Papers in Physics, vol. 13, art. 130003 (2021)

Received: 17 February 2021, Accepted: 17 April 2021
Edited by: O. Fojón
Reviewed by: D. K. Nguyen, Thu Dau Mot University, Vietnam

P. F. Weck, University of Nevada, Las Vegas, USA
Licence: Creative Commons Attribution 4.0
DOI: https://doi.org/10.4279/PIP.130003

www.papersinphysics.org

ISSN 1852-4249

An ab initio study of small gas molecule adsorption on the edge of
N-doped sawtooth penta-graphene nanoribbons

Nguyen Thanh Tien1*, Le Vo Phuong Thuan1, Tran Yen Mi1

Adsorption of the toxic gas molecules carbon monoxide (CO), carbon dioxide (CO2)
and ammonia (NH3) on the edge of N-doped sawtooth penta-graphene nanoribbons
(N:SSPGNRs) was studied using first-principles methods. Basing our study on density
functional theory (DFT), we investigated adsorption configurations, adsorption energy,
charge transfer, and the electronic properties of CO-, CO2- and NH3- adsorbed onto
N:SSPGNRs. We found that CO and CO2 are chemisorbed on the edge of N:SSPGNR,
while NH3 is physisorbed. Current-voltage (I–V) characteristics were also investigated
using the non-equilibrium Green’s function (NEGF) approach. Gas molecules can modify
the current of a device based on N:SSPGNRs. The results indicate the potential of using
N:SSPGNRs for detection of these toxic gas molecules.

I Introduction

Detecting gas molecules using semiconductor gas
sensors is important for agriculture, chemical con-
trols, environmental monitoring, and medical ap-
plications [1, 2]. Low-dimensional systems, espe-
cially material systems based on graphene, have
for many years demonstrated outstanding develop-
ments in sensors and transistor applications [3–8].
However, since the band gap of graphene is al-
most equal to 0, it has not been fully exploited in
the semiconductor industry [9]. The immense suc-
cess of graphene [10–12] was followed by in-depth
studies and encouraging efforts to find other two-
dimensional (2D) nanostructures, such as silicene
[13], phosphorene [14] single-layer graphitic zinc ox-
ide [15], h-boron nitride [16], and transition-metal
dichalcogenides [17]. Penta-graphene (PG), a novel
wide band gap carbon allotrope, and PG-like mate-

*nttien@ctu.edu.vn

1 College of Natural Sciences, Can Tho University, 3-2
Road, Can Tho City 94115, Vietnam

rials were discovered in early 2015 [18–20]. It was
found that PG is ultra-strong, and can sustain a
temperature of 1000 K with grain boundaries. It
displays a quasi-direct intrinsic band gap of 3.2 eV
[18, 21]. Additionally, using the G0W0 approxima-
tion, the PG band gap was calculated as 4.2 eV [22].
In contrast to hydrogenated graphene, hydrogena-
tion of PG leads to a notable increase (76% rise) in
thermal conductivity instead of the 63% reduction
expected due to heat dispersal in device operation
[23]. Furthermore, PG is noteworthy due to its
unique mechanical properties and anisotropic me-
chanical behavior [24]. Unlike graphene, PG has
a buckle structure, which allows it to adsorb gas
molecules in rich configurations. Thus, PG is con-
sidered an excellent base for the development of gas
sensors which can detect harmful gases such as CO,
CO2 and NH3 [25–27].

Cutting 2D-PG sheets in various crystallography
directions obtains more different penta-graphene
nanoribbons (PGNRs). Z. Q. Fan et al. found that
the sawtooth-sawtooth PGNR (SSPGNR) is a more
stable structure than the other three PGNR struc-

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Papers in Physics, vol. 13, art. 130003 (2021) / N. T. Tien et al.

Figure 1: Schematic of possible N:SSPGNR adsor-
bent sites for gas molecules, consisting of a) C-H-
N:SSPGNR, b) H-N-N:SSPGNR, c) C-N-N:SSPGNR.

tures [28]. PGNR receives major attention in semi-
conductor material science since its energy band
gap can be controlled effectively in many ways, such
as by applying an electric field and bending [29],
doping [30, 31], and edge termination [32, 33]. In
our previous studies [31] we discovered that the cur-
rent intensity of N:SSPGNR increases to about 108

times that of pure SSPGNR. This is convenient for
determining current strength in electronic devices,
including sensors. Furthermore, we studied the ad-
sorption feature of the gas molecules (CO, CO2 and
NH3) on the SSPGNR surface [34]. The results
confirm that SSPGNR is sensitive to CO and NH3
molecules, but less sensitive to the CO2 molecule
[26, 27]. However, it is important to study the ab-
sorption configurations at the edges of nanoribbons
[8, 35]. SSPGNR can provide prior adsorption sites
at its edges, which can serve as ideal gas sensor
materials. Nitrogen doping at the carbon edge of
PGNRs allows prior adsorption at this edge with-
out hydrogen passivation. The carbon at the edge
without hydogen passivation presents the dangling
effect that favorably adsorbs CO, CO2 and NH3. In
this study, using DFT and NEGF methods we in-
vestigate theoretically the electronic and transport
properties of N:SSPGNR when gas molecules (CO,
CO2 and NH3) are adsorbed on their edge.

The paper is organized as follows: the subject
and research objectives are presented in the in-
troduction section; in section II the computational
methods are discussed; section III contains the re-
sults and discussion of the electronic and trans-
port properties of N:SSPGNR with the adsorbed

Figure 2: Adsorption configurations of C-H-
N:SSPGNR consist of: a) C-H-N:SSPGNR, b) isolated
gas molecules and c) configurations of C-H-N:SSPGNR
after adsorption gas molecules.

gas molecules on the edge; in section IV the con-
clusions are presented.

II Computational Methods

The electronic and transport properties of
N:SSPGNRs which adsorb gas molecules were
explored by first-principles calculations based on
DFT and NEGF, using the Atomistix ToolKit
(ATK) software package (version 2017.1) [36, 37].
The width of the studied structure was six saw-
tooth chains. A 10 Å vacuum space was introduced
along non periodic (i.e., x and y) directions to
ensure the isolation of N:SSPGNRs from their
periodic replicas.

The samples were optimized using DFT calcu-
lations within the generalized gradient approxima-
tion (GGA) of Perdew Burke Ernzerhof (PBE) [40],
with the following similar conditions: 1 x 1 x 9 k-
point sampling, a cut-off energy of 790 eV and elec-
tron temperature of 300 K. Considering the electric
polarization effect, a double-zeta-polarized basis set
was used to expand the electron wave function. The
self-consistent field tolerance was set as 10−6 Ha.
Furthermore, the ground state configuration was
obtained at the convergence precision of energy for
the maximum energy change, the maximum force,
the maximum stress and the maximum displace-
ment of 2.10−5 eV/atom, 0.05 Ha/Å, 0.05 eV Å−3

and 0.005 Å, respectively.

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Papers in Physics, vol. 13, art. 130003 (2021) / N. T. Tien et al.

Table 1: Adsorption orientations and corresponding numbers for the adsorption structures of CO, CO2 and NH3
on the edge of N:SSPGNR

Gas Configurations Adsorption orientations Notation
of N:SSPGNR

CO C-H-N:SSPGNR Vertical to C and O is downward COCH1
Vertical to C and O is upward COCH2

H-N-N:SSPGNR Vertical to N and O is downward COHN1
Vertical to Nintro and O is upward COHN2

C-N-N:SSPGNR Vertical to C and O is downward COCN1
Vertical to C and O is upward COCN2

Vertical to N and O is downward COCN3
Vertical to N and O is upward COCN4

CO2 C-H-N:SSPGNR Vertical to C CO2CH1
Horizontal to C and CO2 perpendicular to PG CO2CH2

Horizontal to C and CO2 parallel to PG CO2CH3
H-N-N:SSPGNR Vertical to N CO2HN1

Horizontal to N and CO2 perpendicular to PG CO2HN2
Horizontal to N and CO2 parallel to PG CO2HN3

C-N-N:SSPGNR Vertical to C CO2CN1
Horizontal to C and CO2 perpendicular to PG CO2CN2

Horizontal to C and CO2 parallel to PG CO2CN3
Vertical to N CO2CN4

Horizontal to N and CO2 perpendicular to PG CO2CN5
Horizontal to N and CO2 parallel to PG CO2CN6

NH3 C-H-N:SSPGNR Gas molecule is downward NH3CH1
Gas molecule is upward NH3CH2

H-N-N:SSPGNR Gas molecule is downward NH3HN1
Gas molecule is upward NH3HN2

C-N-N:SSPGNR Gas molecule is downward NH3CN1
Gas molecule is upward NH3CN2

Gas molecule is downward NH3CN3
Gas molecule is upward NH3CN4

III Results and Discussion

i Structure Stability

To gauge the capacity of N:SSPGNRs to detect gas
molecules (CO, CO2 and NH3), the adsorption of
gas molecules was investigated on their edges, as
the edge is the most reactive site on the ribbon due
to the presence of dangling bonds.

Figure 1 depicts three possible adsorbent sites on
the edge of an N:SSPGNR, including: a) removing
a passive H atom at the top of the C atom (C-
H-N:SSPGNR), b) removing a passive H atom at
the top of the N atom (H-N-N:SSPGNR), and c)
removing both passive H atoms on the edge of the
ribbon (C-N-N:SSPGNR). To explore the preferred
configuration, we had to identify the model which
the guest molecules would approach uninhibitedly.
We in turn determined the most appropriate config-
uration for each gas molecule: CO, CO2 and NH3.

We first considered possible adsorption config-
urations of the CO molecule on the edge of an
N:SSPGNR; CO can be adsorbed vertically on the
edge with the O atom either upward or downward.
Therefore, there are 8 possible adsorption configu-
rations with the CO molecule. Similarly, there are
12 possible adsorption configurations for the CO2
molecule and 8 for the NH3 molecule. These con-
figurations are listed in Table 1.

To determine the preferred configuration, we cal-
culated the adsorption energy (Ead) of all the con-
figurations considered, as follows [38, 39]:

Ead = Etotal − Eribbon − Egas, (1)

where Etotal, Eribbon and Egas are the total ener-
gies of a considered configuration after gas molecule
adsorption, removing a passive H atom nanorib-
bon and isolated gas molecules, respectively. As
per the definition adopted here, negative adsorp-

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Papers in Physics, vol. 13, art. 130003 (2021) / N. T. Tien et al.

tion energy shows that the process is exothermic
in nature while the magnitude signifies thermody-
namic stability. Computed results indicated that
COCH2, CO2CH2 and NH3CH2 (Fig. 2) were the
preferred configurations of CO, CO2 and NH3 on
N:SSPGNRs, respectively. The adsorption energy
of these samples decreased gradually from -0.26
to -2.96 eV in the following order: Ead(NH3) >
Ead(CO2) > Ead(CO). It is obvious that CO ad-
sorption is the most stable.

In all three adsorption cases, the N:SSPGNR
edge atom closest to gas molecules is a C atom
rather than an N atom. This suggests that the most
effective N:SSPGNR configuration for adsorption of
gas molecules is the C-H-N:SSPGNR configuration.
The adsorption distances of CO, CO2, and NH3
are 1.291 Å, 1.487 Å, and 3.317 Å, respectively, as
shown in Table 2. Therefore, CO- and CO2- ad-
sorbed N:SSPGNRs are more capable of chemical
adsorption than physical adsorption, while an NH3-
adsorbed N:SSPGNR is more likely to adsorb phys-
ically [41].

ii Parameters of structures

Table 3 presents the parameters of three adsorption
structures after relaxation. It can be clearly seen
that the bond lengths of the gas molecules vary
slightly. Namely, after the adsorption, the bond
lengths of two adsorbed gas molecules (CO, CO2)
are longer than those of isolated gas molecules. The
opposite is true of NH3 gas molecules. In addi-
tion, the bond angle of the CO2 molecule is re-
duced from 180◦ to 122◦. The bond angles of the
NH3 gas molecules change negligibly. In particu-
lar, the bond length of the CO adsorption sample
changes the most. This is also one reason the ad-
sorption energy in this sample is the largest. On
the other hand, the bond lengths (d1, d2, d3) and

Table 2: Adsorption energy (Ead), adsorption distance
(h), band gap (Eg) and charge transfer (Q) from gas
molecules to C-H-N:SSPGNR.

Samples Ead h Eg Q
(eV) (Å) (eV) (e)

COCH2 - 1.96 1.291 2.41 0.14
CO2CH2 - 1.31 1.487 2.21 0.47
NH3CH2 -0.26 3.317 1.60 0.03

Figure 3: Density of states of systems: a)
C-H-N:SSPGNR(CO) and C-H-N:SSPGNR; b) C-
H-N:SSPGNR(CO2) and C-H-N:SSPGNR; c) C-H-
N:SSPGNR(NH3) and C-H-N:SSPGNR.

the bond angles (β1, β2, β3) close to the edge of
C-H-N:SSPGNR substrate were also changed after
the gas molecule adsorption. The changes in the
structural parameters due to this interaction is the
basis of the change in electronic properties, which
will be analyzed in the next section.

iii Electronic Properties

The electronic properties of C-H-N:SSPGNR were
studied to understand its capacity to detect CO,
CO2 and NH3. We first investigated the density of
states (DOS) of CO, CO2 and NH3-adsorbed C-H-
N:SSPGNR, as shown in Fig. 3. We also see that
after the adsorption of gas molecules, the DOS of
systems changed, and the band gaps of all three
samples expanded. Specifically, the band gap of
CO-adsorbed C-H-N:SSPGNR showed the largest
increase; its band gap increased to 2.41 eV while the
band gap of C-H-N:SSPGNR was only 1.44 eV. On
the other hand, the sample with the smallest band
gap change was the NH3-adsorbed C-H-N:SSPGNR
sample (Table 2). The trend seen in the calculated
charge transfer (Q) in Table 2 can be understood as
capacity for relative electron donation or electron
withdrawal of the adsorbed molecules. The positive
Q values mean that charge was transferred from the
adsorbed molecules to the C-H-N:SSPGNR in all
three cases, the charge transferred from the CO2 to
the C-H-N:SSPGNR being the largest (Q = 0.47e).

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Papers in Physics, vol. 13, art. 130003 (2021) / N. T. Tien et al.

Table 3: Bond lengths of gas molecules before and after adsorption (l1 to l6), bond angles of gas molecules
before and after adsorption (α1 to α4), bond lengths at edge of C-H-N:SSPGNR before and after gas molecule
adsorption (d1 to d4), and bond angles of C-H-N:SSPGNR before and after adsorption for gas molecules ( β1 to
β4 ).

Samples C-H-N:SSPGNR CO CO2 NH3 COCH2 CO2CH2 NH3CH2

l1 (Å) - 1.128 - - 1.184 - -
l2 (Å) - - 1.128 - - 1.213 -
l3 (Å) - - 1.128 - - 1.213 -
l4 (Å) - - - 1.163 - - 1.022
l5 (Å) - - - 1.163 - - 1.026
l6 (Å) - - - 1.163 - - 1.029
α1 (

◦) - - 180 - - 122 -
α2 (

◦) - - - 107.8 - - 106.0
α3 (

◦) - - - 107.8 - - 106.1
α4 (

◦) - - - 107.8 - - 106.5
d1 (Å) 1.338 - - - 1.339 1.366 1.338
d2 (Å) 1.540 - - - 1.397 1.425 1.536
d3 (Å) 1.508 - - - 1.414 1.409 1.507
β1 (

◦) 122.5 - - - 125.4 132.6 123.1
β2 (

◦) 108.5 - - - 102.9 108.6 108.8
β3 (

◦) 102.9 - - - 108.8 106.3 102.8
β4 (

◦) 120.4 - - - 131.2 111.4 120.2

To better understand the cause of the changes in
band gaps after adsorption, we analyzed the con-
tribution of the gas molecules by drawing the total
density of states (TDOS) and the local density of
states (LDOS), shown in Fig. 4. We also see that
the main contribution to the changes in DOS is
not due to the gas molecules but to changes in the
substrate. In particular, the CO molecule has the
most influence on DOS and the NH3 molecule has
the least. In all cases, the major contribution to
the changes in band gap width is the p orbitals of
the atoms.

On the other hand, as can be see from Fig. 3
and Fig. 4, in all three cases there is an overlap
between the DOS lines, which confirms the connec-
tion between the gas molecules and the substrate.
However, in the case of CO and CO2 adsorption,
there is an overlap and interlacing between TDOS
and LDOS, so we can confirm that there is chemical
bond formation. The adsorption in these two cases
is chemical. In contrast, in the case of NH3 the
adsorption is only the overlapping between TDOS
and LDOS; NH3 can only physically adsorb on the
edge of N:SSPGNR.

Figure 5 shows the electron density difference
(EDD) for all three adsorbed samples. The EDD
was calculated using the following formula:

∆ρ = ρ(T otal) − ρ(ribbon) − ρ(gas). (2)

Here, ρ(T otal) and ρ(ribbon) represent the total elec-
tron densities of the N:SSPGNR with and without
adsorbed gas molecules, respectively, and ρ(gas) is
the electron density of the isolated gas molecules.

Figure 4: TDOS of systems: a) C-H-N:SSPGNR(CO);
b) C-H-N:SSPGNR(CO2); c) C-H-N:SSPGNR(NH3)
and LDOS of the gas molecules (the filled area under
the DOS curve).

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Papers in Physics, vol. 13, art. 130003 (2021) / N. T. Tien et al.

Figure 5: The electron density difference for CO, CO2
and NH3-adsorbed N:SSPGNR. The isosurface value is
taken as 0.009 eV Å−3. The electron density differ-
ence is defined as the valence electron density minus
the neutral atom electron density.

It can be seen from the EDD plots that the charges
were accumulated over the adsorbed gas molecules.

The formation of chemical bonds is evident in
the case of CO and CO2 adsorption. The elec-
tron density at the interface region between CO,
CO2 and N:SSPGNR indicates that the adsorbed
gas molecule does form covalent bonds with the
N:SSPGNR after the adsorption process. In con-
trast, in the case of NH3 adsorption, no formation
of covalent bonds was found, because there is little
electron density difference at the interface between
the NH3 gas molecule and N:SSPGNR.

iv Transport Properties

In the previous section, we showed that the ad-
sorption of gas molecules causes changes in the
electronic band gaps of N:SSPGNR. For further
verification of CO, CO2 and NH3 detection by
N:SSPGNR, we studied the transport properties of
C-H-N:SSPGNR before and after the adsorption of
gas molecules. The current voltage (I-V) charac-
teristics were obtained using a two-probe model.

Figure 6 shows the correlation between the cur-
rent and the bias voltage of the adsorbed samples
and the pure sample. We can see that all of these
lines have the same shape. On the graph there is
a conduction pause although the bias voltage in-
creases. When the bias voltage reaches a certain
limit value (1.6 V), the current begins to increase,
then decreases until saturation at 2.0 V. Specifi-
cally, except for the CO2 adsorption sample, the
current of the remaining samples starts to increase
at the bias voltage of 1.6 V (threshold bias). For
semiconductors, when the polarizing voltage is not

Figure 6: Calculated I-V curves for four struc-
tures: C-H-N:SSPGNR, C-H-N:SSPGNR(CO), C-H-
N:SSPGNR(CO2) and C-H-N:SSPGNR(NH3).

large enough the device stops conducting, but when
it is large enough for an electron to cross the bar-
rier, the device begins to conduct electricity. Thus,
we can conclude that the structures under consid-
eration are semiconductors. The maximum current
obtained for pure C-H-N:SSPGNR, CO-adsorbed
C-H-N:SSPGNR, CO2-adsorbed C-H-N:SSPGNR,
and NH3-adsorbed C-H-N:SSPGNR is 0.3 nA, 0.7
nA, 13.7 nA, and 0.4 nA, respectively. In all four
cases, the maximum currents occur at the bias volt-
age of 1.8 V. The maximum current of the CO2
adsorption sample is the highest, 45 times greater
than that of the pure sample. The maximum cur-
rent of the NH3 adsorption sample is the lowest,
only 1.3 times greater than that of the pure sample.
All these findings suggest that the N:SSPGNR cur-
rent can be distinguished before and after molecule
adsorption [42].

To explain the change in the trend of the I-V
curves in Fig. 6, we considered the bias dependent
transmission spectra, T(E,Vb), of the four stud-
ied structures via Fig. 7 (left-hand panels). We
see that the T(E,Vb) of the pure C-H-N:SSPGNR,
the CO-adsorbed C-H-N:SSPGNR, and the NH3-
adsorbed C-H-N:SSPGNR differ very little. How-
ever, the T(E,Vb) spectrum of the CO2-adsorbed
C-H-N:SSPGNR is very different from the three
other samples. This is also related to the charge
transfer phenomenon mentioned in Table 2. Fur-
thermore, the various maximum currents occur at

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Papers in Physics, vol. 13, art. 130003 (2021) / N. T. Tien et al.

Figure 7: Left-hand panels: The contour of the bias-dependent transmission T(E,Vb); Right-hand panels:
Transmission coefficient at 1.8 V bias of four structures: a) C-H-N:SSPGNR, b) C-H-N:SSPGNR(CO), c) C-H-
N:SSPGNR(CO2) and d) C-H-N:SSPGNR(NH3).

the bias voltage of 1.8 V; the transmission coeffi-
cients at 1.8 V bias of the four structures were cal-
culated and shown in the right-hand panels of Fig.
7. The values and filled zones bounded by the hor-
izontal axis and T(E, Vb = 1.8 V) curves help us
to explain the changing tendency of the maximum
currents of the four structures.

IV Conclusions

In summary, using first-principle calculations we
studied the adsorption geometry, adsorption en-
ergy, charge transfer, density of states, partial den-
sity of states and I-V curves of N:SSPGNR with
gas molecule (CO, CO2 and NH3) adsorption. Our
calculated results show that edge adsorption of CO
and CO2 molecules is more energetically favorable
than edge adsorption of NH3. Moreover, the ad-
sorption of CO and CO2 on the edge of N:SSPGNR

is chemical, while the adsorption of NH3 is physi-
cal. The current voltage (I–V) characteristics were
also investigated using the non-equilibrium Green’s
function (NEGF) approach. The results indicate
that conductance of the CO, CO2, and NH3 adsorp-
tion N:SSPGNR can be distinguished at the bias
voltage of 1.8 V. These changes in electronic and
transport properties make N:SSPGNR a promising
candidate for gas detector development.

Acknowledgements - This research was funded
in part by the Can Tho University Improvement
Project VN14-P6, supported by a Japanese ODA
loan. We are grateful to the information center
and network administrator of Can Tho University
(CTU) for computational support. We also thank
Prof. Yoshitada Morikawa (Osaka University) for
discussing research ideas.

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	Introduction
	Computational Methods
	Results and Discussion
	Structure Stability
	Parameters of structures
	Electronic Properties
	Transport Properties

	Conclusions