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.     

THE MEASUREMENT OF PLASTIC DEFORMATION AND CRACK GROWTH IN CRACKED SPECIMENS BY SAM

In this paper,scanning acoustic microscope(SAM) was used to obtainsome characteristic photographs which explain the mesoscopic information of severalcracked specimens.New results on subsurface information of steel,nickel andaluminium were presented.Plastic deformation and crack initiation were observed andanalysed.The length of crack propagation was measured.SAM is particularly suited tothe study of many mesoscopic phenomena in material science because it can imagemesoscopic subsurface feature without sectioning.It is revealed that SAM has a brightfuture in the field of mesomechanics.     

A Sensitive Nanoporous Gold-Based Electrochemical DNA Biosensor for Escherichia coli Detection

A sensitive electrochemical DNA biosensor based on a mixed monolayer structure self-assembled at nanoporous gold (NPG) electrode surface was prepared for Escherichia coli (E. coli) detection. The NPG was fabricated on gold electrode, onto which thiolated oligonucleotides (SH-DNA) and mercaptohexanol (MCH) were covalently linked forming a mixed self-assembled monolayer (SAM). The hybridization between the SH-DNA/MCH modified biosensor and E. coli DNA was monitored with differential pulse voltammetry measurement using methylene blue (MB) as the hybridization indicator. The biosensor can detect 1 × 10^?12 M DNA target and 50 cfu/μL E. coli without any nucleic acid amplification steps. The detection limit was lowered to 50 cfu/mL after 5.0 h of incubation.     

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.     

Anti-sticking treatment for a nanoimprint stamp

Nanoimprint lithography (NIL), as a low-cost and mass production technique, has played an important role in micro/nano fabrication. However, the sticking problem between the stamp and resist blocks its further application. In order to modify the contact surface, a molecular dynamics (MD) method was used to choose the proper material to coat on the surface of the stamp. According to the MD analysis, CF₂ was found to be a good choice for this purpose. It was applied to the nanoimprint stamp by using the gases in reactive ion etching (RIE). A self-assembly monolayer (SAM) layer was also used in the experiment to release the contact surface energy. Both dry and wet methods were demonstrated as excellent anti-sticking approaches by measuring the contact angles and calculating the surface energy. Both the stamps after anti-sticking treatment can be used more times than the untreated stamps.     

Self-assembling of cyano- and carboxyl-terminated monolayers using short-chain alkylsiloxane

A simple method was developed for the preparation of cyano- and carboxyl-terminated alkylsiloxane monolayers on the hydroxylated surface of the SiO₂/Si substrate through using adsorption and hydrolysis reaction of a short-chain 2-cyanoethyl triethoxysilane [(CH₃CH₂O)₃SiCH₂CH₂CN]. The contact angle and the X-ray photoelectron spectroscopy (XPS) measurements have proved that the cyano terminal group indeed formed on the substrate and was transformed into the carboxylic terminal group after hydrolysis. The ellipsometry shows the presence of an intact monolayer with thickness of around 0.7 nm before and during the hydrolysis reaction. The surface morphology was observed with atomic force microscopy (AFM) imaging. Those all indicate that uniform and ordered self-assembled monolayers (SAMs) were formed on the substrate.     

Effect of humidity and temperature on nano/microtribolgical properties of perfluorinated carboxylic acid and hydrogenated carboxylic acid self‐assembled monolayers deposited on aluminum‐coated silicon substrate

Two series of perfluorinated carboxylic acid (FC) and hydrogenated carboxylic acid (HC) self‐assembled monolayer (SAM) films were prepared on aluminum surfaces separately by chemical vapor deposition. The formation, structure and morphology of these films were characterized by measuring contact angle with ellipsometric method, x‐ray photoelectron spectrometry, and atomic force microscopy, respectively. FC and HC SAMs with long chains formed more densely packed films than those with short chains did. The comparative micro/nanoscale friction and adhesive properties of FC and HC SAMs, with various chain lengths on aluminum‐coated silicon substrate, were investigated. The influence of environmental conditions, such as relative humidity (RH) and temperature, on the friction and adhesion behavior was studied. Micro/nanotribological properties of the films were greatly influenced by their backbones and terminal groups. FC SAMs with long chain exhibited adhesion‐resistance, friction reduction, and environmental independence. Copyright © 2009 John Wiley & Sons, Ltd.     

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.     

Reflection Absorption Infrared Spectroscopy Characterization of SAM Formation from 8-Mercapto-N-(phenethyl)octanamide Thiols with Phe Ring and Amide Groups

Multifunctional amide-containing self-assembled monolayers (SAMs) provide prospects for the construction of interfaces with required physicochemical properties and distinctive stability. In this study, we report the synthesis of amide-containing thiols with terminal phenylalanine (Phe) ring functionality (HS(CH₂)₇CONH(CH₂)₂C₆H₅) and the characterization of the formation of SAMs from these thiols on gold by reflection absorption infrared spectroscopy (RAIRS). For reliable assignments of vibrational bands, ring deuterated analogs were synthesized and studied as well. Adsorption time induced changes in Amide-II band frequency and relative intensity of Amide-II/Amide-I bands revealed two-state sigmoidal form dependence with a transition inflection points at 2.2 ± 0.5 and 4.7 ± 0.5 min, respectively. The transition from initial (disordered) to final (hydrogen-bonded, ordered) structure resulted in increased Amide-II frequency from 1548 to 1557 cm⁻¹, which is diagnostic for a strongly hydrogen-bonded amide network in trans conformation. However, the lateral interactions between the alkyl chains were found to be somewhat reduced when compared with well-ordered alkane thiol monolayers.     

分子间相互作用研究的APF-D密度泛函SAM色散校正方法改进

APF密度泛函色散校正（APF-D）是由B3PW91和PBE0杂化的APF泛函,加上球形原子模型（SAM）色散校正构成的一种有别于Grimme经验色散校正的密度泛函理论色散校正（DFT-D）方法,计算稀有气体及其与小分子复合物结合能和势能面准确性很高,但对常见氢键、C―H…π和π…π等复合物结合能计算结果明显偏大,在一般性分子间相互作用问题研究中一直未被认可和采纳。我们发现APF-D结合能计算结果偏大的原因是APF泛函与SAM色散校正重复计入了一定量的长程色散能;通过引入不依赖于体系的SAM色散能阻力因子ζ,简单而有效地解决了APF-D色散能过度补偿问题,提出了APF-D改进方案APF-D^*;通过S66和L7标准测试集的对照计算表明,APF-D^*结合能准确性远高于原始APF-D,达到和超过目前常用的B3LYPD3和ωB97X-D方法水平,并具有较好的计算效率,期待在大体系分子间相互作用研究中得到广泛应用。