An Investigation into the Interactions Between Self‐Assembled Adenine Molecules and a Au(111) Surface

Abstract

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.

Role of van der Waals interaction in forming molecule-metal junctions: flat organic molecules on the Au(111) surface

“…the molecules can be considered as ''floating'' in a 2D pool: they cannot easily escape from the surface, but can freely move around. This is in agreement with the STM observations 9,11,12 that it is impossible to image small flat molecules on the gold surface at room temperature at small coverages. Our results also imply that the gas-phase modeling, at least in the first approximation, should be adequate for this surface.…”

“…However, in many cases, e.g. for DNA bases 8,11,12,14,16 and melamine molecules on the Au(111) surface, 15,28 perylene-3,4,9,10-tetracarboxylic-3,4,9,10-dianhydride (PTCDA) molecules on the Ag(111) surface, 19,22,23 benzene 26 and PTCDA 30 molecules on the Au(111), Cu(111) and Ag(111) surfaces the calculated adsorption energies are too small (of the order of 0.1-0.2 eV) which is inconsistent with experimental observations of the desorption temperatures for these molecules (around 100-300 1C). This failure of standard generalized gradient approximation (GGA) functionals, such as e.g.…”

“…[42][43][44] If the moleculemolecule interaction dominates, then molecules may move around the surface to form molecular assemblies (providing, of course, that the surface diffusion is not hampered by a too large deposition rate 2,31,32 ); in this case commensurability issues do not arise and the gas-phase modeling of the assemblies, [7][8][9]11,27 i.e. without considering the surface, is justified.…”

Energy Barrier Reduction for the Double Proton-Transfer Reaction in Guanine–Cytosine DNA Base Pair on a Gold Surface

“…[18][19][20][21] Recently, a molecular description of (S)-glutamic acid self-assembly adsorbed on Ag(100) at low-temperature 22 More related to the main aim of the present paper, the formation of planar hydrogen-bonded networks of DNA nucleobases, such as guanine (G) 16 and cytosine (C) 19 adsorbed on an Au(111) surface, has been an issue of great interest. As is noticed in these early works, the symmetry of the functional groups of the C and G molecules allows the self-assembly of ordered network, although in the case of the C molecules their supramolecular structures miss long-range order.…”

Bicomponent Supramolecular Architectures at the Vacuum–Solid Interface

“…312,313,314,315,134,135 For instance, the four nucleobases cytosine (C), 316 guanine (G), 317 adenine (Ad), 103 and thymine (T) 318 form well-organized 1D and 2D structures on Cu, Ag and Au surfaces. The H-bonding in these homomolecular systems is sufficiently strong that the role of the surface can be idealized as a simple support with minimal influence over the self-assembly process.…”