Synthesis of μ2-Oxo-Bridged Iron(III) Tetraphenylporphyrin–Spacer–Nitroxide Dimers and their Structural and Dynamics Characterization by using EPR and MD Simulations

Iron(III) porphyrins have the propensity to form μ₂-oxo-dimers, the structures of which resemble two wheels on an axle. Whereas their crystal structure is known, their solution structure and internal dynamics is not. In the present work, the structure and dynamics of such dimers were studied by means of electron paramagnetic resonance (EPR) spectroscopy and quantum chemistry based molecular dynamics (MD) simulations by using the semiempirical tight-binding method (GFN-xTB). To enable EPR investigation of the dimers, a nitroxide was attached to each of the tetraphenylporphyrin cores through a linear and a bent linker. The inter-nitroxide distance distributions within the dimers were determined by continuous-wave (cw)-EPR and pulsed electron–electron double resonance (PELDOR or DEER) experiments and, with the help of MD, interpreted in terms of the rotation of the porphyrin planes with respect to each other around the Fe–O–Fe axis. It was found that such rotation is restricted to the four registers defined by the phenyl substituents. Within the registers, the rotation angle swings between 30° and 60° in the proximal and between 125° and 145° in the distal register. With EPR, all four angles were found to be equally populated, whereas the 30° and 145° angles are strongly favored to the expense of the 60° and 125° angles in the MD simulation. In either case, the internal dynamics of these dimers thus resemble the motion of a step motor.     

Synthesis,crystal structure and magnetic properties of a new tri‐nuclear iron (II,III) complex,a precursor for the preparation of superparamagnetic Fe3O4 nanoparticles applicable in the removal of Cd2+

This study reports the structural and spectroscopic characterization of a novel metal organic compound formulated as [Fe (bpy)₃] [Fe (dipic)₂]₂.7H₂O ( 1 ) (dipic = pyridine‐2,6‐dicarboxylate and bpy = 2,2^′‐bipyridine). 1 was investigated by elemental analysis, FT‐IR spectroscopy, powder X‐ray diffraction and single crystal X‐ray diffraction (SC‐XRD), which revealed a triclinic structure of expected composition. Thermal degradation of 1 was also investigated. Complex 1 was used as a precursor to prepare superparamagnetic nanoparticles of Fe₃O₄ by thermal analysis. The obtained Fe₃O₄ was characterized by Fourier transformed infrared spectroscopy (FT‐IR), powder X‐ray diffraction (XRD) and scanning electron microscopy (SEM). Fe₃O₄ nanoparticles were used as a nano‐adsorbent to remove Cd²⁺ from water at room temperature. The results showed that this nano‐adsorbent is effective in removing Cd²⁺ from contaminated water sources, and that the maximal effectivity of adsorption occurs at pH = 6. Magnetic measurements of complex 1 and Fe₃O₄ nanoparticles at room temperature revealed paramagnetic and superparamagnetic behavior, respectively.     

Automated chemical resonance generation and structure filtration for kinetic modeling

This work discusses efficient and automated methods for constructing a set of representative resonance structures for arbitrary chemical species, including radicals and biradicals, consisting of the elements H, C, O, N, and S. Determining the representative reactive structures of chemical species is crucial for identification of reactive sites and consequently applying the correct reaction templates to generate the set of important reactions during automated chemical kinetic model generation. We describe a fundamental set of resonance pathway types, accounting for simple resonating structures, as well as global approaches for polycyclic aromatic species. Automatically discovering potential localized structures along with filtration to identify the representative structures was shown to be robust and relatively fast. The algorithms discussed here were recently implemented in the Reaction Mechanism Generator (RMG) software. The final structures proposed by this method were found to be in reasonable agreement with quantum chemical computation results of localized structure contributions to the resonance hybrid.     

Investigation of mononuclear,dinuclear, and trinuclear transition metal (II) complexes derived from an asymmetric Salamo‐based ligand possessing three different coordination modes

A new asymmetric Salamo‐based ligand H₂L was synthesized using 3‐tert‐butyl‐salicylaldehyde and 6‐methoxy‐2‐[O‐(1‐ethyloxyamide)]‐oxime‐1‐phenol. By adjusting the ratio of the ligand H₂L and Cu (II), Co (II), and Ni (II) ions, mononuclear, dinuclear, and trinuclear transition metal (II) complexes, [Cu(L)], [{Co(L)}₂], and [{Ni(L)(CH₃COO)(CH₃CH₂OH)}₂Ni] with the ligand H₂L possessing completely different coordination modes were obtained, respectively. The optical spectra of ligand H₂L and its Cu (II), Co (II) and Ni (II) complexes were investigated. The Cu (II) complex is a mononuclear structure, and the Cu (II) atom is tetracoordinated to form a planar quadrilateral structure. The Co (II) complex is dinuclear, and the two Co (II) atoms are pentacoordinated and have coordination geometries of distorted triangular bipyramid. The Ni (II) complex is a trinuclear structure, and the terminal and central Ni (II) atoms are all hexacoordinated, forming distorted octahedral geometries. Furthermore, optical properties including UV–Vis, IR, and fluorescence of the Cu (II), Co (II), and Ni (II) complexes were investigated. Finally, the antibacterial activities of the Cu (II), Co (II), and Ni (II) complexes were explored. According to the experimental results, the inhibitory effect was found to be enhanced with increasing concentrations of the Cu (II), Co (II), and Ni (II) complexes.     

偏缠绕模的Frobenius性质

主要给出了偏缠绕模的Frobenius性质，推广了缠绕模相应的性质。     

RNAGCN: RNA tertiary structure assessment with a graph convolutional network

RNAs play crucial and versatile roles in cellular biochemical reactions. Since experimental approaches of determining their three-dimensional (3D) structures are costly and less efficient, it is greatly advantageous to develop computational methods to predict RNA 3D structures. For these methods, designing a model or scoring function for structure quality assessment is an essential step but this step poses challenges. In this study, we designed and trained a deep learning model to tackle this problem. The model was based on a graph convolutional network (GCN) and named RNAGCN. The model provided a natural way of representing RNA structures, avoided complex algorithms to preserve atomic rotational equivalence, and was capable of extracting features automatically out of structural patterns. Testing results on two datasets convincingly demonstrated that RNAGCN performs similarly to or better than four leading scoring functions. Our approach provides an alternative way of RNA tertiary structure assessment and may facilitate RNA structure predictions. RNAGCN can be downloaded from https://gitee.com/dcw-RNAGCN/rnagcn.     

一种新型双吡啶悬臂Mn(Ⅱ)配合物的合成、晶体结构及DNA结合能力研究

通过3,3′-((乙烷-1,2-二基双(2-甲基吡啶杂氮二基)双(亚甲基))双(2-羟基-5-甲基苯甲醛)与2-羟基-1,3-丙二胺的缩合反应得到一种具有双吡啶悬臂的双核锰配合物。通过X射线单晶衍射确定了该配合物结构,结果显示其分子式为[Mn₂(C₃₇H₄₃N₆O₆)]·(ClO₄)₂。该配合物属于单斜晶系,P2₁/c空间群,晶胞参数为:a=1.096 50(19) nm, b=1.419 5(3) nm, c=3.109 4(5) nm, β=108.153(5)°。进一步分析表明两个二价锰离子分别与(N_amine)₂(N_imine)₂O₃和(N_imine)₂O₄体系配位,它们与配位原子形成的几何构型分别是十面体和扭曲的八面体。两个中心锰离子距离为0.331 6 nm,由酚氧原子和醋酸根共同桥联。另外,本文也利用伏安法和黏度法对该配合物与小牛胸腺DNA的结合能力进行研究,实验结果表明它们之间的结合方式为弱的插入作用。     

A new generation of visible-light-active photocatalysts—The alkaline earth metal bismuthates: Syntheses,compositions, structures,and properties

Semiconductor materials containing bismuth have attracted the attention of researchers over the past several decades, as a result of their high photocatalytic activity in various reactions and/or high efficiency in their photoelectric conversion of solar energy. This interest originated from the observations that bismuth-containing semiconductors have a sufficiently small bandgap, which makes them sensitive to radiation in the visible spectral range; thus, visible-light-active materials. Among the various bismuth-containing semiconductor materials, the bismuthates of alkaline earth metals are distinguished and describe into separate groups. This article reviews research on the known methods of obtaining bismuthates of various alkaline earth metals (magnesium, calcium, strontium, and barium), and further analyzes their composition, structure, and visible-light-active photocatalytic activity.     

A branch-and-bound method for the minimum k−enclosing ball problem

The minimum k-enclosing ball problem seeks the ball with smallest radius that contains at least k of m given points. This problem is NP-hard. We present a branch-and-bound algorithm on the tree of the subsets of k points to solve this problem. Our method is able to solve the problem exactly in a short amount of time for small and medium sized datasets.