Controlling the orientation of nucleobases by dipole moment interaction with graphene/h-BN interfaces

The interfaces in 2D hybrids of graphene and h-BN provide interesting possibilities of adsorbing and manipulating atomic and molecular entities. In this paper, with the aid of density functional theory, we demonstrate the adsorption characteristics of DNA nucleobases at different interfaces of 2D hybrid nanoflakes of graphene and h-BN. The interfaces provide stronger binding to the nucleobases in comparison to pure graphene and h-BN nanoflakes. It is also revealed that the individual dipole moments of the nucleobases and nanoflakes dictate the orientation of the nucleobases at the interfaces of the hybrid structures. The results of our study point towards a possible route to selectively control the orientation of individual molecules in biosensors.


Introduction
Graphene, 1 the 2D sp 2 -bonded single layer of graphite, is a hot topic of research today due to its unique electrical, 2-4 optical, 5,6 thermal 7,8 and mechanical properties. 9,10 An isoelectronic 2D material, namely hexagonal boron nitride (h-BN), has also gained prominence in this eld, as its electronic structure contains a large band gap, unlike graphene which exhibits a zero band gap. 11,12 Both graphene and h-BN have been studied quite extensively in connection to the adsorption of molecules 13 and nanoclusters 14 by the p electron cloud. 15 To understand the self-assembly process of biological molecules like deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), [16][17][18] interaction of nucleobases and amino acids with graphene and h-BN have been investigated using experiment and theory. These studies indicate that the noncovalent interactions such as p-p stacking and X-p (X ¼ CH, OH, NH etc.) interactions stabilize the nucleobases adsorbed on graphene and h-BN. [19][20][21][22][23][24][25] This shows the potential of using graphene and h-BN in biosensing applications. Moreover, graphene nanoribbons have been proposed to rapidly sequence DNA by measuring the time-dependent conductance as the nucleotides of single-stranded DNA are brought sequentially in contact with the nanoribbon. 26 Recently Lee et al. have studied the interaction of nucleobases with h-BN and graphene using an approach that incorporates van der Waals interactions into the density functional scheme. They found that the binding energies of the different nucleobases with two sheets (h-BN and graphene) are similar and an interfacial dipole is induced between the sheet and base molecule during adsorption. 27 Very recently, 2D hybrids (CBN) of graphene and h-BN have been prepared through chemical vapor deposition method. These hybrids are found to have unusual electronic, magnetic and transport properties including half-metallicity. 28 Gao et al. have explained the formation of CBN with different edges using Rh (111) substrate and they have shown that formation of zigzag edges is more favorable than that of armchair edges. 29 The CBN monolayer can be used as an ultrathin solar cell with PCBM fullerene as an acceptor. 30 Although, the physical properties of these CBN materials have been studied, the interaction of nucleobases with CBN surfaces has not yet been reported. It should be noted that the interaction between the dipoles in the nucleobases and hybrid nanoakes can give rise to non-trivial properties based on the mutual orientations at the interface of dissimilar akes. In the present study, we have carried out density functional calculations to investigate different orientations of nucleobases, namely adenine (A), guanine (G), thymine (T) and cytosine (C) adsorbed on CBN nanoakes with different edges, namely armchair, as well as zigzag with either N-or Btermination. Specically, we have studied the equilibrium geometries, binding characteristics, and role of dipoles in dictating the mutual orientations.

Methodology
Structural models of CBN akes with armchair (Arm) and zigzag (Zig) interfaces were considered from previous studies. 31 Throughout this article, we refer to interfaces with armchair edges as Arm, to those with zigzag edges where N bonds with C as Zig-N, and to those with zigzag edges where B bonds with C as Zig-B. We have employed ab initio calculations based on Density Functional Theory 32,33 (DFT) and the Linear Combination of Atomic Orbitals (LCAO) as implemented in Gaussian09 34 and SIESTA 35 codes. We used two levels of calculations to validate our results and give greater condence in the accuracy of the study: one of them was hybrid meta exchange-correlation functional M06-2X 36 with 6-31+G(d,p) basis set, while for the second one, we used Generalized Gradient Approximation (GGA-PBE) 37 with van der Waals corrections 38,39 to take into account dispersive interactions. For the SIESTA calculations, we considered a box of 30Å 3 to avoid the interactions between periodic images. Double-z polarized basis sets (DZP) and normconserving pseudopotentials 40 were used. To obtain equilibrium structures, forces in three directions on each atom were minimized below 0.01 eVÅ À1 . From here on, meta-GGA is meant to refer to Gaussian09 calculations while GGA + vdW refers to SIESTA calculations.
The stability of the akes was evaluated using the formation energy as per the following equation: In the rst equation, E T , n i , m i , N refer to: total energy of the ake, number of each species in the ake, corresponding chemical potential, and total number of atoms in the ake, respectively. In the second equation, E ake is the total energy of the hybrid ake (Arm, Zig-N, Zig-B). E GR ake is the total energy for the graphene reference system, m i (i ¼ C, N and B) is the chemical potential of each species and N i (i ¼ C, N and B) is the number of extra or missing atoms for a particular species in comparison to the reference graphene ake. N tot is the total number of atoms comprising of C, N and B involved in the equation. , cytosine (C), guanine (G), and thymine (T). We note that due to three possible ake interfaces, the dipole moments have distinct orientations. In Arm, the direction of the dipole moment is along the interface. We note that the total dipole moment (shown in Fig. 1) is formed by the sum of all local dipole moments lying along each BN bond. For the case of Zig-B, the dipole moment is rotated clockwise by 90 degrees compared to Arm ake whereas for Zig-N ake, the direction of the dipole moment is exactly opposite to Zig-B (see Fig. 1(a)-(c)). The dipole moment directions for the nucleobases are shown as yellow arrows in Fig. 1(d). For C, G and T, the arrows point from the oxygen atom (or the center of a pair of oxygen atoms in the case of T) to the opposite side of the nucleobase because the oxygen atom carries excess negative charge. For the nucleobase A, there are three N atoms on one side and two on the other side. The former side has more negative charge than the latter one, which dictates the resulting direction of the dipole moment.

Results and discussion
The cohesive energies for the three akes are given in Table 1, calculated using two different functionals. The results indicate the hierarchy in stability as Zig-N > Arm > Zig-B. The energy differences between Zig-N and Arm (Zig-B) akes are 6.89 (10.69) kJ mol À1 considering GGA + vdW and 3.38 (7.34) kJ mol À1 for meta-GGA respectively. The results follow the same trend using both functionals; the cohesive energy difference between the most stable ake (Zig-N) with the least stable (Zig-B) is about two times bigger than that for the second-most stable (Arm) ake. Next, we have calculated the formation energies for the hybrid akes with GR ake as a reference using the equation given above and the values are 384.32, 473.24, and 479.37 kJ mol À1 for the Zig-N, Arm, and Zig-B ake respectively. This result follows the same trend as that of cohesive energies. It should be noted that the positive formation energies indicate that the akes can be metastable but still  possible to form as seen in experiments. The corresponding values are calculated as À457.68, À368.77, À362.63 kJ mol À1 when a BN ake is considered as the reference. These values indicate that the hybrid akes can be spontaneously formed. The difference in these two cases is related to the growth conditions with different reservoirs. As the ake with the Bterminated zigzag edge (Zig-B) is found to be the least stable in all the cases, we will consider only adsorption complexes involving Zig-N and Arm from now on. Table 2 lists the total dipole moment values for the two most stable akes (Zig-N and Arm) and for the four nucleobases, calculated using two different methods. For the nucleobases, we noted the same hierarchy (G > C > T > A) for both functionals and the results are consistent with the previous studies. 41 For the akes, we note that Zig-N possesses a total dipole moment about 1.5 to 1.7 times bigger than the Arm ake.
As nucleobases and akes possess distinct dipole moment values and orientations, an interesting question can be addressed regarding the mutual interaction and the resulting stability of the complexes formed between the nucleobases and the nanoakes. Specically the relative orientation between a nucleobase and a nanoake is of primary interest to us in the present study. To explore this question, we have investigated two fundamentally different geometries for each complex, in which the dipole moments of the constituting subsystems are either parallel or antiparallel to each other. Fig. 2 illustrates parallel (P) and antiparallel (AP) dipole moment orientations of the hybrid akes and a nucleobase, here shown for the example of Zig-N and guanine. The red and yellow arrows indicate the dipole moments of the isolated ake and the nucleobase, respectively. We have performed geometry optimizations of the complexes to nd the ground state congurations from which the resulting dipole moments can be extracted. The energy differences between the two orientations (DE ¼ E P À E AP ) can provide insights into the relative stabilities and are listed for all explored combinations of Zig-N and Arm akes with the four nucleobases in Table 3. As per the above denition, a positive relative energy would indicate that the antiparallel orientation is more stable than the parallel one.
Indeed it is found that for all nucleobases on either of the two studied nanoakes, the antiparallel conguration is always more stable than the parallel one in the Arm and Zig-N akes, as conrmed by both functionals. However, the nucleobases A and T on Arm are almost degenerate in energy for parallel and antiparallel congurations, indicating no strong preference for either orientation. However, a closer inspection reveals that for GGA + vdW, the antiparallel conguration for A is more stabilized than that for T (5.12 vs. 1.33 kJ mol À1 ), whereas in meta-GGA, the reverse is true (0.54 vs. 2.50 kJ mol À1 ). This difference may occur due to distinct considerations of dispersion corrections in GGA + vdW and meta-GGA.
As we mentioned above, the nucleobase G possesses the largest dipole moment among the four nucleobases while A carries the smallest. Furthermore, it was also found that the Zig-N ake possesses a larger dipole moment than the Arm one. Now we will analyze the total dipole moments of the complexes with the goal to identify a trend. For complexes with Zig-N, we observe the following order for both methods in the total dipole moment for the parallel (P) arrangement: G > C > T > A. It is interesting to note that these results follow the same hierarchy as that of the isolated nucleobases. For the anti-parallel (AP) orientation, the trend is reversed, i.e., we obtain A > T > C > G. This is due to the fact that in this case the dipole moment gets minimized by partial cancellation of the individual dipole moments ( Table 2). The situation is not as straightforward for the Arm ake due to a complex interplay between geometry and charge distribution of the constituents. Hence the resulting total dipole moment cannot be predicted by simple addition or subtraction of the individual dipole moments from Table 2. For Table 2 Calculated dipole moments of the two most stable nanoflakes (Zig-N and Arm) and of the four nucleobases (A, C, G and T) using two functionals (GGA + vdW and meta-GGA)   the parallel conguration, the hierarchy is G > C > T > A for meta-GGA but G z C > T > A for GGA + vdW. In the energetically more favorable anti-parallel orientation, the sequence order is G > A > T > C for meta-GGA and A > G > T > C for GGA + vdW.

System
These results indicate that full-edged ab initio electronic structure calculations are necessary to provide an accurate picture of the dipole moments of these nucleobase-nanoake complexes.
To understand in detail the interaction due to adsorption, we calculated charge density differences between the ake-DNA nucleobase complexes and the sum of the charge densities of akes and DNA nucleobases as described in the following expression: where I ake+DNA is the total charge density for the full system and I ake (I DNA ) is for the ake (DNA), respectively. The charge density difference plots shown in Fig. 3 indicate how the charge is redistributed in the system due to adsorption. The positive charge difference is represented by green and the negative one by orange color. We note that the overall behavior is similar, i.e., the accumulation of positive charge in the graphene side and a negative one in the h-BN side.
Finally, we discuss the binding energies of the nucleobases on different interfaces of CBN akes. For comparison, we have also calculated the binding energies on pure graphene and h-BN akes of the same size as the hybrid systems. These calculations have been carried out using the meta-GGA approach. From the binding energies presented in Fig. 4, it is clear that the hybrid interfaces, especially Zig-N, are better binding agents than the pure akes for all the nucleobases considered here. It is worth mentioning that the nucleobases have a parallel orientation on the graphene ake whereas a tilted orientation is observed on the BN ake. The calculated dipole moments for pure graphene and BN akes were 0 and 0.04 Debye and for graphene/h-BN ake, it was 3.85 Debye. Due to the presence of higher dipole moments, nucleobases strongly interact with the graphene/hexagonal BN ake than pure G and BN akes. This proves the utility of mixed interfaces for stronger adsorption of nucleobases. Moreover, the presence of dipole moments at the interfaces plays an important role in stabilizing certain orientations of the nucleobases.

Conclusions
In the present work, we have performed rst-principles calculations to study the interaction of nucleobases with 2D hybrid nanoakes formed of graphene and h-BN, considering three different types of interfaces. Our results reveal that the dipole moment orientation of the nucleobases relative to the dipole moment of the hybrid nanoake interface plays the decisive role in stabilizing these complexes. The antiparallel orientation of dipole moments of the nucleobases with respect to those of the nanoake interfaces is found to be more stable than the parallel orientation in the armchair and N-terminated zigzag interfaces. Furthermore, the binding energies of the nucleobases on the  hybrid akes are found to be higher than those on both pure graphene and pure boron nitride akes of the same size. Our study hints at the possibilities of using hybrid akes to achieve better sensitivity in detecting and identifying specic nucleobases, e.g., for the purpose of DNA sequencing, by improving the signal-to-noise ratio due to the reduction of spatial uctuations of the nucleobases.

Conflicts of interest
There are no conicts to declare.