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Low Coverage Palladium Adsorption on Graphene: First Principles Study

Article in Quantum Matter · October 2015

DOI: 10.1166/qm.2015.1215

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 RESEARCH ARTICLE
Copyright © 2015 American Scientific Publishers Quantum Matter
All rights reserved
Printed in the United States of America
Vol. 4, 1–6, 2015

Low Coverage Palladium Adsorption on Graphene:

First Principles Study
Yusuf Zuntu Abdullahi1
2 , Md. Mahmudur Rahman1
∗ , Shamsu Abubakar1
3 ,
Rifki Muhida3 , and Henry Setiyanto4
1
Department of Physics, Faculty of Science, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
2
Department of Physics, Faculty of Science, Kaduna State University, P.M.B. 2339, Kaduna State, Nigeria
3
Department of Physics, Faculty of Science, Yobe State University, P.M.B. 1144, Yobe State, Nigeria
3
Department of Physics, Surya College of Education (STKIP Surya), Gedung SURE, Jl. Scientia Boulevard Blok U/7,
Gading Serpong, Tangerang 15810, Banten, Indonesia
4
Analytical Chemistry Research Group, Faculty of Mathematics and Natural Sciences, Institut Teknologi Bandung,
JI Ganesha No. 10, Bandung 40132, Indonesia

In this paper, we investigate stable geometries, electronic and magnetic properties of low coverage palladium
(Pd) atom adsorption on graphene using first principles calculations with the generalized gradient approximation.
Calculations show that single Pd atom located at the top of carbon atom is the energetically favorable config-
uration, and is found to be semiconductor and non-magnetic. We also compute the projected density of states
(PDOS) around Fermi level and beyond. It is found that, C-Pd covalent interaction is mainly dominated by 2pz
of C, 5s and 4d like states of Pd. For low coverage stable Pd dimer, the adsorption is characterized by strong
hybridization between the palladium atoms and the two carbon atoms bonded directly to it. A much weakening
of Pd–Pd bond is observed and the C-Pd covalent bonds mainly dominate by 2pz of C orbital indicating that
planar coating can be achieved. Thus, this work reveals that uniform coating of Pd atom can be achieved and
may be useful in transport measurements.

Keywords: Graphene, Density Functional Theory, Geometric, Electric, Magnetic Properties.

1. INTRODUCTION have theoretically investigated the geometry, electronic and mag-

The fascinating physics of graphene, a single layer of graphite,
has been one of the central interest that fuelled numerous
studies1
10–18 since its isolation.2 Due to its peculiar two dimen-
sional natures, it exhibits, unique properties such as magneto
transport,1 tunable band gap,3 extremely high carrier mobility,4
electron confinement effects5 and Klein tunneling nature.6 While
various groups have succeeded in getting isolated graphene
sheet with different techniques,7 there have also been continuing
efforts simultaneously to explore the effects of various adsorbed
guest atoms8
9 or molecules10
11 on graphene because poten-
tial applications and electronic transports properties measurement
with graphene require contact with metal electrodes.12 Moreover,
graphene has been used experimentally as a substrate for growth
of nanometer-sized crystal structures13 which indicates the possi-
bility of controlling the structure to produce viable future nanode-
vices. Among the widely studied single atoms,14
15 dimers16
17
and molecules10 on graphene, research interest in transition metal
adsorption continue to grow fast and expands the ranges of appli-
cations from catalysis, spintronics to magnetic device. Hu et al.8
∗
Author to whom correspondence should be addressed.
netic properties of fifteen transition metal (TM) single atoms
adsorbed graphene system using density functional theory. Their
results indicated that the graphene properties can be effectively
tuned by TM adsorption and further give an account based on
strong covalent binding that, palladium among others can be
used as a functional material to coat uniformly graphene and
carbon nanotubes. In another recent study, Thapa et al. have stud-
ied Pd adatom and dimer adsorption on graphene with the aim
of revealing the structural, electronic and magnetic properties
and predicted the appearance of magnetic moment for palladium
dimer adsorbed in perpendicular direction,17 although no mag-
netic moment has been confirmed for Pd single atom which is
in perfect agreement with the previous works.8
15 However, they
do not reports the details electronic properties of dimer in par-
allel configurations. As predicted by Ref. [8] that uniform coat-
ing is an attractive properties of Pd different from other metal
which is significant in making contact between electrode and
graphene, therefore, it will be interesting to understand effects
of low coverage palladium atoms on the properties of graphene.
Experimentally, sundaram et al. have observed that, palladium
atoms nucleated at edges and defect of the graphene sheets by

Quantum Matter Vol. 4, No. 4, 2015 2164-7615/2015/4/001/006 doi:10.1166/qm.2015.1215 1

RESEARCH ARTICLE
electro-deposition.18 However, there are no prio reports on the
electronic structure changes of pure graphene uponparallel Pd
dimer adsorption on pure graphene. In view of this, our main
objective of this study is to contribute to the understanding of
this effect of adsorption of low coverage palladium atoms on
graphene properties. To achieve this goal, we have investigated
the various adsorption geometries and then examined the chem-
ical electronic structure of the system based on projected den-
sity of states and charge transfer of the favored configurations.
As a result of our analysis, we find strong covalent interactions
between the carbon atom in the graphene structure and the Palla-
dium atom. Moreover, the Löwdin’s charge analysis and charge
density distribution are computed to support our findings.
2. CALCULATION METHODOLOGY AND
CONVERGENCES
We have performed first principles19 calculations based on
density functional theory implemented in the QUANTUM
ESPRESSO simulation package.20 We used a plane wave basis
set to expand the wave functions. The electron–electron inter-
action is expressed within generalized gradient approximation
(GGA) and spin polarized GGA as parameterized by Perdew-
Burkew-Enzerhof21 exchange correlation scheme. The choice of
GGA is due to the performance in getting ground state proper-
ties of the combined metal graphene system. Electron-ion core
interaction is treated by ultrasoft pseudopotential for C and
Pd(4d9 5s 1 valence orbitals as in the pseudopotential file) atoms.22
All pseudopotentials can be found from the Plane-Wave Self-
Consistent Field(PWSCF) pseudopotential online references.23
To expand the wave functions, we have used plain-wave basis
with the kinetic energy cut-off of 500 eV. For integrals, smearing
is employed to aid convergences and to be specific, Marzari-
Vanderbilt method24 with small Gausian spreading of 0.03 eV
was used. For Brillouin zone (BZ) integrations, we sampled 8 ×
8 × 1 set of k-points with the Mankhorst-Pack scheme.25 In mod-
eling graphene sheet, we used 4 × 4 × 1 supercell containing 32
carbon atoms is constructed in a 3-dimensional periodic boundary
conditions with 2.46 Å in plane lattice constant which is in agree-
ment with the graphene experimental lattice parameter.26 The
graphene sheet constructed is then optimized and the inter-atom
distance was found to be 1.42 Å. To minimize the interaction
between graphene sheet and its neighboring image, a vacuum
(a)
Fig. 1. Possible adsorption sites for Pd atoms on a monolayer graphene and supercell model. (a) Three Pd adatom and dimer (perpendicular) adsorption
sites for with notations; center of hexagon (H), top of carbon atom (T) and bond center (B), (b) most stable Pd adatom adsorption on carbon atom in graphene
sheet named T (c) side view of the adsorbed parallel configuration named RT with two Pd atoms sitting directly above carbon atom in the graphene sheet.
2
Quantum Matter 4, 1–6, 2015
space of 15 Å in vertical direction is considered so that inter
adatoms and dimers interactions can be reduced. In the case
of single Pd adsorption on graphene sheet, three high symmet-
ric sites are considered. The hollow (H) site is at the center of
hexagon, the bridge site (B) at the middle point of carbon–carbon
bond and top (T) site directly above carbon atom as shown in
the Figure 1(a). For Pd atoms adsorption on graphene sheet, six
configurations are employed. Three dimer perpendicular config-
urations with lower atom bonded to graphene sheet at H, B and
T sites are denoted by PH , PB and PT respectively as shown
in Figure (a). Three dimers parallel to graphene sheet for Pd
atoms with configurations denoted as RH , having two atoms sit-
ting above two neighboring H sites, RB with its two atoms sitting
above opposite B sites and RT Having two atoms sitting above
opposite T sites on the same sheets shown in Figure 1(c). The
isolated inter dimer distance is found by optimizing dimer in a
simple cubic cell of (12×12×12 Å) dimension. Only the gamma
points of the BZ are considered during relaxation. To avoid being
trapped at meta-stable structures in the structural optimization
process, a series of static calculations are performed. In this pro-
cess the adatom is fixed at an adsorption sites with several dis-
tances along the line normal to the graphene sheet. The favored
distance from the graphene sheetis obtained from the global min-
imum of the adsorption energy curve of each adsorption site.
The stability curvesare adsorption energy versus Pd-graphene
sheet distances for three sites, H, B and T sites is shown in the
Figure 2. When stable distances for each configuration are found,
the relaxation are performed along all the atomic coordinates
but keeping the cell dimension fixed. We used Broyden-Fletcher-
Goldfarb-Shanno (BFGS) algorithm for the forces and energy
minimization process. However, after full relaxation, the dimers
were found slightly deviate slightly from their original high sym-
metric locations, and the new position shows the nearest possible
configurations.
3. RESULTS AND DISCUSSION
In present work, Pd is considered to be adsorbed on graphene
sheet at three most stable adsorption sites namely, H sites (center
of hexagon), T site (atom top site) and B site (above mid-point
of bond top site) as shown in the Figure 1(a). Table I summarizes
the details geometric stabilities parameters and magnetic moment
(b) (c)
Quantum Matter 4, 1–6, 2015 RESEARCH ARTICLE

disagreement with their favored site. The difference in adatom

Fig. 2. Adsorption energy for Pd-graphene system as a function of distance
between adatom and graphene sheet.
per unit cell for the obtained various adsorbed adatom/dimer
graphene configurations, i.e., the adsorption energy, adsorption
height above the graphene sheet, Löwdin’s charge analysis27 of
the atom in which the difference between the number of neutral
valence electron and Löwdin’s charge is regarded as the number
of electrons transferred, the angle made by atom/dimer-carbon
with bond-graphene sheet angle and the magnetic moment of the
adatom adsorbed graphene. The stability for adatom or dimer is
measured by the adsorption energy defined as
Eads = EGM − EG − nEM
in unit of eV/atom, where EGM represents the spin-polarized total
energy of the Pd graphene system, EM stands for the total energy
of the isolated single or dimer Pd and EG is the total energy
of the isolated graphene per 4 × 4 supercell. Detail discussion is
presented in the following subsections.
3.1. Adsorption of Palladium Adatom on Graphene
The adsorption energies and bond lengths listed in the Table I
suggest that the Pd adatoms are chemisorbed on graphene. The
site with the most negative adsorption energy is referred to as the
most favorable one. The most stable adsorption site for a single
Pd is T-site with corresponding adsorption energy −1.027 eV.
In comparisons to the results of the recent works for palladium
Pd adsorbed graphene8
17 we found that adsorption energy is in
adsorption energy between our calculations and the results in
Refs. [8, 17] are likely due to choices of basis functions and
exchange correlation functionals which are sensitive to the elec-
tronic configurations in the pseudopotentials used. For example,
we employed PBE functional, wave function cut-off energy of
500 eV and a RRKJ ultrasoft pseudopotential while Hu et al.8
used PBE functional, wave function of 400 eV and Vander-
bilt ultasoft pseudopotential. Although Ref. [17] reported closely
lying values between B and T sites, our result is more consis-
tent to the case of cupper (Cu) atom adsorption on graphene
reported by Wu et al.,28 since Pdatomhas similar valence orbital,
it’s expected to have the same way of interactions with the carbon
atom. Furthermore, Pd atom located at the T site shows the low-
est bond length among the rest of the stable configurations indi-
cating strong covalent bond between Pd atom and C of graphene
sheet. Additionally, for the most stable configuration, there is a
slight vertical deformation of the carbon atom right below the Pd
adatom which rises by a distance of about 0.12 Å; this is due to
direct hybridization between the carbon in the graphene and the
adatom. Figure 3(a), shows the top and side view charge den-
sity plots of the energetically stable configurations of Pd atom
and the carbon atom directly bonded. The figure reveals that the
system is stabilized under adatom adsorption with some distri-
butions of electron density between adatom and carbon atoms
around it. Moreover, the bonding between C and Pd shows that
the electronic charge density resides between the adatom and car-
bon atom in the graphene structure which suggests sharing of
(1) electron charge density between adsorbent and graphene resulting
in mutual interaction and this agrees with the a Löwdin’s charge
analysis between Pd and graphene listed in the Table I. For the
various stable adsorption sites investigated, not more than 05e
charge transfer is observed, indicating that the M–G bonds are
of covalent nature. However, in spite of charge transfer between
adatom and graphene, Pd adsorbed system shows no magnetic
moment in all the adsorption sites, which is in perfect agreement
to the reported results.8
17 Moreover, absent of magnetism is as
a result of totally bonded electrons of the Pd adatom-graphene
system, leading to there being no residual spin-polarized charge
in the system as can be seen from Figure 4.
To have an insight into theelectronic structures of the favored
single Pd configuration, Figure 4, shows spin-polarized total and
projected density of states for the most stable configuration of
the Pdadsorbed-graphene system and the nearest bonded C atom.

Table I. Details of the optimized structural properties for Palladium atom and dimer adsorbed on graphene.

Atom Site Eads (eV) h (Å) dMG (Å) dMM (Å)
MC−G   q (e) qd (e) mMG (B)

Pd H −0850 2028 2460 – 54431 9.646 9.524 000

B −0984 2140 2256 – 82015 9.558 9.558 000
T −1027 2225 2109 – 92665 9.733 9.561 000
RH −1012 2223 2657 2824 58034 9.745 (9.748) 9.538 (9.484) 000
RB −1040 2142 2273 2722 87172 9.722 (9.728) 9.482 (9.488) 000
RT −1239 2249 2130 2713 86760 9.760 (9.760) 9.477 (9.477) 000
PH −0362 2103 2536 2534 55638 9.763 (10.058) 9.223 (9.331) 081
PB −0519 2156 2344 2554 66647 9.824 (9.928) 9.355 (9.377) 126
PT −0611 2242 2330 2531 88341 9.802 (10.026) 9.327 (9.369) 215

Notes: The adsorption energies Eads , the average height of adatom over all carbon atoms hA0 , the averaged nearest neighboring metal adatom carbon bond length dMG , Löwdin total
charge q and valence d orbital charge qd , the data outside the bracket are the charge for lower atom directly bonded to graphene and the values inside the bracket are the result for
upper atom in the perpendicular dimer configurations PH PB and PT respectively whereas the parallel configurations (RH , RB and RT ) have their charges results with both atom directly
bind to graphene at their respective adsorption sites depicted by the subscripts in unit of eV, the inter dimer bond length dMM ; the
MC−G bond-graphene sheet angles (degree) and
the magnetic moments mMG of dimer adsorbed on graphene system per unit cell.

3
RESEARCH ARTICLE
Fig. 3. Charge density plots: Scale nr  signifying ranges of isodensity values in a.u. (a) Top and side view charge distribution of the most stable Pd atom-
adsorbed graphene configuration. (b) The corresponding top view charge distribution of the most stable for Pd dimer-adsorbed graphene system (c) Side view
of the perpendicular dimer adsorbed on carbon top i.e., PT configuration with white indicating charge accumulation and light pink charge depletions.
It reveals that, in spite of the low coverage single Pd adsorbed,
the Pd completely destroy the delocalized  orbital there by
modifying the electronic structure of graphene layer from semi-
metal to a semiconducting material with energy band gap of
approximately 0.49 eV at the Fermi level. The symmetric distri-
butions of density of states in both spin up and spin down even at
the vicinity of Fermi level further reveals the reasons for the zero
net magnetic moment in the system. Although charge transfer
is observed between the adatom and the graphene, no polarized
Fig. 4. The spin-polarized total and projected density of states for the ener-
getically stable single Pd adsorbed-graphene system.
4
Quantum Matter 4, 1–6, 2015
charge is found to be visible in either adatom or carbon atom
directly below it. Consistent with valence orbital available in the
pseudopotentials which is stated in Section 2, the states from
approximately −4.0 eV to 2.0 eV is partly contributed by 4d
orbitals like states and mainly dominated by the C-pz like states
with obvious shape peaks within the two regions. Moreover, at
the vicinity of Fermi energy, i.e., within approximately −2.0 eV
to −0.24 eV 3d states dominates in both spin up and spin down
states of Pd and partly contributed by pz of C states.
3.2. Palladium Adsorbed Dimer
To examine quantitatively the geometric features of the dimers Pd
adsorbed graphene system; six configurations have been consid-
ered for relaxations with two palladium atoms bind to graphene
sheet at three adsorption sites either in perpendicular or parallel
directions as discussed in the previous subsections. It is worth
noting that the rationale behind testing different configurations is
to further present an insight on the nature of the stable geometry
of the favored configurations among others even though previous
work tends to give priority to the one that yields viable physi-
cal properties.17 We summarize the adsorption energy, structural
and other physical parameter results for all the relaxed dimer
adsorbed graphene system in Table I. To insure good accuracy of
our analysis, we calculate the bond length of an isolated dimer
Pd in a 12 × 12 × 12 Å simple cubic cell. Our calculated bond
lengths for dimer differ from the previous studies by 0.035 Å.30
Comparedwith the recent reported result,17 the RT (with Pd atom
located on the opposite C atom in the graphene sheet) is energeti-
cally favorable configuration among others, and correspondingly,
the adsorption energy is found to be −1.239 eV. Interestingly, our
results report closely laying values for adsorption energy in paral-
lel configurations as compare to the recent report.17 This is due to
slight tilt by the dimer from its original high symmetric locations
after full structural relaxation in which the new positions show
the nearest stable configurations. Furthermore, from Table I, it
can be observed that, for most dimer configurations, the paral-
lel ones are energetically stable than the perpendicular ones and
correspondingly the height above graphene sheet varies accord-
ing to the adsorption sites indicating strong interactions in some
cases. This is due to net energetic contribution by each Pd atom
in contact with graphene sheet. The bond length for the stable
configuration is 2.713 Å, larger than that for the isolated dimer
by 0.235 Å, and therefore Pd–Pd is much weakened after adsorp-
tion (the bond length changes by approximately 23%). The large
Quantum Matter 4, 1–6, 2015
Fig. 5. The spin-polarized total and projected density of state for the most
stable Pd dimer adsorbed-graphene.
inter-dimer bond length suggests that dimer behaves like two
adjacent adatoms after adsorption. In addition, Figure 3(b), shows
charge distributions of the Pd dimer parallel configurations, the
weakening of the bond is evidenced by the narrow depreciation
in electron charge density between the region of palladium atoms
and carbon atom directly below it. The Löwdin charge analy-
sis (see Table I) indicates that, due to hybridization between 4d
orbitals of both Pd atoms and 5s orbitals, the two Pd atoms trans-
fers the same amount of electron (approximately 048e) to the
carbon in the graphene sheetand this agrees with the depreciation
of electron density isosurface around the region of contact carbon
bond. The rest of the structural parameters for the obtained differ-
ent palladium dimer configurations are listed in the Table I. It can
be seen that the magnetic moment per unit cell in perpendicular
configurations is found to change depending on the adsorption
site, hence induced magnetic moment depends on the adsorp-
tion positions and this is in disagreement with recent reported
result which shows closely laying values in perpendicular config-
uration adsorption sites.17 Additionally, PT configuration which
is energetically stable compare to the rest of perpendicular con-
figurations shows the highest magnetic moment. To have a bet-
ter account for the enhanced magnetic moment among others,
the bond length for the adsorbed Pd dimer, especially the lower
Pd atom directly above the carbon atom in the graphene sheet,
was checked. It can be observed in Table I, that the energetic
RESEARCH ARTICLE
preference and enhanced magnetic moment can be attributed to
the strong interaction between the two Pd atoms leaving the C
atom directly below the lower Pd atom with unpaired electrons.
Moreover, Figure 3(c), depicts the distribution of charges, the
interaction between the lower Pd and the contact carbon atom in
PT is clearly evidenced by the depreciation of the electron charge
density around the region of the interactions. The charge anal-
ysis (see Table I) shows transfer of an electron from the lower
atom to top Pd atom. Thus, lower Pd losses 0198e and a total of
0.172 electrons are transferred to the graphene sheet. This results
in polarized charges around the carbon atom in the graphene.
To explore further insight into the electronic structure changes
of the favored Pd dimer adsorbed graphene system, Figure 5
shows spin-polarized DOS distributed symmetrically for both up
and down spins. The system is found to be metallic with mag-
netic moment completely quenched. It can further be seen that
the states in the energy range from about −4.0 eV to approx-
imately −2.0 eV are primarily contributed by C pz -like states
and the partially from 4d-like orbital states with nearly symmet-
ric contribution in both up and down spins. At nearly −1.25 eV
the C 2p (pz  strongly hybridize with Pd (dx2
−y 2 ) forming 
bond on both majority and minority channels with obvious shape
peaks. The  bond for Pd–Pd (dxy−xy ) dimer position around
−2.0 eV in both majority and minority channel. At the vicinity
of Fermi level the contributions of Pdorbital states is so small in
this case, as such pz states of C completely dominate the region.
4. CONCLUSIONS
The stable geometries, electronic and magnetic properties of low
coverage Pd datom and dimer adsorbed on graphene have been
studied using first principle calculations. As for single Pd adatom,
it is found that single Pdadsorption on top of carbon atom site
is the most stable configuration. The orbital contributions for
C–Pd bond are mainly dominated by C 2pz , and Pd 5s and 4dz2
orbitals. Moreover, the study has revealed that the graphene with
single Pd atomis semiconductor and non-magnetic. For palladium
dimer, it is found that, depending on the configuration of the Pd
dimer parallel or perpendicular configurations two distinct situ-
ations with respect to magnetic behavior can be realized. The
parallel configurations where the bonding between Pd and C is
more strengthened are found to be more stable than the perpen-
dicular configurations. Additionally, Pddimer adsorbing on top
of two carbon atoms site is the energetically favorable compare
to the rest of the parallel configurations and is found to be non-
magnetic. Absent of magnetism results from bonded electrons
of Pd-graphene system leaving no unpaired electron. Further-
more, the study also has revealed that, in spite of low coverage
Pddimer adsorbed graphene the systemis metallic. Additionally,
the Pd–Pd interaction is much weakened compare to an isolated
Pd dimer with nearly symmetric heights above the adsorption
sites and Pd–C bond mainly dominated by C 2pz , indicating that
uniform coating can be attained. This property reveals the pos-
sibility of using palladium metal for making contact between
graphene and electrode. Reasonable magnetic moment is detected
for perpendicular Pd configurations depending on the strength of
the Pd-graphene bond. For favored perpendicular configuration
where magnetic moment is most enhanced, the charge distribu-
tion reveals a uniform electron charge density around the region
of Pd atom and this is mainly caused by the charge transfer
between the Pd dimer leaving the bonding orbitals with more
5
 RESEARCH ARTICLE
deficient electrons. In general, these results demonstrate that the
graphene electronic and magnetic properties can be effectively
modified by Pd dimer metal adsorption and this may serve as a
potential material in nanodevices applications.
Acknowledgments: This work is supported by Univer-
siti Putra Malaysia, Ministry of Higher Education (MOHE),
Malaysia through Fundamental Research Grant Scheme (FRGS)
(Project Code: FRGS/1/11/ST/UPM/02/11). Figure 3 was gener-
ated using the XCRYSDEN program.31
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Received: 2 June 2013. Accepted: 29 June 2013.