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First-principles investigation of defective graphene anchored with

small silicon clusters as a potential anode material for lithium-ion
batteries

Monrudee Liangruksa , Yutthanakon Kanaphan ,

Nonglak Meethong , Annop Klamchuen

PII: S0039-6028(23)00004-3
DOI: https://doi.org/10.1016/j.susc.2023.122250
Reference: SUSC 122250

To appear in: Surface Science

Received date: 17 October 2022

Revised date: 19 December 2022
Accepted date: 12 January 2023

Please cite this article as: Monrudee Liangruksa , Yutthanakon Kanaphan , Nonglak Meethong ,
Annop Klamchuen , First-principles investigation of defective graphene anchored with small sili-
con clusters as a potential anode material for lithium-ion batteries, Surface Science (2023), doi:
https://doi.org/10.1016/j.susc.2023.122250

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First-principles investigation of defective graphene anchored with small silicon clusters

as a potential anode material for lithium-ion batteries

Monrudee Liangruksa1*, Yutthanakon Kanaphan2, Nonglak Meethong2, and Annop

Klamchuen1

1
National Nanotechnology Center (NANOTEC), National Science and Technology

Development Agency (NSTDA), Pathum Thani 12120, Thailand.

2
Materials Science and Nanotechnology Program, Department of Physics, Faculty of Science,

Khon Kaen University, Khon Kaen, 40002, Thailand.

Abstract

The interplay between vacant graphene and silicon (Si) provides a viable way to tune the

properties for successful implementation as a promising anode material of lithium-ion batteries.

Therefore, understanding the interaction of such defects when coupled with silicon clusters is

of particular importance. Using first-principles methods, we investigate the atomic adsorption

on graphene with a single vacancy and a double vacancy, as well as the structural and electrical

properties. The presence of defects strongly enhances the interaction between the defective

graphene and Si clusters, dependent on Si type. We observe that SiO strongly adsorbed on the

divacancy graphene with the adsorption energy of -4.59 eV could provide extra intercalation

places for Li atoms, augmenting the adsorption energy of Li from -1.18 eV to -4.15 eV

compared to the pristine graphene. Moreover, it exhibits a threefold increase in the lithiation

/de-lithiation potential and the superior Li storage capacity. The enrichment of Li adsorption

and uptake is also observed in the hybrid Si6/single-vacancy graphene. Thus, the interface

engineering via deposition of various Si clusters on the vacant graphene could be a new strategy

to achieve a promising anode material for Li-ion batteries.

1
Keywords: DFT, Si cluster, 2D-materials, adsorption energy, lithiation potential, Li-ion battery

1. Introduction

Li-ion batteries (LIBs) represent state-of-the-art energy storage technology widely used in

laptops, cellphones, wearable devices and a prospective candidate for hybrid electric cars [1,

2]. The selection of anode material determines the performance of LIBs, so it has always been

a challenge to explore a novel, electrochemically active, abundant material that can achieve

excellent charge capacity and better cycling performance [3]. One of the promising and most

used anode materials for LIBs is graphite because of the reversible intercalation of Li between

carbon layers [4-9]. However, the limited capacity of 3D graphite hampers the feasible use as

the anode material for LIBs. Alternatively, anode materials with low dimensionality can

achieve higher capacity.

Graphene, a two-dimensional material, also stands out for its excellent characteristics,

such as its mechanical strength, large specific surface area, excellent electronic mobility, and

ability to tolerate volume changes, which meet the prerequisites for the candidate anode

material of LIBs [4, 5, 10-12]. The enhanced Li capacity of the graphene-based anode has been

tremendously explored. The previous studies showed that the enhancement was ascribed to the

surface adsorption of Li ions on both sides of graphene or the high surface areas and large d-

spacing in graphene-based materials [5, 13-18]. However, the increased Li contents on

graphene preferably form the cluster, potentially nucleating Li dendrites. Such nanoclusters

can lead to issues with the stability and the failure of the separator layer and LIBs [19]. To

overcome the Li-nanoclusters issue, the adsorption energy of Li on graphene should be more

than the cohesive energy of the bulk Li. Thus, the surface modifications, such as point defects

[20], edge [21], grain boundary [22], and doping [23-26], are the typical techniques to

circumvent the binding energies between Li atoms to prevent cluster formation.

2
 In addition, the high-capacity graphene nanomaterials were achieved by employing O-

containing functional groups and carbon defects, such as reduced graphene oxides or oxidized

graphene nanoribbons [27-29]. The effects of the edge functional groups, i.e., hydrogen,

carbonyl, ether, carboxyl, and hydroxyl groups, on a Li atom's adsorption on graphene

nanoribbons were investigated theoretically using first-principles calculations [17, 18]. The

presence of ketone and carboxyl groups was reported to increase the binding energy of a single

Li atom on graphene nanoribbons due to the formation of covalent bonding between Li atoms

and the edge-oxidized groups [17, 18]. Recent theoretical studies revealed that the

chemisorption of Li ions on graphene was enhanced by epoxy and hydroxyl groups on the basal

plane, thereby increasing the Li capacity of reduced graphene oxides [14, 30].

Silicon (Si) has shown to be an alternative choice of anode materials due to its low cost,

natural abundance, and outstanding theoretical capacity of 3,579 mAh g-1 [31-34], which is

more significant than graphite (372 mAh g-1) [35, 36]. However, Si has some issues and

drawbacks on low electrical conductivity and irreversible electrode damage when it is charged

and discharged because of a volume change up to 380% [37-39]. Several studies proposed to

mix Si with graphene, taking advantage of the high storage capacity of Si and the long-life

cycle and considering the excellent conductivity of graphene [10, 12, 38, 40, 41]. The

multilayer heterostructure of graphene/Si has been constructed experimentally and investigated

the electrochemical performance as the anode material for LIBs [42]. Nonetheless, the desired

hybrid structure could be successfully achieved; it suffers from the weak interaction between

graphene and Si, as indicated by first-principles calculations [43].

Introducing surface defects will be another way to improve the stability of Si adsorbed

structures. Using a graphitic scaffold with in-plane carbon vacancy defects to construct

Si/graphene composite, Zhao et al. demonstrated the benefits of nanometer-sized vacancies on

ion transport for battery electrode applications [10]. In addition, the Si-encapsulated graphene

3
by a self-assembly approach exhibited a fairly good cycling performance of 1,205 mAh g-1

after 150 cycles [44]. Despite these merits, this structure also suffers from unstable solid

electrolyte interphases (SEI) on the surface of nano-sized silicon. Therefore, hollow and yolk-

shell structures of Si composite coated with carbon-based materials were proposed to be an

efficient way to solve this problem [45-50]. Moreover, contact engineering and defect

incorporation of the Si/carbon nanohybrids merit further exploration of the specific defect

identities and types of silicon clusters and their roles in battery performance.

Motivated by this, we propose a new hybrid material of vacancy graphenes and small Si or

Si-oxide clusters. Based on the similar system and the first-principles method, the preceding

works have shown the potential applications of small Si clusters and carbon-based materials as

the Li-battery anode [43, 51-53]. However, their calculations did not consider the O-contained

Si clusters and some electrochemical properties. Herein, we apply the first-principles method

to evaluate the structural stability, electronic conductivity, and lithiation/de-lithiation process

of Si and Si-oxide clusters on defective graphenes for LIB applications. In addition, the uptake

of many Li atoms on each structure and the corresponding redox potentials are computed and

discussed. This work aims to gain fundamental and atomic insights into the influence of Si and

Si-oxide clusters decorated on the defective graphene as an ideal anode material, mitigating the

structural stability and facilitating Li adsorption/desorption for LIB applications. The resulting

calculations and analyses could provide preliminary direction to experimentalists to synthesize

and fabricate Si-cluster decorated defective graphenes as the promising electrode material.

2. Computational details

The first-principles method based on density functional theory (DFT) was performed to

compute all atomic structures, energetics, and electronic properties, as implemented in the

Vienna ab initio simulation package (VASP) with a projector augmented wave (PAW) method

4
[54, 55]. The electron exchange-correlation interactions were treated by the generalized

gradient approximation (GGA) in the form of the Perdew-Burke-Ernzerhof (PBE) functional

[56]. The cut-off energy for the plane-wave basis expansion was 450 eV. The Van der Waals

corrections were taken into account using the DFT-D3 method [57]. During relaxations, the

positions of all atoms were allowed to fully relax until the force on each atom was less than -

0.01 eV/Angstrom between two ionic steps, and the convergence of the electronic self-

consistent energy was less than 10-6 eV. Integration over the Brillouin zone was performed by

using the Monkhorst-Pack scheme [58] with (5x5x1) and (9x9x1) for the geometry

optimization and electronic structure calculations, respectively.

The stability of adsorbed Si atom on the graphene surface can be defined in terms of the

𝑆𝑖
adsorption energy (𝐸𝑎𝑑𝑠 ) as 𝐸𝑎𝑑𝑠 = 𝐸𝑆𝑖𝑥 𝐺𝑟 − 𝐸𝐺𝑟 − 𝐸𝑆𝑖 . Herein, 𝐸𝑆𝑖𝑥 𝐺𝑟 , 𝐸𝐺𝑟 and 𝐸𝑆𝑖 are the

total energies of Si or Si oxide clusters adsorbed graphene, graphene, and isolated Si clusters.

𝐿𝑖
The Li adsorption on the Si-modified graphene is defined as: 𝐸𝑎𝑑𝑠 = 𝐸𝐿𝑖@𝑆𝑖𝑥 𝐺𝑟 − 𝐸𝑆𝑖𝑥 /𝐺𝑟 −

𝐸𝐿𝑖 , where 𝐸𝐿𝑖@𝑆𝑖𝑥 𝐺𝑟 is the energy of Six-modified graphene after Li adsorption, 𝐸𝑆𝑖𝑥 /𝐺𝑟 is the

energy of Six-modified graphene, and 𝐸𝐿𝑖 is the energy of one Li atom. This quantity is used to

assess the stability of the Li atom and Si cluster adsorbed on defective graphene.

It was previously reported that the 4 × 4 cell was sufficiently large to provide adequate

results for atom adsorption on SV graphene [59, 60]. The 5 x 5 supercell (consisting of 50 C

atoms) was thus applied in the current work. Vacancies were introduced into the graphene sheet

by removing one and two atoms for monovacancy and divacancy, respectively. The vacancy

formation energy, 𝐸𝑣𝑓 , made by removing n carbon atoms can be calculated using [61]:

1
𝐸𝑣𝑓 = 𝑛 × [𝐸𝑆𝑉,𝐷𝑉 + 𝑛𝐸𝐶 − 𝐸𝐺𝑟 ], (1)

5
where 𝐸𝑆𝑉,𝐷𝑉 is the total energy of single vacancy or double vacancy graphene, 𝐸𝐺𝑟 is the total

energy of graphene, 𝐸𝐶 is the total energy of a carbon atom, and n is the number of carbon

atoms of graphene. The small molecules, including Si, SiO, Si2, Si2O, Si3, and Si6, were

considered and optimized before they were set to anchor on the graphene sheet, as shown in

Figure S1 in Supplementary Materials.

Bader charge analysis, carried out using Henkelman’s Group program [62-64], was applied

to determine the charge transfer between atoms. It defines the atomic charges and well-defined

kinetic energies as integrals over the Bader volumes. The charge analysis was calculated using

the Monkhorst-Pack scheme with (9x9x1). The Bader charge transfer of SV/DV graphenes

with Si clusters was calculated and shown in Fig. S5.

The lithiation potential

In the following, the lithiation potential of the bulk lithium deposition was evaluated using

the equation [43]:

∆𝐺
𝑉𝑙𝑖𝑡 = − 𝑧𝐹 , (2)

where ∆𝐺 denotes the change of Gibb’s free energy per mol for the lithiated structure from the

bulk lithium and the substrate, F is the Faraday constant, and z is the number of electrons

involved in the electrochemical reaction (one in this case). Noting that ∆𝐺 can be approximated

to be about the internal energy change for the formation of the lithiated structure as obtained

from DFT (~∆𝐸𝑓 ) by neglecting the entropy and pressure terms [9]. This ∆𝐸𝑓 can be computed

using the following equation:

∆𝐸𝑓 = 𝐸𝐿𝑖𝑦 @𝑆𝑖𝑥 𝐺𝑟 − 𝐸𝑆𝑖𝑥 𝐺𝑟 − 𝑦𝐸𝐿𝑖𝑏𝑢𝑙𝑘 , (3)

where 𝐸𝐿𝑖𝑦 @𝑆𝑖𝑥 𝐺𝑟 is the energy of the lithiated structure, 𝐸𝑆𝑖𝑥 𝐺𝑟 is the energy of the graphene

layer modified with silicon, and 𝐸𝐿𝑖𝑏𝑢𝑙𝑘 is the energy of bulk Li in a body-centered cubic

6
structure. The value of ∆𝐸𝑓 in the unit of eV can be associated with the experimentally

measured potential in volts for the Li-lithiated structure versus Li+/Li0 by this relation [9]:

∆𝐸
𝑉𝑙𝑖𝑡 = − 𝑦𝑒𝑓 , (4)
0

where y is the number of Li atoms involved in the electrochemical reaction, and 𝑒0 is the

elementary charge. Negative values of ∆𝐸𝑓 mean Li insertion is energetically favorable

compared to Li bulk formation.

Storage of Li within the Six-modified graphene sheets

Many Li-ions are really involved in the actual electrochemical reaction of a battery. Therefore,

an understanding of Li-Li interaction is needed to be addressed. Also, it is vital to examine the

feasibility of Li cluster formation, which strongly affects cyclic efficiency. To address the issue

of Li storage capacity, Li's formation (adsorption) energy can be calculated using Eq.(3) listed

above. The maximum number of Li uptake near the Si clusters at the vacancy represents its Li

storage capacity.

The equilibrium redox potential

The equilibrium redox potential measured from bulk lithium metal corresponds to Li

movement into and out of a graphene sheet. Equivalently, it corresponds to lithium injection

from m to m+n atoms in the computational cell or lithium extraction from m+n to m atoms,

which can be expressed by the following equation [61, 65, 66],

1 𝐸(𝑔𝑟𝑎𝑝ℎ𝑒𝑛𝑒 + 𝐿𝑖(𝑚)) + 𝑛𝐸(𝐿𝑖)

𝑉𝑟𝑒𝑑𝑜𝑥(𝑚↔𝑚+𝑛) = 𝑛 × [ ], (5)
−𝐸(𝑔𝑟𝑎𝑝ℎ𝑒𝑛𝑒 + 𝐿𝑖(𝑚 + 𝑛))

where 𝐸(𝑔𝑟𝑎𝑝ℎ𝑒𝑛𝑒 + 𝐿𝑖(𝑛)) and 𝐸(𝐿𝑖) represents the total energy of the substrate containing

n lithium atoms and the total energy of bulk lithium. The average potential for lithium removal

or injection can be estimated by ignoring entropy, volume change, and temperature effects [66].

7
Positive potential indicates Li intercalation is energetically favorable compared to bulk Li

metal precipitation.

3. Results and discussion

Si-cluster modified defective graphene and Li adsorption

We first constructed and optimized a graphene sheet without a carbon vacancy, as

shown in Fig. 1. The 5 x 5 supercell (consisting of 50 C atoms) was used to simulate the isolated

sheet while allowing the vacuum region of 15 Å in the z-direction to avoid the interaction of

the close periodical images. The Si or Si oxide clusters were fully optimized before they were

set to anchor on the graphene to find the most stable structure. Theoretical and experimental

studies have shown the 2D-3D transition of Si clusters when Si atoms are greater than 5 due to

the preference of sp3 hybridization [67-70]. It should be noted that Si6 is stable among small

Sin clusters (n=2-13) [71], and it is found abundantly in experimental mass spectra. The

optimized Si6 geometry agrees with the previous calculations [51, 52]. Figure 1(c) displays the

Si adsorption on various sites: on top of a carbon atom, at the bridge between two nearest C

atoms, and at the center of the 6-membered C rings of graphene (hollow). The bridge site seems

to be one of the most energetically favorable sites for Si atom with Eads=-0.5 eV and the

adsorption length of 2.21 Å, which corresponds to the literature data [43]. Therefore, the Si

atom is first placed at the top, and hollow sites move to the bridge site in the course of geometry

optimization. Interestingly, the interaction between pristine graphene and Si atoms reveals

relatively weak adsorption compared to the strong covalent bonds between each carbon atom

of the graphene sheet. As a result, no distortion of the graphene is observed after Si adsorption,

as shown in Fig. 1(c).

8
Figure 1: (a) The optimized structure of graphene used in the calculations. The 5 x 5 supercell

(consisting of 50 C atoms) was used to simulate the isolated sheet, while the vacuum region of

15 Å was expanded in the z-direction for the unit cell. (b) The optimized small Si-clusters,

including Si, Si2, SiO, Si2O, Si3, and Si6. Grey: C atom, brown: Si atom, and red: O atom. (c)

Optimized structures of graphene, Si, and Si3 adsorbed on graphene (left) and DOS plots of

graphene, Si, and Si3 adsorbed on graphene (right).

It is worth noticing that the Si3 cluster weakly adsorbed onto the graphene surface with

𝑆𝑖
𝐸𝑎𝑑𝑠 = -0.037 eV. This can be understood by the distribution of charges of neighboring Si

atoms, resulting in the weaker Si-graphene interaction where the absolute values of (Eads)Si >

(Eads)Si3. Considering the aforementioned studies to strengthen this weakened interaction, it has

been shown that carbon nanotube (CNT) functionalization could increase the binding energy

between Si clusters and CNT [52]. In addition, the silicon carbide at the Si/HOPG (Highly

Ordered Pyrolytic Graphite) interface, which can be generated by intermixing induced by the

Ar-ion beam, is another approach to improve the adhesivity of silicon and carbon [72]. An

alternative method of graphene’s defects has also been proposed to improve the Si-carbon

interaction.

9
 Herein, the monovacancy and divacancy graphenes were constructed when single and

double carbon atoms were removed, respectively. We calculated the vacancy formation

energies (𝐸𝑣𝑓 ) using Eq.(1) listed above. The 𝐸𝑣𝑓 for the single vacancy and divacancy

graphene are 7.64 eV and 3.86 eV, in agreement with the prior studies [73, 74]. The results

suggest that single vacancy graphene with higher formation energy is less stable than graphene

with double vacancies. We then examined the Si atom on various sites on the single (SV) and

double (DV) graphenes, as shown in Table 1 and Fig. 2. The Si’s binding energy of the

defective graphene has a significantly high value of -8.24 eV and -7.64 eV for SV/Si and

DV/Si, respectively. The Si-C length of SV, lSi-C, defined as the distance between the Si atom

and its nearest C atom in the graphene sheet, is 1.76 Å. The bond length of DV (lSi-C) is 1.89

Å, displaying the stretched bond in this case. It is evident that the adsorption energy of Si is

favorable and robust, producing changes in the geometry of the defective graphene. As a result,

the Si atom and its neighboring C atoms of SV/Si are protruded out of the plane, indicating a

tetrahedral geometry (sp3 hybridization), as shown in Fig. 2(a).

10
 𝑆𝑖
Table 1: The calculated adsorption energy (𝐸𝑎𝑑𝑠 ) of small Si-clusters on defective graphenes,

𝐿𝑖
𝐸𝑎𝑑𝑠 denotes the Li adsorption energy on the substrate, d is the shortest atom-to-atom distance

between the molecule and the surface, and the charge transfer (ΔQ). The positive value of ΔQ

indicates an electronic charge transfer from the Si clusters and Li atoms to the substrate.

Configuration 𝑬𝑺𝒊
𝒂𝒅𝒔 (eV) dSi-C (Å) 𝑬𝑳𝒊
𝒂𝒅𝒔 (eV) d (Å) ∆𝑸 (e) Vlit (V)

SV/Si -8.24 1.76 -1.57 Li-C, 2.10 2.72 -0.07

SV/SiO -4.59 1.83 -3.99 Li-O 1.64 2.21 2.36
SV/Si2 -6.80 1.80 -2.32 Li-C 2.20 2.80 0.69
SV/Si2O -7.24 1.77 -1.65 Li-O, 1.91 3.06 0.02
SV/Si3 -6.32 1.77 -2.56 Li-C, 2.21 2.64 0.92
SV/Si6 -4.76 1.83 -2.99 Li-C, 2.23 2.17 1.35
DV/Si -7.64 1.89 -2.22 Li-C, 2.18 3.35 0.59
DV/SiO -4.49 1.80 -4.15 Li-O, 1.71 2.20 0.64
DV/Si2 -7.29 1.88 -1.93 Li-C, 2.23 3.35 0.30
DV/Si2O -6.58 1.85 -2.46 Li-O, 1.91 3.49 0.83
DV/Si3 -6.51 1.97 -1.87 Li-C, 2.21 4.12 0.24
DV/Si6 -4.24 1.86 -2.48 Li-C, 2.20 3.36 0.59

In the case of a double-vacancy defect, the silicon atomic orbital shows an sp2 d

hybridization, allowing the silicon atom to remain in the graphene plane as shown in Fig 2(b)

for Si adsorption in good agreement with other theoretical reports [43]. Such optimized

geometries of SV/Si and DV/Si are in accordance with the experimental report [75], showing

that the Si atom bonds with three other atoms in an SV site or with four atoms in a DV site.

We also calculated the Li adsorption/insertion energies (Eads) on carbon vacancies of SV/DV,

as shown in Table 1 and Fig. 2(c). The results show that the Li atom binds with C atoms of the

defective graphene with Eads = -1.57 eV (lLi-C = 2.10 Å) and -2.22 eV (lLi-C = 2.18 Å) for

11
Li@SV/Si and Li@DV/Si, respectively. The shortest separation between Si from SV graphene

plane and Li atom is found to be 1.81˚A.

Figure 2: Optimized configurations for Si, SiO, Si2, Si2O, Si3, and Si6 adsorbed on (a) single-

vacancy graphene and (b) double vacancy graphene (side view) without and with Li adsorption.

The brown, blue, red, and green spheres represent the C, Si, O, and Li atoms. (c) Adsorption

𝑆𝑖 𝐿𝑖
energies of Si and Si oxide clusters (𝐸𝑎𝑑𝑠 ) and of lithium atom (𝐸𝑎𝑑𝑠 ) upon (a) single vacancy

graphene and (b) double vacancy graphene, respectively.

The binding energies of other small Si-clusters on SV graphene range from -4.59 to -

8.24 eV, with the weakest adsorption due to SV/SiO. All optimized configurations are

illustrated in Fig. 2 (side view) and Fig. S1 (top view) of Supplementary Materials. With the

12
double vacancy, Si can also be adsorbed effectively on defect graphene with the most immense

binding energy up to -7.64 eV for DV/Si and the most minor binding energy of -4.49 eV for

DV/SiO (See Table 1 and Fig. 2). The Si atom thus exhibits a more vital interaction with SV

than the pristine graphene and DV, inducing substantial out-of-plane distortions to the graphene

𝑆𝑖
sheet. For lithium adsorption, both SV/SiO and DV/SiO reveal the two largest values of 𝐸𝑎𝑑𝑠

= -3.99 eV and -4.15 eV exhibiting strong Li-O bonds with lLi-O = 1.64 Å and 1.71 Å,

respectively. Noticeably from Fig. 2, the Li atom preferably binds to the O atom of Si oxide

clusters rather than the carbon atoms of the defective graphene. The interaction between the O-

contained Si cluster and SV/DV is considerably strong, and due to this interaction, their

optimized structures undergo dramatic structure changes (See Fig. 2).

Both SV and DV demonstrate weaker adsorption when the cluster is larger. In addition,

most Si-clusters are situated above the graphene plane according to their sizes. A decrease is

observed in the calculated adsorption energies of the Si2, Si3, and Si6 upon encountering the

defective graphenes, ranging from -6.80 eV to -4.76 eV and -7.29 eV to -4.24 eV for SV and

DV, respectively. The weaker interaction is responsible for the large cluster finding Si

neighbors. At the same time, the adsorption length (lSi-C) ensures that the Si-clusters adhere

𝑆𝑖
firmly to the carbon atoms of defect graphenes. The Si6 cluster binds with SV and DV at 𝐸𝑎𝑑𝑠

𝑆𝑖
of -4.76 eV and -4.24 eV, respectively, which are smaller than Si on the SV graphene (𝐸𝑎𝑑𝑠 =-

8.24 eV). However, as shown in Table 1, Si/SV demonstrates a weaker Li adsorption of -1.57

eV than that of Si6/SV (-2.99 eV). This means that the presence of the Si cluster, particularly

Si6, is more efficient in terms of Li storage capacity.

Electronic properties of Si cluster on pristine and defective graphenes

The density of states (DOS) and the charge analyses were calculated to discuss how the

electronic structure of graphene was modified by point defects, Si-clusters, and the adsorbed

13
Li atom. DOS of graphene, Si, and Si3 adsorbed on graphene was simulated comparatively, as

shown in Fig. 1(c). Their states are almost identical except for the peaks around the Fermi level

generated by the presence of Si atoms in C/Si and C/Si3. It can be seen that the presence of the

Si atom strongly affects the electronic configuration around the Fermi level, leading to the new

𝑆𝑖
states due to the 3p orbitals of Si atoms. Though 𝐸𝑎𝑑𝑠 becomes smaller as the number of Si

atoms increases, the DOS levels are slightly narrower and shift upward to a higher energy than

the pristine graphene. For the pristine graphene upon Li adsorption, the computed DOS profile

in Fig. 1 is almost unchanged except for the Ef shift towards the higher energy state (conduction

state). This is due to the addition of an electronic charge from Li. It is also evident that the Li

atom acts as a dopant near the Fermi level donating its electron to the neighboring carbon atoms

as indicated in the Bader charge analysis in Fig. S3(a) of Supplementary Materials.

Similar to the DOS of SV and DV, their overall DOS after Si, Si2, or Si3 adsorption

demonstrates Si peaks around the Fermi level (Fig. 3 and Fig. 4), according to the strong

interaction between Si atom and C atoms of the defect graphene. It can be observed that the

DOS of Si/SV is like that of graphene because of the replacement of the C atom with the Si

atom creating Si-C covalent bonds (See Figs. 1(c) and 3). This observation is in agreement with

an sp3 hybridization for SV. Meanwhile, Si/DV demonstrates an sp2 d hybridization associated

with the optimized geometry of silicon atom remaining in the defective graphene’s plane, as

depicted in Fig. S1 of Supplementary Materials. In addition, the inclusion of Si-clusters in the

structure notably affects the shift of Ef to the higher energy, as shown in Fig. 3. While the O-

contained Si cluster displays the Ef shift to the lower energy, coinciding with the electronic

charge transfer from the cluster to the vacant graphene, as shown in Table 1. After lithiation,

Li@SV/Six and Li@DV/Six reveal more sharp peaks around the Fermi level, resulting in

narrower bandgaps than SV/Six and DV/Six (See Figs. 5(a,b) and 6(a,b)). The emergence of the

sharp peaks indicates that it is easier for electrons to jump from the valence band to the

14
conduction band, showing a higher electronic conductivity. As a result, the levels are slightly

shifted to the conduction band and become partially occupied.

Figure 3: Density of states (DOS) of Si-clusters adsorbed on single-vacancy graphene.

Figures 5 and 6 indicate the system's partial density of states (PDOS) of Si-clusters

adsorbed on SV after lithiation, revealing the overlaps between the Si states and Li atoms.

There is a weak hybridization between Si-2p and Li–1s orbitals near the Fermi level, as shown

in Fig. 5(a). Similarly, the hybridization of orbitals of Si and Li in Fig. 5(b) can be observed in

Li@SV/Si2, which becomes weaker for Li@SV/Si3 and barely seen for Li@SV/Si6. This

reflects the interaction of Si and Li atoms that the larger Si cluster shows weaker adsorption to

Li, as can be observed by the stretched lSi-Li bond lengths in Table 1. Remarkably, the DOS of

Li@SV/SiO and Li@SV/Si2O has shifted to higher energy levels, as illustrated in Fig. 5(b),

resulting in peaks at the Fermi level. Meanwhile, the small hybridization between Li-1s and O-

15
2p orbitals of the small SiO and SiO2 near the Fermi level can be observed in Fig. 5(b). This

could refer to the interaction between Li and O atoms of oxide-contained silicon clusters.

Figure 4: Density of states (DOS) of Si-clusters adsorbed on double-vacancy graphene.

DOS of DV without Si (Fig. S2) indicates the Fermi level as distinct from the pristine

graphene. However, the inclusion of Si to DV results in the emergence of states mostly near

the Fermi level, and the EF shifts to the higher energy level shown in Fig.4. The Si2 cluster on

DV mainly exhibits a very sharp peak at the Fermi level. After the lithiation process, the DOS

of Li@DV/Si and Li@DV/SiO in Fig. 6(a) have no evident changes compared to their electrical

structures without lithium atoms (DV/Si and DV/SiO). However, unlike DV/Si2, DV/Si2O,

DV/Si3, and DV/Si6 upon Li adsorption reveal the DOS shifts upwards the higher energy levels

with the sharp peaks at the Fermi level for Si3, and Si6 clusters adsorbed onto the structure (see

Fig. 6(b)). In addition to DOS, there is a hybridization between Si-2p and Li-1s orbitals around

2 eV above the Fermi level in Li@DV/Si3 and Li@DV/Si6, as shown in Figs. 6(b). It can be

noticed that O-2p and Li-1s of Li@DV/SiO and Li@DV/Si2O show orbital hybridization above

16
the Fermi level. While their peaks around the Fermi level of Li@DV/Si2O are contributed

mainly by Si-3p, as depicted in Fig. 6(b).

Figure 5: Density of states (DOS) and partial density of states (PDOS) of single-vacancy

graphene modified with Si, SiO, and Si2 (a) and Si2O, Si3, and Si6 (b) upon lithiation denoted

as Li@SV/Six. Blue, red, and green lines in PDOS correspond to Si-3p, O-2p, and Li-2s,

respectively. The corresponding isosurface of charge density difference due to incorporating a

Li atom on single-vacancy graphenes decorated with small Si-clusters (c, d). The yellow and

cyan regions represent the charge accumulation and depletion, respectively, and the value for

the isosurface is 0.000903721 e/A3.

The charge density differences are calculated and shown in for Si-cluster decorated-

single vacancy graphene (Figs. 5(c,d)) and for double vacancy graphene (Figs. 6(c,d)) after the

lithiation process. Electronic charge depletion around the Li atom is represented by cyan. The

results suggest the charge accumulation (yellow region) around Si and O atoms. The isosurface

17
of the charge density differences was computed using, ∆𝜌 = 𝜌𝑡𝑜𝑡𝑎𝑙 − 𝜌𝐺𝑟 − 𝜌𝑆𝑖𝑥 +𝐿𝑖 , where

𝜌𝑡𝑜𝑡𝑎𝑙 , 𝜌𝐺𝑟 , 𝜌𝑆𝑖𝑥 +𝐿𝑖 are the charge densities of the total system, the defective graphene, and the

adsorbed Six clusters and Li atom, respectively.

The electrons are mainly located near the surface in all cases, implying electrons

transferred from the adsorbed molecule to the substrate following the results of ∆𝑸 as observed

in Table 1 and Figs. 5(c,d) and 6(c,d). The charge transfer is computed using Bader charge

analysis which the details are listed in the calculation part. Si is less electronegative than

carbon, making the electrons move from Si to neighboring carbon atoms. Therefore, the Bader

charge state of the Si atom (Li@DV/Si) interacting with the neighboring C atoms indicates a

more robust charge transfer than the Li@SV/Si (Fig. 6(c)), corresponding to the more

pronounced ∆𝑸 of 3.35 e.

18
Figure 6: Density of states (DOS) and partial density of states (PDOS) of double-vacancy

graphene modified with Si, SiO, and Si2 (a) and Si2O, Si3, and Si6 (b) upon lithiation denoted

as Li@DV/Six. Blue, red, and green lines in PDOS correspond to Si-3p, O-2p, and Li-2s,

respectively. The corresponding isosurface of charge density difference due to incorporating a

Li atom on double-vacancy graphenes decorated with small Si-clusters (c, d). The yellow and

cyan regions represent the charge accumulation and depletion, respectively, and the value for

the isosurface is 0.000903721 e/A3.

The largest ∆𝑸 for each defective graphene are 3.06 e and 4.12 e for Li@SV/Si2O and

Li@DV/Si3, respectively. This is associated with the relatively larger value of the Bader charge

state of the C atoms interacting with the Si, O, and Li atoms, as shown in Figure S3 of

Supplementary Materials. Additionally, ∆𝑸 of Li@DV/Si2O in Fig. 6(d) is relatively high up

to 3.49 e, comparable to ∆𝑸 of Li@SV/Si2O (3.06 e) in Fig. 5(d). It should be noted that there

is a larger charge transfer in DV than SV, demonstrating evident changes occurring in the local

electronic structure of double-vacancy graphene. Given the significant charge transfer of DV

anchored with Si clusters, it is speculated to show the greater capacity of the anode material.

The lithiation potential can be calculated from Eqs. (3) and (4). The computed 𝑉𝑙𝑖𝑡 for

the perfect graphene shows a negative value of -0.45 V (data not shown), agreeing with the

previous report [43]. The negative sign indicates that Li adsorption on pure graphene is not

favorable. It becomes less negative, i.e., -0.07 V in the case of SV/Si as indicated in Table 1,

meaning a better situation for Li inserting. The structure facilitating the most lithiation process

is SV/SiO, showing Vlit=2.36 V as listed in Table 1. A single Li atom prefers to bind at the Si-

Si bridge site of SV/Si6, providing a relatively large Vlit of 1.35 V.

𝐿𝑖
However, only a single Li atom is focused on the 𝐸𝑎𝑑𝑠 and 𝑉𝑙𝑖𝑡 calculations. The

situation may change when there are a lot of Li ions diffusing in the anode materials. The ease

19
of Li insertion on a given structure profoundly affects the Li storage capacity. In the following,

we selected SV/SiO, SV/Si6, DV/SiO, and DV/Si6 based on their considerable Li binding

energy and 𝑉𝑙𝑖𝑡 for further evaluating the Li-Li interaction, as shown in Fig.7. Though SV/Si3

and DV/Si2O present relatively large charge transfer, it may pose the dendrite formation issue

due to the small Li-binding energy. Note that the substrate that can bear more Li content can

potentially carry and store more charges, leading to a larger capacity. The number of Li uptake

of each structure is varied to which the 𝐸𝑓 is negative, Li is no longer adsorbed at the Six cluster,

or the cluster is deformed according to the excess Li adsorption. This represents the upper limit

of Li uptake around the defect and the Si cluster. It is worth noting that this Li capacity is not

the same as the specific capacity (expressed in mAh g-1) of anode material. The result of 𝐸𝑓 of

pristine graphene reveals the positive value of +0.46 eV upon one Li adsorption as listed in

Table 2, implying the possible Li clustering formation.

Table 2: The calculated formation energies (𝐸𝑓 ) and redox potentials of the Li adsorption on

pristine, monovacancy, and divacancy graphenes (SV and DV), compared with the defective

graphenes contained SiO or Si6 cluster (SV/SiO, SV/Si6, DV/SiO, and DV/Si6).

System n (Li Formation Redox System n (Li Formation Redox

(single) atoms) energy potential (double) atoms) energy potential

(𝐸𝐹 , 𝑒𝑉) (𝑉𝑟𝑒𝑑 , 𝑉) (𝐸𝐹 , 𝑒𝑉) (𝑉𝑟𝑒𝑑𝑜𝑥 , 𝑉)

Pristine 1 0.46 -0.46 N/A N/A N/A N/A

graphene

SV 3 -0.88 -0.52 DV 2 -0.56 -0.11

SV/SiO 3 -2.78 -0.72 DV/SiO 4 -5.41 0.17

SV/Si6 6 -2.07 -0.51 DV/Si6 3 -3.20 0.87

20
 Using Eq. (3), 𝐸𝑓 of the representative structures were computed as depicted in Fig. 7

and Table 2. The positive value of 𝐸𝑓 indicates the possible clustering of Li. Thus, it is evident

that defects and Si-clusters of all the structures could promote Li adsorption while mitigating

the Li dendrite nucleation. As a result, SV/Si6 has the highest capacity and can store up to 6 Li

atoms with 𝐸𝑓 =-2.07 eV (See Fig. 7). In terms of the largest negative 𝐸𝑓 , DV/SiO exhibits the

value of -5.41 eV, while it can store a relatively great number of Li up to 4 atoms. The structural

modification by Si6 and SiO clusters thus plays a crucial role in creating a sufficiently spatial

site for Li addition.

Figure 7: (a) Formation energy (𝐸𝑓 ) and (b) equilibrium redox potential (Vred) of the Li

adsorption on the hybrid Si-cluster/single-vacancy and double-vacancy graphene.

It is known that DFT calculations could be used to estimate the redox potential (𝑉𝑟𝑒𝑑𝑜𝑥 )

without using any experimental parameters to predict many properties [76]. As a result, the

𝑉𝑟𝑒𝑑𝑜𝑥 of SV/Si6 displays the negative value of -0.06 V since the 4th Li insertion as depicted in

21
Fig. 7. Meanwhile, DV/SiO shows the positive value of 𝑉𝑟𝑒𝑑𝑜𝑥 (0.17 V) up to the 4th Li

adsorption, while the extra addition of a Li atom leads to a negative value (data not shown).

Thus, the upper limit of the lithium storage capacity on DV/SiO and SV/Si6 in terms of 𝑉𝑎𝑣 are

4 and 3 atoms, respectively. Together, the SiO-adsorbed divacancy graphene demonstrates the

energetically favorable Li insertion (Ef) and the more pronounced influence for Li movement

towards the electrode (Vav). Moreover, it exhibits structural and electrical properties

satisfactorily suitable for LIB applications, as shown in Eads and DOS. Besides DV/SiO, SV/

Si6 is an attractive candidate as the anode material for future developments because of its

satisfactory properties.

4. Conclusions

In summary, the novel structure of hybrid defective graphene and small Si clusters has been

proposed as a potential anode material for LIBs. Using the first-principles calculations based

on DFT, the effects of small Si clusters and the interfacial phenomena on single-vacancy and

double-vacancy graphenes are investigated. The design of elaborated nanostructures includes

incorporating graphene defects to ensure the host's stability and minimize the undesired volume

expansion of Si clusters. From our calculations, the interaction between Si clusters and the

defective graphene is quite strong, forming Si-C bonds with the underlying support surface.

Furthermore, the bonding is significantly varied by the size of Si clusters, while the interaction

is weakened when the cluster becomes larger.

The Li uptake ability has been examined by computing the adsorption energy and the

lithiation potential of a single Li atom. Meanwhile, the formation energy and the redox

potential are calculated in the case of many Li atoms adsorbed at the cluster. We find the hybrid

nanostructure could strongly uptake more Li atoms than the pristine graphene and the defective

graphene. Specifically, the double-vacancy graphene with SiO and single-vacancy graphene

22
with Si6 reveal the enhanced structural, electrical properties and Li storage capacity. This study

highlights the importance of interface engineering in the design of hybrid Si clusters/defective

graphene as an anode material for batteries and supercapacitors.

Declaration of competing interest

The authors declare no competing interest.

Acknowledgments

ML acknowledges NSTDA Supercomputer Center (ThaiSC) for providing computing

resources.

Data availability

The data that support the findings of this study are available from the corresponding author

upon reasonable request.

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