How does huperzine A enter and leave the binding gorge of acetylcholinesterase? Steered molecular dynamics simulations

The entering and leaving processes of Huperzine A (HupA) binding with the long active-site gorge of Torpedo californica acetylcholinesterase (TcAChE) have been investigated by using steered molecular dynamics simulations. The analysis of the force required along the pathway shows that it is easier for HupA to bind to the active site of AChE than to disassociate from it, which for the first time interprets at the atomic level the previous experimental result that unbinding process of HupA is much slower than its binding process to AChE. The direct hydrogen bonds, water bridges, and hydrophobic interactions were analyzed during two steered molecular dynamics (SMD) simulations. Break of the direct hydrogen bond needs a great pulling force. The steric hindrance of bottleneck might be the most important factor to produce the maximal rupture force for HupA to leave the binding site but it has a little effect on the binding process of HupA with AChE. Residue Asp72 forms a lot of water bridges with HupA leaving and entering the AChE binding gorge, acting as a clamp to take out HupA from or put HupA into the active site. The flip of the peptide bond between Gly117 and Gly118 has been detected during both the conventional MD and SMD simulations. The simulation results indicate that this flip phenomenon could be an intrinsic property of AChE and the Gly117-Gly118 peptide bond in both HupA bound and unbound AChE structures tends to adopt the native enzyme structure. At last, in a vacuum the rupture force is increased up to 1500 pN while in water solution the greatest rupture force is about 800 pN, which means water molecules in the binding gorge act as lubricant to facilitate HupA entering or leaving the binding gorge.     

甘氨酸与氯化碱金属在水中的焓相互作用参数

氨基酸在混合溶液中的热力学性质及相互作用的研究不论对溶液化学还是生命科学都是十分重要的．对此国内已有不少的研究h，’1．利用偿效应的方法研究氨基酸与电解质间的相互作用是很有效的卜一句，但大多数的工作都是在低浓度下研究一个氨基酸分子和一个电解质离子对间的相互作用烩．本文测定了甘氨酸在水中和在LICI、NaCI、KCI的水溶液中的溶解偿，计算出甘氨酸与各个公在水中的偿对相互作用参数和三相互作用参数，并由此讨论了甘氨酸与这些盐的对分子相互作用和三分子相互作用．1实验部分试剂：甘氨酸为ARfa，K甲醇一水重结晶．LI…     

Oligodeoxyribonucleotide analogues with bridging dimethylene sulfide,sulfoxide, and sulfone groups. Toward a second-generation model of nucleic acid structure

Short DNA analogues with bridging dimethylene sulfide, sulfoxide, and sulfone groups replacing the phosphate diesters (S-DNAs) were synthesized from building blocks prepared via two routes, both starting from D-glucose. Building blocks for RNA analogues were prepared by stereoselective introduction of nucleobase into a 2'-acylated ribose analogue. The ribose analogues were converted to deoxyribose analogues by replacement of a 3'-OH group by a thioacetyl unit, followed by photolytic deoxygenation or radical-based 2'-deoxygenation. DNA analogues joined via CH(2)(-)S-CH(2) units were prepared by S(N)2 displacement of a 6'-mesyl group on one building block using a thiolate nucleophile of another. 4,4'-Dimethoxytrityl protection and deprotection schemes were established for both the thiol and hydroxyl groups. The corresponding sulfoxide DNA analogues were obtained by oxidation with hydrogen peroxide. Sulfone DNA analogues were obtained by oxidation of the sulfide DNA with persulfate or hydrogen peroxide in the presence of a titanium silicate catalyst. The physical properties of several representative oligonucleotide analogues were examined, and interpreted in light of a "second-generation" model for DNA strand-strand recognition, a model that emphasizes the role of the polyanionic backbone in diminishing unwanted tendencies of highly functionalized molecules to form "structure" in solution. Even short sulfide-linked DNA analogues displayed association properties different from those displayed by standard DNA molecules. Complex formation observed with sulfide-linked tetramers by HPLC study in different solvents suggested that the complex is formed using hydrogen bonding. Sulfone-linked dinucleotides display Watson-Crick behavior; the tetramer, however, displayed self-structure. Self-structure and self-aggregation become more prominent as the length of the oligonucleotide analogues increases. The tendency to self-aggregate can be decreased by adding a charged sulfonate group to the 3'-end of the DNA analogue. Features of the second-generation model are important for many areas of nucleic acid chemistry, from the design of nucleic acid therapeutic agents to the search for life on other planets.     

A Novel Fluorescent Aminoacid Designed for Fluorometric Detection of Cu （Ⅱ）

A fluorescent aminoacid was designed for selective and sensitive detection of Cu(II) in aqueous solution. The designing of this Cu(II) fluorescent chemosensing molecule, N ± (1‐naphthyl). aminoacetic acid (NAA), was based on the binding of Cu(II) to aminoacetic acid and the novel charge transfer photophysics of 1‐aminonaphthalenes. The fluorescence of NAA was found quenched by Cu (II) and several other metal ions of similar electronic structure such as Co(II), Ni(II) and Zn(II). The quenching was shown to occur via electron transfer within the metal‐NAA complex, which required an optimal combination of high binding affinity and favorable redox properties of the components in the metal‐NAA complex and hence afforded selective fluorometric detection of Cu(II). The calibration graph obeyed Stern‐Volmer theory and was shown for Cu(II) over the range of 0–2.75 ± 10–⁴ mol/L. The quenching constant of Cu(II) was measured as 8.0 ± 10³ mol/L that was two orders of magnitude higher than those of Co(II), Ni(II) and Zn(II). The 3SD limit of detection for Cu(II) was 8.00 ± 10^?6 mol/L with a coefficient of variation of 1.65%. Linear range for quantitative detection of Cu(II) was 2.67 ± 10^?5‐2.75 ± 10^?4 mol/L. The method was applied to synthetic sample measurements which gave recoveries of 105%‐112%.     

Ab initio global potential-energy surface for H5(+) --> H3(+) + H2

An accurate global potential-energy surface (PES) is reported for H5(+) based on more than 100,000 CCSD(T)/aug-cc-pVTZ ab initio energies. This PES has full permutational symmetry with respect to interchange of H atoms and dissociates to H3(+) and H2. Ten known stationary points of H5(+) are characterized and compared to previous ab initio calculations. Quantum diffusion Monte Carlo calculations are performed on the PES to obtain the zero-point energy of H5(+) and the anharmonic dissociation energy (D0) of H5(+) --> H3(+) + H2. The rigorous zero-point state of H4D+ is also calculated and discussed within the context of a strictly classical approach to obtain the branching ratio of the reaction H4D+ --> H3(+) + HD and H2D+ + H2. Such an approach is taken using the PES and critiqued based on the properties of the quantum zero-point state. Finally, a simple procedure for adding the long range-interaction energy is described.     

Low-dimensional hybrid copper halides with novel D6R Cu(6)I(6) cores

Two low-dimensional hybrid copper halides, (2,2'-bipy)Cu(3)I(3) (1) and (2,2'-bipy)Cu(4)I(4) (2) (2,2'-bipy = 2,2'-bipyridine), with novel D6R (double six-membered rings) Cu(6)I(6) cores were synthesized by hydro(solvo)thermal reactions and characterized by single-crystal X-ray diffraction.     

一阶导数差示脉冲极谱法用于甲硝唑的定量研究

本实验运用一阶导数差示脉冲极谱法对甲硝唑及其制剂进行了定量研究。在０．００１ｍｏｌ／Ｌ氯化钾－０．００１ｍｏｌ／Ｌ盐酸－水（１＋０．２＋４８）的底液中，甲硝唑于－０．８００Ｖ（ｖｓ Ａｇ／ＡｇＣｌ）处出现一良好的一阶导数差示脉冲极谱峰，在５０～３００μｇ／ｍＬ范围内，药物浓度与其导数峰幅值呈线关系，检测限为８．０×１０＾－８ｍｏｌ／Ｌ。本法操作简便，快速，灵敏，结果准确。     

Further Daphniphyllum Alkaloids from the Leaves of Daphniphyllum macropodum Miq.

Five new polycyclic Daphniphyllum alkaloids, macropodumines F ( 1 ) and G ( 2 ), 17‐oxoyuzurimine ( 3 ), and macropodumines H ( 4 ) and I ( 5 ), were isolated from the leaves of D. macropodum Miq ., collected in Sichuan Province, China. The structures and relative configurations of the new compounds – as well as of four known, related alkaloids – were elucidated on the basis of in‐depth spectroscopic and mass‐spectrometric analyses, by chemical derivatization, and by comparison of spectroscopic data with those of known compounds.     

Binding sites of nitrogenase: kinetic and theoretical studies of cyanide binding to extracted FeMo-cofactor derivatives

The first kinetic study of a substrate (CN(-)) binding to the isolated active site (extracted FeMo-cofactor) of nitrogenase is described. The kinetics of the reactions between CN(-) and various derivatives of extracted FeMo-cofactor [FeMoco-L; where L is bound to Mo, and is NMF, Bu(t)NC, or imidazole (ImH)] have been followed using a stopped-flow, sequential-mix method in which the course of the reaction is followed indirectly, by monitoring the change in the rate of the reaction of the cofactor with PhS(-). The kinetic results, together with DFT calculations, indicate that the initial site of CN(-) binding to FeMoco-L is controlled by a combination of the electron-richness of the cluster core and lability of the Mo-L bond. Ultimately, the reactions between FeMoco-L and CN(-) involve displacement of L and binding of CN(-) to Mo. These reactions occur with a variety of rates and rate laws dependent on the nature of L. For FeMoco-NMF, the reaction with CN(-) is complete within the dead-time of the apparatus (ca. 4 ms), while with FeMoco-CNBu(t) the reaction is much slower and exhibits first order dependences on the concentrations of both FeMoco-CNBu(t) and CN(-) (k = 2.5 +/- 0.5 x 10(4) dm(3) mol(-1) s(-1)). The reaction of FeMoco-ImH with CN(-) occurs at a rate which exhibits a first order dependence on FeMoco-ImH but is independent of the concentration of CN(-) (k = 50 +/- 10 s(-1)). The results are interpreted in terms of CN(-) binding directly to the Mo site for FeMoco-NMF and FeMoco-ImH, but with FeMoco-CNBu(t) initial binding at an Fe site is followed by movement of CN(-) to Mo. Complementary DFT calculations are consistent with this interpretation, indicating that, in FeMoco-L, the Mo-L bond is stronger for L = ImH than for L = CNBu(t) and the binding of CN(-) to Mo is stronger than to any Fe atom in the cofactor.     

Self-assembly of electron donor-acceptor dyads into ordered architectures in two and three dimensions: surface patterning and columnar "double cables"

We report the synthesis and characterization of covalent dyads and multiads of electron acceptors (A) and donors (D), with the purpose of exploiting their nanophase separation behavior toward (a) two-dimensional (2D) surface patterning with well-defined integrated arrays of dissimilar molecular electronic features and (b) bulk self-assembly to noncovalent columnar versions of the so-called "double cable" systems, the likes of which could eventually provide side-by-side percolation pathways for electrons and holes in solar cells. Soluble, alkylated hexa-peri-hexabenzocoronenes (HBCs) bearing tethered anthraquinones (AQs) are shown by scanning tunneling microscopy (STM) to self-assemble at the solution-graphite interface into either defect-rich polycrystalline monolayers or extended 2D crystalline domains, depending on the number of tethered AQs. In the bulk, the thermal stability of the room-temperature HBC columnar phase is increased, which is attributed to the desired nanotriphase separation of HBC columns, insulating alkyl sheaths, and AQ units. Homeotropic alignment (columns normal to surfaces), predicted to be ideal for potential exploitation of such "double cables" in photovoltaic devices, is demonstrated.