Physisorption of Nucleobases on Graphene
Physisorption of Nucleobases on Graphene
S. Gowtham1, Ralph H. Scheicher1,2, Rajeev Ahuja2,3, Ravindra Pandey1,∗ and Shashi P. Karna4
1Department of Physics and Multi-Scale Technologies Institute,
Michigan Technological University, Houghton, Michigan 49931, USA
2Condensed Matter Theory Group, Department of Physics,
Box 530, Uppsala University, S-751 21 Uppsala, Sweden
3Applied Materials Physics, Department of Materials and Engineering,
Royal Institute of Technology (KTH), S-100 44 Stockholm, Sweden and
4US Army Research Laboratory, Weapons and Materials Research Directorate,
ATTN: AMSRD-ARL-WM; Aberdeen Proving Ground, Maryland 21005-5069, USA
(Dated: October 24, 2018)
We report the results of our first-principles investigation on the interaction of the nucleobases
adenine (A), cytosine (C), guanine (G), thymine (T), and uracil (U) with graphene, carried out
within the density functional theory framework, with additional calculations utilizing Hartree–Fock
plus second–order Møller–Plesset perturbation theory. The calculated binding energy of the nucle-
obases shows the following hierarchy: G > T ≈ C ≈ A > U, with the equilibrium configuration
being very similar for all five of them. Our results clearly demonstrate that the nucleobases exhibit
significantly different interaction strengths when physisorbed on graphene. The stabilizing factor
in the interaction between the base molecule and graphene sheet is dominated by the molecular
polarizability that allows a weakly attractive dispersion force to be induced between them. The
present study represents a significant step towards a first-principles understanding of how the base
sequence of DNA can affect its interaction with carbon nanotubes, as observed experimentally.
PACS numbers: 68.43.-h, 81.07.De, 82.37.Rs
DNA-coated carbon nanotubes represent a hybrid sys-
tem which unites the biological regime and the nanoma-
terials world. They possess features which make them
attractive for a broad range of applications, e.g., as an
efficient method to separate carbon nanotubes (CNTs)
according to their electronic properties [1, 2, 3], as highly
specific nanosensors, or as an in vivo optical detector for
ions. Potential applications of single-stranded DNA (ss-
DNA) covered CNTs range from electron sensing of vari-
ous odors [4], to probing conformational changes in DNA
triggered by shifts in the surrounding ionic concentration
[5], and detection of hybridization between complemen-
tary strands of DNA [6, 7]. The interaction of DNA with
CNT is not limited to the outer surface of the tube; it
has also been experimentally demonstrated that ssDNA
can be inserted into a CNT [8], further enhancing the
potential applications of this nano-bio system.
The details of the interaction of DNA with CNTs
have not yet been fully understood, though it is gen-
erally assumed to be mediated by the π-electron net-
works of the base parts of DNA and the graphene-like
surface of CNTs. One would like to obtain a better un-
derstanding of the binding mechanism, and the relative
strength of base-CNT binding as it is indicated experi-
mentally from sequence-dependent interactions of DNA
with CNTs [3, 4]. In this Letter, we present the results
of our first-principles study of the interaction of nucle-
obases with a graphene sheet as a significant step towards
a deeper understanding of the interaction of ssDNA with
∗Corresponding authors. E-mail: rhs@mtu.edu, pandey@mtu.edu
CNTs.
Previous theoretical studies focused on the adsorption
of the nucleobase adenine on graphite [9]. In the present
study, we have considered all five nucleobases of DNA
and RNA, namely the two purine bases adenine (A) and
guanine (G), and the three pyrimidine bases cytosine (C),
thymine (T), and uracil (U). Our specific interest is to
assess the subtle differences in the adsorption strength of
these nucleobases on graphene, which in turn will allow
us to draw conclusions for the interaction of DNA and
RNA with CNTs as well.
Calculations were performed using the plane-wave
pseudopotential approach within the local density ap-
proximation (LDA) [10, 11] of density functional theory
(DFT) [16], as implemented in the Vienna Ab-initio Sim-
ulation Package (vasp) [17]. The cutoff energy was set
to 850 eV. For k-point sampling of the Brillouin zone
we used the 1 × 1 × 1 Monkhorst-Pack grid [18], which
we found from benchmark calculations to yield identical
results as a 3× 3× 1 Monkhorst-Pack grid would.
A 5×5 array of the graphene unit cell in the x-y plane
and a separation of 15 Å between adjacent graphene
sheets in the z-direction was found to be a suitable choice
to represent the supercell. The base molecules were ter-
minated at the cut bond to the sugar ring with a methyl
group in order to generate an electronic environment in
the nucleobase more closely resembling the situation in
DNA and RNA rather than that of just individual iso-
lated bases by themselves. This has the additional bene-
fit that a small magnitude of steric hindrance can be ex-
pected from the methyl group, quite similar to the case
in which a nucleobase with attached sugar and phosphate
group would interact with graphene.
http://arxiv.org/abs/0704.1316v1
mailto:rhs@mtu.edu, pandey@mtu.edu
For each of the five nucleobases, an “initial force re-
laxation” calculation step determined the preferred ori-
entation and optimum height of the planar base molecule
relative to the graphene sheet. A slice of the potential
energy surface was then explored by translating the re-
laxed base molecules in a fixed orientation parallel to the
graphene plane in steps of 0.246 Å along the lattice vec-
tors of graphene, covering its entire unit cell by a mesh
of 10 × 10 scan points. The separation between base
molecule and graphene sheet was held fixed at the opti-
mum height determined previously. The determination
of the minimum total energy configuration was then fol-
lowed by a 360◦ rotation of the base molecules in steps of
5◦ to probe the dependence of the energy on the orienta-
tion of the base molecules with respect to the underlying
2-D graphene sheet. The configuration yielding the mini-
mum total energy was used in the final optimization step
in which all atoms in the system were free to relax. We
would like to emphasize here that for all five nucleobases,
the eventually determined equilibrium configuration was
characterized by a separation between base and graphene
sheet that was equal to the optimum height chosen in the
previous lateral potential energy surface scan.
An additional set of calculations was performed us-
ing the ab initio Hartree–Fock approach coupled with
second–order Møller–Plesset perturbation theory (MP2)
as implemented in the gaussian 03 suite of programs
[19]. Due to the use of localized basis sets (rather than
plane-wave), the system here consisted of the five nucle-
obases on top of a patch of nanographene [20], i.e., a finite
sheet containing 28 carbon atoms. The LDA optimized
configuration and the 6-311++G(d,p) basis sets for C,
H, N and O atoms were used for the MP2 calculations.
The first optimization step involving the “initial force
relaxation” led to a configuration of all five nucleobases
in which their planes are likewise oriented almost exactly
parallel to the graphene sheet with a separation of about
3.5 Å, characteristic for π–π stacked systems [21]. The in-
teraction of the attached methyl group with the graphene
sheet results in a very small tilt of the molecule, with an-
gles less than 5◦.
The base is translated 2.461 Å along both graphene
lattice unit vectors respectively (maintaining a constant
vertical distance of 3.5 Å from the sheet, as determined
in the previous step), and rotated 360◦ in the equilibrium
configuration with respect to the configuration obtained
after the “initial force relaxation” step in the optimiza-
tion procedure. From the optimization steps involving
the translational scan of the energy surface, it is appar-
ent that the energy barriers to lateral movement of a
given base can range from 0.04 to 0.10 eV (Fig. 1), thus
considerably affecting the mobility of the adsorbed nucle-
obases on the graphene sheet at room temperature, and
constricting their movement to certain directions. The
rotational scans carried out by us found energy barriers
of up to 0.10 eV, resulting in severe hindrance of changes
in the orientation of the adsorbed nucleobase.
In their equilibrium configuration, three of the five
bases tend to position themselves on graphene in a con-
figuration reminiscent of the Bernals AB stacking of two
adjacent graphene layers in graphite (Fig. 2). Virtu-
ally no changes in the interatomic structure of the nu-
cleobases were found in their equilibrium configurations
with respect to the corresponding gas-phase geometries,
as it could be expected for a weakly interacting system
such as the one studied here. A notable exception is the
RC−O in guanine which shows a 10% contraction upon
physisorption of the molecule on graphene.
The stacking arrangement shown in Fig. 2 can be un-
derstood from the tendency of the π–orbitals of the nucle-
obases and graphene to minimize their overlap, in order
to lower the repulsive interaction. The geometry deviates
from the perfect AB base-stacking as, unlike graphene,
the six- and five-membered rings of the bases possess a
heterogeneous electronic structure due to the presence of
both nitrogen and carbon in the ring systems. In ad-
dition, there exist different side groups containing CH3,
NH2, or O, all of which contribute to the deviation from
the perfect AB base-stacking as well. Adenine, thymine
and uracil display the least deviation from AB stacking
(Fig. 2) out of the five nucleobases. For guanine and cy-
tosine on the other hand, there is almost no resemblance
to the AB stacking configuration recognizable (Fig. 2).
We calculated the binding energy for all five nucle-
obases. The binding energy of the system consisting of
the nucleobase and the graphene sheet is taken as the
energy of the equilibrium configuration with reference to
the asymptotic limit obtained by varying the distance be-
tween the base and the graphene sheet in the z-direction
(Table I). Within LDA, we found adenine, cytosine and
thymine to all possess nearly identical binding energies
of about 0.49 eV, while guanine with 0.61 eV is bound
more strongly, and uracil with 0.44 eV somewhat more
weakly.
It is somewhat surprising that guanine and adenine
would possess such different physisorption energies, de-
spite both containing a five- and a six-membered ring
and featuring relatively similar molecular structures. A
closer analysis of the various contributions to the total
energy (Fig. 3) reveals that the Kohn-Sham kinetic en-
ergy displays a slightly more pronounced minimum for
guanine than for adenine, and that the position of that
minimum is shifted by about 0.25 Å towards the graphene
sheet. The exchange-correlation energy drops off some-
what more rapidly in the case of adenine; however, the
difference to the case for guanine is only very small.
Table I also includes the polarizabilities of the nucle-
obases calculated at the MP2 level of theory. The polar-
izability of the nucleobase [22], which represents the de-
formability of the electronic charge distribution, is known
to arise from the regions associated with the aromatic
rings, lone pairs of nitrogen and oxygen atoms. Accord-
ingly, the purine base guanine appears to have the largest
value, whereas the pyrimidine base uracil has the small-
est value among the five nucleobases. Our calculations
confirm this behavior.
A remarkable correlation is found when the molecu-
lar polarizabilities of the base molecules are compared
with the binding energies, in particular when the latter
are also determined at the MP2 level of theory (Table
I). Clearly, the polarizability of a nucleobase is the key
factor which governs the strength of interaction with the
graphene sheet. This behavior is expected for a system
that draws its stabilization from van der Waals (vdW)
dispersion forces, since the vdW energy is proportional
to the polarizabilities of the interacting entities. The
observed correlation thus strongly suggests that vdW in-
teraction is indeed the dominant source of attraction be-
tween graphene and the nucleobases.
The MP2 binding energies are systematically larger
than those calculated within the LDA approximation
(Table I). This is due to the well established fact that
MP2 provides a more accurate treatment of the vdW
interaction than LDA. We note that the adsystem con-
sisting of the base and the sheet is not bound at the
Hartree-Fock level of theory, which underscores the im-
portance of electron correlation in describing the weak
vdW interactions in this system.
In the equilibrium configuration, a redistribution of the
total charge density within a given base seems to appear.
From an analysis of the Mulliken charges for the MP2
calculations, we also find a negligible charge transfer (<
0.02 e) between any of the five nucleobases and patch
of nanographene in the equilibrium configuration. Elec-
trostatic interactions in the adsystem are therefore very
unlikely to contribute to the interaction energy.
In summary, we investigated the physisorption of
the five DNA/RNA nucleobases on a planar sheet of
graphene. Our first-principles results clearly demon-
strate that the nucleobases exhibit significantly differ-
ent interaction strengths when physisorbed on graphene.
This finding represents an important step towards a bet-
ter understanding of experimentally observed sequence-
dependent interaction of DNA with CNTs [3, 4]. The
calculated trend in the binding energies strongly sug-
gests that the polarizability of the base molecules de-
termines the interaction strength of the nucleobases with
graphene. As graphene can be regarded as a model sys-
tem for CNTs with very small surface curvature, our con-
clusions should therefore also hold for the physisorption
of nucleobases on large-diameter CNTs. Further stud-
ies involving the investigation of nucleobases interacting
with small-diameter CNTs are currently underway.
The authors acknowledge helpful discussions with Prof.
Roberto Orlando of the University of Turin, Italy, and
with Dr. Takeru Okada and Prof. Rikizo Hatakeyama of
Tohoku University, Japan. S.G., R.H.S., and R.P. would
like to thank DARPA for funding. R.H.S. and R.A. are
grateful to the Swedish National Infrastructure (SNIC)
for computing time. R.H.S. acknowledges support from
EXC!TiNG (EU Research and Training Network) under
contract HPRN-CT-2002-00317. The research reported
in this document was performed in connection with con-
tract DAAD17-03-C-0115 with the U.S. Army Research
Laboratory.
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base Eb(LDA) [eV] Eb(MP2) [eV] α [e
G 0.61 1.07 131.2
A 0.49 0.94 123.7
T 0.49 0.83 111.4
C 0.49 0.80 108.5
U 0.44 0.74 97.6
TABLE I: Binding energy Eb of the DNA/RNA nucleobases
with graphene as calculated within LDA are compared with
binding energy and polarizability α from MP2 calculations.
FIG. 1: Potential energy surface (PES) plot (in eV) for gua-
nine on graphene. Qualitatively similar PES plots were ob-
tained for the other four nucleobases. Approximately a 3 × 3
repetition of the unit cell is shown. The energy range between
peak and valley is approximately 0.1 eV. Energy barriers of
only about 0.04 eV separate adjacent global minima.
FIG. 2: Equilibrium geometry of nucleobases on top of
graphene: (a) guanine, (b) adenine, (c) thymine, (d) cyto-
sine, and (e) uracil.
-1.0 -0.5 0.0 0.5 1.0
displacement [A]
-1.0 -0.5 0.0 0.5 1.0
displacement [A]
FIG. 3: Plot of the relative total (black), exchange-correlation
(blue) and kinetic energy (red) of guanine (top) and adenine
(bottom) adsorbed on graphene calculated as a function of
the displacement from their respective equilibrium position.
