分子逻辑器件研究进展

分子器件具有尺寸小、设计合成可控、存储量大、反应速度快、人工智能等诸多优点,是当今化学、物理和材料等领域研究最为重要的一个交叉领域.综述了近些年来分子逻辑器件领域的研究进展.介绍了各种类型的分子逻辑门、半(加)减法器、分子逻辑线路以及DNA分子和固态分子计算.最后提出了分子器件存在的问题并展望了其应用前景.     

A fast parallel clustering algorithm for molecular simulation trajectories

We implemented a GPU‐powered parallel k‐centers algorithm to perform clustering on the conformations of molecular dynamics (MD) simulations. The algorithm is up to two orders of magnitude faster than the CPU implementation. We tested our algorithm on four protein MD simulation datasets ranging from the small Alanine Dipeptide to a 370‐residue Maltose Binding Protein (MBP). It is capable of grouping 250,000 conformations of the MBP into 4000 clusters within 40 seconds. To achieve this, we effectively parallelized the code on the GPU and utilize the triangle inequality of metric spaces. Furthermore, the algorithm's running time is linear with respect to the number of cluster centers. In addition, we found the triangle inequality to be less effective in higher dimensions and provide a mathematical rationale. Finally, using Alanine Dipeptide as an example, we show a strong correlation between cluster populations resulting from the k‐centers algorithm and the underlying density. © 2012 Wiley Periodicals, Inc.     

生物分子计算进展*

由于生物分子在化学反应中具有高度的并行性和识别能力,使生物分子计算在解决组合优化问题中显示出巨大的优势。生物分子计算已成功地应用于计算哈密顿路径、最大集合以及逻辑运算中的SAT类问题等NP完全问题。本文总结了生物分子计算的基本思想与计算方法、生物分子计算的应用与进展,并对生物分子计算的发展趋势作了评述。     

Temperature Development of Homo- and Hetero-Clustering in Saturated Vapors

Computational findings of temperature increase of clustering degree in saturated vapors are analyzed. A thermodynamic proof is presented and a simple criterion derived. Illustrations are based on saturated steam, magnesium and carbon vapor. The results are applicable to synthesis of fullerenes, metallofullerenes, and heterofullerenes, chemical vapor deposition technique, or atmospheric chemistry.     

Cobalt-thioalkylazoimidazole complexes: Structures, spectra and redox properties

1-Alkyl-2-{(o-thioalkyl)phenylazo}imidazole (SRaaiNR^/, 1) reacts with Co(ClO₄)₂·6H₂O to form [Co(SRaaiNR^/)₂](ClO₄)₂ (2). The single crystal X-ray structure of one of the complexes of 2 shows a tridentate chelation N(imidazole), N(azo), S(thioether) system. In the structure one of ClO₄⁻ anions shows disorder and forms an (imidazole)C–H···O(ClO₃) interaction leading to a 1-D chain. Co(OAc)₂.4H₂O and SRaaiNR^/ react in the presence of NH₄SCN (1:1:2 mole ratio) in methanol and the complex [Co(SRaaiNR^/)₂(SCN)₂] (3) has been separated. The single crystal X-ray structure determination has established the structure of the complexes in which the ligand SRaaiNR^/ acts in a bidentate N(imidazole), N(azo) chelation mode. A cyclic voltammogram shows a Co(III)/Co(II) oxidative response at 0.6–0.8 V and azo reductions. DFT computation using optimized geometry support the electronic spectral and redox properties of the complexes.     

将密度泛函理论计算纳入高等化学教学初探——对乙酸乙酯碱性水解机理的理论研究

使用Gaussian 09软件对乙酸乙酯碱性水解反应的机理进行了研究。本研究融合了本科教学中有机化学、物理化学和结构化学的相关知识,以乙酸乙酯水解机理为问题导向,阐述了研究和解决问题的思路和方法,探索了将第一性原理计算引入高等教育的方式。     

距离边数矢量与分子相似度的计算

化学环境编码算法;分子相似度计算;距离边数矢量与分子相似度的计算     

LiNbO_3晶体中Pr~(3+)离子的配位场能级计算

在C3v点群对称场中,运用双层点电荷配位场(DSCPCF)模型计算了LiNbO3晶体中Pr3+离子的40个配位场能级,与实验值相比,其均方根偏差为19.94 cm-1,优于文献值(44.22 cm-1).所得晶体场参数也明显好于文献值,说明双层点电荷模型能更好地拟合实验结果,对于研究C3v对称场中稀土离子的光谱特性具有非常重要的意义.     

Basis Sets Dependency in Constructing Spectroscopy-Accuracy Ab Initio Global Electric Dipole Moment Functions

Recently, more attention have been paid on the construction of dipole moment functions (DMF) using theoretical methods. However, the computational methods to construct DMFs are not validated as much as those for potential energy surfaces do. In this letter, using Ar...He as an example, we tested how spectroscopyaccuracy DMFs can be constructed using ab initio methods. We especially focused on the basis set dependency in this scenario, i.e., the convergence of DMF with the sizes of basis sets, basis set superposition error, and mid-bond functions. We also tested the explicitly correlated method, which converges with smaller basis sets than the conventional methods do. This work can serve as a pictorial sample of all these computational technologies behaving in the context of constructing DMFs.     

基于甲酸和氢氧化钠的衍生移动反应界面的数值计算与实验验证(英文)

在甲酸（α相）和氢氧化钠（γ相）缓冲液形成的移动反应界面的基础上,提出了一种衍生移动反应界面模型。模型表明在α相和γ相之间会形成一个新的β相,β相和α相形成衍生移动反应界面,β相和γ相形成移动界面。为了验证该模型的有效性,该文给出了相关理论及数值推导过程。此外,基于毛细管电泳和自制装置进行了相关实验。结果表明,若使用以前的移动反应界面,实验结果与理论计算存在较大误差,而采用该文提出的衍生移动反应界面,实验数据与理论计算结果高度一致。该文提出的衍生移动反应界面理论及模型对于电泳,特别是毛细管电泳中样品的分离与富集具有重要的意义。