Hierarchical Self-Assembly of Noncanonical Guanine Nucleobases on Graphene

Molecular dynamics simulation to predict assembly structures of bowl-shaped π-conjugated molecules

The proposed computational method using molecular dynamics simulation investigating the structural stability and dynamics of the molecular assembly could predict bulk crystal structures for the rationally designed bowl-shaped π-conjugated molecules. In addition, the process of the formation of the columnar assemblies was reproduced by our simulated annealing simulation.

Engineering GaN/AuNC core-shell nanowire heterojunctions by gold nanoclusters with excitation-dependent behavior for enhancing the responsivity and stability of self-driven photodetectors

Self-driven broadband photodetectors (PDs) with low-power consumption have great potential applications in the wide range of next-generation optoelectronic devices. In this study, a self-driven broadband PD responding to an ultraviolet-visible range based on gallium nitride/gold nanocluster (GaN/AuNC) core-shell nanowire heterojunctions is fabricated for the first time. By introducing the AuNCs onto the GaN nanowire surfaces, the GaN/AuNC core-shell nanowire heterojunctions can be formed efficiently. It is crucial that AuNCs have the functions of light collectors and hole conductors in heterojunctions due to the suitable energy level alignment. Under the optimized conditions of AuNCs, it is found that GaN/AuNC core-shell nanowires can significantly increase the photocurrent and responsivity of PDs, mainly resulting from the light interreflection within the heterojunctions and the effective improvement of carrier transport. Owing to the excitation-dependent emission behavior of AuNCs, the responsivity of PD with GaN/AuNC core-shell nanowire heterojunctions can be enhanced by around 330% compared with that of PD without AuNCs under visible illumination. Furthermore, GaN/AuNC hybrid nanowires with excitation-dependent fluorescence behavior can modulate the enhanced amplitude performance of broadband PDs. Owing to the high stability of AuNCs, the photocurrent of the PD with AuNCs is still quite stable after continuous operation for more than 20 000 s. Therefore, this study provides an effective method for developing new broadband PDs with high performance and low energy consumption.

Self-assembly of rylene-decorated guanine ribbons on graphene surface for optoelectronic applications: a theoretical study

We are witnessing a change of paradigm from the conventional top-down to the bottom-up fabrication of nanodevices and particularly optoelectronic devices. A promising example of the bottom-up approach is self-assembling of molecules into layers with predictable and reproducible structural, electronic and optical properties. Nucleobases possess extraordinary ability to self-assembly into one-, two-, and three-dimensional structures. Optical properties of nucleotides are not suitable for wider application to optoelectronics and photovoltaics due to their large optical band gap, which is in contrast to rylene-based dyes that have been intensively investigated in organic optoelectronics. However, these lack the self-assembly capability of nucleobases. Combinations of covalently decorated guanine molecules with rylene type chromophores present 'the best of the both worlds'. Due to the large size of such compounds and its flexible nature their self-assemblies have not been fully understood yet. Here, we use a theoretical approach to study the structural, energetic and optical properties of rylene-based dye decorated guanine (GPDI), as self-assembled on a graphene sheet. Particularly we utilize the density-functional based tight-binding method to study atomic structure of these systems including the potential energy surface of GPDI and stability and organization of single- and multilayered GPDIs on graphene sheet. Using density-functional theory (DFT) we employ the energy decomposition analysis to gain a deeper insight into the contributions of different moieties to stability of GPDI films. Using time dependent DFT we analyze optical properties of these systems. We find that atomically thin films consisting of only a few molecular layers with large surface areas are more favorable than isolated thick islands. Our study of excited states indicates existence of charge separated states similar to ones found in the well-studied hydrogen bonded organic frameworks. The self-assembly characterized with a large homogeneous coverage and long-living charge-separated states provide the great potential for optoelectronic applications.

Polarization influences the evolution of nucleobase-graphene interactions

In recent years, graphene has attracted attention from researchers as an atomistically thin solid state material for the study on the self-assembly of nucleobases. Non-covalent interactions between nucleobases and graphene sheets play a fundamental role in understanding the self-assembly of nucleobases on the graphene sheet. A fundamental understanding of the effect of molecular polarizability on these non-covalent interactions between the nucleobases and the underlying graphene sheet is absent in the literature. In this paper, we present the results from polarizable molecular dynamics simulation studies to understand the effect of polarization on the strength of non-covalent interactions. To this end, we report the development of Drude parameters for describing the polarizable graphene sheet. The developed parameters were used to study the self-aggregation phenomenon of nucleobases on a graphene support. We observe a significant change in the interaction patterns upon the inclusion of polarization into the system, with polarizable simulations yielding results that closely resemble the experimental studies. Two of the key observations were the probability of the formation of stacks in guanine-rich systems, and the spontaneous formation of H-bonded structures over the graphene sheet, which allude to the importance of the DNA sequence and composition. Both these effects were not observed in the additive simulations. The present study sheds light on the effect of polarization on the adsorption of DNA nucleobases on a graphene sheet, but the methodology can be extended to include a variety of small molecules and complete DNA strands.

Predictions of Pattern Formation in Amino Acid Adlayers at the In Vacuo Graphene Interface: Influence of Termination State

Controlled self-assembly of biomolecules on graphene offers a pathway for realizing its full potential in biological applications. Microscopy has revealed the self-assembly of amino acid adlayers into dimer rows on nonreactive substrates. However, neither the spontaneous formation of these patterns, nor the influence of amino acid termination state on the formation of patterns has been directly resolved to date. Molecular dynamics simulations, with the ability to reveal atomic level details and exert full control over the termination state, are used here to model initially disordered adlayers of neutral, zwitterionic, and neutral-zwitterionic mixtures for two types of amino acids, tryptophan and methionine, adsorbed on graphene in vacuo. The simulations of the zwitterion-containing adlayers exhibit the spontaneous emergence of dimer row ordering, mediated by charge-driven intermolecular interactions. In contrast, adlayers containing only neutral species do not assemble into ordered patterns. It is also found that the presence of trace amounts of water reduces the interamino acid interactions in the adlayers, but does not induce or disrupt pattern formation. Overall, the findings reveal the balance between the lateral interamino acid interactions and amino acid-graphene interactions, providing foundational insights for ultimately realizing the predictable pattern formation of biomolecules adsorbed on unreactive surfaces.

Dynamics of self-assembled cytosine nucleobases on graphene

Molecular self-assembly of cytosine (C _n ) bases on graphene was investigated using molecular dynamics methods. For free-standing C _n bases, simulation conditions (gas versus aqueous) determine the nature of self-assembly; the bases prefer to aggregate in the gas phase and are stabilized by intermolecular H-bonds, while in the aqueous phase, the water molecules disrupt base-base interactions, which facilitate the formation of π-stacked domains. The substrate-induced effects, on the other hand, find the polarity and donor-acceptor sites of the bases to govern the assembly process. For example, in the gas phase, the assembly of C _n bases on graphene displays short-range ordered linear arrays stabilized by the intermolecular H-bonds. In the aqueous phase, however, there are two distinct configurations for the C _n bases assembly on graphene. For the first case corresponding to low surface coverage, the bases are dispersed on graphene and are isolated. The second configuration archetype is disordered linear arrays assembled with medium and high surface coverage. The simulation results establish the role of H-bonding, vdW π-stacking, and the influence of graphene surface towards the self-assembly. The ability to regulate the assembly into well-defined patterns can aid in the design of self-assembled nanostructures for the next-generation DNA based biosensors and nanoelectronic devices.