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Atomic clusters

Massimiliano Bartolomei, Ricardo Pérez de Tudela, Kilian Arteaga, Tomás González-Lezana, Marta I Hernández, José Campos-Martínez, Pablo Villarreal, Javier Hernández-Rojas, José Bretón, Fernando Pirani
Benchmark interaction energies between coronene, C24H12, and molecular hydrogen, H2, have been computed by means of high level electronic structure calculations. Binding energies, equilibrium distances and strengths of the long range attraction, evaluated for the basic configurations of the H2-C24H12 complex, indicate that the system is not too affected by the relative orientations of the diatom, suggesting that its behavior can be approximated to that of a pseudoatom. The obtained energy profiles have confirmed the noncovalent nature of the bonding and serve to tune-up the parameters of a new force field based on the atom-bond approach which correctly describes the main features of the H2-coronene interaction...
September 22, 2017: Physical Chemistry Chemical Physics: PCCP
Tomás F Beltrán, Guillermo Zaragoza, Lionel Delaude
The reaction of [Fe2(CO)9] with two representative imidazolium-2-dithiocarboxylate zwitterions derived from common N-heterocyclic carbenes (NHCs) bearing mesityl (IMes) or 2,6-diisopropylphenyl substituents on their nitrogen atoms (IDip) unexpectedly afforded two small bimetallic iron-carbonyl clusters with the generic formula [Fe2(CO)6(μ-κ(2)-S,S'-κ(2)-S,S'-S3C·NHC)]. After a brief optimization of the reaction conditions, these two "sulfur-enriched" products were isolated in low yields. They were fully characterized by IR, NMR, UV/Visible, and ESI-MS techniques, and their molecular structures were determined by single crystal X-ray diffraction analysis...
September 22, 2017: Dalton Transactions: An International Journal of Inorganic Chemistry
J Hermenau, J Ibañez-Azpiroz, Chr Hübner, A Sonntag, B Baxevanis, K T Ton, M Steinbrecher, A A Khajetoorians, M Dos Santos Dias, S Blügel, R Wiesendanger, S Lounis, J Wiebe
A cluster of a few magnetic atoms on the surface of a nonmagnetic substrate is one suitable realization of a bit for spin-based information technology. The prevalent approach to achieve magnetic stability is decoupling the cluster spin from substrate conduction electrons in order to suppress destabilizing spin-flips. However, this route entails less flexibility in tailoring the coupling between the bits needed for spin-processing. Here, we use a spin-resolved scanning tunneling microscope to write, read, and store spin information for hours in clusters of three atoms strongly coupled to a substrate featuring a cloud of non-collinearly polarized host atoms, a so-called non-collinear giant moment cluster...
September 21, 2017: Nature Communications
Salma Kassem, Alan T L Lee, David A Leigh, Vanesa Marcos, Leoni I Palmer, Simone Pisano
It has been convincingly argued that molecular machines that manipulate individual atoms, or highly reactive clusters of atoms, with Ångström precision are unlikely to be realized. However, biological molecular machines routinely position rather less reactive substrates in order to direct chemical reaction sequences, from sequence-specific synthesis by the ribosome to polyketide synthases, where tethered molecules are passed from active site to active site in multi-enzyme complexes. Artificial molecular machines have been developed for tasks that include sequence-specific oligomer synthesis and the switching of product chirality, a photo-responsive host molecule has been described that is able to mechanically twist a bound molecular guest, and molecular fragments have been selectively transported in either direction between sites on a molecular platform through a ratchet mechanism...
September 20, 2017: Nature
Jishi Chen, Yanze Pan, Zonghua Wang, Peng Zhao
A series of tiara like structural Pdn(SR)2n (5 ≤ n ≤ 20) nanoclusters were synthesized by using a modified Brust-Schiffrin route and isolated via thin layer chromatography, and further measured using MALDI-MS. A new crystal structure of tiara like structural Pd6(SC2H4Ph)12 was determined by single-crystal X-ray crystallography. The atomic distance of PdPd increased and the Pd-S bond length decreased with the increase in the n value in the optimized structure of Pdn(SR)2n (5 ≤ n ≤ 10), which were optimized by density functional theory at the B3LYP level...
September 21, 2017: Dalton Transactions: An International Journal of Inorganic Chemistry
Fahri Alkan, Sean T Holmes, Cecil Dybowski
Calculations of (19)F magnetic shielding in various materials are presented. In calculations on gas-phase molecules, the variation of magnetic shielding with the amount of Hartree-Fock exchange (HFX) in the functional demonstrates that excellent agreement with experiment is obtained with an admixture of 50%, here denoted PBE0 (50%). Calculations at the PBE, PBE0 (25%), and PBE0 (50%) levels on 10 crystalline organofluorines and 15 crystalline inorganic fluorides, in which a cluster <I>ansatz</I> is used to model the lattice environment, were performed...
September 20, 2017: Journal of Chemical Theory and Computation
Kara Elizabeth Ranaghan, William G Morris, Laura Masgrau, Kittusamy Senthilkumar, Linus O Johannissen, Nigel S Scrutton, Jeremy N Harvey, Frederick R Manby, Adrian J Mulholland
Aromatic amine dehydrogenase (AADH) and related enzymes are at the heart of debates on the roles of quantum tunnelling and protein dynamics in catalysis. The reaction of tryptamine in AADH involves significant quantum tunnelling in the rate-limiting proton transfer step, shown e.g. by large H/D primary kinetic isotope effects (KIEs), with unusual temperature dependence. We apply correlated ab initio combined quantum mechanics/molecular mechanics (QM/MM) methods, at levels up to local coupled cluster theory (LCCSD(T)/(aug)-cc-pVTZ), to calculate accurate potential energy surfaces for this reaction, which are necessary for quantitative analysis of tunnelling contributions and reaction dynamics...
September 20, 2017: Journal of Physical Chemistry. B
Jorge Quintero-Saumeth, David A Rincón, Markus Doerr, Martha C Daza
We have carried out a computational study on the reactivity of catechol (1,2-dihydroxybenzene) towards superoxide radical anion (O2˙(-)) in water, N,N-dimethylformamide (DMF), pentyl ethanoate (PEA) and vacuum using density functional theory and the coupled cluster method. Five reaction mechanisms were studied: (i) sequential proton transfer followed by hydrogen atom transfer (PT-HT), (ii) sequential hydrogen atom transfer followed by proton transfer (HT-PT), (iii) single electron transfer (SET), (iv) radical adduct formation (RAF) and (v) concerted double proton-transfer electron-transfer (denoted as global reaction, GR)...
September 20, 2017: Physical Chemistry Chemical Physics: PCCP
Alvaro Muñoz-Castro, Ivan A Popov, Alexander I Boldyrev
A correlation between the long-range characteristics of the magnetic response of toroidal boron-based structures is given, involving the uncoordinated B16 cluster and the hypercoordinated [Co@B16](-/3-) counterparts. It is found that the perfectly symmetrical doubly aromatic systems share common features, involving a continuous shielding region for the orientation-averaged response (isotropic), and a long-ranged shielding cone under a perpendicularly oriented applied field (B). In contrast, the conflicting aromatic structure given by the slightly distorted species, exhibits an enhanced deshielding cone under B, which dominates the isotropic character of the response...
September 20, 2017: Physical Chemistry Chemical Physics: PCCP
Krishnendu Bera, Priyanka Rani, Gaurav Kishor, Shikha Agarwal, Antresh Kumar, Durg Vijay Singh
ATP-Binding cassette (ABC) transporters play an extensive role in the translocation of diverse sets of biologically important molecules across membrane. EchnocandinB (antifungal) and EcdL protein of Aspergillus rugulosus are encoded by the same cluster of genes. Co-expression of EcdL and echinocandinB reflects tightly linked biological functions. EcdL belongs to Multidrug Resistance associated Protein (MRP) subfamily of ABC transporters with an extra transmembrane domain zero (TMD0). Complete structure of MRP subfamily comprising of TMD0 domain, at atomic resolution is not known...
September 20, 2017: Journal of Biomolecular Structure & Dynamics
Michael Charles Thompson, Jacob Ramsay, J Mathias Weber
We report infrared photodissociation spectra of manganese-CO2 cluster anions,[Mn(CO2)n](-) (n = 2 - 10) to probe structural motifs characterizing the interaction between Mn and CO2 in the presence of an excess electron. We interpret the experimental spectra through comparison with infrared spectra predicted from density functional theory calculations. The cluster anions consist of core ions combining a Mn atom with a variety of ligands, solvated by additional CO2 molecules. Structural motifs of ligands evolve with increasing cluster size from simple monodentate and bidentate CO2 ligands to oxalate ligands and combinations of these structural themes...
September 19, 2017: Journal of Physical Chemistry. A
Jiao-Jiao Chen, Ting Zhang, Mei-Qi Zhang, Qing-Yu Liu, Xiao-Na Li, Sheng-Gui He
Neutral manganese oxide clusters Mn2NO3N+x (N = 2-22; x = -1, 0, 1) with dimensions up to a nanosize were prepared by laser ablation and reacted with C2H4 in a fast flow reactor. The size-dependent reactivity of C2H4 adsorption on these clusters was experimentally identified and the adsorption reactivity decreases generally with the increase of cluster size. Density functional theory calculations were performed to study the geometrical and electronic structures of Mn2NO3N (N = 1-6) clusters. The calculated results indicated that the coordination number and the charge distribution of the metal centers are responsible for the experimentally observed size-dependent reactivity...
September 19, 2017: Chemistry: a European Journal
Md Abu Bakar, Mizuho Sugiuchi, Mitsuhiro Iwasaki, Yukatsu Shichibu, Katsuaki Konishi
It is well known that various transition elements can form M···H hydrogen bonds. However, for gold, there has been limited decisive experimental evidence of such attractive interactions. Herein we demonstrate an example of spectroscopically identified hydrogen bonding interaction of C-H units to Au atoms in divalent hexagold clusters ([Au6](2+)) decorated by diphosphine ligands. X-ray crystallography reveals substantially short Au-H/Au-C distances to indicate the presence of attractive interactions involving unfunctionalized C-H moieties...
September 18, 2017: Nature Communications
Xujian Li, Xing Zhang, Heng Yang, Qi Zhou
The control of dispersity and size of metal particles deposited on substrate surface are always the major challenges for fabricating the efficient and stable metallic nanoparticles-decorated composite. Herein, we proposed a simple liquid-phase atomic layer deposition (L-ALD) method to obtain an atomic-layered MnO2 nanoparticles loaded palygorskite nanorod (MnO2@Pal), involving two-step procedures comprised of the solid-liquid interfacial reaction between organic manganese precursor and surface hydroxyl groups of palygorskite, and then a calcination treatment to activate surface Mn, which is used as a powerful adsorbent for recovery of REE ions from wastewater...
September 9, 2017: Journal of Colloid and Interface Science
Jeong-Wan Jo, Yong-Hoon Kim, Joohyung Park, Jae Sang Heo, Seongpil Hwang, Won-June Lee, Myung-Han Yoon, Myung-Gil Kim, Sung Kyu Park
Oxide dielectric materials play a key role in a wide range of high-performance solid-state electronics from semiconductor devices to emerging wearable and soft bio-electronic devices. Although lots of previous advances are noteworthy, their typical processing temperature still far exceeds the thermal limitations of soft materials, impeding their wide utilization in these emerging fields. Here, we report an innovative route to form highly reliable aluminum-oxide dielectric films using an ultralow temperature (< 60 ˚C) solution process with a class of oxide nanocluster precursors...
September 18, 2017: ACS Applied Materials & Interfaces
Dmitri G Fedorov, Kazuo Kitaura
A many-body expansion of the Fock matrix in the fragment molecular orbital method is derived up to three-body terms for restricted Hartree-Fock and density functional theory in the atomic orbital basis and compared to the expansion in the basis of fragment molecular orbitals (MOs). The physical nature of many-body corrections is revealed in terms of charge transfer terms. An improvement of the fragment MO expansion is proposed by adding exchange to the embedding. The accuracy of all developed methods is demonstrated in comparison to unfragmented results for polyalanines, a water cluster, Trp-cage (PDB: 1L2Y) and crambin (PDB: 1CRN) proteins, a zeolite cluster, a Si nano-wire, and a boron nitride ribbon...
September 14, 2017: Journal of Chemical Physics
Nathaniel R Gunby, Sarah L Masters, Deborah L Crittenden
Molecular properties depend on molecular structure, so the first step in any computational chemistry investigation is to generate all thermally accessible conformers. Typically it is necessary to make a trade-off between the number of conformers to be explored and the accuracy of the method used to calculate their energies. Ab initio potential energy surface scans can, in principle, be applied to any molecule, but their conformational cost scales poorly with both molecular size and dimensionality of the search space...
September 6, 2017: Journal of Molecular Graphics & Modelling
Boon K Teo, Huayan Yang, Juanzhu Yan, Nanfeng Zheng
Understanding the nucleation and growth pathways of nanocrystallites allows precise control of the size and shape of functional crystalline nanomaterials of importance in nanoscience and nanotechnology. This paper provides a detailed analysis of the stereochemical and electronic requirements of three series of nanoclusters based on face-centered cubes (fcc) as the basic building blocks, namely, 1-, 2-, and 3-D assemblages of fcc to form superrods (n), supersquares (n(2)), and supercubes (n(3)). The generating functions for calculating the numbers (and arrangements) of surface and interior metal atoms, as well as the number and dispositions of the ligands, for these particular sequences of fcc metal clusters of the general formula [Mm(SR)l(PR'3)8](q) (where M = coinage metals; SR = thiolates (or group XI ligands), and PR'3 = phosphines) are presented...
September 15, 2017: Inorganic Chemistry
Zhiyu Jia, Yongjun Li, Zicheng Zuo, Huibiao Liu, Changshui Huang, Yuliang Li
Graphdiyne (GDY) is a flat material comprising sp(2)- and sp-hybridized carbon atoms with high degrees of π conjugation that features uniformly distributed pores. It is interesting not only from a structural point of view but also from the perspective of its electronic, chemical, mechanical, and magnetic properties. We have developed an in situ homocoupling reaction of hexaethynylbenzene on Cu foil for the fabrication of large-area ordered films of graphdiyne. These films are uniform and composed of graphdiyne multilayers...
September 15, 2017: Accounts of Chemical Research
Frederico V Prudente, Jorge M C Marques, Francisco B Pereira
A new analytical potential for Li(+)Ar2 including three-body interactions has been modeled by employing ab initio energies that were calculated within the CCSD(T) framework and a quadruple-zeta basis-set (i.e., cc-pVQZ for lithium and aug-cc-pVQZ for argon) and, then, corrected for the basis-set superposition error (BSSE) with the counterpoise method. Departing from this function, we have constructed the potential energy surface for Li(+)Arn clusters by summing over all two-body and three-body terms. We have employed our evolutionary algorithm (EA) to perform a global geometry optimization that allows for the study of a Li(+) ion microsolvated with argon atoms...
September 15, 2017: Physical Chemistry Chemical Physics: PCCP
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