Enhancement in the rate of conversion of peptide Cys-Pro esters to peptide thioesters by structural modification

We previously reported that the peptide containing a Cys-Pro ester (CPE) moiety is spontaneously transformed into a peptide thioester via an N to S acyl shift followed by diketopiperazine formation. In an attempt to identify more reactive structures for the formation of a peptide thioester, we modified the CPE structure, in which the Pro residue in the CPE moiety was replaced with N-substituted glycine derivatives. These peptides were transformed into a peptide thioester more rapidly. Alternatively, the addition of an amino acid residue at the C-terminus of the CPE moiety also accelerated thioester formation.     

On the induced‐fit mechanism of substrate‐enzyme binding structures of nylon‐oligomer hydrolase

We present a detailed computational investigation of the induced‐fit motion in a nylon‐oligomer hydrolase (NylB) upon substrate binding. To this aim, we resort on the recently introduced parallel cascade selection molecular dynamics approach, allowing for an accelerated access to the set of conformational changes from an open‐ to a closed‐state structure to form the enzyme‐substrate complex in a specific induce‐fit mechanism. The structural investigation is quantitatively complemented by free energy analyses within the umbrella sampling algorithm accompanied by weighted histogram analysis. We find that the stabilization free energy is about 1.4 kcal/mol, whereas the highest free energy barrier to be overcome is about 2.3 kcal/mol. Conversely, the energetic contribution for the substrate binding is about 20 kcal/mol, as estimated from Generalized Born/Surface Area. This means that the open‐close induced‐fit motion could occur frequently once the substrate binds to the open state of NylB. © 2014 Wiley Periodicals, Inc.     

A Defective Nanotube Molecule of C552H496N24 with Pyridinic and Pyrrolic Nitrogen Atoms

A 3-nm molecule comprising a cylindrical core and cross-shaped rims was designed and synthesized by developing a modular synthetic route. By using a cyclic precursor from previous studies as a starting material, multiple carbazole units were installed at the rims of the defective cylinder. The defective cylinder was synthetically doped with two types of nitrogen atoms, that is, pyridinic and pyrrolic nitrogen atoms, which resulted in solvatochromic shifts in fluorescence by charge-transfer interactions. The structure of the large, C₅₅₂H₄₉₆N₂₄ molecule was fully disclosed by crystallographic analyses, and the unique helical arrangement of nitrogen-doped cylinders in the crystal was revealed.     

Acidic‐pH‐Activatable Fluorescence Probes for Visualizing Exocytosis Dynamics

Live imaging of exocytosis dynamics is crucial for a precise spatiotemporal understanding of secretion phenomena, but current approaches have serious limitations. We designed and synthesized small‐molecular fluorescent probes that were chemically optimized for sensing acidic intravesicular pH values, and established that they can be used to sensitively and reliably visualize vesicular dynamics following stimulation. This straightforward technique for the visualization of exocytosis as well as endocytosis/reacidification processes with high spatiotemporal precision is expected to be a powerful tool for investigating dynamic cellular phenomena involving changes in the pH value.     

Three Distinct Redox States of an Oxo‐Bridged Dinuclear Ruthenium Complex

A series of [{(terpy)(bpy)Ru}(μ‐O){Ru(bpy)(terpy)}]ⁿ⁺ ( [RuORu]ⁿ⁺ , terpy=2,2′;6′,2′′‐terpyridine, bpy=2,2′‐bipyridine) was systematically synthesized and characterized in three distinct redox states (n=3, 4, and 5 for Ru^II,III₂ , Ru^III,III₂ , and Ru^III,IV₂ , respectively). The crystal structures of [RuORu]ⁿ⁺ (n=3, 4, 5) in all three redox states were successfully determined. X‐ray crystallography showed that the Ru? O distances and the Ru‐O‐Ru angles are mainly regulated by the oxidation states of the ruthenium centers. X‐ray crystallography and ESR spectra clearly revealed the detailed electronic structures of two mixed‐valence complexes, [Ru^IIIORu^IV]⁵⁺ and [Ru^IIORu^III]³⁺ , in which each unpaired electron is completely delocalized across the oxo‐bridged dinuclear core. These findings allow us to understand the systematic changes in structure and electronic state that accompany the changes in the redox state.     

“非保护型”金属胶体纳米簇形成机理研究

碱-乙二醇法制备的"非保护型"金属及合金纳米簇由表面吸附的溶剂分子和简单离子实现稳定化,它们被广泛用于制备高性能复相催化剂和研究复相催化剂中的尺寸、组成、载体表面基团以及修饰剂对催化性能的影响。关于此类非保护金属纳米簇的形成过程及机理的认识尚有待进一步深化。本文采用原位快速扫描X射线吸收精细结构谱(QXAFS)、原位紫外-可见(UV-Vis)吸收光谱、透射电子显微镜和动态光散射技术研究了碱-乙二醇法合成中非保护型金属胶体纳米簇的形成过程与机理。结果表明,在碱-乙二醇法合成非保护型Pt金属纳米簇的过程中,室温下即有部分Pt(IV)被还原至Pt(II)。随着反应温度的升高,OH-逐渐取代与Pt离子配位的Cl-,在Pt―Pt键形成之前,反应体系的UV-Vis吸收光谱中可观察到明显的纳米粒子的散射信号,原位QXAFS分析表明Pt纳米簇是由Pt氧化物纳米粒子还原所形成的;在Ru金属纳米簇的形成过程中,OH-首先取代了Ru Cl_3中的Cl~-,形成羟基配合物Ru(OH) _6~(3-),后者进一步缩合形成氧化钌纳米粒子,最终Ru金属纳米簇由乙二醇还原氧化钌纳米粒子形成。由于先形成了氧化物纳米粒子,后续的还原反应被限制在氧化物纳米粒子内,使最终得到的非保护型金属纳米簇具有尺寸小、分布窄的特点。本工作所获得的知识对发展高性能能源转化催化剂、精细化学合成催化剂、传感器等功能体系具有重要意义。     

Biosynthesis of Indole Diterpene Lolitrems: Radical‐Induced Cyclization of an Epoxyalcohol Affording a Characteristic Lolitremane Skeleton

Lolitrems are tremorgenic indole diterpenes that exhibit a unique 5/6 bicyclic system of the indole moiety. Although genetic analysis has indicated that the prenyltransferase LtmE and the cytochrome P450 LtmJ are involved in the construction of this unique structure, the detailed mechanism remains to be elucidated. Herein, we report the reconstitution of the biosynthetic pathway for lolitrems employing a recently established genome‐editing technique for the expression host Aspergillus oryzae. Heterologous expression and bioconversion of the various intermediates revealed that LtmJ catalyzes multistep oxidation to furnish the lolitrem core. We also isolated the key reaction intermediate with an epoxyalcohol moiety. This observation allowed us to establish the mechanism of radical‐induced cyclization, which was firmly supported by density functional theory calculations and a model experiment with a synthetic analogue.     

Half‐Sandwich Iridium Complexes Bearing a Diprotic Glyoxime Ligand: Structural Diversity Induced by Reversible Deprotonation

Synthesis and deprotonation reactions of half‐sandwich iridium complexes bearing a vicinal dioxime ligand were studied. Treatment of [{Cp*IrCl(μ‐Cl)}₂] (Cp*=η⁵‐C₅Me₅) with dimethylglyoxime (LH₂) at an Ir:LH₂ ratio of 1:1 afforded the cationic dioxime iridium complex [Cp*IrCl(LH₂)]Cl ( 1 ). The chlorido complex 1 undergoes stepwise and reversible deprotonation with potassium carbonate to give the oxime–oximato complex [Cp*IrCl(LH)] ( 2 ) and the anionic dioximato(2?) complex K[Cp*IrCl(L)] ( 3 ) sequentially. Meanwhile, twofold deprotonation of the sulfato complex [Cp*Ir(SO₄)(LH₂)] ( 4 ) resulted in the formation of the oximato‐bridged dinuclear complex [{Cp*Ir(μ‐L)}₂] ( 5 ). X‐ray analyses disclosed their supramolecular structures with one‐dimensional infinite chain ( 1 and 2 ), hexagonal open channels ( 3 ), and a tetrameric rhomboid ( 4 ) featuring multiple intermolecular hydrogen bonds and electrostatic interactions.     

Organic electroluminescent device with aromatic amine-containing polymer as a hole transport layer (II): Poly(arylene ether sulfone)-containing tetraphenylbenzidine

Organic electroluminescent devices were fabricated using a poly(arylene ether sulfone)-containing tetraphenylbenzidine (PTPDES) and tris(8-quinolinolato)-aluminum(III) complex, Alq, as the hole transport layer and the electron-transporting emitter layer, respectively. A device structure of glass substrate/indium—tin oxide (ITO)/PTPDES/Alq/Mg : Ag was employed. Hole injection from ITO through the PTPDES layer to the Alq layer and concomitant electroluminescence from the Alq layer were observed. Bright green light with a luminance of 14,000 cd/m² was observed at a drive voltage of 14 V, indicating that the polymer possesses a high hole mobility and a high electron-blocking capability.     

Strategy for structural elucidation of drugs and drug metabolites using (MS)n fragmentation in an electrospray ion trap

Triple-stage quadrupole (TSQ) electrospray ionization (ESI) tandem mass spectrometry (MS/MS) and ion trap ESI-MS/MS can be used to cleave protonated molecules to produce carbocations and neutral molecules in the positive ion mode. Dissociation products which correspond to protonated forms of neutral fragment molecules can also be trapped and detected. These protonated molecules in turn can cleave via carbocation cleavage, ipso cleavage, onium cleavage or McLafferty or related rearrangements. One can elucidate the structures of metabolites from the differences in m/z ratios of the fragments arising from the original drug compound and its metabolite. This strategy for structural elucidation is further facilitated by estimates of the reactivity of drugs with oxygen diradicals involved in cytochrome P-450 cycles.