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Understanding the disorder of the DNA base cytosine on the Au(111) surface
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10.1063/1.3001585
/content/aip/journal/jcp/129/18/10.1063/1.3001585
http://aip.metastore.ingenta.com/content/aip/journal/jcp/129/18/10.1063/1.3001585

Figures

Image of FIG. 1.
FIG. 1.

Development of the cytosine structure with increasing coverage. (a) The herringbone reconstruction is not lifted and the zigzag branches are able to move in a whiplike manner (indicated by the black arrows). (b) Confined areas contain a number of blurs, which consist of moving C clusters; branches are usually terminated by fivefold rings, and junctions between interconnecting branches are often established by sixfold rings. (c) With increasing coverage, the number of mobile C molecules in blurred spots decreases, while the number of sixfold rings increases. (d) At high coverages, the structure is still disordered, and the basic units such as zigzag filaments and rings are clearly observed; blurred formations confined in very small nanocages are less mobile and can sometimes be identified as five- or sixfold rings (indicated by white arrows). C coverage, image size, , : (a) 0.22, , , ; (b) 0.22, , , ; (c) 0.54, , , ; (d) 0.75, , , . Note that no change in the observed structures could be found by changing the voltage polarity.

Image of FIG. 2.
FIG. 2.

Counts of five- (a) and sixfold (b) rings per area vs total cytosine coverage on the surface. 0.75 is the highest coverage observed, which corresponds to 1 ML. The number of fivefold rings stays nearly constant (within the error bars), while the number of sixfold rings clearly grows with increasing coverage. Closed symbols are total counts, while open symbols are either fivefold rings found as termination of branches (a) or sixfold rings found in branch junctions. The error bars correspond to the errors due to: (a) blurs and (b) cutoff heights for filaments (see text).

Image of FIG. 3.
FIG. 3.

The cytosine molecule in configuration . The chiral counterpart, the configuration , is obtained from upon flipping in the molecular plane. The seven binding sites which can participate in forming a double hydrogen bond between cytosine homopairs are explicitly indicated. Site 8 which contains 3 atoms is the combination of sites 5 and 6.

Image of FIG. 4.
FIG. 4.

Relaxed one-dimensional cytosine filaments, denoted , where in brackets indicates the order of stability according to Table I.

Image of FIG. 5.
FIG. 5.

[(a)–(c)] All of the possible end-to-end filament connections. (d) and (e) show the two common trimers which cause the change between (or provide the connection with) two filaments. The calculated stabilization energies of the molecular complexes are also given (in eV), as well as the corresponding sum of dimer energies from Ref. 43 (in brackets).

Image of FIG. 6.
FIG. 6.

Possible end-to-side filament connections to C-1D(1) [(a)–(d)] and C-1D(2) [(e)–(k)] filaments. Only possibilities associated with the attachment to site 3 of the side of the C-1-D(1) filament are shown in (a)–(d); another four possibilities arise in a similar way when attaching to site 2 of it (not shown). On the right, unit cells of 1D structures (with the lattice vector also indicated, in green) which model the connections employed in all cases [(a)–(k)] are shown; these contain a part of the corresponding filaments (running horizontally) with a single monomer attached. The calculated stabilization energies (in eV) of the relaxed connection structures are also shown together with the stabilization energies of the corresponding individual dimers (in brackets) for comparison. The stabilization energies of the connections were obtained by subtracting the energies of an individual filament and a molecule from the total energy in each case, including the appropriate BSSE correction.

Image of FIG. 7.
FIG. 7.

Schematic of a fivefold ring with the center at point O (not shown). The segment angles and the corresponding molecular sizes are explicitly indicated.

Image of FIG. 8.
FIG. 8.

Selected fivefold ring models. These rings are given in order of stability indicated by the number in the brackets.

Image of FIG. 9.
FIG. 9.

The cytosine sextuplets with three- [structures C-6(1) and C-6(2)] and sixfold [structures from C-6(3) to C-6(5)] symmetries. These rings are given in order of stability indicated by the numbers in the brackets in their label.

Image of FIG. 10.
FIG. 10.

[(a)–(c)] Calculated models for joining molecules to the side of a ring. The stability (in eV) of each pair involved in the ring-monomer binding (which was calculated as the binding energy of a single molecule to the ring, including the BSSE correction) is also given (in eV), together with the stability of each isolated dimer (in brackets) for comparison. (d) A model of the roundabout junction.

Tables

Generic image for table
Table I.

Five most stable cytosine filaments formed by periodically repeating two molecules in one dimension. Shown are the two dimers involved [the number in the brackets corresponds to the order of stability according to DFT calculations of dimers (Ref. 43)]; , , , and are the interaction, deformation, BSSE correction, and stabilization energies (including the BSSE corrections), respectively, and is the sum of all dimer energies taken from Ref. 43, and, finally, the length of the lattice vector (in Å) in the direction of periodicity.

Generic image for table
Table II.

Structure and energetics of the cytosine fivefold rings. , , , and are the interaction, deformation, BSSE correction, and stabilization energies (including the BSSE corrections), respectively, and is the sum of all dimer energies taken from Ref. 43. is the stabilization energy per molecule.

Generic image for table
Table III.

Energies of the cytosine sixfold ring structures. , , , and are the interaction, deformation, BSSE correction, and stabilization energies (including the BSSE corrections), respectively, and is the sum of all dimer energies taken from Ref. 43. is the stabilization energy per molecule.

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/content/aip/journal/jcp/129/18/10.1063/1.3001585
2008-11-14
2014-04-25
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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: Understanding the disorder of the DNA base cytosine on the Au(111) surface
http://aip.metastore.ingenta.com/content/aip/journal/jcp/129/18/10.1063/1.3001585
10.1063/1.3001585
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