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Atomic clusters

Yaxun Fan, Hua Wang, Chengqian He, Fulin Qiao, Shu Wang, Yilin Wang
The interactions between a star-shaped hexameric cationic quaternary ammonium surfactant PAHB and calf thymus DNA and induced DNA condensation were investigated by ζ-potential, dynamic light scattering, atomic force microscopy, isothermal titration calorimetry, ethidium bromide exclusion assay, circular dichroism and cytotoxicity assay. With the addition of PAHB, long extended DNA molecules exhibit successive conformational transitions from elongated coil to partially condensed cluster-like aggregate, globules-on-a-string structure, and then to fully condensed globule until the saturation point of interaction between PAHB and DNA, which is slightly above their charge neutralization point...
June 22, 2017: ACS Applied Materials & Interfaces
C-Z Gao, P M Dinh, P-G Reinhard, E Suraud
We study from a theoretical perspective the ionization of molecules and clusters induced by irradiation of a combined two-color laser field consisting of a train of attosecond XUV pulses in the presence of an IR field. We use time-dependent density-functional theory (TDDFT) in real time and real space as a theoretical tool. The calculated results are compared to experimental data when available. We also compare TDDFT with results obtained using a time-dependent Schrödinger equation (TDSE), which is well suited to simple systems while TDDFT allows dealing with more complex molecules and clusters...
June 21, 2017: Physical Chemistry Chemical Physics: PCCP
Yury Minenkov, Heng Wang, Zhandong Wang, S Mani Sarathy, Luigi Cavallo
Computational electronic structure calculations are routinely undertaken to predict thermodynamic properties of the various species. However, the application of highly accurate wave function theory methods, such as the "gold standard" coupled cluster approach including single, double and partly triple excitations in perturbative fashion, CCSD(T), to large molecules is limited due to high computational cost. In this work, the promising domain based local pair natural orbital coupled cluster approach, DLPNO-CCSD(T), has been tested to reproduce 113 accurate formation enthalpies of medium-size molecules (few dozens heavy atoms) important for bio- and combustion chemistry via the reaction based Feller-Peterson-Dixon approach...
June 21, 2017: Journal of Chemical Theory and Computation
Seung-Tae Hong
Quasicrystals (QCs) are well-ordered but aperiodic crystals with classically forbidden symmetries (such as 5-fold). High-dimensional (HD) crystallography is a standard method to locate atom positions explicitly. However, in practice, it is still challenging because of its complexity. Here, we report a new simple approach to three-dimensional (3D) atomic modeling derived from X-ray diffraction data, and apply it to the icosahedral QC Al0.63Cu0.25Fe0.12. Electron density maps were calculated directly from 3D diffraction data indexed with noninteger (fractional) numbers as measured, with proper phases; each of 2(5) = 32 possible phase assignments for the five strongest reflections was used for Fourier synthesis...
June 21, 2017: Inorganic Chemistry
Kazuo Kobayashi
Bacteria possess molecular biosensors that enable responses to a variety of stressful conditions, including oxidative stress, toxic compounds, and interactions with other organisms, through elaborately coordinated regulation of gene expression. In Escherichia coli and related bacteria, the transcription factor SoxR functions as a sensor of oxidative stress and nitric oxide (NO). SoxR protein contains a [2Fe-2S] cluster essential for its transcription-enhancing activity, which is regulated by redox changes in the [2Fe-2S] cluster...
June 21, 2017: Accounts of Chemical Research
Obaidur Rahaman, Maria Kalimeri, Marina Katava, Alessandro Paciaroni, Fabio Sterpone
We introduce a novel strategy to quantify the disorder of extended water-water hydrogen-bond (HB) networks sampled in particle-based computer simulations. The method relies on the conformational clustering of the HB connectivity states. We successfully applied it to unveil the fine relationship among the protein dynamical transition in hydrated powder, which marks the activation of protein flexibility at Td∽240 K, and the sudden increase of the configurational disorder of the water HB network enveloping the proteins...
June 21, 2017: Journal of Physical Chemistry. B
Shin Nakamura, Takumi Noguchi
Photosynthetic water oxidation is performed at the Mn4CaO5 cluster in photosystem II (PSII). The protonation structures of amino acid residues and water molecules around the Mn4CaO5 cluster are crucial in water oxidation reactions. In this study, we determined the protonation state of a key His residue in water oxidation, D1-H337, which is directly hydrogen bonded with the oxygen atom of the Mn4CaO5 cluster, using polarized attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectroscopy. Flash-induced polarized ATR-FTIR difference spectra upon the S1→S2 transition of oriented PSII membranes showed broad negative and positive features around 2600 and 2900 cm-1, respectively, with large dichroic ratios, accompanied with several minor peaks attributable to the Fermi resonance of a His NH vibration...
June 21, 2017: Journal of the American Chemical Society
Qisheng Lin, Kaiser Aguirre, Scott M Saunders, Timothy A Hackett, Yong Liu, Valentin Taufour, Durga Paudyal, Sergey Budko, Paul C Canfield, Gordon J Miller
Planar hydrocarbon-like metal clusters may foster new insights linking organic molecules with conjugated - bonding interactions and inorganic structures in terms of their bonding characteristics. However, such clusters are uncommon in polar intermetallics. Herein, we report two polar intermetallic phases, Pr5Co2Ge3 and Pr7Co2Ge4, both of which feature such planar metal clusters, viz., ethylene-like [Co2Ge4] clusters plus the concatenated forms and polyacene-like [Co2Ge2]n ribbons in Pr5Co2Ge3, and 1,2,4,5-tetramethylbenzene-like [Co4Ge6] cluster in Pr7Co2Ge4...
June 19, 2017: Chemistry: a European Journal
Mona Habibi, Jörg Rottler, Steven S Plotkin
Mechanical unfolding of mutated apo, disulfide-reduced, monomeric superoxide dismutase 1 protein (SOD1) has been simulated via force spectroscopy techniques, using both an all-atom (AA), explicit solvent model and a coarse-grained heavy-atom Gō (HA-Gō) model. The HA-Gō model was implemented at two different pulling speeds for comparison. The most-common sequence of unfolding in the AA model agrees well with the most-common unfolding sequence of the HA-Gō model, when the same normalized pulling rate was used...
June 16, 2017: Biochimica et Biophysica Acta
Alvaro Rafael Muñoz-Castro, Franck Gam, Dayan Paez-Hernandez, Ramiro Arratia-Perez, C W Liu, Samia Kahlal, Jean-Yves Saillard
Coinage-metal atomically precise nanoclusters are made of a well-defined metallic core embedded in a ligand-protecting outer shell. Whereas gold derivatives are particularly well documented, examples of silver nanoclusters are somewhat limited and copper species remain particularly scare. Our DFT relativistic calculations on superatomic metallic cores indicate that copper species are almost as stable as gold clusters and more stable than their silver counterparts. Thus, for silver superatomic cores, the role of the stabilizing ligands is more crucial in the stabilization of the overall structure, in comparison to copper and gold...
June 19, 2017: Chemistry: a European Journal
M H Yang, J H Li, B X Liu
In the present study, atomistic simulation reveals that the microscopic mechanism of the relaxation dynamics in amorphous materials is governed by the activating atoms that jump more than half of the average nearest neighbor distance within a given time. Based on the unsupervised machine-learning algorithm, hierarchical clustering analysis shows that the activating atoms are excited in a cooperative and avalanche-like model to form activating units. Correlation analysis suggests that large free volumes facilitate the formation of activating atoms...
June 19, 2017: Physical Chemistry Chemical Physics: PCCP
Zhongwei Hu, Lasse Jensen
The two-photon absorption (TPA) cross-sections of small thiolate-protected gold clusters have been shown to be much larger than typical small organic molecules. In comparison with larger nanoparticles, their TPA cross-sections per gold atom are also found to be larger. Theoretical simulations have suggested that the large enhancement of these TPA cross-sections comes from a one-photon double-resonance mechanism. However, it remains difficult to simulate TPA cross-sections of thiolate-protected gold clusters due to their large system size and a high density of states...
June 1, 2017: Chemical Science
Yantao Chen, Carl-Johan Aurell, Anna Pettersen, Richard J Lewis, Martin A Hayes, Matti Lepistö, Anna C Jonson, Hanna Leek, Linda Thunberg
Saccharin is a well-known scaffold in drug discovery. Herein, we report the synthesis and preclinical property comparisons of three bioisosteres of saccharin: aza-pseudosaccharins (cluster B), and two new types of aza-saccharins (clusters C and D). We demonstrate a convenient protocol to selectively synthesize products in cluster C or D when primary amines are used. Preclinical characterization of selected matched-pair products is reported. Through comparison of two diastereomers, we highlight how stereochemistry affects the preclinical properties...
June 8, 2017: ACS Medicinal Chemistry Letters
Wenjun Yu, Rongshui Wang, Haiyan Huang, Huijun Xie, Shuning Wang
Agrobacterium tumefaciens S33 can grow with nicotine as the sole source of carbon, nitrogen, and energy via a novel hybrid of the pyridine pathway and the pyrollidine pathway. Characterization of the enzymes involved in the hybrid pathway is important for understanding its biochemical mechanism. Here we report that the molybdenum-containing nicotine dehydrogenase (NdhAB), which catalyzes the initial step of nicotine degradation, is located in the periplasm of strain S33, while the 6-hydroxynicotine oxidase and 6-hydroxypseudooxynicoine oxidase are in the cytoplasm...
June 16, 2017: Applied and Environmental Microbiology
Yasutaka Kuwahara, Yukihiro Yoshimura, Hiromi Yamashita
Liquid-phase oxidation of alkylaromatics with molecular O2 was examined using a microporous Mn-based metal-organic framework (Mn-MOF-74). Mn-MOF-74 consisting of trimeric Mn clusters and 2,5-dihydroxyterephthalate (dhtp) linkers exhibits superior catalytic activity with good ketone selectivity compared to conventional oxide-supported Mn catalysts without showing any lengthy induction period. Combined analyses by means of XRD, FE-SEM, N2 physisorption and Mn K-edge XAFS reveal that the superior catalytic performance is attributed to the inherently-formed Mn(iii)2(dhtp) moieties embedded in the Mn-MOF-74 framework rather than structural factors associated with the MOF...
June 16, 2017: Dalton Transactions: An International Journal of Inorganic Chemistry
Xiaoyan Sun, Shaodong Zhou, Lei Yue, Maria Schlangen, Helmut Schwarz
The thermal reduction of N₂O by CO mediated by the metal-free cluster cations [Si₂Ox]*+ (x = 2-5) has been examined in the gas phase using Fourier transform-ion cyclotron resonance (FT-ICR) mass spectrometry in conjunction with quantum chemical calculations. Three successive oxidation/reduction steps occur starting from [Si₂O₂]*+ and N₂O to form eventually [Si₂O₅]*+; the latter as well as the intermediate oxide cluster ions react sequentially with CO molecules to regenerate [Si₂O₂]*+. Thus, full catalytic cycles occur at ambient conditions in the gas phase...
June 16, 2017: Angewandte Chemie
Gabriel Merino, Maryel Contreras, Sudip Pan, Mesias Orozco-Ic, Jose Luis Cabellos
Extensive potential energy surface explorations of 25 clusters with formula E3M3+ (E = Group 14 element and M = Group 1 element) via density functional theory and high level ab initio computations reveal that the lowest energy isomer for all these systems corresponds to a nonclassical D3h star-like structure in singlet state, where three M atoms interact electrostatically with the triangular E3 core, occupying three bridging positions around it. More than 18,200 calculations were done in the search for the minima structures, starting with a first phase at PBE0/LANL2DZ and ending with an analysis of the most representative clusters at CCSD(T)/def2-TZVP//PBE0/def2-TZVP level...
June 16, 2017: Chemistry: a European Journal
Mathew J Cherukara, Badri Narayanan, Henry Chan, Subramanian K R S Sankaranarayanan
We perform massively-parallel classical molecular dynamics (MD) simulations to study the long timescale monolayer silicene growth on an Ir (111) surface. We observe an intricate multi-stage growth process driven by atomic and cluster migration on the surface. Initial growth involves formation of sub-nanometer clusters via adatom surface diffusion. Subsequently, these clusters rearrange spontaneously with each additional Si atom, forming clusters containing 4-7 member rings. Growth of each cluster through adatom adhesion is accompanied by the formation of larger islands through cluster migration and coalescence...
June 15, 2017: Nanoscale
Takaaki Ikuno, Jian Zheng, Aleksei Vjunov, Maricruz Sanchez-Sanchez, Manuel A Ortuño, Dale Pahls, John L Fulton, Donald M Camaioni, Zhanyong Li, Debmalya Ray, B Layla Mehdi, Nigel D Browning, Omar K Farha, Joseph T Hupp, Christopher J Cramer, Laura Gagliardi, Johannes A Lercher
Copper oxide clusters synthesized via atomic layer deposition on the nodes of the metal-organic framework NU-1000 are active for oxidation of methane to methanol under mild reaction conditions. Analysis of chemical reactivity, in situ X-ray absorption spectroscopy, and density functional theory calculations are used to determine structure/activity relations in the Cu-NU-1000 catalytic system. The Cu-loaded MOF contained Cu as clusters of a few atoms each. The Cu was present at ambient conditions as a mixture of ~15 % Cu(+) and ~ 85 % Cu(2+)...
June 14, 2017: Journal of the American Chemical Society
Xiaoyu Li, Xiaoqing You, Chung K Law, Donald G Truhlar
In order to explore the hydrogen abstraction reaction kinetics of unsaturated methyl esters by hydrogen atoms, we selected two molecules for study, in particular methyl 3-butenoate and methyl 2-butenoate, whose C[double bond, length as m-dash]C double bonds are at different locations. We first determined an accurate and efficient electronic structure method for the investigation by considering eight hydrogen abstraction reactions and comparing their barrier heights and reaction energies computed using several exchange-correlation density functionals to those obtained from CCSD(T)-F12a/jun-cc-pVTZ coupled cluster calculations...
June 14, 2017: Physical Chemistry Chemical Physics: PCCP
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