Protein-ligand binding free energy estimation using molecular mechanics and continuum electrostatics. Application to HIV-1 protease inhibitors

A method is proposed for the estimation of absolute binding free energy of interaction between proteins and ligands. Conformational sampling of the protein-ligand complex is performed by molecular dynamics (MD) in vacuo and the solvent effect is calculated a posteriori by solving the Poisson or the Poisson-Boltzmann equation for selected frames of the trajectory. The binding free energy is written as a linear combination of the buried surface upon complexation, SASbur, the electrostatic interaction energy between the ligand and the protein, Eelec, and the difference of the solvation free energies of the complex and the isolated ligand and protein, deltaGsolv. The method uses the buried surface upon complexation to account for the non-polar contribution to the binding free energy because it is less sensitive to the details of the structure than the van der Waals interaction energy. The parameters of the method are developed for a training set of 16 HIV-1 protease-inhibitor complexes of known 3D structure. A correlation coefficient of 0.91 was obtained with an unsigned mean error of 0.8 kcal/mol. When applied to a set of 25 HIV-1 protease-inhibitor complexes of unknown 3D structures, the method provides a satisfactory correlation between the calculated binding free energy and the experimental pIC5o without reparametrization.     

手性钯络合物催化下2-硝基环酮的不对称烯丙基化反应

在用氮杂冠醚改良的手性二茂铁膦与钯的络合物催化下, 2-硝基环酮可进行不对称烯丙基化反应. 讨论了配位基的形状, 反应物的构造, 碱的类型以及反应时间对反应速率和立体选择性的影响. 通过增加反应的空间位阻改进了反应的立体选择性 .     

苯二甲酰基桥联铁硫配合物［（μ－RS）Fe_2（CO）_6］_2（μ－OCC_6

通过由Ｆｅ３（ＣＯ）１２、ＲＳＨ和Ｅｔ３Ｎ所形成的［（μ－ＣＯ）（μ－ＲＳ）Ｆｅ２（ＣＯ）６］Ｅｔ３ＮＨ于室温下分别与对或间苯二甲酰氯的原位反应，首次合成６个结构新颖的苯二甲酰基桥联铁硫配合物［（μ－ＲＳ）·Ｆｅ２（ＣＯ）６］２（μ－ｐ－ＯＣＣ６Ｈ４ＣＯ－ｐ－μ）（Ｒ＝Ｅｔ，ｎ－Ｂｕ，ｔ－Ｂｕ）以及［（μ－ＲＳ）Ｆｅ２（ＣＯ）６］２（μ－ｍ－ＯＣＣ６Ｈ４ＣＯ－ｍ－μ）（Ｒ＝ｎ－Ｐｒ，ｎ－Ｂｕ，ｔ－Ｂｕ）。经元素分析、ＩＲ光谱及１ＨＮＭＲ表征了它们的结构，并讨论了产物的生成过程。此外，还提出了合成对苯二甲酰氯的一种新方法。     

Kinetic studies of nickel speciation in model solutions of a well-characterized humic acid using the competing ligand exchange method

Publications on the binding characteristics of metals with humic acid (HA) are sparse. Here we investigated the release of nickel from Ni(II)-HA complexes using model solutions of three different [Ni(II)]/[HA] mole ratios at three different pH values; we also compared the results with those of [Ni(II)]/[FA] complexes from previous work in this laboratory. Ligand exchange kinetics using the competing ligand exchange method (CLEM) were studied using two different techniques: graphite furnace atomic absorption spectrometry (GFAAS) with Chelex 100 resin as the competing ligand, and adsorptive cathodic stripping voltammetry (AdCSV) with dimethylglyoxime as the competing ligand to measure the rate of dissociation of Ni(II)-HA complexes. The results of the kinetic studies showed that as the [Ni(II)]/[HA] mole ratio was decreased, the rate of dissociation of Ni(II)-HA complexes decreased, and the proportion of free Ni²⁺ ions plus very labile nickel complexes decreased while the proportion of the less labile kinetically distinguishable components increased. Generally, the rate of dissociation of Ni(II)-HA complexes was slower than that of Ni(II)-FA complexes. Studies on the validity of the kinetic model showed that the concentrations of chemical species varied in a reasonable way with pH and the [Ni(II)]/[HA] mole ratios, indicating that the kinetically distinguishable components have chemical significance and the kinetic model is valid.     

Synthesis and Crystal Structure of a New 2D Honeycomb-like Cadmium(II) Complex with Tripodal Ligand

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Affinity Chromatography of Insulin with a Heptapeptide Ligand Selected from Phage Display Library

A heptapeptide phage display library was screened with insulin to find its ligands for affinity chromatography. The peptide was synthesized and coupled to EAH Sepharose 4B (5.4 mol mL^–1 bed). Then, insulin chromatography was carried out with mobile phases of different pH values and by the addition of urea and ethylene glycol. It was found that electrostatic interactions were predominant for the affinity binding, and hydrogen bonding might also contribute somewhat to the affinity. Finally, frontal analysis was performed and the dynamic binding capacity of the affinity column for insulin at 50% breakthrough was estimated at 60.6 mg mL^–1 bed, which was about two times higher than the theoretical binding capacity of the monomeric insulin. The result suggests that insulin was bound in dimer state in a stoichiometric relationship with the coupled peptide, indicating the high binding efficiency of the peptide ligand for insulin.     

Molecular and crystal structures of ruthenium and osmium arene clusters

The molecular and crystal structures of a number of ruthenium and osmium clusters of nuclearity between three and six containing arene fragments such as C₆H₆, C₆H₃Me₃, C₆H₄Me₂ and C₆H₅Me have been investigated. Attention has been focused on the relationship between the terminal ( ⁶-coordination) and face-capping ( ₃: ²: ²: ²-coordination) bonding modes. Empirical packing potential energy calculations have been employed to investigate the intermolecular organization in the crystal. It has been shown that the arene fragments in mono-arene clusters form ribbons, while in bis-arene clusters graphitic-like interactions throughout the crystal are established. The factors controlling the ease of arene reorientational motion in the solid state has also been investigated in relation to the shape, size and geometry of the molecules and of their interlocking modes.     

取代乙酸配体对乙炔二聚反应催化剂性能的影响

研究了取代乙酸配体作为Ｎｉｅｕｌａｎ催化剂对乙炔二聚反应性能的影响。结果表明，不同功能结构数目的影响，结果表明，不同功能结构数目的的氨羧配体均使催化剂的选择性提高。乙炔转化率略有下降，巯基乙酸配体的加入，则改变了乙炔二聚反应的机理，得到以乙醛为主的产物。     

Trifluoromethylated amino alcohols as chiral ligands for highly enantioselective Reformatsky reaction

The enantioselective Reformatsky reaction of PhCHO was achieved by the use of trifluoromethylated amino alcohols as chiral ligands to afford the corresponding optically active β-hydroxy ester with up to 90% ee.