Micro- and nanofabrication of robust reactive arrays based on the covalent coupling of dendrimers to activated monolayers

We report on methods to fabricate robust micro- and nanopatterned platforms, comprising high functional group densities and quasi three-dimensional structures, for possible applications in biochip array technologies. For this purpose, amine-terminated poly(amidoamine) (PAMAM) dendrimers were immobilized via amide linkage formation on 11,11'-dithiobis(N-hydroxysuccinimidylundecanoate) (NHS-C10) self-assembled monolayers (SAMs) on gold surfaces. The coupling reaction and the resulting assemblies were characterized by grazing incidence reflection Fourier transform infrared spectroscopy, contact angle measurements, X-ray photoelectron spectroscopy (XPS), and atomic force microscopy; the obtained surface coverage values were successfully fitted with a Langmuir isotherm. The fraction of unreacted peripheral primary amine groups of the surface-immobilized PAMAM dendrimers was 28% as determined by XPS analysis of trifluoroacetic anhydride-labeled assemblies. Patterning of the PAMAM dendrimers on NHS-C10 SAMs on the micrometer and sub-100-nm scale was achieved by microcontact printing and dip pen nanolithography. The resulting patterns are characterized by their high degree of order and stability of the transferred molecules due to covalent attachment.     

Inverted chemical force microscopy: following interfacial reactions on the nanometer scale

Atomic force microscopy (AFM) with chemical specificity using chemically modified AFM probes, so-called chemical force microscopy, was applied to study surface chemical reactions on the nanometer scale. To overcome the typical limitations of conventional AFM in following reactions in real-time, i.e. slow data acquisition, as well as thermal and instrumental drifts, we have introduced a new approach, named inverted chemical force microscopy (iCFM). In iCFM the reactants are immobilized on the AFM tip rather than on the substrate. The chemical reactions take place at the surface of the tip and are probed in real-time by force-displacement measurements on an inert octadecanethiol-covered Au substrate. The reactions studied were the hydrolysis and aminolysis of 11,11^′-dithiobis(N-hydroxysuccinimidylundecanoate) (NHS-C₁₀). By iCFM intermolecular interactions and hence reaction kinetics can be quantitatively studied on the level of ∼10-100 molecules. In particular, our iCFM data showed that the aminolysis reaction with n-butylamine on SAMs of NHS-C₁₀ is a spatially heterogeneous reaction. In addition, information about the defect density of reactive SAMs was obtained.     

A tetrafluorophenyl activated ester self-assembled monolayer for the immobilization of amine-modified oligonucleotides

A tetrafluorophenyl (TFP) ester-terminated self-assembled monolayer (SAM) for the fabrication of DNA arrays on gold surfaces is described. Activated ester SAMs are desirable for biomolecule array fabrication because they readily react with amine-containing molecules to form a stable amide linkage. N-Hydroxysuccinimide (NHS) ester SAMs are commonly used for this purpose but are subject to a competing hydrolysis side reaction, limiting their effectiveness under basic conditions. TFP was evaluated here as an alternative activated ester leaving group with a potentially greater stability under basic conditions. It is shown that TFP SAMs are much more stable to basic pH than their NHS analogs and are also more hydrophobic, which is an advantage in the fabrication of high-density spotted arrays. DNA arrays prepared on TFP SAMs at pH 10 have a 5-fold greater surface density of DNA molecules, reduced fluorescence background, and smaller spot radii than those prepared on NHS SAM analogs.     

Synthesis and self-assembly of 2,9,16-tri(tert-butyl)-23-(10-mercaptodecyloxy)phthalocyanine and the application of its self-assembled monolayers in organic light-emitting diodes

2,9,16-Tri(tert-butyl)-23-(10-mercaptodecyloxy)phthalocyanine (8) and its disulfide (9) have been synthesized and characterized, and their self-assembling behaviors on gold substrates have been studied. Characteristic Q-bands were observed at about 630 nm in the UV/visible spectra of the self-assembling monolayers (SAMs). They were broadened and blue-shifted relative to those observed in solution. Binding energies for S2p have the same values (161.70 eV) and are in accord with those for gold thiolates. The application of the SAMs in organic light-emitting diode was investigated. It shows that the SAM promotes the hole injection process from the anode.     

Attachment of Amine‐ and Maleimide‐Containing Ferrocene Derivatives onto Self‐Assembled Alkanethiol and Alkanedithiol Monolayers: Voltammetric Evaluation of Cross‐Linking Efficiencies and Surface Coverage of Electroactive Groups

Ferrocene derivatives containing primary amines and maleimide groups were attached covalently onto N‐hydrosuccinimidyl (NHS)‐terminated alkanethiol self‐assembled monolayers (SAMs) and SAMs of alkanedithiol. The surface coverage and efficiencies of the two cross‐linking reactions were evaluated with cyclic voltammetry. All the ferrocene derivatives attached onto the alkanethiol or alkanedithiol SAMs exhibit reversible redox waves. The surface coverage of the aminated ferrocene groups was compared to that of N‐hydrosuccinimidyl (NHS)‐terminated alkanethiol SAM. The covalent attachment of β‐ferrocenylethylamine onto a 11,11′‐dithio‐bis(succinimidylundecanoate) SAM yielded an efficiency as high as 63.1%. The cross‐linking efficiency of this reaction was found to increase with the nucleophilicity of the amino groups. SAMs of longer alkyl chains favor the attachment of a greater number of ferrocene derivatives. As for the Michael‐type electrophilic addition between the sulfhydryl groups of the alkanedithiol SAMs and the ferrocenyl maleimide, the cross‐linking efficiencies were found to range from 6.5% to 25.7%, depending on the alkanedithiol chain length. The difference in the efficiencies between the two types of cross‐linking reactions might be partially attributable to the steric hindrance imposed by the SAMs and the relative sizes of the functional groups.     

两个4,4'-二甲基-2,2'-联吡啶锰(Ⅱ)配合物切割DNA的动力学研究

对2个4,4'-二甲基-2,2'-联吡啶锰(Ⅱ)配合物在生理条件及H2O2的存在下对DNA切割的动力学进行了研究.结果表明,这2个配合物分别存在下的DNA切割反应具有相似的动力学反应特征.其中对超螺旋DNA切割成缺口DNA步骤,均表现为三级反应,即反应速率分别与底物DNA的浓度、配合物的浓度和H2O2的浓度的一次方成正比;同时得到了2个反应的速率常数、活化能(Ea)、活化焓(△H≠)和活化熵(△S≠)等动力学参数,并根据这些结果提出了一个可能的氧化切割反应机理.     

Nucleotide recognition and phosphate linkage hydrolysis at a lipid cubic interface

Mononucleotides, when entrapped within a mono-olein-based cubic Ia3d liquid crystalline phase, have been found to undergo hydrolysis at the sugar-phosphate ester bond in spite of their natural inertness toward hydrolysis. Here, kinetics of the hydrolysis reaction and interactions between the lipid matrix and the mononucleotide adenosine 5'-monophosphate disodium salt (AMP) and its 2'-deoxy derivative (dAMP) are thoroughly investigated in order to shed some light on the mechanism of the nucleotide recognition and phosphate ester hydrolysis. Experiments evidenced that molecular recognition occurs essentially through the sn-2 and the sn-3 alcoholic OH groups of mono-olein. As deduced from the apparent activation energies, the mechanism underlying the hydrolysis reaction is the same for AMP and dAMP. Nevertheless, the reaction proceeds slower for the latter, highlighting a substantial difference in the chemical behavior of the two nucleotides. A model that explains the hydrolysis reaction is presented. Remarkably, the hydrolysis mechanism appears to be highly specific for the Ia3d phase.     

'Shape effects' in metal oxide supported nanoscale gold catalysts

We report the activity of shape-controlled metal oxide (CeO(2), ZnO and Fe(3)O(4)) supported gold catalysts for the steam reforming of methanol (SRM) and the water gas shift (WGS) reactions. Metal oxide nanoshapes, prepared by controlled hydrolysis and thermolysis methods, expose different crystal surfaces, and consequently disperse and stabilize gold differently. We observe that similar to gold supported on CeO(2) shapes exposing the {110} and {111} surfaces, gold supported on the oxygen-rich ZnO {0001} and Fe(3)O(4) {111} surfaces shows higher activity for the SRM and WGS reactions. While the reaction rates vary among the Au-CeO(2), Au-ZnO and Au-Fe(3)O(4) shapes, the apparent activation energies are similar, indicating a common active site. TPR data further indicate that the reaction lightoff coincides with the activation of Au-O-M species on the surface of all three oxide supports evaluated here. Different shapes contain a different number of binding sites for the gold, imparting different overall activity.     

Kinetic evidence for hydrophobically stabilized encounter complexes formed by hydrophobic esters in aqueous solutions containing monohydric alcohols.

The pH-independent hydrolysis of four esters, p-methoxyphenyl 2,2-dichloroethanoate (1a), p-methoxyphenyl 2,2-dichloropropanoate (1b), p-methoxyphenyl 2,2-dichlorobutanoate (1c), and p-methoxyphenyl 2,2-dichloropentanoate (1d), in dilute aqueous solution has been studied as a function of the molality of added cosolutes ethanol, 1-propanol, and 1-butanol. The rate constants for the neutral hydrolysis decrease with increasing cosolute concentration. These kinetic medium effects respond to both the hydrophobicity of the ester and of the monohydric alcohol. The observed rate effects were analyzed using both a thermodynamic and a kinetic model. The kinetic model suggests a molecular picture of a hydrophobically stabilized encounter complex, with equilibrium constants K(ec) often smaller than unity, in which the cosolute blocks the reaction center of the hydrolytic ester for attack by water. The formation of these encounter complexes leads to a dominant initial-state stabilization as follows from the thermodynamic model. Decreases in both apparent enthalpies and entropies of activation for these hydrolysis reactions correspond to unfavorable enthalpies and favorable entropies of complexation, which confirms that the encounter complexes are stabilized by hydrophobic interactions.     

Understanding the mechanism of short-range electron transfer using an immobilized cupredoxin

The hydrophobic patch of azurin (AZ) from Pseudomonas aeruginosa is an important recognition surface for electron transfer (ET) reactions. The influence of changing the size of this region, by mutating the C-terminal copper-binding loop, on the ET reactivity of AZ adsorbed on gold electrodes modified with alkanethiol self-assembled monolayers (SAMs) has been studied. The distance-dependence of ET kinetics measured by cyclic voltammetry using SAMs of variable chain length, demonstrates that the activation barrier for short-range ET is dominated by the dynamics of molecular rearrangements accompanying ET at the AZ-SAM interface. These include internal electric field-dependent low-amplitude protein motions and the reorganization of interfacial water molecules, but not protein reorientation. Interfacial molecular dynamics also control the kinetics of short-range ET for electrostatically and covalently immobilized cytochrome c. This mechanism therefore may be utilized for short-distance ET irrespective of the type of metal center, the surface electrostatic potential, and the nature of the protein-SAM interaction.     

Binding maps for the study and prediction of bimetallic catalyst surface reactions: The case of methanol oxidation

Focusing on the competing pathways of methanol oxidation on platinum and platinum/gold bimetallic catalysts, we explore a novel density functional theory (DFT)‐based approach to the study of reactions on catalyst surfaces. Traditionally, DFT has been used to compute binding energies of products and intermediates as proxies for catalytic activity, and to compute full reaction pathways and their activation energy barriers. Merging the computational simplicity and intuitive clarity of binding energy calculations with the site sensitivity of transition state calculations, we construct maps of the binding energies of relevant atoms and molecules at all sites on a surface. We show that knowledge of the arrangement of strong and weak binding sites on a surface is powerful in rationalizing the ease with which a reaction step proceeds on a given local motif of surface atoms. We highlight the prospects and challenges of this approach toward catalyst screening and prediction.     

Ab initio calculations of the reaction mechanisms for metal-nitride deposition from organo-metallic precursors onto functionalized self-assembled monolayers

An atomistic mechanism has been derived for the initial stages of the adsorption reaction for metal-nitride atomic layer deposition (ALD) from alkylamido organometallic precursors of Ti and Zr on alkyltrichorosilane-based self-assembled monolayers (SAMs). The effect of altering the terminal functional group on the SAM (including -OH, -NH2, -SH, and -NH(CH3)) has been investigated using the density functional theory and the MP2 perturbation theory. Reactions on amine-terminated SAMs proceed through the formation of a dative-bond complex with an activation barrier of 16-20 kcal/mol. In contrast, thiol-terminated SAMs form weak hydrogen-bonded intermediates with activation barriers between 7 and 10 kcal/mol. The deposition of Ti organometallic precursors on hydroxyl-terminated SAMs proceeds through the formation of stronger hydrogen-bonded complexes with barriers of 7 kcal/mol. Zr-based precursors form dative-bonded adducts with near barrierless transitions. This variety allows us to select a kinetically favorable substrate for a chosen precursor. The predicted order of reactivity of differently terminated SAMs and the temperature dependence of the initial reaction probability have been confirmed for Ti-based precursors by recent experimental results. We predict that the replacement of methyl groups by trifluoromethyl groups on the SAM backbone decreases the activation barrier for amine-terminated SAMs by 5 kcal/mol. This opens a route to alter the native reactivities of a given SAM termination, in this case making amine termination energetically viable. The surface distribution of SAM molecules has a strong effect on the adsorption kinetics of Ti-based precursors. Unimolecular side decomposition reactions were found to be kinetically competitive with adsorption at 400 K.     

Understanding the kinetics of spin-forbidden chemical reactions

Many chemical reactions involve a change in spin-state and are formally forbidden. This article summarises a number of previously published applications showing that a form of Transition State Theory (TST) can account for the kinetics of these reactions. New calculations for the emblematic spin-forbidden reaction HC + N(2) are also reported. The observed reactivity is determined by two factors. The first is the critical energy required for reaction to occur, which in spin-forbidden reactions is often defined by the relative energy of the Minimum Energy Crossing Point (MECP) between potential energy surfaces corresponding to the different spin states. The second factor is the probability of hopping from one surface to the other in the vicinity of the crossing region, which is largely defined by the spin-orbit coupling matrix element between the two electronic wavefunctions. The spin-forbidden transition state theory takes both factors into account and gives good results. The shortcomings of the theory, which are largely analogous to those of standard TST, are discussed. Finally, it is shown that in cases where the surface-hopping probability is low, the kinetics of spin-forbidden reactions will be characterised by unusually unfavourable entropies of activation. As a consequence, reactions involving a spin-state change can be expected to compete poorly with spin-allowed reactions at high temperatures (or energies).     

Insights into Sonogashira cross-coupling by high-throughput kinetics and descriptor modeling

A method is presented for the high-throughput monitoring of reaction kinetics in homogeneous catalysis, running up to 25 coupling reactions in a single reaction vessel. This method is demonstrated and validated on the Sonogashira reaction, analyzing the kinetics for almost 500 coupling reactions. First, one-pot reactions of phenylacetylene with a set of 20 different meta- and para-substituted aryl bromides were analyzed in the presence of 17 different Pd-phosphine complexes. In addition, the temperature-dependent Sonogashira reactions were examined for 21 different ArX (X=Cl, Br, I) substrates, and the corresponding activation enthalpies and entropies were determined by means of Eyring plots: ArI (DeltaH(not equal)=48-62 kJ mol(-1); DeltaS(not equal)=-71--39 J mol(-1) K; NO(2)-->OMe), ArBr (DeltaH(not equal)=54-82 kJ mol(-1), DeltaS(not equal)=-55-11 J mol(-1) K), and ArCl (DeltaH(not equal)=95-144 kJ mol(-1), DeltaS(not equal)=-6-100 J mol(-1) K). DFT calculations established a linear correlation of DeltaH( not equal) and the Kohn-Sham HOMO energies of ArX (X=Cl, Br, I) and confirmed their involvement in the rate-limiting step. However, despite different C--X bond energies, aryl iodides and electron-deficient aryl bromides showed similar activation parameters.     

An electrochemical platform for acetylcholinesterase activity assay and inhibitors screening based on Michael addition reaction between thiocholine and catechol-terminated SAMs

An electrochemical platform for acetylcholinesterase (AChE) activity assay and its inhibitors screening is developed based on the Michael addition reaction of thiocholine, the hydrolysis product of acetylthiocholine (AsCh) in the presence of AChE, with the electrogenerated o-quinone of catechol-terminated SAMs on a gold electrode. For understanding and confirming the mechanism of the reaction, the electrochemical behaviors of Michael addition reaction of two model compounds, cysteine (CYS) and glutathione (GSH), towards the catechol-terminated SAMs have been studied. The enzyme kinetics and the inhibition effects of three types of AChE inhibitors, which are tacrine, carbofuran and parathion-methyl, have been investigated using an amperometric method. Among these three inhibitors, tacrine exhibits the strongest inhibiting effect, which is reinforced by the resulting data of kinetic studies on each inhibitor's influence upon the enzyme activity.     

Odd-even variations in the wettability of n-alkanethiolate monolayers on gold by water and hexadecane: a molecular dynamics simulation study

Molecular dynamics (MD) simulations were performed to investigate odd-even chain length dependencies in the wetting properties of self-assembled monolayers (SAMs) of n-alkanethiols [CH3(CH2)n-1SH] on gold by water and hexadecane. Experimentally, the contact angle of hexadecane on the SAMs depends on whether n is odd or even, while contact angles for water show no odd-even dependence. Our MD simulations of this system included a microscopic droplet of either 256 water molecules or 60 hexadecane molecules localized on an n-alkanethiolate SAM on gold with either an even or odd chain length. Contact angles calculated for these nanoscopic droplets were consistent with experimentally observed macroscopic trends in wettability, namely, that hexadecane is sensitive to structural differences between odd- and even-chained SAMs while water is not. Structural properties for the SAMs (including features such as chain tilt, chain twist, and terminal methyl group tilt) were calculated during the MD simulations and used to generate IR spectra of these films that compared favorably with experimental spectra. MD simulations of SAMs in contact with slabs of water and hexadecane revealed that the effects of these solvents on the structure of the SAM was restricted to the chain terminus and had no effect on the inner structure of the SAM. The density profiles for water and hexadecane on the SAMs were different in that water displayed a significant depletion in its density at the liquid/SAM interface from its bulk value, while no such depletion occurred for hexadecane. This difference in contact may explain the lack of an odd-even variation in the wetting characteristics of water on these surfaces, because the water molecules are positioned further away from the surface and, therefore, are not sensitive to the structural differences in the average orientations for the terminal methyl groups in odd- and even-chained SAMs. In contrast, the differences in the wetting properties of hexadecane on the odd- and even-chained SAMs may reflect the closer proximity of these molecules to the SAM surface and a resulting greater sensitivity to the differences in the terminal methyl group orientations in the SAMs. SAM-solvent interaction energies were calculated during the MD simulations, yielding interaction energies that differed on the even- and odd-chained surfaces by approximately 10% for hexadecane and negligibly for water, in accord with estimates using experimental wetting results.     

Gas-phase ion-mobility characterization of SAM-functionalized Au nanoparticles

We present results of a systematic examination of functionalized gold nanoparticles (Au-NPs) by electrospray-differential mobility analysis (ES-DMA). Commercially available, citrate-stabilized Au colloid solutions (10-60 nm) were sized using ES-DMA, from which changes in particle size of less than 0.3 nm were readily discerned. It was found that the formation of salt particles and the coating of Au-NPs by salt during the electrospray process can interfere with the mobility analysis, which required the development of sample preparation and data correction protocols to extract correct values for the Au-NP size. Formation of self-assembled monolayers (SAMs) of alkanethiol molecules on the Au-NP surface was detected from a change in particle mobility, which could be modeled to extract the surface packing density of SAMs. A gas-phase temperature-programmed desorption (TPD) kinetic study of SAMs on Au-NPs found the data to be consistent with a second-order Arrhenius-based rate law, yielding an Arrhenius factor of 1.0 x 10 (11) s (-1) and an activation energy approximately 105 kJ/mol. For the size range of SAM-modified Au-NP we considered, the effect of surface curvature on the energetics of binding of carboxylic acid terminated SAMs is evidently negligible, with binding energies determined by TPD agreeing with those reported for the same SAMs on planar surfaces. This study suggests that the ES-DMA can be added to the tool set of characterization methods used to study the structure and properties of coated nanoparticles.     

Gold adatom as a key structural component in self-assembled monolayers of organosulfur molecules on Au(1 1 1)

Chemisorption of organosulfur molecules, such as alkanethiols, arenethiols and disulfide compounds on gold surfaces and their subsequent self-organization is the archetypal process for molecular self-assembly on surfaces. Owing to their ease of preparation and high versatility, alkanethiol self-assembled monolayers (SAMs) have been widely studied for potential applications including surface functionalization, molecular motors, molecular electronics, and immobilization of biological molecules. Despite fundamental advances, the dissociative chemistry of the sulfur headgroup on gold leading to the formation of the sulfur–gold anchor bond has remained controversial. This review summarizes the recent progress in the understanding of the geometrical and electronic structure of the anchor bond. Particular attention is drawn to the involvement of gold adatoms at all stages of alkanethiol self-assembly, including the dissociation of the disulfide (S–S) and hydrogen-sulfide (S–H) bonds and subsequent formation of the self-assembled structure. Gold adatom chemistry is proposed here to be a unifying theme that explains various aspects of the alkanethiol self-assembly and reconciles experimental evidence provided by scanning probe microscopy and spectroscopic methods of surface science. While several features of alkanethiol self-assembly have yet to be revisited in light of the new adatom-based models, the successes of alkanethiol SAMs suggest that adatom-mediated surface chemistry may be a viable future approach for the construction of self-assembled monolayers involving molecules which do not contain sulfur.     

Self-assembled monolayers of dendritic polyglycerol derivatives on gold that resist the adsorption of proteins

Highly protein-resistant, self-assembled monolayers (SAMs) of dendritic polyglycerols (PGs) on gold can easily be obtained by simple chemical modification of these readily available polymers with a surface-active disulfide linker group. Several disulfide-functionalized PGs were synthesized by N,N'-dicyclohexylcarbodiimide-mediated ester coupling of thioctic acid. Monolayers of the disulfide-functionalized PG derivatives spontaneously form on a semitransparent gold surface and effectively prevent the adsorption of proteins, as demonstrated by surface plasmon resonance (SPR) kinetic measurements. A structure-activity relationship relating the polymer architecture to its ability to effectuate protein resistance has been derived from results of different surface characterization techniques (SPR, attenuated total reflectance infrared (ATR-IR), and contact-angle measurements). Dendritic PGs combine the characteristic structural features of several highly protein-resistant surfaces: a highly flexible aliphatic polyether, hydrophilic surface groups, and a highly branched architecture. PG monolayers are as protein resistant as poly(ethylene glycol) (PEG) SAMs and are significantly better than dextran-coated surfaces, which are currently used as the background for SPR spectroscopy. Due to the higher thermal and oxidative stability of the bulk PG as compared to the PEG and the easy accessibility of these materials, dendritic polyglycerols are novel and promising candidates as surface coatings for biomedical applications.     

Directed growth of poly(isobenzofuran) films by chemical vapor deposition on patterned self-assembled monolayers as templates

This paper describes a method to direct the formation of microstructures of poly(isobenzofuran) (PIBF) by chemical vapor deposition (CVD) on chemically patterned, reactive, self-assembled monolayers (SAMs) prepared on gold substrates. We examined the growth dependence of PIBF by deposition onto several different SAMs each presenting different surface functional groups, including a carboxylic acid, a phenol, an alcohol, an amine, and a methyl group. Interferometry, Fourier transform infrared (FT-IR) spectroscopy, X-ray photoelectron spectroscopy (XPS), gel permeation chromatography (GPC), and optical microscopy were used to characterize the PIBF films grown on the various SAMs. Based on the kinetic and the spectroscopic analyses, we suggest that the growth of PIBF is surface-dependent and may follow a cationic polymerization mechanism. Using the cationic polymerization mechanism of PIBF growth, we also prepared patterned SAMs of 11-mercapto-1-undecanol (MUO) or 11-mercaptoundecanoic acid (MUA) by microcontact printing (microCP) on gold substrates as templates, to direct the growth of the PIBF. The directed growth and the formation of microstructures of PIBF with lateral dimensions of 6 microm were investigated using atomic force microscopy (AFM). The average thickness of the microstructures of PIBF films grown on the MUO and the MUA patterns were 400 +/- 40 nm and 490 +/- 40 nm, respectively. SAMs patterned with carboxylic acid salts (Cu2+, Fe2+, or Ag+) derived from MUA led to increases in the average thickness of the microstructures of PIBF by 10%, 12%, or 27%, respectively, relative to that of control templates. The growth dependence of PIBF on the various carboxylic acid salts was also investigated using experimental observations of the growth kinetics and XPS analyses of the relative amount of metal ions present on the template surfaces.