茂金属卡宾配合物{(eta~5-C_5H_5)MoX(CO)_2[C(CH_2)_2CH_2O]}(X:Cl、Br、I)的电子结构研究

运用G98W程序,采用Lanl2dz基组,对茂金属配合物{(eta~5-C_5H_5)MoX(CO)_2[C(CH_2)_2CH_2O]}(X:Cl、Br、I)进行从头算研究,探讨配合物结构单元的稳定性、分子轨道能量、原子净电荷布居规律,以及一些前沿分子轨道的组成特征等。结果表明,标题配合物结构在能量上是稳定的,因而能作为结构单元而存在。为茂金属配合物的合成、分子组装提供理论参考。     

论(Cl_2BN_3)_n(n=1-4)簇合物

用密度泛函论B3LYP/6-311+G*法,计算(C1_2BN_3)_n(n=1-4)簇合物的结构和性质.发现,多聚体(C1_2BN_3)_n(n=2-4)的优化构型原来是由不同子体系的叠氮基α-N和B原子相连而形成的环状结构。几何参数的比较分析还发现N_α-B、N_α-N_β、N_β-N_Υ和B-Cl的键长与聚合度密切相关,环状构型中B-N_α-B键角总比N_α-B-N_α大。同时计算所有优化构型的振动频率,将其IR谱归类.通过热力学计算,发现簇合物的稳定性为3A>3B;4A>4B.由焓变可知,从单体形成二聚体于热力学不利,而形成最稳定三聚体和四聚体的温度分别达800K和500K仍是有利的.     

1-环丙基-5-取代-7-(4-甲基哌嗪基）-6,8-二氟-1,4-二氢 -4-氧-3-喹啉羧酸的定量构效关系

通过量子化学AM1和Monte Carlo模拟计算,对1-环丙基-5-取代-7-(4-甲基哌嗪基）-6,8-二氟-1,4-二氢-4-氧-3-喹啉羧酸的定量构效关系进行了研究,结果显示5-位取代基的体积V、表面积S、与母核紧连原子的净电荷、指示变量等对抗菌活性有很大影响,回归得到了相关性好的方程：((4)R=0.9,(5)R=0.94),(6)R=0.95)。5-位小的取代基、4-位和5-位形成氢键对抗菌活性有利。计算表明5-为被甲基取代后具有更好的抑制金葡萄菌和绿脓杆菌的抗菌活性。     

Analysis of I/O Performance on an Amazon EC2 Cluster Compute and High I/O Platform

Cloud computing is currently being explored by the scientific community to assess its suitability for High Performance Computing (HPC) environments. In this novel paradigm, compute and storage resources, as well as applications, can be dynamically provisioned on a pay-per-use basis. This paper presents a thorough evaluation of the I/O storage subsystem using the Amazon EC2 Cluster Compute platform and the recent High I/O instance type, to determine its suitability for I/O-intensive applications. The evaluation has been carried out at different layers using representative benchmarks in order to evaluate the low-level cloud storage devices available in Amazon EC2, ephemeral disks and Elastic Block Store (EBS) volumes, both on local and distributed file systems. In addition, several I/O interfaces (POSIX, MPI-IO and HDF5) commonly used by scientific workloads have also been assessed. Furthermore, the scalability of a representative parallel I/O code has also been analyzed at the application level, taking into account both performance and cost metrics. The analysis of the experimental results has shown that available cloud storage devices can have different performance characteristics and usage constraints. Our comprehensive evaluation can help scientists to increase significantly (up to several times) the performance of I/O-intensive applications in Amazon EC2 cloud. An example of optimal configuration that can maximize I/O performance in this cloud is the use of a RAID 0 of 2 ephemeral disks, TCP with 9,000 bytes MTU, NFS async and MPI-IO on the High I/O instance type, which provides ephemeral disks backed by Solid State Drive (SSD) technology.     

还原型牛红细胞Cu(I)Zn-SOD的量化计算

运用G94W量子化学程序,在B3YIP/Lan12dz基组的水平上,对于还原型牛红细胞中CU(I)Zn-SOD活性中心进行了从头计算。研究了分子轨道能量,电荷分布,前线轨道的贡献。结果表明:前沿分子轨道能量均为负值,其电子光谱稳定,与金属配位的咪唑环电荷表现正负交替现象。在前线轨道贡献上Cu(I)的占有轨道贡献大,空轨道的贡献小,不易于接受O_O~-自由基的不成对电子。     

法尼基丙酮的合成方法及其结构的量子化学研究

以橙花叔醇和乙酰乙酸甲酯为原料,采用改良的Carroll反应制得法尼基丙酮。通过探讨合成过程中的各种因素对产品收率的影响,确定了合成标题化合物的最佳实验条件。用分子轨道理论中的AM1方法,通过能量梯度全优化计算,给出了标题化合物两种异构体的稳定几何构型、电子结构和生成热、偶极矩、前线分子轨道能级等分子的基本性质,联系有机电子结构理论进行了讨论。     

基于AM1量子化学方法的醇胺类缓蚀剂在模拟混凝土孔溶液中对钢筋缓蚀作用研究

用电化学极化曲线的方法评价了几种醇胺化合物在混凝土模拟孔溶液中对钢筋的缓蚀效果,用Gaussian03程序中的AM1方法计算了这几种醇胺化合物的量子化学参数,并采用最小二乘法,分别将它们的前线分子轨道能级、氮氧原子上的净电荷、分子偶极距以及热力学参数与相对缓蚀效率进行拟合.用所拟合的方程预测了这些醇胺的缓蚀效率,预测结果与实验结果基本相符.     

环氧酶/5-脂氧酶双重抑制剂的定量构效关系研究

目的:寻找COX/5-LO双重抑制剂的生物活性与化学结构之间的关系,为设计合成新型COX/5-LO双重抑制剂提供理论依据。方法:选择16个活性较强的COX/5-LO双重抑制剂,利用CNDO/2程序进行化合物的量子化学参数计算以及定量构效关系研究。结果:这些化合物对5-LO的抑制作用主要与LUMO和HOMO本征值之差以及分子偶极矩呈正相关;抑制COX作用主要与电子总能量呈负相关,与分子总能量和分子偶极矩呈正相关。结论:增加分子偶极矩,有可能同时增强COX/5-LO双重抑制作用,从而得到高效低毒的非甾体抗炎药。     

I-SOLV: a new surface-based empirical model for computing solvation free energies

We have developed a new empirical model, I-SOLV, for computing solvation free energies of neutral organic molecules. It computes the solvation free energy of a solute molecule by summing up the contributions from its component atoms. The contribution from a certain atom is determined by the solvent-accessible surface area as well as the surface tension of this atom. A total of 49 atom types are implemented in our model for classifying C, N, O, S, P, F, Cl, Br and I in common organic molecules. Their surface tensions are parameterized by using a data set of 532 neutral organic molecules with experimentally measured solvation free energies. A head-to-head comparison of our model with several other solvation models was performed on a test set of 82 molecules. Our model outperformed other solvation models, including widely used PB/SA and GB/SA models, with a mean unsigned error as low as 0.39 kcal/mol. Our study has demonstrated again that well-developed empirical solvation models are not necessarily less accurate than more sophisticated theoretical models. Empirical models may serve as appealing alternatives due to their simplicity and accuracy.     

碳原子簇Cn(n=2-20)的结构优化及构型转换

将并行快速退火演化算法结合Brenner势能函数用于小碳原子簇Cn(n=2—20)的结构优化，得到了最稳定构型：C2-C4为线型结构；C5-C17，为单环；C18和C19为类富勒烯的笼状结构；C30为最小的富勒烯。在Brenner势中使用了关于键级的修正项Fij以考虑成键轨道的非正常重叠和非、局域效应，研究了Fij项对碳原子簇键级以及结构转变产生的影响和原因，结果表明该修正项可以降低多环碳原子簇的键级，使得原子簇C18和C20的最稳定结构发生从多环到笼状的转变。     

二氧化碳水合物小晶穴和大晶穴的密度泛函研究

本文通过B3LYP方法,在6-31G(d,p)水平下对结构Ⅰ型二氧化碳水合物的十二面体小晶穴和十四面体大晶穴的结构进行优化,并计算了其振动频率.13C-NMR化学屏蔽常数及电子密度.结果表明,水合物晶穴的氢键键能强于水分子二聚体和冰晶格中的氢键键能.由此可以看出结构Ⅰ型二氧化碳水合物的晶穴是由氢键组成的稳定结构.通过CO2分子与大、小晶穴的范德华能比较,发现C02分子在大晶穴中更稳定.所计算出的C=O键的不对称伸缩振动频率和13C-NMR化学屏蔽常数与文献中的实验值基本一致.通过分析CO2与晶穴的电子密度,其结果与氢键键能计算结果一致,计算结果还表明,CO2在大晶穴中的稳定性较在小晶穴中的稳定性强.     

氧分子在镍钛合金(100)表面吸附行为的研究

NiTi形状记忆合金作为一种广泛使用的生物医学材料，表面形成的氧化膜是其具有良好生物相容性的基础。氧分子在NiTi合金表面的吸附是其形成氧化膜的关键，应用离散变分Xα方法，首次对O2分子在B2结构NiTi(100)表面的吸附过程进行了理论研究，分别计算了在两种不同的O2分子吸附方式中Ti-O原子间的键级和电荷分布。结果表明：O2分子垂直接近NiTi(100)表面对其发生吸附更为有利。在吸附过程中，O2分子中只有一个氧原子被其最近邻的一个表面铁原子所吸附，而合金中其它表面原子及体相原子的电子结构没有变化。Mulliken集居数及局域态密度分析表明，吸附过程中铁原子与氧原子之间的相互作用主要是由2p(O)电子和4s，4p(Ti)电子贡献。     

Theoretical study of aluminum arsenide clusters: equilibrium geometries and electronic structures of Al(n)As(n) (n=1-4)

The geometry, electronic configurations, harmonic vibrational frequencies and stability of the structural isomers of Al(n)As(n) clusters (n=1-4) have been investigated using density functional theory. For dimers and trimers, the lowest energy structures are planar cumulenic rings (IIs, VIs) with D(nh) symmetry. The caged structure with T(d) symmetry (IXs) lie lowest in energy among the tetramers. The AlAs bond dominates the structures for many isomers so that one preferred dissociation channel is loss of the AlAs monomer. The atomic charges, hybridization and chemical bonding in the different structures are also discussed. Comparisons with valence-isoelectronic Si(2n), Al(n)P(n) and Ga(n)As(n) clusters of same size, the properties of the aluminum arsenide clusters are analogous to those of their corresponding Al(n)P(n), Si(2n) counterparts. The results can explain the modification and refinement of Si phase in AlSi alloy in the molecular level.     

铁卟啉化合物与氧气分子形成的体系的密度泛函理论研究(英文)

采用密度泛函理论B3LYP方法在6-31G(d)基组水平下对氯化铁(+3)卟啉与氧气分子形成的体系进行了研究,得到了几何构型,电子性质及分子轨道结构等相关数据.对两个体系不同自旋状态下的几何构型参数和电子性质对比发现:受体系立体构型对称性的影响,在两个体系中凡是与卟啉环上N原子相关的几何参数及电子性质均呈现出相同规律性.又采用密度泛函理论UB3LYP/6-311G*//UB3LYP/6-31G*方法对这两个体系不同自旋状态下的能量进行了计算,分析表明自旋多重度越高体系越稳定.然后分别分析了两个体系在最稳定自旋状态下的分子轨道占据情况及中心Fe原子最外层3d轨道的电子分布情况,结果表明Fe原子的3d二和3dxz/3dyz与氧气分子的单占据反键轨道HOMO π*2px/π*2py之间存在相互作用,这种相互作用引起铁卟啉环与O2分子间的电子转移并使O2活化.然而,根据分析在通常状态下铁卟啉对O2分子的活化作用是微弱的.     

基于改进TLSER模型的定量结构-疏水性关系

针对理论线性溶剂化能关系模型中氢键碱度的描述进行了改进，应用于一类结构独特的多环七碳化合物及其衍生物的定量结构－疏水性关系的研究中，取得了较为满意的结果。     

(OsB)_n(n=1-6)团簇结构与稳定性的第一性原理研究

基于第一性原理,采用密度泛函理论(DFT)中的广义梯度近似(GGA)对(OsB)_n(n=1-6)团簇各种可能的构型进行了几何结构优化,得出了各团簇的最稳定构型,并对最稳定构型的能量、结合能、二阶能量差分、能隙等性质进行了理论研究。研究结果表明:n=2、3时,体系的基态结构分别为棱形和锅盖形;n=4时,体系的基态结构是对称性为T_d的立方体形状,是本文对称性最高的构型;从n=4开始立方体构型主导着团簇基态结构的生长行为,表明团簇的稳定性不仅与团簇的尺寸大小有关,还与团簇的对称性有关。团簇(OsB)_4的能隙、结合能与能量的二阶差分比邻近的值都大,说明团簇(OsB)_4有较高的稳定性,n=4是团簇的幻数。     

Computational alanine scanning and free energy decomposition for E. coli type I signal peptidase with lipopeptide inhibitor complex

A thorough investigation of different roles of Escherichia coli type I signal peptidase residues binding to lipopeptide inhibitor has been performed by a combination of computational alanine scanning mutagenesis and free energy decomposition methods. PB and GB models are both used to evaluate the binding free energy in computational alanine scanning method and only GB model can be used to decompose the binding free energy on a per-residue basis. The regression analysis between the PB and GB model and also between the computational alanine scanning and free energy decomposition have been reported with a correlation coefficient of 0.96 and 0.83, respectively, which suggest they are both in fair agreement with each other. Moreover, the contribution components from van der Waals, electrostatic interaction, non-polar and polar energy of solvation, have been determined as well as the effects of backbones and side-chains. The results indicate that Lys145 is the most important residue for the binding but also acts as a general base, activating Ser90 to increase its nucleophility, recognizing and stabilizing the binding of lipopeptide inhibitor to the E. coli SPase. The hydroxyl group of Ser88 plays a key role for the binding of the inhibitor. Ser90 contributes more to the intramolecular interaction than to the intermolecular interaction. Tyr143 and Phe84 contribute larger van der Waals interaction energies, indicating that these residues can be important for the selection based on the shape of the inhibitors. The contributions from other several interfacial residues of the E. coli SPase are also analyzed. This study can be a guide for the optimization of lipopeptide inhibitors and future design of new therapeutic agents for the treatment of bacterial infections.     

How to sort N items using a sorting network of fixed I/O size

Sorting networks of fixed I/O size p have been used, thus far, for sorting a set of p elements. Somewhat surprisingly, the important problem of using such a sorting network for sorting arbitrarily large datasets has not been addressed in the literature. Our main contribution is to propose a simple sorting architecture whose main feature is the pipelined use of a sorting network of fixed I/O size p to sort an arbitrarily large data set of N elements. A noteworthy feature of our design is that no extra data memory space is required, other than what is used for storing the input. As it turns out, our architecture is feasible for VLSI implementation and its time performance is virtually independent of the cost and depth of the underlying sorting network. Specifically, we show that by using our design N elements can be sorted in Θ(N/p log N/p) time without memory access conflicts. Finally, we show how to use an AT²-optimal sorting network of fixed I/O size p to construct a similar architecture that sorts N elements in Θ(N/p log N/p log p) time     

A model of checkpoint behavior for applications that have I/O

Due to the increase and complexity of computer systems, reducing the overhead of fault tolerance techniques has become important in recent years. One technique in fault tolerance is checkpointing, which saves a snapshot with the information that has been computed up to a specific moment, suspending the execution of the application, consuming I/O resources and network bandwidth. Characterizing the files that are generated when performing the checkpoint of a parallel application is useful to determine the resources consumed and their impact on the I/O system. It is also important to characterize the application that performs checkpoints, and one of these characteristics is whether the application does I/O. In this paper, we present a model of checkpoint behavior for parallel applications that performs I/O; this depends on the application and on other factors such as the number of processes, the mapping of processes and the type of I/O used. These characteristics will also influence scalability, the resources consumed and their impact on the IO system. Our model describes the behavior of the checkpoint size based on the characteristics of the system and the type (or model) of I/O used, such as the number I/O aggregator processes, the buffering size utilized by the two-phase I/O optimization technique and components of collective file I/O operations. The BT benchmark and FLASH I/O are analyzed under different configurations of aggregator processes and buffer size to explain our approach. The model can be useful when selecting what type of checkpoint configuration is more appropriate according to the applications’ characteristics and resources available. Thus, the user will be able to know how much storage space the checkpoint consumes and how much the application consumes, in order to establish policies that help improve the distribution of resources.

     

Metal (IV) tetras (8‐hydroxyquinoline) (M = Zr,Hf) used as electroluminescent material and electron‐transport layer in OLEDs

Abstract— In this paper, we report on the utilization of zirconium (IV) tetras (8‐hydroxyquinoline), Zrq₄, and hafnium (IV) tetras (8‐hydroxyquinoline), Hfq₄, as an electroluminescent material in fluorescent organic light‐emitting diodes (OLED) and as electron transport layer (ETL) for high‐efficiency electrophosphorescent organic light‐emitting diodes (PHOLEDs). Structural studies show that the metal tetraquinolates (Mq₄) have a very low dipole moment (<0.1 D), in contrast to Alq₃ which has an estimated dipole moment of 4.7 D. Mobility measurements show that Mq₄ complexes give mobilities of (3.5 ± 0.5) × 10^?6 cm²/V‐sec, which are close to the values reported for Alq₃, i.e., (2.3–4.3) × 10^?6 cm²/V‐sec. OLEDs were prepared with the structure ITO/NPD (400 Å)/Mq_n (500 Å)/LiF/Al (NPD = 4‐4′‐bis[N‐(1‐naphthyl)‐N‐phenyl‐amino]bi phenyl, Mq_n = Alq₃, Zrq₄, Hfq₄. The Mq₄‐based OLEDs gave external efficiencies of 1.1%, while the Alq₃‐based devices of the same structure gave efficiencies of 0.7%. PHOLEDs have been fabricated with the structure ITO/NPD (500 Å)/CBP‐8% Ir(ppy)³ (250 Å)/BCP (150 Å)/Mq_n (250 Å)/LiF/Al (CBP = N,N′‐dicarbazolyl‐4‐4′‐biphenyl, Ir(ppy)³ = fac‐tris(2‐phenylpyrridine)iridium, BCP = bathocruprione). PHOLEDs with Mq₄ ETLs showed a greatly improved efficiency, when compared to Alq₃‐based PHOLEDs. The Zrq₄‐based PHOLEDs gave a peak external quantum efficiency of 14% at 0.3 mA/cm² (150 cd/m²), while the Hfq₄ based PHOLED gave a peak external quantum efficiency of 15% at 0.6 mA/cm² (300 cd/m²). Comparable PHOLEDs with an Alq₃ ETL give peak external quantum efficiencies of 8.0% at 0.5 mA/cm². The devices gave an electroluminescence (EL) spectrum consisting only of fac‐tris(2‐phenylpyrridine)iridium (Ir(ppy)³) dopant emission (CIE coordinates of 0.26, 0.66), with no Mq₄ emission observed at any bias level.