Supplemental Material for
Nucleobase adsorbed at graphene devices: enhance
bio-sensorics?
Bo Song, 1* Gianaurelio Cuniberti,2 Stefano Sanvito,3 Haiping Fang1,†
1
Laboratory of Physical Biology, Shanghai Institute of Applied Physics, Chinese
Academy of Sciences, P.O. Box 800-204, Shanghai 201800, China
2
Institute for Materials Science and Max Bergmann Center of Biomaterials, Dresden
University of Technology, 01062 Dresden, Germany
3
†
School of Physics and CRANN, Trinity College, Dublin 2, Ireland
Corresponding author. Email: fanghaiping@sinap.ac.cn
*Corresponding author. Email: bosong@sinap.ac.cn
SI. Methods for the density functional theory (DFT) calculation
The devices were investigated by using ab initio calculations based on density
functional theory (DFT) as implemented in the SIESTA packageS1,S2 and with the
Perdew-Burke-Ernzerhof (PBE) form of the generalized gradient approximation
(GGA) to the exchange-correlation functional.S3 In the calculations, only the valence
orbitals were treated self-consistently, namely we consider 1s for H, 2s2p for C, N and
O, and 3s3p for S and Al. The interaction between the valence electrons and the core
ions were treated at the level of norm-conserving pseudopotentialsS4 with separable
non-local operators.S5 Atomic orbitals with a double-ζ polarization were used to
expand the electron wave functionsS1,S2,S6 with a real-space equivalent mesh energy
cutoff of 180 Ry. We used 0.02 Ry as the confinement-energy shift that defines the
cutoff radii of the atomic orbitals. All of the geometries were optimized using the
conjugate gradient method39 until the residual Hellmann-Feynman forces acting on
any atom were smaller than 0.05 eV/Å.
SII. Setup of the molecular device for studying the nucleobase effects on GNR
A seven-armchair GNR, 15.63 Å  7.38 Å in size, formed the conducting channel for
all of the devices investigated. The GNR lattice was terminated in an armchair
structure along the long side, and the edges were passivated by hydrogen. Along the
small ends, the lattice had a zigzag configuration, and it was connected by three sulfur
atoms to the hollow sites of the Al(111) electrodes. The experimental lattice constant
of Al, a = 4.050 Å, was used for the two electrodes,S7 which were periodic and
defined by a supercell containing 10 Al atoms. The scattering region cell (the
junction), namely the region for which the electrostatic potential is calculated
self-consistently, included the GNR, the six sulfur atoms and part of the electrodes, as
shown in Fig. 1 in our manuscript. Overall, our scattering region had a chemical
composition of Al100S6C56H16, since five Al monolayers were included at each side of
the GNR. This setup is sufficient to ensure appropriate electron screening and
therefore to correctly impose the transport boundary conditions. After fixing the
electrode atoms in their bulk positions at an electrode-electrode distance of 23.0 Å,
the geometry was optimized. This optimized structure was then used to investigate the
effect of the adsorption of nucleobases on the electronic transport across the
nano-ribbon.
SIII.
Methods for the calculations of electron transport
Our calculations for the electronic transport were based on DFT and the
non-equilibrium Green’s function method (NEGF-DFT), as implemented in the
Smeagol code.S8-S10 An electronic temperature of 300 K was applied throughout the
calculation. To reduce the computational overheads and to make the calculations more
tractable, a single ζ was used as the basis set for Al, whereas a double ζ basis was
adopted for the orbitals of the other species (C, H, N, O and S). The use of a reduced
basis for the electrodes is a well-established practice that has been justified and
documented in the literature.S11,S12 In calculating the charge density, the complex part
of the Green’s function integral was computed using 400 energy points on the
imaginary semicircle, 50 points along the line parallel to the real axis, and 20 poles. In
addition, 1000 integration points were taken for the integral over the real energies
necessary at finite bias. All of the calculations for electrodes were carried out with
periodic boundary conditions over the plane perpendicular to the transport direction
by sampling 100 k-points in the Brillouin zone.
SIV.
Methods for molecular dynamics (MD) simulations
The entire device was first immersed in TIP3P water molecules,S13 and its atomic
positions were not allowed to relax. MD was then performed for only the nucleobase
and the water. Our MD simulations were performed with Gromacs 4.0 S14 and the
Amber03 force field,S15 within a constant-temperature (300 K) and constant-volume
canonical ensemble. A cut-off of 1.0 nm was applied to the Lennard-Jones interaction,
and the reciprocal space portion of the electrostatic interactions was treated with the
PME method.S16
SV. Nucleobase skating on the GNR surface and its discussion
Our molecular-dynamics simulations showed that the nucleobase was efficiently
confined to the graphene nanoribbon (GNR) and skated on the surface of GNR, as
presented in the mpg-file (animation_top-view.mpg) for the top view of the skating,
the mpg-file (animation_side-view.mpg) for the side view. To describe such
phenomena clearly, we calculated the atomic distribution of the nucleobases A and C
in the direction vertical to the GNR surface for all MD simulation times. The results
are presented in Fig. S1. The full width at half maximum (FWHM) of the distribution
was only 0.6 Å for both nucleobases, indicating that the distribution was narrow, and
the nucleobases parallel to the GNR surface remained there even in water at room
temperature. Here, it is noted that in a real device, GNR would be on a substrate. If
the applied substrate cannot confine the nucleobases of an ssDNA well like the
graphene does, namely, the adsorption energy of the base on the substrate is clearly
less than the case on the graphene, the nucleobasis of ssDNA only slide within the
nanoribbon, and cannot slide off. In this case, the detection is feasible.
FIG. S1. (Color online) Probability of the atoms in the nucleobases A (red curve)
and C (blue curve) as a function of the distance above the GNR surface.
SVI.
Transmission spectra for the electronic transport
To explain the details of the I-V curves, in Fig. S2 we present the transmission spectra
T(E−EF) as a function of energy, E (EF is the Fermi energy of the electrodes), at the
following four voltages: 0.0 V, 0.2 V, 0.4 V and 0.6 V. We present three cases: 1)
GNR, 2) A-on-GNR and 3) G-on-GNR.
FIG. S2. (Color online) Transmission spectra as a function of energy for the
pristine GNR (left), and for the GNRs with adsorbed A (middle) and G (right).
The curves are plotted for different applied biases: 0.0 V (first row), 0.2 V
(second row), 0.4 V (third row) and 0.6 V (fourth row). The two vertical blue
lines denote the bias window.
First, we noted that, under zero-bias conditions, the spectrum of A-on-GNR was
almost identical to that of the pristine GNR over the entire explored energy window,
indicating that the effect of the adsorbed adenine on the electronic structure of the
GNR is weak. In contrast, the spectrum of G-on-GNR around E = -0.1 eV was
different from that of the nano-ribbon alone. This difference is an indication of
stronger electrical coupling between graphene and the adsorbate. However, the
differences were almost negligible around EF, so that the low bias current was similar
for all three structures. As the bias window opens to 0.2 V (see the second row in Fig.
S1), the spectra of the pristine GNR, A-on-GNR and G-on-GNR become similar.
Consequently, the current is also similar. A further bias increase to 0.4 V did not
induce any appreciable difference between the spectra of A-on-GNR and GNR, but
the spectrum of G-on-GNR began to differ. This point is when the G-on-GNR current
became lower than that of the pristine GNR and of A-on-GNR. Finally, at V = 0.6 V,
the differences between G-on-GNR and both the pristine GNR and A-on-GNR were
amplified in T(E). The spectrum of guanine appeared to become sparser across the
considered bias window. This finding correlates well with the smaller electrical
current for G-on-GNR presented in Fig. 3(a) in our manuscript.
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