Super-Robust Xanthine-Sodium Complexes on Au(111).

A widely accepted theory is that life originated from the hydrothermal environment in the primordial ocean. Nevertheless, the low desorption temperature from inorganic substrates and the fragileness of hydrogen-bonded nucleobases do not support the required thermal stability in such an environment. Herein, we report the super-robust complexes of xanthine, one of the precursors for the primitive nucleic acids, with Na. We demonstrate that the well-defined xanthine-Na complexes can only form when the temperature is ≥430 K, and the complexes keep adsorbed even at ≈720 K, presenting as the most thermally stable organic polymer ever reported on Au(111). This work not only justifies the necessity of high-temperature, Na-rich environment for the prebiotic biosynthesis but also reveals the robustness of the xanthine-Na complexes upon the harsh environment. Moreover, the complexes can induce significant electron transfer with the metal as inert as Au and hence lift the Au atoms up.

Subsurface-Carbon-Induced Local Charge of Copper for an On-Surface Displacement Reaction.

Transition-metal carbides have sparked unprecedented enthusiasm as high-performance catalysts in recent years. Still, the catalytic properties of copper carbide remain unexplored. By introducing subsurface carbon to Cu(111), a displacement reaction of a proton in a carboxyl acid group with a single Cu atom is demonstrated at the atomic scale and room temperature. Its occurrence is attributed to the C-doping-induced local charge of surface Cu atoms (up to +0.30 e/atom), which accelerates the rate of on-surface deprotonation via reduction of the corresponding energy barrier, thus enabling the instant displacement of a proton with a Cu atom when the molecules adsorb on the surface. This well-defined and robust Cuδ+ surface based on subsurface-carbon doping offers a novel catalytic platform for on-surface synthesis.

Graphene-Like Covalent Organic Framework with a Wide Band Gap Synthesized On Surface via Stepwise Reactions.

Developing graphene-like two-dimensional materials naturally possessing a band gap has sparked enormous interest. Thanks to the inherent wide band gap and high mobility in the 2D plane, covalent organic frameworks containing triazine rings (t-COFs) hold great promise in this regard, whilst the synthesis of single-layer t-COFs remains highly challenging. Herein, we present the fabrication of a well-defined graphene-like t-COF on Au(111). Instead of single/multiple-step single-type reactions commonly applied for on-surface synthesis, distinct stepwise on-surface reactions, including alkynyl cyclotrimerization, C-O bond cleavage, and C-H bond activation, are triggered on demand, leading to product evolution in a controlled step-by-step manner. Aside from the precise control in sophisticated on-surface synthesis, this work proposes a single-atomic-layer organic semiconductor with a wide band gap of 3.41 eV.

Xanthine Quartets on Au(111).

The quartet of xanthine (X), a purine base ubiquitously distributed in most human body tissues and fluids, has been for the first time fabricated and visualized, as the first alternative purine quartet besides the known guanine (G)-quartet. The X-quartet network is demonstrated to be the most stable phase on Au(111). Unlike guanine, the fabrication of the X-quartets is not dependent on the presence of metal atoms, which makes it the first metal-free purine quartet. The X-quartet holds great promise to potentially construct artificial new DNA quadruplexes for genetic regulation and antitumor therapy. Moreover, both the X-quartet itself and the quartet networks favor homochirality, suggesting homochiral xanthine oligomers and the networks may have been formed as the precursors of the pristine oligonucleotides on primitive Earth.

Formation of Hypoxanthine Tetrad by Reaction with Sodium Chloride: From Planar to Stereo.

By reacting with NaCl on Au(111), the formation of hypoxanthine (HX) tetrads is demonstrated at the atomic scale in real space. These results directly demonstrate that alternative purine tetrads can be formed in both planar and non-planar configuration, and that ionic bonding plays a crucial role for the formation and planar-to-stereo transformation of the tetrads, providing deeper insight for constructing artificial DNA/RNA quadruplexes. Moreover, both the tilted HXs and Na show strong charge transfer with the substrate in the non-planar phase. The insights gained by this work also open up new routes to tune the electrostatic nature of metal-organic interfaces and design stereo-nanostructures on surfaces.

Formation mechanism for a hybrid supramolecular network involving cooperative interactions.

A novel mechanism of hybrid assembly of molecules on surfaces is proposed stemming from interactions between molecules and on-surface metal atoms which eventually got trapped inside the network pores. Based on state-of-the-art theoretical calculations, we find that the new mechanism relies on formation of molecule-metal atom pairs which, together with molecules themselves, participate in the assembly growth. Most remarkably, the dissociation of pairs is facilitated by a cooperative interaction involving many molecules. This new mechanism is illustrated on a low coverage Melamine hexagonal network on the Au(111) surface where multiple events of gold atoms trapping via a set of so-called "gate" transitions are found by kinetic Monte Carlo simulations based on transition rates obtained using ab initio density functional theory calculations and the nudged elastic band method. Simulated STM images of gold atoms trapped in the pores of the Melamine network predict that the atoms should appear as bright spots inside Melamine hexagons. No trapping was found at large Melamine coverages, however. These predictions have been supported by preliminary STM experiments which show bright spots inside Melamine hexagons at low Melamine coverages, while empty pores are mostly observed at large coverages. Therefore, we suggest that bright spots sometimes observed in the pores of molecular assemblies on metal surfaces may be attributed to trapped substrate metal atoms. We believe that this type of mechanism could be used for delivering adatom species of desired functionality (e.g., magnetic) into the pores of hydrogen-bonded networks serving as templates for their capture.

Self-assembly of artificial nucleobase 1H-benzimidazole-4,7-dione at the liquid/solid interface.

Self-assembly at the liquid/solid interface of an electrochemically active DNA nucleobase analogue, 1H-benzoimidazole-4,7-dione (Q), has been studied by means of scanning tunneling microscopy (STM). High-resolution STM images revealed the formation of well-ordered two-dimensional (2D) supramolecular nanostructures when the Q molecules are adsorbed onto the graphite surface from a 1-octanol solution. Detailed analysis shows that the observed 2D nanostructures are mainly dominated by hydrogen-bonded Q molecules. Since Q can be considered as a molecule mimicking the nucleobase guanine (G), which is known to form Watson-Crick base pairs with its complementary nucleobase cytosine (C), we have examined the binding ability of Q with C realized by available hydrogen-bonding sites on both Q and C molecules. Upon deposition of a mixture of Q and C molecules onto a graphite surface, one might expect that hydrogen-bonded QC dimers were observed in a new 2D self-assembled structure governed by inter- and intramolecular hydrogen-bonding interactions between Q and C molecules. However, our STM experiments showed that no well-ordered structures are formed and instead phase separation occurs where large-scale homodomains are formed consisting of the individual QQ and CC dimers. To gain further insight into the possible molecular arrangements of the Q and C nucleobases in the mixture phase, the high-resolution STM images are compared with the results from ab initio density functional theory (DFT) calculations.

Adenine monolayers on the Au(111) surface: structure identification by scanning tunneling microscopy experiment and ab initio calculations.

From an interplay between scanning tunneling microscopy (STM) and ab initio density functional theory (DFT) we have identified and characterized two different self-assembled adenine (A) structures formed on the Au(111) surface. The STM observations reveal that both structures have a hexagonal geometry in which each molecule forms double hydrogen bonds with three nearest neighbors. One of the A structures, with four molecules in the primitive cell, has p2gg space group symmetry, while the other one, with two molecules in the cell, has p2 symmetry. The first structure is observed more frequently and is found to be the dominating structure after annealing. Experimental as well as theoretical findings indicate that the interaction of A molecules with the gold surface is rather weak and smooth across the surface. This enabled us to unequivocally characterize the observed structures, systematically predict all structural possibilities, based on all known A-A dimers, and provisionally optimize positions of the A molecules in the cell prior to full-scale DFT calculations. The theoretical method is a considerable improvement compared to the approach suggested previously by Kelly and Kantorovich [Surf. Sci. 589, 139 (2005)]. We propose that the less ordered p2gg symmetry structure is observed more frequently due to kinetic effects during island formation upon deposition at room temperature.

Two-dimensional supramolecular nanopatterns formed by the coadsorption of guanine and uracil at the liquid/solid interface.

A novel supramolecular nanostructure formed by the coadsorption of the complementary nucleobases guanine (G) and uracil (U) at the liquid (1-octanol solvent)/solid (graphite) interface is revealed by scanning tunneling microscopy (STM). The GU supramolecular structure is distinctly different from the structures observed by STM when the individual nucleobases (NB) are adsorbed on graphite in the control experiments. Using a systematic methodology and ab initio density functional theory (DFT), an atomistic structural model is proposed for the supramolecular coadsorbed GU structure, which consists of a periodic repetition of cyclic units based on the strongest GU base pairing.

An investigation into the interactions between self-assembled adenine molecules and a Au(111) surface.

Two molecular phases of the DNA base adenine (A) on a Au(111) surface are observed by using STM under ultrahigh-vacuum conditions. One of these phases is reported for the first time. A systematic approach that considers all possible gas-phase two-dimensional arrangements of A molecules connected by double hydrogen bonds with each other and subsequent ab initio DFT calculations are used to characterize and identify the two phases. The influence of the gold surface on the structure of A assemblies is also discussed. DFT is found to predict a smooth corrugation potential of the gold surface that will enable A molecules to move freely across the surface at room temperature. This conclusion remains unchanged if van der Waals interaction between A and gold is also approximately taken into account. DFT calculations of the A pairs on the Au(111) surface show its negligible effect on the hydrogen bonding between the molecules. These results justify the gas-phase analysis of possible assemblies on flat metal surfaces. Nevertheless, the fact that it is not the most stable gas-phase monolayer that is actually observed on the gold surface indicates that the surface still plays a subtle role, which needs to be properly addressed.

Understanding the disorder of the DNA base cytosine on the Au(111) surface.

Using ultrahigh vacuum scanning tunneling microscopy (STM) and ab initio density functional theory, we have investigated in detail structures formed by cytosine on the Au(111) surface in clean ultrahigh vacuum conditions. In spite of the fact that the ground state of this DNA base on the surface is shown to be an ordered arrangement of cytosine one-dimensional branches (filaments), this structure has never been observed in our STM experiments. Instead, disordered structures are observed, which can be explained by only a few elementary structural motifs: filaments, five- and sixfold rings, which randomly interconnect with each other forming bent chains, T junctions, and nanocages. The latter may have trapped smaller structures inside. The formation of such an unusual assembly is explained by simple kinetic arguments as a liquid-glass transition.

Coexistence of homochiral and heterochiral adenine domains at the liquid/solid interface.

In this work, the self-assembly of the DNA base molecule adenine (A) is imaged with high-resolution scanning tunneling microscopy (STM) at the liquid (1-octanol)/solid (HOPG) interface at room temperature. Rather surprisingly, the STM results reveal, for the first time, the spontaneous formation of two coexisting distinct (homo- and heterochiral) domains of adenine, which are formed at the liquid/solid interface without changing any experimental conditions. Ab initio density functional theory (DFT) calculations support our STM findings and suggest the existence of various A networks of nearly similar stability that all are constructed from the most stable A dimer.

Homochiral xanthine quintet networks self-assembled on Au(111) surfaces.

Xanthine molecule is an intermediate in nucleic acid degradation from the deamination of guanine and is also a compound present in the ancient solar system that is found in high concentrations in extraterrestrial meteorites. The self-assembly of xanthine molecules on inorganic surfaces is therefore of interest for the study of biochemical processes, and it may also be relevant to the fundamental understanding of prebiotic biosynthesis. Using a combination of high-resolution scanning tunneling microscopy (STM) and density functional theory (DFT) calculations, two new homochiral xanthine structures have been found on Au(111) under ultrahigh vacuum conditions. Xanthine molecules are found to be self-assembled into two extended homochiral networks tiled by two types of di-pentamer units and stabilized by intermolecular double hydrogen bonding. Our findings indicate that the deamination of guanine into xanthine leads to a very different base pairing potential and the chemical properties of the base which may be of relevance to the function of the cell and potential development of human diseases. Moreover, the adsorption of xanthine molecules on inorganic surfaces leading to homochiral assemblies may be of interest for the fundamental understanding of the emerged chirality at early stages of life.

Homopairings of the artificial nucleobase 1H-benzoimidazole-4,7-dione.

All planar homopairings of the artificial nucleobase 1H-benzoimidazole-4,7-dione are reported for the first time in this study. Using the idea of binding sites discussed in our previous work and an ab initio density functional theory method we predict 13 homopairs. The stabilization energies of the homopairs vary from -0.13 to -0.69 eV. The collected data on all the planar homopairs reported here may be useful when constructing assemblies of this artificial base on various solid substrates.

Elementary structural motifs in a random network of cytosine adsorbed on a gold(111) surface.

Nonsymmetrical organic molecules adsorbed on solid surfaces may assemble into random networks, thereby providing model systems for organic glasses that can be directly observed by scanning tunneling microscopy (STM). We investigated the structure of a disordered cytosine network on a gold(111) surface created by thermal quenching, to temperatures below 150 K, of the two-dimensional fluid present on the surface at room temperature. Comparison of STM images to density functional theory calculations allowed us to identify three elementary structural motifs (zigzag filaments and five- and six-membered rings) that underlie the whole supramolecular random network. The identification of elementary structural motifs may provide a new framework for understanding medium-range order in amorphous and glassy systems.