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.     

On-line identification of tropane alkaloids from Erythroxylum vacciniifolium by liquid chromatography-UV detection-multiple mass spectrometry and liquid chromatography-nuclear magnetic resonance spectrometry

The bark of catuaba (Erythroxylum vacciniifolium Martius, Erythroxylaceae), a tree native to the northern part of Brazil, was investigated for its alkaloid content. With the aim of obtaining preliminary structure information on-line, the alkaloid extract was analysed by high-performance liquid chromatography coupled to diode array UV detection, to mass spectrometry and to nuclear magnetic resonance. Interpretation of on-line spectroscopic data obtained from this extract led to structural elucidation of six new alkaloids and partial identification of 18 potentially original alkaloids bearing the same tropane skeleton esterified in positions 3 and 6 by 1-methyl-1H-pyrrol-2-carboxylic acid and/or 4-hydroxy-3,5-dimethoxybenzoic acid.     

Synthesis of 3-amino-5-nitrobenzaldehyde oxime and its conversion into 3,4-bis(3-amino-5-nitrophenyl)furoxan and isomeric 3(4)-(3-amino-5-nitrophenyl)-4(3)-nitrofuroxans

The oxime of the hitherto unknown 3-amino-5-nitrobenzaldehyde was synthesized by the reaction of 3-amino-5-nitrobenzaldehyde phenylhydrazone with excess of (NH₂OH)₂·H₂SO₄. The oxime obtained was used as the starting compound for the synthesis of novel diaryl- and arylnitrofuroxans. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 12, pp. 2232–2235, December, 1997.     

Observation of self-ion-molecule reactions during collisionally activated dissociation in an ion-trap mass spectrometer

This paper describes the formation of protonated molecules ([M + H]+) and adduct ions by self-ion-molecule reactions (SIMR) during collisionally activated decomposition (CAD) of methyne addition ions ([M + CH]+) produced from chemical ionization (CI) or SIMR in both an external and internal source ion-trap mass spectrometer (ITMS). The CAD results for the methyne addition ions of dopamine produced from both SIMR and dimethyl ether CI undertaken in the external and internal source ITMS were compared in order to prove the occurrence of SIMR during CAD processes. Compared with the external source ITMS, the internal source ITMS is much more easily applicable to this type of reaction owing to the large population of neutral analytes present in the trap.     

异亚硝基乙酰乙酸乙酯亚胺Pd(Ⅱ)配合物的合成、表征和tran Pd(p-CH3C6H4-IEAI)2的晶体结构

Six palladium(Ⅱ) complexes with isonitrosoethylacetoacetate imine Schiff base ligands, Pd(R-IEAI)₂, were prepared and characterized by IR, Raman and electronic spectra. Complex tran Pd(p-CH₃C₆H₄-IEAI)₂ (2) cry- stallizes in the monoclinic system, space group P2₁/c,with a=1.2002(2),b=0.9972(2),c=1.1121(2)nm,β=90.43(3)°,Z=2,F(000)=616,μ=7.44cm^-1. The final R and wR are 0.0244 and 0.0625 for 2620 ob-served reflections with I≥2σ(I), respectively. The geometry around the Pd(Ⅱ) ions in those complexes has a distorted PdN₄ square plane, the Schiff base ligands R-IEAI^- being coordinated through their oximino-nitrogen atoms and imino-nitrogen atoms.     

N-取代苯甲酰基-N'-取代芳基硫脲的合成、晶体结构及生物活性

为了寻找新的高活性农药, 利用工业易得的三氟羧草醚及其中间体为起始原料, 设计合成了9个未见报道的N-取代苯甲酰基-N'-取代芳基硫脲化合物, 结构经IR, ¹H NMR, 元素分析确认. X射线衍射测定了化合物4b的晶体结构, 结果表明: 其分子属于三斜晶系, 空间群P-1, a＝0.51588(19) nm, b＝1.0766(4) nm, c＝2.0596(8) nm, α＝81.113(6)°, β＝89.702(6)°, γ＝78.131(6)°, V＝1.1056(7) nm³, D_c＝1.445 Mg/m³, Z＝2, F(000)＝492, μ＝0.319 mm^－1. 初步生物活性测试结果表明, 部分化合物具有较好的除草活性.     

Determining the chromophore in the amylopectin–iodine complex by theoretical and experimental studies

A partial hydrolysis of amylose followed by the addition of iodine provides a spectrum almost identical to that of the amylopectin–iodine (API) complex suggesting the involvement of smaller “amylose-like” units in the API complex. Our theoretical studies on different polyiodine and polyiodide species suggest that a nearly linear I₄ unit stabilized within the cavity of a small “amylose-like” helix is responsible for the characteristic API spectrum. Since there are 2.75 anhydroglucose residues (AGU) for every iodine atom in the amylose–iodine (AI) complex and a structural similarity exists between the API and the AI (amylose–iodine) complexes, we identify (C₆H₁₀O₅)₁₁I₄ to be the chromophore in the API complex. © 1994 John Wiley & Sons, Inc.     

Organoelement Compounds with Al?Al,Ga?Ga,and In?In Bonds

In the attempt to synthesize compounds with aluminum in a low oxidation state and an Al Al bond, by the reduction of alkylaluminum halides with alkali metals, analogous to a Wurtz coupling, in general the deposition of elemental aluminum and the formation of the corresponding trialkylaluminum compounds is observed. Thus, tetrasubstituted dialuminum compounds R₂Al AlR₂, apart from a few poorly characterized examples, were for a long time considered part of an unverified class of substances. Only with the sterically very highly shielded tetrakis[bis(trimethylsilyl)methyl]dialuminum did we achieve the synthesis of the first completely characterized organoelement compound with unlimited stability, which shows aluminum in the oxidation state + II and has an Al Al bond. In the meantime, corresponding compounds for the elements gallium and indium have been obtained. With the simple access to tetrasubstituted dimetal compounds, a fascinating new research area has opened for preparative chemistry, in which the particular interest will naturally lie in the reactive properties of the metal-metal bond.     

Probing in vitro digestion at oil–water interfaces

Interfacial layers have been widely applied to study the formation and stability of emulsion-based systems. However, the application of isolated interfaces to address digestibility of emulsions is often limited because of the complexity of experimental methods and results. This review summarizes the latest developments in analytical methods and literature data on effects of digestion on interfacial layers. Particular emphasis is given to understand the changes on interfacial magnitudes during oral, gastric, and duodenal digestion, either applied separately or sequentially. Limitations of interfacial aspects and key factors that influence emulsion microstructure in bulk and lipid digestion are identified. Understanding the behavior of interfacial layers upon gastrointestinal digestion promotes an accurate tracking of the physiological fate of emulsions.     

Fermentation characteristics and the dynamic trend of chemical components during fermentation of Massa Medicata Fermentata

As a representative of traditionally fermented Chinese medicine, Massa Medicata Fermentata (MMF) shows the functions of invigorating the spleen and stomach and promoting digestion, which plays an important role in the treatment of gastrointestinal diseases. The fermentation mechanism and the key factors that affect the quality of MMF have not been revealed yet, which has become an urgent issue that limits its clinical application. This article aims to systematically and comprehensively reveal the transformation of physical properties and the dynamic trend of chemical components including substrate components, volatile components, and lactic acid as anaerobic fermentation product during MMF fermentation. Along with obvious hyphae growth observed for MMF, the weight of MMF decreased, and the moisture and temperature increased. Through the quantified 14 components from substrate, ferulic acid increased from 45.53 ± 6.94 to 141.89 ± 78.40 μg/g, while glycosides and phenolic acids declined except caffeic acid. Also, within the 66 volatile components analyzed, alcohols and acids increased, while aldehydes and ketones decreased. Lactic acid was not detected in the fermentation substrate, but an apparent increase in lactic acid content was observed along with the increased fermentation days, resulting in 2.54 ± 0.15 mg/g on day 8. Based on the tested components, the fermentation process of MMF was discriminated into three distinct stages by principal component analysis, and an optimal fermentation time of four days was proposed. The results of this study will be of great significance to clarify the characteristics of fermentation and conduce to improving quality standards of MMF.