Dynamics of self-assembled cytosine nucleobases on graphene

Abstract

Molecular self-assembly of cytosine (C ) bases on graphene was investigated using molecular dynamics methods. For free-standing C 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 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 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.

Effects on the aromatic character of DNA/RNA nucleobases due to its adsorption onto graphene

“…Because it is know that purine ( A and G ) and pyrimidine bases ( C, T , and U ) can self‐assemble onto crystalline solids, the interaction of nucleobases with nanostructured materials has been extensively studied due to its potential biotechnological applications in nanosciences and medicine, this is to develop materials for resembling, sensing and/or sequencing of DNA/RNA constituents, and or to obtain new biological‐friendly interfaces . Among the layered materials, graphene has shown a superior ability to interact with nucleobases, where experimental and theoretical analyses have determined a high adsorption stability in these cases (even in aqueous conditions), and revealing the processes as biomolecules interact at graphene biointerfases …”

“…The stability of nucleobases–graphene systems has been revised from theoretical studies at the Hartree–Fock, Molecular‐Mechanics, and DFT level of theory . These analyses show that nucleobases are physisorbed onto graphene at shorter interplane distances (∼3 Å) and with adsorption energies in the range of 0.4–1.1 eV; the order of stability is commonly sorted as G > A ≥ C ≥ T > U , where the stability of C, A , and T is very similar depending on the different theoretical methodologies .…”

Simulation of graphene–fullerene nanohybrid structure

“…The force field parameters for the graphene and fullerene carbon atoms were taken from the aromatic carbon atoms of the CHARMM27 force field [47]. In the literature, the CHARMM27 force field parameters [48][49][50][51][52] have been reported to yield significant results for the graphene and fullerene systems. Sathe et al [48] have used the CHARMM27 force field parameters for graphene to study the detection of DNA by graphene nanopores.…”

“…Luo et al [49] have employed the CHARMM27 force field parameters for the polyethylene glycol-functionalized graphene oxide nanosheets to investigate their interactions with the cell membrane. Saikia et al [50] have applied CHARMM27 force field parameters for graphene to describe the self-assembly of cytosine bases on graphene. Kraszewski et al [51] have modelled functionalized fullerene using the CHARMM27 force field parameters to study their interactions with the model cell membrane.…”

Capturing Concentration-Induced Aggregation of Nucleobases on a Graphene Surface through Polarizable Force Field Simulations

“…Controlled supramolecular assemblies formed by small molecules on two-dimensional (2D) supports have attracted significant attention in the scientific community. − Noncovalent interactions such as hydrogen bonding, π–π stacking, and electrostatic interactions play a fundamental role in stabilizing such supra-molecular assemblies . Here, nucleobases offer a viable pathway to the realization of both structured and amorphous self-assemblies due to the presence of multiple hydrogen bond donors and acceptors. − Chemical moieties with a nucleobase core can act as starting blocks for rosette nanotubes , and other self-assemblies. − Self-assemblies formed by nucleobases or their derivatives have found applications in bionanotechnology − and catalysis. , A fundamental understanding of the behavior of nucleobases at the solid–liquid interface is also crucial in understanding the evolution of life from simple chemical moieties. , …”