NKChemSQL——针对MySQL的化学信息学扩展

化学数据库是进行化学信息学研究的重要资源,分子属性与指纹计算、分子结构格式转换、分子相似度匹配、精确匹配和子结构匹配以及分子结构图片导出等,都是必需的基本服务内容。应用广泛的数据库系统MySQL却缺乏这些功能,难以满足化学信息处理、网站开发等开发的需求。NKChemSQL是自行编制的MySQL扩展库,通过对开源软件OpenBabel的功能进行包装,以SQL语言的格式完成相应操作。NKChemSQL具有良好的运行表现,经过对含26万余条分子结构信息的NCI数据库进行的测试,全结构匹配只需不到1秒而子结构匹配达300个结构/秒,相似度匹配则达1万个结构/秒。NKChemSQL为开发化学信息学软件和网站提供了非常便利的新方式。     

Feature Activated Molecular Dynamics: Parallelization and Application to Systems with Globally Varying Mechanical Fields

A recently developed hybrid molecular dynamics method (Feature Activated Molecular Dynamics, or FAMD), which was originally designed to extend the scope of certain types of molecular dynamics simulations, is extended here in two ways. First, the method is modified to execute on parallel computer architectures using the MPI communication interface. The parallel FAMD algorithm is demonstrated to be computationally efficient and to substantially increase the length scales accessible with molecular dynamics. The performance of the parallel algorithm is demonstrated using a crystalline system containing 1× 10⁶ atoms, in which 1000 supersaturated self-interstitials are introduced and allowed to aggregate for about 4 ns. In the second part of this paper, the FAMD method is applied to problems in which spatio-temporally varying stress fields are present throughout the simulation cell. In particular, we consider the evolution of a spherical void in a hydrostatically stressed silicon crystal and show that the method can capture the extremely rapid void cavitation dynamics following material failure. Once again, the FAMD approach is demonstrated to provide substantial computational advantages over standard molecular dynamics.     

纳米WO3材料的制备、应用及研究趋势

结合近年来国内外相关文献，综述了纳米WO3材料的研究现状与进展，重点概述了超细WO3粉体和纳米WO3薄膜的各种制备方法及各自优缺点，并介绍了纳米WO3薄膜的稀有金属掺杂研究等；分析了纳米WO3材料的研究意义，介绍了纳米WO3材料在变色及催化等方面的应用。最后分析了纳米WO3材料应用的发展趋势。     

海湾扇贝g型溶菌酶基因cDNA的克隆与分析

通过EST和锚定PCR技术,从海湾扇贝(Argopecten irradians)中克隆得到一种溶菌酶基因的全长cDNA(全长659bp,编码200个氨基酸)。BLASTx分析的结果显示,它和脊椎动物g型溶菌酶相似性较高,却不同于无脊椎动物中已发现的c型和i型溶菌酶。在其编码的氨基酸序列中发现了g型溶菌酶的活性中心(Glu82,Asp97,Asp108),同时6个保守的半胱氨酸也与鸟类和鱼类的g型溶菌酶相一致。结合BLASTX分析的结果,可以确认所获得的cDNA序列是一种在无脊椎动物中首次发现的g型溶菌酶的编码序列。采用Clustalw软件,对多种脊椎动物c型、g型溶菌酶和无脊椎动物c型、i型溶菌酶以及本研究发现的无脊椎动物g型溶菌酶进行了分析,结果发现,无脊椎动物c型、i型溶菌酶和脊椎动物c型溶菌酶同源性较高,而海湾扇贝g型溶菌酶和脊椎动物g型溶菌酶同源性较高。由此说明c型、g型溶菌酶从无脊椎到脊椎动物的进化是平行发生的,这对进一步研究溶菌酶及其分子进化具有重要意义。     

尖晶石相型LiM_(0.2)Mn_(1.8)O_4(M=Mg、Cd)相的晶格畸变与红外吸收峰频移

通过室温固相法制备了不同元素掺杂的前驱体,并采用分步煅烧法获得了尖晶石型LiMn2O4和LiM0.2Mn1.8O4(M=Mg、Cd)相。采用XRD和FTIR技术就元素掺杂对产物晶格畸变、Mn—O键长和键能强度等微观结构参数和光谱频移现象进行分析。结果表明,不同元素掺杂导致产物产生不同程度的晶格畸变。Mg元素掺杂使晶格收缩,Mn(Ⅳ)—O和Mn(Ⅲ)—O键收缩和键能强度增加,对应吸收峰发生蓝移;Cd元素掺杂使晶格膨胀,Mn(Ⅳ)—O和Mn(Ⅲ)—O键增长和键能强度降低,对应吸收峰发生红移。     

Effect of postmolding heat treatment on in vitro properties of a polyanhydride implant containing gentamicin sulfate

A polyanhydride implant containing gentamicin sulfate was fabricated using a laboratory-scale injection-molding machine. After injection molding, the implants were subject to heat treatment at 60°C for various time periods with or without nitrogen protection. The impact of this heat treatment on the in vitro properties of the implants including copolymer molecular weights, mechanical properties, and in vitro drug-release profiles was investigated. This heat treatment caused a drastic drop in the molecular weight of the copolymer. Heating without nitrogen protection resulted in the hardening of the implant, but heating in the presence of nitrogen rendered the implant less rigid. It was also found that a faster in vitro drug release profile was shown by implants heated without nitrogen protection and a pronounced slowing down in drug release was exhibited by implants heated with nitrogen protection.     

Fullerene材料的现状与发展趋势

富勒烯（Ｆｕｌｅｒｅｎｅ）和碳纳米管（ＣＮＴ）可能是本世纪末材料科学领域最重大的发现之一。进入９０年代以来，其制备方法、物化特性及可能的应用领域等成为人们的研究热点，并对材料物理、微电子、介观量子效应等众多科研领域产生了重大的冲击。根据目前进展，富勒烯／碳纳米管的应用研究很可能首先在ＣＮＴ缺陷研究、分子工具（Ｍｏｌｅｃｕｌａｒｔｏｏｌｓ）、纳米装置（Ｎａｎｏ－ｄｅｖｉｃｅ）应用和新一代贮能材料等方面取得突破。     

Crystallinity and electrical conductivity of sulfur-containing microcrystalline diamond thin film

Hydrogen sulfide (H₂S) was introduced into a microwave plasma chemical vapor deposition of microcrystalline diamond thin film. Secondary-ion mass spectroscopy showed that sulfur concentration was controlled from 2 × 10¹⁵ to 9 × 10¹⁷ cm^− 3 by controlling the H₂S/CH₄ ratio, while that of hydrogen concentration was around 5 × 10²⁰ cm^− 3 and was independent of the H₂S/CH₄ ratio. Electrical conductance increased linearly as the S concentration increased from 2 × 10¹⁵ to 3 × 10¹⁶ cm^− 3 without significant deterioration of film crystallinity, i.e., the amount of sp² phase did not increase. Non-ohmic conduction was converted to ohmic conduction when the S concentration reached 9 × 10¹⁷ cm^− 3 by increasing the H₂S/CH₄ ratio to 30,000 ppm. This modification was consistent to the formation of a graphitic phase by heavy S-doping, which was identified by Raman spectra and surface morphology.     

Nanobody Paratope Ensembles in Solution Characterized by MD Simulations and NMR

Variable domains of camelid antibodies (so-called nanobodies or V_HH) are the smallest antibody fragments that retain complete functionality and therapeutic potential. Understanding of the nanobody-binding interface has become a pre-requisite for rational antibody design and engineering. The nanobody-binding interface consists of up to three hypervariable loops, known as the CDR loops. Here, we structurally and dynamically characterize the conformational diversity of an anti-GFP-binding nanobody by using molecular dynamics simulations in combination with experimentally derived data from nuclear magnetic resonance (NMR) spectroscopy. The NMR data contain both structural and dynamic information resolved at various timescales, which allows an assessment of the quality of protein MD simulations. Thus, in this study, we compared the ensembles for the anti-GFP-binding nanobody obtained from MD simulations with results from NMR. We find excellent agreement of the NOE-derived distance maps obtained from NMR and MD simulations and observe similar conformational spaces for the simulations with and without NOE time-averaged restraints. We also compare the measured and calculated order parameters and find generally good agreement for the motions observed in the ps–ns timescale, in particular for the CDR3 loop. Understanding of the CDR3 loop dynamics is especially critical for nanobodies, as this loop is typically critical for antigen recognition.     

Photopharmacology of Antimitotic Agents

Antimitotic agents such as the clinically approved vinca alkaloids, taxanes and epothilone can arrest cell growth during interphase and are therefore among the most important drugs available for treating cancer. These agents suppress microtubule dynamics and thus interfere with intracellular transport, inhibit cell proliferation and promote cell death. Because these drugs target biological processes that are essential to all cells, they face an additional challenge when compared to most other drug classes. General toxicity can limit the applicable dose and therefore reduce therapeutic benefits. Photopharmacology aims to avoid these side-effects by introducing compounds that can be applied globally to cells in their inactive form, then be selectively induced to bioactivity in targeted cells or tissue during a defined time window. This review discusses photoswitchable analogues of antimitotic agents that have been developed by combining different photoswitchable motifs with microtubule-stabilizing or microtubule-destabilizing agents.