Transition mechanism of the coverage-dependent polymorphism of self-assembled melamine nanostructures on Au(111).

Molecular self-assembled films have recently attracted increasing attention within the field of nanotechnology as they offer a route to obtain new materials. However, careful selection of the molecular precursors and substrates, as well as exhaustive control of the system evolution is required to obtain the best possible outcome. The three-fold rotational symmetry of melamine molecules and their capability to form hydrogen bonds make them suitable candidates to synthesize this type of self-assembled network. In this work, we have studied the polymorphism of melamine nanostructures on Au(111) at room temperature. We find two coverage-dependent phases: a honeycomb structure (α-phase) for submonolayer coverage and a close-packed structure (ß-phase) for full monolayer coverage. A combined scanning tunnel microscopy and density functional theory based-calculations study of the transition regime where both phases coexist allows describing the mechanism underlying this coverage driven phase transition in terms of the changes in the molecular lateral tension.

On-Surface Hydrogen-Induced Covalent Coupling of Polycyclic Aromatic Hydrocarbons via a Superhydrogenated Intermediate.

The activation, hydrogenation, and covalent coupling of polycyclic aromatic hydrocarbons (PAHs) are processes of great importance in fields like chemistry, energy, biology, or health, among others. So far, they are based on the use of catalysts which drive and increase the efficiency of the thermally- or light-induced reaction. Here, we report on the catalyst-free covalent coupling of nonfunctionalized PAHs adsorbed on a relatively inert surface in the presence of atomic hydrogen. The underlying mechanism has been characterized by high-resolution scanning tunnelling microscopy and rationalized by density functional theory calculations. It is based on the formation of intermediate radical-like species upon hydrogen-induced molecular superhydrogenation which favors the covalent binding of PAHs in a thermally activated process, resulting in large coupled molecular nanostructures. The mechanism proposed in this work opens a door toward the direct formation of covalent, PAH-based, bottom-up synthesized nanoarchitectures on technologically relevant inert surfaces.

Differential pulse voltammetric determination of the carcinogenic diamine 4,4'-oxydianiline by electrochemical preconcentration on a MoS2 based sensor.

An electrochemical sensor for the carcinogen 4,4'-oxydianiline (Oxy) is described. The method is based on the ability of MoS2 nanosheets to preconcentrate Oxy. A glassy carbon electrode (GCE) was covered, by drop-casting, with MoS2 nanosheets that were obtained by exfoliation. X-Ray photoemission spectroscopy indicates that Oxy accumulates on the MoS2 nanosheets through an electropolymerization process similar to that reported for aniline. Both electrochemical impedance spectroscopy and atomic force microscopy were used to characterize the electrode surface at the different stages of device fabrication. Employing the current measured at +0.27 V vs. Ag/AgCl after Oxy adsorption, the modified GCE enables the voltammetric detection of Oxy at 80 nM levels with relative errors and relative standard deviations of <8.3 and <5.6%, respectively, at all the concentrations studied. The method was applied to the selective determination of Oxy in spiked river water samples. Very good selectivity and recoveries of around 95% in average are found. Graphical abstractSchematic representation of 4,4-oxydianiline electrochemical polymerization and preconcentration onto molybdenum disulfide nanosheets for the diamine determination in river waters.

Size-Selective Carbon Clusters as Obstacles to Graphene Growth on a Metal.

Chemical vapor deposition (CVD) on metals is so far the best suited method to produce high-quality, large-area graphene. We discovered an unprecedentedly large family of small size-selective carbon clusters that form together with graphene during CVD. Using scanning tunneling microscopy (STM) and density functional theory (DFT), we unambiguously determine their atomic structure. For that purpose, we use grids based on a graphene moiré and a dilute atomic lattice that unambiguously reveal the binding geometry of the clusters. We find that the observed clusters bind in metastable configurations on the substrate, while the thermodynamically stable configurations are not observed. We argue that the clusters are formed under kinetic control and establish that the evolution of the smallest clusters is blocked. They are hence products of surface reactions in competition with graphene growth, rather than intermediary species to the formation of extended graphene, as often assumed in the literature. We expect such obstacles to the synthesis of perfect graphene to be ubiquitous on a variety of metallic surfaces.

A magnesium-induced RNA conformational switch at the internal ribosome entry site of hepatitis C virus genome visualized by atomic force microscopy.

The 5' untranslated region of hepatitis C virus (HCV) genomic RNA contains an internal ribosome entry site (IRES) element, composed of domains II-IV, which is required for cap-independent translation initiation. Little information on the 3D structure of the whole functional HCV IRES is still available. Here, we use atomic force microscopy to visualize the HCV IRES conformation in its natural sequence context, which includes the upstream domain I and the essential, downstream domains V and VI. The 574 nt-long molecule analyzed underwent an unexpected, Mg(2+)-induced switch between two alternative conformations: from 'open', elongated morphologies at 0-2 mM Mg(2+) concentration to a 'closed', comma-shaped conformation at 4-6 mM Mg(2+). This sharp transition, confirmed by gel-shift analysis and partial RNase T1 cleavage, was hindered by the microRNA miR-122. The comma-shaped IRES-574 molecules visualized at 4-6 mM Mg(2+) in the absence of miR-122 showed two arms. Our data support that the first arm would contain domain III, while the second one would be composed of domains (I-II)+(V-VI) thanks to a long-range RNA interaction between the I-II spacer and the basal region of domain VI. This reinforces the previously described structural continuity between the HCV IRES and its flanking domains I, V and VI.

Acrylates Polymerization on Covalent Plasma-Assisted Functionalized Graphene: A Route to Synthesize Hybrid Functional Materials.

The modification of the surface properties of graphene with polymers provides a method for expanding its scope into new applications as a hybrid material. Unfortunately, the chemical inertness of graphene hinders the covalent functionalization required to build them up. Developing new strategies to enhance the graphene chemical activity for efficient and stable functionalization, while preserving its electronic properties, is a major challenge. We here devise a covalent functionalization method that is clean, reproducible, scalable, and technologically relevant for the synthesis of a large-scale, substrate-supported graphene-polymer hybrid material. In a first step, hydrogen-assisted plasma activation of p-aminophenol (p-AP) linker molecules produces their stable and covalent attachment to large-area graphene. Second, an in situ radical polymerization reaction of 2-hydroxyethyl acrylate (HEA) is carried out on the functionalized surface, leading to a graphene-polymer hybrid functional material. The functionalization with a hydrophilic and soft polymer modifies the hydrophobicity of graphene and might enhance its biocompatibility. We have characterized these hybrid materials by atomic force microscopy (AFM), X-Ray photoelectron spectroscopy (XPS) and Raman spectroscopy and studied their electrical response, confirming that the graphene/p-AP/PHEA architecture is anchored covalently by the sp3 hybridization and controlled polymerization reaction on graphene, retaining its suitable electronic properties. Among all the possibilities, we assess the proof of concept of this graphene-based hybrid platform as a humidity sensor. An enhanced sensitivity is obtained in comparison with pristine graphene and related materials. This functional nanoarchitecture and the two-step strategy open up future potential applications in sensors, biomaterials, or biotechnology fields.

Correction: In situ observation of the on-surface thermal dehydrogenation of n-octane on Pt(111).

Correction for 'In situ observation of the on-surface thermal dehydrogenation of n-octane on Pt(111)' by Daniel Arribas et al., Nanoscale, 2023, https://doi.org/10.1039/d3nr02564k.

In situ observation of the on-surface thermal dehydrogenation of n-octane on Pt(111).

The catalytic dehydrogenation of alkanes constitutes a key step for the industrial conversion of these inert sp3-bonded carbon chains into other valuable unsaturated chemicals. To this end, platinum-based materials are among the most widely used catalysts. In this work, we characterize the thermal dehydrogenation of n-octane (n-C8H18) on Pt(111) under ultra-high vacuum using synchrotron-radiation X-ray photoelectron spectroscopy, temperature-programmed desorption and scanning tunneling microscopy, combined with ab initio calculations. At low activation temperatures, two different dehydrogenation stages are observed. At 330 K, n-C8H18 effectively undergoes a 100% regioselective single C-H bond cleavage at one methyl end. At 600 K, the chemisorbed molecules undergo a double dehydrogenation, yielding double bonds in their carbon skeletons. Diffusion of the dehydrogenated species leads to the formation of carbon molecular clusters, which represents the first step towards poisoning of the catalyst. Our results reveal the chemical mechanisms behind the first stages of alkane dehydrogenation on a platinum model surface at the atomic scale, paving the way for designing more efficient dehydrogenation catalysts.

Attomolar detection of hepatitis C virus core protein powered by molecular antenna-like effect in a graphene field-effect aptasensor.

Biosensors based on graphene field-effect transistors have become a promising tool for detecting a broad range of analytes. However, their performance is substantially affected by the functionalization protocol. In this work, we use a controlled in-vacuum physical method for the covalent functionalization of graphene to construct ultrasensitive aptamer-based biosensors (aptasensors) able to detect hepatitis C virus core protein. These devices are highly specific and robust, achieving attomolar detection of the viral protein in human blood plasma. Such an improved sensitivity is rationalized by theoretical calculations showing that induced polarization at the graphene interface, caused by the proximity of covalently bound molecular probe, modulates the charge balance at the graphene/aptamer interface. This charge balance causes a net shift of the Dirac cone providing enhanced sensitivity for the attomolar detection of the target proteins. Such an unexpected effect paves the way for using this kind of graphene-based functionalized platforms for ultrasensitive and real-time diagnostics of different diseases.

Epitaxial growth and characterization of SnSe phases on Au(111).

Two-dimensional (2D) layered group IV-VI semiconductors attract great interest due to their potential applications in nanoelectronics. Depending on the dimensionality, different phases of the same material can present completely different electronic and optical properties, expanding its applications. Here, we present a combined experimental and theoretical study of the atomic structure and electronic properties of epitaxial SnSe structures grown on a metallic Au(111) substrate, forming almost defect-free 2D layers. We describe a coverage-dependent transition from a metallicß-SnSe to a semiconductingα-SnSe phase. The combination of scanning tunneling microscopy/spectroscopy, non-contact atomic force microscopy, x-ray photoelectron spectroscopy/diffraction and angle-resolved photoemission spectroscopy, complemented by density functional theory, provides a comprehensive study of the geometric and electronic structure of both phases. Our work demonstrates the possibility to grow two distinct SnSe phases on Au(111) with high quality and on a large scale. The strong interaction with the substrate allows the stabilization of the previously experimentally unreportedß-SnSe, while the ultra-thin films of orthorhombicα-SnSe are structurally and electronically equivalent to bulk SnSe.

Steering Hydrocarbon Selectivity in CO2 Electroreduction over Soft-Landed CuOx Nanoparticle-Functionalized Gas Diffusion Electrodes.

The use of physical vapor deposition methods in the fabrication of catalyst layers holds promise for enhancing the efficiency of future carbon capture and utilization processes such as the CO2 reduction reaction (CO2RR). Following that line of research, we report in this work the application of a sputter gas aggregation source (SGAS) and a multiple ion cluster source type apparatus, for the controlled synthesis of CuOx nanoparticles (NPs) atop gas diffusion electrodes. By varying the mass loading, we achieve control over the balance between methanation and multicarbon formation in a gas-fed CO2 electrolyzer and obtain peak CH4 partial current densities of -143 mA cm-2 (mass activity of 7.2 kA/g) with a Faradaic efficiency (FE) of 48% and multicarbon partial current densities of -231 mA cm-2 at 76% FE (FEC2H4 = 56%). Using atomic force microscopy, electron microscopy, and quasi in situ X-ray photoelectron spectroscopy, we trace back the divergence in hydrocarbon selectivity to differences in NP film morphology and rule out the influence of both the NP size (3-15 nm, >20 µg cm-2) and in situ oxidation state. We show that the combination of the O2 flow rate to the aggregation zone during NP growth and deposition time, which affect the NP production rate and mass loading, respectively, gives rise to the formation of either densely packed CuOx NPs or rough three-dimensional networks made from CuOx NP building blocks, which in turn affects the governing CO2RR mechanism. This study highlights the potential held by SGAS-generated NP films for future CO2RR catalyst layer optimization and upscaling, where the NPs' tunable properties, homogeneity, and the complete absence of organic capping agents may prove invaluable.

LiCl Photodissociation on Graphene: A Photochemical Approach to Lithium Intercalation.

The interest in the research of the structural and electronic properties between graphene and lithium has bloomed since it has been proven that the use of graphene as an anode material in lithium-ion batteries ameliorates their performance and stability. Here, we investigate an alternative route to intercalate lithium underneath epitaxially grown graphene on iridium by means of photon irradiation. We grow thin films of LiCl on top of graphene on Ir(111) and irradiate the system with soft X-ray photons, which leads to a cascade of physicochemical reactions. Upon LiCl photodissociation, we find fast chlorine desorption and a complex sequence of lithium intercalation processes. First, it intercalates, forming a disordered structure between graphene and iridium. On increasing the irradiation time, an ordered Li(1 × 1) surface structure forms, which evolves upon extensive photon irradiation. For sufficiently long exposure times, lithium diffusion within the metal substrate is observed. Thermal annealing allows for efficient lithium desorption and full recovery of the pristine G/Ir(111) system. We follow in detail the photochemical processes using a multitechnique approach, which allows us to correlate the structural, chemical, and electronic properties for every step of the intercalation process of lithium underneath graphene.

Silicon and Hydrogen Chemistry under Laboratory Conditions Mimicking the Atmosphere of Evolved Stars.

Silicon is present in interstellar dust grains, meteorites and asteroids, and to date thirteen silicon-bearing molecules have been detected in the gas-phase towards late-type stars or molecular clouds, including silane and silane derivatives. In this work, we have experimentally studied the interaction between atomic silicon and hydrogen under physical conditions mimicking those at the atmosphere of evolved stars. We have found that the chemistry of Si, H and H2 efficiently produces silane (SiH4), disilane (Si2H6) and amorphous hydrogenated silicon (a-Si:H) grains. Silane has been definitely detected towards the carbon-rich star IRC+10216, while disilane has not been detected in space yet. Thus, based on our results, we propose that gas-phase reactions of atomic Si with H and H2 are a plausible source of silane in C-rich AGBs, although its contribution to the total SiH4 abundance may be low in comparison with the suggested formation route by catalytic reactions on the surface of dust grains. In addition, the produced a-Si:H dust analogs decompose into SiH4 and Si2H6 at temperatures above 500 K, suggesting an additional mechanism of formation of these species in envelopes around evolved stars. We have also found that the exposure of these dust analogs to water vapor leads to the incorporation of oxygen into Si-O-Si and Si-OH groups at the expense of SiH moieties, which implies that, if this type of grains are present in the interstellar medium, they will be probably processed into silicates through the interaction with water ices covering the surface of dust grains.

INFRA-ICE: An ultra-high vacuum experimental station for laboratory astrochemistry.

Laboratory astrochemistry aims at simulating, in the laboratory, some of the chemical and physical processes that operate in different regions of the universe. Amongst the diverse astrochemical problems that can be addressed in the laboratory, the evolution of cosmic dust grains in different regions of the interstellar medium (ISM) and its role in the formation of new chemical species through catalytic processes present significant interest. In particular, the dark clouds of the ISM dust grains are coated by icy mantles and it is thought that the ice-dust interaction plays a crucial role in the development of the chemical complexity observed in space. Here, we present a new ultra-high vacuum experimental station devoted to simulating the complex conditions of the coldest regions of the ISM. The INFRA-ICE machine can be operated as a standing alone setup or incorporated in a larger experimental station called Stardust, which is dedicated to simulate the formation of cosmic dust in evolved stars. As such, INFRA-ICE expands the capabilities of Stardust allowing the simulation of the complete journey of cosmic dust in space, from its formation in asymptotic giant branch stars to its processing and interaction with icy mantles in molecular clouds. To demonstrate some of the capabilities of INFRA-ICE, we present selected results on the ultraviolet photochemistry of undecane (C11H24) at 14 K. Aliphatics are part of the carbonaceous cosmic dust, and recently, aliphatics and short n-alkanes have been detected in situ in the comet 67P/Churyumov-Gerasimenko.

The Chemistry of Cosmic Dust Analogues from C, C2, and C2H2 in C-Rich Circumstellar Envelopes.

Interstellar carbonaceous dust is mainly formed in the innermost regions of circumstellar envelopes around carbon-rich asymptotic giant branch (AGB) stars. In these highly chemically stratified regions, atomic and diatomic carbon, along with acetylene are the most abundant species after H2 and CO. In a previous study, we addressed the chemistry of carbon (C and C2) with H2 showing that acetylene and aliphatic species form efficiently in the dust formation region of carbon-rich AGBs whereas aromatics do not. Still, acetylene is known to be a key ingredient in the formation of linear polyacetylenic chains, benzene and polycyclic aromatic hydrocarbons (PAHs), as shown by previous experiments. However, these experiments have not considered the chemistry of carbon (C and C2) with C2H2. In this work, by employing a sufficient amount of acetylene, we investigate its gas-phase interaction with atomic and diatomic carbon. We show that the chemistry involved produces linear polyacetylenic chains, benzene and other PAHs, which are observed with high abundances in the early evolutionary phase of planetary nebulae. More importantly, we have found a non-negligible amount of pure and hydrogenated carbon clusters as well as aromatics with aliphatic substitutions, both being a direct consequence of the addition of atomic carbon. The incorporation of alkyl substituents into aromatics can be rationalized by a mechanism involving hydrogen abstraction followed by methyl addition. All the species detected in gas phase are incorporated into the nanometric sized dust analogues, which consist of a complex mixture of sp, sp2 and sp3 hydrocarbons with amorphous morphology.

Copper-assisted oxidation of catechols into quinone derivatives.

Catechols are ubiquitous substances often acting as antioxidants, thus of importance in a variety of biological processes. The Fenton and Haber-Weiss processes are thought to transform these molecules into aggressive reactive oxygen species (ROS), a source of oxidative stress and possibly inducing degenerative diseases. Here, using model conditions (ultrahigh vacuum and single crystals), we unveil another process capable of converting catechols into ROSs, namely an intramolecular redox reaction catalysed by a Cu surface. We focus on a tri-catechol, the hexahydroxytriphenylene molecule, and show that this antioxidant is thereby transformed into a semiquinone, as an intermediate product, and then into an even stronger oxidant, a quinone, as final product. We argue that the transformations occur via two intramolecular redox reactions: since the Cu surface cannot oxidise the molecules, the starting catechol and the semiquinone forms each are, at the same time, self-oxidised and self-reduced. Thanks to these reactions, the quinone and semiquinone are able to interact with the substrate by readily accepting electrons donated by the substrate. Our combined experimental surface science and ab initio analysis highlights the key role played by metal nanoparticles in the development of degenerative diseases.

Thermal wet decomposition of Prussian Blue: implications for prebiotic chemistry.

The complex salt named Prussian Blue, Fe4[Fe(CN)6]3 x 15 H2O, can release cyanide at pH > 10. From the point of view of the origin of life, this fact is of interest, since the oligomers of HCN, formed in the presence of ammonium or amines, leads to a variety of biomolecules. In this work, for the first time, the thermal wet decomposition of Prussian Blue was studied. To establish the influence of temperature and reaction time on the ability of Prussian Blue to release cyanide and to subsequently generate other compounds, suspensions of Prussian Blue were heated at temperatures from room temperature to 150 degrees at pH 12 in NH3 environment for several days. The NH3 wet decomposition of Prussian Blue generated hematite, alpha-Fe2O3, the soluble complex salt (NH4)4[Fe(CN6)] x 1.5 H2O, and several organic compounds, the nature and yield of which depend on the experimental conditions. Urea, lactic acid, 5,5-dimethylhydantoin, and several amino acids and carboxylic acids were identified by their trimethylsilyl (TMS) derivatives. HCN, cyanogen (C2N2), and formamide (HCONH2) were detected in the gas phase by GC/MS analysis.

Synthesis of cobalt ferrite core/metallic shell nanoparticles for the development of a specific PNA/DNA biosensor.

Controlled synthesis of cobalt ferrite superparamagnetic nanoparticles covered with a gold shell has been achieved by an affinity and trap strategy. Magnetic nanoparticles are functionalized with a mixture of amino and thiol groups that facilitate the electrostatic attraction and further chemisorption of gold nanoparticles, respectively. Using these nanoparticles as seeds, a complete coating shell is achieved by gold salt-iterative reduction leading to monodisperse water-soluble gold-covered magnetic nanoparticles, with an average diameter ranging from 21 to 29 nm. These constitute a versatile platform for immobilization of biomolecules via thiol chemistry, which is exemplified by the immobilization of peptide nucleic acid (PNA) oligomers that specifically hybridize with complementary DNA molecules in solution. Hybridation with DNA probes has been measured using Rhodamine 6G fluorescence marker and the detection of a single nucleotide mutation has been achieved. These results suggest the PNA-nanoparticles application as a biosensor for DNA genotyping avoiding commonly time-consuming procedures employed.

Identification of PAH Isomeric Structure in Cosmic Dust Analogues: the AROMA setup.

We developed a new analytical experimental setup called AROMA (Astrochemistry Research of Organics with Molecular Analyzer) that combines laser desorption/ionization techniques with ion trap mass spectrometry. We report here on the ability of the apparatus to detect aromatic species in complex materials of astrophysical interests and characterize their structures. A limit of detection of 100 femto-grams has been achieved using pure polycyclic aromatic hydrocarbon (PAH) samples, which corresponds to 2x108 molecules in the case of coronene (C24H12). We detected the PAH distribution in the Murchison meteorite, which is made of a complex mixture of extraterrestrial organic compounds. In addition, collision induced dissociation experiments were performed on selected species detected in Murchison, which led to the first firm identification of pyrene and its methylated derivatives in this sample.