Adsorption of 4-mercaptopyridine on Au(111: a periodic DFT study

4-Mercaptopyridine-Modified Sensor for the Sensitive Electrochemical Detection of Mercury Ions

As a highly toxic heavy metal ion, mercury ion (Hg²⁺) pollution has caused serious harm to the environment and human health. In this paper, 4-mercaptopyridine (4-MPY) was selected as the sensing material and decorated on the surface of a gold electrode. Trace Hg²⁺ could be detected by both differential pulse voltammetry (DPV) and electrochemical impedance spectroscopy (EIS) methods. The proposed sensor displayed a wide detection range from 0.01 μg/L to 500 μg/L with a low limit of detection (LOD) of 0.002 μg/L by EIS measurements. Combined with molecular simulations and electrochemical analyses, the chelating mechanism between Hg²⁺ and 4-MPY was explored. Through the analysis of binding energy (BE) values and stability constants, 4-MPY showed an excellent selectivity for Hg²⁺. In the presence of Hg²⁺, the coordination of Hg²⁺ with the pyridine nitrogen of 4-MPY was generated at the sensing region, which caused a change in the electrochemical activity of the electrode surface. Due to the strong specific binding capability, the proposed sensor featured excellent selectivity and an anti-interference capability. Furthermore, the practicality of the sensor for Hg²⁺ detection was validated with the samples of tap water and pond water, which demonstrated its potential application for on-site environmental detection.

Inductive Effect Alone Cannot Explain Lewis Adduct Formation and Dissociation at Electrode Interfaces

Understanding breaking and formation of Lewis bonds at an electrified interface is relevant to a large range of phenomena, including electrocatalysis and electroadsorption. The complexities of interfacial environments and associated reactions often impede a systematic understanding of this type of bond at interfaces. To address this challenge, we report the creation of a main group classic Lewis acid-base adduct on an electrode surface and its behavior under varying electrode potentials. The Lewis base is a self-assembled monolayer of mercaptopyridine and the Lewis acid is BF₃, forming a Lewis bond between nitrogen and boron. The bond is stable at positive potentials but cleaves at potentials more negative of approximately -0.3 V vs Ag/AgCl without an associated current. We also show that if the Lewis acid BF₃ is supplied from a reservoir of Li⁺BF₄^- electrolyte, the cleavage is completely reversible. We propose that the N-B Lewis bond is affected both by the field-induced intramolecular polarization (electroinduction) and by the ionic structures and ionic equilibria near the electrode. Our results indicate that the second effect is responsible for the Lewis bond cleavage at negative potentials. This work is relevant to understanding the fundamentals of electrocatalytic and electroadsorption processes.

Nanoscale chemical analysis of 2D molecular materials using tip-enhanced Raman spectroscopy

Two-dimensional (2D) molecular materials have attracted immense attention due to their unique properties, promising a wide range of exciting applications. To understand the structure-property relationship of these low-dimensional materials, sensitive analytical tools capable of providing structural and chemical characterisation at the nanoscale are required. However, most conventional analytical techniques fail to meet this challenge, especially in a label-free and non-destructive manner under ambient conditions. In the last two decades, tip-enhanced Raman spectroscopy (TERS) has emerged as a powerful analytical technique for nanoscale chemical characterisation by combining the high spatial resolution of scanning probe microscopy and the chemical sensitivity and specificity of surface-enhanced Raman spectroscopy. In this review article, we provide an overview of the application of TERS for nanoscale chemical analysis of 2D molecular materials, including 2D polymers, biomimetic lipid membranes, biological cell membranes, and 2D reactive systems. The progress in the structural and chemical characterisation of these 2D materials is demonstrated with key examples from our as well as other laboratories. We highlight the unique information that TERS can provide as well as point out the common pitfalls in experimental work and data interpretation and the possible ways of averting them.

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.

Molecular-Scale Chemical Imaging of the Orientation of an On-Surface Coordination Complex by Tip-Enhanced Raman Spectroscopy

Metal-organic coordination structures at interfaces play an essential role in many biological and chemical systems. Understanding the molecular specificity, orientation, and spatial distribution of the coordination complexes at the nanometer scale is of great importance for effective molecular engineering of nanostructures and fabrication of functional devices with controllable properties. However, fundamental properties of such coordination systems are still rarely studied directly. In this work, we present a spectroscopic approach on the basis of tip-enhanced Raman spectroscopy (TERS) to investigate cobalt(II) tetraphenyl-porphyrine coordination species on the scale of a single molecule under ambient conditions. Coordination species anchored on gold surfaces modified with pyridine thiol self-assembled monolayers can be spectroscopically distinguished and mapped with ca. 2 nm resolution. In addition, in combination with density functional theory simulations, the adsorption configuration and molecular orientation of the coordination complexes are also revealed using TERS imaging.

Hydrogen Peroxide Oxidation Reaction on a 4-Mercaptopyridine Self-Assembled Monolayer on Au(111) Metallized by Platinum Nanoislands

A systematic investigation of the hydrogen peroxide oxidation reaction (HPOR) in phosphate buffer (pH = 7.3) on an Au(111) single crystal modified with a 4-mercaptopyridine self-assembled monolayer (SAM) has been conducted before and after metallization with Pt. While bare Au(111) shows considerable electrocatalytic activity towards the HPOR, the inhibition of the oxidation reaction after modification with the SAM implies that adsorbed 4-mercaptopyridine molecules do not catalyze the HPOR. However, SAM-modified Au(111) recovers catalytic activity for the HPOR already after a single metallization step fabricating Pt islands on-top. Hydrogen peroxide (HP) may then either react at the (non-metallic) Pt nanoislands or on reactivated Au sites, made accessible by structural changes of the SAM induced by the metallization. The shape of the voltammetric profiles for the HPOR on repeatedly metallized SAMs suggests that the contribution of Au to the total current density gradually diminishes with increasing Pt coverage while the contribution of the Pt islands increases. The electrochemical behavior is dominated by the Pt islands at a coverage of 0.5 ML obtained by three subsequent metallization steps.

Graphical abstract

Discrimination between hydrogen bonding and protonation in the spectra of a surface-enhanced Raman sensor

Adsorbed mercaptopyridine can sense hydrogen-bonding because the ring breathing mode has a different frequency from bare and protonated species.

Surface Structure of 4-Mercaptopyridine on Au(111): A New Dense Phase

4-Mercaptopyridine (4MPy) self-assembled on Au(111) has been studied by in situ electrochemical scanning tunneling microscopy (EC-STM) in HClO₄, cyclic voltammetry, X-ray photoelectron spectroscopy (XPS) and density functional theory (DFT). Samples prepared by varying the immersion time at constant concentration named short time (30 s) and long time (3 min) adsorption have been studied. Cyclic voltammetry and XPS showed that the chemistry of the adsorbed molecules does not depend on the adsorption time resulting in a well established chemisorbed thiol self-assembled monolayer on Au(111). EC-STM study of the short time adsorption sample revealed a new self-assembled structure after a cathodic desorption/readsorption sweep, which remains stable only if the potential is kept negative to the Au(111) zero charge potential (E_PZC). DFT calculations have shown a correlation between the observed structure and a dense weakly adsorbed phase with a surface coverage of θ = 0.4 and a (5 × √3) lattice configuration. At potentials positive to the E_PZC, the weakly adsorbed state becomes unstable, and a different structure is formed due to the chemisorption driven by the electrostatic interaction. Long time adsorption experiments, on the other hand, have shown the typical (5 × √3) structure with θ = 0.2 surface coverage (chemisorbed phase) and are stable over the whole potential range. The difference observed in long time and short time immersion can be explained by the optimization of molecular interactions during the self-assembly process.

The role of the crystalline face in the ordering of 6-mercaptopurine self-assembled monolayers on gold

Well-ordered molecular films play an important role in nanotechnology, from device fabrication to surface patterning. Self-assembled monolayers (SAMs) of 6-mercaptopurine (6MP) on the Au(100)-(1 × 1) and Au(111)-(1 × 1) have been used to understand the interplay of molecule-substrate interactions for heterocyclic thiols capable of binding to the surface by two anchors, which spontaneously form a highly disordered film on Au(111). Our results reveal that for the same surface coverage the simple change of the substrate from Au(111)-(1 × 1) to Au(100)-(1 × 1) eliminates molecular disorder and yields well-ordered SAMs. We discuss these findings in terms of differences in the surface mobility of 6MP species on these surfaces, the energetics of the adsorption sites, and the number of degrees of freedom of these substrates for a molecule with reduced surface mobility resulting from its two surface anchors. These results reveal the presence of subtle molecule-substrate interactions involving the heteroatom that drastically alter SAM properties and therefore strongly impact on our ability to control physical properties and to build devices at the nanoscale.

From porphyrins to pyrphyrins: adsorption study and metalation of a molecular catalyst on Au(111)

The molecular ligand pyrphyrin, a tetradentate bipyridine based macrocycle, represents an interesting but widely unexplored class of molecules. It resembles the well-known porphyrin, but consists of pyridyl subunits instead of pyrroles. Metal complexes based on pyrphyrin ligands have recently shown promise as water reduction catalysts in homogeneous photochemical water splitting reactions. In this study, the adsorption and metalation of pyrphyrin on a single crystalline Au(111) surface is investigated in an ultrahigh vacuum by means of scanning tunneling microscopy, low-energy electron diffraction, X-ray photoelectron spectroscopy and density functional theory. Pyrphyrin coverages of approximately one monolayer and less are obtained by sublimation of the molecules on the substrate kept at room temperature. The molecules self-assemble in two distinct phases of long-range molecular ordering depending on the surface coverage. The deposition of cobalt metal and subsequent annealing lead to the formation of Co-ligated pyrphyrin molecules accompanied by a pronounced change of the molecular self-assembly. Electronic structure calculations taking the herringbone reconstruction of Au(111) into account show that the molecules are physisorbed, but preferred adsorption sites are identified where Co and the N atoms of the two terminal cyano groups are optimally coordinated to the surface Au atoms. An intermediate state of the metalation reaction is observed and the reaction steps for the Co metalation of pyrphyrin molecules on Au(111) are established in a joint experimental and computational effort.

Chemical speciation of heavy metals by surface-enhanced Raman scattering spectroscopy: identification and quantification of inorganic- and methyl-mercury in water

Chemical speciation of heavy metals has become extremely important in environmental and analytical research because of the strong dependence that toxicity, environmental mobility, persistence and bioavailability of these pollutants have on their specific chemical forms. Novel nano-optical-based detection strategies, capable of overcoming the intrinsic limitations of well-established analytic methods for the quantification of total metal ion content, have been reported, but the speciation of different chemical forms has not yet been achieved. Here, we report the first example of a SERS-based sensor for chemical speciation of toxic metal ions in water at trace levels. Specifically, the inorganic Hg(2+) and the more toxicologically relevant methylmercury (CH₃Hg(+)) are selected as analytical targets. The sensing platform consists of a self-assembled monolayer of 4-mercaptopyridine (MPY) on highly SERS-active and robust hybrid plasmonic materials formed by a dense layer of interacting gold nanoparticles anchored onto polystyrene microbeads. The co-ordination of Hg(2+) and CH₃Hg(+) to the nitrogen atom of the MPY ring yields characteristic changes in the vibrational SERS spectra of the organic chemoreceptor that can be qualitatively and quantitatively correlated to the presence of the two different mercury forms.

Temperature effects in the vibrational spectra of self-assembled monolayers

The vibrational spectrum of a thiolate-based self-assembled monolayer fabricated by the adsorption of benzylmercaptan on a Au(111) substrate is studied using a combined experimental and theoretical approach employing infrared reflection absorption spectroscopy and density functional theory. The vibrational spectra are derived both using a finite differences approach and from ab initio molecular dynamics simulations at various temperatures. In addition, the possibility of adsorbate-induced reconstructions of the Au(111) substrate is taken into account. It turns out that the measured spectra can only be understood by taking finite temperatures into account.

Influence of the solvent on the stability of bis(terpyridine) structures on graphite

The effect of solvation on the adsorption of organic molecules on graphite at room temperature has been addressed with force-field molecular dynamics simulations. As a model system, the solvation of a bis(terpyridine) isomer in water and 1,2,4-trichlorobenzene was studied with an explicit solvation model. The inclusion of solvation has a noticeable effect on adsorption energies. Although the results of the various considered force fields differ quite significantly, they all agree that the adsorption of BTP from the TCB solvent is almost thermoneutral. The substrate simply acts as a template to allow a planar arrangement of the network, which is stabilized by the intermolecular interaction. Using an atomic thermodynamics approach, the order of the stability of various network structures as a function of the chemical potential is derived yielding a sequence in agreement with the experiment.

One-step vs stepwise immobilization of 1-D coordination-based Rh-Rh molecular wires on gold surfaces

Reaction of dimeric [Rh(II)(2)(phen)(2)(μ-OAc)(2)(MeCN)(2)](BF(4))(2) (phen =1,10-phenanthroline) with pyrazine (pz) in a 1:2 ratio leads to the new 1-D metal-metal-bonded coordination oligomer {[Rh(II)(2)(phen)(2)(μ-OAc)(2)(pz)](BF(4))(2)}(n) (Rh-Rhpz)(n) (1), where each Rh atom of the dimeric unit (Rh-Rh) is coordinated in the equatorial plane to a nitrogen atom of a rigid and linear bifunctionalized organic linker (pz). Single X-ray diffraction analysis reveals the 1-D straight oligomeric chain structure (molecular wire, MW) consists of alternating (Rh-Rh) units and pz linking ligands with free BF(4)(-) as counteranions, and each metal center has a slightly distorted octahedral arrangement. The presence of accessible labile MeCN groups on both ends of these MWs ("free ends") enables functionalization of a 4-mercaptopyridine-gold coordinating platform (Au/MP) to form in one step a layer of coordination oligomer (Au/MP(Rh-Rhpz)(n); n ≈ 50). Furthermore (Rh-Rhpz)(n) (n = 1-6) MWs were grafted to Au/MP surfaces by a conventional step-by-step assembly construction involving coordination reactions between the Rh dimer ([Rh(2)(phen)(2)(μ-OAc)(2)(MeCN)(2)](BF(4))(2) (2)) and pz. A detailed physicochemical study (UV-vis, RAIR, QCM-D, ellipsometry, contact angle measurements, as well as impedance spectroscopy and cyclic voltammetry) has been made during both assembly methods to characterize the resulting surface-anchored coordination molecular wire (CMW) layers (Au/MP(Rh-Rhpz)(n)). The results indicate that the immobilized molecular assemblies (MAs) were successfully fabricated using both methods of assembly. The efficiency of the two methods is discussed.

Complex surface chemistry of 4-mercaptopyridine self-assembled monolayers on Au(111)

The adsorption of 4-mercaptopyridine on Au(111) from aqueous or ethanolic solutions is studied by different surface characterization techniques and density functional theory calculations (DFT) including van der Waals interactions. X-ray photoelectron spectroscopy and electrochemical data indicate that self-assembly from 4-mercaptopyridine-containing aqueous 0.1 M NaOH solutions for short immersion times (few minutes) results in a 4-mercaptopyridine (PyS) self-assembled monolayer (SAM) with surface coverage 0.2. Scanning tunneling microscopy images show an island-covered Au surface. The increase in the immersion time from minutes to hours results in a complete SAM degradation yielding adsorbed sulfur and a heavily pitted Au surface. Adsorbed sulfur is also the main product when the self-assembly process is made in ethanolic solutions irrespective of the immersion time. We demonstrate for the first time that a surface reaction is involved in PyS SAM decomposition in ethanol, a surface process not favored in water. DFT calculations suggest that the surface reaction takes place via disulfide formation driven by the higher stability of the S-Au(111) system. Other reactions that contribute to sulfidization are also detected and discussed.

Tip-enhanced Raman spectroscopic imaging of patterned thiol monolayers

Full spectroscopic imaging by means of tip-enhanced Raman spectroscopy (TERS) was used to measure the distribution of two isomeric thiols (2-mercaptopyridine (2-PySH) and 4-mercaptopyridine (4-PySH)) in a self-assembled monolayer (SAM) on a gold surface. From a patterned sample created by microcontact printing, an image with full spectral information in every pixel was acquired. The spectroscopic data is in good agreement with the expected molecular distribution on the sample surface due to the microcontact printing process. Using specific marker bands at 1000 cm(-1) for 2-PySH and 1100 cm(-1) for 4-PySH, both isomers could be localized on the surface and semi-quantitative information was deduced from the band intensities. Even though nanometer size resolution information was not required, the large signal enhancement of TERS was employed here to detect a monolayer coverage of weakly scattering analytes that were not detectable with normal Raman spectroscopy, emphasizing the usefulness of TERS.

Towards a scalable and accurate quantum approach for describing vibrations of molecule-metal interfaces

We present a theoretical framework for the computation of anharmonic vibrational frequencies for large systems, with a particular focus on determining adsorbate frequencies from first principles. We give a detailed account of our local implementation of the vibrational self-consistent field approach and its correlation corrections. We show that our approach is both robust, accurate and can be easily deployed on computational grids in order to provide an efficient computational tool. We also present results on the vibrational spectrum of hydrogen fluoride on pyrene, on the thiophene molecule in the gas phase, and on small neutral gold clusters.

Influence of water on the properties of an Au/Mpy/Pd metal/molecule/metal junction

The geometric and electronic structure of the metal-molecule interface in metal/molecule/metal junctions is of great interest since it affects the functionality of such units in possible nanoelectronic devices. We have investigated the interaction between water and a palladium monolayer of a Au(111)/4-mercaptopyridine/Pd junction by means of DFT calculations. A relatively strong bond between water and the palladium monolayer of the Au/Mpy/Pd complex is observed via a one-fold bond between the oxygen atom of the water molecule and a Pd atom. An isolated H(2)O molecule adsorbs preferentially in a flat-lying geometry on top of a palladium atom that is at the same time also bound to the nitrogen atom of a Mpy molecule of the underlying self-assembled monolayer. The electronic structure of these Pd atoms is considerably modified which is reflected in a reduced local density of states at the Fermi energy. At higher coverages, water can be arranged in a hexagonal ice-like bilayer structure in analogy to water on bulk metal surfaces, but with a much stronger binding which is dominated by O-Pd bonds.

In situ STM evidence for the adsorption geometry of three N-heteroaromatic thiols on Au(111)

The electrochemical behavior of three heteroaromatic thiols (MBs) (2-mercaptobenzimidazole (MBI), 2-mercaptobenzothiazole (MBT), and 2-mercaptobenzoxazole (MBO)) on a Au(111) surface has been investigated by electrochemical scanning tunneling microscopy (ECSTM) and cyclic voltammetry (CV) in 0.1 M HClO(4) solution. All three thiols form oriented molecular cluster lines along the reconstruction line direction at 0.55 V. With the electrode potential shifting negatively, the molecules undergo a disordered-ordered structural transition. Molecularly resolved STM images show that all three molecules form striped adlayers in the desorption region on the Au(111) surface. The different heteroatoms in the heteroaromatic rings result in different electrochemical behavior of the MB self-assembled monolayers (SAMs). MBI, MBT, and MBO are proposed to interact with the substrate via the S-Au bonds from thiol group and the coordination interaction of N, S, and O with the substrate from the heteroaromatic ring, respectively. These results provide direct evidence of the electrochemical behavior and the adlayer structures of MB SAMs on the Au electrode.

Bis(terpyridine)-based surface template structures on graphite: a force field and DFT study

Host-guest networks formed by ordered organic layers are promising candidates for applications in molecular storage and quantum computing. We have studied 2-dimensionally ordered surface template structures of bis(terpyridine)-derived molecules (BTPs) on graphite using force field and DFT methods and compared the results to recent experimental observations. In order to determine the force field best suited for surface calculations, bond lengths and angles, torsional potentials, adsorption and stacking energies of smaller aromatic molecules were calculated with different force fields (Compass, UFF, Dreiding and CVFF). Density functional perturbation theory calculations were used to study the intermolecular interactions between 3,3'-BTP molecules. Structural properties, adsorption energies and rotational barriers of the 3,3'-BTP surface structure and its host-guest systems with phthalocyanine (PcH(2)) or excess 3,3'-BTP as guest molecules have been addressed. In addition, STM images of oligopyridine and phthalocyanine molecules were simulated based on periodic and local density functional theory calculations.