Nature of the ring-closure process along the rearrangement of octa-1,3,5,7-tetraene to cycloocta-1,3,5-triene from the perspective of the electron localization function and catastrophe theory

We analyze the behavior of the energy profile of the ring‐closure process for the transformation of (3Z,5Z)‐octa‐1,3,5,7‐tetraene 5 to (1Z,3Z,5Z)‐cycloocta‐1,3,5‐triene 6 through a combination of electron localization function (ELF) and catastrophe theory (CT). From this analysis, concepts such as bond breaking/forming processes, formation/annihilation of lone pairs, and other electron pair rearrangements arise naturally through the reaction progress simply in terms of the different ways of pairing up the electrons. A relationship between the topology and the nature of the bond breaking/forming processes along this rearrangement is reported. The different domains of structural stability of the ELF occurring along the intrinsic reaction path have been identified. The reaction mechanism consists of six steps separated by fold and cusp catastrophes. The transition structure is observed in the third step, d(C1? C8) = 2.342 Å, where all bonds have topological signature of single bonds (C? C). The “new” C1? C8 single bond is not formed in transition state and respective catastrophe of the ELF field (cusp) is localized in the last step, d(C1? C8) ≈ 1.97 Å, where the two monosynaptic nonbonding basins V(C1) and V(C8) are joined into single disynaptic bonding basin V(C1,C8). The V(C1,C8) basin corresponds to classical picture of the C1? C8 bond in the Lewis formula. In cycloocta‐1,3,5‐triene 6 the single C1? C8 bond is characterized by relatively small basin population 1.72e, which is much smaller than other single bonds with 2.03 and 2.26e. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011     

Water PMF for predicting the properties of water molecules in protein binding site

Water is an important component in living systems and deserves better understanding in chemistry and biology. However, due to the difficulty of investigating the water functions in protein structures, it is usually ignored in computational modeling, especially in the field of computer‐aided drug design. Here, using the potential of mean forces (PMFs) approach, we constructed a water PMF (wPMF) based on 3946 non‐redundant high resolution crystal structures. The extracted wPMF potential was first used to investigate the structure pattern of water and analyze the residue hydrophilicity. Then, the relationship between wPMF score and the B factor value of crystal waters was studied. It was found that wPMF agrees well with some previously reported experimental observations. In addition, the wPMF score was also tested in parallel with 3D‐RISM to measure the ability of retrieving experimentally observed waters, and showed comparable performance but with much less computational cost. In the end, we proposed a grid‐based clustering scheme together with a distance weighted wPMF score to further extend wPMF to predict the potential hydration sites of protein structure. From the test, this approach can predict the hydration site at the accuracy about 80% when the calculated score lower than ?4.0. It also allows the assessment of whether or not a given water molecule should be targeted for displacement in ligand design. Overall, the wPMF presented here provides an optional solution to many water related computational modeling problems, some of which can be highly valuable as part of a rational drug design strategy. © 2012 Wiley Periodicals, Inc.     

Effect of metal cations [Li+, Na+, K+, Be2+, Mg2+, and Ca2+] on the structure of 2‐(3′‐hydroxy‐2′‐pyridyl)benzoxazole: A theoretical investigation

Density functional theory calculations were performed at the B3LYP/6‐311++G(d,p) level to systematically explore the geometrical multiplicity and binding strength for the complexes formed by alkaline and alkaline earth metal cations, viz. Li⁺, Na⁺, K⁺, Be²⁺, Mg²⁺, and Ca²⁺ (Mⁿ⁺, hereinafter), with 2‐(3′‐hydroxy‐2′‐pyridyl)benzoxazole. A total of 60 initial structures were designed and optimized, of which 51 optimized structures were found, which could be divided into two different types: monodentate complexes and bidentate complexes. In the cation‐heteroatom complex, bidentate binding is generally stronger than monodentate binding, and of which the bidentate binding with five‐membered ring structure has the strongest interaction. Energy decomposition revealed that the total binding energies mainly come from electrostatic interaction for alkaline metal ion complexes and orbital interaction energy for alkaline earth metal ion complex. In addition, the electron localization function analysis show that only the Be? O and Be? N bond are covalent character, and others are ionic character. © 2012 Wiley Periodicals, Inc.     

Experimental shift allowance in the deconvolution of SIMS depth profiles

We study the deconvolution of the secondary ion mass spectrometry (SIMS) depth profiles of silicon and gallium arsenide structures with doped thin layers. Special attention is paid to allowance for the instrumental shift of experimental SIMS depth profiles. This effect is taken into account by using Hofmann's mixing‐roughness‐information depth model to determine the depth resolution function. The ill‐posed inverse problem is solved in the Fourier space using the Tikhonov regularization method. The proposed deconvolution algorithm has been tested on various simulated and real structures. It is shown that the algorithm can improve the SIMS depth profiling relevancy and depth resolution. The implemented shift allowance method avoids significant systematic errors of determination of the near‐surface delta‐doped layer position. Copyright © 2013 John Wiley & Sons, Ltd.     

An analytical depth resolution function for the MRI model

The mixing roughness information depth model is frequently used for the quantification of sputter depth profiles. In general, the solution of the convolution integral for any kind of in‐depth distributions is achieved by numerical methods. For a thin delta layer, an analytical depth resolution function is presented, which enables a simple and user‐friendly quantification of measured delta layer profiles in AES, XPS and SIMS. Copyright © 2013 John Wiley & Sons, Ltd.     

Polymer chain diffusion in polymer blends: A theoretical interpretation based on a memory function formalism

The diffusion of polymer chains in miscible polymer blends with large dynamic asymmetry—those where the two blend components display very different segmental mobility—is not well understood yet. In the extreme case of the blend system of poly(ethylene oxide) (PEO) and poly(methyl methacrylate)(PMMA), the diffusion coefficient of PEO chains in the blend can change by more than five orders of magnitude while the segmental time scale hardly changes with respect to that of pure PEO. This behavior is not observed in blend systems with small or moderate dynamic asymmetry as, for instance, polyisoprene/poly(vinyl ethylene) blends. These two very different behaviors can be understood and quantitatively explained in a unified way in the framework of a memory function formalism, which takes into account the effect of the collective dynamics on the chain dynamics of a tagged chain. © 2019 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2019 , 57, 1239–1245     

Synthesis,Crystal Structure,and Selected Properties of [Au(S2CNH2)2]SCN: A Precursor for Gold Macro-Needles Consisting of Gold Nanoparticles Glued by Graphitic Carbon Nitride

A new preparation route is developed for the synthesis of needle-like crystals of [Au(S₂CNH₂)₂]SCN, which avoids disproportionation of the Au^I salt used as a starting material. In the crystal structure, the two crystallographically independent Au^III centers are in a square-planar environment of two S₂CNH₂ ligands. The Hirshfeld surface analysis reveals the presence of noncovalent intermolecular S⋅⋅⋅S interactions, which are essential for the spatial arrangement of the molecules. Density functional theory (DFT) calculations including dispersion and damping corrections result in a unit cell volume very close to the value determined experimentally. Thermal decomposition in an inert atmosphere generates black needles with lengths of up to 500 μm. X-ray powder diffraction and pair distribution function analyses demonstrate that the needles are composed of nanosized crystals with a volume-weighted average domain size of 20(1) nm. According to results of X-ray photoemission experiments, the black needles are covered by a nitrogen-rich carbon nitride with composition near (CN)₂N. ¹³C solid-state NMR investigations indicate that two different carbon species are present, with signals corresponding well to heptazine units as in melon and triazine units as in poly(triazin imide) type compounds. Scanning transmission electron microscopy tomography evidences that the needles are composed of slightly elongated nanoparticles.     

X-射线荧光分析散射幂函数法原理及其应用I·RhKα相干散射平方法

本文发现6~40号元素对能量为20keV的X_射线的质量吸收系数和质量相干散射系数之间呈二次幂函数关系,并据此提出了X_射线荧光定量分析校正基体效应的新方法——RhKa相干散射平方法.用国家标准物质GBW对该原理进行了验证.本法用于硅酸盐地质样品中微量元素的测定取得令人满意的结果.     

聚合物体系散射函数的热力学基础

利用链段浓度和链头浓度的概念，根据热力学涨落理论，给出了聚合物二元共混体系ｄｅＧｅｎｎｅｓ散射函数的一个普遍的热力学证明，指出了这个函数和Ｆｌｏｒｙ－Ｈｕｇｇｉｎｓ共混自由能公式一样，也依赖于忽略构象涨落的假设．