A multireference configuration interaction method based on the separated electron pair wave functions

A multireference configurational interaction method based on the separated electron pair (SEP) wave functions, SEP‐CI approach, has been developed as an approximation to the traditional CASSCF method. It differs from the CASSCF method in that active orbitals are obtained from the SEP wave function without further optimization in the subsequent CI calculations, and the active space is automatically constructed according to the occupation coefficients of SEP natural orbitals. These features make the present SEP‐CI method computationally much less demanding than the CASSCF method. The applicability of the SEP‐CI method is illustrated with sample calculations on the insertion reaction of BeH₂ and dissociation energies of LiH, BH, FH, H₂O, and N₂. © 2005 Wiley Periodicals, Inc. J Comput Chem 27: 39–47, 2006     

ClF-分子离子的结构与势能函数

采用单、双取代包括三重激发的二次组态相互作用[QCISD(T)]方法和单、双取代包括非迭代三重激发的耦合簇理论[CCSD(T)]方法, 结合相关一致基组aug-cc-pVXZ (X=D, T, Q, 5)对基态³⁵ClF^-和³⁷ClF^- (X²Σ⁺)分子离子进行了结构优化计算. 对CCSD(T)方法的计算结果用四种方法分别外推至基组极限, 得到了体系在基组极限的平衡结构常数. 在CCSD(T)/aug-cc-pVXZ (X=D, T, Q, 5)理论水平进行了单点能扫描. 对扫描计算结果进行基组外推并用Murrell-Sorbie 势能函数拟合得到了体系的解析势能函数表达式, 并进一步得到了³⁵ClF^-和³⁷ClF^-的光谱常数. 拟合所得势能曲线准确地再现了其离解能和平衡结构特征. 对ClF 中性自由基采用完全相同的理论方法进行了计算. 所得结果与有关文献中的实验结果符合得很好, 而且在一定程度上证明了将该理论方法应用于ClF^-分子离子的计算是合适而可靠的. ClF 自由基的优化计算结果还被用于计算其电子亲和能.ClF^-的垂直解离能也同时计算得出. 基于ClF^-的结构优化和单点能扫描计算结果, 通过求解核运动的径向薛定谔方程, 得到了无转动³⁵ClF^-和³⁷ClF^-(X²Σ⁺)的全部振动态及相应的分子常数.     

Increasing the accuracy of mass isotopomer analysis through calibration curves constructed using biologically synthesized compounds

Mass isotopomer analysis is an important technique to measure the production and flow of metabolites in living cells, tissues, and organisms. This technique depends on accurate quantifications of different mass isotopomers using mass spectrometry. Constructing calibration curves using standard samples is the most universal approach to convert raw mass spectrometry measurements into quantitative distributions of mass isotopomers. Calibration curve approach has been, however, of very limited use in comprehensive analyses of biological systems, mainly suffering from the lack of extensive range of standard samples with accurately known isotopic enrichment. Here, we present a biological method capable of synthesizing specifically labeled amino acids. These amino acids have well‐determined and estimable mass isotopomer distributions and thus can serve as standard samples. In this method, the bacterium strain Methylobacterium salsuginis sp. nov. was cultivated with partially ¹³C‐labeled methanol as the only carbon source to produce ¹³C‐enriched compounds. We show that the mass isotopomer distributions of the various biosynthesized amino acids are well determined and can be reasonably estimated based on proposed binomial approximation if the labeling state of the biomass reached an isotopic steady state. The interference of intramolecular inhomogeneity of ¹³C isotope abundances caused by biological isotope fractionation was eliminated by estimating average ¹³C isotope abundance. Further, the predictions are tested experimentally by mass spectrometry (MS) spectra of the labeled glycine, alanine, and aspartic acid. Most of the error in mass spectrometry measurements was less than 0.74 mol% in the test case, significantly reduced as compared with uncalibrated results, and this error is expected to be less than 0.4 mol% in real experiment as revealed by theoretical analysis. Copyright © 2009 John Wiley & Sons, Ltd.     

Real Time Electrochemical Monitoring of DNA/PNA Dissociation by Melting Curve Analysis

An immobilization‐free electrochemical method is reported for real‐time monitoring of the DNA hybrid dissociation between a ferrocene labeled peptide nucleic acid (PNA) and a fully‐complementary or single‐base‐mismatched DNA. This method takes advantages of electrostatic charge characteristics and interactions among the neutrally charged PNA, the negatively charged DNA and the negatively charged electrode surface made of indium tin oxide (ITO). When a ferrocene labeled PNA (Fc‐PNA) sequence is hybridized to a complementary DNA strand, electrostatic repulsion between the negatively charged PNA/DNA hybrid and the negative ITO surface retards the diffusion of the electroactive Fc to the electrode, resulting in a much reduced electrochemical signal. On the other hand, when the Fc‐PNA is dissociated from the hybrid at elevated temperatures, the neutrally charged Fc‐PNA easily diffuses to the electrode with an enhanced electrochemical signal. Therefore, an electrochemical melting curve of the Fc‐PNA/DNA hybrid can be obtained by measuring the Fc signal with the increasing temperature. This strategy allows monitoring of the dissociation of the DNA hybrid in real time, which might lead to a simple detection method for single nucleotide polymorphism (SNP) analysis.     

Second-order advantage from kinetic-spectroscopic data matrices in the presence of extreme spectral overlapping A multivariate curve resolution--alternating least-squares approach

Multivariate curve resolution coupled to alternating least-squares (MCR-ALS) has been employed to model kinetic-spectroscopic second-order data, with focus on the achievement of the important second-order advantage, under conditions of extreme spectral overlapping among sample components. A series of simulated examples shows that MCR-ALS can conveniently handle the studied analytical problem unlike other second-order multivariate calibration algorithms, provided matrix augmentation is implemented in the spectral mode instead of in the usual kinetic mode. The approach has also been applied to three experimental examples, which involve the determination of: (1) the antiparkinsonian carbidopa (analyte) in the presence of levodopa as a potential interferent, both reacting with cerium (IV) to produce the fluorescent species cerium (III) with different kinetics; (2) Fe(II) (analyte) in the presence of the interferent Zn(II), both catalyzing the oxidation of methyl orange with potassium bromate; and (3) tartrazine (analyte) in the presence of the interferent brilliant blue, both oxidized with potassium bromate, with the interferent leading to a product with an absorption spectrum very similar to tartrazine. The results indicate good analytical performance towards the analytes, despite the intense spectral overlapping and the presence of unexpected constituents in the test samples.     

新型微填充柱－毛细管柱二维色谱系统过程的动力学研究

从色谱动力学角度对新型微填充柱－毛细管柱二维色谱系统过程中双柱条件与流出曲线及柱效之间的依赖关系加以系统研究。结果表明：由于双柱条件之间存在关联，双柱系统流出曲线特征与单柱系统存在一定的差异，流出曲线一阶矩和二、三阶中心矩以及双柱系统的柱效皆由预柱和主柱条件综合确定。     

RECENT PROGRESS OF NANO-MECHANICAL MAPPING

 Nano-mechanical mapping by atomic force microscopy has been developed as an useful application to measure mechanical properties of soft materials at nanometer scale. To date, the Hertzian theory was used for analyzing force-distance curves as the simplest model among several contact mechanics between elastic bodies. However, the preexisting methods based on this theory do not consider the adhesive interaction in principle, which cannot be neglected in the ambient condition. A new analytical method was introduced to estimate the elasticity and the adhesive energy simultaneously by means of the JKR theory, describing adhesive contact between elastic materials. Poly(dimethylsiloxane) (PDMS) and isobutylene-co-isoprene rubber (IIR) were analyzed to verify the applicable limit of the JKR analysis. For elastic samples such as PDMS, the force-deformation plots obtained experimentally were consistent with JKR theoretical curves. Meanwhile, for viscoelastic samples, especially for IIR, the experimental plots revealed large deviations from JKR curves depending on scanning velocity and maximum loading force. Some nano-rheological arguments were employed based on the difference between these specimens.     

平面C-B样条的奇拐点分析

平面C-B样条曲线是三次均匀B样条的推广.通过移动C-B样条曲线段的一个控制点而固定其余三个控制点的方法,讨论了在曲线上形成零曲率点的移动控制点的轨迹,得到了C-B样条曲线段的尖点判别曲线、拐点判别区域,同时也给出了在曲线段上生成重结点的移动控制点的轨迹区域.     

Relation of structure to performance characteristics of monolithic and perfusive stationary phases

Commercially available polymer-based monolithic and perfusive stationary phases were evaluated for their applicability in chromatography of biologics. Information on bed geometry, including that from electron microscopy (EM), was used to interpret and predict accessible volumes, binding capacities, and pressure drops. For preparative purification of biologics up to at least 7 nm in diameter, monoliths and perfusive resins are inferior to conventional stationary phases due to their low binding capacities (20–30 g/L for BSA). For larger biologics, up to several hundred nanometers in diameter, calculations from EM images predict a potential increase in binding capacity to nearly 100 g/L. The accessible volume for adenovirus calculated from the EM images matched the experimental value. While the pores of perfusive resins are essentially inaccessible to adenovirus under binding conditions, under non-adsorbing conditions the accessible intrabead porosity is almost as large as the interbead porosity. Modeling of breakthrough curves showed that the experimentally observed slow approach to full saturation can be explained by the distribution of pore sizes.     

Visco-penalization of the sum of two monotone operators

A new type of approximating curve for finding a particular zero of the sum of two maximal monotone operators in a Hilbert space is investigated. This curve consists of the zeros of perturbed problems in which one operator is replaced with its Yosida approximation and a viscosity term is added. As the perturbation vanishes, the curve is shown to converge to the zero of the sum that solves a particular strictly monotone variational inequality. As an off-spring of this result, we obtain an approximating curve for finding a particular zero of the sum of several maximal monotone operators. Applications to convex optimization are discussed.