Electropolymerized Pyrrole‐Substituted Manganese Phthalocyanine Films for the Electroassisted Biomimetic Catalytic Reduction of Molecular Oxygen

We report for the first time on the electroassisted biomimetic activation of molecular oxygen by a newly prepared electropolymerized polypyrrole‐manganese phthalocyanine film. The prepared films and their intervention in the electroassisted catalytic reduction of molecular oxygen were analyzed by cyclic voltammetry and UV‐visible spectrophotometry on optically transparent electrodes. The obtained results demonstrate the probable existence of the key‐steps responsible for the suggested formation of the highly reactive manganese oxo intermediate.     

A variational coupled cluster theory for closed shells using a propagator modification procedure

A general partial summation method for including arbitrary classes of diagrams to all orders in the coupled cluster based size consistent energy functional for closed shell states is developed. Since the various reduced density matrices which appear in the energy functional are essentially the time-independent analogues of the corresponding many body Green functions, it is possible to derive Dyson-like equations for these quantities. By expanding the associated proper self energy parts in terms of the T-amplitudes, one can carry out partial summations in the reduced density matrices and thus in energy. At a higher level, higher order terms in a proper self energy can also be generated by renormalizing the internal propagators in it, and considering only the irreducible self-energy terms.     

DNAzyme amplification of molecular beacon signal

This paper reports an improved catalytic molecular beacon. Addition of the target oligonucleotide activates a DNA enzyme (DNAzyme), which, in turn, activates multiple copies of molecular beacons (MB) and gives rise to a strong fluorescence signal. In a previous design, the activated DNAzyme could oligomerize, especially dimerize, and result in inactivation of the DNAzyme. The current design avoids this problem, upon activated by the target DNA, the DNAzyme will stay constantly active. With the improved method, a detection of 10 pM DNA has been demonstrated, which is 1000 times more sensitive than the method previously reported.     

Functionality map analysis of the active site cleft of human thrombin

Summary The Multiple Copy Simultaneous Search methodology has been used to construct functionality maps for an extended region of human thrombin, including the active site. This method allows the determination of energetically favorable positions and orientations for functional groups defined by the user on the three-dimensional surface of a protein. The positions of 10 functional group sites are compared with those of corresponding groups of four thrombin-inhibitor complexes. Many, but not all features, of known thrombin inhibitors are reproduced by the method. The results indicate that certain aspects of the binding modes of these inhibitors are not optimal. In addition, suggestions are made for improving binding by interaction with functional group sites on the thrombin surface that are not used by the thrombin inhibitors. Abbreviations: MCSS, multiple copy simultaneous search; PPACK, d-phenylalanyl-l-propyl-l-arginine chloromethane; NAPAP, N -(2-naphthylsulfonylglycyl)-d-para-amidinophenylalanylpiperidine; argatroban, (2R,4R)-4-methyl-1-[N -(3-methyl-1,2,3,4-tetrahydro-8-quinolinylsulfonyl)-l-arginyl]-2-piperidine carboxylic acid; rms, root mean square. The thrombin residues are numbered according to the chymotrypsin-based numbering by Bode et al. [8]. P1, P2, P3, etc., denote the peptide inhibitor residues on the amino-terminal side of the scissile peptide bond, and S1, S2, S3, etc., the corresponding subsites of thrombin     

Molecular mechanics (MM2) calculations and cone angles of phosphine ligands

Molecular mechanics (MM2) calculations were performed on 54 conformations of 18 phosphines (PH₃; PH_3−nR_n, where n = 1,…3, and R = Me and Et, n = 1 or 2 and R =ⁱPr, and n = 1 and R =^tBu, PMe₂Et, PMeEt₂, and PPhMe₂, and PPh₂R where R = Me, Et, ⁱPr, ^tBu and Ph). The results are compared to those previously obtained from MINDO/3 and MNDO calculations, and to experimental data. Single conformer cone angles and weighted average cone angles were calculated from MM2 optimized geometries employing Tolman's general definition, and they are compared to Tolman's values, MINDO/3 results, and T.L. Brown's E_R values. Of the cone angle definitions used, the weighted average values are suggested as the best single representation of phosphine ligand sizes. The steric parameters (cone angle and E_R values) alone, and in conjunction with electronic parameters, are correlated with experimental data.     

A molecular mechanics approach for analyzing tensile nonlinear deformation behavior of single-walled carbon nanotubes

In this paper, by capturing the atomic information and reflecting the behaviour governed by the nonlinear potential function, an analytical molecular mechanics approach is proposed. A constitutive relation for single-walled carbon nanotubes (SWCNT’s) is established to describe the nonlinear stress-strain curve of SWCNT’s and to predict both the elastic properties and breaking strain of SWCNT’s during tensile deformation. An analysis based on the virtual internal bond (VIB) model proposed by P. Zhang et al. is also presented for comparison. The results indicate that the proposed molecular mechanics approach is indeed an acceptable analytical method for analyzing the mechanical behavior of SWCNT’s. The project supported by the National Natural Science Foundation of China (10121202, 90305015 and 10328203), the Key Grant Project of Chinese Ministry of Education (0306) and the Research Grants Council of the Hong Kong Special Administrative Region, China (HKU 7195/04E).     

一例含阴离子水簇的钴配合物的合成、结构及理论研究

金属配合物中的水簇研究为研究宏观意义上的水以及与蛋白质分子有关的水分子提供了有效途径。本文合成了一个含有阴离子水簇的带状超分子配合物[Co(2,2-bipy)₂(N₃)₂](N₃)_0.5Cl_0.5·2H₂O(1,2, 2-bipy=2, 2-联吡啶)。单晶结构解析表明,配合物属于三斜晶系,P-1空间群,晶胞参数为:a=0.822 54(7) nm,b=1.175 58(9) nm,c=1.237 06(10) nm,α=91.379 0(10)°,β=92.151 0(10)°,γ=108.119 0(10)°,V=1.135 27(16) nm³,由一个单核[Co(2,2-bipy)₂(N₃)₂]⁺配合物阳离子、两个非配位水分子、0.5个游离的叠氮离子和0.5个氯离子组成,叠氮离子和氯离子位置无序,占有率各为50%。两个客体水分子通过强烈的分子间氢键作用形成了环状水四聚体,且与无序的N^-₃和Cl^-通过氢键作用形成了一个[(H₂O)₄(N₃)Cl]^2- 阴离子水簇。此外,本文基于密度泛函理论(DFT)对配合物[Co(2,2-bipy)₂(N₃)₂]⁺阳离子进行了量子化学计算,分析了其单点能和原子电荷,并计算了中心金属离子的氧化态,计算结果与实验相吻合。     

Stationary states of crystal growth in three dimensions

A new Markov process describing crystal growth in three dimensions is introduced. States of the process are configurations of the crystal surface, which has a terrace-edge-kink structure. The states are continuous along edges but discrete across edges, in accordance with the very different rates for the two types of captures of particles. Stationary distributions, describing steady crystal growth, are found in general. To our knowledge, these are the first examples of stationary distributions for layered crystal growth in three dimensions. The steady growth rate and other quantities are obtained explicitly for two interacting edges. For many interacting edges, growth behavior is determined (a) in various asymptotic regimes including thermodynamic limits, (b) via simulations, and (c) using series (cluster) expansions in the slope of the surface, the first three coefficients being computed. The theoretical growth rates show a marked dependence on surface dimensions. This may contribute to the size dependence and dispersion in the observed growth rate of small crystals.     

Ion beam mixing of α-MoSi2

Abstract

Using molecular dynamics simulation, we study the mixing of an α-MoSi₂ crystal by 1 keV Ar ions. The observed order of magnitude of the mixing is compatible with a spike model of ion beam mixing. The influence of the target surface and of chemical effects are discussed.     

Response to the comments by J.H. Evans on ‘On the onset of void ordering in metals under neutron or heavy-ion irradiation’

Evans's comments are related only loosely to the main body of our paper, which is devoted to the onset of void ordering: his Monte Carlo simulations of this early stage of ordering are in a qualitative agreement with our results. They question, however, the basic mechanisms of damage accumulation revealed by a number of scientists using various techniques over the years. Here we argue that his views are erroneous due to overlooking some essential features of one-dimensional defect transport.