Physisorption of DNA nucleobases on h-BN and graphene: vdW-corrected DFT calculations
Jun-Ho Lee, Yun-Ki Choi, Hyun-Jung Kim, Ralph H. Scheicher, Jun-Hyung Cho
aa r X i v : . [ c ond - m a t . m e s - h a ll ] F e b Physisorption of DNA nucleobases on h-BN and graphene: vdW-correctedDFT calculations
Jun-Ho Lee, Yun-Ki Choi, Hyun-Jung Kim, Ralph H. Scheicher, and Jun-Hyung Cho ∗ Department of Physics and Research Institute for Natural Sciences,Hanyang University, 17 Haengdang-Dong,Seongdong-Ku, Seoul 133-791, Korea Division of Materials Theory, Department of Physics and Astronomy,˚Angstr¨om Laboratory, Uppsala University,Box 516, SE-751 20, Uppsala, Sweden (Dated: October 16, 2018)
Abstract
We present a comparative study of DNA nucleobases [guanine (G), adenine (A), thymine (T), and cyto-sine (C)] adsorbed on hexagonal boron nitride ( h -BN) sheet and graphene, using local, semilocal, and vander Waals (vdW) energy-corrected density-functional theory (DFT) calculations. Intriguingly, despite thevery different electronic properties of BN sheet and graphene, we find rather similar binding energies for thevarious nucleobase molecules when adsorbed on the two types of sheets. The calculated binding energiesof the four nucleobases using the local, semilocal, and DFT+vdW schemes are in the range of 0.54 ∼ ∼ ∼ > A > T > C, but also a very weak hybridization between the molecularlevels of the nucleobases and the p -states of the BN sheet or graphene. This physisorption of G, A, T, andC on the BN sheet (graphene) induces a small interfacial dipole, giving rise to an energy shift in the workfunction by 0.11 (0.22), 0.09 (0.15), − PACS numbers: 68.43.Bc, 82.39.Pj, 68.43.-h
Typeset by REVTEX 1 . INTRODUCTION
The interaction of DNA nucleobases with inert surfaces has attracted much attention becauseof its importance for molecular recognition and self-organization processes.
Indeed, a greatnumber of theoretical studies for the adsorption of the four DNA nucleobases [guanine (G), ade-nine (A), thymine (T), and cytosine (C)] on graphene have been performed to explore the bindingmechanism and the relative binding strength of G, A, T, and C.
These essentially planar base-graphene model systems can simplify the structural complexity of a full three-dimensional DNAdouble-stranded or single-stranded polymer adsorbed on graphene, to provide a possibility for di-rect experimental characterization of the molecular interactions with graphene. According to pre-vious density-functional theory (DFT) calculations carried out within the local density approxima-tion (LDA), the binding energy of the nucleobases on graphene varies in the following hierarchy:G > A ≈ T ≈ C. Calculations using the more accurate second-order Møller-Plesset perturbation the-ory (MP2), as well as other calculations utilizing DFT methods including van der Waals (vdW)interactions, obtained binding energy strengths of nucleobases with graphene in the orderingof G > A > T > C, consistent with the single solute adsorption isotherm study at the graphite-waterinterface. The same trend was also confirmed using isothermal titration calorimetry. In con-trast to the relatively large number of studies involving graphene, there have been relatively fewstudies concentrating on the interaction of DNA with the heterogeneous boron nitride (BN) sheet,which has been successfully fabricated through the micromechanical cleavage method and thechemical-solution-derived method. The hexagonal BN sheet exhibits the same honeycomb lattice structure as graphene. However,the electronic properties of the two sheets are drastically different from each other: graphene is agapless semimetal with the nonpolar nature of the homonuclear C − C bond, while the BN sheet isan insulator with the polar nature underlying the charge transfer between its constituent B and Natoms.
It is thus interesting to investigate and compare how such different electronic propertiesof the BN sheet and graphene affect the binding mechanism and the relative binding strength of thefour nucleobases. Using LDA, Lin et al . showed that the nucleobase molecules are bound to theBN sheet via a polar electrostatic interaction, indicating that the interaction in the base-BN systemsis somewhat different from the p - p interaction between the nucleobases and the nonpolar graphenesheet. However, calculations based on LDA may not be reliable for this base-BN systems, sinceLDA cannot correctly describe the long-ranged vdW interactions.2n the present work, we investigate the adsorption of the four DNA nucleobases on the BNsheet and graphene, using vdW energy-corrected DFT (DFT+vdW scheme ) calculations and, forcomparison, LDA as well as generalized gradient approximation (GGA) calculations. Somewhatsurprisingly, we find that the binding energy for a given base molecule is very similar on both theBN sheet and graphene. According to our analysis, it is revealed that despite the large differencesin the individual atomic polarizabilities between the BN sheet and graphene, the vdW energybetween adsorbed molecule and the BN sheet is nearly equal to the corresponding one in thebase-graphene system, resulting in very similar contributions of vdW interactions to the bindingenergy. We find that the vdW interactions between base molecule and its substrate determine thesequence of the binding energy as G > A > T > C. Here, the contribution of vdW interactions tothe binding energy amounts to ∼ II. COMPUTATIONAL METHODS
The DFT+vdW, GGA, and LDA calculations were performed using the FHI-aims codefor an accurate, all-electron description based on numeric atom-centered orbitals, with “tight”computational settings and accurate tier 2 basis sets. Calculations with larger tier 3 basis setsshow that our binding energies are converged to within 0.01 eV. For the exchange-correlationenergy, we employed the LDA functional of Ceperley-Alder and the GGA functional of Perdew-Burke-Ernzerhof (PBE). The DFT+vdW scheme was combined with the PBE functional, sincePBE tends to underestimate the binding energy at organic/graphene interfaces. In this PBE+vdWscheme, the total energy is composed of the PBE energy ( E PBE ) and the vdW energy ( E vdW ) whichis given by a sum of pairwise interatomic C R − terms: E vdW = − (cid:229) A , B f damp ( R AB , R A , R B ) C , AB R − AB , (1)where R AB is the distance between atoms A and B , C , AB is the corresponding C coefficient, R A and R B are the vdW radii, and f damp ( R AB , R A , R B ) is a damping function eliminating the R − AB singularityat small distances. Here, the C coefficients were computed in a first principles way from the PBEground-state electron density using the recently developed DFT+vdW scheme. × k -spaceintegration was done with a single G point in the Brillouin zone of the 5 × III. RESULTS AND DISCUSSION
We begin by describing the equilibrium structures of adsorbed G, A, T, and C on graphene ob-tained using the LDA, PBE, and PBE+vdW schemes. On the basis of previous theoretical calcula-tions, we optimize the AB-stacking-like arrangements of all four nucleobases on graphene.Here, we use the optimized lattice constant of graphene as 2.445, 2.467, and 2.465 ˚A (see TableI) for LDA, PBE, and PBE+vdW, respectively. The optimized AB-stacking-like structures for ad-sorbed G, A, T, and C on graphene are very similar to the corresponding ones on the BN sheet (seeFig. 1). Table II lists the vertical distance between the base molecule and graphene sheet, obtainedusing LDA, PBE, and PBE+vdW. We find that LDA, PBE, and PBE+vdW give the values of thevertical distance ranging 3.08 ∼ ∼ ∼ E b for the four base-graphene systems using LDA, PBE, andPBE+vdW are listed in Table III. We find that LDA (PBE; PBE+vdW) gives E b = 0.72 (0.14;1.18), 0.55 (0.06; 1.00), 0.54 (0.08; 0.95), and 0.56 (0.13; 0.93) eV for adsorbed G, A, T, andC on graphene, respectively. Thus, the binding sequence of the four nucleobases is G > A ≈ T ≈ Cfor LDA and G > A > T > C for PBE+vdW. This trend of the binding sequence for the four base-graphene systems agree well with previous theoretical results (see Table III), though the mag-nitudes of E b vary depending on the employed implementations of various computational meth-ods. It is notable that PBE gives lower binding energies of less than ∼ a) (b)(c) (d) FIG. 1: (Color online) Top and side views of the optimized structures of adsorbed (a) G, (b) A, (c) T, and(d) C on the BN sheet, respectively. The circles represent B, C, N, O, and H atoms with decreasing size.For distinction, N atoms on the BN sheet (nucleobases) are drawn in light (dark) color. The vertical planealong the dashed line is taken for the contour plot in Fig. 4. relatively larger vertical distances around ∼ p − p stacking interactions between the base molecule and graphene. We also notethat LDA predicts relatively lower binding energies yet smaller vertical distances compared withthose obtained using PBE+vdW.To assess the contribution of vdW interactions to the binding energy, we decompose thePBE+vdW binding energy into two parts computed from E PBE and E vdW : E b = E b , PBE + E b , vdW , (2)where E b , PBE = − [ E PBE ( base / sub ) − E PBE ( base ) − E PBE ( sub ) ] and E b , vdW = − [ E vdW ( base / sub ) − E vdW ( base ) − E vdW ( sub ) ], in which “sub” stands for “substrate”. Figure 2 shows E b , vdW for the5 ABLE I: Optimized lattice constant (in ˚A) of the BN and graphene sheets obtained using LDA, PBE, andPBE+vdW, in comparison with previous theoretical results.LDA PBE PBE+vdWBN This 2.489 2.513 2.510Ref. 32 2.49Ref. 33 2.511graphene This 2.445 2.467 2.465Ref. 30 2.445Ref. 31 2.47TABLE II: Calculated vertical distance (in ˚A) between the base molecule and BN or graphene sheet,obtained using LDA, PBE, and PBE+vdW. G A T CBN LDA 3.03 3.04 3.08 3.12PBE 3.80 3.94 3.96 4.04PBE+vdW 3.21 3.25 3.27 3.24graphene LDA 3.08 3.17 3.10 3.12PBE 3.95 4.00 4.02 3.97PBE+vdW 3.26 3.29 3.29 3.27 four base-graphene systems. We find that adsorbed G, A, T, and C on graphene have E b , vdW ( E b , PBE ) = 1.18, 1,10, 1,02, and 0.94 (0.00, − − − E b = 1.18,1.00, 0.95, and 0.93 eV, respectively. Thus, for all four nucleobases, the contribution of vdWinteractions to the binding energy amounts to ∼ E b , vdW due to the use of two different adsorption structures inthe PBE+vdW and PBE calculations (see Table II). It is likely that the relatively shorter verticaldistance in PBE+vdW compared with that in PBE gives rise to the Pauli repulsion between p E b , PBE . G A T C E b , v d W ( e V ) M-C
G A T C E b , v d W ( e V ) M-N M-B
FIG. 2: (Color online) Calculated E b , vdW for adsorbed G, A, T, and C on the graphene (top panel) and BNsheets (bottom panel). M-C represents the value for the base-graphene systems. For the base-BN systems,the two components are decomposed: M-B (M-N) represents the component arising from the atomic pairsbetween the constituent atoms in the base molecule and the B (N) atom.TABLE III: Calculated binding energies (in eV) of G, A, T, and C adsorbed on the BN and graphene sheets,in comparison with previous theoretical results. G A T CBN LDA This 0.75 0.56 0.57 0.59Ref. 22 0.69 0.58 0.56 0.54PBE This 0.15 0.07 0.08 0.13PBE+vdW This 1.18 1.01 0.94 0.93graphene LDA This 0.72 0.55 0.54 0.56Ref. 10 0.61 0.49 0.49 0.49PBE This 0.14 0.06 0.08 0.13PBE+vdW This 1.18 1.00 0.95 0.93Ref. 12 0.99 0.85 0.76 0.76vdW-DF Ref. 12 0.74 0.63 0.60 0.58 In Fig. 2, it is clearly seen that the binding energy sequence G > A > T > C is determined byvdW interactions between the base molecule and graphene. Since the vdW energy in the presentPBE+vdW scheme is given by a sum of pairwise interatomic C R − terms, we can say that the7agnitude of the effective C , i j coefficient between the base molecule and the C atom of grapheneis in the same order of G > A > T > C as the binding energy, consistent with a previous theoreticalstudy that the strength of the binding energy is governed by the polarizabilities of the basemolecules which are in the order of G > A > T > C.Next, we study the adsorption of four nucleobases on the BN sheet using the LDA, PBE, andPBE+vdW schemes. The optimized PBE+vdW structures for adsorbed G, A, T, and C on the BNsheet are respectively shown in the panels (a), (b), (c), and (d) of Fig. 1, showing the same AB-stacking-like arrangement as the case of the base-graphene systems. In Table II, we find that LDA,PBE, and PBE+vdW give the values of the vertical distance ranging 3.03 ∼ ∼ ∼ − N bond. On the other hand, either PBE or PBE+vdW gives almostthe same binding energy on the graphene and BN sheets, indicating that each base molecule bindsto the two sheets with a nearly equal binding strength. Indeed, PBE+vdW predicts that adsorbedG, A, T, and C on the BN sheet have E b , vdW = 1.16, 1.09, 0.99, and 0.93 eV, respectively. Thesevalues are very close to the corresponding ones (1.18, 1,10, 1,02, and 0.94 eV) on graphene. Tounderstand this similarity of E b , vdW on the two substrates, we decompose E b , vdW obtained on theBN sheet into two components: i.e., one (the other) component arising from the atomic pairsbetween the constituent atoms in base molecule and the B (N) atom. Such decompositions forthe four base-BN systems are displayed in Fig. 2. We find that the ratio of magnitudes of thetwo components in all base-BN systems is about 8:5, indicating that the effective C , i j coefficientbetween the base molecule (M) and the B atom is greater than that between M and the N atomby a factor of ∼ E b , vdW in the base-graphene and base-BN systemsare very close to each other, the value of ( C , M − B + C , M − N )/2 can be nearly equal to the value of C , M − C . The interesting conclusion from these results is that, despite the different bonding natures(i.e., non-polar and polar) of the graphene and BN sheets, the vdW interactions between eachnucleobase molecule and the two substrates are close to each other, resulting in similar bindingenergies in the base-graphene and base-BN systems (see Table III). It is noteworthy that the in-8lane polarizability of graphene and BN sheet would be very different, in the sense that the morelocalized electronic density of the polar network of B- and N-atom in the latter is more difficultto deform (from an energetic point of view) than in the more delocalized electronic density ofthe non-polar network of C-atoms in graphene. Despite this in-plane difference in polarizability,the main contribution to the vdW interaction with the p – p stacked nucleobases seems to arisehowever mainly from the eponymous p -orbitals belonging to the substrate (which are much closerin distance to the corresponding p -orbitals of the nucleobases). It is thus likely that the p − p stacking interactions on the BN sheet will be very close to those on graphene, resulting in theoverall quantitatively similar binding energy for a given nucleobase on both the BN sheet andgraphene. (a)(b) E ne r g y ( e V ) E ne r g y ( e V ) G KM G A T CG A T C
FIG. 3: (Color online) Calculated band structures of adsorbed G, A, T, and C on the (a) graphene and (b)BN sheets. The band dispersions are plotted along the symmetry lines of the Brillouin zone of the 5 × Figure 3(a) and 3(b) show the calculated PBE+vdW band structures for adsorbed G, A, T, and9 on the graphene and BN sheets, respectively. It is seen that the molecular orbitals of the fournucleobases hardly hybridize with the p states of the graphene or BN sheet. We note that theHOMO of adsorbed G, A, T, and C on the graphene (BN) sheet locates at 0.93 (1.80), 1.23 (2.04),1.53 (2.31), and 1.33 (2.17) eV below the Fermi level, respectively. Here, the HOMO positionsfollow the order of the ionization energies for the isolated base molecules G, A, T, and C which arecalculated to be 5.39, 5.48. 5.79, and 5.60 eV, respectively. Our analysis of the Mulliken chargesin the PBE+vdW calculations shows a very small charge transfer of less than 0.03 e between anyof the four nucleobases and the graphene or BN sheet. To see the rearrangement of charge at thebase-substrate interface, we calculate the charge density difference defined as Dr = r M / sub − ( r M + r sub ) , (3)where r M / sub , r M , and r sub denote the charge densities of the base-substrate system and its sepa-rated systems, i.e., isolated layer of base molecules and clean substrate, respectively. Figure 4(a)and 4(b) show Dr for adsorbed G on the graphene and BN substrates, respectively. It is seen thatthe two base-substrate systems involve charge rearrangement at the interface. This charge rear-rangement gives rise to an interfacial dipole, thereby causing the work-function shift. Thecalculated work-function shifts of all base-substrate systems are listed in Table IV. We find that,upon adsorption of G, A, T, and C on the graphene (BN) sheet, the work function increases relativeto the value of 4.24 (3.48) eV at the isolated graphene (BN) sheet by 0.22 (0.11), 0.15 (0.09), 0.01( − × value ( ∼ The work-function shift D W can be correlated with the induced interfacial dipole D p bya simple electrostatics relation D W = e D p /( e A ), where A is the area of 5 × D p as 0.065 (0.032), 0.045 (0.028), 0.002 ( − e ˚Afor adsorbed G, A, T, and C on the graphene (BN) sheet, respectively. Note that D p correspondsto the normal component of induced dipole moment directed from base molecule to substrate. Onthe basis of our PBE+vdW results, we can say that, although the binding mechanism between thenucleobases and the graphene or BN sheet is driven by the vdW interactions, the interfacial dipoleis induced upon adsorption to yield the work-function shift in the order of G > A > C > T. Here, wenote that the values of D p for adsorbed T on the graphene and BN sheets are close to zero, possiblybecause of the cancelation of inhomogeneous interfacial dipole moments.10 a)(b) FIG. 4: (Color online) Calculated charge density difference Dr for adsorbed G on the (a) graphene and (b)BN substrates. The contour plot in (a) is drawn in the vertical plane along the dashed line in Fig. 1(a).The same vertical plane is also used in (b). The first solid (dashed) line is at 0.0004 ( − e / ˚A withspacings of 0.0004 e / ˚A .TABLE IV: Calculated work-function shift (in eV) upon physisorption of nucleobases G, A, T, and C onthe BN and graphene sheets. The reference work functions of pristine BN and graphene sheets are given inthe last column (in eV). G A T C pristineBN + + − + + + + + IV. SUMMARY
We have investigated the adsorption of the four DNA nucleobases on the BN sheet and ongraphene, using the LDA, PBE, and PBE+vdW schemes. The calculated binding energies of thefour nucleobases on the two different substrates were predicted in the order of PBE+vdW > LDA > PBE. We found that the vdW interactions between each base molecule and the two sheets arevery close to each other, giving rise to similar binding energies in the base-BN and base-graphene11ystems. Here, the magnitudes of the vdW interactions range from 0.9 to 1.2 eV, indicating astrong physisorption. We also found that the variation of vdW interactions depending on the basemolecules determines the sequence of the binding energy as G > A > T > C, following the hierarchyof polarizabilities of the four DNA nucleobases. Our analysis shows that this physisorption inducesan interfacial dipole between the base molecule and the substrate, leading to a small change in thework function relative to isolated graphene and BN sheets.
Acknowledgement.
This work was supported by a National Research Foundation of Korea (NRF)grant funded by the Korean Government (MEST) (no. 2011-0031286), the Sweden-Korea Re-search Cooperation Programme of the Swedish Foundation for International Cooperation in Re-search and Higher Education (STINT) through Grant no. 2011/036, and KISTI supercomputingcenter through the strategic support program for the supercomputing application research (KSC-2012-C3-18). J.H.L. acknowledges support from the TJ Park Foundation. ∗ Corresponding author: [email protected] Z. S. Siwy and M. Davenport, Nat. Nanotechnol. , 697 (2010). M. Liu, H. Zhao, S. Chen, H. Yu, and X. Quan, Chem. Commun. , 564 (2012). H. W. Ch. Postma, Nano Lett. , 420 (2010). F. Lu, F. Wang, L. Cao, C. Y. Kong, and X. Huang, Nanosci. Nanotechnol. Lett. , 949 (2012). R. H. Scheicher, A. Grigoriev, and R. Ahuja, J. Mater. Sci. , 7439 (2012). S. Mukhopadhyay, R. H. Scheicher, R. Pandey, and S. P. Karna, J. Phys. Chem. Lett. , 2442 (2011). S. 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