Synthesis of Molecular Tripods Based on a Rigid 9,9′-Spirobifluorene Scaffold

The efficient synthesis of a new tripodal platform based on a rigid 9,9′-spirobifluorene with three acetyl protected thiol groups in the positions 2, 3′ and 6′ for deposition on Au(111) surfaces is reported. The modular 9,9′-spirobifluorene platform provides both a vertical arrangement of the molecular rod in position 7 and its electronic coupling to the gold substrate. To demonstrate the validity of the molecular design, the model compound <b>24</b> exposing a <i>para</i>-cyanophenylethynyl rod is synthesized. Our synthetic approach is based on a metal–halogen exchange reaction of 2-iodobiphenyl derivative and his subsequent reaction with 2,7-disubstituted fluoren-9-one to afford the carbinol <b>16</b>. Further electrophilic cyclization and separation of regioisomers provided the corresponding 2,7,3′,6′-tetrasubstituted 9,9′-spirobifluorene <b>17</b> as the key intermediate. The molecular structure of <b>17</b> was determined by single-crystal X-ray diffraction crystallography. The self-assembly features of the target compound <b>24</b> were analyzed in preliminary UHV-STM experiments. These results already demonstrated the promising potential of the concept of the tripodal structure to stabilize the molecule on a Au(111) surface in order to control the spatial arrangement of the molecular rod

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. © 2008 American Institute of Physics.</p

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 property addressed.</p