Surface-mediated Reactions Research Articles

Surface-Assisted Reactions toward Formation of Graphene Nanoribbons on Au(110) Surface

Scanning tunneling microscopy and X-ray spectroscopy measurements are combined to first-principles simulations to investigate the formation of graphene nanoribbons (GNRs) on Au(110), as based on the surface-mediated reaction of 10,10′-dibromo-9,9′-bianthracene (DBBA) molecules. At variance with Au(111), two different pathways are identified for the GNR self-assembly on Au(110), as controlled by both the adsorption temperature and the surface coverage of the DBBA molecular precursors. Room-temperature DBBA deposition on Au(110) leads to the same reaction steps obtained on Au(111), even though with lower activation temperatures. For DBBA deposition at 470 K, the cyclodehydrogenation of the precursors preceds their polymerization, and the GNR formation is fostered by increasing the surface coverage. While the initial stages of the reaction are found to crucially determine the final configuration and orientation of the GNRs, the molecular diffusion is found to limit in both cases the formation of high-density...

Ullmann coupling mediated assembly of an electrically driven altitudinal molecular rotor.

Surface-bound molecular rotation can occur with the rotational axis either perpendicular (azimuthal) or parallel (altitudinal) to the surface. The majority of molecular rotor studies involve azimuthal rotors, whereas very few altitudinal rotors have been reported. In this work, altitudinal rotors are formed by means of coupling aryl halides through a surface-mediated Ullmann coupling reaction, producing a reaction state-dependent altitudinal molecular rotor/stator. All steps in the reaction on a Cu(111) surface are visualized by low-temperature scanning tunneling microscopy. The intermediate stage of the coupling reaction is a metal-organic complex consisting of two aryl groups attached to a single copper atom with the aryl rings angled away from the surface. This conformation leads to nearly unhindered rotational motion of ethyl groups at the para positions of the aryl rings. Rotational events of the ethyl group are both induced and quantified by electron tunneling current versus time measurements and are only observed for the intermediate structure of the Ullmann coupling reaction, not the starting material or finished product in which the ethyl groups are static. We perform an extensive set of inelastic electron tunneling driven rotation experiments that reveal that torsional motion around the ethyl group is stimulated by tunneling electrons in a one-electron process with an excitation energy threshold of 45 meV. This chemically tunable system offers an ideal platform for examining many fundamental aspects of the dynamics of chemically tunable molecular rotor and motors.

Surface-mediated selective photocatalytic aerobic oxidation reactions on TiO2 nanofibres

The interaction between photocatalyst surface and the reactants may outweigh its light absorption ability in photocatalytic activities.

Polluted dust promotes new particle formation and growth.

Understanding new particle formation and their subsequent growth in the troposphere has a critical impact on our ability to predict atmospheric composition and global climate change. High pre-existing particle loadings have been thought to suppress the formation of new atmospheric aerosol particles due to high condensation and coagulation sinks. Here, based on field measurements at a mountain site in South China, we report, for the first time, in situ observational evidence on new particle formation and growth in remote ambient atmosphere during heavy dust episodes mixed with anthropogenic pollution. Both the formation and growth rates of particles in the diameter range 15–50 nm were enhanced during the dust episodes, indicating the influence of photo-induced, dust surface-mediated reactions and resulting condensable vapor production. This study provides unique in situ observations of heterogeneous photochemical processes inducing new particle formation and growth in the real atmosphere, and suggests an unexpected impact of mineral dust on climate and atmospheric chemistry.

Single‐chain factor XII exhibits activity when complexed to polyphosphate

The mechanism underpinning factorXII autoactivation was originally characterized with non-physiological surfaces, such as dextran sulfate (DS), ellagic acid, and kaolin. Several 'natural' anionic activating surfaces, such as platelet polyphosphate (polyP), have now been identified. To analyze the autoactivation of FXII by polyP of a similar length to that found in platelets (polyP70 ). PolyP70 showed similar efficacy to DS in stimulating autoactivation of FXII, as detected with amidolytic substrate. Western blotting revealed different forms of FXII with the two activating surfaces: two-chain αFXIIa was formed with DS, whereas single-chain FXII (scFXII; 80kDa) was formed with polyP70 . Dissociation of scFXII from polyP70 abrogated amidolytic activity, suggesting reversible exposure of the active site. Activity of scFXII-polyP70 was enhanced by Zn(2+) and was sensitive to NaCl concentration. A bell-shaped concentration response to polyP70 was evident, as is typical of surface-mediated reactions. Reaction of scFXII-polyP70 with various concentrations of S2302 generated a sigmoidal curve, in contrast to a hyperbolic curve for αFXIIa, from which a Hill coefficient of 3.67 was derived, indicative of positive cooperative binding. scFXII-polyP70 was more sensitive to inhibition by H-d-Pro-Phe-Arg-chloromethylketone and corn trypsin inhibitor than αFXIIa, but inhibition profiles for C1-inhibitor were similar. Active scFXII-polyP70 was also able to cleave its physiological targets FXI and prekallikrein to their active forms. Autoactivation of FXII by polyP, of the size found in platelets, proceeds via an active single-chain intermediate. scFXII-polyP70 shows activity towards physiological substrates, and may represent the primary event in initiating contact activation invivo.

Highly efficient reduction of 4-nitrophenol by heterostructured gold-magnetite nanocatalysts

In this study, the catalytic reduction of 4-nitrophenol by heterostructured Au–Fe3O4 nanocatalysts using NaBH4 as the reducing agent was investigated under various environmental conditions. The electron behaviors at the interface of Au and Fe3O4 nanoparticles were examined to elucidate the reaction mechanisms for 4-nitrophenol reduction. The transmission electron microscopic images show that the average particle size of Au–Fe3O4 heterostructures increases slightly from 14 to 18nm after phase transfer from oil phase to aqueous solution. The X-ray photoelectron and X-ray absorption near edge spectroscopic results show the electron flow from Au seeds to Fe3O4, resulting in the formation of positively charged Au surface to accelerate the catalytic reduction efficiency and rate of 4-nitrophenol. In addition, the reduction of 4-nitrophenol is a surface-mediated reaction and the catalytic efficiency and rate of 4-nitrophenol is highly dependent on the initial 4-nitrophenol concentration, pH, and reaction temperature. The increase in pH lowers the reduction efficiency and rate of 4-nitrophenol and a 2.4-fold decrease in the pseudo-first-order rate constant is observed when pH increases from 5 to 9. In addition, the Au–Fe3O4 nanocatalysts show a good separation ability and reusability which can be repeatedly applied for complete reduction of 4-nitrophenol for at least six successive cycles without the loss of morphology and saturation magnetization. Results obtained in this study clearly demonstrate that the Au–Fe3O4 heterostructures are excellent nanocatalysts which can be applied in heterogeneous catalysis, water treatment, and green chemistry.

Molecular dynamics simulations of the amino acid-ZnO (10-10) interface: a comparison between density functional theory and density functional tight binding results.

We investigate the adsorption behavior of four different amino acids (glutamine, glutamate, serine, cysteine) on the zinc oxide (101̄0) surface, comparing the geometry and energy associated with a number of different adsorption configurations. In doing this, we highlight the benefits and limits of using density-functional tight-binding (DFTB) with respect to standard density functional theory (DFT). The DFTB method is found to reliably reproduce the DFT adsorption geometries. Analysis of the adsorption configurations emphasizes the fundamental role of the first hydration layer in mediating the interactions between the amino acids and the surface. Direct surface-molecule bonds are found to form predominantly via the carboxylate groups of the studied amino acids. No surface-mediated chemical reactions are observed, with the notable exception of a proton transfer from the thiol group of cysteine to a hydroxyl group of the surface hydration layer. The adsorption energies are found to be dominated both by the formation of direct or indirect surface-molecule hydrogen bonds, but also by the rearrangement of the hydrogen-bond network in surface proximity in a non-intuitive way. Energetic comparisons between DFTB and DFT are made difficult on one side by the long time necessary to achieve convergence of potential energy values in MD simulations and on the other side by the necessity of including higher-order corrections to DFTB to obtain a good description of the hydrogen bond energetics. Overall, our results suggest that DFTB is a good reference method to set the correct chemical states and the initial geometries of hybrid biomolecule/ZnO systems to be simulated with non-reactive force fields.

Computational investigation of surface reactivity of functionalized silicon surfaces in deposition processes

Recent advances in chemical vapor deposition and atomic layer deposition coupled with the ever-increasing demand for better control over the interface formation driven by practical applications require understanding and controlling chemical reactions, leading to the deposition of metal-based films onto semiconductor substrates at a truly atomic level. Computational investigation of possible surface-mediated reactions of metalorganic precursors used to deposit thin films used in practical applications allows for an efficient screening of the parameters needed to optimize the process of interface formation. Here, we will use a simple frontier orbital analysis coupled with cluster calculations to explore the surface reactions of functionalized silicon surfaces with test metalorganic precursor molecules. Two molecular precursors are investigated. Trimethylaluminum allows us to investigate the contribution of relatively simple C–Al and C–H dissociation processes in determining the mechanism of surface reaction with a silicon surface either terminated with hydrogen or modified with several nitrogen- or oxygen-containing functional groups. Following similar processes with tetrakis(dimethylamido)titanium provides an opportunity to expand the type of processes investigated and to decouple electronic and steric factors determining surface reactivity.

Surface [4 + 2] Cycloaddition Reaction of Thymine on Si(111)7×7 Observed by Scanning Tunneling Microscopy

The early stage of thymine (Thy) adsorption on Si(111)7×7 surface is studied with scanning tunneling microscopy (STM) and density functional theory (DFT)-based computational method. Bright protrusions corresponding to the adsorbed thymine molecules are observed in both empty-state and filled-state STM images. These bright protrusions in the empty-state images exhibit three different degrees [lower (L), medium (M), and higher (H)] of intensities. The L and M protrusions are found on the adatom–restatom pairs in the 7 × 7 unit cell, indicating bidentate configurations for Thy adsorption. A free Thy molecule has been found to interact with the Si surface by a two-step process: Thy first undergoes keto–enol tautomerization to form the more stable dienol tautomer, which then binds to the Si adatom–restatom pair via the [4 + 2] cycloaddition reaction, leading to two different adproducts. Our DFT/B3LYP/6-31++G(d,p) calculations show three plausible cycloaddition products, with the 1,4-cyclohexadiene adproduct being more stable than 3,6- and 2,5-cyclohexadienes. Our calculations also suggest the viability of formation of a Thy molecule hydrogen-bonded with the bidentate Thy adproducts already on the surface. Statistical analysis for three different exposures of Thy on the 7 × 7 surface reveals that the L protrusion has the highest relative surface concentration (80%), with the M (16%) and H features (4%) being significantly less popular. These results lead us to attribute the L and M protrusions to the 1,4- and the 3,6-cycloaddition products, respectively, with the least popular H protrusion assigned to a Thy molecule hydrogen-bonded to the bidentate Thy, all attached to an adatom–restatom pair. The observation of [4 + 2] cycloaddition products on the Si surface confirms the formation of precursor dienol Thy tautomer. This surface-mediated two-step reaction pathway for Thy is unique for surfaces, in contrast to keto–enol tautomerization that is mainly observed in the solution phase either by acid- or base-catalyzed pathways. Our STM study coupled with our separate XPS work have demonstrated that this type of tautomerization can also be observed on Si surfaces, and this can initiate the subsequent cycloaddition reactions of Thy molecule with the surface.

Competing reactions during metalorganic deposition: Ligand-exchange versus direct reaction with the substrate surface

Surface-mediated reactions of metalorganic compounds on solid substrates are key processes in film deposition technology, especially in atomic layer deposition (ALD) or chemical vapor deposition. Since most applications of thin films require high purity, understanding and controlling the mechanisms of desired and undesired surface reactions are of the utmost importance. This work outlines a general approach to understand potential surface reactions during deposition through density functional theory calculations, considering precursors containing the most commonly used types of ligands, namely alkyl (Al(CH3)3), alkoxide (Ti[OC3H7]4), alkylamide (Hf[N(CH3)2]4), diketonate (Cu(acac)2), amidinate (Ni[Pr-amd]2), and cyclopentadienyl (Hf(Cp)2(CH3)2). In all cases, the “desired” ligand-exchange reaction (the basis of most ALD processes) is compared to “undesired” surface reactions, where the ligands of the precursor interact with reactive surface sites and can undergo uncontrolled decomposition pathways, incorporating undesired elements into the growing film. To be able to make an effective comparison across precursor types, all calculations were made considering the same surface model, that of a Si(100) surface, and the same level of theory. Our results show that the undesired ligand-mediated adsorption on reactive sites can often compete (both thermodynamically and kinetically) with the desired ligand-exchange reaction, particularly in the case of alkoxides, alkylamides, and diketonates. The intrinsic reactivity of each precursor (based on their frontier molecular orbitals) is found to determine the manner in which it will react with the surface. This article emphasizes that undesired reactions can often be predicted and evaluated based on the chemical reactivity of each precursor. This approach, applied to specific cases, will be important for probing the chemical performance of a deposition precursor.

Surface‐Mediated Synthesis of Dimeric Rhodium Catalysts on MgO: Tracking Changes in the Nuclearity and Ligand Environment of the Catalytically Active Sites by X‐ray Absorption and Infrared Spectroscopies

The preparation of dinuclear rhodium clusters and their use as catalysts is challenging because these clusters are unstable, evolving readily into species with higher nuclearities. We now present a novel synthetic route to generate rhodium dimers on the surface of MgO by a stoichiometrically simple surface-mediated reaction involving [Rh(C(2)H(4))(2)] species and H(2). X-ray absorption and IR spectra were used to characterize the changes in the nuclearity of the essentially molecular surface species as they formed, including the ligands on the rhodium and the metal-support interactions. The support plays a key role in stabilizing the dinuclear rhodium species, allowing the incorporation of small ligands (ethyl, hydride, and/or CO) and enabling a characterization of the catalytic performance of the supported species for the hydrogenation of ethylene as a function of the metal nuclearity and ligand environment. A change in the nuclearity from one to two Rh atoms leads to a 58-fold increase in the catalytic activity for ethylene hydrogenation, a reaction involving unsaturated, but stable, dimeric rhodium species.

Kinetics of Active Surface-Mediated Diffusion in Spherically Symmetric Domains

We present an exact calculation of the mean first-passage time to a target on the surface of a 2D or 3D spherical domain, for a molecule alternating phases of surface diffusion on the domain boundary and phases of bulk diffusion. We generalize the results of Bénichou et al. in (J. Stat. Phys. 142:657, 2011) and consider a biased diffusion in a general annulus with an arbitrary number of regularly spaced targets on a partially reflecting surface. The presented approach is based on an integral equation which can be solved analytically. Numerically validated approximation schemes, which provide more tractable expressions of the mean first-passage time are also proposed. In the framework of this minimal model of surface-mediated reactions, we show analytically that the mean reaction time can be minimized as a function of the desorption rate from the surface.

Dechlorination of chlorinated hydrocarbons by bimetallic Ni/Fe immobilized on polyethylene glycol-grafted microfiltration membranes under anoxic conditions

In this study, the dechlorination of chlorinated hydrocarbons including trichloroethylene (TCE), tetrachloroethylene (PCE) and carbon tetrachloride (CT) by bimetallic Ni/Fe nanoparticles immobilized on four different membranes was investigated under anoxic conditions. Effects of several parameters including the nature of membrane, initial concentration, pH value, and reaction temperature on the dechlorination efficiency were examined. The scanning electron microscopic images showed that the Ni/Fe nanoparticles were successfully immobilized inside the four membranes using polyethylene glycol as the cross-linker. The agglomeration of Ni/Fe were observed in poly(vinylidene fluoride), Millex GS and mixed cellulose ester membranes, while a relatively uniform distribution of Ni/Fe was found in nylon-66 membrane because of its hydrophilic nature. The immobilized Ni/Fe nanoparticles exhibited good reactivity towards the dechlorination of chlorinated hydrocarbons, and the pseudo-first-order rate constant for TCE dechlorination by Ni/Fe in nylon-66 were 3.7–11.7 times higher than those in other membranes. In addition, the dechlorination efficiency of chlorinated hydrocarbons followed the order TCE > PCE > CT. Ethane was the only end product for TCE and PCE dechlorination, while dichloromethane and methane were found to be the major products for CT dechlorination, clearly indicating the involvement of reactive hydrogen species in dechlorination. In addition, the initial rate constant for TCE dechlorination increased upon increasing initial TCE concentrations and the activation energy for TCE dechlorination by immobilized Ni/Fe was 34.9 kJ mol −1, showing that the dechlorination of TCE by membrane-supported Ni/Fe nanoparticles is a surface-mediated reaction.

Process intensification of heterogeneous photocatalysis with static mixer: Enhanced mass transfer of reactive species

The process intensification (PI) of heterogeneous photocatalysis using the Kenics static mixer was investigated and its mechanism was proposed. Three model compounds (phenol, Cr(VI), and acid orange 7 (AO7)) with different photocatalytic reaction mechanisms were selected. The use of the Kenics static mixer increased the degradation rate of phenol from 20% to 150%, but appeared to have no effect on the photodegradation of Cr(VI) and AO7. However, with the addition of formic acid and NaF to the Cr(VI) and AO7 systems, respectively, the reaction mechanism shifted from a surface-mediated reaction to a radical-mediated reaction, and the photoreduction of Cr(VI) and photo-oxidation of AO7 using the Kenics static mixer exhibited higher reaction rates. In addition, the results of experiments with the terephthalic acid (TA) fluorescence probe indicated that the Kenics static mixer increased the yield of hydroxyl radicals. Based on the reaction mechanisms, we propose that the Kenics static mixer played a role in heterogeneous photocatalysis by creating intense mixing and increasing the interfacial mass transfer, which resulted in the enhanced mobility of reactive radicals from the catalyst surface or boundary layer to the solution. This approach intensified the heterogeneous photocatalysis process by enhancing the mass transfer of the reactive species rather than the reactant substrate, provided an alternative to the PI of heterogeneous photocatalysis, and allowed for easier engineering applications.

Extended Two-Dimensional Metal–Organic Frameworks Based on Thiolate–Copper Coordination Bonds

Self-assembly and surface-mediated reactions of 1,3,5-tris(4-mercaptophenyl)benzene--a three-fold symmetric aromatic trithiol--are studied on Cu(111) by means of scanning tunneling microscopy (STM) under ultrahigh-vacuum (UHV) conditions. In order to reveal the nature of intermolecular bonds and to understand the specific role of the substrate for their formation, these studies were extended to Ag(111). Room-temperature deposition onto either substrate yields densely packed trigonal structures with similar appearance and lattice parameters. Yet, thermal annealing reveals distinct differences between both substrates: on Cu(111) moderate annealing temperatures (~150 °C) already drive the emergence of two different porous networks, whereas on Ag(111) higher annealing temperatures (up to ~300 °C) were required to induce structural changes. In the latter case only disordered structures with characteristic dimers were observed. These differences are rationalized by the contribution of the adatom gas on Cu(111) to the formation of metal-coordination bonds. Density functional theory (DFT) methods were applied to identify intermolecular bonds in both cases by means of their bond distances and geometries.

Mean First-Passage Time of Surface-Mediated Diffusion in Spherical Domains

We present an exact calculation of the mean first-passage time to a target on the surface of a 2D or 3D spherical domain, for a molecule alternating phases of surface diffusion on the domain boundary and phases of bulk diffusion. The presented approach is based on an integral equation which can be solved analytically. Numerically validated approximation schemes, which provide more tractable expressions of the mean first-passage time are also proposed. In the framework of this minimal model of surface-mediated reactions, we show analytically that the mean reaction time can be minimized as a function of the desorption rate from the surface.

Formation of PCDD/Fs from the copper oxide-mediated pyrolysis and oxidation of 1,2-dichlorobenzene.

Formation of polychorinated dibenzo-p-dioxins (PCDDs) has been demonstrated to occur via surface-mediated reactions of chlorinated phenols. However, polychlorinated dibenzofurans (PCDFs) are observed in much lower yields in laboratory studies than in full-scale combustors where PCDFs are in higher concentrations than PCDDs. This has led to the suggestion that at least PCDFs are formed from elemental carbon in the de novo process. However, the potential for PCDF formation from reactions of chlorinated benzenes has been largely overlooked. In this study, we investigated the potential contribution of chlorinated benzenes to formation of PCDD/Fs using 1,2-dichlorobenzene as a surrogate for reactions of other chlorinated benzenes and CuO/silica (3 wt % Cu) as a surrogate for fly ash. Results were similar for oxidative and pyrolytic conditions with a slight increase in more chlorinated products under oxidative conditions. Reaction products included chlorobenzene, polychlorinated benzenes, phenol, 2-monochlorophenol (2-MCP), dichlorophenols, and trichlorophenols with yields ranging from 0.01 to 2% for the phenols and from 0.01 to 10% for chlorinated benzenes. 4,6-Dichlorodibenzo furan (4,6-DCDF) and dibenzofuran (DF) were observed in maximum yields of 0.2% and 0.5%, respectively, under pyrolytic conditions and 0.1% and 0.3%, respectively, under oxidative conditions. In previous studies of the pyrolysis of 2-MCP under identical conditions, 4,6-DCDF and dibenzo-p-dioxin (DD) were observed with maximum yields of ∼0.2% and ∼0.1%, respectively, along with trace quantities of 1-monochlorodibenzo-p-dioxin (1-MCDD). Under oxidative conditions, 1-MCDD, DD, and 4,6-DCDF were observed with maximum yields of 0.3%, 0.07% and 0.1%, respectively. When combined with the fact that measured concentrations of chlorinated benzenes are 10-100× that of chlorinated phenols in full-scale combustion systems, the data suggest surface-mediated reactions of chlorinated benzenes can be a significant source of PCDD/F emissions.

Surface-mediated chain reaction through dissociative attachment

Chain reactions on a surface offer an important route to linear nanopatterning. We recently reported cooperative reactions on a silicon surface in which the reaction of one halogen atom with a silicon atom of a silicon dimer induced the halogenation of its neighbouring silicon atom through surface-mediated charge transfer. The reaction was unable to propagate further but here we describe how, by chemically bridging the gaps between the rows of these silicon dimers, this mechanism is able to form extended chains. The agents for chain growth are CH(3)Cl molecules that dissociatively attach CH(3) groups and chlorine atoms to silicon atoms from different dimers. By means of charge transfer through the surface, this gives rise to dangling bonds adjacent to the CH(3) groups and chlorine atoms (in effect, 'free radicals') that dissociate further incoming CH(3)Cl molecules, thereby providing the growing points for chains of indefinite length. This versatile mechanism of chain growth is examined in experiments and using ab initio theory.

ChemInform Abstract: Surface-Mediated Solid Phase Reaction: Dramatic Improvement of Michael Reaction on the Surface of Alumina.

Abstract The Michael reaction of several 1,3-dicarbonyl compounds, nitro- alkanes, and thiols as donors with methyl vinyl ketone, acrolein, methyl acrylate, methyl methacrylate, and mesityl oxide as acceptors on the surface of alumina without any solvent proceed very efficiently and furnish high yield of adducts.

ChemInform Abstract: Surface-Mediated Solid Phase Michael Reaction: Dramatic Acceleration on Alumina.

Abstract The Michael reaction of several β-dicarbonyl compounds, ethyl cyanoacetate, and diethyl malonate as donors with methyl vinyl ketone, acrolein and methyl acrylate as acceptors are carried out very efficiently on Al 2 O 3 surface without any solvent.