Secondary structure analysis of peptides with relevance to iron–sulfur cluster nesting

Peptides coordinated to iron–sulfur clusters, referred to as maquettes, represent a synthetic strategy for constructing biomimetic models of iron–sulfur metalloproteins. These maquettes have been successfully employed as building blocks of engineered heme-containing proteins with electron-transfer functionality; however, they have yet to be explored in reactivity studies. The concept of iron–sulfur nesting in peptides is a leading hypothesis in Origins-of-Life research as a plausible path to bridge the discontinuity between prebiotic chemical transformations and extant enzyme catalysis. Based on past biomimetic and biochemical research, we put forward a mechanism of maquette reconstitution that guides our development of computational tools and methodologies. In this study, we examined a key feature of the first stage of maquette formation, which is the secondary structure of aqueous peptide models using molecular dynamics simulations based on the AMBER99SB empirical force field. We compared and contrasted S…S distances, [2Fe-2S] and [4Fe-4S] nests, and peptide conformations via Ramachandran plots for dissolved Cys and Gly amino acids, the CGGCGGC 7-mer, and the GGCGGGCGGCGGW 16-mer peptide. Analytical tools were developed for following the evolution of secondary structural features related to [Fe-S] cluster nesting along 100 ns trajectories. Simulations demonstrated the omnipresence of peptide nests for preformed [2Fe-2S] clusters; however, [4Fe-4S] cluster nests were observed only for the 16-mer peptide with lifetimes of a few nanoseconds. The origin of the [4Fe-4S] nest and its stability was linked to a “kinked-ribbon” peptide conformation. Our computational approach lays the foundation for transitioning into subsequent stages of maquette reconstitution, those being the formation of iron ion/iron–sulfur coordinated peptides. © 2018 Wiley Periodicals, Inc.     

Partial stripping of Ag atoms from silver bilayer on a Au(111) surface accompanied with the reductive desorption of hexanethiol SAM

The interfacial structures of Ag bilayer prepared by underpotential deposition on Au(111) (Ag(2ML)/Au(111)) were determined by ex situ scanning tunneling microscopy and in situ surface X-ray scattering measurements before and after oxidative adsorption and after reductive desorption of a self-assembled monolayer (SAM) of hexanethiol (C₆SH) in alkaline ethanol solution. While no structural change was observed after oxidative formation of C₆SH SAM on the Ag(2ML)/Au(111) in an ethanol solution containing 20 mM KOH and 0.1 mM C₆SH, some of the Ag atoms in the bilayer were stripped when the SAM was reductively desorbed. Dedicated to Professor J. O’M. Bockris on the occasion of his 85th birthday.     

金表面不同链长烷基硫醇自组装单分子膜表面电势的变化规律

从Helmholtz模型出发,对生长在金表面不同链长烷基硫醇自组装单分子膜(SAM)表面电势的变化规律进行了理论研究.利用量子化学软件Gaussian03和MOPAC,讨论了分子偶极矩、相对介电常数以及分子的倾斜角对SAM表面电势的影响.研究表明,不同链长烷基硫醇SAM中分子的倾斜角随烷基链长度的规律性变化是引起SAM表面电势变化的主要原因.从SAM形成机制出发,对金表面不同链长烷基硫醇SAM表面电势的变化规律及其成因提出了新的解释.     

Synthesis and SAM formation of water soluble functional carboxymethylcelluloses: thiosulfates and thioethers

Functional thiomethyl and thiosulfate derivatives of carboxymethylcellulose (CMC, DS = 0.9) were synthesized by nucleophilic displacement reactions. Alkylation of CMC by allyl glycidyl ether took mainly place at the primary positions of the cellulose backbone and yielded a 6-O-(3-allyloxy-2-hydroxypropyl)-CMC 1 with a partial DS of 3-allyloxy-2-hydroxypropyl substituents DSallyl of up to 0.43. Addition of tetrathionate to the allyl groups gave rise to 6-O-(2,3-bis(thiosulfato)propoxy-2-hydroxypropyl)-CMC 2. As the addition of tetrathionate was sluggish and incomplete, alternatively bromine was added and the resulting dibromide was substituted by thiosulfate. A 40% conversion of the allyl groups was achieved by this two-step procedure. On the other hand, the addition of bromine to 1 in aqueous solution almost quantitatively yielded the bromohydrin derivative which was converted by displacement reaction with thiosulfate to 6-O-(2-hydroxy-3-thiosulfatopropoxy-2-hydroxypropyl)-CMC 4. 6-Thiomethyl-6-deoxy-CMC 6 was synthesized by displacement reaction of 6-O-tosylcellulose with sodium methylsulfide and subsequent carboxymethylation of the cellulose backbone. A partial DS of thiomethyl substituents DSThM=0.65 exclusively at the primary positions was obtained. All functional CMC derivatives, 2, 4, and 6 were readily available in gram quantities, rather stable and highly water soluble for pH > 3. On gold surfaces they form self-assembled monolayers (SAMs) with thicknesses of 1.2 to 2.4 nm as determined by surface plasmon resonance (SPR).     

Study of phenothiazine and N‐methyl phenothiazine by infrared,raman, 1H‐, and 13C‐NMR spectroscopies

A complete vibrational analysis of the Fourier transform (FT) infrared (IR) and FT‐Raman spectra of both molecules was carried out using quantum chemical calculations. The structure of phenothiazine (PTZ) and N‐methylphenothiazine (N‐MePTZ) were studied by semiempirical, and ab initio methods. Different basis sets and two new procedures for scaling the frequencies of the ring modes were used. Vibrational data of the methyl group in N‐MePTZ were interpreted in terms of the different molecular conformations in the solid state. The ¹H‐ and ¹³C–nuclear magnetic resonance (NMR) data were interpreted in terms of the electron densities on the atoms and the stacking solute–solute association in dimethyl sulfoxide solution. Chemical shifts were related to the Merz‐Kollman atomic charges. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002     

Synthesis, characterization, and SAMs electroactivity of ruthenium complexes with sulfur containing ligands

The vibrational and ¹H NMR data hints that the coordination of the 2,2′-dithiodipyridine (2-pySS) ligand to the [Ru(CN)₅]³⁻ metal center occurs through the sulfur atom instead of the nitrogen atoms which is usually observed for N-heterocyclic ligands. Electrochemical results show that this coordination mode implies an additional thermodynamic stabilization of the Ru^II over Ru^III oxidation state due to a relative stronger π-back-bonding interaction with the empty low-lying dπ orbitals of the sulfur atom. Computational data reinforce the experimental results showing that the 2-pySS Lewis base centers are located on the sulfur atoms. Ligands containing only sulfur atoms as coordination sites (2,2′-dithiodipyridine N-oxide (2-pySSNO), 1,4-dithiane (1,4-dt), and 2,6-dithiaspiro[3.3]heptane (asp)) were also coordinated to the [Ru(CN)₅]³⁻ metal center to undoubtedly correlate the electrochemical results with the ligand coordination atom. Among the synthesized compounds, the [Ru(CN)₅(1,4-dt)]³⁻ and [Ru(CN)₅(asp)]³⁻ complexes showed to be able to form self-assembled monolayers (SAMs) on gold. These SAMs, which were characterized by SERS (surface-enhanced Raman scattering) spectroscopy, successfully assessed the heterogeneous electron transfer reaction of the cytochrome c metalloprotein in physiological medium.     

SERRS study of [Ru(CN)<Subscript>5</Subscript>(pyS)]<Superscript>4−</Superscript> SAM and cytochrome c: A suggestion toward the heterogeneous molecular recognition

Surface-Enhanced Raman Scattering (SERS) spectra of [Ru(CN)₅(pyS)]⁴⁻ (RupyS) complex self-assembled monolayer (SAM) were obtained on gold and silver surfaces at 632.8 and 413.1 nm excitation radiations, respectively. The bands assigned to the heme iron of the cytochrome c (cyt c) metalloprotein group were observed by using the RupyS SAM on silver at 413.1 nm. The Surface-Enhanced Resonance Raman Scattering (SERRS) spectra of the RupyS SAM on silver in the cyt c solution obtained at −0.2 and +0.2 V present bands at 1,365 and 1,374 cm⁻¹ characteristic of the heme group, indicating the reduced and oxidized states of this protein, respectively. The bands observed at 1,464, 1,504, and 1,638 cm⁻¹ are used to confirm the redox state of cyt c. The presence of the oxidized and reduced bands in function of different applied potential is an evidence that the protein is interacting with the modifier. This paper is dedicated to Prof. Francisco Nart, in memoriam.     

自组装膜结构与电化学行为的关系

报导了组装时间对４－乙氧基－４＇－Ｎ（２″－巯基－乙基）羧基酰胺－偶氮苯（Ｃ２ＡｚｏＣ２）自组装膜电化学行为的影响。接触角与界面电容的数据表明，组装时间的增长使自组装膜表面覆盖度增加。从循环伏安图中可以观察到氧化峰与还原峰之间的距离增大，同时计算得到的表观电极反应速率常数显著减小。基于偶氮苯基团的自身结构及其在电化学反应过程中所经历的构型改变，认为有序体系中组装结构的致密性阻碍偶氮苯基团的构型变化     

固体薄层纵深分析研究——Ⅱ.钢、铝合金和钛合金溅射速率的测定

用PHI 600型扫描俄歇探针、200型台阶仪和Q-920型图象分析仪,测定了35Cr Ni3MoV钢、Al-5.5 Zn-1.4Mg合金和Ti-5Al-2.5Sn合金的溅射速率,提出了对蚀坑分部位确定溅射速率的方法。文中给出了详细的测定结果。