The crystal and molecular structure of benzoyl-pentafluoropropionylmethylene triphenylarsorane

Benzoyl-pentafluoropropionylmethylene triphenylarsorane contains two strongly electron-withdrawing groups in alkylidene moiety. Single crystals obtained from CH₃OH-H₂O solution are triclinic, the space group is \documentclass{article}\pagestyle{empty}\begin{document}$ {\rm{P}}\bar 1 $\end{document}, with a = 12.292Å, b = 13.457Å, c = 15.318Å, α = 90.562° β = 90.516°, γ = 92.820°, and Z = 4. The X-ray diffraction intensity data were collected with a four-circle diffractometer. The structure has been solved by heavy-atom method and refined by block-diagonal least-squares method. The final R was 0.061 for 8393 independent observed reflections. The ylide carbon is planar sp² hybridized. The bond length of As-C_ylide is 1.888Å, much longer than As = C, and also longer than the corresponding bond length in other arsonium ylides previously reported, indicating a smaller contribution of “double bond” canonical form to the overall structure. On the other hand, the easier delocalization of negative charge due to the two strongly electron-withdrawing groups results in the greater chemical stability.     

The further crystallographic refinement of trichosanthin at 2.7A resolution and the comparison among the three molecular structures in two crystal forms

The three-dimensional structure of trichosanthin at 2.7A resolution has been improved further, by refitting one of the C-terminal tails, adjusting 16 residues in the molecular surface regions, discarding some water molecules with high B values, and adjusting weights during the further refinement. The R-factor has been reduced to 18.5% and the r.m.s deviations from ideal geometry are also improved. The structures of the two molecules in the monoclinic asymmetric unit and the only molecule in the orthorhombic asymmetric unit are compared with one another. The main-chain structures for most of the residues in the three molecules are substantially the same. However, the courses of the three C-terminal tails are completely different, and the intermolecular interactions resulting from the particular packing of the molecules in the crystals account for the differences. The strand Be-2 and the preceding B-turn in small domain show large r.m.s. deviations among the three molecules and they are also involved in i     

Crystal structure of the complex of trichosanthin with NADPH at 0.172 nm resolution

The orthorhombic crystal structure of the complex of trichosanthin with nicotinamide adenine dinucleotide phosphate has been determined by molecular replacement method using one of the molecules of the monoclinic crystal structure of trichosanthin at 0.27 nm resolution as the search model. The crystallographic refinement at 0.172 nm resolution led to a final R-factor of 17.4% with root-mean-square deviations of 0.0013 nm and 3.8 from the ideal bond lengths and bond angles, respectively. The quality of the structure, the polypeptide chain fold and the comparison of it with that of the monoclinic trichosanthin structure, the location of nicotinamide adenine dinucleotide phosphate, the active site structure as well as the solvent structure are described.     

2’-脱氧腺苷-5’-磷酸与羟基自由基反应所形成的自由基

运用可靠的B3LYP/DZP++方法研究了2'-脱氧腺苷-5'-单磷酸(dAMP)与羟基自由基(HO·)的反应中所产生的20余种自由基. 结果表明, 反应的初始产物包括HO·加成到dAMP碱基C8、C4位上所形成的羟基加合物自由基, 以及dAMP碱基环上氨基的脱氢自由基. 而且,反应最初形成的C4位羟基加合物自由基具有脱水产生dAMP碱基环上氨基脱氢自由基的热力学趋势, 脱水形成的两种氨基脱氢自由基都是强氧化剂.尽管HO·加成到dAMP碱基C2位上所形成的加成产物比C4位的加成产物更稳定, 但dAMP与HO·的氧原子间较强的静电排斥作用却使得HO·难以靠近C2原子, 导致C2位的羟基加成产物难以形成. 上述结论不但与有关实验结果一致, 而且还对一些实验现象作出了合理的解释.     

The improvement of Cα atom positions of trichosanthin—–An application of phase filtering procedure to three-dimensional structure determination of protein

Wang's phase filtering procedure has been applied to the structure study of trichosanthin crystals belonging to space group C2. The MIR phases at 3Å resolution have been improved with the accumulative phase shift of 31.8° and the figure of merit has been improved from 0.54 to 0.84. The resulted electron density map at 3Å resolution has been much improved with a higher ratio of the electron density of the protein to the noise in the solvent region. The minimap has been interpreted more reasonably than the previous maps, giving the overall course of the polypeptide chain substantially the same as previously reported except for containing more secondary structure and a few short segments traced differently. The first 85 C_α atoms of the polypeptide chain are located in about the same positions as determined previously with an exception of a short segment but the amino acid residues after that shift along the chain with a maximum shift of about 15 residues. The electron density of side chains agrees better with the primary structure. The conformation and the three-dimensional structure as well as the major heavy-atom binding sites for the two molecules in an asymmetric unit are substantially the same. The structure of trichosanthin shows more similarity to ricin A chain than that reported previously.     

Structure-charge transport relationship of 5,15-dialkylated porphyrins

5,15-Dialkyl-substituted porphyrins that are symmetrically capped with ethyl (C(2)-Por), butyl (C(4)-Por) and hexyl (C(6)-Por) were synthesized and characterized. Molecular structure versus physical property relationship has been established through the analysis of planar charge transport using thin film transistor (TFT) structure.     

Improving performance of polymer solar cell by adjusting crystallinity and nanoscale phase separation

In this paper, we report a high-performance P3HT/PCBM bulk-heterojunction solar cell with a power conversion efficiency of 4.85% fabricated by adjusting polymer crystallinity and nanoscale phase separation using an ultrasonic irradiation mixing approach of the polymer. The results of grazing incidence X-ray diffraction, UV/Vis spectroscopic, and atomic force microscopic measurements of the P3HT/PCBM blend films reveal that the P3HT/PCBM film fabricated by ultrasonic irradiation mixing P3HT and PCBM solutions for 10 min has higher degree of crystallinity, higher absorption efficiency, and better phase separation, which altogether account for the higher charge transport properties and photovoltaic cell performance.     

Structural and chromotropism properties of copper(II) complexes with 3,3′-((pyridin-2-ylmethyl)azanediyl)dipropanamide ligand

Transition Metal Chemistry - A tetra-dentate ligand L [3,3′-((pyridin-2-ylmethyl)azanediyl)dipropanamide] was synthesized and characterized by spectroscopic and structural methods. The...     

The three-dimensional structure of trichosanthin refined at 2.7resolution

The three-dimensional structure of trichosanthin crystallizing in space group C2 has beenrefined at 2.7 resolution from a previously reported starting model at 3 resolution based on asolvent flattened map and the revised primary structure consisting of 247 amlno-acids.The finalR-factor is 19.2% with the root mean-square deviations of 0.018 from ideal bond lengths andof 2.2° from ideal bond angles.Trichosanthin molecule is composed of two domains,the largedomain consisting of 181 amino-acld residues starting from N-terminus and the small domain con-sisting of the rest of the amino-acid residues.The molecule contains eight α-helices,five β-sheetsmade of sixteen β-strands,and some reverse turns.It is noteworthy that some of the α-helicesand β-sheets show irregular hydrogen bonding patterns.Six of the thirteen residues absolutelyconserved in eleven ribosome-inactivating proteins are located in a cleft near the interface ofthe two domains and they are likely to be active sites.Three additional conservative residueslocated in the cleft region might make some functional contribution as well.     

Bulk heterojunction photovoltaic cells based on tetra-methyl substituted copper(II) phthalocyanine:P3HT:PCBM composite

Insoluble CuMePc nanocrystals were incorporated into P3HT:PCBM bulk heterojunction photovoltaic cells to increase the carrier mobility and photon harvesting. The P1C1-based (weight ratio of P3HT:?CuMePc = 1:1) OPV cell exhibited the best photovoltaic performance with a J(SC) of 16.3 mA cm(-2), V(OC) of 0.58 V, FF of 0.56 and PCE of 5.3%.