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Journal of Molecular Modeling (2017) 23:355

https://doi.org/10.1007/s00894-017-3521-7

ORIGINAL PAPER

Effects of shape, size, and pyrene doping on electronic properties


of graphene nanoflakes
Thanawit Kuamit 1 & Manussada Ratanasak 1 & Chompoonut Rungnim 2 & Vudhichai Parasuk 1

Received: 16 May 2017 / Accepted: 6 November 2017


# Springer-Verlag GmbH Germany, part of Springer Nature 2017

Abstract
Effects of size, shape, and pyrene doping on electronic properties of graphene nanoflakes (GNFs) were theoretically investigated
using density functional theory method with PBE, B3PW91, and M06-2X functionals and cc-pVDZ basis set. Two shapes of
zigzag GNFs, hexagonal (HGN) and rhomboidal (RGN), were considered. The energy band gap of GNF depends on shape and
decreases with size. The HGN has larger band gap energy (1.23–3.96 eV) than the RGN (0.13–2.12 eV). The doping of pyrene
and pyrene derivatives on both HGN and RGN was also studied. The adsorption energy of pyrene and pyrene derivatives on GNF
does not depend on the shape of GNFs with energies between 21 and 27 kcal mol−1. The substituent on pyrene enhances the
binding to GNF but the strength does not depend on electron withdrawing or donating capability. The doping by pyrene and
pyrene derivatives also shifts the HOMO and LUMO energies of GNFs. Both positive (destabilizing) and negative (stabilizing)
shifts on HOMO and LUMO of GNFs were seen. The direction and magnitude of the shift do not follow the electron withdrawing
and donating capability of pyrene substituents. However, only a slight shift was observed for doped RGN. A shift of 0.19 eV was
noticed for HOMO of HGN doped with 1-aminopyrene (pyNH2) and of 0.04 eV for LUMO of HGN doped with 1-
pyrenecarboxylic acid (pyCOOH).

Keywords Pristine graphene . Pyrene doping . Diode . Graphene nanoflake . DFT calculations

Introduction [8–11]. Graphene can be potentially used for logic devices


by inducing a band gap between its π and π* states. There
Graphene is a crystalline allotrope of carbon with two- are several methods for introducing band gap to graphene.
dimensional properties that can be described as a one-atom Traditionally, this could be achieved by doping graphene with
thick layer of graphite [1]. Graphene has good conductivities, boron or nitrogen atoms. The atomic doping technique can
good thermal properties, extremely high surface area, light induce the band gap and make p- or n-type graphene
weight, etc. [2–7]. Moreover, graphene is also known as a [12–16]. However, the atomic doping is difficult to control
zero-band gap semiconductor. Thus, it has been interesting and often destroys the band structure of graphene. Another
to large numbers of researchers for its wide applicability technique for band gap modification is by using chemisorbed
adsorbates, the chemical doping method [17–20]. The chem-
Electronic supplementary material The online version of this article ical doping changes the hybridization of carbon on graphene
(https://doi.org/10.1007/s00894-017-3521-7) contains supplementary from sp2 to sp3 and hence alters the band structure. However,
material, which is available to authorized users. this technique causes an undesired adjustment or disrupting of
the basic electronic properties of graphene. Another method
* Vudhichai Parasuk
for the electronic-property modification of graphene is by
vudhichai.p@chula.ac.th
using physisorbed adsorbates, the physisorption technique.
1
Center of Excellence in Computational Chemistry, Department of The advantage of the physisorption technique is that the
Chemistry, Faculty of Science, Chulalongkorn University, unique electronic property of graphene can be protected, since
Bangkok 10330, Thailand
the physisorption just slightly changes the band structure
2
National Nanotechnology Center National Science and Technology [21–29]. Lee et al. [30] modified electronic properties of re-
Development Agency, 130 Thailand Science Park, Paholyothin Rd,
duced graphene oxide (rGO) by using noncovalent
Klong Luang, Pathumthani 12120, Thailand
355 Page 2 of 9 J Mol Model (2017) 23:355

interactions with aromatic molecules through π-π interaction. The knowledge could provide a new insight into the de-
Because pyrene could stably bind to the graphene through sign of a complete circuit of donor- and acceptor-type
strong π-π interactions [31–34] and electron withdrawing or graphene diodes.
donating substituents can be attached to pyrene with simple
reactions and facile purification [35, 36]. They then doped
rGO with pyrene and pyrene derivatives and successfully de- Computational models and methods
vised a bottom-gated field-effect transistor. Several theoretical
studies have been carried out regarding the properties of Two different shapes of zigzag-edge GNFs, HGN and
physisorbed graphene. Deng et al. [37] using density function- RGN, were selected for the study. The hexagonal carbon
al theory (DFT) suggested that the computed band gap energy ring is the core structure for the construction of HGN,
of fully H-terminated armchair- and zigzag-edge graphene which expands along the C2 symmetry axis as C6 exten-
decreases with increasing size of nanosheet. Zhou and sion within the D6h point group. Thus, it expands along
Zhang [38] theoretically investigated the adsorption behavior the C2’ axis within D6h symmetry as zigzag circles around
of a series of benzene derivatives physisorbed on graphene. the nanoflake. The total number of C atoms in HGN is
They suggested that adsorption energies were insensitive to 6n2, where n is the peripheral zigzag circle of HGN. Our
the adsorption sites (hollow, bridging, on-top), since energy HGN models were generated for n = 2–6, which contains
differences between these sites are within 1 kcal mol−1. C24H12, C54H18, C96H24, C150H30, and C216H36, respec-
Moreover, the adsorption energies for all the derivatives are tively. For RGN, the m x m model was used to generate
larger than that of benzene. This can be ascribed to the increas- GNFs, where m is the number of benzene rings. Our RGN
ing orbital overlap of substituents with graphene. models were produced for m = 3–8, which are comprised
A graphene nanoflakes (GNF) is a finite sized of C 3 0 H 1 4 C 4 8 H 1 8 , C 7 0 H 2 2 , C 9 6 H 2 6 , C 1 2 6 H 3 0 , and
graphene. It can be prepared by both bottom up [39] and C160H34, respectively. All molecular structures were fully
top down [40–48] approaches. Whilst it has properties optimized by DFT method [52] using Perdew Burke
similar to graphene, it can be made into many sizes and Ernzerhof (PBE) functional [53] and cc-pVDZ basis set
shapes. Nagai et al. [49] have studied electrical properties [54]. Geometry optimizations were performed in gas
of functionalized GNFs with various shapes and sizes and phase using the Gaussian 09 software [55]. Illustrations
found that electrical properties of GNFs can be tuned by of the HGNs and RGNs being investigated in this study
making them the proper size and shape. Shakourian-Fard are given in Fig. 1.
et al. [50] used M06-2X/cc-pVDZ level of theory to study To address the dispersion-type interaction for the study
the effect of defect types on electronic and optical prop- of physisorption, we chose the Minnesota M06-2X func-
erties of GNFs physisorbed by ionic liquids (ILs). They tional [56] with cc-pVDZ basis set in cooperation with
reported that the increasing size of the defective GNF BSSE correction since from our previous study we found
affects the geometry of the surface and enhances the bind- that the method could yield a reasonable description for
ing affinity of ILs by about 10%. Chutia et al. [51] inves- the dispersion interaction (π-π stacking) [57]. Two differ-
tigated the properties of GNFs by modifying their surface ent adsorption sites, on-top and hollow, were investigated
chemistry and stacking conformation. They have shown for both doped HGN and RGN (Fig. 2). We chose the C96
that there is a remarkable relationship between the chem- model to study the physisorption because in this model
ical hardness with electrical conductivity of GNFs. They both HGN and RGN have the same number of carbon
also revealed that HOMO-LUMO energy gap can directly atoms. Doped GNF structures at the two positions were
be related with the chemical hardness and hence the elec- obtained by fully optimizing the structures in Fig. 2 at
trical conductivity. Like graphene, electronic properties of BSSE corrected M06-2X/cm3-pVDZ level of theory.
GNF can also be modified by doping with π-conjugated Energies of HOMO and LUMO and band gap energies (Eg)
compound. of HGNs, RGNs, and their physisorbed complexes were de-
In this work, geometries and electronic properties of termined using the DFT method with B3PW91 hybrid func-
two shapes of graphene nanoflakes, rhomboidal (RGN) tional [58, 59] and cc-pVDZ basis set. The B3PW91 hybrid
and hexagonal (HGN), at various sizes were investigated functional has been shown to provide excellent prediction for
using DFT calculations. Moreover, the physisorption on band gap energies of 70 insulating compounds [60]. Band gap
HGN and RGN by pyrene and its derivatives with various energies of both HGNs (C24H12, C54H18, C96H24, C150H30,
electron withdrawing/donating substituents and their ef- C216H36) and RGNs (C30H14, C48H18, C70H22, C96H26,
fects on electronic properties of GNF were discussed. C126H30, C160H34) were estimated by:
This research aimed to understand the fundamental that
Eg ¼ ELUMO  EHOMO ð2Þ
governs electronic properties of GNF and graphene re-
garding shape and size and especially pyrene doping. where E LUMO is the energy of the lowest unoccupied
J Mol Model (2017) 23:355 Page 3 of 9 355

Fig. 1 Hexagonal graphene nanoflakes (a) and rhomboidal graphene nanoflakes (b)

molecular orbital and EHOMO is the energy of the highest All HGNs being studied have large band gap. They could be
occupied molecular orbital. classified as semiconductors. From the relation between the
number of carbon atoms on HGN and its band gap energy,
HGN will have zero band gap when the number of carbon
atoms is beyond 480 (see Fig. S1). Thus, very large HGN will
Results and discussion have electronic properties similar to graphene. However, mod-
erately large RGNs (C > 200) have negligible band gap energy
Size and shape dependent and they show the properties of metals. Though, for small
RGNs there remains a sizable band gap and they can be made
HOMO and LUMO energies of five HGNs, C24H12, C54H18,
into semiconductors.
C96H 24, C150H30, and C216H 36 and six RGNs, C30H 14,
To understand why HOMO and LUMO energies of GNFs
C48H18, C70H22, C96H26, C126H30, and C160H34 are displayed
depend on shape, we compared HOMO and LUMO orbitals
in Fig. 3. The relation between band gap energies and numbers
of C96H24 (HGN) and C96H26 (RGN), Fig. S2 and S3. HOMO
of carbon atoms are given in Fig. S1. Corresponding band gap
and LUMO orbitals of HGN look very distinct; however,
energies for HGNs are 3.96, 2.76, 2.06, 1.58, and 1.23 eV,
HOMO and LUMO orbitals of RGN appear to be similar.
respectively and for RGNs are 2.12, 1.16, 0.62, 0.34, 0.20,
Thus, while HGN has large band gap, HOMO and LUMO
and 0.13 eV, respectively. It can be seen that HOMO and
of RGN have similar energy and hence negligible band gap.
LUMO energies and hence band gap energies depend on
shape and size of GNFs. The decreasing of band gap energy
with the increasing of size was observed for both HGN and Physisorption
RGN consistent with the result of Deng et al. [37]. Thus, the
observation could be explained by the increment of free π Adsorption energies (Ead1) and BSSE corrected adsorption
electrons in occupied orbitals perpendicular to the GNF plane energies (Ead2) of pyrene and seven pyrene derivatives
(pz orbital). RGN generally has a band gap smaller than HGN. adsorbed on HGN and RGN were given in Table 1. The

Fig. 2 Pyrene doped HGN (a) and RGN (b) at on-top and hollow adsorbed positions
355 Page 4 of 9 J Mol Model (2017) 23:355

mol−1 were observed. So, in general there is no distinct pref-


erential adsorption site.
From Table 1, strong bindings between HGN/RGN and
adsorbates were observed. Although, the BSSE is reasonably
large (4–7 kcal mol−1), it is still an order of magnitude smaller
than the binding affinity. The BSSE corrected adsorption en-
ergies for all adsorbates are between 21 and 27 kcal mol−1.
Adsorption energies of pyrene/pyrene derivatives on HGN
and RGN are similar. The binding of GNF with pyrene/
pyrene derivatives is 2–3 times stronger than that between
nucleobase and graphene (9–14 kcal mol−1) [57]. This is prob-
ably because pyrene has more benzene rings than the
nucleobase. This binding affinity between π-conjugated com-
pound and graphene is, however, one order of magnitude
smaller than that between ion and graphene [61]. This sug-
Fig. 3 HOMO, LUMO energies (eV) of HGNs and RGNs with various gests the different nature of the interaction with graphene for
sizes
the two systems. Intriguingly, all pyrene derivatives have
stronger binding with GNF than the unsubstituted one in
preferred adsorption site for each physisorbed complex was
agreement with Zhou and Zhang [38]. Thus, it could be ratio-
denoted in parenthesis, where t refers to on-top site and h to
nalized that the substituent on pyrene allows greater orbital
hollow site. Optimized structures of adsorption complexes of
overlap between the GNF and the adsorbate. Computed ad-
HGN and RGN with pyrene/seven pyrene derivatives
sorption energies do not seem to depend on the electron
were displayed in Figs. 4 and 5, respectively. For most adsorp-
donating/withdrawing capability of the substituents.
tion complexes, the energy difference between the complex at
However, they are more or less contingent to the size of sub-
the hollow and the on-top sites is < 1 kcal mol−1 (see Table S1
stituent or rather to the surface area, Fig. S4. The py-
and S2) in agreement with Zhao and Zhang [38]. However, for
NHCOCH3 has the largest surface area and thus the strongest
RGN-pyNH2, HGN-pyNH2, HGN-pyCH3, and HGN-pyNO2
binding to GNF. This again agrees with Zhou and Zhang’s
the respective variances of 5.65, 1.88, 1.88, and 1.26 kcal
observation [38], while disagreeing with the Hunter–Sanders
rules (electron donating substituents weaken binding whereas
electron withdrawing substituents enhance binding) [62, 63].
Table 1 Adsorption energies (Ead1) and BSSE corrected adsorption
energies (Ead2) of pyrene and seven derivatives adsorbed on HGN and We cannot find any relation between the adsorbate-GNF dis-
RGN in kcal mol−1 together with the distance between pyrene/pyrene tance (rPG) and the adsorption energy. The rPG between 3.0
derivatives and GNF (rPG) in Å and remarks of adsorption sites in paren- and 3.2 Å was reported for HGN and RGN, where those for
thesis (h=hollow, t=on-top) RGN are slightly shorter.
GNF+adsorbates Ead1 (kcal mol−1) Ead2 (kcal mol−1) rPG (Å)
Effect of pyrenes doping
HGN-PyH(h) 25.64 21.74 3.115
HGN-PyNO2(h) 30.70 23.33 3.029 HOMO and LUMO energies of HGN (C96H24) and RGN
HGN-PySO3H(h) 31.49 23.90 3.144 (C96H26) doped with pyrene and seven pyrene derivatives
HGN-PyCOOH(h) 29.76 23.61 3.156 are presented in Figs. 6 and 7, respectively. The variation of
HGN-PyNHCOCH3(h) 31.45 26.75 3.064 HOMO and LUMO energies were observed for both HGN
HGN-PyCH3(h) 28.40 22.98 3.185 and RGN.
HGN-PyOH(h) 28.32 23.36 3.098 The change of HOMO and LUMO energies could be better
HGN-PyNH2(h) 30.74 23.95 3.156 described by the shift of HOMO/LUMO energy of doped
RGN-PyH(h) 25.21 21.64 3.043 GNF as compared to the undoped one as listed in Tables 2
RGN-PyNO2(h) 30.53 24.48 3.020 and 3 for HGN and RGN, respectively. Positive (energy
RGN-PySO3H(h) 29.67 23.65 3.052 higher than undoped GNF) and negative (energy lower than
RGN-PyCOOH(h) 29.94 24.04 3.041 undoped GNF) shifts were observed for HOMO of HGN dop-
RGN-PyNHCOCH3(t) 32.79 26.95 2.999 ing with pyrene/pyrene derivatives, while only positive shifts
RGN-PyCH3(h) 27.17 23.03 3.083 were seen for LUMO of HGN doping with pyrene/pyrene
RGN-PyOH(h) 28.31 23.10 3.012 derivatives and HOMO/LUMO of pyrene/pyrene derivatives
RGN-PyNH2(h) 27.18 22.62 3.032 doped RGN. However, we could not find any relation between
the electron withdrawing/donating capability of the
J Mol Model (2017) 23:355 Page 5 of 9 355

Fig. 4 Optimized structures for adsorption complexes of pyrene/seven pyrene derivatives and HGN (top view)

substituents on pyrene and the HOMO/LUMO energy shift. as their magnitude do not have any relation with the electron
For RGNs, only a small shift around 0.01–0.08 eV were withdrawing/donating capability of the substituent. Thus, the
noted. electronic effect on pyrene ring does not have any direct in-
Thus, it could be concluded that the doping has a minimal fluence on the electronic properties of GNF. This conclusion
effect on the electronic structure of RGN. However, it should surprised us. To see whether the electronic effect of the sub-
be noticed that the doping with pyNH2 (the strongest electron stituent on pyrene affects its electronic structure, we carried
donating substituents) provides the largest positive shift. For out B3PW91/cc-pVDZ calculations for pyrene and seven
HGN, the more pronounced positive shift was observed on pyrene dervatives. More pronouced shifts on HOMO (0.01–
HOMO energy when doping with pyNH2 (0.19 eV), while 0.55 eV) and LUMO (0.03–1.03 eV) as compared to those of
HGN with pyCOOH doping provides the smallest postive physisorbed complexes were found, see Table S3. The nega-
shift (0.04 eV) on LUMO energy. Likewise, the positive and tive shift was noticed to be associated with pyrene with elec-
the negative shifts on HOMO/LUMO energy of HGN as well tron withdrawing substituents, while the positive shift was

Fig. 5 Optimized structures for adsorption complexes of pyrene/seven derivatives and RGN (top view)
355 Page 6 of 9 J Mol Model (2017) 23:355

Table 2 Energy shifts of HOMO and LUMO (eV) upon doping as


compared to undoped HGN

Substituent LUMO (eV) HOMO (eV)

HGN-pyH 0.10 −0.01


HGN-pyNO2 0.09 0.00
HGN-pySO3H 0.12 0.04
HGN-pyCOOH 0.04 −0.05
HGN-pyNHCOCH3 0.08 −0.01
HGN-pyCH3 0.10 −0.01
HGN-pyOH 0.09 −0.01
HGN-pyNH2 0.07 0.19

softness of those complexes have the same trend as their


Fig. 6 HOMO and LUMO energies (eV) of HGN (C96H24) and HGN
doped with pyrene (−H) and pyrene derivatives (electron donating -NH2,
HOMO-LUMO gap. However, they could not explain the
−OH, −CH 3, −NHCOCH 3, electron withdrawing -NO2 , −SO3H,- shift of HOMO/LUMO energies in physisorbed complexes
COOH) of pyrene/pyrene derivatives and GNFs because no relation-
ship between values of chemical hardness and softness and
found for those with electron donating substituents. In addi- HOMO/LUMO energy shifts was observed. To understand
tion, the magnitude of the shift is also in accordance with the HOMO/LUMO energy shifts of the physisorbed complexes,
Hammett sigma constant, see Fig. S5. Hence, the electronic we performed population analysis for pyrenes in the complex
effect of substituents correlates with HOMO/LUMO energy using the natural population analysis (NPA) method. Table 4
shifts on pyrene. Unlike the physisorbed complex, direct sub- represents the sum of the atomic net charge of the adsorbate
stitution has a stronger effect on the electronic structure of the (pyrene/pyrene derivatives) in HGN and RGN complexes.
aromatic compound since it interacts with π electrons directly. From Table 4, for both HGN and RGN complexes pyrene
Therefore, we could not easily control the shift of HOMO and and all pyrene dervatives have negative net charge suggesting
LUMO energies of GNF by just adding substituents on the that the adsorbate pulls electrons from GNF. Thus, all adsor-
adsorbate. Chutia et al. [51] suggested that the electrical con- bates act as the elecron withdrawing group such that regard-
ductivity is related to the chemical hardness and softness. The less of the substituent they all provide the same electronic
chemical hardness and softness of complexes between pyrene/ effect to GNF and changing electron withdrawing/donating
pyrene derivatives and HGN/RGN were calculated and listed capabilites of the substituent on pyrene will not have any
in Table S6 and S7. Indeed, the chemical hardness and substantial effect on the electronic property of GNF.
One application for nanoelectronic devices of graphene is
diode. The diode is a fundamental electronic device, which
consists of donor and acceptor. Thus, it allows electricity to
flow in one direction when voltage is applied.
Typically, the donor is the n-type semiconductor and the
acceptor is the p-type semiconductor. For organic

Table 3 Enegy shifts of HOMO and LUMO (eV) upon doping as


compared to undoped RGN

Substituent LUMO (eV) HOMO (eV)

RGN-pyH 0.05 0.01


RGN-pyNO2 0.06 0.03
RGN-pySO3H 0.05 0.02
RGN-pyCOOH 0.05 0.02
RGN-pyNHCOCH3 0.06 0.02
RGN-pyCH3 0.05 0.01
Fig. 7 HOMO and LUMO energies (eV) of RGN (C96H26) and RGN
doped with pyrene (−H) and pyrene derivatives (electron donating -NH2, RGN-pyOH 0.04 0.00
−OH, −CH 3 , −NHCOCH 3 , electron withdrawing -NO 2 , −SO 3 H, RGN-pyNH2 0.08 0.06
−COOH)
J Mol Model (2017) 23:355 Page 7 of 9 355

Table 4 Sum of atomic net charge of pyrene/pyrene derivatives in HGN 3.96 eV). Thus, large RGNs have electronic properties closer
and RGN complexes
to graphene. Very large HGNs with twice the number of car-
Adsorbates Net charge bon atoms as large RGNs will also have a close-to-zero band
gap. Pyrene and all pyrene derivatives have large binding
HGN complex RGN complex affinity with GNFs (21–27 kcal mol−1, BSSE corrected).
PyH −0.0191 −0.01548
Adsorption energies with pyrene and pyrene derivatives are
similar for RGNs and HGNs. The strenght of adsorption does
PyNO2 −0.01755 −0.01643
not depend on the type of substituent (whether it is electron
PySO3H −0.01253 −0.01423
withdrawing or donating). All pyrene derivatives adsorbed to
PyCOOH −0.01559 −0.01348
GNF stronger than pyrene due to the orbital overlap of the
PyNHCOCH3 −0.01459 −0.01030
substituent. Doping can shift HOMO and LUMO of GNF
PyCH3 −0.01643 −0.01355
but the magnitude and the direction of the shift does not follow
PyOH −0.01045 −0.00800
the electron withdrawing/donating capability of the substitu-
PyNH2 −0.00699 −0.01085
ent. Thus, the shift of HOMO and LUMO in GNFs cannot be
controlled by the physisorption since all pyrene dervatives act
as electron withdrawing groups. Therefore, the substituent on
pyrene does not provide a substantially different electronic
effect on GNF. A slight shift in HOMO and LUMO was ob-
served for RGN, while a more significant shift is noticed for
HGN doped with pyNH 2 (0.19 eV). HGN doped with
pyCOOH provides the least positive shift on LUMO
(0.04 eV). Therefore, HGN-pyNH2 and HGN-pyCOOH can
be made into a diode.

Acknowledgments The authors would like to acknowledge the 90th an-


niversary of Chulalongkorn University for Mr.Thanawit Kuamit’s schol-
arship and Ratchadapisek Somphot Endownment Fund of Chulalongkorn
University RES560530184-AM and CU-57-038-AM (Advanced
Material Cluster) and the world class university grant of the comission
for higher education WCU-031-AM-57 for funding this work.
Additionally, the Center of Excellence in Computational Chemistry
(CECC), Department of Chemistry, Chulalonkorn University and the
National Electronics and Computer Technology Center (NECTEC) under
Fig. 8 Schemetic drawing for organic diode with p- and n-type junction the National e-Science Consortium are gratefully acknowledged for their
support in computing facilities.
semiconductor [64, 65], the electron will move from HOMO This work is devoted to the remembrance of His Majesty King
Bhumibol Adulyadej (1927-2016), for his life-time dedication to
of the donor to LUMO of the acceptor as illustrated in Fig. 8. Thailand.
The HGN doped with pyNH2 has the highest positive shift of
HOMO (0.19 eV) and slight positive shift of LUMO
(0.07 eV), whereas the HGN doped with pyCOOH has the
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