Nanopatterning the surface with ordered supramolecular architectures of N9-alkylated guanines: STM reveals

Ciesielski, Artur; Perone, Rosaria Carmela; Pieraccini, Silvia; Spada, Gian Piero; Samorı́, Paolo

doi:10.1039/c0cc00443j

Cited by 26 publications

(21 citation statements)

References 42 publications

(7 reference statements)

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“…Previous STM studies on the self‐assembly of lipophilic guanosine derivatives40 and different N9‐alkylated G mole‐cules41 at the liquid–solid interface have revealed similar ribbon structures as observed here for G and 9mG. This comparison indicates that alkylation of G at position 9 generally results in ribbon‐like assembly of the molecules, as is the case for nonalkylated G. Only a blocking of the Watson–Crick binding face at position 1 and the introduction of a methyl group at position 8 force the molecules to assemble into more complex 2D nanostructures.…”

Section: Resultsmentioning

confidence: 99%

Control of Self‐Assembled 2D Nanostructures by Methylation of Guanine

Bald

Wang

Dong

et al. 2011

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Methylation of DNA nucleobases is an important control mechanism in biology applied, for example, in the regulation of gene expression. The effect of methylation on the intermolecular interactions between guanine molecules is studied through an interplay between scanning tunneling microscopy (STM) and density functional theory with empirical dispersion correction (DFT-D). The present STM and DFT-D results show that methylation of guanine can have subtle effects on the hydrogen-bond strength with a strong dependence on the position of methylation. It is demonstrated that the methylation of DNA nucleobases is a precise means to tune intermolecular interactions and consequently enables very specific recognition of DNA methylation by enzymes. This scheme is used to generate four different types of artificial 2D nanostructures from methylated guanine. For instance, a 2D guanine windmill motif that is stabilized by cooperative hydrogen bonding is revealed. It forms by self-assembly on a graphite surface under ambient conditions at the liquid-solid interface when the hydrogen-bonding donor at the N1 site of guanine is blocked by a methyl group.

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Section: Resultsmentioning

confidence: 99%

Control of Self‐Assembled 2D Nanostructures by Methylation of Guanine

Bald

Wang

Dong

et al. 2011

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“…(1) strongly interacting benzenecarboxylic acids, such as isophthalic acid (ISA), 36 terephthalic acid (TRA), 36 and trimesic acid (TMA); 16,37 (2) two bases, N 9 -ethyl guanine (GUA) 38 and melamine (MEL), 39 whose self-assembly is steered by multiple hydrogen bonds; (3) a series of linear alkanes with a chain length of twelve that are substituted at one terminus with one carboxylic group (A12), 14 one hydroxyl group (B12), 40 one chlorine group (L12), 41 or nothing (C12); [40][41][42] and (4) two large poly-aromatic hydrocarbons, coronene (COR) 30,43 and perchlorocoronene (CLC). 30 An illustration of the modeled SAMs, which span a wide range of molecular size, density of packing and energy of interaction is given in Fig.…”

Section: Chemical Potential Of the Unit Cellmentioning

confidence: 99%

Predicting molecular self-assembly at surfaces: a statistical thermodynamics and modeling approach

Conti

Cecchini

2016

Phys. Chem. Chem. Phys.

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Molecular self-assembly at surfaces and interfaces is a prominent example of self-organization of matter with outstanding technological applications. The ability to predict the equilibrium structure of a self-assembled monolayer (SAM) is of fundamental importance and would boost the development of bottom-up strategies in a number of fields. Here, we present a self-consistent theory for a first-principles interpretation of 2D self-assembly based on modeling and statistical thermodynamics. Our development extends the treatment from finite-size to infinite supramolecular objects and delineates a general framework in which previous approaches can be recovered as particular cases. By proving the existence of a chemical potential per unit cell, we derive an expression for the surface free energy of the SAM (γ), which provides access to the thermodynamic stability of the monolayer in the limit of the ideal gas approximation and the model of energetics in use. Further manipulations of this result provide another expression of γ, which makes the concentration dependence as well as the temperature dependence of 2D self-assembly explicit. In the limit of the approximations above, this second result was used to analyze competitive equilibria at surfaces and rationalize the concentration- and temperature-dependent polymorphism in 2D. Finally, the theory predicts that there exists a critical aggregation concentration (C) of monomers above which 2D self-assembly can be viewed as a "precipitation" in a solubility equilibrium. Numerical analysis of thirteen model SAMs on graphene shows that the value of C sets an absolute scale of 2D self-assembly propensity, which is useful to compare chemically distinct and apparently unrelated self-assembly reactions.

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“…To achieve an in‐depth understanding of the self‐assembly of guanine at the solid/liquid interface, we performed a sub‐molecularly resolved STM study of physisorbed monolayers on graphite of a series of N(9)‐alkylated guanines with linear alkyl side‐chains from –C 2 H 5 up to –C 18 H 37 ( G3 – G11 ) . This comparative study was carried out by applying a drop of a solution of the chosen alkyl‐substituted guanine in 1,2,4‐trichlorobenzene (TCB) on freshly cleaved HOPG surface.…”

Section: Self‐assembly In 2dmentioning

confidence: 99%

“…STM current images of monolayers of alkylated guanines showing ribbon‐like (a,f,g–i), crystalline (b,e), and dimeric (c,d) structures formed at the HOPG/solution interface. Reproduced with permission . Copyright 2010, the Royal Society of Chemistry.…”

Section: Self‐assembly In 2dmentioning

confidence: 99%

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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Nanopatterning the surface with ordered supramolecular architectures of N9-alkylated guanines: STM reveals

Abstract: STM study of the self-assembly at the solid-liquid interface of substituted guanines exposing in the N(9)-position alkyl side chains with different lengths revealed the formation of distinct crystalline nanopatterns.

Cited by 26 publications

References 42 publications

Control of Self‐Assembled 2D Nanostructures by Methylation of Guanine

Control of Self‐Assembled 2D Nanostructures by Methylation of Guanine

Predicting molecular self-assembly at surfaces: a statistical thermodynamics and modeling approach

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

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