Feature vector clustering molecular pairs in computer simulations

A clustering framework is introduced to analyze the microscopic structural organization of molecular pairs in liquids and solutions. A molecular pair is represented by a representative vector (RV). To obtain RV, intermolecular atom distances in the pair are extracted from simulation trajectory as components of the key feature vector (KFV). A specific scheme is then suggested to transform KFV to RV by removing the influence of permutational molecular symmetry on the KFV as the predicted clusters should be independent of possible permutations of identical atoms in the pair. After RVs of pairs are obtained, a clustering analysis technique is finally used to classify all the RVs of molecular pairs into the clusters. The framework is applied to analyze trajectory from molecular dynamics simulations of an ionic liquid (trihexyltetradecylphosphonium bis(oxalato)borate ([P_6,6,6,14][BOB])). The molecular pairs are successfully categorized into physically meaningful clusters, and their effectiveness is evaluated by computing the product moment correlation coefficient (PMCC). (Willett, Winterman, and Bawden, J. Chem. Inf. Comput. Sci. 1986, 26, 109–118; Downs, Willett, and Fisanick, J. Chem. Inf. Comput. Sci. 1994, 34, 1094–1102) It is observed that representative configurations of two clusters are related to two energy local minimum structures optimized by density functional theory (DFT) calculation, respectively. Several widely used clustering analysis techniques of both nonhierarchical (k-means) and hierarchical clustering algorithms are also evaluated and compared with each other. The proposed KFV technique efficiently reveals local molecular pair structures in the simulated complex liquid. It is a method, which is highly useful for liquids and solutions in particular with strong intermolecular interactions. © 2019 Wiley Periodicals, Inc.     

Studies of conventional sulfur vulcanization of SBR rubber: Analysing the reaction products from thermal degradation of the accelerator by means of MCC-IMS technique

A combination of knowledge on curing process of rubber mixes with novel methods of chemical analysis, a new unconventional approach to analysis of rubber vulcanization is presented in this study. Six SBR samples containing various N-tert-butyl-2-benzothiazole sulfenamide (TBBS) accelerator: sulfur ratios (within) the range of conventional (CV) sulfur vulcanization system were studied using multi-capillary column ion mobility spectrometry (MCC-IMS) technique. For these analysis, calibration/dilution curves were established. Moreover, data from MCC-IMS were correlated with other parameters of the rubber vulcanizates – their crosslink density and structure as well as their tensile strength and modulus at elongation. For such comparison, one of the reaction products from thermal decomposition of TBBS, benzothiazole was selected. Furthermore, the concentration of benzothiazole released during the vulcanization process corresponded well with the crosslink density of the rubber vulcanizates studied. It was even possible to calculate the crosslink density from the concentration of benzothiazole determined by MCC-IMS, using Boltzmann fitting curve. The presented results could be an important contribution in understanding the mechanisms occurring during rubber vulcanization, demonstrating a new approach to testing and evaluation of the process.     

A Polypyridyl‐Based Layered Complex as Dual‐Functional Co‐catalyst for Photo‐Driven Organic Dyes Degradation and Water Splitting

With the ever‐increasing concerns on environmental pollution and energy crisis, it is of great urgency to develop high‐performance photocatalyst to eliminate organic pollutants from wastewater and produce hydrogen via water splitting. Herein, a polypyridyl‐based mixed covalent Cu^I/II complex with triangular {Cu₃} and rhombic {Cu₂Cl₄} subunits alternately extended by mixed SCN^– and Cl^– heterobridges [Cu₄(DNP)(SCN)Cl₄]_n ( 1 ) [DNP = 2,6‐bis(1,8‐naphthyridine‐2‐yl)pyridine] was solvothermally synthesized and employed as a dual‐functional co‐photocatalyst. Resulting from a narrowed band‐gap of 1.07 eV with suitable redox potential and unsaturated Cu^I/II sites, the complex together with H₂O₂ can effectively degrade Rhodamine B and methyl orange up to 87.4 and 88.2 %, respectively. Meanwhile, the complex mixed with H₂PtCl₆ can also accelerate the photocatalytic water splitting in the absence of a photosensitizer with the hydrogen production rate of 27.5 μmol · g^–1 · h^–1. These interesting findings may provide informative hints for the design of the multiple responsive photocatalysts.     

层状复合氧化物La4BaCu5-xMxO13+λ的制备、表征及对CO还原NO的活性

 采用柠檬酸爆炸法合成了系列层状钙钛矿型复合氧化物La4BaCu5-xMxO13+λ(M=Mn, Co; x=0~5)催化剂. 用TPD, TPR和化学分析法对催化剂进行了表征,考察了催化剂在CO还原NO中的催化活性.结果表明,掺杂Mn, Co后催化剂中的活性氧含量及氧化还原性质发生了变化. 掺杂少量Mn, Co可使催化剂在CO还原NO中的催化活性明显提高,且掺杂Co的样品比掺杂Mn的样品活性提高更明显.这是由于Cu-Mn与Cu-Co之间的协同作用不同导致的结果.     

2-溴-4,4'-二硝基-3'-二甲基锍-2'-联苯酚内盐的合成、结构及性质的研究

在胺存在下,3,7-二硝基二苯并溴五环硫酸氢盐与二甲基亚砜反应生成2-溴-4,4'-二硝基-3'-二甲基锍-2'-联苯酚内盐(3).3的X射线晶体结构分析数据表明其分子具有内盐结构但酚氧负离子的负电荷是部分离域的,分子内两苯环所成的两面角为117.3°.3在熔解时发生重排及热分解分别生成2-溴-2'-甲氧基-3'-甲硫基-4,4'-二硝基联苯(6)及3,7-二硝基-4-甲硫基-二苯并呋喃(7).3与盐酸反应生成相应的锍盐(8).     

K6In2Q6 (Q = S,Se, Te): Missing Links in the Series of Alkali Chalcogenido Ditrielates(III)

The chalcogenido indates K₆In₂Q₆ (Q = S, Se, Te) were synthesized from melts of the pure elements at a maximum temperature of 700 °C. All three potassium salts contain dinuclear units [In₂Q₆]^6– of two edge-sharing [InQ₄] tetrahedra. The sulfido and the selenido indate are isotypic and crystallize in the K₆Mn₂O₆-type structure [monoclinic, space group P2₁/c, a = 784.32(9)/809.32(3), b = 1274.58(14)/1322.37(4), c = 836.48(9)/870.53(3) pm, β = 97.900(2)/97.5877(8)°, Z = 2, R₁ = 0.0123/0.0109; for Q = S/Se]. The tellurido indate K₆In₂Te₆ crystallizes in a new orthorhombic structure type [space group Pnma, a = 1793.70(12), b = 1491.55(11), c = 837.40(6) pm, Z = 4, R₁ = 0.0157]. In this structure, the telluride anions form a hexagonal close packing, in which K⁺ cations occupy all octahedral voids; the In³⁺ ions take 1/6 (but always adjacent) tetrahedral voids. This structure-chemical relation to the h.c.p. packing, which is similarly found for most of the sodium dimetallates (e.g. Na₆Fe₂S₆), is substantiated by a full crystallographic group-subgroup tree. The crystal chemistry of the new indates is discussed and compared with that of alkali chalcogenido metallates(III) of Fe, Al and Ga containing [M₂Q₆]^6– dimers, which overall form as many as ten different structure types. DFT band structure calculations of the three title compounds exhibit bandgaps, which continuously decrease from the S to the Te compound and which are also in accordance with the pale yellow (S), bright yellow (Se) and red-brown (Te) color of the compounds. The chemical bonding in the salts and within the metallate anion is discussed on the basis of the partial DOS and a Bader analysis of the calculated electron density.     

SrIrIn6 – An Intergrowth of SrIrIn4 with Indium Slabs

The indium-rich intermetallic compound SrIrIn₆ was synthesized from the elements in a sealed tantalum ampoule at 1173 K, followed by slow cooling for crystal growth. SrIrIn₆ crystallizes with a new structure type which was characterized by X-ray powder and single crystal diffraction: Pmma, a = 852.34(2), b = 434.54(5), c = 1059.18(6) pm, wR₂ = 0.0178, 884 F² values, and 32 variables. The SrIrIn₆ structure shows two basic building units: (i) Ir@In₉ tricapped trigonal prisms (261–292 pm Ir–In) and (ii) distorted bcc In@In₈ cubes (301 to 329 pm In–In). The strontium cations fill cages within the complex three-dimensional [IrIn₆] network and have coordination number 13 (Sr@In₁₃) in form of a tricapped pentagonal prism. The SrIrIn₆ structure can be described as a simple intergrowth variant of SrIrIn₄ (LaCoAl₄ type) with indium slabs. The crystal chemical similarities with the structures of SrIrIn₄, SrIr₂In₈ and Eu₃Ir₂In₁₅ are discussed.     

痂囊腔菌素A的结构

对实验室生物合成方法制得的痂囊腔菌素A做X射线晶体衍射测定,与文献对照,所属品系及空间群相同,晶胞参数接近,但发现北醌母体外的侧基构型有明显差异,主要表现在两个手性碳原子是R-R型而非S-S型,分别以衍射数据和分子力学优化数据为起始结构,进行STO-3G水平上的结构全优化。计算结果表明所制得的痂囊腔菌素A是一种新的光学活性对映体,由此推测痂囊腔菌素A的高光敏活性可能与手性结构特征有关。     

Analytical challenges and the development of biomarkers to measure and to monitor the effects of ocean acidification

Changing ocean-carbonate chemistry caused by oceanic uptake of anthropogenic atmospheric carbon dioxide leads to the formation of carbonic acid, thus lowering the pH of the sea with predictions of a decrease from current levels at 8.15 to 7.82 by the end of the century. The exact measurement of subtle pH changes in seawater over time presents significant analytical challenges, as the equilibrium constants are governed by water temperature and pressure, salinity effects, and the existence of other ionic species in seawater.Here, we review these challenges and how pH also affects dissolved inorganic and organic chemicals that affect biological systems. This includes toxic compounds (xenobiotics) as well as chemicals that are beneficial for marine organisms, such as the chemical signals (i.e. pheromones) that are utilized to coordinate animal behavior. We review how combining analytical, molecular and biochemical tools can lead to the development of biosensors to detect pH effects to enable predictive modeling of the ecological consequences of ocean acidification.     

Copper(I) complexes of N-(aryl)pyridine-2-aldimines: Spectral, electrochemical and catalytic properties

The reactions of N-(aryl)pyridine-2-aldimines (L-R; R = OCH₃, CH₃, H, Cl and NO₂), derived from pyridine-2-aldehyde and para-substituted anilines, with CuI in methanol under ambient conditions afford a series of brown complexes of the type [{Cu(L-R)I}₂]. The structure of the [{Cu(L-OCH₃)I}₂] complex has been determined by X-ray crystallography. In these dimeric complexes the two copper centers are linked through an iodo-bridge, and the L-R ligands are coordinated to the metal center through the pyridine-nitrogen and imine-nitrogen. All the complexes show characteristic ¹H NMR signals and intense MLCT transitions in the visible region. These complexes also show an emission near 465 nm, whilst they are excited at 340 nm, with relatively poor quantum yields (φ ∼0.002 at 298 K). Cyclic voltammetry on all the complexes shows two successive Cu(I)-Cu(II) oxidations on the positive side of SCE, and a reduction of the coordinated imine ligand on the negative side. These copper(I) complexes are found to efficiently catalyze Suzuki type C-C coupling reactions.