keyword
MENU ▼
Read by QxMD icon Read
search

Atomic clusters

keyword
https://www.readbyqxmd.com/read/28346939/a-b12-dependent-radical-sam-enzyme-involved-in-oxetanocin-a-biosynthesis
#1
Jennifer Bridwell-Rabb, Aoshu Zhong, He G Sun, Catherine L Drennan, Hung-Wen Liu
Oxetanocin A (OXT-A) is a potent antitumour, antiviral and antibacterial compound. Biosynthesis of OXT-A has been linked to a plasmid-borne Bacillus megaterium gene cluster that contains four genes: oxsA, oxsB, oxrA and oxrB. Here we show that both the oxsA and oxsB genes are required for the production of OXT-A. Biochemical analysis of the encoded proteins, a cobalamin (Cbl)-dependent S-adenosylmethionine (AdoMet) radical enzyme, OxsB, and an HD-domain phosphohydrolase, OxsA, reveals that OXT-A is derived from a 2'-deoxyadenosine phosphate in an OxsB-catalysed ring contraction reaction initiated by hydrogen atom abstraction from C2'...
March 27, 2017: Nature
https://www.readbyqxmd.com/read/28343039/study-of-trace-metal-imbalances-in-the-blood-scalp-hair-and-nails-of-oral-cancer-patients-from-pakistan
#2
Muhammad Abdul Qayyum, Munir H Shah
Oral cancer is an important cause of cancer morbidity and mortality globally and exposure to trace metals alongside tobacco, alcohol and HPV are the important etiological factors in its development. Selected essential and toxic trace metals (Cd, Cr, Cu, Fe, Mn, Ni, Pb and Zn) were measured in the blood, scalp hair and nails of oral cancer patients and counterpart controls by atomic absorption spectrometry. Mean concentrations of Cd, Ni and Pb were found to be significantly higher (p<0.05) and those of Cu, Fe and Zn were considerably lower in the blood, scalp hair and nails of the patients than the controls...
March 23, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28342572/exploring-the-atomic-structure-of-1-8nm-monolayer-protected-gold-clusters-with-aberration-corrected-stem
#3
Jian Liu, Nan Jian, Isabel Ornelas, Alexander J Pattison, Tanja Lahtinen, Kirsi Salorinne, Hannu Häkkinen, Richard E Palmer
Monolayer-protected (MP) Au clusters present attractive quantum systems with a range of potential applications e.g. in catalysis. Knowledge of the atomic structure is needed to obtain a full understanding of their intriguing physical and chemical properties. Here we employed aberration-corrected scanning transmission electron microscopy (ac-STEM), combined with multislice simulations, to make a round-robin investigation of the atomic structure of chemically synthesised clusters with nominal composition Au144(SCH2CH2Ph)60 provided by two different research groups...
November 22, 2016: Ultramicroscopy
https://www.readbyqxmd.com/read/28341861/minimum-vertex-type-sequence-indexing-for-clusters-on-square-lattice
#4
Longguang Liao, Yu-Jun Zhao, Zexian Cao, Xiao-Bao Yang
An effective indexing scheme for clusters that enables fast structure comparison and congruence check is desperately desirable in the field of mathematics, artificial intelligence, materials science, etc. Here we introduce the concept of minimum vertex-type sequence for the indexing of clusters on square lattice, which contains a series of integers each labeling the vertex type of an atom. The minimum vertex-type sequence is orientation independent, and it builds a one-to-one correspondence with the cluster...
March 24, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28339265/topology-scaling-identification-of-layered-solids-and-stable-exfoliated-2d-materials
#5
Michael Ashton, Joshua Paul, Susan B Sinnott, Richard G Hennig
The Materials Project crystal structure database has been searched for materials possessing layered motifs in their crystal structures using a topology-scaling algorithm. The algorithm identifies and measures the sizes of bonded atomic clusters in a structure's unit cell, and determines their scaling with cell size. The search yielded 826 stable layered materials that are considered as candidates for the formation of two-dimensional monolayers via exfoliation. Density-functional theory was used to calculate the exfoliation energy of each material and 680 monolayers emerge with exfoliation energies below those of already-existent two-dimensional materials...
March 10, 2017: Physical Review Letters
https://www.readbyqxmd.com/read/28338266/accelerated-oxygen-atom-transfer-and-c-h-bond-oxygenation-by-remote-redox-changes-in-fe3-mn-iodosobenzene-adducts
#6
Graham de Ruiter, Kurtis M Carsch, Sheraz Gul, Ruchira Chatterjee, Niklas B Thompson, Michael K Takase, Junko Yano, Theodor Agapie
We report the synthesis, characterization, and reactivity of [LFe3 (PhPz)3 OMn((s) PhIO)][OTf]x (3: x=2; 4: x=3), where 4 is one of very few examples of iodosobenzene-metal adducts characterized by X-ray crystallography. Access to these rare heterometallic clusters enabled differentiation of the metal centers involved in oxygen atom transfer (Mn) or redox modulation (Fe). Specifically, (57) Fe Mössbauer and X-ray absorption spectroscopy provided unique insights into how changes in oxidation state (Fe(III)2 Fe(II) Mn(II) vs...
March 24, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28330355/fast-divide-and-conquer-algorithm-for-evaluating-polarization-in-classical-force-fields
#7
Dominique Nocito, Gregory J O Beran
Evaluation of the self-consistent polarization energy forms a major computational bottleneck in polarizable force fields. In large systems, the linear polarization equations are typically solved iteratively with techniques based on Jacobi iterations (JI) or preconditioned conjugate gradients (PCG). Two new variants of JI are proposed here that exploit domain decomposition to accelerate the convergence of the induced dipoles. The first, divide-and-conquer JI (DC-JI), is a block Jacobi algorithm which solves the polarization equations within non-overlapping sub-clusters of atoms directly via Cholesky decomposition, and iterates to capture interactions between sub-clusters...
March 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28327708/facile-embedding-of-single-vanadium-atoms-at-the-anatase-tio2-101-surface
#8
Stig Koust, Logi Arnarson, Poul G Moses, Zheshen Li, Igor Beinik, Jeppe V Lauritsen, Stefan Wendt
To understand the structure-reactivity relationships for mixed-metal oxide catalysts, well-defined systems are required. Mixtures of vanadia and titania (TiO2) are of particular interest for application in heterogeneous catalysis, with TiO2 often acting as the support. By utilizing high-resolution scanning tunneling microscopy, we studied the interaction of vanadium (V) with the anatase TiO2(101) surface in the sub-monolayer regime. At 80 K, metallic V nucleates into homogeneously distributed clusters onto the terraces with no preference for nucleation at the step edges...
March 22, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28327547/iron-based-magnetic-superhalogens-with-pseudohalogens-as-ligands-an-unbiased-structure-search
#9
Li Ping Ding, Peng Shao, Cheng Lu, Fang Hui Zhang, Li Ya Wang
We have performed an unbiased structure search for a series of neutral and anionic FeL4 (L = BO2, CN, NO2, NO3, OH, CH3, NH2, BH4 and Li2H3) clusters using the CALYPSO (Crystal structure Analysis by Particle Swarm Optimization) structure search method. To probe the superhalogen properties of neutral and anionic FeL4 clusters, we used density-functional theory with the B3LYP functional to examine three factors, including distribution of extra electron, pattern of bonding and the nature of the ligands. Theoretical results show that Fe(BO2)4, Fe(NO3)4 and Fe(NO2)4 can be classified as magnetic superhalogen due to that their electron affinities even exceed those of the constituent ligands...
March 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28325114/complexes-of-dna-bases-and-watson-crick-base-pairs-interaction-with-neutral-silver-agn-n-8-10-12-clusters-a-dft-and-tddft-study
#10
Ruby Srivastava
We study the binding of the neutral Agn (n = 8, 10, 12) to the DNA base- adenine (A), guanine (G) and Watson-Crick -adenine-thymine (AT), guanine-cytosine (GC) pairs. Geometries of complexes were optimized at the DFT level using the hybrid B3LYP functional. LANL2DZ effective core potential (ECP) was used for silver and 6-31+G(**) was used for all other atoms. NBO charges were analyzed using the Natural population analysis. The absorption properties of Agn-A,G/WC complexes were also studied using time-dependent density functional theory (TDDFT)...
March 21, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28325049/antibody-subclass-detection-using-graphene-nanopores
#11
Amir Barati Farimani, Mohammad Heiranian, Kyoungmin Min, Narayana R Aluru
Solid-state nanopores are promising for label-free protein detection. The large thickness, ranging from several tens of nanometers to micrometers and larger, of solid-state nanopores prohibits atomic-scale scanning or interrogation of proteins. Here, a single-atom thick graphene nanopore is shown to be highly capable of sensing and discriminating between different subclasses of IgG antibodies despite their minor and subtle variation in atomic structure. Extensive molecular dynamics (MD) simulations, rigorous statistical analysis with a total aggregate simulation time of 2...
March 28, 2017: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/28323432/electronic-structures-and-oh-induced-atmospheric-degradation-of-cf3nsf2-a-potential-green-dielectric-replacement-for-sf6
#12
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
https://www.readbyqxmd.com/read/28320902/a-global-optimization-perspective-on-molecular-clusters
#13
REVIEW
J M C Marques, F B Pereira, J L Llanio-Trujillo, P E Abreu, M Albertí, A Aguilar, F Pirani, M Bartolomei
Although there is a long history behind the idea of chemical structure, this is a key concept that continues to challenge chemists. Chemical structure is fundamental to understanding most of the properties of matter and its knowledge for complex systems requires the use of state-of-the-art techniques, either experimental or theoretical. From the theoretical view point, one needs to establish the interaction potential among the atoms or molecules of the system, which contains all the information regarding the energy landscape, and employ optimization algorithms to discover the relevant stationary points...
April 28, 2017: Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences
https://www.readbyqxmd.com/read/28320489/on-the-analysis-of-clustering-in-an-irradiated-low-alloy-reactor-pressure-vessel-steel-weld
#14
Kristina Lindgren, Krystyna Stiller, Pål Efsing, Mattias Thuvander
Radiation induced clustering affects the mechanical properties, that is the ductile to brittle transition temperature (DBTT), of reactor pressure vessel (RPV) steel of nuclear power plants. The combination of low Cu and high Ni used in some RPV welds is known to further enhance the DBTT shift during long time operation. In this study, RPV weld samples containing 0.04 at% Cu and 1.6 at% Ni were irradiated to 2.0 and 6.4×1023 n/m2 in the Halden test reactor. Atom probe tomography (APT) was applied to study clustering of Ni, Mn, Si, and Cu...
March 21, 2017: Microscopy and Microanalysis
https://www.readbyqxmd.com/read/28319381/effects-of-second-metal-al-v-co-doping-on-the-no-reactivity-of-small-rhodium-cluster-cations
#15
Shinichi Hirabayashi, Masahiko Ichihashi
Reactions of pure and doped rhodium cluster cations, RhnX(+) (n = 2-6; X = Al, V, Co, Rh), with NO molecules were investigated at near-thermal energy using a guided ion beam tandem mass spectrometer. We found that the doping with Al and V increases the total reaction cross section mostly. Under single-collision conditions, Rh2X(+) reacts with NO to produce Rh2N(+) with release of metal monoxide, XO, whereas RhnX(+) (n = 3-6) adsorb NO. For the specific clusters RhnAl(+) (n = 3 and 4) and RhnV(+) (n = 4-6), the NO adsorption is often accompanied by the release of one Rh atom...
March 28, 2017: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/28317986/experimental-and-theoretical-evidence-for-the-ferromagnetic-edge-in-wse2-nanosheets
#16
Lei Tao, Fanchen Meng, Shudong Zhao, Yongli Song, Jianxin Yu, Xianjie Wang, Zhiguo Liu, Yi Wang, Bingsheng Li, Yang Wang, Yu Sui
Bulk TMDCs are diamagnetic materials; however, two-dimensional TMDCs exhibit spin polarized edge states, which results in a coupling between the unsaturated transition metal and chalcogenide atoms at the edges. The magnetism in two-dimensional TMDCs broadens their applications in spintronic and multi-functional devices. Herein, by combining macro/micro-magnetic experimental measurements and density functional theory (DFT) calculations, we demonstrate that among five possible edge-terminated WSe2 nanosheets only two types have a magnetic ground state, corresponding to the 100% Se edge terminated and 50% Se edge terminated nanosheets, respectively...
March 20, 2017: Nanoscale
https://www.readbyqxmd.com/read/28317055/electronic-and-relativistic-contributions-to-ion-pairing-in-polyoxometalate-model-systems
#17
Dylan J Sures, Stefano A Serapian, Károly Kozma, Pedro I Molina, Carles Bo, May Nyman
Ion pairs and solubility related to ion-pairing in water influence many processes in nature and in synthesis including efficient drug delivery, contaminant transport in the environment, and self-assembly of materials in water. Ion pairs are difficult to observe spectroscopically because they generally do not persist unless extreme solution conditions are applied. Here we demonstrate two advanced techniques coupled with computational studies that quantify the persistence of ion pairs in simple solutions and offer explanations for observed solubility trends...
March 20, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28314143/a-hybrid-molecular-dynamics-study-on-the-non-newtonian-rheological-behaviors-of-shear-thickening-fluid
#18
Kaihui Chen, Yu Wang, Shouhu Xuan, Xinglong Gong
To investigate the microstructural evolution dependency on the apparent viscosity in shear-thickening fluids (STFs), a hybrid mesoscale model combined with stochastic rotation dynamics (SRD) and molecular dynamics (MD) is used. Muller-Plathe reverse perturbation method is adopted to analyze the viscosities of STFs in a two-dimensional model. The characteristic of microstructural evolution of the colloidal suspensions under different shear rate is studied. The effect of diameter of colloidal particles and the phase volume fraction on the shear thickening behavior is investigated...
July 1, 2017: Journal of Colloid and Interface Science
https://www.readbyqxmd.com/read/28306180/selective-nanoscale-mass-transport-across-atomically-thin-single-crystalline-graphene-membranes
#19
Piran R Kidambi, Michael S H Boutilier, Luda Wang, Doojoon Jang, Jeehwan Kim, Rohit Karnik
Atomically thin single crystals, without grain boundaries and associated defect clusters, represent ideal systems to study and understand intrinsic defects in materials, but probing them collectively over large area remains nontrivial. In this study, the authors probe nanoscale mass transport across large-area (≈0.2 cm(2) ) single-crystalline graphene membranes. A novel, polymer-free picture frame assisted technique, coupled with a stress-inducing nickel layer is used to transfer single crystalline graphene grown on silicon carbide substrates to flexible polycarbonate track etched supports with well-defined cylindrical ≈200 nm pores...
March 17, 2017: Advanced Materials
https://www.readbyqxmd.com/read/28304408/evidence-of-a-strong-effect-of-defect-free-metal-oxide-supports-on-pt-nanoparticles
#20
Ashkan Moradabadi, Shideh Ahmadi, Payam Kaghazchi
Influence of metal oxide (MO) supports on nanoparticle (NP) catalysts is still under investigation. Theoretical studies demonstrate that active defect sites on the surface of a MO support can affect the structure and activity of metal clusters. In the present work, we show that even defect-free surfaces of MOs can cause considerable restructuring and accumulation of interfacial charges on Pt NPs of size 1 nm (Pt55). Independent of the type of MO support, we find that supported Pt55 behaves like a conductor since the binding energy of a test adsorbate on top of it is similar to that on an intact Pt55...
March 17, 2017: Nanoscale
keyword
keyword
82153
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"