Stability of Nucleobases and Base Pairs Adsorbed on Graphyne and Graphdiyne

Abstract

A theoretical understanding of the structure and energetics of the interaction of nucleobases (NBs) and amino acids with extended carbon-based network structures is crucial for understanding phenomena occurring at the nanobio interface. Herein, we investigate the adsorption of NBs and base pairs (BPs) on the new network materials in the carbon family, graphyne (GY), and graphdiyne (GDY) using dispersioncorrected density functional theory (ωB97XD functional) with a basis set of triple-ζ quality. Systematic investigations on the orientation dependence of the interaction of each of the NBs with a series of model compounds along with their superstructures reveal that the binding strengths of NBs on GY and GDY follow the order G > A > C > T > U, while those of BPs follow the order GC > AT > AU. The NBs and the BPs are found to adsorb at distances of ∼3 Å from the GY and GDY sheets, and the adsorption strengths are higher for GY than GDY. The small decrease in the hydrogen bond energies of the BPs subsequent to adsorption suggests that GY and GDY can serve as promising templates for the self-assembly of DNA and RNA. Our first-principles studies on how the NBs interact with GY and GDY can serve as a first and significant step toward the aim of understanding the interactions of DNA and RNA with GY and GDY as well as designing biomolecular devices based on GY and GDY. We believe that our findings will motivate several studies toward understanding the interface of biology and the nanoworld.

Defect‐Based Modulation of Optoelectronic Properties for Biofunctionalized Hexagonal Boron Nitride Nanosheets

“…where j is the current density, A is the Richardson constant [A m À2 ], T is the temperature [K], k B is the Boltzmann constant, and F is the work function of the material. Hence, the work functionv alues andt heir changes are calculated according to Equations (5) and (6): [28] F ¼ E inf ÀE f ð5Þ…”

“…[1,2] h-BN has been demonstrated to be an excellent platform for DNA sequencing andD NA hybridization.A denine( A), guanine (G), cytosine (C), and thymine (T) are fundamental constituents of DNA and have ak ey role in the storageo fg enetic information. Studies have focused on the adsorption behavioro ft hese nucleobases (NBs) on solid surfaces such as graphene, [3,4] graphyne and graphdiyne, [5] graphene oxide, [4] molybdenumd isulfide (MoS 2 ), [6] silicon, [7] silicene, [8] and h-BN [3,[9][10][11] to investigatet he mechanism of their self-assembly and the performance of thesem aterials as biosensors.A nalogous to what occurs with carbon nanomaterials, the boron nitride nanomaterials used in experimental synthesis are not alwaysp ure and defect-free. Experimental and theoretical reportsh ave demonstrated the existence of various defects such as Stone-Wales, vacancies and adatoms in these nanostructures.…”

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

“…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 . Furthermore, the spontaneous self‐assembly of hydrogen‐bonded base‐pairs is expected as a consequence of the high physisorption stability of nucleobases and slight effects into the hydrogen bond energies of its base‐pairs upon binding on graphene .…”

Computational study on the interaction of nucleobases with boron‐rich boron nitride nanotubes

“…The optimized geometries and harmonic frequencies were obtained using the dispersion corrected density functional theory (DFT‐D) with ωB97XD at 6‐31G(d,p) basis set, which are widely used to study the interaction between NBs and various nanomaterials . The convergence criteria for the self‐consistent field energy at each step of the optimization are RMS and maximum density matrix values of 10 −8 and 10 −6 , respectively.…”

“…For example, recent investigations have established that the doping of graphene with silicon, nickel, gallium, and aluminum increase the adsorption strength of NBs when compared to pristine gaphene . Several studies on the adsorption of NBs on graphene oxide, graphyne, and graphdiyne are already reported . The adsorption of modified NBs on the pristine, boron‐doped, nitrogen‐doped, and silicon‐doped graphene have been explored .…”