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Adenine monolayers on the Au(111) surface: Structure identification by scanning tunneling microscopy experiment and ab initio calculations
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10.1063/1.3046690
/content/aip/journal/jcp/130/2/10.1063/1.3046690
http://aip.metastore.ingenta.com/content/aip/journal/jcp/130/2/10.1063/1.3046690

Figures

Image of FIG. 1.
FIG. 1.

Adenine grows in well-ordered 2D structures; note that the herringbone reconstruction of the Au(111) can be seen as corrugation on top of the A layer. Adenine molecules are mobile on the surface [see the noisy left part in (a)] until they attach to islands. A minimum observed island size of several tens of molecules is shown in (b). Two different structures can be found with [(a) and (c)] four and [(b) and (d)] two molecules in the unit cell, respectively. The unit cell is indicated by the corresponding lattice vectors and . From the high-resolution images in (e) the space group symmetry of the unit cell can be extracted (see text).

Image of FIG. 2.
FIG. 2.

(a) The adenine molecule in configuration (top view). The configuration is obtained from by flipping in the molecular plane. The six possible pairs of nearest N and H atoms (bonding sites) which can participate in forming two adjacent hydrogen bonds between two adenine molecules are explicitly indicated as well as atom labels. (b) The six most stable pairs (given by the number in brackets) are shown with the notation that corresponds to a dimer with chiral monomers, while corresponds to a pair with nonchiral monomers. The indices and indicate explicitly the sites of the two molecules [as adopted in (a)] engaged in the two hydrogen bonds in each pair. Note that all possible 21 A pairs are described in detail in Ref. 28.

Image of FIG. 3.
FIG. 3.

Schematic of the relative position of two neighboring chains and of adenine molecules (shown by solid circles) in a structure with a hexagonal ordering. The primitive unit cell is formed by four molecules, e.g., 1, 2, 3, and 4. The molecules within and across chains bind to each other by means of double hydrogen bonds. The bonds across the two chains are facilitated by connecting molecules 3 and of one chain with the molecules and of the other, respectively. Each molecule has three sites (denoted , , and ) involved in the structure, positions of some sites are indicated explicitly by site vectors from the molecules centers, where . The site vectors depend on the actual orientation of the molecules. Dashed circles indicate expected positions of molecules , , and (denoted as , , and ) for the corresponding dimers , , and to be “ideal” (i.e., relaxed isolated dimers). Correspondingly, vectors , , and show the displacements of the positions of the molecules binding sites in the actual structure as compared to the ideal dimer positions.

Image of FIG. 4.
FIG. 4.

Models for the adenine structure on the Au(111) surface: (a) The proposed structure; [(b) and (c)] other much less stable structures.

Image of FIG. 5.
FIG. 5.

Models for the adenine structure seen on the Au(111) surface: (a) The proposed structure ; (b) another less stable structure .

Image of FIG. 6.
FIG. 6.

Schematics of the two highest stability structures (a) and (b) found. The binding sites participating in each double hydrogen bond or connecting any two molecules are explicitly indicated by numbers . Two possible chiralities are distinguished by the open and gray circles. The unit cell in is indicated by molecules marked , , , and , while the unit cell for is formed by either molecules marked , or , .

Tables

Generic image for table
Table I.

Adenine monolayer possibilities. For every pair in the monolayer, the binding sites (see Fig. 2) used in the construction are given. For the sake of clarity, the four distinct pairs along the chain are shown separately from the two pairs associated with binding two adjacent chains (see Fig. 3). The lengths (in ) of the two lattice vectors, and , and the angle (in degrees) between them, , are given before (i.e., for the predicted geometry) and after DFT relaxation; the predicted and the DFT calculated stabilization energies are also given. Note that the first lattice vector used here is not the same as defined in Sec. III B; these are related as follows: for monolayers and for monolayers.

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/content/aip/journal/jcp/130/2/10.1063/1.3046690
2009-01-14
2014-04-16
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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: Adenine monolayers on the Au(111) surface: Structure identification by scanning tunneling microscopy experiment and ab initio calculations
http://aip.metastore.ingenta.com/content/aip/journal/jcp/130/2/10.1063/1.3046690
10.1063/1.3046690
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