Chemical transformations drive complex self-assembly of uracil on close-packed coinage metal surfaces

Scanning Probe Microscopy Characterization of Biomolecules enabled by Mass-Selective, Soft-landing Electrospray Ion Beam Deposition

Scanning probe microscopy (SPM), in particular at low temperature (LT) under ultra-high vacuum (UHV) conditions, offers the possibility of real-space imaging with resolution reaching the atomic level. However, its potential for the analysis of complex biological molecules has been hampered by requirements imposed by sample preparation. Transferring molecules onto surfaces in UHV is typically accomplished by thermal sublimation in vacuum. This approach however is limited by the thermal stability of the molecules, i. e. not possible for biological molecules with low vapour pressure. Bypassing this limitation, electrospray ionisation offers an alternative method to transfer molecules from solution to the gas-phase as intact molecular ions. In soft-landing electrospray ion beam deposition (ESIBD), these molecular ions are subsequently mass-selected and gently landed on surfaces which permits large and thermally fragile molecules to be analyzed by LT-UHV SPM. In this concept, we discuss how ESIBD+SPM prepares samples of complex biological molecules at a surface, offering controls of the molecular structural integrity, three-dimensional shape, and purity. These achievements unlock the analytical potential of SPM which is showcased by imaging proteins, peptides, DNA, glycans, and conjugates of these molecules, revealing details of their connectivity, conformation, and interaction that could not be accessed by any other technique.

Multiple Molecular Interactions between Alkyl Groups and Dissociated Bromine Atoms on Ag(111)

Multiple intermolecular interactions offer a high-degree of controllability of on-surface molecular assemblies. Here, two kinds of molecular networks were formed by depositing 11,11,12,12-tetrabromo-1,4,5,8-tetraaza-9,10-anthraquinodimethane derivatives with two different alkyl groups in...

Quantitative Insights into the Adsorption Structure of Diindeno[1,2-a;1',2'-c]fluorene-5,10,15-trione (Truxenone) on a Cu(111) Surface Using X-ray Standing Waves

The adsorption structure of truxenone on Cu(111) was determined quantitatively using normal-incidence X-ray standing waves. The truxenone molecule was found to chemisorb on the surface, with all adsorption heights of the dominant species on the surface less than ∼2.5 Å. The phenyl backbone of the molecule adsorbs mostly parallel to the underlying surface, with an adsorption height of 2.32 ± 0.08 Å. The C atoms bound to the carbonyl groups are located closer to the surface at 2.15 ± 0.10 Å, a similar adsorption height to that of the chemisorbed O species; however, these O species were found to adsorb at two different adsorption heights, 1.96 ± 0.08 and 2.15 ± 0.06 Å, at a ratio of 1:2, suggesting that on average, one O atom per adsorbed truxenone molecule interacts more strongly with the surface. The adsorption geometry determined herein is an important benchmark for future theoretical calculations concerning both the interaction with solid surfaces and the electronic properties of a molecule with electron-accepting properties for applications in organic electronic devices.

Selectively Scissoring Hydrogen-Bonded Cytosine Dimer Structures Catalyzed by Water Molecules

A single-molecule-level understanding of the activity of solvating water molecules in hydrogen-bonded assemblies would provide insights into the properties of the first hydration shells. Herein, we investigate the solvation of one of the DNA bases, cytosine, whose glassy-state network formed on Au(111) contains diverse types of hydrogen-bonded dimer configurations with hierarchical strengths. Upon water exposure, a global structural transformation from interwoven chain segments to extended chains was identified by scanning tunneling microscopy and atomic force microscopy. Density functional theory calculation and coarse-grained molecular dynamics simulation indicate that water molecules selectively break the weak-hydrogen-bonded dimers at T-junctions, while the stable ones within chains remain intact. The resulting hydrated chain segments further self-assemble into molecular chains by forming strong hydrogen bonds and spontaneously releasing water molecules. Such an intriguing transformation cannot be realized by thermal annealing, indicating the dynamic nature of water molecules in the regulation of hydrogen bonds in a catalytic manner.

Snapshots of Dynamic Adaptation: Two-Dimensional Molecular Architectonics with Linear Bis-Hydroxamic Acid Modules

Linear modules equipped with two terminal hydroxamic acid groups act as the building block of diverse two-dimensional supramolecular motifs and patterns with room-temperature stability on the close-packed single-crystal surfaces of silver and gold, revealing a complex self-assembly scenario. By combining multiple investigation techniques (scanning tunneling microscopy, atomic force microscopy, X-ray photoelectron spectroscopy, and density functional theory calculations), we analyze the characteristics of the ordered assemblies which range from close-packed structures to polyporous networks featuring an exceptionally extended primitive unit cell with a side length exceeding 7 nm. The polyporous network shows potential for hosting and promoting the formation of chiral supramolecules, whereas a transition from 1D chiral randomness to an ordered racemate is discovered in a different porous phase. We correlate the observed structural changes to the adaptivity of the building block and surface-induced changes in the chemical state of the hydroxamic acid functional group.

Quantum Tunneling Mediated Interfacial Synthesis of a Benzofuran Derivative

Reaction pathways involving quantum tunneling of protons are fundamental to chemistry and biology. They are responsible for essential aspects of interstellar synthesis, the degradation and isomerization of compounds, enzymatic activity, and protein dynamics. On-surface conditions have been demonstrated to open alternative routes for organic synthesis, often with intricate transformations not accessible in solution. Here, we investigate a hydroalkoxylation reaction of a molecular species adsorbed on a Ag(111) surface by scanning tunneling microscopy complemented by X-ray electron spectroscopy and density functional theory. The closure of the furan ring proceeds at low temperature (down to 150 K) and without detectable side reactions. We unravel a proton-tunneling-mediated pathway theoretically and confirm experimentally its dominant contribution through the kinetic isotope effect with the deuterated derivative.

Nickel Adatoms Induced Tautomeric Dehydrogenation of Thymine Molecules on Au(111)

Tautomerization of nucleobases may induce base mismatches resulting in the abnormal disturbance of gene replication and expression, which has therefore attracted widespread interests in many disciplines. Metal atoms participating in a variety of important biological processes are found to be able to affect the nucleobase tautomerization as evidenced by many theoretical and spectroscopic studies. To get the real-space evidence and to unravel the underlying mechanism for the metal-induced tautomerization, especially from the keto form to the enol one, the interplay of high-resolution scanning tunneling microscopy imaging/manipulation and density functional theory (DFT) calculations has been employed. We present a process showing the Ni adatom-induced keto-enol tautomeric dehydrogenation of thymine molecules on Au(111). The key to making such a process feasible is the Ni atoms which greatly lower the energy barrier for the tautomerization from keto to enol form, which is rationalized by extensive DFT-based transition-state search calculations.

The self-assembly and metal adatom coordination of a linear bis-tetrazole ligand on Ag(111)

We employ a linear linker molecule consisting of a benzene functionalised with two tetrazole moieties at para positions. Its self-assembly and coordination with the native silver adatoms and codeposited Fe adatoms on a Ag(111) surface under ultra high vacuum conditions are investigated by means of scanning tunnelling microscopy and X-ray photoelectron spectroscopy. We discover a rich spectrum of room-temperature stable Ag and Fe2+ coordination nodes depending on the formation temperature.

Two-dimensional self-assembled nanostructures of nucleobases and their related derivatives on Au(111)

The construction of two-dimensional (2D) self-assembled nanostructures has been one of the considerably interesting areas of on-surface chemistry in the past few decades, and has benefited from the rapid development and improvement of scanning probe microscopy techniques. In this research field, many attempts have been made in the controllable fabrication of well-ordered and multifunctional surface nanostructures, which attracted interest because of the prospect for artificial design of functional molecular nanodevices. DNA and RNA are considered to be programmable self-assembly systems and it is possible to use their base sequences to encode instructions for assembly in a predetermined fashion at the nanometer scale. As important constituents of nucleic acids, nucleobases, with intrinsic functional groups for hydrogen bonding, coordination bonding, and electrostatic interactions, can be employed as a potential system for the versatile construction of various biomolecular nanostructures, which may be used to structure the self-assembly of DNA-based artificial molecular constructions and play an important role in novel biosensors based on surface functionalization. In this article, we will review the recent progress of on-surface self-assembly of nucleobases and their derivatives together with different reactants (e.g., metals, halogens, salts and water), and as a result, various 2D surface nanostructures are summarized.

Tuning the ease of formation of on-surface metal-adatom coordination polymers featuring diketones

We use pyrene-4,5,9,10-tetraketone molecules with substituents of varying bulkiness in the 2,7 positions to probe the generality and versatility of the previously reported on-surface coordination of two diketones with a single metal atom, leading to one-dimensional coordination polymers. Three different low index surfaces of group 11 metals (Cu, Ag and Au) are used to provide both the support and the metal atoms for metal-organic coordination. By real space visualisation with single molecule resolution employing scanning tunnelling microscopy we investigate the molecular self-assembly and show how this can be substantiated with the formation of metal-organic linear and cyclic oligomers, depending on the employed substrate.

Real-space evidence of Watson-Crick and Hoogsteen adenine-uracil base pairs on Au(111)

From the interplay of high-resolution scanning tunneling microscopy imaging and density functional theory calculations, we show the real-space evidence of the formation of Watson-Crick and Hoogsteen adenine-uracil base pairs on an Au(111) surface with the employment of base derivatives, and further investigate the relative stability of the two types of adenine-uracil base pairs.

Influence of Transition Metal Cationization versus Sodium Cationization and Protonation on the Gas-Phase Tautomeric Conformations and Stability of Uracil: Application to [Ura+Cu]+ and [Ura+Ag]<sup/>

The gas-phase conformations of transition metal cation-uracil complexes, [Ura+Cu]⁺ and [Ura+Ag]⁺, were examined via infrared multiple photon dissociation (IRMPD) action spectroscopy and theoretical calculations. IRMPD action spectra were measured over the IR fingerprint and hydrogen-stretching regions. Structures and linear IR spectra of the stable tautomeric conformations of these complexes were initially determined at the B3LYP/6-31G(d) level. The four most stable structures computed were also examined at the B3LYP/def2-TZVPPD level to improve the accuracy of the predicted IR spectra. Two very favorable modes of binding are found for [Ura+Cu]⁺ and [Ura+Ag]⁺ that involve O2N3 bidentate binding to the 2-keto-4-hydroxy minor tautomer and O4 monodentate binding to the canonical 2,4-diketo tautomer of Ura. Comparisons between the measured IRMPD and calculated IR spectra enable elucidation of the conformers present in the experiments. These comparisons indicate that both favorable binding modes are represented in the experimental tautomeric conformations of [Ura+Cu]⁺ and [Ura+Ag]⁺. B3LYP suggests that Cu⁺ exhibits a slight preference for O4 binding, whereas Ag⁺ exhibits a slight preference for O2N3 binding. In contrast, MP2 suggests that both Cu⁺ and Ag⁺ exhibit a more significant preference for O2N3 binding. The relative band intensities suggest that O4 binding conformers comprise a larger portion of the population for [Ura+Ag]⁺ than [Ura+Cu]⁺. The dissociation behavior and relative stabilities of the [Ura+M]⁺ complexes, M⁺ = Cu⁺, Ag⁺, H⁺, and Na⁺) are examined via energy-resolved collision-induced dissociation experiments. The IRMPD spectra, dissociation behaviors, and binding preferences of Cu⁺ and Ag⁺ are compared with previous and present results for those of H⁺ and Na⁺. Graphical Abstract ᅟ.

Unveiling the Self-Assembling Behavior of 5-Fluorouracil and its N,N'-Dimethyl Derivative: A Spectroscopic and Microscopic Approach

Under physiological conditions, 5-fluorouracil (5-FU), an anticancer drug, self-assembles into fibrils by strong hydrogen-bonding network, whereas its N,N'-dimethyl derivative, 5-fluoro-1,3-dimethyluracil (5-FDMU), does not make fibrils due to lack of strong hydrogen-bonding motif. In vitro, 5-FU self-assembly is sensitive to physicochemical conditions like the pH and ionic strength of the solution, which tune the strength of the noncovalent driving forces. Here we report a surprising finding that the buffer, which is necessary to control the pH and is typically considered to be inert, also significantly influences 5-FU self-assembly, which indicates an important role of counterions in the fibril formation. We have also monitored concentration- and time-dependent fibrillar growth of 5-FU. Again, fibril growth process is probed under dynamic conditions using microfluidic platform. The self-assembly of 5-FU compared with its N,N'-dimethyl derivative shows lower cytotoxicity to the cultured human erythroleukemic cells (K562 cells), which plausibly states the reason behind the greater effectiveness of 5-FU derivative drugs than 5-FU itself.

Towards interference free HPLC-SERS for the trace analysis of drug metabolites in biological fluids

Sofosbuvir metabolite, 2'-deoxy-2'-fluoro-2'-C-methyluridine (PSI-6206) was studied for the first time by surface enhanced Raman spectroscopy (SERS) using the paper-based SERS substrate. The quantification limit of PSI-6206 by SERS was found to be 13ngL^-1 (R² value=0.959, RSD=5.23%). For the structural and quantitative analysis of PSI-6206 in blood plasma, an interference-free HPLC-SERS method was developed and compared to HPLC-DAD and HPLC-MS methods. The SERS quantification of the drug by the paper substrate was 4 orders of magnitude more sensitive than that by the diode array detector. In addition, the SERS detection provided unique structural identification of the drug in blood plasma, similar to Mass spectroscopy detector. Due to the disposable nature of the SERS substrate, the new method does not suffer from the known "memory effect" which is known to lead to false positive identification in traditional HPLC-SERS methods. Therefore, the presented HPLC-paper SERS platform holds great potential for the sensitive and cost effective determination of drugs and their metabolites in biological fluids.

Synthesis of Pyrene-Fused Pyrazaacenes on Metal Surfaces: Toward One-Dimensional Conjugated Nanostructures

We investigated the synthesis of one-dimensional nanostructures via Schiff base (imine) formation on three close-packed coinage metal (Au, Ag, and Cu) surfaces under ultrahigh vacuum conditions. We demonstrate the feasibility of forming pyrene-fused pyrazaacene-based oligomers on the Ag(111) surface by thermal annealing of tetraketone and tetraamine molecules, which were designed to afford cyclocondensation products. Direct visualization by scanning tunneling microscopy of reactants, intermediates, and products with submolecular resolution and the analysis of their statistical distribution in dependence of stoichiometry and annealing temperature together with the inspection of complementary X-ray photoelectron spectroscopy signatures provide unique insight in the reaction mechanism, its limitations, and the role of the supporting substrate. In contrast to the reaction on Ag(111), the reactants desorb from the Au(111) surface before reacting, whereas they decompose on the Cu(111) surface during the relevant thermal treatment.

Formation of Ordered Coronene Clusters in Template Utilizing the Structural Transformation of Hexaphenylbenzene Derivative Networks on Graphite Surface

In the present work, we report the fabrication of regular coronene (COR) clusters on surfaces in ambient conditions in the two-dimensional network formed by hexaphenylbenzene derivatives (HPB) via structural transformation. HPB could form a stable snowflake network structure on the highly oriented pyrolytic graphite surface at the air-solid interface. When COR molecules were introduced into the system, the HPB snowflake network could transform to honeycomb structures, and the COR heptamers were subsequently aggregated and entrapped into the cavity. Scanning tunneling microscopic was employed to monitor the assembly behavior of both HPB and HPB/COR at a submolecule scale level, and density functional theory calculations were utilized to reveal that the structural transformation and the entrapment are the energetically favorable. The pores formed from HPB might also give a clue to immobilizing some functional molecule clusters, like COR, to fabricate their ordered monolayer in ambient conditions, so as to obtain complex supramolecular surface structures.

Self-assembly of Natural and Unnatural Nucleobases at Surfaces and Interfaces

The self-assembly of small organic molecules interacting via non-covalent forces is a viable approach towards the construction of highly ordered nanostructured materials. Among various molecular components, natural and unnatural nucleobases can undergo non-covalent self-association to form supramolecular architectures with ad hoc structural motifs. Such structures, when decorated with appropriate electrically/optically active units, can be used as scaffolds to locate such units in pre-determined positions in 2D on a surface, thereby paving the way towards a wide range of applications, e.g., in optoelectronics. This review discusses some of the basic concepts of the supramolecular engineering of natural and unnatural nucleobases and derivatives thereof as well as self-assembly processes on conductive solid substrates, as investigated by scanning tunnelling microscopy in ultra-high vacuum and at the solid/liquid interface. By unravelling the structure and dynamics of these self-assembled architectures with a sub-nanometer resolution, a greater control over the formation of increasingly sophisticated functional systems is achieved. The ability to understand and predict how nucleobases interact, both among themselves as well as with other molecules, is extremely important, since it provides access to ever more complex DNA- and RNA-based nanostructures and nanomaterials as key components in nanomechanical devices.

Formation of a thermally stable bilayer of coadsorbed intact and deprotonated thymine exploiting the surface corrugation of rutile TiO2(110)

Adsorption of thymine on rutile TiO₂(110) leads to a room temperature stable bilayer which follows the corrugation of the oxide surface and consists of both intact and deprotonated molecules.

Cyano-Functionalized Triarylamines on Coinage Metal Surfaces: Interplay of Intermolecular and Molecule-Substrate Interactions

The self-assembly of cyano-functionalized triarylamine derivatives on Cu(111), Ag(111) and Au(111) was studied by means of scanning tunnelling microscopy, low-energy electron diffraction, X-ray photoelectron spectroscopy and density functional theory calculations. Different bonding motifs, such as antiparallel dipolar coupling, hydrogen bonding and metal coordination, were observed. Whereas on Ag(111) only one hexagonally close-packed pattern stabilized by hydrogen bonding is observed, on Au(111) two different partially porous phases are present at submonolayer coverage, stabilized by dipolar coupling, hydrogen bonding and metal coordination. In contrast to the self-assembly on Ag(111) and Au(111), for which large islands are formed, on Cu(111), only small patches of hexagonally close-packed networks stabilized by metal coordination and areas of disordered molecules are found. The significant variety in the molecular self-assembly of the cyano-functionalized triarylamine derivatives on these coinage metal surfaces is explained by differences in molecular mobility and the subtle interplay between intermolecular and molecule-substrate interactions.

Functionalisation and immobilisation of an Au(110) surface via uracil and 2-thiouracil anchored layer

We study surface functionalisation by uracil and 2-thiouracil, and immobilisation of several DNA moieties on functionalised gold surfaces. The combination of X-ray photoelectron and near-edge X-ray absorption spectroscopy allowed us to obtain a complete understanding of complex interfacial processes, starting from adsorption of biomolecules onto the metallic surface and progressing towards a specific surface functionality for interactions with other biologically related adsorbates. Au(110) surfaces were functionalised by deposition of uracil and 2-thiouracil molecules under vacuum conditions, and then tested for their selectivity by immobilisation of different DNA moieties deposited from aqueous solutions. We observed that adenine, adenosine, and RNA polymer (polyadenylic acid) from saturated solutions were immobilized successfully on the 2-thiouracil, but those from dilute (1%) solutions were not. However, cytosine failed to adsorb even from saturated solution. The chemical states of the biologically related adsorbates were investigated and the geometrical orientation of uracil and 2-thiouracil on the Au(110) surface was determined using both spectroscopic techniques.

Controllable Scission and Seamless Stitching of Metal-Organic Clusters by STM Manipulation

Scanning tunneling microscopy (STM) manipulation techniques have proven to be a powerful method for advanced nanofabrication of artificial molecular architectures on surfaces. With increasing complexity of the studied systems, STM manipulations are then extended to more complicated structural motifs. Previously, the dissociation and construction of various motifs have been achieved, but only in a single direction. In this report, the controllable scission and seamless stitching of metal-organic clusters have been successfully achieved through STM manipulations. The system presented here includes two sorts of hierarchical interactions where coordination bonds hold the metal-organic elementary motifs while hydrogen bonds among elementary motifs are directly involved in bond breakage and re-formation. The key to making this reversible switching successful is the hydrogen bonding, which is comparatively facile to be broken for controllable scission, and, on the other hand, the directional characteristic of hydrogen bonding makes precise stitching feasible.

Self-assembly and chemical modifications of bisphenol a on Cu(111): interplay between ordering and thermally activated stepwise deprotonation

Bisphenol A (BPA) is a chemical widely used in the synthesis pathway of polycarbonates for the production of many daily used products. Besides other adverse health effects, medical studies have shown that BPA can cause DNA hypomethylation and therefore alters the epigenetic code. In the present work, the reactivity and self-assembly of the molecule was investigated under ultra-high-vacuum conditions on a Cu(111) surface. We show that the surface-confined molecule goes through a series of thermally activated chemical transitions. Scanning tunneling microscopy investigations showed multiple distinct molecular arrangements dependent on the temperature treatment and the formation of polymer-like molecular strings for temperatures above 470 K. X-ray photoelectron spectroscopy measurements revealed the stepwise deprotonation of the hydroxy groups, which allows the molecules to interact strongly with the underlying substrate as well as their neighboring molecules and therefore drive the organization into distinct structural arrangements. On the basis of the combined experimental evidence in conjunction with density functional theory calculations, structural models for the self-assemblies after the thermal treatment were elaborated.

Control of active semiconducting layer packing in organic thin film transistors through synthetic tailoring of dielectric materials

The influence of dielectric material's property on the solid state structure packing of active semiconducting layer in OTFTs has been carefully studied by employing a whole new family of dielectric materials based on the rigid, tetrahedral bulky moleculei.e.adamantane, a smallest cage structure of diamond.

Direct visualization of molecule deprotonation on an insulating surface

Elucidating molecular-scale details of basic reaction steps on surfaces is decisive for a fundamental understanding of molecular reactivity within many fields, including catalysis and on-surface synthesis. Here, the deprotonation of 2,5-dihydroxybenzoic acid (DHBA) deposited onto calcite (101;4) held at room temperature is followed in situ by noncontact atomic force microscopy. After deposition, the molecules form two coexisting phases, a transient striped phase and a stable dense phase. A detailed analysis of high-resolution noncontact atomic force microscopy images indicates the transient striped phase being a bulk-like phase, which requires hydrogen bonds between the carboxylic acid moieties to be formed. With time, the striped phase transforms into the dense phase, which is explained by the deprotonation of the molecules. In the deprotonated state, the molecules can no longer form hydrogen bonds, but anchor to the surface calcium cations with their negatively charged carboxylate group. The deprotonation step is directly confirmed by Kelvin probe force microscopy images that unravel the change in the molecular charge.