Binding Ensembles of p53-MDM2 Peptide Inhibitors by Combining Bayesian Inference and Atomistic Simulations

Designing peptide inhibitors of the p53-MDM2 interaction against cancer is of wide interest. Computational modeling and virtual screening are a well established step in the rational design of small molecules. But they face challenges for binding flexible peptide molecules that fold upon binding. We look at the ability of five different peptides, three of which are intrinsically disordered, to bind to MDM2 with a new Bayesian inference approach (MELD × MD). The method is able to capture the folding upon binding mechanism and differentiate binding preferences between the five peptides. Processing the ensembles with statistical mechanics tools depicts the most likely bound conformations and hints at differences in the binding mechanism. Finally, the study shows the importance of capturing two driving forces to binding in this system: the ability of peptides to adopt bound conformations (ΔGconformation) and the interaction between interface residues (ΔGinteraction).     

Crystallization of binary carboxylic acids characterized with streaming potential measurement

The streaming potential of supersaturated solution of binary carboxylic acids, which have even carbon atoms, was determined to characterize crystallization under different temperatures. The value of the streaming potential was related to the type and solubility of the acids and the starting temperature of crystallization, and was easily influenced by the pressure difference of the liquid or the rate of temperature decline. When the temperature was declined to the point where a crystal nucleus appeared, the streaming potential reached the minimum. Thereafter, as the temperature was sequentially lowered, some minicrystals grew, and the streaming potential presented an ascendant tendency. The higher the starting temperature of the acids saturated solution, the higher is the temperature corresponding to the streaming potential minimum. The less the carbon atoms in the acids and the greater the solubility of the acids are, the higher is the temperature of the streaming potential minimum. Copyright © 2007 John Wiley & Sons, Ltd.     

Biocatalytic Synthesis of Highly Enantiopure 1,4-Benzodioxane-2-carboxylic Acid and Amide

Catalyzed by Rhodococcus erythropolis AJ270, a nitrile hydratase and amidase containing microbial whole-cell catalyst, at 10 ℃ and with the use of methanol as a co-solvent, nitrile and amide biotransformations produce 2S-1,4-benzodioxane-2-carboxamide and 2R-1,4-benzodioxane-2-carboxylic acid in high yields with excellent enantioselectivity.     

A new convenient synthesis of N-acyl-2-(dimethoxyphosphoryl)glycinates

Easily accessible N-acyl-2-triphenylphosphonioglycinate tetrafluoroborates react smoothly with trimethylphosphite in the presence of methyltriphenylphosphonium iodide to give N-acyl-2-(dimethoxyphosphoryl)glycinates in good or very good yields. The dimethoxyphosphorylglycinates may be isolated by column chromatography, or used directly for the Wadsworth-Emmons synthesis of α,β-dehydro-α-amino acids in a one-pot procedure without purification.     

Synthesis,crystal structure and characterization of a 2-D network organic-inorganic hybrid polymer with α-BW_(12)O_(40) ~(5-) as building blocks

A two-dimensional network compound [Ce(DMF)4(H2O)][α-BW12O40]·H2O·(HDMA)2 (HDMA = protoned dimethylamine, DMF = N,N-dimethylformamide) was synthesized from α-H5BW12O40·nH2O, Ce(NO3)3·6H2O and DMF and characterized by IR, UV spectra and TG-DTA. The result of the X-ray single crystal diffraction indicates that the crystal is monoclinic, space group P21/n, with unit cell dimensional: a = 1.1983(3), b = 2.4216(5), c = 1.9517(4) nm, β = 92.91(3)°, Z = 4, R1 = 0.07710, wR2 = 0.1416. Structural analysis indicates that every [Ce(DMF)4(H2O)]3 building block is surrounded by three adjacent [α-BW12O40]5- polyanions, meanwhile, every [α-BW12O40]5- polyanion interconnects with three neighboring [Ce(DMF)4(H2O)]3 subunits, by making use of which two-dimensional network structure can be constructed. The result of thermogravimetric analysis manifests that the title compound has two-stage weight loss and the decomposition temperature of the title polyanionic framework is 560℃ . The electrochemical analysis shows the title polyanion has three-step redox processes in the pH = 4―7 media.     

H2CCF自由基与HNCO反应机理的理论研究

采用密度泛函理论的B3LYP方法, 在6-311＋＋G(d,p)基组水平上研究了H₂CCF自由基与HNCO的微观反应机理, 优化了反应过程中的反应物、中间体、过渡态和产物, 为了获得更精确的能量信息, 还在QCISD(T)/6-311＋＋G(d,p)基组水平上计算了各物质的能量．振动分析结果和IRC分析结果证实了中间体和过渡态的真实性, 计算所得的成键临界点电荷密度的变化也确认了反应过程．对于H₂CCF自由基与HNCO反应, 我们找到了六条可行的反应通道, 结果分析表明通道H₂CCF＋HNCO→IM3→TS5→H₂CCFH＋NCO控制步骤活化能最低, 是该反应的主要通道, 在此反应过程中有稳定的氢键复合物IM3生成, 还表现出氢原子迁移的反应特征．     

Diastereoselective addition of organolithiums to 1,3-oxazolidines complexed with aluminum tris(2,6-diphenylphenoxide) (ATPH)

1,3-Oxazolidines were easily obtained by condensation of N-substituted (R)-phenylglycinol with aldehydes. Addition of organolithium reagents to 1,3-oxazolidines by complexation with the bulky Lewis acid aluminum tris(2,6-diphenylphenoxide) (ATPH) readily produced the corresponding chiral amines with good yield and high diastereoselectivity. The configuration of the new stereogenic center was shown to be opposite to that of adducts obtained for the same 1,3-oxazolidines using Grignard reagents. The best diastereoselectivity was achieved using N-isopropyl-1,3-oxazolidines. The mechanism of addition was deduced by determining the stereochemistry of the iminium-aluminum complex by NOE experiments.     

新型手性Salen双核锌配合物的分子识别研究

合成了新型手性Salen配体（H3L）及新型手性Salen双核锌配合物（主体）.通过研究主体对咪唑类客体及氨基酸酯类客体的分子识别行为,测定了这些配位反应的缔合常数.主体对咪唑类客体分子识别的缔合常数顺序为:K(Im) >K(2-MeIm) >K(2-Et-4-MeIm).主体对氨基酸酯类客体分子识别的缔合常数顺序为:K(LeuOCH3) >K(ValOCH3) >K(AlaOCH3) >K(SerOCH3),配位数均为2.主体与D、 L型氨基酸酯分子识别反应在不同温度下的缔合常数结果表明,随着温度的升高,对映选择性下降.实验发现反应体系中存在焓熵补偿关系. CD光谱的研究结果也反映了主体对不同客体识别能力的差异.     

Rapid analysis of triterpenic acids by liquid chromatography using porous graphitic carbon and evaporative light scattering detection

An original system which uses Porous Graphitic Carbon as support and a mixture of organic solvents as mobile phase is proposed for the analysis of triterpenic acids by liquid chromatography. The separation of betulinic acid, ursolic acid, oleanolic acid, and 18alpha- and 18beta-glycyrrhetinic acids was carried out within a short time and monitored by evaporative light scattering detection as universal detection method. Molecular modelling studies show that the main contribution to the selectivity comes from the electrostatic interaction characterised by the dipole moment of the products.     

Ab Initio High Pressure Investigations of InI

The high pressure behaviour of InI is studied by DFT‐calculations and compared with experimental data. The existence of a 5s² electron pair in In⁺ represents an unfavourable bonding situation for high symmetry structures because of effective closed shell repulsion. Since cations with a ns² electron pair are highly polarizable and the electronic situation is more favourable in the low symmetry structure InI prefers a TlI‐type structure at ambient pressure. A pressure induced transition to the more densely packed high symmetry CsCl‐type structure takes place at about 19 GPa according to our calculations. At ambient pressure the interactions are predominantly ionic. However with increasing pressure the distances between In⁺ cations in the TlI‐type structure diminish drastically, mainly due to the changing space requirement of the lone electron pair. Apart from ionic interactions further bonding interactions between the In⁺ cations occur. At elevated pressure the electron localization function (ELF) as well as the band structure diagrams suggest metallic bonding between the In⁺ within the zigzag chain, i. e. increasing bonding interactions between the In⁺ cations due to the electron pair and its s‐p‐mixing. At ambient pressure In‐In interactions are rather weak and the space requirement of the lone electron pair mainly determines the characteristic arrangement of the ions. At elevated pressure the In‐In interactions become stronger and stabilise themselves additionally the specific structural arrangement.