Effect of nematic ordering on the elasticity and yielding in disordered polymeric solids

The relation between elasticity and yielding is investigated in a model polymer solid by Molecular‐Dynamics simulations. By changing the bending stiffness of the chain and the bond length, semicrystalline and disordered glassy polymers — both with bond disorder — as well as nematic glassy polymers with bond ordering are obtained. It is found that in systems with bond disorder the ratio τ_Y/G between the shear yield strength τ_Y and the shear modulus G is close to the universal value of the atomic metallic glasses. The increase of the local nematic order in glasses leads to the increase of the shear modulus and the decrease of the shear yield strength, as observed in experiments on nematic thermosets. A tentative explanation of the subsequent reduction of the ratio τ_Y/G in terms of the distributions of the per‐monomer stress is offered. © 2017 Wiley Periodicals, Inc. J. Polym. Sci. Part B: Polym. Phys. 2017 , 55, 1760–1769     

Organometallic Molecular Wires with Thioacetylene Backbones,trans-{RS-(C≡C)n}2Ru(phosphine)4: High Conductance through Non-Aromatic Bridging Linkers

In this work, the design, synthesis, and single-molecule conductance of ethynyl- and butadiynyl-ruthenium molecular wires with thioether anchor groups [RS=n-C₆H₁₃S, p-tert-Bu−C₆H₄S), trans-{RS−(C≡C)_n}₂Ru(dppe)₂ (n=1 ( 1^R ), 2 ( 2^R ); dppe: 1,2-bis(diphenylphosphino)ethane) and trans-(n-C₆H₁₃S−C≡C)₂Ru{P(OMe)₃}₄ 3^hex ] are reported. Scanning tunneling microscope break-junction study has revealed conductance of the organometallic molecular wires with the thioacetylene backbones higher than that of the related organometallic wires having arylethynylruthenium linkages with the sulfur anchor groups, trans-{p-MeS−C₆H₄-(C≡C)_n}₂Ru(phosphine)₄ 4 ⁿ (n=1, 2) and trans-(Th−C≡C)₂Ru(phosphine)₄ 5 (Th=3-thienyl). It should be noted that the molecular junctions constructed from the butadiynyl wire 2^R , trans-{ Au −RS−(C≡C)₂}₂Ru(dppe)₂ ( Au : gold metal electrode), show conductance comparable to that of the covalently linked polyynyl wire with the similar molecular length, trans-{ Au −(C≡C)₃}₂Ru(dppe)₂ 6³ . The DFT non-equilibrium Green's function (NEGF) study supports the highly conducting nature of the thioacetylene molecular wires through HOMO orbitals.     

Synthesis,characterization, density functional theory,X‐ray study,thermal stability,and biological and MOE relevance of metal complexes of griseofulvin

Metal(II) and metal(III) coordination compounds of griseofulvin (GFV) drug were synthesized. The structure of the ligand was determined on the basis of elemental analyses, infrared and ¹H NMR spectroscopies and thermal studies. GFV behaved as a neutral tridentate chelating agent and coordinated to metal ions through three oxygen atoms: two methoxy groups and oxygen atom of furan ring. Metal complexes were characterized by means of elemental analyses and molar conductance, spectral (infrared, electron spin resonance) and thermal studies. All the complexes showed molar conductance behaviour corresponding to an electrolytic nature. All the complexes showed octahedral geometry, except [Zn(GFV)Cl]Cl that showed tetrahedral geometry. Density functional theory (DFT) calculations were employed to understand and estimate the contribution of each interaction in the formation of the assembly using several theoretical models. The computed parameters from DFT calculations for structure optimizations and vibrational frequencies were in good agreement with the experimental data. Newly synthesized metal complexes in addition to GFV were examined against opportunistic pathogens. The biological applications of complexes were studied with two Gram‐positive bacteria (Bacillus subtilis and Staphylococcus aureus) and two Gram‐negative bacteria (Escherichia coli and Neisseria gonorrhoeae) as well as their antifungal activity against Candida albicans. Results suggested that metal complexes were more biologically sensitive than free ligand. The complexes showed a moderate inhibition of MCF7 breast cancer cell line growth. Molecular docking studies further helped in understanding the mode of action of the compounds through their various interactions with the crystal structures of: human serum albumin (PDB: 5FUO), Staphylococcus aureus nucleoside (PDB: 3Q8U), human acetylcholinesterase (PDB: 1B41) and the human DNA–Topo I complex (PDB: 1SC7).     

基于酸度诱导的HSA与BDE154的光谱和计算模拟研究

在不同酸度条件下（pH＝3.0，6.0，7.4，9.0）诱导人血清白蛋白（HSA）进行质子化或去质子化，以研究其与小分子2，2'，4，4'，5，6'-六溴联苯醚（BDE154）的结合情况.首先将HSA与BDE154进行半柔性对接，发现BDE154与HSA周围的残基，如：酪氨酸150、赖氨酸195、赖氨酸199等存在较强的疏水相互作用.然后通过分子动力学模拟技术研究HSA在不同质子化状态下的动力学行为和热力学性质，可知过多的正电荷使HSA或者HSA-BDE154的系统稳定性变差.最后对HSA-BDE154的结合自由能进行预测，并对分子动力学模拟结果进行二级结构分析，结果表明HSA-BDE154复合物体系中随着酸度的增大，配体的结合对HSA的去螺旋过程有促进的作用.     

鲍曼不动杆菌LpxC的同源模建及分子对接

鲍曼不动杆菌已成为最普遍的医院致病菌,且耐药情况严峻.LpxC作为新抗菌药物靶点被大量研究,但鲍曼不动杆菌LpxC晶体尚未解析得到,基于其结构的药物设计等工作无法开展.以铜绿假单胞菌LpxC晶体结构为模板,通过同源模建方法获得鲍曼不动杆菌LpxC结构模型.较好的Ramachandran plot分布和Profile-3D结果验证了模型的合理性.用分子动力学模拟优化鲍曼不动杆菌LpxC模型,修补部分不合理构象.后续分子对接结果显示S构型的苄氧乙酰基羟肟酸类抑制剂比R构型分子能更有效地结合在F191,H237和K238组成的较浅口袋中,这可能是S构型抑制剂活性更高的主要因素,模拟结果与实验数据吻合较好.     

Rhorix: An interface between quantum chemical topology and the 3D graphics program blender

Chemical research is assisted by the creation of visual representations that map concepts (such as atoms and bonds) to 3D objects. These concepts are rooted in chemical theory that predates routine solution of the Schrödinger equation for systems of interesting size. The method of Quantum Chemical Topology (QCT) provides an alternative, parameter‐free means to understand chemical phenomena directly from quantum mechanical principles. Representation of the topological elements of QCT has lagged behind the best tools available. Here, we describe a general abstraction (and corresponding file format) that permits the definition of mappings between topological objects and their 3D representations. Possible mappings are discussed and a canonical example is suggested, which has been implemented as a Python “Add‐On” named Rhorix for the state‐of‐the‐art 3D modeling program Blender. This allows chemists to use modern drawing tools and artists to access QCT data in a familiar context. A number of examples are discussed. © 2017 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.