Properties of spanning water networks at protein surfaces

The formation of a spanning two-dimensional hydrogen-bonded water network at the surface of proteins via a percolation transition enables their biological function. We show in detail how the spanning (percolating) water network appears at the surfaces of model hydrophilic spheres and at the surface of a single protein (lysozyme) molecule. We have found essential correlations of the linear extension, radius of gyration, and position of the center of mass of the largest water cluster with its size. The specific two-peak structure of the probability distribution of the largest cluster size allowed us to study various properties separately for spanning and nonspanning largest clusters. The radius of gyration of the spanning cluster always exceeds the radii of the spheres or the effective radius of the protein. Any spanning cluster envelops essentially more than half of the surface area. The temporal decay of the spanning networks shows a stretched exponential character. Their average lifetime at the percolation threshold is about the lifetime of a water-water hydrogen bond.     

Manipulating 2D metal-organic networks via ligand control

High-resolution scanning tunneling microscopy has revealed how ligand control can be successfully employed to eliminate isomeric phases and defects in 2D coordination networks that are self-assembled at a surface support by replacing symmetric dicarboxylato linker ligands to dissymmetric carboxylpyridyl linker ligands.     

Thermal breaking of spanning water networks in the hydration shell of proteins

The presence of a spanning hydrogen-bonded network of water at the surface of biomolecules is important for their conformational stability, dynamics, and function. We have studied by computer simulations the clustering and percolation of water in the hydration shell of a small elastinlike peptide (ELP) and the medium-size protein staphylococcal nuclease (SNase), in aqueous solution. We have found that in both systems a spanning network of hydration water exists at low temperatures and breaks up with increasing temperature via a quasi-two-dimensional percolation transition. The thermal breaking of the spanning water network occurs at biologically relevant temperatures, in the temperature range, which is close to the temperature of the "inverse temperature transition" of ELP and the unfolding temperature of SNase, respectively.     

Nature of percolation phase transition in hydration water films around immersed bodies

The phenomenological vector model of water is used to clarify the nature of the percolation phase transition in hydration water films around the surface of immersed bodies, which is found in molecular dynamic calculations. The transition is explained by the emergence of ordering in the directions of projections of water dipole moments on the body surface at the lower critical temperature, i.e. by the formation of ferroelectric water film. The evaluation of this temperature is given, which is consistent with numerical calculations.     

Dehydrogenative silane coupling on silicon surfaces via early transition metal catalysis

Derivatization of silicon surfaces is an area of intense interest due to the centrality of silicon in the microelectronics industry and because of potential promise for a myriad of other applications. In this paper, we investigate the feasibility of Si-Si bond formation directly on the surface to contrast with the more widely studied Si-C and Si-O bond forming reactions. Functionalization of hydride-terminated silicon surfaces with silanes is carried out via early transition metal mediated dehydrogenative silane coupling reactions. Zirconocene and titanocene catalyst systems were evaluated for heterocoupling of a molecular silane, RSiH3, with a surface Si-H group on Si(s). The zirconocene catalysts proved to be much more reactive than the titanium system, and so the former was examined exclusively. The silanes, aromatic or aliphatic, are bonded to the silicon surface through direct Si-Si bonds, although the level of incorporation of the trihydroarylsilanes was substantially higher than that of the aliphatic silanes. The reaction proceeds on nanocrystalline hydride-terminated porous silicon surfaces, as well as flat Si(100)-H(x) and Si(111)-H interfaces. The reactions were studied by a variety of techniques, including FTIR, SIMS, and XPS.     

Formation of infinite 2D water layers in a crystal host

A self-assembled,(H_2O)_(38) cluster stabilized by a mono-nuclear copper(Ⅱ) complex 1 namely {[Cu(phen)_2(CO_3)]·7H_2O} is characterized by X-ray diffraction studies.The adjacent(H_2O)_(38) clusters connect together resulting in an infinite 2D water layer structure.The water morphology is stable at room temperature,but upon thermal decomposition,the water loss is irreversible.     

Formation of large 2D nanosheets via PVP-assisted assembly of anatase TiO2 nanomosaics

We demonstrate an unusual formation of large 2D nanosheets from nanomosaic building blocks of anatase TiO(2) nanosheets with exposed (001) facets. It is proposed that large PVP molecules adsorbed on the (001) facets serve as the linker that brings building blocks together, at the same time prevents them from stacking along the c-axis.     

Formation of mesoscopic water networks in aqueous systems

Formation of the macroscopically-infinite hydrogen-bonded water network in various aqueous systems occurs via 3D percolation transition when the probability of finding a spanning water cluster exceeds 95%. As a result, in a wide interval of water content below the percolation threshold, rarefied quasi-2D water networks span over the mesoscopic length scale. Formation and topology of spanning water networks, which affect various properties of aqueous systems, can be described within the framework of the percolation theory.     

Formation of smooth, conformal molecular layers on ZnO surfaces via photochemical grafting

We have investigated the photochemical grafting of organic alkenes to atomically flat ZnO(10 ?10) single crystals and ZnO nanorods as a way to produce functional molecule-semiconductor interfaces. Atomic force microscopy shows that photochemical grafting produces highly conformal, smooth molecular layers with no detectable changes in the underlying structure of the ZnO terraces or steps. X-ray photoelectron spectroscopy measurements show that grafting of a methyl ester-terminated alkene terminates near one monolayer, while alkenes bearing a trifluoroacetamide-protected amine form very smooth multilayers. Even with multilayers, it is possible to deprotect the amines and to link a second molecule to the surface with excellent efficiency and without significant loss of molecules from the surface. This demonstrates that the use of photochemical grafting, even in the case of multilayer formation, enables multistep chemical processes to be conducted on the ZnO surface. Photoresponse measurements demonstrate that functionalization of the surface does not affect the ability to induce field effects in the underlying ZnO, thereby suggesting that this approach to functionalization may be useful for applications in sensing and in hybrid organic-inorganic transistors and related devices.     

Carbon on transition metal surfaces

The review surveys the conditions of formation and properties of four forms of surface carbon on transition metals, to wit, adsorbed atoms and clusters, surface carbide and graphite, and their role in the physical and chemical processes on the surface. The first-order phase transition in the adlayer, when graphite islands coexist with carbon gas, are considered. The effect of intercalation, when atoms (Cs, K, Na, Ba, Pt, Si) penetrate spontaneously under the graphite islands physisorbed on the metal, and its mechanism are discussed. An analysis is made of the poisoning of platinum-group metal catalysts in the reaction of dissociation, when graphite islands characterized by extreme adsorption and catalytic passivity form in the adlayer. The method of CsCl dissociation to probe the surface carbon is treated. Attention is drawn to the adsorption of a number of atoms (Cs, K, Ba, Pt) on a graphite monolayer on metals, and the properties of such systems are discussed. The effects observed in coadsorption of CsCl molecules with K, Na, Ba, Tm atoms on a graphite monolayer on metals are covered. By analogy with the bulk carbides, surface carbides of fixed stoichiometry and very strong metal-carbon bonding have been revealed to form on the surface of transition metals (W, Re, Mo). The effect of displacement of surface carbon into the bulk of the metal stimulated by the adsorption of some atoms (Si, S, O) is discussed. The carbon clusters adsorbed on metals are considered. The transport of surface carbon, its desorption and diffusion between the surface and the bulk of the metal with a single- and double-phase adlayer are reviewed.     

Ab initio studies of a water layer at transition metal surfaces

This paper presents a detailed study of a water adlayer adsorbed on Pt(111) and Rh(111) surfaces using periodic density functional theory methods. The interaction between the metal surface and the water molecules is assessed from molecular dynamics simulation data and single point electronic structure calculations of selected configurations. It is argued that the electron bands around the Fermi level of the metal substrate extend over the water adlayer. As a consequence in the presence of the water layer the surface as a whole still maintains its metallic conductivity-a result of a crucial importance for understanding the process of electron transfer through the water/metal interface and electrochemical reactions in particular. Our results also indicate that there exists a weak bond between the hydrogen of the water and the Rh metal atoms as opposed to the widespread (classical) models based on purely repulsive interaction. This suggests that the commonly used classical interactions potentials adopted for large scale molecular dynamics simulations of water/metal interfaces may need revision. Two adsorption models of water on transition metals with the OH bonds pointing towards or away of the surface are also examined. It is shown that due to the very close values of their adsorption energies one should consider the real structure of water on the surface as a mixture of these simple "up" and "down" models. A model for the structure of the adsorbed water layer on Rh(111) is proposed in terms of statistical averages from molecular dynamics simulations.     

Glycan–protein cross-linking mass spectrometry reveals sialic acid-mediated protein networks on cell surfaces

A cross-linking method is developed to elucidate glycan-mediated interactions between membrane proteins through sialic acids. The method provides information on previously unknown extensive glycomic interactions on cell membranes. The vast majority of membrane proteins are glycosylated with complicated glycan structures attached to the polypeptide backbone. Glycan–protein interactions are fundamental elements in many cellular events. Although significant advances have been made to identify protein–protein interactions in living cells, only modest advances have been made on glycan–protein interactions. Mechanistic elucidation of glycan–protein interactions has thus far remained elusive. Therefore, we developed a cross-linking mass spectrometry (XL-MS) workflow to directly identify glycan–protein interactions on the cell membrane using liquid chromatography-mass spectrometry (LC-MS). This method involved incorporating azido groups on cell surface glycans through biosynthetic pathways, followed by treatment of cell cultures with a synthesized reagent, N-hydroxysuccinimide (NHS)–cyclooctyne, which allowed the cross-linking of the sialic acid azides on glycans with primary amines on polypeptide backbones. The coupled peptide–glycan–peptide pairs after cross-linking were identified using the latest techniques in glycoproteomic and glycomic analyses and bioinformatics software. With this approach, information on the site of glycosylation, the glycoform, the source protein, and the target protein of the cross-linked pair were obtained. Glycoprotein–protein interactions involving unique glycoforms on the PNT2 cell surface were identified using the optimized and validated method. We built the GPX network of the PNT2 cell line and further investigated the biological roles of different glycan structures within protein complexes. Furthermore, we were able to build glycoprotein–protein complex models for previously unexplored interactions. The method will advance our future understanding of the roles of glycans in protein complexes on the cell surface.

The cell surface glycocalyx is highly interactive defined by extensive covalent and non-covalent interactions. A method for cross-linking and characterizing glycan–peptide interactions in situ is developed.     

Formation and healing of micrometer-sized channel networks on highly mobile Au(111) surfaces

Practical protocols are presented to reproducibly prepare micrometer-sized Au(111) substrates. Au(111) terraces of micrometer dimensions and atomic smoothness were crystallized by flame-annealing vacuum-deposited gold films on glass and on millimetric amorphous gold shots. Gold films and shots that were slowly cooled in a moderately applied stream of nitrogen gas exhibited large and stable crystal surfaces with Au(111) morphologies. Similarly, flame-annealed gold samples cooled with another protocol--in much rougher streams of nitrogen gas--produced morphologically unstable and highly mobile Au(111) layers. Within the first hour after preparation, however, rapid microscale restructuring in the layers produced complex morphologies of hexagonal channel networks and islands that were predominantly triangular. These channeled gold layers fused slowly in the following hours, with velocities of 0.01-0.2 A/s, as quantified by digital image correlation (DIC). Atomically smooth, stable, and predominantly triangular Au(111) terraces on the scale of micrometers were observed approximately 24 h after the sample preparations.     

Amino-carboxylic recognition on surfaces: from 2D to 2D + 1 nano-architectures

The control of the electronic properties of the interfaces between small organic molecules and the substrate is key for the development of efficient and reliable organic-based devices. A promising and widely covered route is to interpose a Self-Assembled Monolayer (SAM) to bridge the molecular film and the electrode. The morphology and the electronic level alignment of the triple substrate-SAM-organic layered system can be tuned by properly selecting the SAM composition. We have recently proposed a novel approach to the problem where, under ultra-high vacuum conditions, a molecular film is anchored to the SAM by exploiting the recognition between molecules functionalized, respectively, with -NH(2) and -COOH end-groups. Here we briefly review the role of the amino-carboxylic interaction in the formation of ordered organic 2-dimensional architectures on solid surfaces. We then describe the anchoring process of carboxylic molecules on amine based SAMs we have recently reported on. New results are presented showing how multiple anchoring sites per molecule may be exploited for tailoring the molecular orientation as well as the density of the anchored molecules.     

How protein surfaces induce anomalous dynamics of hydration water

Water around biomolecules slows down with respect to pure water, and both rotation and translation exhibit anomalous time dependence in the hydration shell. The origin of such behavior remains elusive. We use molecular dynamics simulations of water dynamics around several designed protein models to establish the connection between the appearance of the anomalous dynamics and water-protein interactions. For the first time we quantify the separate effect of protein topological and energetic disorder on the hydration water dynamics. When a static protein structure is simulated, we show that both types of disorder contribute to slow down water diffusion, and that allowing for protein motion, increasing the spatial dimensionality of the interface, reduces the anomalous character of hydration water. The rotation of water is, instead, altered by the energetic disorder only; indeed, when electrostatic interactions between the protein and water are switched off, water reorients even faster than in the bulk. The dynamics of water is also related to the collective structure--à voir the hydrogen bond (H-bond) network--formed by the solvent enclosing the protein surface. We show that, as expected for a full hydrated protein, when the protein surface offers pinning sites (charged or polar sites), the superficial water-water H-bond network percolates throughout the whole surface, hindering the water diffusion, whereas it does not when the protein surface lacks electrostatic interactions with water and the water diffusion is enhanced.     

Line of percolation in supercritical water

The percolation transition of the hydrogen-bonded clusters of molecules is investigated in supercritical water by Monte Carlo computer simulations. Simulations have been performed at four thermodynamic state points located above the supercritical extension of the vapor-liquid coexistence curve on the p-T phase diagram and at four state points located below this curve. It is found in a temperature range of a few hundred Kelvin that the extension of the vapor-liquid coexistence curve separates the supercritical thermodynamic states in which the water molecules form infinite hydrogen-bonded clusters from those in which the hydrogen-bonded clusters are isolated oligomers. However, the difference between the size of the hydrogen-bonded clusters at thermodynamic states located at the two sides of the extension of the coexistence curve is found to decrease with increasing temperature, and the present results suggest that this difference is likely to vanish at high enough temperatures.     

Photolysis of water vapor on titanium/TiO2 surfaces

The photolysis of water vapor on the surface of titanium coated polycrystalline n-TiO₂ at a temperature of 380°C is reported. A quantum conversion efficiency for hydrogen production of 2% is measured for excitation above the band gap of TiO₂. The experiments demonstrate the catalytic nature of the reaction with respect to the active material and also suggest an important role played by the titanium metal in the observations.     

过渡金属表面上水生成经典Horiuti-Polanyi机理与非Horiuti-Polanyi机理选择的总体趋势（英文）

在非均相催化加氢反应中,氢气(H₂)一直被公认为是通过两步基元步骤参加还原反应的,包括第一步的分子解离和之后的反应物与原子氢键合,即所谓的Horiuti-Polanyi(HP)机理.直到我们研究组在Ag或Au催化丙烯醛加氢还原反应理论研究中发现非HP机理加氢路径存在时,新的机理才被提出,并引起广大研究者的浓厚兴趣.考虑到表面羟基(OH)和氧(O)在非均相催化体系中广泛存在,如常见的过渡金属催化的费托合成、甲烷重整、水汽转化及氨氧化等反应,基于第一性原理的密度泛函理论计算方法,我们对OH/O在一系列过渡金属催化作用下还原生成水的微观机理进行了系统全面的探究.研究发现,不同金属对应于不同的催化氢化反应活性,以及不同的催化反应机理.在某些金属上H₂以分子形式进攻反应物种的非HP机理有利,而在其它金属上经典的H₂解离后参与氢化还原反应的HP机理更容易发生.详细分析显示, H₂的解离活性决定了反应机理的种类:在对H₂解离具有催化活性的金属(如Pt、Ni)表面,不论是(211)台阶面还是(...