In-situ scanning tunneling microscopy study of uracil on Au(100)

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.

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.

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

We address the interplay of adsorption, chemical nature, and self-assembly of uracil on the Ag(111) and Cu(111) surfaces as a function of molecular coverage (0.3 to 1 monolayer) and temperature. We find that both metal surfaces act as templates and the Cu(111) surface acts additionally as a catalyst for the resulting self-assembled structures. With a combination of STM, synchrotron XPS, and NEXAFS studies, we unravel a distinct polymorphism on Cu(111), in stark contrast to what is observed for the case of uracil on the more inert Ag(111) surface. On Ag(111) uracil adsorbs flat and intact and forms close-packed two-dimensional islands. The self-assembly is driven by stable hydrogen-bonded dimers with poor two-dimensional order. On Cu(111) complex structures are observed exhibiting, in addition, a strong annealing temperature dependence. We determine the corresponding structural transformations to be driven by gradual deprotonation of the uracil molecules. Our XPS study reveals unambiguously the tautomeric signature of uracil in the contact layer and on Cu(111) the molecule's deprotonation sites. The metal-mediated deprotonation of uracil and the subsequent electron localization in the molecule determine important biological reactions. Our data show a dependence between molecular coverage and molecule-metal interaction on Cu(111), as the molecules tilt at higher coverages in order to accommodate a higher packing density. After deprotonation of both uracil N atoms, we observe an adsorption geometry that can be understood as coordinative anchoring with a significant charge redistribution in the molecule. DFT calculations are employed to analyze the surface bonding and accurately describe the pertaining electronic structure.

Condensation of nucleobases at mercury/aqueous solution interface--a structural perspective using hydrogen bonding considerations

The two-dimensional condensation behavior exhibited by nucleobases at a mercury/aqueous solution interface is analyzed on the basis of their hydrogen-bonded quadruplex structures, and the experimentally observed critical temperatures are rationalized incorporating different types of hydrogen bonding, surface coordination effects, and stacking considerations. The proposed methodology provides a structural basis for the interpretation of critical temperatures and enables the calculation of the same pertaining to different modified nucleobases. The applicability of the procedure to order-disorder transitions of water dipoles at Hg electrodes is also indicated.