Atomic-Scale Investigation on the Facilitation and Inhibition of Guanine Tautomerization at Au(111) Surface

Kong, Huihui; Sun, Qiang; Wang, Likun; Tan, Qinggang; Zhang, Chi; Sheng, Kai; Xu, Wei

doi:10.1021/nn4061918

Cited by 39 publications

(48 citation statements)

References 28 publications

(39 reference statements)

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“…4:1) on Au(111) at room temperature (RT) and further annealing at 390 Kf or 10 min results in the formation of ar homboid network structure as shown in Figure 1a.F rom the close-up STM image ( Figure 1b), we identify that the network structure is composed of two kinds of elementary motifs (that is,the trimeric and the dimeric ones as indicated by the corresponding contours). Tw oe nantiomers of the trimeric motif are also observed as indicated by green and blue trimeric contours where the individual molecular chiralities are denoted by Ra nd L. As experienced with coordination schemes between DNAb ases and transition metals, [7,9,[26][27][28] after extensive structural search, we assign this trimeric motif to aG 3 Ni 1 metal-organic structure as highlighted in Figure 1c.F rom the DFT-optimized model superimposed on the corresponding STM image,w ed istinguish that it is formed by three Gm olecules (with different chiralities) coordinating with one Ni atom via one N7 site and two O6 sites,and the intermolecular NH···O and NH···N hydrogen bonds further stabilize the structure.T he dimeric structure (depicted by the white contour in Figure 1b)i s assigned to ah ydrogen-bonded dimer according to the morphology and the well-established NH···O hydrogen bonds involved. These two elementary structural motifs are also linked together via hydrogen bonds.…”

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confidence: 78%

Structural Transformation and Stabilization of Metal–Organic Motifs Induced by Halogen Doping

et al. 2017

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The structural transformation of supramolecular nanostructures with constitutional diversity and adaptability by dynamic coordination chemistry would be of fundamental importance for potential applications in molecular switching devices. The role of halogen doping in the formation of elementary metal-organic motifs on surfaces has not been reported. Now, the 9-ethylguanine molecule (G) and Ni atom, as a model system, are used for the structural transformation and stabilization of metal-organic motifs induced by iodine doping on Au(111). The iodine atoms are homogeneously located at particular hydrogen-rich locations enclosed by G molecules by electrostatic interactions, which would be the key for such an unexpected stabilizing effect. The generality and robustness of this approach are demonstrated in different metal-organic systems (G/Fe) and also by chlorine and bromine.

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confidence: 78%

Structural Transformation and Stabilization of Metal–Organic Motifs Induced by Halogen Doping

et al. 2017

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“…In biological systems, the transformation of nucleobases from canonical to their noncanonical forms could induce a mismatch of base pairing and further disturb the genetic codes . Direct real‐space evidence of the existence of different G tautomers and further investigation into the effect of metals on G tautomerisation at surfaces has been recently reported by Xu and co‐workers . From the interplay of STM imaging under UHV and DFT calculations, the authors show that the tautomerisation of G from G/N(9)–H ( G1 ) to G/N(7)–H ( G12 ) is facilitated on Au(111) surfaces by annealing, whereas such a tautomerisation process is effectively inhibited by introducing Ni atoms due to its preferential coordination at the N(7) site of G/N(9)–H tautomer.…”

Section: Self‐assembly In 2dmentioning

confidence: 97%

Self‐assembly of Natural and Unnatural Nucleobases at Surfaces and Interfaces

Ciesielski

Garah

Masiero

et al. 2015

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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.

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“…First, we built up structural models of the triangular clusters based on the canonical form of the Umolecule;however, we identified that the most stable parallelogrammic model did not agree with the experimental configuration as illustrated in Figure S3. As it is known that the nucleobases can undergo tautomerization on surfaces, [39][40][41] we then re-built our models taking into account the non-canonical forms of the Umolecule.A fter an extensive structural search and comparison with STM images,w ei dentified the energetically favorable models of the triangular and parallelogrammic clusters,which were overlaid on the corresponding simulated STM images ( Figure 1e); good agreements are achieved when comparing them with the experimental morphologies and dimensions. Theoptimized models showed that the triangular cluster was formed by three Umolecules coordinating to three Ni atoms, and that the parallelogrammic cluster was formed by two homochiral triangular clusters linked together through double NÀH···O hydrogen bonds.Interestingly,wefound that the two dim molecules mentioned above are just the ones that are involved in the formation of hydrogen bonds.W ethus believe that the change in apparent heights of molecules 1a nd 2 ( Figure 1c,d)s hould be attributed to the corresponding change in their molecular adsorption configurations upon hydrogen-bond formation.…”

Section: Angewandte Communicationsmentioning

confidence: 99%

Controllable Scission and Seamless Stitching of Metal–Organic Clusters by STM Manipulation

et al. 2015

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Scanning tunneling microscopy( STM) manipulation techniques have proven to be ap owerfulm ethod for advanced nanofabrication of artificial molecular architectures on surfaces.With increasing complexity of the studied systems, STM manipulations are then extended to more complicated structural motifs.Previously,the dissociation and construction of various motifs have been achieved, but only in as ingle direction. In this report, the controllable scission and seamless stitching of metal-organic clusters have been successfully achieved through STM manipulations.T he system presented here includes two sorts of hierarchical interactions where coordination bonds hold the metal-organic elementary motifs while hydrogen bonds among elementary motifs are directly involved in bond breakage and re-formation. The key to making this reversible switching successful is the hydrogen bonding,w hichi sc omparatively facile to be broken for controllable scission, and, on the other hand, the directional characteristic of hydrogen bonding makes precise stitching feasible.The direct identification of intermolecular interactions and the delicate tailoring of structural motifs with molecular precision on solid surfaces have recently attracted considerable interest because of the prospect for artificial design of functional molecular nanostructures and nanodevices.S canning tunneling microscopy (STM), especially under ultrahigh vacuum (UHV) conditions,h as proven to be ap owerful method for the precise manipulation of single molecules to trigger various single-molecule behaviors,s uch as translation, [1][2][3] rotation, [3][4][5][6][7][8][9] flipping, [10] cis-trans isomerization, [11][12][13] tautomerization, [14][15][16] dehydrogenation, [17][18][19] and dehalogenation.[20] Not limited to single molecules,S TM manipulations have also been extended to larger molecular structural motifs with great progress in the following aspects:1 )moving clusters, [21] chains, [22][23][24][25] and patches; [26] 2) dissociating dimers, clusters,a nd complexes by breaking hydrogen bonds, [27] coordination bonds, [28][29][30] and carbon-metal bonds, [31] respectively;3)constructing structural motifs by forming new bonds ranging from hydrogen bonds, [32] coordination bonds, [30,33] to robust covalent bonds; [20,34,35] and 4) probing different hierarchical interactions [36] and identifying hydrogen-bonding configurations [27] and covalent bonding sites.[37] Most of the previous studies mentioned above mainly exhibited either the dissociation or construction of various structural motifs. However,t ot he best of our knowledge,t he reversible switching of complicated structural motifs by controllable breakage and re-formation of certain bonds through STM manipulations has not been reported to date.Itistherefore of great interest to explore the feasibility of utilizing STM manipulations to achieve controllable scission and precise stitching of complicated structural motifs in ac omparatively facile manner, which may open anew avenue for the artificial ...

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Atomic-Scale Investigation on the Facilitation and Inhibition of Guanine Tautomerization at Au(111) Surface

Cited by 39 publications

References 28 publications

Structural Transformation and Stabilization of Metal–Organic Motifs Induced by Halogen Doping

Structural Transformation and Stabilization of Metal–Organic Motifs Induced by Halogen Doping

Self‐assembly of Natural and Unnatural Nucleobases at Surfaces and Interfaces

Controllable Scission and Seamless Stitching of Metal–Organic Clusters by STM Manipulation

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