Molecular dynamics on a distributed-memory multiprocessor

Dynamics simulations of molecular systems are notoriously computationally intensive. Using parallel computers for these simulations is important for reducing their turnaround time. In this article we describe a parallelization of the simulation program CHARMM for the Intel iPSC/860, a distributed memory multiprocessor. In the parallelization, the computational work is partitioned among the processors for core calculations including the calculation of forces, the integration of equations of motion, the correction of atomic coordinates by constraint, and the generation and update of data structures used to compute nonbonded interactions. Processors coordinate their activity using synchronous communication to exchange data values. Key data structures used are partitioned among the processors in nearly equal pieces, reducing the memory requirement per node and making it possible to simulate larger molecular systems. We examine the effectiveness of the parallelization in the context of a case study of a realistic molecular system. While effective speedup was achieved for many of the dynamics calculations, other calculations fared less well due to growing communication costs for exchanging data among processors. The strategies we used are applicable to parallelization of similar molecular mechanics and dynamics programs for distributed memory multiprocessors. © 1992 by John Wiley & Sons, Inc.     

Fluorescence immunoassay of alpha-fetoprotein with iron(III) tetrasulfonatophthalocyanine as a mimetic enzyme labeling reagent

A new fluorimetric immunoassay for alpha-fetoprotein (AFP) has been developed using a novel promising mimetic peroxidase, iron(III) tetrasulfonatophthalocyanine (FeTSPc), as a labeling reagent to catalyze the fluorescence reaction of P- hydroxyphenylacetic acid (P-HPA) and hydrogen peroxide (H2O2). In the competitive immunoassay, anti-AFP antibody was coated on a 96-well plate (polystyrene) and a constant amount of FeTSPc-labeled AFP and a known amount of test solution were added. Non-labeled and FeTSPc-labeled AFP compete for binding to the plate-bound antibody. After the immunoreaction, the immunochemically adsorbed FeTSPc-AFP conjugate moiety was determined by measuring the fluorescence produced in a solution containing P-HPA and H2O2. AFP can be determined in the concentration range of 1-300 ng mL(-1) with a detection limit of 0.5 ng mL(-1).     

Systems-based design of bi-ligand inhibitors of oxidoreductases: filling the chemical proteomic toolbox

Genomics-driven growth in the number of enzymes of unknown function has created a need for better strategies to characterize them. Since enzyme inhibitors have traditionally served this purpose, we present here an efficient systems-based inhibitor design strategy, enabled by bioinformatic and NMR structural developments. First, we parse the oxidoreductase gene family into structural subfamilies termed pharmacofamilies, which share pharmacophore features in their cofactor binding sites. Then we identify a ligand for this site and use NMR-based binding site mapping (NMR SOLVE) to determine where to extend a combinatorial library, such that diversity elements are directed into the adjacent substrate site. The cofactor mimic is reused in the library in a manner that parallels the reuse of cofactor domains in the oxidoreductase gene family. A library designed in this manner yielded specific inhibitors for multiple oxidoreductases.     

Characterization of cyclodextrin-modified infrared chemical sensors: Part I. Modeling the mechanisms of interaction

To explore the properties of cyclodextrins (CDs) as an optical sensing phase, the behavior of immobilized CD in interaction with analytes was studied in this work. CDs having different cavity sizes were immobilized onto the surface of infrared (IR) internal reflection-sensing element (IRE) to kinetically monitor the behavior of CD in interaction with analytes. Several aromatic compounds having various molecular sizes and functional groups were used to characterize the interaction mechanism. A two-layer modification method was proposed in this work, which utilized a thin hydrophobic film (polyvinyl benzyl chloride) to stick on the IRE and to covalently bond to the CDs through an ethylene diamine linker. The synthesized CD phases exhibited high stability in aqueous solution. To analyze the behavior during the formation of complexes between the guest molecules and the CD phases, we modeled the interaction behavior and treated the kinetic data with the theoretical equations developed in this work. The results indicate that the behavior of the interaction between guest molecules and CDs was explained by considering the formation of two types of complexes: adsorbed complexes and inclusion complexes. The formation of the inclusion complexes was relatively fast, the time required to reach equilibrium could be shorter than a few minutes. The adsorbed complexes were also observed, but their rate of formation was relatively slow; equilibrium could be reached at times greater than 60 min. Based on the signals observed under equilibrium conditions, the concentration of inclusion complexes was approximately three times than that of the adsorbed complexes.     

非水溶剂中铁酞菁的“in—situ”可见紫外光谱电化学

用循环伏安与现场可见紫外光谱电化学方法研究了氯化４－特丁基苯氧基铁酞菁［（ＴｂＰｃ）Ｆｅ（Ⅲ）Ｃｌ］电化学行为．结果表明，在四氢呋喃溶剂中其正电位区经历了两步氧化过程，对应于Ｆｅ（Ⅲ）／Ｆｅ（Ⅳ）以及Ｆｅ（Ⅳ）／阳离子自由基的生成反应，负电位区还原过程经历了Ｆｅ（Ⅲ）／Ｆｅ（Ⅱ），Ｆｅ（Ⅱ）／Ｆｅ（Ⅰ）和Ｆｅ（Ⅰ）／阴离子自由基生成的３个步骤，阐述了配位效应对氧化还原机理的影响．指出Ｆｅ（Ⅳ）不寻常价态的出现，是阴离子Ｃｌ－的轴向配位对超常价态起到稳定作用的结果．     

8－羟基喹啉纤维微柱分离富集ICP－AES测定多种痕量元素

制备了８－羟基喹啉纤维滤纸片，作为微柱填充物，同时富集了九种痕量元素，并分离了样品中的高盐组分。富集后的痕量组分采用电感耦合等离子体原子发射光谱法（ＩＣＰ－ＡＥＳ）测定，回收率为９０％～１０２％。     

Two new C18-norditerpenoid alkaloids from Aconitum delavayi

Further phytochemical investigation of the unique C18-norditerpenoid alkaloids from the roots of Aconitum delavayi Franch ledto the isolation of two new norditerpenoid alkaloids,delavaconitine F 1 and delavaconitine G 2.Their structures were determinedfrom spectroscopic evidence.     

Zeolite NaY-mediated oxidation of dyes with H2O2: unique heterogeneous non-transition metal center cleavage of H2O2 under visible light irradiation

This study investigated the visible-light catalysis mediated by zeolite NaY on the oxidation of dyes with H₂O₂. The results demonstrated that zeolite NaY acts as a sink for the electron from the photo-excited dye in the heterogeneous catalysis. Furthermore, the electron can effectively activate H₂O₂ to produce ^·OH radical that is a powerful oxidant for the oxidation of dye at room temperature. The effects of the framework topology, Si/Al ratio, and exchangeable cation of the zeolite on the oxidation of various dyes were also shown.     

Voltammetry and electrocatalytic properties of cobalt (1,4,8,12-tetraazacyclopentadecane) in aqueous solution

Summary The spectrochemical, electrochemical and electrocatalytic properties of Co[15]aneN₄ ([15]aneN₄ = 1,4,8,12-tetraazacyclopentadecane) have been investigated. The results show that, in aqueous solution, this compound mainly exists as three species whose axial coordination positions are occupied by water and/or hydroxy ligands; it is marginal whether other substrates such as Cl^– and NO _inf3 ^sup– interact with the central ion in acid-base solutions. The approximate Pourbaix diagram of Co^III/II[15]ane N₄ was determined. There is an electrochemically-induced isomerization between two trans conformational isomers of the Co[15]aneN₄ complexes in acid and netural solutions. The Co[15]aneN₄ complex has electrocatalytic properties for reduction of nitrate and nitrite only in strong alkaline solution.     

酵母核糖核酸在碳纳米管修饰电极上的电化学行为及其分析测定

研究了酵母核糖核酸（yRNA）在碳纳米管（MWNT）修饰电极上的电化学行为，优化了测定参数，在此基础上建立了一种直接测定yRNA的电分析测试方法。yRNA在碳纳米管修饰电极上于磷酸盐缓冲溶液中在0．758V处产生不可逆的氧化电流峰，峰电流与yRNA的质量浓度在1～10mg／mL之间有良好的线性关系，线性回归方程为：Iρ=0．0813ρ＋0．1807，相关系数r为0．9980，检出限为0．6mg／mL。