a proton transfer, with low activation barriers only if one of the two distinct peptide/peptidic ligands (the one that occupies the side position) is substituted...
February 17, 2017: Nanoscale
#18
Daigo Masuzaki, Toshiaki Nagata, Fumitaka Mafune
Thermal dissociation of cationic niobium oxide clusters (NbnOm+) was investigated by gas phase thermal desorption spectrometry. The dominant species formed at 300 K were NbnO2.5n+p (n = 2, 4, 6, …; p = 0, 1, 2, …) and NbnO2.5n-0.5+q (n = 3, 5,…; q = 0, 1, 2, …). At higher temperatures, the more oxygen-rich clusters were observed to release O2. However, the desorption of O2 from NbnOm+ was found to be insignificant in comparison with VnOm+ because Nb tends to have a +5 oxidation state exclusively, whereas V can have both +4 and +5 oxidation states...
February 16, 2017: Journal of Physical Chemistry. A
#19
Mark W Kelly, Sarah C Halliwell, W Jeff Rodgers, Jason D Pattle, Jeremy N Harvey, Michael N R Ashfold
Quantum mechanical and hybrid quantum mechanical/molecular mechanical (QM/MM) cluster models have been used to investigate possible reaction mechanisms whereby gas phase NHx (x = 0-2), CNHx (x = 0, 1) and OH radicals can add to, and incorporate in, a C-C dimer bond on the C(100):H 21 diamond surface during chemical vapor deposition from microwave activated C/H containing gas mixtures containing trace amounts of added N or O. Three N incorporation routes are identified, initiated by N, NH and CN(H) addition to a surface radical site, whereas only OH addition was considered as the precursor to O incorporation...
February 16, 2017: Journal of Physical Chemistry. A
#20
Allaa R Hilal, Rifaat Hilal
The photo dissociation of nitrosyl fluorite, FONO, a potential source of atmospheric fluorine, underlies its active role in ozone depletion and other activities in the troposphere. In the present work, the electronic structure of FONO is revisited at high level of ab initio and density functional theory (DFT) theoretical levels. Several different post SCF methods were used to compute excited states, vertical excitation energies and intensities, namely configuration interaction with single excitations (CIS), equation of motion coupled cluster with single and double excitations (EOM-CCSD), and symmetry adopted cluster configuration interaction (SAC-CI) methods...
March 2017: Journal of Molecular Modeling
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