Adsorption of mercaptopropionic acid onto Au(1 1 1)

Molecular planting of a single organothiol into a "gap-site" of a 2D patterned adlayer in an electrochemical environment

The self-assembled inclusion of molecules into two-dimensional (2D) porous networks on surfaces has been extensively studied because 2D functional materials consisting of organic molecules have become an important research topic. However, the isolation of a single molecular thiol remains a challenging goal. Here, we report a method of planting and isolating organothiols onto a 2D patterned organic adlayer at an electrochemical interface. In situ scanning tunneling microscopy revealed that the phase transition of an ovalene adlayer is electrochemically induced and that the gap site created by three ovalene molecules serves as a 2D molecular template to isolate thiol molecules and to standardize the distance between them via the formation of precise selective open spaces, suggesting that electrochemical "molecular planting" opens applications for 2D patterns of isolated single organothiol molecules.

Tracking interfacial single-molecule pH and binding dynamics via vibrational spectroscopy

Understanding single-molecule chemical dynamics of surface ligands is of critical importance to reveal their individual pathways and, hence, roles in catalysis, which ensemble measurements cannot see. Here, we use a cascaded nano-optics approach that provides sufficient enhancement to enable direct tracking of chemical trajectories of single surface-bound molecules via vibrational spectroscopy. Atomic protrusions are laser-induced within plasmonic nanojunctions to concentrate light to atomic length scales, optically isolating individual molecules. By stabilizing these atomic sites, we unveil single-molecule deprotonation and binding dynamics under ambient conditions. High-speed field-enhanced spectroscopy allows us to monitor chemical switching of a single carboxylic group between three discrete states. Combining this with theoretical calculation identifies reversible proton transfer dynamics (yielding effective single-molecule pH) and switching between molecule-metal coordination states, where the exact chemical pathway depends on the intitial protonation state. These findings open new domains to explore interfacial single-molecule mechanisms and optical manipulation of their reaction pathways.

A New Approach for Quantitative Surface-Enhanced Raman Spectroscopy through the Kinetics of Chemisorption

Surface enhanced Raman spectroscopy (SERS) is a non-destructive, highly sensitive, and rapid analytical tool, which has been widely used in different fields, especially for trace quantities of analyte. However, using SERS for reliable quantitative sample analysis is still a great challenge. Herein, a new approach to quantitative SERS analysis at nanostructured substrates that does not require an internal standard or well-ordered nanostructured SERS substrates is developed. This method is based on the kinetics of chemisorption, that is, on a homogeneous surface, the time taken for adsorption of an adsorbate (adenine or melamine) to reach equilibrium negatively correlates with the concentration of the adsorbate. Quantitative analysis is achieved by using in situ SERS to acquire the adsorption profile of the adsorbate and enabling the adsorption equilibrium time to be calculated. There is excellent correlation between the adenine and melamine SERS response over adsorption equilibrium time with concentration, and the correlation coefficients are 0.9906 and 0.9682, respectively. Moreover, milk sample spiked with the melamine is also studied, and the standard recovery rate is 106%. This work demonstrates a novel, non-destructive, and cost-effective quantitative SERS detection technique, which can broaden applications across multiple fields.

Amperometric Aptasensor for Amyloid-β Oligomer Detection by Optimized Stem-Loop Structures with an Adjustable Detection Range

Amyloid-β oligomers (AβO) have become representative biomarkers for early diagnosis of Alzheimer's disease. Here, we report on an aptasensor based on stem-loop probes for sensitive and specific detection of AβO by an amperometric transducer principle using alternating current voltammetry (ACV). Stem-loop probes with redox-active moieties are immobilized on a gold substrate as a receptor element. The signal transduction mechanism relies on redox ferrocene (Fc) reporting via charge transfer on a molecular recognition event involving a conformational change of the molecular beacon. The stem-loop structures were optimized by considering the aptamers' stem length, spacer, and different ferrocene terminals. In addition, the sensor assembly and signal recording including aptamer concentration and ACV frequency dependence are discussed. Using the optimized stem-loop probe (B-3' Fc), the aptasensor showed a decrease of the Fc peak current induced by AβO binding within the broad concentration range spanning 6 orders of magnitude. Furthermore, the detection limit of the sensor can be further decreased by optimizing the ACV frequency, however at the cost of a narrowed detection range. In this work, a label-free electrochemical aptasensor is demonstrated, which facilitates the quantification of the concentration of AβO with high selectivity and subpicomolar sensitivity, which may be conducive to improving the diagnosis and pharmacology studies of Alzheimer's disease.

CO2 electrochemical reduction at thiolate-modified bulk Au electrodes

Simple modification of polycrystalline bulk Au by an appropriate thiol can selectively enhance electrochemical CO₂RR at the expense of HER.

Nucleotide and structural label identification in single RNA molecules with quantum tunneling spectroscopy

Although a number of advances have been made in RNA sequencing and structural characterization, the lack of a method for directly determining the sequence and structure of single RNA molecules has limited our ability to probe heterogeneity in gene expression at the level of single cells. Here we present a method for direct nucleotide identification and structural label mapping of single RNA molecules via Quantum Molecular Sequencing (QMSeq). The method combines non-perturbative quantum tunneling spectroscopy to probe the molecular orbitals of ribonucleotides, new experimental biophysical parameters that fingerprint these molecular orbitals, and a machine learning classification algorithm to distinguish between the ribonucleotides. The algorithm uses tunneling spectroscopy measurements on an unknown ribonucleotide to determine its chemical identity and the presence of local chemical modifications. Combining this with structure-dependent chemical labeling presents the possibility of mapping both the sequence and local structure of individual RNA molecules. By optimizing the base-calling algorithm, we show a high accuracy for both ribonucleotide discrimination (>99.8%) and chemical label identification (>98%) with a relatively modest molecular coverage (35 repeat measurements). This lays the groundwork for simultaneous sequencing and structural mapping of single unknown RNA molecules, and paves the way for probing the sequence-structure-function relationship within the transcriptome at an unprecedented level of detail.

Surface-enhanced Raman scattering study of the kinetics of self-assembly of carboxylate-terminated n-alkanethiols on silver

Adsorption of 11-mercaptoundecanoic acid (MUA) on silver from methanol and aqueous solutions was monitored in situ by surface-enhanced Raman scattering (SRES) spectroscopy. While adsorption of MUA from methanol is a one-step formation of a thiol-bound monolayer, SERS spectra reveal that monolayer formation from aqueous solution involves interactions of both carboxylate and thiol groups of MUA with the silver surface. Several Raman scattering bands, including the ν(C-S), ν(s)(COO(-)), and ν(C-C), were used to investigate the evolution of the structure of adsorbed MUA on silver surfaces. The time-dependent profiles of these bands for assembly from aqueous solution indicate a multistep process, which is initiated by the binding of both carboxylate and thiol groups to silver, producing a mixture of gauche and trans conformations. In a subsequent step, the COO-Ag interactions are displaced by stronger S-Ag bonds, leading to ordering of the resulting monolayer with formation of a complete SAM with all-trans conformations. The results also showed that the adsorption process depended strongly on the solution pH and surface potential of the metal. These factors can significantly affect the participation and displacement of -COO(-) during self-assembly of MUA from aqueous solution.

Electrochemically controlled self-assembled monolayers characterized with molecular and sub-molecular resolution

Self-assembled organization of functional molecules on solid surfaces has developed into a powerful and sophisticated tool for surface chemistry and nanotechnology. A number of reviews on the topic have been available since the mid 1990s. This perspective article aims to focus on recent development in the investigations of electronic structures and assembling dynamics of electrochemically controlled self-assembled monolayers (SAMs) of thiol containing molecules on gold surfaces. A brief introduction is first given and particularly illustrated by a Table summarizing the molecules studied, the surface lattice structures and the experimental operating conditions. This is followed by discussion of two major high-resolution experimental methods, scanning tunnelling microscopy (STM) and single-crystal electrochemistry. In Section 3, we briefly address choice of supporting electrolytes and substrate surfaces, and their effects on the SAM structures. Section 4 constitutes the major body of the article by offering some details of recent studies for the selected cases, including in situ monitoring of assembling dynamics, molecular electronic structures, and the key external factors determining the SAM packing. In Section 5, we give examples of what can be offered by theoretical computations for the detailed understanding of the SAM electronic structures revealed by STM images. A brief summary of the current applications of SAMs in wiring metalloproteins, design and fabrication of sensors, and single-molecule electronics is described in Section 6. In the final two sections (7 and 8), we discuss the current status in understanding of electronic structures and properties of SAMs in electrochemical environments and what could be expected for future perspectives.

3-Mercapto-1-propanesulfonic acid and Bis(3-sulfopropyl) disulfide adsorbed on Au(111): in situ scanning tunneling microscopy and electrochemical studies

3-Mercapto-1-propanesulfonic acid (MPS) and bis(3-sulfopropyl) disulfide (SPS) adsorbed on a Au(111) electrode were studied by using in situ scanning tunneling microscopy (STM). Although the adsorptions of MPS and SPS are known to be oxidative and reductive, respectively, on an Au(111) electrode, these two admolecules behave similarly in terms of phase evolution, surface coverage, potential for stripping, and characteristics of cyclic voltammetry. However, different adsorption mechanisms of these molecules result in different structures. Raising electrode potential causes more MPS and SPS molecules to adsorb, yielding ordered adlattices between 0.67 and 0.8 V (vs reversible hydrogen electrode). The ordered adlattices of MPS and SPS appear as striped and netlike structures with molecules adsorbed parallel to the Au(111) surface. Switching potential to 0.9 V or more positive still does not result in upright molecular orientation, possibly inhibited by electrostatic interaction between the end group of -SO(3)(-) and the Au(111) electrode. Lowering the potential to 0.4 V disrupted the ordered adlayer. Stripping voltammetric experiments show that MPS and SPS admolecules are desorbed from Au(111) at the same potential, suggesting that these molecules are both adsorbed via their sulfur headgroups. The S-S bond in SPS is likely broken upon its adsorption on Au(111).

Structures of dense glycine and alanine adlayers on chiral Cu(3,1,17) surfaces

Density Functional Theory calculations have been used to predict the structures of dense glycine and alanine adlayers on Cu(3,1,17)(S). Facets of this chiral Cu surface result from adsorbate-induced surface reconstruction when glycine or alanine are adsorbed and annealed on Cu(100). We have calculated the surface energy changes associated with this surface reconstruction. Our results allow the enantiospecificity of this reconstruction following adsorption of enantiopure or racemic alanine on Cu(100) to be discussed. The overall stability of glycine and alanine adlayers on Cu(3,1,17)(S) arises from an interplay between the formation of chemical bonds with the Cu surface, deformations in the adsorbed molecules during adsorption, and intermolecular hydrogen bonds within the adlayer; none of these factors individually dominates.

Engineered Superoxide Dismutase Monomers for Superoxide Biosensor Applications

Because of its high reaction rate and specificity, the enzyme superoxide dismutase (SOD) offers great potential for the sensitive quantification of superoxide radicals in electrochemical biosensors. In this work, monomeric mutants of human Cu,Zn-SOD were engineered to contain one or two additional cysteine residues, which could be used to bind the protein to gold surfaces, thus making the use of promotor molecules unnecessary. Six mutants were successfully designed, expressed, and purified. All mutants bound directly to unmodified gold surfaces via the sulfur of the cysteine residues and showed a quasi-reversible, direct electron transfer to the electrode. Thermodynamic and kinetic parameters of the electron transfer were characterized and showed only slight variations between the individual mutants. For one of the mutants, the interaction with the superoxide radical was studied in more detail. For both partial reactions of the dismutation, an interaction between protein and radical could be shown. In an amperometric biosensorial approach, the SOD-mutant electrode was successfully applied for the detection of superoxide radicals. In the oxidation region, the electrode surpassed the sensitivity of the commonly used cytochrome c electrodes by approximately 1 order of magnitude while not being limited by interferences, but the electrode did not fully reach the sensitivity of dimeric Cu,Zn-SOD immobilized on MPA-modified gold.

Scanning probe microscopic studies of the oriented attachment and membrane reconstitution of cytochrome C oxidase to a gold electrode

Scanning probe microscopy was used to monitor the resulting surface of the oriented incorporation of cytochrome c oxidase into electrode supported lipid bilayer at four crucial stages with molecular resolution. We were able to reveal the formation of a densely packed monolayer of the active ester dithio(succiniimidylepropionate) (DTSP) and the covalent linkage of the nitrilotriacetic acid (NTA) to the thiol anchored DTSP by scanning tunneling microscopy. Atomic force microscopy investigations showed that the detergent solubilized oxidase is immobilized as monomers and small aggregates via histidine residues. Finally, the reconstitution of the proteins within the supported membrane was verified. The amount of oxidase immobilized within the solid supported membrane was estimated.

Role of surface heterogeneity and molecular interactions in the charge-transfer process through self-assembled thiolate monolayers on Au(111)

A comparative study of charge-transfer processes from/to methyl-terminated and carboxylate-terminated thiolate-covered Au(111) surfaces to/from immobilized methylene blue (MB) molecules is presented. Scanning tunneling microscopy images with molecular resolution reveal the presence of molecular-sized defects, missing rows, and crystalline domains with different tilts that turn the thickness of the alkanethiolate SAM (the spacer) uncertain. The degree of surface heterogeneity at the SAMs increases as the number of C units (n) in the hydrocarbon chain decreases from n = 6. Defective regions act as preferred paths for MB incorporation into the methyl-terminated SAMs, driven by hydrophobic forces. The presence of negative-charged terminal groups at the SAMs reduces the number of molecules that can be incorporated, immobilizing them at the outer plane of the monolayer. Only MB molecules incorporated into the SAMs close to the Au(111) surface (at a distance < 0.5 nm) are electrochemically active. MB molecules trapped in different defects explain the broad shape and humps observed in the voltammogram of the redox couple. The heterogeneous charge-transfer rate constants for MB immobilized into methyl-terminated thiolate SAMs are higher than those estimated for carboxylate- terminated SAMs, suggesting a different orientation of the immobilized molecule in the thiolate environment.