Determination of adsorption and speciation of chromium species by saltbush (Atriplex canescens) biomass using a combination of XAS and ICP-OES

Studies were performed to determine the effect of pH on chromium (Cr) binding by native, esterified, and hydrolyzed saltbush (Atriplex canescens) biomass. In addition, X-ray absorption spectroscopy studies were performed to determine the oxidation state of Cr atoms bound to the biomass. The amounts of Cr adsorbed by saltbush biomass were determined by inductively coupled plasma-optical emission spectroscopy (ICP-OES). For Cr(III), the results showed that the percentages bound by native stems, leaves, and flowers at pH 4.0 were 98%, 97%, and 91%, respectively. On the other hand, the Cr(VI) binding by the three tissues of the native and hydrolyzed saltbush biomass decreased as pH increased. At pH 2.0 the stems, leaves, and flowers of native biomass bound 31%, 49%, and 46%, of Cr(VI), respectively. The results of the XAS experiments showed that Cr(VI) was reduced in some extend to Cr(III) by saltbush biomass at both pH 2.0 and pH 5.0. The XANES analysis of the Cr(III) reaction with the saltbush biomass parts showed an octahedral arrangement of oxygen atoms around the central Cr(III) atom. The EXAFS studies of saltbush plant samples confirmed these results.     

酞菁（H_2TAP）的X－射线光电子能谱（XPS）

酞菁（Ｈ_２ＴＡＰ）的Ｘ－射线光电子能谱（ＸＰＳ）朱志昂，卜显和，刘月霞（南开大学化学系天津３０００７１）ＰａｕｌＧ．Ｇａｓｓｍａｎ（美国明尼苏达大学化学系）关键词酞青，ＸＰＳ，Ｃ１ｓ电子结合能，Ｎ１ｓ电子结合能酞菁及其金属配合物作为叶绿素，血红素的?..     

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.     

Metabolomic-based investigation of Yinlan alleviating hyperlipidemia by inhibiting blood stasis and phlegm turbidity through the PXR-CYP3A4-ABCB1-FXR pathway

Yinlan lipid regulatory capsule (YL) is a composite traditional Chinese medicine (TCM) new drug to alleviate hyperlipidemia, while its therapeutic mechanism in vivo was not clarified with nontargeted metabolomics investigation. An animal model was established in rats fed a high-fat diet, and their body weights, body mass index (BMI) and blood cholesterol levels were measured. Serum, liver and kidney tissue samples were also extracted for PXR-CYP3A4-ABCB1-FXR signaling pathway research using PCR and UHPLC–MS. The obtained plasma samples were analyzed by UHPLC-Q-TOF-MS metabolomic investigation, which revealed PXR-CYP3A4-related metabolites and changes induced by YL. Finally, the key metabolites were chosen as index components, and their levels in the serum, liver, small intestine and bile were used for simultaneous UHPLC–MS-MS determination. The results indicated that YL was effective in rebalancing blood TG and TC levels (compared to controls). With respect to the PXR-CYP3A4-ABCB1 pathway, as a result of YL’s effect, gene expression or activity of the two targets decreased significantly in both the liver and kidney. The same trend was observed in the serum samples mentioned above. Metabolomics screening and data revealed that 44 metabolites can be regarded as biomarkers related to hyperlipidemia, fatty acids synthesis, and body energy consumption, as well as synthesis, transportation and exertion of cholesterol. YL’s treatment focused on 26 of them, primarily bile acids, indicating that the antihyperlipidemic effect of this drug lies in its inhibitory activity of cholesterol metabolism. Subsequent analysis of those in vivo components revealed that significant increases (compared to the model group) occurred in the blood, liver, small intestine and bile in groups that received medium and high doses of YL (while the low dose was relatively unchanged). Those target components exhibit a close relationship with PXR and/or CYP3A4. The use of YL repressed PXR expression and subsequently decreased CYP3A4 activity. As a result, synthesis of related bile acids increased, while cholesterol levels decreased, consequently leading to the attenuation of hyperlipidemia. This study comprehensively investigated the antihyperlipidemia mechanism of YL based on its repression of PXR-CYP3A4 activity and related metabolite yield, establishing an accurate method for evaluating the therapeutic effect of YL.     

Hydrogen-bonded assembly and binding affinity of the multi-point acceptor and isophthalic acid

Supermolecular complexes formed by oligophenyleneethynylene derivatives and isophthalic acid were studied using AM1 method to obtain binding energy. Electronic spectra and IR spectra of the complexes were calculated by INDO/CIS and AM1 methods based on AM1 geometries. Results indicated that the dimer could be formed by the monomers via hydrogen bonding because of the negative binding energy. Binding energy of the complexes was affected by electronegativity and steric effects of the substituents. The first UV absorptions and IR frequencies of N-H bonds of the complexes were both red-shifted compared with those of the monomers. The complexes could bind small molecules via hydrogen bonds, resulting in the change in UV absorptions and an increase in IR frequencies of N-H bonds.     

Synthesis and peptide-binding properties of a luminescent pyrimidine zinc(II) complex

The synthesis and peptide-binding properties of a Zn(II)nitrilotriacetate complex substituted with pyrimidine hydrazine amides are reported. The metal complex provides millimolar binding affinity in aqueous buffer to peptides bearing N-terminal His. The pyrimidine heterocycles intermolecularly interact with the bound peptide and quench the emission of nearby Trp residues by energy transfer.     

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.     

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).     

Golden crowns: cation binding by macrocyclic gold(I) crown ether derivatives

The polyether bis(alkynes) α,ω-bis(O-propargyl)triethylene glycol and α,ω-bis(O-4-propargyloxyphenoxy)triethylene glycol reacted with [AuCl(SMe₂)] in the presence of base to form the corresponding oligomeric gold(I) acetylide complexes (AuCCCH₂O(CH₂CH₂O)₃CH₂CCAu)_n and (AuCCCH₂OC₆H₄O(CH₂CH₂O)₃C₆H₄OCH₂CCAu)_n. These digold(I) diacetylide complexes reacted with diphosphine ligands to give macrocyclic digold(I) complexes of the type [Au₂(μ-CC)(μ-PP)], where CC is the diacetylide and PP is a diphosphine ligand. These digold(I) complexes bind the cations Li⁺, Na⁺, K⁺ and Cs⁺, as studied by electrospray mass spectrometry.     

UO22＋•nH2O和PuO22＋•nH2O (n＝2, 4, 5, 6)密度泛函理论研究

首先用密度泛函理论(DFT)方法研究了铀酰和钚酰离子的几何与电子结构, 计算结果与实验基本符合, 表明DFT方法也能用于含铀和钚重原子的化合物计算. 然后对铀酰和钚酰水合离子的几何构型、Mulliken集居数分布以及铀酰(钚酰)与配体水分子的结合能进行计算, 计算结果表明UO₂^2＋•5H₂O和PuO₂^2＋•5H₂O分别为铀酰和钚酰系列水合离子中最稳定的配合物.