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Yttrium doped graphene oxide as a new adsorbent for H2O, CO, and ethylene
molecules: Dispersion-corrected DFT calculations

Leila Tabari, Davood Farmanzadeh

PII: S0169-4332(19)32845-4
DOI: https://doi.org/10.1016/j.apsusc.2019.144029
Reference: APSUSC 144029

To appear in: Applied Surface Science

Received Date: 17 May 2019

Revised Date: 7 September 2019
Accepted Date: 14 September 2019

Please cite this article as: L. Tabari, D. Farmanzadeh, Yttrium doped graphene oxide as a new adsorbent for H2O,
CO, and ethylene molecules: Dispersion-corrected DFT calculations, Applied Surface Science (2019), doi: https://
doi.org/10.1016/j.apsusc.2019.144029

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Yttrium doped graphene oxide as a new adsorbent for H2O, CO, and
ethylene molecules: Dispersion-corrected DFT calculations

Leila Tabari* and Davood Farmanzadeh

Email address:tabari1384@yahoo.com
Department of Physical Chemistry, Faculty of Chemistry, University of Mazandaran, P. O. Box: 453,
Babolsar, I. R. Iran

ABSTRACT
A Grimme dispersion-corrected density functional theory (DFT-D) calculations are performed
to explore the electronic structures and adsorption behaviors of graphene oxide (GO) and Yttrium
doped graphene oxide (Y doped GO) toward the adsorption of H2O, CO, and C2H4 molecules. The
HOMO and LUMO spatial distributions, the electrostatic potential charges, and the field that
corresponds to the electrostatic potential are evaluated to understand the effect of the Yttrium
doping on the electronic properties of the pristine graphene oxide. Calculated molecular and
thermodynamic parameters indicate that the electronic structure of GO is obviously affected by
the presence of yttrium atom. It can be seen that the adsorption energies of H2O, CO, and C2H4
molecules adsorption increase from 69.5, 17.4 and 34.7kJ/mol over the pristine GO to 133.1, 182.4
and 214.2kJ/mol for the Yttrium doped GO. We believe that the obtained results will provide
beneficial insights for experimental research about the potential application of metal-doped
graphene oxides as nanoscale adsorbents for water, carbon monoxide, and ethylene molecules.

Keywords: Graphene oxide, Yttrium doped graphene oxide, Grimme dispersion-

corrected density functional theory, Electrostatic potential.

1
 1. Introduction
Graphene oxide (GO) is an admirable layered material for electronics[1], refine filters[2],
optical applications [3], nanocomposites [4] and catalytic activity [5]. Since the first time synthesis
of graphene oxide in 1859 [6], has received much attention via experimental and theoretical
methods due to the interesting properties and potentials [7-10].
The Brodie, Staudenmaier [11], and Hummers [12] methods are the three basic classes for GO
synthesis, which all exploit exfoliation of graphite oxide with strong oxidizing acids. The oxidized
groups of produced graphene oxide depend on the oxidation conditions and oxidants combination.
In 2018 water electrolytic oxidation of graphite has been reported as a high efficiency green
method to graphene oxide synthesize. Based on this method, Pei et al. presented a new industrial
synthesis technique with fast, easy and environmentally friendliness characters [13].
Lian et al. demonstrated the considerable desorption capacity of water on the laminated
structure of graphene oxide due to the high capillary pressure in GO laminates [14]. Magnetite
graphene oxide composites have been synthesized and proposed as a tunable targeted drug delivery
[15].
DFT study of chloroform adsorption on GO showed the graphene oxide can be a potential
candidate for refining the chlorinated water [16].
Investigation of the adsorption behavior of GO toward aniline, nitrobenzene, and
chlorobenzene, from water revealed that the graphene oxide can be used efficiently for the removal
of these aromatic compounds due to the notable properties of it [17]. The graphene oxide-based
materials are getting great attention as sensors for different biomolecules, and environmental gas
molecules [18-20]. Roy et al. introduced an electrochemical immunosensor to tracing the
antibody–antigen interactions using the interaction of carboxylic groups of graphene oxide and
protein molecules [21]. Gan et al. performed an experimental study on the humidity sensing
properties of graphene oxide coated photonic crystal cavity. The results stablished the high
efficiency of the GO based material for humidity sensing [22]. In 2016 Chen et al. synthesized the
GO/cellulose hydrogel for metal ions adsorption. The obtained results showed the good adsorption
capacity of GO/cellulose composite for Zn2+, Fe3+, and Pb2+[23]. In 2017 water adsorption has
been studied on graphene oxide papers with different oxygen functional groups. The results
showed the characterized papers are promising compounds for moisture adsorption and food
longer-term keeping [24].

2
In 2014 Yttrium doped graphene oxide nanoflake structure was synthesized by hydrothermal
technique. Analysis of photo electrochemical properties by investigation of decomposition of
methylene blue molecules demonstrate the better photocatalytic performance of Yttrium-doped
graphene oxide rather than pristine GO and Y2O3[25].
Adsorption of dodecyl amine hydrochloride cationic surfactant on graphene oxide has been
examined by Chen et al. The findings showed the electrostatic interaction and hydrogen
bonding between cationic surfactant and GO make a good adsorbent for dodecyl amine removal
[26].
Experimental investigation in 2018 showed the graphene oxide with a chemical cross-link with
poly (vinyl alcohol) sponges have high water permeability and continuous flow adsorption
capacity which make them a good candidate for wastewater refinement [27]. The results of
experimental investigations clearly reveal the effect of oxidation degree on the adsorption
behavior of graphene oxide [28,29].
The ability of Al and Si decorated graphene oxide for the adsorption of ethylene, acetylene,
formaldehyde and methanol molecules was investigated using the quantum chemical calculations.
The obtained results demonstrated that the Al/Si-GO can be used as an efficient adsorbent for the
adsorption of these molecules [30,31].
In the present work, we are interested in to investigate the adsorption properties of H2O, CO, and
C2H4 molecules on the surface of the graphene oxide and Yttrium doped graphene oxide by the
density functional theory calculations. Studies of water and simple gases adsorption clarify the
intrinsic mechanism of these molecules adsorption [32-35]. Adsorption of water has been widely
investigated for over a century, because of its notable effect on different chemical and physical
processes. Moreover, adsorption of humidity has received great attention because of its role in
food storage, environmental monitoring, surface characterization methods, and industrial
productions [36-38].
Investigation of carbon monoxide molecule adsorption is important environmentally and
industrially. Detection and adsorption of CO from different gas mixtures have received extensive
attention due to its high toxicity to humans [39,40]. Furthermore, CO can decrease the performance
of polymer electrolyte membrane fuel cells by adsorbing on to the electrocatalyst surface [41,42].
Ethylene is considered as a growth-stimulating hormone of the plant which can cause early
senescence and ripening in many vegetables and fruits. In addition, the ethylene catalyzes

3
chlorophyll degradation speed in flowers and leafy products. For these reasons, the adsorption of
ethylene needs very comprehensive investigation and consideration [43-45]. In this paper, the
geometries, thermodynamic properties and the electrostatic potential charge of the pristine and
Yttrium doped GO and the adsorption energies and the Mulliken and Hirshfeld charge transfer of
adsorption structures were investigated systematically to explore the effect of H2O, CO, and C2H4
adsorption on the geometries and electronic properties of the adsorbent sheets.

2. Methods
The electronic structure and energetics of molecules and surfaces were modeled with the
DMol3 program using density functional theory (DFT) [46]. The Van der Waals forces are difficult
to describe in the framework of local or semi local density functional theory due to long-range
correlation effects. To deal with this problem semiempirically, a number of dispersion corrections
are available in DMol3. Grimme is one of the most well-known hybrid semiempirical solutions
that introduce damped atom-pairwise dispersion corrections of the form C6R-6 in the DFT
formalism [47]. Therefore, DFT-D with the Grimme dispersion correction method was applied for
the van der Waals forces in all calculations.
The PBE (Perdew, Burke and Enzerhof) generalized gradient corrected (GGA) functional [48]
were applied in which the exchange part of the functional is similar to the Becke formula [49], and
the correlation part is close to the Perdew-Wang functional [50]..This functional has a reliable
numerical performance and it is mostly used in DFT calculations. Double numerical plus
polarization (DNP) basis set with the fine quality were employed using hexadecapole for
multipolar expansion. Using the numerical basis set and exact DFT spherical atomic orbitals, basis
set superposition effects [51] are minimized and it is possible to obtain an excellent description,
even for weak bonds. The fine settings and thermal smearing of 0.01 Hartree are designed to
produce accurate quantitative results and speed up convergence. In our calculations, the adsorption
energies are calculated by the following equation:

Eads  Eadsorbent/adsorbed molecule Eadsorbent Eadsorbed molecule (1)

Where Eadsorbent , Eadsorbed molecule and Eadsorbent/adsorbed molecule are total electronic energies
of the ground state of the adsorbent sheet, adsorbed species (H2O, CO, and C2H4 molecules) and
the adsorption structure in the gas phase, respectively. Using this valuation, the positive and

4
negative quantities of 𝐸𝑎𝑑𝑠 define the endothermic and exothermic adsorption process,
respectively. Energetically, negative adsorption energies are desirable for adsorption process and
the positive adsorption energies show the adsorption of those species on the surface is unfavorable.

3. Results and discussions

3.1. Graphene oxide model

Graphene oxide is introduced as a trigonal hybridized carbon surface which obtained some
oxygen containing functional groups such as hydroxyl, epoxy and carboxyl groups. These
connecting groups make GO amphiphile by water soluble edges and hydrophobic basic sheet.
Kim et al. showed the amphiphilicity of GO is size-dependent and can be controlled by PH
[52]. The experimental obtained results showed that the contents of functional groups are greatly
depended on the synthesis conditions [53].
In this work, we considered a model of graphene oxide consist of 110 atoms corresponding to a
C:O ratio of 6:1 with two epoxy groups, two hydroxyl groups and four carboxyl groups. Figure 1 shows the
optimized structure of modeled graphene oxide.

Figure 1. Optimized model of graphene oxide with three considered adsorption sites
(A, B and C).

The carbon-carbon bond lengths in basal plane of GO are varied from 1.37 to 1.48Å. These
values are close to C-C bond length of graphite planar structure [54]. The C-C bond length of
epoxide group is about 1.53Å which corresponds to sp3-sp3 carbon -carbon bond length. To
5
confirm that geometry is computed correctly, vibrational frequencies have been calculated. Lack
of imaginary frequencies show the optimized structure is stable and locates at the minimum of the
potential energy.

3.2. Adsorption of H2O, CO, and C2H4 on the GO surface

In order to investigate the adsorption properties, H2O, CO, and C2H4 molecules has been
placed on the different sites of the surface of the GO and geometry optimizations have been
performed. To obtain the most stable adsorption structure, we first consider three most possible
adsorption sites (A site: near the epoxide and hydroxyl groups, B site: on top of the carboxylic acid
group and C site: on the basal carbon plane), as shown in figure 1.
Figure 2 shows the optimized structures of the H2O, CO, and C2H4 molecules on the A, B and
C sites of the surface of graphene oxide. From the figure, in most structures after relaxation, the
adsorbates tend to adsorb near the oxygen-containing groups.

Figure 2. The optimized structures of the H2O, CO, and C2H4 molecules on the different adsorption position on the
surface of graphene oxide. Distances are in angstrom.

6
 In order to investigate the electronic properties of obtained adsorption structures, we calculated
the adsorption energies the H2O, CO, and C2H4 molecules adsorption on the surface of GO using
DFT-D.
Table 1 shows the adsorption energy and energy gap (𝐸𝐿𝑈𝑀𝑂 -𝐸𝐻𝑂𝑀𝑂) of H2O, CO, and C2H4
adsorption on the A, B, and C sites of GO surface.
As shown in table 1, the adsorption energies of the H2O, CO, and C2H4 at the A site (near the
epoxide and hydroxyl groups) are -0.72,-0.18, and -0.36eV, which indicate the A site is the most
stable configuration with the largest adsorption energies and therefore, all adsorbed molecules prefer
to place more stably close to the oxygen containing groups.
From the results of table 1, it is clear that the energy gap of GO (0.13eV) changes negligible after
adsorption process. Consequently, the conductivity of the graphene oxide will not change
significantly.

Table 1. The calculated adsorption energies (𝐸𝑎𝑑𝑠) and energy gaps (𝐸𝑔) of H2O, CO, and C2H4 adsorbed on the A, B
and C sites of GO. (All energies are in eV)

Adsorption sites A (oxygen-containing groups) B (Carboxylic acid site) C (Basal carbon plane)

Eads Eg Eads Eg Eads Eg

G.O+H2O -0.72 0.12 -0.44 0.14 -0.24 0.13

G.O+CO -0.18 0.13 -0.13 0.14 -0.13 0.13
G.O+C2H4 -0.36 0.13 -0.36 0.11 -0.23 0.13

3.3. Yttrium doped graphene oxide

In order to design the Yttrium doped GO configuration, a carbon atom of graphene oxide was
replaced with an Yttrium atom and the structure optimized whiteout restriction. In this study,

7
Yttrium atom was located near the oxygen containing groups which is the most favorable site in
adsorption process. Figure 3 shows the optimized structure of Yttrium doped graphene oxide.

Figure 3. The optimized structure of Yttrium doped graphene oxide.

distances are in Å.

The C-C and C-Y bond lengths of the optimized structure of Yttrium doped GO are also shown
in Figure 3. It can be seen that the length of the C-Y bonds are longer than that of the C-C bonds
(the average C-C bond length is 2.30Å). Therefore, there is a local outward distortion along the
vertical direction to the graphene oxide surface. The doping reaction enthalpy at 298.15K (
∆𝐻298.15𝐾
𝑟𝑒𝑎𝑐𝑡𝑖𝑜𝑛) was calculated using the below phrase:

∆𝐻298.15𝐾
𝑟𝑒𝑎𝑐𝑡𝑖𝑜𝑛 = (𝐸𝑡𝑜𝑡𝑎𝑙 + 𝐻𝑡𝑜𝑡𝑎𝑙)𝑝𝑟𝑜𝑑𝑢𝑐𝑡 ― (𝐸𝑡𝑜𝑡𝑎𝑙 + 𝐻𝑡𝑜𝑡𝑎𝑙)𝑟𝑒𝑎𝑐𝑡𝑎𝑛𝑡 (2)
Where Etotaland Htotal, are the total electronic energy and enthalpy of product (Y doped GO
and carbon atom) and reactant (GO and Yttrium atom).
The negative ΔH refers to the exothermic reaction. On the other hand, positive ΔH shows
the endothermic reaction that is the overall increase in enthalpy is achieved by the heat adsorption.
Gibbs free energy change (ΔG) computed by the same path as that of ΔH. The positive sign of the
free energy indicates that this reaction will not occur spontaneously at room temperature.
The ∆H298.15K 298.15K
reaction and ∆Greaction for the Yttrium doping reaction are evaluated 104.42 and

99.96kcal/mol, respectively, which show the doping reaction is unfavorable for enthalpy and
entropy.

8
 Experimental results showed the Yttrium doped graphene oxide nanocomposite has been
successfully synthesized by hydrothermal method. In this method Y doped GO was prepared with
various solvents via a heating at 180°C for 16 hours which confirm that the process can't be
composited with Yttrium at room temperature [25].
In order to further investigate the Yttrium atom effect on the electronic properties of GO, the
highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO)
spatial distribution, the electrostatic potential (ESP) charges and the field that corresponds to the
electrostatic potential of both GO and Y doped GO have been studied by means of dispersion
corrected density functional theory.
The HOMO and LUMO are especially important in determining the chemical reactivity of a
system. These molecular orbitals are the single-particle wave functions constructed from linear
combinations of atomic orbitals. The spatial distribution of HOMO and LUMO of the pristine GO
and Y doped GO are shown in Fig. 4.
From the plots of the frontier molecular orbitals, in the pristine GO (Figure 4a) both the
HOMO and LUMO are more localized at the same edge of GO molecule. After Yttrium
substitution, it is obviously seen that the LUMO is drawn towards an opposite side of the graphene
oxide. As shown in Figure 4b, by doping of Yttrium atom, HOMO and LUMO are localized at the
either end of the graphene oxide.

9
 Figure 4. The HOMO and LUMO spatial distribution of the pristine GO (a) and Y doped GO
(b).

It is well known that the atomic charges rearrangements can cause the change in molecular
orbitals distribution. Thus, ESP charges and the field that accord with the electrostatic potential
could give us information on the electronic structure of GO and Y doped GO.
The electrostatic potential derived charges are generated in the molecule space and can be
calculated from the positions of the atomic nuclei, the electron density, the integration weight and
the Coulomb potential at selected point. The reliable results of ESP fitted charges in simulations
of biochemical systems confirm the validity of this technique [55,56].
Electrostatic potential produces a volumetric data of the Coulomb potential. Positive regions
(red color) of the electrostatic, or Coulomb, potential correspond to electron-deficient areas and
are subject to nucleophilic attack and the negative regions (yellow color) correspond to electron-
rich areas and are subject to electrophilic attack.
Therefore, we have calculated ESP fitted charges and the electrostatic potential surface of
pristine and Y doped GO. As can be seen from Fig. 5, Y doped GO are designed by substitution
of one carbon atom with ESP charge of -0.015e by one Yttrium atom with ESP charge of 1.491e

10
in the GO sheet. The positive charge of Yttrium can be explained by the small electronegativity of
Y atoms (1.22) rather than carbon atoms (2.55).
After Yttrium substitution, it can also be observe that the atomic charge of carbon atoms which
are connected to Yttrium atom changes from -0.039,-0.019 and -0.029e to -0.179,-0.219 and -
1.176e, respectively. Moreover, ESP charges of oxygen atoms of hydroxyl and epoxide groups are
more negative than that of the pristine GO.
Electrostatic potential plot of the pristine and Y doped GO confirms the calculated results of
ESP derived charges. As shown in in Figure 5, in the Yttrium doped GO, the rejoins around the
Yttrium and oxygen atoms are intensively red (positive charge) and yellow (negative charge),
respectively.

Figure 5. The calculated ESP-fitted charges and the electrostatic potential surface of pristine (a) and Y
doped GO (b). In the Electrostatic potential isosurfaces, the red and yellow colors correspond to electron-
deficient and electron-rich areas, respectively.

3.4. H2O, CO, and C2H4 adsorption on the surface of Yttrium doped GO

11
 In order to investigate the adsorption of H2O, CO, and C2H4 molecules on the surface of Y-
doped GO, different possible primary adsorption geometries were considered. Figure 6 shows the
most stable adsorption configurations, which are calculated after full relax optimization.
The geometry analysis reveals that the adsorption of these molecules can cause the structural
changes in the adsorbent. As shown in the figure 6, the average bond length of Y-C bond increase
from 2.30Å to 2.33Å, 2.41 and 2.42Å by adsorption of H2O, CO, and C2H4, respectively. From
the obtained results, the Y-C bond length in figure 6 b and c are close to the related bond in the
five-coordinated binaphthylamido alkyl ate Yttrium complexes (2.423Å) [57].
As shown in the figure 6 a and b, the distances between the O atoms of H2O and CO from Y
atom are 2.45 and 2.85Å, respectively which are close to the experimental results of Y-O bond
length [58].
Moreover, as shown in figure 6 b and c, after CO and C2H4 adsorption the length of C-O bond
between sheet and hydroxyl group is elongated from 1.62 to 4.09 and 4.16Å, respectively which
indicate that the O atom of hydroxyl moves closer to the Yttrium atom and the relevant C‒O bond
becomes weaker.
The adsorption process can be further investigated by analyzing the adsorption energies,
HOMO and LUMO energies, and energy gap, which are listed in table 2.

Table 2. HOMO and LUMO energy surfaces, energy gap (𝐸𝑔) and adsorption energy (𝐸𝑎𝑑𝑠) in eV of the GO and
Y doped GO and adsorption structures.
HOMO LUMO 𝐸𝑔 𝐸𝑎𝑑𝑠
Graphene oxide (GO) -4.73 -4.60 0.13 ---
GO+H2O -4.72 -4.60 0.12 -0.72
GO+CO -4.72 -4.59 0.13 -0.18
GO+C2H4 -4.72 -4.59 0.13 -0.36
Y doped GO -4.66 -4.52 0.14 ---
Y doped GO+H2O -4.59 -4.49 0.10 -1.38
Y doped GO+CO -4.84 -4.63 0.21 -1.89
Y doped GO+C2H4 -4.74 -4.60 0.14 -2.22

The calculated values of table 2 show the adsorption of H2O, CO, and C2H4 molecules can't
significantly affect the HOMO and LUMO electronic energies, thus there aren’t obvious changes
in the energy gaps. As a result, the adsorption of H2O, CO and C2H4 can't affect the conductivity

12
of the GO and Yttrium doped GO, signally. It is clear that the significant change of energy gap
upon the adsorption process implies the sensitivity of the adsorbent for the adsorbed species [59].
Therefore, it was concluded that the GO and Y doped GO are not sensitive toward H2O, CO, and
C2H4 molecules.
From the results of table 2, for the pristine GO, adsorption energies of H2O, CO, and C2H4 are
calculated -0.72(-69.5), -0.18(-17.4), -0.36(-34.7) eV(kJ/mol), respectively. After Yttrium
substitution, the adsorption energies increases to -1.38(133.6), -1.89(182.4) and -2.22(214.2)
eV(kJ/mol), respectively which means that the doping of Yttrium atom leads to energetic
favorability of the H2O, CO, and C2H4 adsorption compared with the pristine GO.
It can be suggested that the electron rich part of the H2O, CO and C2H4 molecules tends to
interact with electron poor Yttrium atom of the Y doped GO, which causes the significantly
changes of the adsorption energies. The π-bond in the ethylene molecule and O atom of H2O and
CO are regions of high electron density, thus it can cause the high quantities of the adsorption
energies.

13
Figure 6. The most stable adsorption configurations of H2O, CO, and
C2H4 molecules adsorbed over the Y doped GO. Distances are in Å.

14
 To gain further understanding, Mulliken and Hirshfeld atomic charge values are calculated by the
Grimme method of the dispersion corrected DFT calculations.
The Mulliken analysis is one of the most common types of charge that is sensitive to the choice of
basis set [60].Therefore; we also have calculated the Hirshfeld partitioned charges of all adsorption
structures. The Hirshfeld charge analysis is based on the deformation density, which is more stable with
respect to the basis set than Mulliken charge analysis [61]. Table 3 shows the calculated results for the
Mulliken and Hirshfeld charge values of adsorbed molecules on the pristine and Y doped GO.

Table 3. The calculated Hirshfeld and Mulliken charge values of adsorbed H2O, CO, and C2H4 on the pristine
and Y doped graphene oxide.
Adsorption structures Hirshfeld charge (e) Mulliken atomic charge (e)

GO+H2O 0.031 0.039

GO+CO -0.007 0.000
GO+C2H4 -0.039 0.018
Y doped GO+H2O 0.070 0.044
Y doped GO+CO 0.108 0.020
Y doped GO+C2H4 0.120 0.114

As evident from the obtained results, doping of GO with Y atom can enhance both the
Mulliken and Hirshfeld charges of adsorbed molecules. The larger transferred charge values verify
the stronger adsorption energies in these systems.
On the other hand, the calculated results for adsorption energies and charge transfer reflect the
strong interaction between the H2O, CO, and C2H4 and Y doped GO. According to the atomic
charge analysis, the large negative adsorption energy of C2H4 adsorption over Y doped GO is also
confirmed by the 0.120e (0.114e) Hirshfeld (Mulliken) atomic charge of ethylene molecule.
The results of this investigation are useful for future studies about the potential of graphene
oxide based materials into building nanoscale adsorbents.

Conclusions
This paper reports a DFT-D theoretical study about the influence of Yttrium doping on the
geometry and electronic properties of graphene oxide. Based on the frontier molecular orbital and
the electrostatic potential charge analyses, it can be concluded that the substituted Yttrium atom
can affect the electronic properties of graphene oxide molecule. The adsorption energies and
charge transfers were evaluated to compare the ability of GO and Y doped GO toward the
15
adsorption of H2O, CO, and C2H4 molecules. It was found that Yttrium doping leads to a noticeable
increase in the adsorption energies. Moreover, it can be seen that the adsorption process can't affect
the energy gap and consequently the conductance of the studied adsorbent. The results give useful
data for designing new adsorbent for small molecules and further theoretical and experimental
works are required to explore the interesting properties of Yttrium doped graphene oxide.

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Graphical abstract

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Highlight
 A Grimme dispersion corrected density functional theory calculations are performed to
the influence of Yttrium doping on the geometry and electronic properties of graphene
oxide.
 The adsorption energies and charge transfers were evaluated to compare the ability of GO
and Y doped GO toward the adsorption of H2O, CO and C2H4 molecules.

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