Quantum chemical characterization of the reactions of guanine with the phenylnitrenium ion.

Density functional calculations at the B3LYP/6-311+G(2d,p)//pBP/DN level predict all cationic adducts combining guanine, at either its N2, O6, N7, or C8 positions, with phenylnitrenium ion, at either its N, 2, or 4 positions, to be lower in energy than the separated reactants. This relative stability of all adducts is preserved after addition of aqueous solvation free energies computed at the SM2 level, although some leveling of the adduct relative energies one to another is predicted. Cations having the lowest relative energies in solution correspond structurally to those adducts most commonly found when guanine reacts with larger, biologically relevant nitrenium ions in vitro and in vivo. One of these, the N-C8 adduct, is stabilized both by a rearomatized phenyl ring and by the operation of an anomeric effect not found in any of the others. On the basis of energetic analysis, direct conversion of an N-N7 cation to an N-C8 cation according to a previously proposed mechanism is unlikely; however, an alternative rearrangement converting a 2-N7 cation to an N-C8 cation via the intermediacy of a five-membered ring may be operative in nitrenium ions with aromatic frameworks better able than phenyl to stabilize endocyclic cationic charge.     

An investigation of the chemical stability of arsenosugars in basic environments using IC-ICP-MS and IC-ESI-MS/MS

This paper evaluates the chemical stability of four arsenosugars using tetramethylammonium hydroxide (TMAOH) as an extraction solvent. This solvent was chosen because of the near quantitative removal of these arsenicals from difficult to extract seafood (oysters and shellfish). Four arsenosugars (3-[5'-deoxy-5'-(dimethylarsinoyl)-beta-ribofuranosyloxy]-2-hydroxypropylene glycol--As(328), 3-5'-deoxy-5'-(dimethylarsinoyl)-beta-ribofuranosyloxy]-2-hydroxypropanesulfonic acid--As(392), 3-[5'-deoxy-5'-(dimethylarsinoyl)-beta-ribofuranosyloxy]-2-hydroxypropyl hydrogen sulfate--As(408), and 3-[5'-deoxy-5'-(dimethylarsinoyl)-beta-ribofuranosyloxy]-2-hydroxypropyl-2,3-hydroxypropyl phosphate--As(482)) were evaluated. The stability of these four arsenosugars were studied independently in a solution of 2.5% TMAOH at 60 degrees C over a period of up to 8 h. Two arsenosugars, As(328) and As(392), were found to be relatively stable in this solution for up to 8 h. However, As(408) and As(482) formed detectable quantities of dimethylarsinic acid (DMAA) and As(328) within 0.5 and 2 h, respectively. It was found that 97% of As(408) degrades after 8 h of treatment producing 3.4 times as much DMAA as As(328). This is contrary to As(482), which produces 13 times as much As(328) as DMAA and only 37% of the As(482) was converted by the 8 h treatment at 60 degrees C. These degradation products led to the investigation of weaker TMAOH extraction solvents. Three different concentrations (2.5%, 0.83% and 0.25%) were used to determine the effect of TMAOH concentration on the degradation rate of As(408). By reducing the TMAOH concentration to 0.83%, the conversion of the arsenosugar to As(328) and DMAA is nearly eliminated (less than 5% loss). Arsenosugars, As(408) and As(482), were also studied in 253 mM NaOH to verify the degradation products. The NaOH experiments were conducted to investigate a possible hydroxide based reaction mechanism. Similar degradation plots were found for each arsenosugar when compared to the 2.5% TMAOH data. A mechanism has been proposed for the formation of As(328) from As(408) and As(482) in base via an SN2 reaction (hydroxide attack) at the side chain carbon adjacent to the inorganic ester. The formation of DMAA is observed in all arsenosugars after prolonged exposure. This probably occurs via an SN2 attack at the arsenic atom.     

Pulsed fluorescence measurements of trapped molecular ions with zero background detection

Sensitive methods have been developed to measure laser-induced fluorescence from trapped ions by reducing the detection of background scattering to zero levels during the laser excitation pulse. The laser beam diameter has been reduced to approximately 150 microm to eliminate scattering on trap apertures and the resulting laser-ion interaction is limited to a volume of approximately 10(-5) cm which is approximately 0.03-0.15 of the total ion cloud volume depending on experimental conditions. The detection optics collected fluorescence only from within the solid angle defined by laser-ion interaction volume. Rhodamine 640 and Alexa Fluor 350 ions, commonly used as fluorescence resonance energy transfer (FRET) fluorophores, were generated in the gas phase by using electrospray ionization and injected into a radiofrequency Paul trap where they were stored and exposed to Nd:YAG laser pulses at 532 and 355 nm for times up to 10 m. Fluorescence emitted by these ions was investigated for several trap q(z) values and ion cloud temperatures. Analysis of photon statistics indicated an average of approximately 10 photons were incident on the PMT detector per 15 ns pulse for approximately 10(3) trapped ions in the interaction volume. Fluorescence measurements displayed a dependence on trapped ion number which were consistent with calculations of the space charge limited ion density. To investigate the quantitative capability of these fluorescence techniques, the laser-induced fragmentation of trapped Alexa Fluor 350 ions was measured and compared with a rate equation model of the dynamics. Decay of the fluorescence signal as well as the parent ion number compared closely with quantitative predictions of the photofragmentation model.     

D3R grand challenge 4: blind prediction of protein–ligand poses,affinity rankings,and relative binding free energies

Journal of Computer-Aided Molecular Design - The Drug Design Data Resource (D3R) aims to identify best practice methods for computer aided drug design through blinded ligand pose prediction and...     

Nickel cluster structure determined from the adsorption of molecular nitrogen: Ni49-Ni71

The geometrical structures of nickel clusters in the size range from 49 to 71 atoms are studied by the chemical probe method. Saturation coverages of molecular nitrogen are determined for each cluster and from this data specific structures are proposed (except for Ni₆₆ and Ni₆₇). The results indicate that icosahedral packing is the dominant structural configuration throughout this size range, in agreement with earlier results based on water and ammonia adsorption. In addition, it seems that for clusters larger than Ni₅₄ the excessive strain in the surface of the 55-atom regular icosahedron often leads to rear-rangements of the surface atoms to relieve that strain. Ni₅₅, in particular, is found to have two isomers, the regular icosahedron and a structure in which a single apex atom is displaced to the center of an opposite face. Ni₇₁ occurs as a 55-atom regular icosahedron with a 16-atom cap. The results suggest that the atoms in the cap adopt an ABA configuration relative to the underlying icosahedron rather than an icosahedral arrangement. For some clusters the saturation with nitrogen causes a small degree of surface reconstruction that leads to the adsorption of additional nitrogen molecules.Work supported by the U.S. Department of Energy, Office of Basic Energy Sciences, Division of Chemical Sciences, under Contract No. W-31-109-Eng-38     

Reactions of cobalt clusters with deuterium

The kinetics of chemical reactions of cobalt clusters Co_n with deuterium are described. Absolute rate constants have been measured in the size range n=7–68 at 293 K. The rate constants are found to be a strong function of cluster size, varying by a factor of 400. This size dependence is most prominent for n=7 to 25: Co₁₅ is the most reactive cluster, and Co_7–9 and Co_19–20 are particularly unreactive. Abrupt changes in the rate constants from one cluster size to the next are observed. For the clusters above n=25, the rate constants show several less prominent maxima and minima superimposed on a slow, nearly monotonic increase with cluster size.     

昆虫信息素研究III: 拟蚜虫警戒素的研究

合成了一系列碳数为十五和十四的倍半萜类蚜虫警戒素,并进行了生物活性测定,从中筛选有效化合物.     

Communication Roles, Perceived Effectiveness, and Satisfaction in an Environmental Management Program

Earlier research has shown a relationship between various forms of structural centrality and perceived leadership and role satisfaction in small experimental groups. The limited amount of research on this topic in naturally occurring social networks has yielded results that often conflict with one another. Different results have generally been attributed to possible differences in task environments. This paper examines the relationship between two types of structural centrality and perceived influence, role satisfaction, and perceived effectiveness in an environmental resource management program. Findings in this paper suggest that the observed differences in relationships between the network and other variables is partly a function of global network properties (e.g., marginality of subgroups) and related task environments. This revised version was published online in August 2006 with corrections to the Cover Date.     

Micromechanical modeling of the elasto-viscoplastic behavior of semi-crystalline polymers

A micromechanically based constitutive model for the elasto-viscoplastic deformation and texture evolution of semi-crystalline polymers is developed. The model idealizes the microstructure to consist of an aggregate of two-phase layered composite inclusions. A new framework for the composite inclusion model is formulated to facilitate the use of finite deformation elasto-viscoplastic constitutive models for each constituent phase. The crystalline lamellae are modeled as anisotropic elastic with plastic flow occurring via crystallographic slip. The amorphous phase is modeled as isotropic elastic with plastic flow being a rate-dependent process with strain hardening resulting from molecular orientation. The volume-averaged deformation and stress within the inclusions are related to the macroscopic fields by a hybrid interaction model. The uniaxial compression of initially isotropic high density polyethylene (HDPE) is taken as a case study. The ability of the model to capture the elasto-plastic stress-strain behavior of HDPE during monotonic and cyclic loading, the evolution of anisotropy, and the effect of crystallinity on initial modulus, yield stress, post-yield behavior and unloading-reloading cycles are presented.     

Three-dimensional micromechanical modeling of voided polymeric materials

A three-dimensional micromechanical unit cell model for particle-filled materials is presented. The cell model is based on a Voronoi tessellation of particles arranged on a body-centered cubic (BCC) array. The three-dimensionality of the present cell model enables the study of several deformation modes, including uniaxial, plane strain and simple shear deformations, as well as arbitrary principal stress states.The unit cell model is applied to studies on the micromechanical and macromechanical behavior of rubber-toughened polycarbonate. Different load cases are examined, including plane strain deformation, simple shear deformation and principal stress states. For a constant macroscopic strain rate, the different load cases show that the macroscopic flow strength of the blend decreases with an increase in void volume fraction, as expected. The main mechanism for plastic deformation is broad shear banding across inter-particle ligaments. The distributed nature of plastic straining acts to reduce the amount of macroscopic strain softening in the blend as the initial void volume fraction is increased. In the case of plane strain deformation, the plastic flow is observed to initiate across inter-particle ligaments in the direction of constraint. This particular mode of deformation could not have been captured using a two-dimensional, plane strain idealization of cylindrical voids in a matrix.The potential for localized crazing and/or cavitation in the matrix is addressed. It is observed that the introduction of voids acts to relieve hydrostatic stress in the matrix material, compared to the homopolymer. It is also seen that the predicted peak hydrostatic stress in the matrix is higher under plane strain deformation than under triaxial tension (with equal lateral stresses), for the same macroscopic stress triaxiality.The effect of void volume fraction on the macroscopic uniaxial tension behavior of the different blends is examined using a Considère construction for dilatant materials. The natural draw ratio was predicted to decrease with an increase in void volume fraction.