Cluster and periodic DFT calculations of adsorption and activation of CO2 on the Cu(hkl) surfaces

The adsorption behavior and thermal activation of carbon dioxide on the Cu(1 1 1), Cu(1 0 0), and Cu(1 1 0) surfaces have been investigated by means of density functional theory calculations and cluster models and periodic slabs. According to the cluster models, the optimized results indicate that the basis set of C and O atoms has a distinct effect on the adsorption energy, but an indistinct one on the equilibrium geometry. For the CO₂/Cu(hkl) adsorption systems studied here, the final structure of adsorbed CO₂ is near linear and the preferred modes for the adsorption of CO₂ onto the Cu(1 1 1), Cu(1 0 0), and Cu(1 1 0) surfaces are the side-on adsorption at the cross bridge site with an adsorption energy of 13.06 kJ/mol, the side-on adsorption at the short bridge site (13.54 kJ/mol), and the end-on adsorption on the on-top site with C–O bonds located along the short bridge site (26.01 kJ/mol), respectively. However, the calculated adsorption energies from periodic slabs are lower as compared to the experimental data as well as the cluster model data, indicating that the periodic slab approach of generalized gradient approximation in the density function theory may be not suitable to obtain quantitative information on the interaction of CO₂ with Cu(hkl) surfaces.     

Drug metabolite cluster centers-based strategy for comprehensive profiling of Neomangiferin metabolites in vivo and in vitro and network pharmacology study on anti-inflammatory mechanism

Neomangiferin (NMF) is an extremely special xanthone that could be simultaneously attributed to C-glycoside and O-glycoside with a variety of biological activities, such as anti-inflammatory, antitumor, antipyretic, and so on. So far as we know, the metabolism profiling has been insufficient until now. Herein, Drug Metabolite Cluster Centers (DMCCs)-based Strategy has been developed to profile the NMF metabolites in vivo and in vitro. Firstly, the DMCCs was proposed depending on literature-related and preliminary analysis results. Secondly, the specific metabolic rule was implemented to screen the metabolites of candidate DMCCs from the acquired Ultra High Performance Liquid Chromatography Quadrupole Exactive Orbitrap Mass Spectrometry (UHPLC-Q-Exactive Orbitrap MS) data by extracted ion chromatography (EIC) method. Thirdly, candidate metabolites were accurately and tentatively identified according to the pyrolysis law of mass spectrometry, literature reports, comparison of reference substances, and especially the diagnostic product ions (DPIs) deduced preliminarily. Finally, network pharmacology was adopted to elucidate the anti-inflammatory action mechanism of NMF on the basis of DMCCs. As a result, 3 critical metabolites including NMF, Mangiferin (MF) and Norathyriol (NA) were proposed as DMCCs, and a total of 61 NMF metabolites (NMF included) were finally screened and characterized coupled with 3 different biological sample preparation methods including solid phase extraction (SPE), acetonitrile precipitation and methanol precipitation. Among them, 32 metabolites were discovered in rat urine, 30 in rat plasma, 12 in rat liver, 9 metabolites in liver microsomes and 8 in rat faeces, respectively. Our results also illustrated that NMF primarily underwent deglucosylation, glucuronidation, methylation, sulfation, dihydroxylation and their composite reactions in vivo and in vitro. Additionally, network pharmacology analysis based on DMCCs revealed 85 common targets of disease-metabolites, and the key targets were TNF, EGFR, ESR1, PTGS2, HIF1A, IL-2, PRKCA and PRKCB. They exerted anti-inflammatory effects mainly through the pathways of inflammatory response, calcium-dependent protein kinase C activity, nitrogen metabolism, pathways in cancer and so on. In general, our study constructed a novel strategy to comprehensive elucidate the biotransformation pathways of NMF in vivo and in vitro, and provided vital reference for further understanding its anti-inflammatory action mechanism. Moreover, the established strategy could be generalized to the metabolism and action mechanism study of other natural products.     

Si4+Si3反应动力学：振动激发态对反应的影响

用准经典轨线方法研究了处于振动激发态的硅原子团簇与硅原子团簇碰撞的反应动力学，计算表明，对于Ｓｉ４＋Ｓｉ３反应，当反应物团簇处于振动激发态时，有利于生成更小团簇的碎片，而对生成Ｓｉ６＋Ｓｉ及Ｓｉ５＋Ｓｉ２的影响不大。     

ToF-SIMS analysis of surface-anchored organometallic clusters

ToF-SIMS analysis of the organometallic cluster Os₃(μ-H)(CO)₁₀(μ-SCH₂CH₂SH) chemically attached onto a silver or gold surface, and of the cluster fragment Os₃(μ-H)(CO)₁₀(μ-OSi) on a silica surface, allows for identification of the surface organometallic species, and also gives information on its reactivity.     

Polynuclear manganese grids and clusters—A magnetic perspective

High nuclearity paramagnetic, spin-coupled transition metal clusters and grids are fascinating chemists and physicists partly because of their structural beauty, and the challenge of creating them, but also because of their novel physical properties. Magnetic interactions between the spin centers are a primary focus. This review will examine a selection of Mn(II) polynuclear grids and clusters, with nuclearities in the range Mn₄ to Mn₉. Theoretical treatments of the magnetic properties are discussed, and approaches to solving the exchange problem for ‘large’ spin systems related to computational difficulties. A freely available software package (MAGMUN4.1) is presented as a means of dealing simply with spin-coupled clusters in general, and symmetry reduction methods are discussed briefly as a means of dealing with ‘large’ spin systems.     

Supramolecular cluster catalysis: facts and problems

By checking the chemistry underlying the concept of “supramolecular cluster catalysis” we identified two major errors in our publications related to this topic, which are essentially due to contamination problems. (1) The conversion of the “closed” cluster cation [H₃Ru₃(C₆H₆)(C₆Me₆)₂(O)]⁺ (1) into the “open” cluster cation [H₂Ru₃(C₆H₆)(C₆Me₆)₂(O)(OH)]⁺ (2), which we had ascribed to a reaction with water in the presence of ethylbenzene is simply an oxidation reaction which occurs in the presence of air. (2) The higher catalytic activity observed with ethylbenzene, which we had erroneously attributed to the “open” cluster cation [H₂Ru₃(C₆H₆)(C₆Me₆)₂(O)(OH)]⁺ (2), was due to the formation of RuO₂ · nH₂O, caused by a hydroperoxide contamination present in ethylbenzene.     

Modeling the cluster formation during infrared and ultraviolet matrix-assisted laser desorption ionization of oligonucleotides in succinic acid matrix with molecular mechanics

A large succinic acid (HOOC(CH₂)₂COOH) matrix containing 7 × 7 × 7 unit cells with guest oligonucleotide AGCAGCT was modeled with molecular dynamics simulation for infrared matrix-assisted laser desorption ionization. We simulated the laser heating of the succinic acid (this data is still missing from the literature) with λ=2.94 μm infrared laser pulses and compared it to ultraviolet excitation. We did this in order to elucidate the cluster formation of succinic acid in the gas phase in itself and around the analyte. At this wavelength, the laser energy is coupled into the matrix through the OH vibrations of the carboxyl groups. The most pronounced difference we observed at 1,500 K simulation is that infrared heating generates about 10–15 more succinic acid molecules bound to the analyte in noncovalent complex form than the ultraviolet mode, which generates about 2 molecules thus bound. We report energy redistribution within the matrix between the host and guest species as well as other dynamical properties. The parameter and topology data for succinic acid that we used are reported and ready for use in CHARMM computer code environment for simulation. Revised: 12 October 2001 / Accepted: 27 February 2002 / Published online: 13 June 2002     

OH stretch IR spectra of (H2O)3 and benzene-(H2O)3

The OH stretch IR spectrum of (H₂O)₃ is significantly altered upon complexation of the cluster with a benzene molecule. Theoretical calculations show that the differences in the OH stretch spectra of (H₂O)₃ and benzene-(H₂O)₃ are primarily due to mode localization induced by the benzene molecule. Received: 27 January 1997 / Accepted: 28 January 1997     

Cs[Er6C]I12 und Cs2Lu[Lu6C]Cl18: Beispiele für quaternäre reduzierte Halogenide der Lanthanide mit isolierten „Clustern”︁

CS[Er₆C]I₁₂ and cs₂Lu[Lu₆C]CI₁₈: Examples for Quaternary Reduced Halides of the Lanthanides with Isolated “Clusters” Cs[Er₆C]I₁₂ and Cs₂Lu[Lu₆C]Cl₁₈ were obtained as byproducts through metallothermic reductions of ErI₃ and LuCl, with cesium in the presence of carbon in sealed tantalum containers at temperatures ranging from 700 to 940 °C. Cs₂Lu[Lu₆C]Cl₁₈ (isostructural with Cs₂Zr[Zr₆H]Cl₁₈, R 3 , a = 981.7 pm, c = 2723.2 pm, Z = 3, R = 0.082, R, = 0.053) contains octahedral [Lu₆C] clusters which are slightly compressed along the threefold axis and edge-bridged by twelve chloride anions to form [Lu₆C]Cl₁₂ units. Six additional Cl in exo positions of the cluster provide octahedral coordination for the seventh Lu³⁺. Cs⁺ occupies anticuboctahedral interstices within the Cl⁺ layers as a part of the (hexagonal) closest packed arrangement. Cs[Er₆C]I₁₂ (trigonal, R 3, a = 1112.0pm, c = 2063.8pm, Z = 3, R = 0.094, R, = 0.068) exhibits [Er₆C]I₁₂ units as well and shows the structural framework of Sc[Sc₆N]Cl₁₂. Instead of Sc³⁺ in octahedral holes, cesium occupies a regular iodide position within the ccp sheets forming [CsI₃] layers. Both halides are compared with other compounds of the lanthanides containing isolated [M₆X₁₂] clusters. The extreme electron deficiency is discussed.