A comparative study of various computational approaches in calculating the structure of pyridoxal 5'-phosphate (PLP)-dependent beta-lyase protein. The importance of protein environment

Various computational approaches, using molecular mechanics (Amber), semiempirical (AM1), density functional (B3LYP), and various ONIOM methods, have been comparatively investigated for the structure of Escherichia coli NifS CsdB protein. The structure of the entire monomer containing 407 amino acid residues and 579 surrounding water molecules has been optimized. The full geometry optimization in the "active site-only" approach (including only active site atoms) has been found to give the largest root-mean-square (RMS) deviation from the X-ray structure; a much better agreement has been achieved by keeping the atoms leading to the backbones of some amino acids frozen in their positions in the X-ray structure. The best agreement has been attained by including the surrounding protein in the calculations using the two-layer ONIOM (B3LYP:Amber) approach. The results presented in this study conclusively demonstrate the importance of the protein/active-site interaction on the active-site structure of the enzyme. The present theoretical study represents the largest system studied at the ONIOM level to date, containing 7992 atoms, including 84 atoms in the QM region and rest in the MM region.     

杂富勒烯的电子结构与性质关系的研究──Ⅱ.C_(57)X_3,C_(56)X_4(X=B、N、P)的位置异构体

用 CNDO／2方法在 586微机上计算了 C57X3C56X4（X=B、N、P）的 234个位置异构体的电子结构。在C57X3（X=B、N、P）位置异构体中，C57X3（1，2，9）（X=B、N、P）分别是最稳定的。对于C56X4（X=B、N、P）位置异构体，C56B4（1，2，9，8），C56N4（1，2，9，12）和C56P4（1，2，9，12）分别是最稳定的，但稳定性都比C60差。其氧化或还原性都比 C60好，将它们和 C60比较，与 X相距一个或两个键的 C原子电荷密度增加或减少较多，其余电或亲核反应性增加；X与 X，X与 C原子之间 Wiberg Order都减少较多，其键的强度削弱；邻近杂原子的 C与 C原子之间 Wiberg Order减少或增加很少，其键的强度稍有削弱或增强。     

不饱和类碳烯H2C(=)CLiBr的DFT研究

采用量子化学计算方法，在B3LYP／6－311G^*水平上全优化得到了不饱和类碳烯H2C＝CLiBr的平衡结构，结果表明，不饱和类碳烯H2C＝CLiBr只有两种平衡结构，对这两种平衡结构之间相互转化的过渡态进行计算，求得了转化势垒，根据计算得到的微观性质，采用统计热力学方法，研究了两种平衡结构之间相互转化的热力学性质，进而讨论了两种平衡结构在不同温度下的稳定性问题，在计算得到振动频率及强度的基础上，模拟了稳定平衡结构的红外光谱图。     

Pseudobond ab initio QM/MM approach and its applications to enzyme reactions

This perspective article mainly focuses on the development and applications of a pseudobond ab initio QM/MM approach to study enzyme reactions. The following aspects of methodology development are discussed: the approaches for the QM/MM covalent boundary problem, an efficient iterative optimization procedure, the methods to determine enzyme reaction paths, and the approaches to calculate free energy change in enzyme reactions. Several applications are described to illustrate the capability of the methods. Finally, future directions are discussed.     

Determination of rare earth impurities in high purity uranium by isotope dilution analysis

Summary An isotope dilution method for the determination of rare earth impurities in uranium has been developed and Ce, Nd, Sm, Eu and Gd have been determined in uranium oxide samples. The method involves isotopic dilution with enriched isotopes of the rare earths being measured, followed by the separation of rare earths from uranium. A mass spectrometer with thermionic source was used to determine the relative isotopic abundances in each of these rare earths. All these five elements were analysed selectively by preferential evaporation technique. Trace concentrations down to parts per billion range can be measured with good sensitivity and accuracy.

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Bestimmung von Verunreinigungen an Seltenen Erden in hochreinem Uran durch Isotopenverdünnungsanalyse

Zusammenfassung Eine Isotopenverdünnungsmethode wurde ausgearbeitet zur Bestimmung von Ce, Nd, Sm, Eu und Gd in Uranoxidproben. Das Verfahren umfaßt isotopische Verdünnung mit angereicherten Isotopen der zu bestimmenden Elemente und nachfolgende Abtrennung der Seltenen Erden von Uran. Die relativen Isotopenhäufigkeiten wurden mit Hilfe eines Massenspektrometers mit thermischer Ionenquelle bestimmt. Alle fünf Elemente wurden durch selektive Verdampfung analysiert. Spurenkonzentrationen bis herab zum ppb-Bereich konnten mit guter Empfindlichkeit und Genauigkeit erfaßt werden.

     

On the configuration interaction method for singlet states

The direct CI method, which avoids explicit calculation of the Hamiltonian matrix, is presented in a new form. The method is linked with Davidson's algorithm for iterative evaluation of the ground state eigenvector. The viability of the method is indicated by the test calculations on water which are described.     

Bacterial response to eukaryotic cells. Analysis of differentially expressed proteins using nano liquid chromatography-electrospray ionization tandem mass spectrometry

Host-bacteria interactions have mostly been investigated with regard to the host response or to activities of pathogenic bacteria. In contrast, we aim to identify reactions of non-pathogenic bacteria that result from their contact with host cells of the gastrointestinal tract. In a proteomic approach, the response of non-pathogenic human Escherichia coli bacteria on gut epithelial cells (rat IEC-6) was investigated in an in vitro co-culture model. For this purpose, a sensitive analytical procedure was developed based on the identification of two-dimensional polyacrylamide gel electrophoresis separated proteins by online nanoLC-electrospray ionization MS/MS using a quadrupole time-of-flight tandem mass spectrometer for accurate mass determination. We demonstrate here the efficiency of this technique by the identification of a total of 43 differentially expressed proteins, out of which 25 were up-regulated and 18 were down-regulated. They represent a wide range of molecular weight and different metabolic and physiological functions.     

Ag@Au core/shell triangular nanoplates with dual enzyme-like properties for the colorimetric sensing of glucose

Due to the serious harm of diabetes to human health, development of sensitive assays for glucose level is of high significance for early prevention and treatment of diabetes. Currently, most conventional enzyme-based glucose sensors suffer from high cost and low stability due to the inherent defects of natural enzymes. Herein, we develop a pure nanozyme-based glucose detection method using Ag@Au core/shell triangular nanoplates (TNPs), which combines glucose oxidase (GOD)- and horseradish peroxidase (HRP)-like activities of the Au shell and inherent plasmonic properties of Ag TNPs. The sensing mechanism is based on the fact that the Au shell possessed GOD-like activity, enabling the oxidation of glucose to produce H₂O₂, which can further etch the silver core, leading to the decrease of absorbance at 800 nm and the color change from blue to colorless. Compared with the previous nanozymes-based glucose sensors, our method avoids the use of enzymes and organic chromogenic agent. Moreover, the stability of the Ag@Au core/shell TNPs is much better than that of Ag TNPs due to the protection by the coating of the Au shell. This method was successfully applied to the detection of urine samples from patients with diabetes, indicating its practical applicability for real sample analysis.     

FT合成沉淀Fe／Cu／K催化剂有效因子的计算Ⅰ．工业颗粒催化剂有效因子的计算

用包括水抑制作用的动力学方程，根据建立的反应扩散模型和ＦＴ合成化学计量关系，计算了工业原颗粒ＦＴ合成沉淀Ｆｅ／Ｃｕ／Ｋ催化剂在工业操作条件下的有效因子。根据不同的产物组成，建立了三种化学计量关系式，比较了气相反应和气液反应的有效因子，确立了ＦＴ合成沉淀Ｆｅ／Ｃｕ／Ｋ催化剂有效因子的计算方法。在ＦＴ合成反应条件下，产物蜡充满了催化剂的微孔，各组分在蜡中的扩散系数要比纯气相中的扩散系数小得多。在工况操作条件下（５２３Ｋ，２．５ＭＰａ，５００ｈ￣（－１），尾气循环比３．０），工业原颗粒（ｄ＿ｐ＝２．５ｍｍ，ｌ＿ｐ＝５～１０ｍｍ）催化剂的实际有效因子是纯气相反应的一半左右，计算的平均有效因子分别为０．４０和０．４２。     

1H NMR Detection of σ-Adducts in S NH Reactions of Nitroquinolines with Chloromethyl Phenyl Sulfone

The intermediate -adducts of chloromethyl phenyl sulfone with 3-nitro-, 5-nitro-, 6-nitro-, 7-nitro- and 8-nitroquinoline are detected by ¹H NMR spectroscopy.