Fully quantum mechanical energy optimization for protein-ligand structure

We present a quantum mechanical approach to study protein-ligand binding structure with application to a Adipocyte lipid-binding protein complexed with Propanoic Acid. The present approach employs a recently develop molecular fractionation with a conjugate caps (MFCC) method to compute protein-ligand interaction energy and performs energy optimization using the quasi-Newton method. The MFCC method enables us to compute fully quantum mechanical ab initio protein-ligand interaction energy and its gradients that are used in energy minimization. This quantum optimization approach is applied to study the Adipocyte lipid-binding protein complexed with Propanoic Acid system, a complex system consisting of a 2057-atom protein and a 10-atom ligand. The MFCC calculation is carried out at the Hartree-Fock level with a 3-21G basis set. The quantum optimized structure of this complex is in good agreement with the experimental crystal structure. The quantum energy calculation is implemented in a parallel program that dramatically speeds up the MFCC calculation for the protein-ligand system. Similarly good agreement between MFCC optimized structure and the experimental structure is also obtained for the streptavidin-biotin complex. Due to heavy computational cost, the quantum energy minimization is carried out in a six-dimensional space that corresponds to the rigid-body protein-ligand interaction.     

Phasentransferkatalysatoren auf Basis von Saccharose-Ethylenoxid-Addukten

Sucrose ethyleneoxide adducts have been prepared by reaction of sucrose with various amounts of ethyleneoxide inDMSO. The resulting polypode molecules were found to be efficient phase transfer catalysts in nucleophilic substitutions, oxidation and dichlorcarbene generation. Polymerisable polypodes have been obtained by reaction of sucrose ethyleneoxide adducts with methacrylic anhydride or methacryloylchloride in pyridine. Free radical polymerisation of the resulting mixtures of mono- and polyfunctional methacrylic esters of sucrose ethyleneoxide adducts yielded crosslinked gels. These polymer-supported octopus-molecules were found to be efficient triphase catalysts.

     

Synthesis, structure, and spectroscopy of phenylacetylenylene rods incorporating meso-substituted dipyrrin ligands

The synthesis, structure, and spectroscopic characterization of a series of phenylacetylenylene rodlike molecules containing dipyrromethene (dipyrrin) ligands are described. The combination of the phenylacetylenylene groups with the porphyrinogenic dipyrrin moieties results in a rich absorption spectroscopy for these compounds, although the fluorescence of the phenylacetylenylene moiety is quenched by presence of the dipyrrin chelator. The Cu(2+) and Fe(3+) complexes of these ligands have been prepared and three of these compounds have been structurally characterized by using single-crystal X-ray diffraction. Unlike other octahedral metal-dipyrrin complexes described to date, one of the iron complexes demonstrates ideal threefold symmetry in the solid-state. The elongated structure and high symmetry of these complexes suggests the use of these meso-substituted phenylacetylenylene ligands as an interesting class of extended, branched molecules for the construction of supramolecular architectures.     

铬(Ⅲ)含β一二酮混合配体配合物的合成和表征

首次合了五种Cr(β-dik)Cl_2py_2型(其中β-dik分别为乙酰丙酮、苯甲酰丙酮、三氟乙酰丙酮、2—噻吩甲酰三氟丙酮、二苯甲酰甲烷)和一种Cr(pmbp)Cl_2(thf)混合配体配合物、一种Cr(pmbp)_3配合物。并对上述化合物进行了电子光谱、红外光谱等的表征工作。     

Phospha-adamantanes as ligands for organopalladium chemistry: aminations of aryl halides

The use of Pd₂dba₃·CHCl₃ and 1,3,5,7-tetramethyl-2,4,8-trioxa-6-phenyl-6-phospha-adamantane has been shown to facilitate the effective amination of aryl halides with aromatic or aliphatic amines in high yields.     

一种新型可溶性高聚物负载手性配体的合成及其催化烯烃的不对称双羟化反应研究

在碱性条件下, 聚乙二醇单甲醚(HO\|OPEG\|OMe)与1,4-二氟蒽醌进行亲核单取代反应生成中间体F\|AQN-OPEG-OMe, 产率88%. F-AQN-OPEG-OMe与奎宁锂进行亲核取代反应, 以95.6%的产率得到新型手性配体QN\|AQN\|OPEG-Me. QN-QN\|OPEG-Me与OsO4原位配位生成的均相催化剂在4种烯烃的不对称双羟化反应中表现出较高的对映选择性(92%~99%e.e.)和化学产率(80%~94%). 催化活性和立体选择性与Sharpless手性配体(DHQ)2AQN相当. 反应结束后, 配体可用乙醚沉淀回收, 循环使用5次, 催化剂的催化活性和立体选择性无明显改变, 配体的回收率均在95%~97%之间.     

Plasma-Catalytic Decomposition of Phenols in Atmospheric Pressure Dielectric Barrier Discharge

This study investigated the processes for the destruction of phenol and its derivatives (resorcin and pyrocatechol) in aqueous solutions under the action of an oxygen dielectric barrier discharge (DBD) at atmospheric pressure in the presence or absence of catalysts in the plasma zone. It was shown that the DBD had a high decomposition efficiency for phenol and its derivatives (up to 99%). Phenol was the most stable and pyrocatechol was the least. In a plasma-catalytic hybrid process, the effective rate constants for phenol, resorcin and pyrocatechol decomposition were 11, 4 and 2.5 times higher, respectively, than those for the DBD treatment without catalysts. The process also resulted in a 1.4, 1.6 and 1.2 times higher rate of carboxylic acid formation for phenol, resorcin and pyrocatechol, respectively. The fractional conversion into the respective carboxylic acids reached 56% for phenol and 68% for resorcin and pyrocatechol.     

Chelating Behaviour of Substituted 1-Benzoyl-4-Phenylthiosemicarbazide

The preparation and characterization of a series of new coordination compounds of Co(II), Ni(II), Cu(II), Zn(II) and Cd(II) containing o-methyl- or o-chlorobenzoyl-4-phenyl-3-thiosemicarbazide (HMBPT, HCBPT=HL) are reported. The reaction products were investigated by analyses, electrolytic conductance, magnetic susceptibility, reflectance and IR spectral studies. The IR spectra show that HMBPT and HCBPT coordinate with the metal ions via different coordination sites (NS and/or NO). The spectral data support the suggestion that the ligands form his-chelates with Ni(II) and Cu(II) of square planar stereochemistry and of general formulae ML₂·H₂O, where L is the uninegatively charged bidentate ligand. The Co(II) ion forms octahedral and tetrahedral structures with HMBPT and HCBPT, respectively. The ligand field parameters (D₄, B and β) for the Co(II) chelates were calculated using the averaged-ligand-field approximation. The influence of the benzene ring substituents (o-chloro or o-methyl) on the stereochemistry are discussed. Also, the formation of the complexes in solution was tested by the pH-metric method.     

Ligand-protein docking using a quantum stochastic tunneling optimization method

A novel hybrid optimization method called quantum stochastic tunneling has been recently introduced. Here, we report its implementation within a new docking program called EasyDock and a validation with the CCDC/Astex data set of ligand-protein complexes using the PLP score to represent the ligand-protein potential energy surface and ScreenScore to score the ligand-protein binding energies. When taking the top energy-ranked ligand binding mode pose, we were able to predict the correct crystallographic ligand binding mode in up to 75% of the cases. By using this novel optimization method run times for typical docking simulations are significantly shortened.     

四核钴羰基簇合物Co4(CO)8(μ-CO)2(μ4-PSR)2的合成和晶体结构

The title compounds Co4(CO)8(μ-CO)2 (μ4-PSR) [R=-CH3, -C2H5, -C(CH3)3,-(CHa)4CH3] were synthesized by the reaction of Co2(CO)8 with RSPCl2. They were characterized by IR, 1HNMR, elemental analysis. The crystal and molecular structure of Co4(Co)8(μ-CO)2 (μ4-PSC2H5) has been determined by single crystal diffraction method. Crystal data: monoclinic, space group P21 /c, with a=8-445(3), 6=8.562(3), c= 17.125(6)Å, β=104.26 (3)' 9 V=1200.1Å3, Z=2, Dc=1.937gcm-3. Its molecular structure contains an octahedral Co4P2 skeleton which consists of a rectangular four cobalt atoms core and the Co4 core is capped above and below by two quadruply bridging PSR ligands.