A simulation strategy for the atomistic modeling of flexible molecules covalently tethered to rigid surfaces: Application to peptides

A computational strategy to model flexible molecules tethered to a rigid inert surface is presented. The strategy is able to provide uncorrelated relaxed microstructures at the atomistic level. It combines an algorithm to generate molecules tethered to the surface without atomic overlaps, a method to insert solvent molecules and ions in the simulation box, and a powerful relaxation procedure. The reliability of the strategy has been investigated by simulating two different systems: (i) mixed monolayers consisting of binary mixtures of long‐chain alkyl thiols of different lengths adsorbed on a rigid inert surface and (ii) CREKA (Cys‐Arg‐Glu‐Lys‐Ala), a short linear pentapeptide that recognizes clotted plasma proteins and selectively homes to tumors, covalently tethered to a rigid inert surface in aqueous solution. In the first, we examined the segregation of the two species in the monolayers using different long‐chain:short‐chain ratios, whereas in the second, we explored the conformational space of CREKA and ions distribution considering densities of peptides per nm² ranging from 0.03 to 1.67. Results indicate a spontaneous segregation in alkyl thiol monolayers, which enhances when the concentration of longest chains increases. However, the whole conformational profile of CREKA depends on the number of molecules tethered to the surface pointing out the large influence of molecular density on the intermolecular interactions, even though the bioactive conformation was found as the most stable in all cases. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011     

Electrochemical detection of cytosine and 5-methylcytosine on Au(111) surfaces

In this communication we report a voltammetric study of the adsorption–desorption of cytosine (C) and methylcytosine (mC) on well-defined gold (Au) electrodes. The voltammetric measurements clearly indicate that these processes are extremely sensitive to the Au surface structure and in particular to the presence of (111) surface domains. Interestingly, on Au(111) surfaces, a linear correlation between the C and mC concentrations (logarithm scale) and the peak potential of the main voltammetric feature is found. In addition, in the simultaneous presence of both molecules, mC governs the electrochemical response, which has allowed its accurate quantification in C-mC mixtures. In situ FTIR spectroscopic measurements have been carried out to deepen on this mC electrochemical sensitivity. This research may contribute to the future development of an electrochemical sensor for the determination of the degree of methylation in DNA.     

Electrochemical impedance spectroscopy of tethered bilayer membranes

The electrochemical impedance spectra (EIS) of tethered bilayer membranes (tBLMs) were analyzed, and the analytical solution for the spectral response of membranes containing natural or artificially introduced defects was derived. The analysis carried out in this work shows that the EIS features of an individual membrane defect cannot be modeled by conventional electrical elements. The primary reason for this is the complex nature of impedance of the submembrane ionic reservoir separating the phospholipid layer and the solid support. We demonstrate that its EIS response, in the case of radially symmetric defects, is described by the Hankel functions of a complex variable. Therefore, neither the impedance of the submembrane reservoir nor the total impedance of tBLMs can be modeled using the conventional elements of the equivalent electrical circuits of interfaces. There are, however, some limiting cases in which the complexity of the EIS response of the submembrane space reduces. In the high frequency limit, the EIS response of a submembrane space that surrounds the defect transforms into a response of a constant phase element (CPE) with the exponent (α) value of 0.5. The onset of this transformation is, beside other parameters, dependent on the defect size. Large-sized defects push the frequency limit lower, therefore, the EIS spectra exhibiting CPE behavior with α ≈ 0.5, can serve as a diagnostic criterion for the presence of such defects. In the low frequency limit, the response is dependent on the density of the defects, and it transforms into the capacitive impedance if the area occupied by a defect is finite. The higher the defect density, the higher the frequency edge at which the onset of the capacitive behavior is observed. Consequently, the presented analysis provides practical tools to evaluate the defect density in tBLMs, which could be utilized in tBLM-based biosensor applications. Alternatively, if the parameters of the defects, e.g., ion channels, such as the diameter and the conductance are known, the EIS data analysis provides a possibility to estimate other physical parameters of the system, such as thickness of the submembrane reservoir and its conductance. Finally, current analysis demonstrates a possibility to discriminate between the situations, in which the membrane defects are evenly distributed or clustered on the surface of tBLMs. Such sensitivity of EIS could be used for elucidation of the mechanisms of interaction between the proteins and the membranes.     

Organized arrays of individual DNA molecules tethered to supported lipid bilayers

An unappreciated aspect of many single-molecule techniques is the need for an inert surface to which individual molecules can be anchored without compromising their biological integrity. Here, we present new methods for tethering large DNA molecules to the surface of a microfluidic sample chamber that has been rendered inert by the deposition of a supported lipid bilayer. These methods take advantage of the "bio-friendly" environment provided by zwitterionic lipids, but still allow the DNA molecules to be anchored at fixed positions on the surface. We also demonstrate a new method for constructing parallel arrays of individual DNA molecules assembled at defined positions on a bilayer-coated, fused silica surface. By using total internal reflection fluorescence microscopy to visualize the arrays, it is possible to simultaneously monitor hundreds of aligned DNA molecules within a single field-of-view. These molecular arrays will significantly increase the throughput capacity of single-molecule, fluorescence-based detection methods by allowing parallel processing of multiple individual reaction trajectories.     

Potential-induced phase transition of low-index Au single crystal surfaces in propylene carbonate solution

In situ scanning tunneling microscopy (STM) was employed to examine the surface structures of Au(111), Au(100), and Au(110) single crystals in propylene carbonate (PC) containing tetrabutylammonium perchlorate (TBAP). All three electrodes exhibited potential-induced phase transition between the reconstructed and unreconstructed (1 × 1) structures at negative and positive potentials, respectively. The potential-induced phase transition of the Au electrode surfaces is attributed to the interaction of the TBA cation and the perchlorate anion at the electrode surface, which is similar to that which takes place in aqueous solutions. In addition to static atomic structures, dynamic processes of both the reconstruction and the lifting of the reconstruction were investigated by means of in situ STM. The lifting of reconstructed Au(111)-(√3 × 22) on Au(111) to the (1 × 1) structure is completed within 1 min at a positive potential. The diffusion of Au atoms on the Au(100) plane in the PC solution proceeds more rapidly than that in the aqueous solution, suggesting that the PC solvent plays an important role in accelerating the diffusion of Au atoms.     

Electrochemical oxidative formation of ordered monolayers of thiol molecules on Au(111) surface

Electrochemical oxidative formation of thiolate monolayers on a Au(111) surface in KOH ethanol solutions of various thiol concentrations is described. The formation process was investigated by electrochemistry, in situ scanning tunneling microscopy (STM), and surface X‐ray diffraction (SXRD). The reductive charge in the linear sweep voltammogram after keeping the potential at +0.1 V increased with holding time and reached the saturated value of 103 µC cm^?2, corresponding to the full monolayer coverage of the ( ) structure. The desorption peak shifted negatively with holding time even after the monolayer was formed, suggesting that ordering of the monolayer requires a much longer time than full coverage adsorption. The herringbone structure, corresponding to the ( × 23) structure, was observed on the Au(111) surface in KOH ethanol solution by in situ STM, which shows that a clean surface was exposed. When hexanethiol ethanol solution was added into the ethanol solution at ?450 mV so that the final thiol concentration was higher than ca. 5 µM, generation of vacancy islands (VIs) was observed, which shows the potentiostatic monolayer formation. When the potential was scanned positively from ?950 mV where a clean reconstructed Au(111) surface was exposed, generation of VIs was observed accompanied by anodic current flow. During both oxidative adsorption and reductive desorption of the monolayer, the shape of the steps of the gold surface changed drastically, which suggests that the gold atoms on the surface are extremely mobile during the monolayer formation. SXRD measurement confirmed the surface reconstruction lifting upon monolayer formation. © 2009 The Japan Chemical Journal Forum and Wiley Periodicals, Inc. Chem Rec 9: 199–209; 2009: Published online in Wiley InterScience ( www.interscience.wiley.com ) DOI 10.1002/tcr.200900002     

Adhesion of amphipathic molecules to solid surfaces

Summary Oil/water contact angles, coefficient of friction and electron diffraction have been used to study the adsorption of three long chain surface-active substances (a fatty acid, a sulphate and a substituted amine, from aqueous solution on to electropolished copper, aluminium and iron. According to the p_H of the solution, the adsorption occurs by one of the following processes (a) physical adsorption, (b) chemisorption, (c) adherence of a precipitate, (d) sensitised adsorption to form a mixed film. Certain applications e.g. lubrication and the prevention of fretting corrosion, are discussed in relation to the structure and rate of adsorption of the four types of film. The first requirement for an efficient lubricant film is the chemisorption of the long chain compound as a basic metal soap. The film is considerably strengthened by subsequent adsorption of a less polar compound, such as cholesterol, by process (d). A suitable vehicle for the two compounds is an oil/water emulsion.Electron diffraction has been used to determine the physical and chemical nature of the electropolished metal surfaces. Adsorbed monolayers can only be detected on extremely smooth surfaces. A new technique is described for depositing insoluble monolayers on reactive metals, which avoids the roughening of the metal surface experienced in the normal Langmuir-Blodgett method.

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Zusammenfassung Randwinkel öl-Wasser, Reibungskoeffizient und Elektronenstrahlbeugung wurden benutzt zum Studium der Adsorption dreier langkettiger Substanzen (eine Fettsäure, ein Sulfat und ein substituiertes Amin) aus wäßriger Lösung heraus auf elektropoliertes Kupfer, Aluminium und Eisen. Entsprechend dem p_H-Wert der Lösung geschieht die Adsorption durch einen der folgenden Prozesse:a) Physikalische Adsorption, b) Chemisorption, c) Haftung eines Niederschlags und d) sensibilisierte Adsorption unter Bildung eines Mischfilms.Einige Anwendungen, z. B. Schmierung und die Verhinderung von Reibungskorrosion, wurden unter BerÜcksichtigung der Struktur und der Adsorptionsgeschwindigkeit der vier genannten Typen von Adsorptionsschichten diskutiert. Die erste Bedingung fÜr wirksame Schmierung ist die Chemisorption der langkettigen Substanz als basische, metallorganische VerdÜnnung (Seife). Der erhaltene Adsorptionsfilm erfährt eine beachtliche Verfestigung durch nachfolgende Adsorption (nach dem Prozeß d) einer schwächer polaren Substanz, wie des Cholesterols. Ein brauchbarer Träger fÜr beide Komponenten ist eine öl-Wasser-Emulsion.Zur Aufklärung der chemischen und physikalischen Eigenschaften der elektropolierten Metalloberflächen wurde die Elektronenstrahlbeugung eingesetzt. Adsorbierte Monoschichten können nur auf extrem ebenen Oberflächen beobachtet werden. Zur Verhinderung der Aufrauhung von Metalloberflächen, wie sie von der Langmuir-Blodgett-Methode her bekannt ist, wurde eine neue Auftragungstechnik fÜr unlösliche Monoschichten auf reaktionsfähige Metalloberflächen entwickelt.

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This work was carried out during the tenure of Consolidated Zinc Studentships at Trinity Hall, Cambridge, on the part of two of the authors (R. B. W. & J. A. S.). Further financial support was provided by Almin Limited and C. S. I. R. O. (Australia).     

Electrochemical self-assembly of alkanethiolate molecules on Ni(111) and polycrystalline Ni surfaces

In this work, the electrochemical formation of alkanethiolate self-assembled monolayers (SAMs) on Ni(111) and polycrystalline Ni surfaces from alkanethiol-containing aqueous 1 M NaOH solutions was studied by combining Auger electron spectroscopy (AES), X-ray photoelectron spectroscopy (XPS), electrochemical techniques, and density functional theory (DFT) calculations. Results show that alkanethiolates adsorb on Ni concurrent with NiO electroreduction. The resulting surface coverage depends on the applied potential and hydrocarbon chain length. Electrochemical and XPS data reveal that alkanethiolate electroadsorption at room temperature takes place without S-C bond scission, in contrast to previous results from gas-phase adsorption. A complete and dense monolayer, which is stable even at very high cathodic potentials (-1.5 V vs SCE), is formed for dodecanethiol. DFT calculations show that the greater stability against electrodesorption found for alkanethiolate SAMs on Ni, with respect to SAMs on Au, is somewhat related to the larger alkanethiolate adsorption energy but is mainly due to the larger barrier to interfacial electron transfer present in alkanethiolate-covered Ni. A direct consequence of this work is the possibility of using electrochemical self-assembly as a straightforward route to build stable SAMs of long-chained alkanethiolates on Ni surfaces at room temperature.     

Toward Raman fingerprints of single dye molecules at atomically smooth Au(111)

The creation of a highly enhanced electromagnetic (EM) field underneath a scanning tunneling microscope (STM) tip enables Raman spectroscopic studies of organic submonolayer adsorbates at atomically smooth single crystalline surfaces. To study the sensitivity of this technique, tip-enhanced resonance Raman (TERR) spectra of the dye malachite green isothiocyanate on Au(111) in combination with the corresponding STM images of the probed surface region were analyzed. The detection limit for unambiguous identification of the dye and semiquantitative determination of the surface coverage reaches < or =0.7 pmol/cm(2), or approximately five molecules present in the enhanced-field region, which is confirmed by STM images. Because of well-defined adsorption sites at atomically smooth Au(111) surfaces, no variation in band positions or relative band intensities was observed at the single- or few-molecule detection level when employing TERR spectroscopy.     

Adhesion of single polyelectrolyte molecules on silica, mica, and bitumen surfaces

In a recent study (Energy Fuels 2005, 19, 936), a partially hydrolyzed polyacrylamide (HPAM) was used as a process aid to recover bitumen from oil sand ores. It was found that HPAM addition at the bitumen extraction step not only improved bitumen recovery but also enhanced fine solids settling in the tailings stream. To understand the role of HPAM, single-molecule force spectroscopy was employed for the first time to measure the desorption/adhesion forces of single HPAM molecules on silica, mica, and bitumen surfaces using an atomic force microscope (AFM). Silicon wafers with an oxidized surface layer and newly cleaved mica were used, respectively, to represent sand grains and clays in oil sands. The force measurements were carried out in deionized water and in commercial plant process water under equilibrium conditions. The desorption/adhesion forces of HPAM obtained on mica, silica, and bitumen surfaces were approximately 200, 40, and 80 pN in deionized water and approximately 100, 50, and 40 pN in the plant process water, respectively. The measured adhesion forces together with the zeta potential values of these surfaces indicate that the polymer would preferentially adsorb onto clay surfaces rather than onto bitumen surfaces. It is the selective adsorption of HPAM that benefits both bitumen recovery and tailings settling when the polymer was added directly to the bitumen extraction process at an appropriate dosage.     

UV-induced immobilization of tethered zirconocenes on H-terminated silicon surfaces

A tethered ethylenebis(indenyl) zirconocene was covalently immobilized on H-terminated Si(111) surfaces using UV-mediated alkene hydrosilylation, thus making possible the development of structured catalytic surfaces with highly controlled properties.     

Initiation and inhibition of dealloying of single crystalline Cu3Au (111) surfaces

Dealloying is widely utilized but is a dangerous corrosion process as well. Here we report an atomistic picture of the initial stages of electrochemical dealloying of the model system Cu(3)Au (111). We illuminate the structural and chemical changes during the early stages of dissolution up to the critical potential, using a unique combination of advanced surface-analytical tools. Scanning tunneling microscopy images indicate an interlayer exchange of topmost surface atoms during initial dealloying, while scanning Auger-electron microscopy data clearly reveal that the surface is fully covered by a continuous Au-rich layer at an early stage. Initiating below this first layer a transformation from stacking-reversed toward substrate-oriented Au surface structures is observed close to the critical potential. We further use the observed structural transitions as a reference process to evaluate the mechanistic changes induced by a thiol-based model-inhibition layer applied to suppress surface diffusion. The initial ultrathin Au layer is stabilized with the intermediate island morphology completely suppressed, along an anodic shift of the breakdown potential. Thiol-modification induces a peculiar surface microstructure in the form of microcracks exhibiting a nanoporous core. On the basis of the presented atomic-scale observations, an interlayer exchange mechanism next to pure surface diffusion becomes obvious which may be controlling the layer thickness and its later change in orientation.     

From smart polymer molecules to responsive nanostructured surfaces

A heteroarm star block copolymer made from seven polystyrene and seven poly(2-vinylpyridine) arms was grafted onto a solid substrate to fabricate a responsive polymer surface consisting of a densely packed monolayer of copolymer molecules. The grafted layer demonstrates a two-level hierarchical response upon external stimuli combining core-shell transitions of single stars with cooperative transitions of the interacting arms between "dimple" and "ripple" morphologies of the monolayer. The response allows for the switching of the surface properties upon changing solvent selectivity or pH of the aqueous environment.     

Kondo effect in single cobalt phthalocyanine molecules adsorbed on Au(111) monoatomic steps

The Kondo effect in single dehydrogenated cobalt phthalocyanine (CoPc) molecules adsorbed on Au(111) monoatomic steps was studied with a low temperature scanning tunneling microscope. The CoPc molecules adsorbed on Au(111) monoatomic steps show two typical configurations, which can be dehydrogenated to reveal Kondo effect. Moreover, the Kondo temperatures (T(K)) measured for different molecules vary in a large range from approximately 150 to approximately 550 K, increasing monotonically with decreasing Co-Au distance. A simple model consisting of a single Co 3d(z) (2) orbital and a Au 6s orbital is considered and gives a qualitative explanation to the dependence. The large variation of T(K) is attributed to the variation of the interaction between the magnetic-active cobalt ion and the Au substrate resulted from different Co-Au distances.     

Electrochemical detection of osmium tetroxide-labeled PCR-products by means of protective strands

This communication reports about how single-stranded 136 base polymerase chain reaction (PCR) products labeled with electrochemically active osmium tetroxide bipyridine can be detected voltammetrically by hybridization with probe strands immobilized on gold electrodes. These electroactive ssDNA targets have been obtained by means of Lambda Exonuclease treatment of the double-stranded PCR products followed by hybridization of the remaining single strands with short protective strands and covalent labeling with osmium tetroxide bipyridine. Square-wave voltammetric signals of these osmium labels have been obtained only upon hybridization with the immobilized probe strands. An optimal 50 °C hybridization temperature has been found with a saturation of the probe layer at 30 min hybridization time and 7.5 nmol/l target concentration. The blank capture probe layer alone did not yield any signal. Unprotected strands produced almost no interference. Such double-selective switch-on electrochemical hybridization assays hold great promise for the specific detection of PCR products.     

电镀铂/金的金电极上As(Ⅲ)电化学行为的电化学石英晶体微天平研究

采用电化学石英晶体微天平(EQCM)技术研究了Britton-Robinson(B-R,pH=1.8～11.2)缓冲溶液和H2SO4介质中电镀铂淦的金电极上As(Ⅲ)的循环伏安行为.通过实时监测EQCM频率等参数的变化过程并利用预电沉积As(O)放大电极响应信号,考察了两电极上As.(O)的电沉积、AsⅢ皿和AsⅤ助组...     

Adsorption of organic molecules on rutile TiO2 and anatase TiO2 single crystal surfaces

The interaction of organic molecules with titanium dioxide surfaces has been the subject of many studies over the last few decades. Numerous surface science techniques have been utilised to understand the often complex nature of these systems. The reasons for studying these systems are hugely diverse given that titanium dioxide has many technological and medical applications. Although surface science experiments investigating the adsorption of organic molecules on titanium dioxide surfaces is not a new area of research, the field continues to change and evolve as new potential applications are discovered and new techniques to study the systems are developed. This tutorial review aims to update previous reviews on the subject. It describes experimental and theoretical work on the adsorption of carboxylic acids, dye molecules, amino acids, alcohols, catechols and nitrogen containing compounds on single crystal TiO(2) surfaces.     

Biomimetics with a self-assembled monolayer of catalytically active tethered isoalloxazine on Au

A new biomimetic nanostructured electrocatalyst comprised of a self-assembled monolayer (SAM) of flavin covalently attached to Au by reaction of methylformylisoalloxazine with chemisorbed cysteamine is introduced. Examinations by Fourier transform infrared spectroscopy and scanning tunneling microscopy (STM) show that the flavin molecules are oriented perpendicular to the surface with a 2 nm separation between flavin molecules. As a result of the contrast observed in the STM profiles between areas only covered by unreacted cysteamine and those covered by flavin-cysteamine moieties, it can be seen that the flavin molecules rise 0.7 nm above the chemisorbed cysteamines. The SAM flavin electrocatalyst undergoes fast electron transfer with the underlying Au and shows activity toward the oxidation of enzymatically active beta-NADH at pH 7 and very low potential (-0.2 V vs Ag/AgCl), a requirement for use in an enzymatic biofuel cell, and a 100-fold increase in activity with respect to the collisional reaction in solution.