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.     

d,h-m̈-Alkoxoalkylphosphonato-e-m̈-alkoxo-f-m̈-oxo-bis[trichloroantimon(V)]-Verbindungen

d,h-m?-Alkoxoalkylphosphonato-e-m?-alkoxo-f-m?-oxo-bis[trichloroantimony(V)] Compounds The binuclear antimony(V) complexes Cl₃Sb(O)[R³(R¹O)PO₂](OR²)SbCl₃ 1 to 7 with R¹, R² and R³ = Me or Et in solution slowly exchanges the R² groups between the equatorial oxygen atoms of the Sb₂O₂ ring. The SbO(3)PO(3)Sb ringsystem makes rapid pseudorotation. The resulting isomeres are detected by nmr spectroscopy.     

Copolymerization of butadiene and styrene with a gadolinium tricarboxylate catalyst

Homo- and copolymerizations of butadiene (BD) and styrene (St) were carried out by gadolinium catalysts having various tricarboxylate ligands [Gd(OCOR)₃: R = CH₃, CH₂Cl, CHCl₂, CCl₃, and CF₃], to investigate the effects of ligands and discuss the cis polymerization mechanism. Polymerization of BD with Gd(OCOR)₃—(i—Bu)₃Al—Et₂AlCl catalysts was carried out in hexane at 50°C. By each catalyst, poly(BD) having a high cis content (cis = 97–99%) in 22–85% yields for 2–24 h were obtained. The ligands with low pKa values increased the polymerization activity as follows: R of Gd(OCOR)₃: CF₃ > CCl₃ > CHCl₂ > CH₂Cl ～ CH₃. On the other hand, in the polymerization of St or copolymerization of BD and St under similar conditions, the highest activity was attained by a Gd(OCOCCI₃)₃- based catalyst. The difference in the optimum ligand among the homo- and copolymerization of BD and St was discussed on the basis of energy levels of the catalysts. In the copolymers of BD and St, the cis-1,4 content of the BD unit decreased with increasing St content. Furthermore, according to the diad analysis of copolymers (St content ～ 14.5 mol %) by ¹³C NMR spectroscopy, the low cis value of the BD unit was observed in the St-BD diad (cis/trans/vinyl = 24/53/23), while the high cis value of the BD unit remained in the BD-BD diad (cis/trans/vinyl = 89/10/1). These results suggest that the terminal BD unit is controlled by the cis configuration by the coordination between the penultimate cis vinylene unit and the gadolinium metal catalyst, whereas the presence of the penultimate St unit interferes with cis polymerization of the terminal BD unit. The difference in the coordination mechanism in the course of polymerization between rare earth metal and transition metal catalysts such as the Ni(acac)₂ and Co(acac)₃-based catalyst was also discussed. © 1995 John Wiley & Sons, Inc.     

Synthesis and electrochemistry of Group 6 tetracarbonyl (N,N′-bis(ferrocenylmethylene)ethylenediamine)metal(0) complexes

Thermal substitution reaction of Cr(CO)₄(η^2:2-1,5-cyclooctadiene), Mo(CO)₄(η^2:2-norbornadiene), and W(CO)₅(η²-bis(trimethylsilyl)ethyne) with N,N′-bis(ferrocenylmethylene)ethylenediamine (bfeda) yields M(CO)₄(bfeda) complexes which could be isolated from the reaction solution and characterized by elemental analysis, MS, IR, and NMR spectroscopy. In the case of tungsten, W(CO)₅(bfeda) is formed as intermediate and then undergoes the ring closure reaction yielding the ultimate product W(CO)₄(bfeda). The electrochemical behavior of the M(CO)₄(bfeda) complexes was studied by using cyclic voltammetry (CV) and differential pulse voltammetry (DPV) in dichloromethane with tetrabutylammonium tetrafluoroborate as electrolyte. Constant potential electrolysis of the complexes was performed successively at their peak potentials at 0 °C in their CH₂Cl₂ solution and the electrolysis was followed by in situ recording the electronic absorption spectra in every 5 mC. In the electrolysis of Cr(CO)₄(bfeda), the central Cr(0) is oxidized first and electrolysis continues with oxidations of two ferrocenyl groups until the end of totally three moles of electron passage per mole of complex. In the electrolysis of Mo(CO)₄(bfeda) and W(CO)₄(bfeda) the first oxidation occurs on the central atom forming a short-lived species which undergoes an intramolecular one-electron transfer and is reduced back to M(0) while one of the ferrocene units is oxidized to the ferrocenium cation at the same time. This indicates that the electron is transferred from iron to the central metal atom.     

Synthesis and structural characterization of ferrocene-based bis(pyrazol-1-yl)borate ligands: FcB(Me)pz2K, Fc2Bpz2K, and 1,1′-fc[B(Me)pz2]2K2 (Fc: ferrocenyl, fc: ferrocenylene, pz: pyrazolyl)

Reaction of the ferrocenyl(dimethylamino)boranes FcB(Me)NMe₂, Fc₂BNMe₂, and 1,1′-fc[B(Me)NMe₂]₂ with 1:1 mixtures of pyrazole and potassium pyrazolide in refluxing THF gave the potassium salts of the ferrocene-based bis(pyrazol-1-yl)borate ligands FcB(Me)pz₂K, Fc₂Bpz₂K, and 1,1′-fc[B(Me)pz₂]₂K₂ in good yield (Fc: ferrocenyl, fc: ferrocenylene, pz: pyrazolyl). In the solid state, FcB(Me)pz₂K and Fc₂Bpz₂K form centrosymmetric dimers with short K?Cp contacts suggesting an η⁵ coordination mode of the potassium ion. The crystal lattice of the ditopic ligand 1,1′-fc[B(Me)pz₂]₂K₂ consists of coordination polymer strands featuring essentially the same structural motif that has been observed for the monotopic derivatives. All three scorpionate ligands are thus promising building blocks for the preparation of ferrocene-containing multiple-decker sandwich complexes.     

Surface diffusion in reversed-phase liquid chromatography using silica gels bonded with C1 and C18 ligands of different densities

Surface diffusion in reversed-phase liquid chromatography (RPLC) using silica gels bonded with C₁ and C₁₈ alkyl ligands of different densities was studied from the viewpoints of two extrathermodynamic relationships, i.e., enthalpy-entropy compensation (EEC) and linear free energy relationship (LFER). First, according to the four methods proposed by Krug et al., the values of surface diffusion coefficient (D_s) were analyzed to confirm that an actual EEC resulting from substantial physico-chemical effects takes place for surface diffusion. Then, it was also demonstrated that a LFER is observed between surface diffusion and the retention equilibrium. The establishment of EEC and LFER suggests a mechanistic similarity of molecular migration by surface diffusion, irrespective of the alkyl chain length and the densities of C₁ and C₁₈ ligands. Finally, a thermodynamic model for the LFER based on the real EEC was used to estimate D_s values under various RPLC conditions. The D_s values can be estimated with a mean square deviation of about 25–30%. The agreement between the D_s values estimated and those experimentally measured suggests that the total mass flux by surface diffusion consists of the two contributions due to C₁ and C₁₈ ligands and that the contribution of each ligand is proportional to the ligand density.     

Synthesis and Characterization of a [Mn12O12(O2CR)16(H2O)4] Complex Bearing Paramagnetic Carboxylate Ligands. Use of a Modified Acid Replacement Synthetic Approach

Summary.  A new modified approach for the synthesis of Mn₁₂ clusters, based on the use of complex [Mn₁₂O₁₂(O₂C ^t Bu)₁₆(H₂O)₄] (2) as starting material to promote the acidic ligand replacement, is presented here. This new synthetic approach allowed us to obtain complex [Mn₁₂O₁₂(O₂CC₆H₄N(O^•) ^t Bu)₁₆(H₂O)₄] (3), whose preparation remained elusive by direct replacement of the acetate groups of Mn₁₂Ac (1). Complex 3 bearing open-shell radical units, was prepared to increase the total spin number of its ground state, and consequently, to increase T _B , with the expectation that the radical ligands may couple ferromagnetically with the Mn₁₂ core. Unfortunately, magnetic measurements of complex 3 revealed that the sixteen radical carboxylate ligands interact antiferromagnetically with the Mn₁₂ core to yield a S = 2 magnetic ground state. Corresponding author. E-mail: vecianaj@icmab.es Received March 27, 2002; accepted May 2, 2002     

Scoring functions: A view from the bench

Computational approaches to drug design are presently hindered by the complexity of the physical chemistry which underlies weak, non- covalent interactions between protein targets and small molecule ligands. Although a number of programs are now available for the design of novel potential ligands, it remains a key problem to rank these rapidly and reliably by estimated binding affinity. Such a step is necessary to select only the most promising candidates for synthesis and experimental characterisation. To calculate ligand affinity quickly and reliably is an extremely difficult problem, but it may well prove possible to estimate sufficiently accurately given an appropriate set of parameters to score individual protein–ligand interactions. Improvements in the situation will require a wider set of thermodynamically characterised systems than is currently available.     

(μ3-S)FeCo2(CO)7(dppfe)的合成和晶体结构

通过简单取代反应,合成了一个新的混金属簇合物(μ3-S)FeCo2(CO)7(dppfe) (2) (dppfe=Ph2PC5H4FeC5H4PPh2).利用IR,1H NMR,MS 和 X-ray单晶衍射的方法对簇合物2进行了结构表征.簇合物2的晶体属于三斜晶系,空间群为Pī.晶胞参数: a=1.132 4(15) nm, b=1.3670(17) nm, c=1.5769(2) nm,α=114.646(2)°,β=100.340(2)°,γ=100.113(3)°, V=2.0953(5) nm3.