Tuning Adsorption of Methylamine and Methanethiol on Twisted

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C: Physical Processes in Nanomaterials and Nanostructures

Tuning Adsorption of Methylamine and Methanethiol on Twisted-Bilayer Graphene Francisco Hidalgo, Alberto Rubio-Ponce, and Cecilia Noguez J. Phys. Chem. C, Just Accepted Manuscript • DOI: 10.1021/acs.jpcc.9b02577 • Publication Date (Web): 03 Jun 2019 Downloaded from http://pubs.acs.org on June 4, 2019

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The Journal of Physical Chemistry

Tuning Adsorption of Methylamine and Methanethiol on Twisted-Bilayer Graphene Francisco Hidalgo,∗,† Alberto Rubio-Ponce,† and Cecilia Noguez‡ †Departamento de Ciencias Básicas, Universidad Autónoma Metropolitana-Azcapotzalco, Av. San Pablo 180, Cd. de México C.P. 02200, México ‡Instituto de Física, Universidad Nacional Autónoma de México - Apartado Postal 20-364, Cd. de México C. P. 01000, México E-mail: [email protected]

Abstract The influence of a second graphene layer on the adsorption of methanethiol and methylamine is studied using density functional theory. Exploring different adsorption sites, we compare adsorption energies of both molecules on the monolayer, A-B stacked bilayer and three different twisted-bilayer graphene systems. Results show that both molecules are physisorbed with energies larger than room temperature on determined sites, where methylamine is stronger adsorbed than methanethiol. In A-B stacking, adsorption energies are always smaller than those found in the monolayer. However, at some relative angles between the top and bottom graphene layers, the adsorption energy increases suggesting a molecular-adsorption tuning effect. Although the electronic charge at the interlayer and vacuum regions suffer a rearrangement, there is no charge transfer between molecules and graphene layers. It is expected that these results motivate further studies of molecule adsorption using as additional parameter the relative angle in twisted-bilayer graphene.

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Abbreviations DFT, mLG, bLG, tbLG.

1. Introduction Molecular adsorption is the physical phenomenon inherently associated with functionalization, sensors design and self-assembly. Nanostructures such as nanoparticles, slabs, and surfaces 1–4 are the main candidates to explore these novel topics, with the purpose of developing the new technological age. Among them, two-dimensional materials, structures with a large surface-volume ratio at the nanoscale with only a few atoms for thickness, open a vast possibility to discover new physical and chemical properties useful, for instance, in materials science, catalysis, sensor design, biological engineering, and photovoltaic devices 5–8 to name but a few. Pristine monolayer graphene (mLG), a two-dimensional material structured as a honeycomb of carbon atoms, exhibits an excellent set of physical properties: chemical stability, mechanical flexibility, high optical transparency, high carrier mobilities, good biocompatibility, and excellent thermal and electrical conductivities. 9–13 However, the use of pristine graphene for electronic devices or sensors is not proper because of the lacking of a bandgap, as well as inertness to reactions. Hence, functionalization of graphene, the chemical process focused on adding new features, capabilities or properties changing its surface chemistry, is crucial for future applications on electronic devices. 7,11,14,15 Such functionalization can be accomplished through covalent bonding 16,17 or non-covalent interactions. 7,15,18 Noncovalently functionalized graphene is considered for potential applications in biomedicine and biosensing, involving mainly detection, diagnostic, cell imaging, and drug delivery. 7,15,19,20 Further, bilayer graphene (bLG) exhibits characteristics that make it different from the single layer. 21–23 While mLG and bLG have no band gap between the valence and conduction bands, their low-energy band structure is different: a quadratic dispersion for bLG 2


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rather than a linear dispersion for mLG. In principle, it is possible to functionalize each layer differently, thus generating new physical and chemical properties. 18,24,25 Additionally, a relative twist angle between the top and bottom layer in the bLG originates a twisted-bilayer graphene (tbLG) with specific moiré pattern, a new periodic feature associated with the new symmetry of the structure. 23,26 The possible angles are limited by the symmetry condition of the hexagonal lattice, i.e., 0◦ < θ < 60◦ , which forms a discrete set of rotation angles due to commensurate conditions. 23,26 For angles 10◦ < θ < 50◦ , the two layers can be considered decoupled, exhibiting a linear dispersion of electronic bands near to Fermi level similar to those of mLG. 27 Instead, small angles induce strongly correlated electrons, which generates all a new whole of interesting and fascinating physical properties: an angle-dependence of van Hove singularities, 28,29 the existence of superconductivity for certain magic angles, 30,31 flat bands near to Fermi level, 27,32 a reduction of the Fermi velocity for angles lower than a critical value, 27,30,33 just to mention a few. In view of the above, it is interesting to elucidate whether a twist angle in tbLG induces changes in the adsorption energy of molecule respect to mG or bLG cases. This is the main target of this work. Herein, we study the adsorption of methylamine and methanethiol on mG, bLG, and three tbLGs. Both molecules are formed by different functional groups, which are essential constituents of many different organic molecules, like cysteine. Hence, before to study the adsorption of more complex molecules, it is advantageous to understand the behavior of individual functional groups through small molecules. The three tbLGs have twist angles of 13.17◦ , 32.20◦ and 44.80◦ . Small twist angles require large unit cells, which increases the computational effort. Hence, through these tBLGs we study the molecular adsorption in the decoupled regime of graphene layers. This manuscript is organized as follows. Section 2 summarizes the computational method. In section 3, the atomic models of graphene layers and molecules are described; also, adsorption sites are defined. The final configuration of structures and adsorption energies for each molecule adsorbed on graphene layers are shown and discussed in section 4. Section 5 summarizes our main results. 3



2. Computational details All calculations are based on density functional theory (DFT) through the siesta package. 34 Local density approximation (LDA) in the Perdew and Zunger functional form 35 describes the exchange-correlation part of the total energy. It has been widely discussed that LDA calculations for determining structural and electronic properties of graphene-based interfaces get an excellent agreement in comparison with other functionals. 36,37 All calculations employ a basis set constituted by double-ζ polarized orbitals. siesta uses strictly localized atomic orbitals; 34,38 then, the basis set has to be large enough to describe vacuum and interface regions. For a correct description of the electronic properties of systems such as surfaces, twodimensional structures, and long-range interactions, an extended basis set must be considered whenever the basis set is strictly localized. 39 Hence, we employ an extended atomic basis set by including diffuse orbitals, as proposed by García-Gil et al., for noble metal surfaces. 39 Therefore, 3p diffuse orbitals for carbon and nitrogen atoms, as well as 4p orbitals for sulfur atoms are included to enlarge the basis set. Comparison between the standard and extended basis set is discussed in Supporting Information to keep continuity in the manuscript (see Figure S1 and Table S1). Here, all unit cells have more than 20 Å of vacuum along the normal direction to graphene layers, which avoids spurious interactions between periodic replicas along this direction. Additionally, our calculations include a dipole correction to cancel the artificial electric field generated by the periodic boundary conditions imposed on the electrostatic potential inherent to asymmetric slabs, as suggested by Bengtsson. 40 For accurate Brillouin zone (BZ) integrations, the Monkhorst and Pack scheme 41 is employed with a (11 × 11 × 1) k-grid. Finally, geometrical optimizations were carried out keeping fixed the cell parameters, but allowing a structural relaxation up to interatomic forces were smaller than 0.01 eV/Å in each atom.

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3. Atomic models and adsorption sites Here, mLG is simulated by a 6 × 6 supercell containing 72 carbon atoms and a corresponding 2

surface area of ∼ 189 Å , as shown in Figure 1(a). We found that this is the minimum size cell to obtain negligible molecule-molecule electrostatic interactions between neighboring unit cells when periodic conditions are applied on the plane direction. Lattice vectors are √ √ a1 = 6 × a0 23 , 12 and a2 = 6 × a0 23 , − 21 , where a0 = 2.459 Å is the lattice parameter of graphene with a corresponding C C bond length of 1.420 Å. 22,42 For all the structures studied here, a0 is kept fixed. bLG in A-A stacking consists of two graphene layers, locating one of them (the top layer) exactly above the other (the bottom layer), such that, all carbon atoms at the top and bottom layers are vertically aligned. However, A-A bLG is considered as metastable structure as reported by just a few experimental groups. 22,23,43,44 Therefore, A-A bLG it is not included in this work. However, A-B stacking, also called the Bernal stacking, is constructed from the A-A stacking by just displacing the top layer respect to the bottom one by exactly a C C bond length and along the binding direction, as it is shown in Figure 1(b) and 1(c). All carbon atoms in the top layer of A-B bLG are either top (t) atoms, located atop atoms at the bottom layer; or hole (h) atoms, situated at the center of a hexagon of the bottom layer. Using similar criteria to those described above in mLG, bLG is also simulated with a 6 × 6 supercell, now containing 144 carbon atoms but with the same lattice vectors and surface area than mLG, as shown in Figure 1. A-A and A-B stacking represent bLG with zero relative angles between the top and bottom layers. tbLG emerges when an angle is generated by a relative rotation of the top layer respect to the bottom around a perpendicular axis to both planes. 23,26 In principle, there are not experimental limitations to obtain any relative angle between layers, except for good control over it. 26,45,46 However, in computational simulations of infinite 2D systems, structures must obey strictly periodic and commensurable conditions. 23,26,47 Otherwise, it would be necessary to apply computational methods used for quasicrystals, which are computationally more demanding. Although commensurability and periodic conditions are assured, 5



Figure 1: Top view of 6 × 6 supercells of (a) mLG and (b) A-B stacked bLG. (c) Side view of bLG with an interlayer distances dt−b . Adsorption sites in mLG are: top (T), hollow (H), and bridge between nearest neighbors (B) and second neighbors (B2). Adsorption sites in bLG are: Top aligned with an atom on the second layer, (Tt ), or aligned with a hole (Th ), bridge between nearest neighbors in the top layer (B), between second neighbors in two different configurations, (Bt ) or (Bh ), and hollow (H). Open circles indicate top (t) and hole (h) atoms in the first layer. the viable theoretically relative angles are still restricted by the number of atoms in the unit cell. 23,26,46 Commonly, two integers (n, m) help to denote commensurated tbLG. 47 In this work, we study three tbLG with relative angles θ = 13.17◦ , 32.20◦ , and 44.80◦ that correspond to (n, m) integers: (3, 2), (3, 1), and (6, 1). Their corresponding structural parameters are shown in Table 1. By construction, unit cells of (3, 2) and (3, 1) tbLG have surface areas which are smaller than the corresponding 6 × 6 supercell of mLG. Hence, it is necessary to construct 2 × 1 and 2 × 2 supercells, respectively, to assure that those moleculemolecule interactions are still negligible. Therefore, these tBLG have a reasonable number of atoms in their unit cells and, at the same time, obey the minimum size cell required to avoid molecule-molecule interactions among different unit cells. Figure 2 depicts the supercells of the three tbLG studied here. Furthermore, we construct all bLG and tbLG assuming an initial interlayer distance of dt−b = 3.33 Å, 22,23 as seen in the side view of bLG in Figure 1(c). 6


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Figure 2: (a) 2 × 2 (3,1), (b) 2 × 1 (3,2) and (c) 1 × 1 (6,1) supercells of twisted-bilayer graphene (tbLG). Arbitrary path for each tbLG is denoted in grey, including the eleven equidistant adsorption sites. H and T adsorption sites are also shown for tbLG. Carbon atoms are in brown and orange for the top and bottom layer, respectively. Table 1 details the main structural parameters of each unit cell. After setting up all bLG and tbLG, we bring the structures under a geometry optimization, observing slight structural changes, including a small corrugation in tbLG. Herein, corrugation on graphene is understood as a buckling on the plane and defined as the difference between the maximum and minimum vertical coordinates of carbon atoms in the same graphene layer, i.e., ∆G = zmax − zmin . As a consequence, dt−b has to be redefined because corrugation is no longer zero. Hence,

dt−b

N 1 X top zi − zibottom , = N i=1

(1)

where zi denotes the vertical coordinates of carbon atoms in the top and bottom layers, and N is the number of carbon atoms in each layer. From Eq. 1, dt−b represents the difference between the average of vertical coordinates of carbon atoms in the top and bottom layers.

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Table 1: Structural parameters of unit cells of (n, m) tbLG. (n, m) Lattice vectors ×a0 (3,2) (3,1) (6,1)

√ 3, 4 √ √3 7 , 2 3, 1 ; √ √2 2 7 3 5 , 2 ; 23 , 13 2 2

√ 5 3 1 ; , 2 2

Lattice parameters (Å)

θ (◦ )

Num. of Area atoms (Å2 )

10.718

13.17◦

76

100

8.866

32.20◦

52

68

16.125

44.80◦

172

225

While dt−b = 3.27 Å and ∆Gt = ∆Gb = 0.000 in bLG, the three tbLG exhibit a small increment of the interlayer distance with dt−b = 3.35 Å, because they show corrugations of 0.035 Å, 0.012 Å, and 0.025 Å, for (3, 2), (3, 1), and (6, 1) tbLG, respectively. Interestingly, tbLGs reach the lowest energy configurations when dt−b and ∆G are larger than those found in bLG. Upon relaxation, these structures are used to explore different adsorption sites, as described below. Different theoretical works based on ab-initio calculations have shown that deprotonized cysteine is adsorbed on metal-doped graphene through the presence of an impurity, while adsorption does not happen on pristine graphene. 48–50 Additionally, the adsorption on monolayer graphene of saturated organic molecules, like pyridine 51,52 and aminotriazines, 53 have been reported. Taking into account these previous results, we study the adsorption energy of CH3NH2 and CH3SH molecules on their saturated form (see Figure 3) on mLG, bLG, and tbLG. Amine ( NH2) and thiol ( SH) groups are constituent of a wide range of organic molecules, including cysteine. Hence, the present study can help to elucidate the adsorption of these conformational groups and to distinguish different ways in which graphene adsorbs organic molecules. Whichever the adsorption site is, it is straightforwardly defined when the adsorbate is a single atom like Sc, Co or Ni, 54 or a small molecule like H2O, N2O or CO. 55 For larger molecules, it is necessary to consider a reference atom to define the adsorption site on graphene. Hence, in this work nitrogen (N) and carbon (C) are considered the reference atom for CH3NH2 and CH3SH, respectively, as will be discussed in the Results section. Ini-

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tially, CH3NH2 and CH3SH molecules are oriented on graphene structures such that C S and C N bonds are aligned parallel to the graphene plane and located 3.0 Å above the top layer.

(b)

(a)

Figure 3: Top and side view of (a) CH3NH2 and (b) CH3SH. Brown, yellow, silver and light pink spheres denote carbon, sulfur, nitrogen and hydrogen atoms, respectively. Because of the high symmetry of the honeycomb lattice, there are three different adsorption sites in mLG: top configuration (T), directly above a carbon atom; bridge configuration (B), at the center of two consecutive carbon atoms (nearest neighbors); and hollow configuration (H), at the center of a hexagon. Besides, another bridge configuration (B2) can be defined between two non-consecutive carbon atoms (second neighbors). Figure 1(a) depicts these four adsorption sites in mLG. In A-B stacking, top (t) and hole (h) atoms define new possible adsorption sites (see Figure 1(b)). In a top configuration, the adsorption can be through a top atom (Tt ) or a hole atom (Th ). For bridge configurations, there are three possibilities. One of them is defined at the center of two nearest neighbors (B), which means the bridge configuration comprises a pair of atoms at the top layer over a hole in the bottom layer. Another bridge site occurs when the middle point between two-second neighbors atoms in the top layer is over a bond on the bottom layer, Bh , or when they are not, Bt . All these sites are indicated in Figure 1(b). Finally, there is only one hollow site (H) at the center of a hexagon. All these adsorption sites have been chosen such that they are localized around the center of the unit cell. Note that in tbLG the relative angle between the top and 9



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bottom layers breaks the high symmetry of bLG; hence, it is not possible to identify top and hole atoms. Although top, bridge, and hollow sites can still be defined, the similarity between two comparable adsorption sites is lost because of the lack of high symmetry. For that reason, it is necessary to explore the adsorption on the whole tbLG supercell, which is practically impossible. Therefore, we define the following strategy for the three tbLGs studied here. We choose an arbitrary path along each supercell. Along this path, we define eleven equidistant points, testing each one as an adsorption site for both molecules. Finally, the adsorption energy, Eads , is calculated as usual: 36

Eads = |ES | − |EM | − |EG |,

(2)

where subindex S denotes the total energy of optimized structures of the molecule adsorbed on graphene structures, while M and G are the corresponding energies of the isolated molecule and the isolated graphene structures. According with Eq. 2, if Eads > 0 then the molecular adsorption is feasible. Next, adsorption energies for each molecule are discussed.

4. Results and discussion CH3NH2 adsorbed on mLG, bLG and tbLG Let us start analyzing the adsorption of CH3NH2 on mLG. Table 2 shows the adsorption energies of the four sites defined for mLG in the previous section. All these energies are between 0.411 − 0.461 eV, which are much larger than kB T0 ∼ 0.026 eV, the corresponding energy at room temperature. Additionally, they show similar values than other results from organic molecules physisorption on mLG previously reported. 51–53 The highest adsorption energy (HAE) is found for H site, while T site shows the lowest adsorption energy (LAE). Furthermore, the energy difference between both sites is ≈ 0.050 eV, twice kB T0 . As result of molecular adsorption, mLG is structurally distorted, where a corrugation is found. The 10


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corrugation is similar for all adsorption sites with ∆G ∼ 0.010 Å, which is about 1% of the bonding length of C C atoms in graphene. For the four adsorption sites, CH3NH2 is reoriented after relaxation, such that the N atom of the amine group is closer to graphene than the C atom in the methyl radical, as it can be see in Figure 4. For simplicity, the realignment of CH3NH2 is quantified with the distances between the average vertical position of carbon atoms in graphene and the vertical positions of N and C atoms in the molecule, zN and zC , respectively. The distances are also listed in Table 2. Interestingly, H configuration with the HAE is the one with the shorter zN and zC distances, i.e., CH3NH2 is closer to mLG. In this case the distances between the N atom and the six C atoms in graphene forming the hollow are almost equidistant with values between 3.17 and 3.20 Å. On the other hand, the T site, the one with the LAE, shows larger distances to graphene. So that, the closer the molecule the highest the adsorption energy.

Figure 4: Side view of CH3NH2 (left side) and CH3SH (right side) adsorbed on monolayer graphene. Notice the different orientation of the functional group amine and thiol with respect to graphene, which define the direction of the electric dipole moment (red arrow). Table 2: Eads of CH3NH2 adsorbed on mLG in top (T), bridge (B and B2), and hollow (H) sites. zN and zC are the distances from average vertical position of C atoms of graphene to vertical position of N and C atoms of CH3NH2, respectively. Eads is in eV (kcal mol−1 ) and distances are in Å. Site Eads zN T 0.411 (9.451) 2.966 B 0.412 (9.472) 2.976 B2 0.438 (10.078) 2.911 H 0.460 (10.589) 2.851

zC 3.174 3.173 3.228 3.084

Now, let us discuss the case of CH3NH2 adsorbed on bLG. Table 3 shows the adsorption 11



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energies and the principal structural parameters for the six sites on bLG. Firstly, we found that the adsorption energies have slightly diminished respect to those in mLG., i.e, now they are in the range 0.380 − 0.427 eV. However, they show essentially the same energy difference between HAE and LAE than before, with values that correspond again to H and T sites; specifically, to Th that is the same configuration respect to mLG. Now, corrugation is induced in top (∆Gt ) and bottom (∆Gb ) layers. Here, ∆Gt is 10 times larger than corresponding the corrugation in mLG, while ∆Gb is almost two orders of magnitude smaller than ∆Gt , i.e., even smaller than corrugation in mLG, thus, ∆Gt > ∆GmLG > ∆Gb . As a consequence of corrugation, the distance between graphene layers, dt−b decreases, such that, the larger ∆Gt the smaller dt−b . In agreement with the mLG case, CH3NH2 is reoriented and again the N atom is closer to top layer than the C one. Indeed, HAE configurations exhibit lowest zN values for bLG and mLG as well, as it is shown in Tables 2 and 3. From those tables, we observe that the adsorption energy on bLG is smaller respect to mLG, even when CH3NH2 is closer to the top graphene layer. Therefore, we conclude that the presence of the bottom layer might induce an electronic rearragenment which modifies the electrostatic interaction between the molecule and top layer, by decreasing the adsorption energy and allowing the molecule to be closer. Table 3: Eads of CH3NH2 adsorbed on A-B stacked bLG in top (Tt and Th ), bridge (B, Bt and Bh ), and hollow (H) sites. Corrugation ∆Gt and ∆Gb top and bottom layers, respectively. zN and zC , distance from average vertical position of C atoms of top graphene layer to N and C atoms of CH3NH2, respectively. Eads is in eV (kcal mol−1 ) and distances are in Å. site Eads dt−b ∆Gt Tt 0.384 (8.839) 3.250 0.121 Th 0.379 (8.719) 3.247 0.133 B 0.386 (8.875) 3.239 0.144 Bt 0.386 (8.870) 3.242 0.134 Bh 0.403 (9.264) 3.244 0.135 H 0.427 (9.814) 3.247 0.127

∆Gb 0.004 0.006 0.006 0.006 0.005 0.005

zN 2.904 2.857 2.881 2.818 2.819 2.741

zC 3.103 3.014 3.052 3.102 3.037 2.955

Finally, we discuss the adsorption of CH3NH2 on tbLG. Taking into account the above results for both mLG and bLG cases when the molecule is adsorbed on H and T sites with 12


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corresponding HAE and LAE; we identify both configurations for the three tbLG structures. We confirm the same trend: H and T sites exhibit HAE and LAE, respectively; as shown in Table 4. In the three cases, HAE have similar values among them and are close to that corresponding on mLG. The differences between HAE and LAE for the corresponding (3, 2), (3, 1), and (6, 1) tbLGs are 0.057, 0.051, and 0.043 eV. These intervals are within those differences obtained for mLG and bLG. To confirm that H and T configurations exhibit HAE and LAE, we chose an arbitrary straight path on the unit cell containing both sites for the three tbLG. Along this path, we test eleven equidistant adsorption sites, finding that all adsorption energies fall into the interval defined by H and T configurations. Figure 5 displays all the calculated adsorption energies of CH3NH2 on mLG, bLG and tbLGs, plotted as red dots. Here, the energies close to the upper limit correspond to arrangements similar to H, while those close to the lower limit resemble the T configuration. As in mLG and bLG, CH3NH2 is also reoriented, again N is closer than C to the top layer, which means that zN < zC always, as seen in Table 4. Again, top layers exhibit larger corrugations with similar values to bLG, but now the corrugation of the bottom layers, ∆Gb , increases one order of magnitude with respect to the corresponding values of bLG. In particular, notice that T configuration on (3, 2) tbLG exhibits the smallest adsorption energy and the largest ∆Gt . Notice that the corresponding three tbLG configurations with HAE exhibit also the smallest corrugations, ∆Gt , such that the molecule is closer to the graphene top layer. In contrast, T configurations have the largest corrugations with the molecule slightly further from the graphene top layer. This last tendency is similar to that observed for CH3SH, as we will discuss in the next section. In summary, we found that CH3NH2 is always adsorbed on mLG, bLG and tbLG with energies at least one order of magnitude larger than kB T0 at room temperature, showing a clear dependency on the adsorption site. For all cases, T and H configurations exhibit LAE and HAE, respectively. Also, it is found that the amine group, via the N atom, is closer to graphene than the methyl radical. So, when CH3NH2 is adsorbed on mLG, the 13



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Table 4: Eads of CH3NH2 adsorbed on (3, 2), (3, 1), and (6, 1) tbLG in H and T sites. Interlayer distances, dt−b ), and corrugation ∆Gt and ∆Gb . Eads is in eV and distances in Å. tbLG site (3,2) H (3,2) T (3,1) H (3,1) T (6,1) H (6,1) T

Eads 0.450 0.392 0.452 0.401 0.447 0.405

dt−b 3.333 3.325 3.336 3.323 3.326 3.328

∆Gt 0.120 0.136 0.108 0.147 0.131 0.137

∆Gb 0.040 0.046 0.035 0.035 0.058 0.063

zN 2.840 2.855 2.781 2.861 2.778 2.931

zC 3.061 3.090 3.042 3.030 3.050 3.069

largest adsorption energy is in the H configuration. With a second graphene layer in A-B stacking, the adsorption energy decreases respect to mLG. However, by making a relative angle between top and bottom graphene layers, the adsorption energy increases respect to those observed in bLG, suggesting a tuning effect. Additionally, the adsorption of the molecule induces corrugation in graphene layers. While corrugation in top layers of bLG and tbLG are always larger than those in bottom layers, mLG exhibits the lowest values. This corrugation could modify the electronic properties of graphene layers, changing the local environment and thus, favoring the adsorption process, as we discuss latter.

CH3SH adsorbed on mLG, bLG and tbLG Now, let us discuss the adsorption of the CH3SH molecule, which exhibits quite a different behavior respect to CH3NH2. For instance, the final configuration of CH3SH adsorbed on all the graphene structures shows that now the methyl radical is closer to graphene than the thiol group. It means that for CH3SH the functional group is repulsed by graphene structures and not attracted as in the case of the amine group, as shown in Figure 4. Because of this molecular orientation, all configurations are built assuming the C atom on the methyl as the reference atom. As previously, Figure 5 resumes all the adsorption energies of CH3SH on mLG, bLG and the three tbLG, shown in blue dots. Here, they are compared with the corresponding adsorption energies of CH3NH2 shown in red also in Figure 5. From these results, we found that graphene structures adsorb CH3SH weaker than CH3NH2 molecules. 14


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Figure 5: Comparing adsorption energies of CH3NH2 (red) and CH3SH (blue) on monolayer (mLG), A-B stacked bilayer (bLG), and (3,2), (3,1) and (6,1) twisted-bilayer graphene. For CH3NH2, the upper and lower limits are always giving by H and T configurations, respectively. However, the adsorption of CH3SH is different (see text). Values are reported in eV. We observe that the HAE of CH3SH on mLG corresponds to a B2 configuration of the C atom of the methyl and with the S atom of thiol group in a H configuration. It means that the adsorption energy depends not only on the position of the radical but also on the functional group. This two-sites dependency is not observed in CH3NH2, where the location of the N atom in the H configuration is enough to define the HAE wherever the C atom of methyl is. We remark that, for each molecule, similar adsorption energies do not mean necessarily similar configurations, except for upper values. The energy difference between HAE and LAE on mLG is just 0.020 eV, as listed in Table 5. It means that CH3SH can move along different adsorption sites over graphene at room temperature. Beside giving smaller adsorption energies, a much larger corrugation is obtained. For instance, while ∆G for CH3NH2 on mLG is smaller than 1% of C C bonding, CH3SH induces values up to 8.5% of C C. Now, we define the distances to the S atom, zS , and the methyl C, zC , with respect to the average vertical position of carbon atoms in graphene, as seen in Table 5, and compare

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with zN and zC reported in Table 2 for CH3NH2. While both zC distances are essentially the same, zS > zN , which confirms that thiol group is repulsed by mLG. The difference in the final configurations of CH3NH2 and CH3SH is crucial because it defines differently the direction of the electric dipole moment of each molecule (see Figure 4), which is related with the corrugation induced in graphene structures, as we will discuss later. Table 5: Eads of CH3SH adsorbed on mLG at T, B, B2, and H configurations. ∆G denotes corrugation of mLG. zS and zC are the corresponding distances from S and C atoms of CH3SH to graphene. Eads is in eV (kcal mol−1 ) and distances are in Å. Case T B B2 H

Eads 0.361 0.369 0.380 0.368

(8.305) (8.481) (8.744) (8.470)

∆G 0.048 0.121 0.097 0.112

zS 3.466 3.388 3.383 3.388

zC 3.226 3.168 3.132 3.128

On bLG, adsorption energies of CH3SH decrease and the interval between higher and lower limits is similar to the energy differences found for CH3NH2. Now, we find that HAE and LAE correspond Bh and Th configurations. Here, ∆Gt , ∆Gb , and dt−b are slightly larger than those generated by CH3NH2, and the molecular distances, zS and zC , are slightly reduced respect to mLG. But comparing both molecules, we found that they are still obeying that zS > zN as compared with the CH3NH2 molecule. From these results, we can conclude that a second graphene layer in A-B stacking reduces the adsorption energy in both molecules. Table 6: Eads of CH3SH adsorbed on bLG in Tt , Th , B, Bt , Bh , and H sites. ∆Gt and ∆Gb are the corrugation of top and bottom layers. zS and zC are the distance from graphene to S and C atoms of CH3SH. Eads is in eV (kcal mol−1 ) and distances are in Å. Case Eads dt−b ∆Gt Tt 0.346 (7.951) 3.252 0.142 Th 0.316 (7.265) 3.243 0.176 B 0.340 (7.811) 3.255 0.128 Bt 0.321 (7.375) 3.258 0.128 Bh 0.356 (8.211) 3.242 0.169 H 0.338 (7.777) 3.245 0.170

∆Gb 0.005 0.006 0.005 0.004 0.006 0.005

zS 3.307 3.316 3.394 3.301 3.316 3.314

zC 3.144 3.159 3.205 3.182 3.058 3.132

Following the same methodology used before, we explore different adsorption sites of 16


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CH3SH along an arbitrary straight path on the unit cell of each tbLG. Here, HAE are obtained for the methyl in a B2 configuration and the S atom in a H configuration for all tbLG, see Table 7. While the adsorption energy and dt−b increase, the distance between molecule and graphene decreases respect to bLG, in a similar way that CH3NH2 does, as we have discussed above. It is noteworthy that the induced corrugation on the bottom layer, ∆Gb , increases notably up to values close to ∆Gt . Although this corrugation is also observed in CH3NH2 adsorbed on tbLG, these values are twice larger, so they might be a direct consequence of the interaction between CH3SH and graphene layers, as we will discuss later. Table 7: HAE and sites of CH3SH on (3, 2), (3, 1), and (6, 1) tbLG. Interlayer distance (dt−b ), and corrugations, ∆Gt and ∆Gb . Energies are in eV and distances in Å. tbLG site Eads dt−b ∆Gt ∆Gb zS zC (3,2) B2 0.385 3.314 0.181 0.120 3.233 3.054 (3,1) B2 0.379 3.336 0.128 0.028 3.226 3.113 (6,1) B2 0.390 3.328 0.148 0.112 3.323 3.063 Notice that the relative twist angle between the top and bottom layers brings an increase in the adsorption energy of CH3SH respect to bLG up to values close to mLG, in a similar way that CH3NH2 does. It means that the change in adsorption energy from bLG to tbLG is a consequence of the non-symmetric electronic charge distribution in twisted-graphene structures. Also, the similarity of HAE between tbLGs and mG (see Figure 5) is according to the decoupled regime which the three tbLGs belongs. 27 However, from the results stated above, the adsorption energy and corrugation are a direct result of the molecule-graphene structures interactions. In order to check the presence of corrugation, a couple of fully-relaxed calculations for molecule adsorption on mG was carried on. The lattice parameter of the unit cell increases slightly (≈ 0.6%), and corrugation changes but remains. Corrugation persists because the molecule adsorption is a local interaction on the graphene layer. Besides, the presence of the molecule on the slab breaks the hexagonal symmetry of the graphene supercell, which 17



could change the lattice vectors in fully-relaxed calculations. In this sense, we have kept fixed the cell parameters and, as a consequence, also the hexagonal symmetry, letting that the structural changes induced by the molecule-layer interactions could be just analyzed by the corrugation parameter. To understand the different values of the corrugation induced by either molecule, let us discuss the influence of the molecular electric dipole moment on them. CH3NH2 and CH3SH are polar molecules. They both exhibit an electric dipole moment, µ ~ , which points from the functional groups to the methyl radical. From our DFT calculations, we obtained that |~µCH3NH2 | = 1.32 D and |~µCH3SH | = 1.44 D, which are similar to that exhibited by other polar molecules, like the water molecule (|~µH2O | = 1.85 D). 56 As we have discussed along herein, upon adsorption either molecule are oriented such that zS > zN , whereas the corresponding methyl positions are almost the same. These molecular orientations imply that µ ~ CH3NH2 has a vertical component pointing outside graphene (up), while µ ~ CH3SH does pointing inside graphene (down), as we shown in Figure 4. To explain this difference, we refer to previous works that focused to study the adsorption of polar molecules on metal surfaces from a classical point of view based on electrostatic interactions. 56–60 Although classical electrostatic approximations have been employed considering electric dipoles oriented parallel or perpendicular to the metallic surface, it is not possible to elucidate the influence of pointing direction of perpendicular dipoles (up or down) at shorter distances. In fact, at larger separation distances between the molecule and metal surface, where the discrete nature of the surface can be neglected and quantum-mechanical effects are insignificant, these classical models describe the asymptotic behavior of the adsorption energy excellently. 56,58 However, at shorter separation distances quantum effects begin to be relevant and classical electrostatic models fail, even through using a non-local dielectric approach. 58 Years ago, Holmström and Holloway studied the self-consistent electronic structure of a dipole with a Jellium model of the surface within the local density approximation. 60 They concluded that near the surface strong asymmetries occur in physical quantities, for instance, adsorption energy and electron density distribution, depending on the dipole ori18


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entation (up or down), utterly absent in the far-field limit. They also reported that the up configuration of the dipole is more stable that the down one, which is in qualitative concordance with our results: the adsorption energy of CH3NH2, which has a vertical component of electric dipole moment pointing up, is larger than that of CH3SH for any configuration, which points down. Beyond the electron affinity of the functional group to the metallic surface, or in our case the graphene layers, when the molecule is physisorbed there is not a chemical bonding with the surface and long-range interactions domain the adsorption. 61 However, quantum effects are present. Bagus et al., discussed the emergence of an interface dipole when atoms and molecules are physisorbed on metal surfaces, originated mainly by exchange-like effects. 62 They concluded that the adsorption of noble gases, such as Xenon, on metallic surfaces and the emerging electric dipole at the interface are originated by the Pauli repulsion. This repulsion is also known as the Pauli push-back effect and occurs when electrostatic interactions pulled the atoms towards the surface, and their wavefunctions overlap with those of the metallic surface. 62 Since the overall wave function must obey antisymmetry, some of the metallic charge between molecule and surface is pushed back into the metal, decreasing the wavefunction overlap of molecule and surface. In the case of CH3SH adsorbed on graphene structures, the molecular electric dipole moment has its vertical component pointing down to graphene layers. Then, the positive charge of the molecule is near graphene, hence, attracting its electronic charge. But at the same time, this attraction increases the overlapping of both wavefunctions and the Pauli push-back effect repulses the electronic charge. As a result, there is a competition between both effects that oppose each other. Hence, the Pauli push-back effect could be responsible for the large structural distortions, which gives rise to corrugation on the graphene layers when CH3SH is adsorbed. In contrast, the vertical component of the electric dipole of CH3NH2 points up. Hence, the negative charge of the molecule is near graphene, repelling thereby the electronic charge of the surface in the same way that Pauli push-back effect does. 19



Then, the induced corrugation by CH3NH2 is smaller than that of CH3SH, despite that the N atom is closer to graphene structure than the S atom is. Nonetheless, an explicit study about the contribution of the Pauli push-back effect on the physisorption of polar molecules on graphene layers is beyond the goal of this work. However, we can get some insights on how molecular adsorption modifies the electronic properties of graphene layers, which should be different for both molecules. In Figure 6, the electronic band structures of CH3NH2 adsorbed on mLG (left), bLG (at the middle) and (6, 1) tbLG (right) are shown in the top row using red lines, while the corresponding band structures for the adsorption of CH3SH are shown in the bottom row using blue lines. Also, each case is compared with the band structure of pristine graphene structure in dotted black lines. Upon molecular adsorption, the electronic bands around the Fermi level (pinned at 0 eV) are not modified from those of pristine graphene. The highest occupied molecular orbital (HOMO) electronic states of CH3NH2 and CH3SH are constant along the high-symmetry points, located at −1.2 eV and −0.75 eV that correspond to the horizontal lines in Figures 6(a,b,c) and 6(d,e,f), respectively. At energies lower than −3.0 eV, the electronic band structure of graphene remains undisturbed respect to pristine graphene arrangement upon CH3NH adsorption, as insets shows in the top row of Figure 6. Instead, deviations from pristine bands are observed for the adsorption of CH3SH at the same energies range, as we show in the insets of the bottom row of Figure 6. Such deviations could be associated with the large corrugation generated upon the adsorption of CH3SH. The position of the Fermi level respect to the Dirac cone of the graphene structures did not change upon molecular adsorption, which means that there is not electronic exchange between molecules and graphene structures, confirming the physisorption process. 18,63 From band structures of Figure 6, there is not any evidence of charge transfer around the Fermi level in the cases studied here. However, the thioled molecule induces large deviations of electronic bands at energies lower than −3 eV, which are mainly associated to corrugation. Although a direct comparison between the band structure of the molecule adsorbed on 20


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(a)

(b)

(c)

(d)

(e)

(f)

Figure 6: Electronic band structures of CH3NH2 (top in red) and CH3SH (bottom in blue) adsorbed on mLG (left), bLG (middle) and (6, 1) tbLG (right). Fermi level is pinned at 0.0 eV. For comparison, band structures of corresponding pristine graphene are also plotted in black dotted lines. graphene and pristine graphene can help distinguish deviations of the electronic properties, it is necessary to compare with the graphene unit cell band structure, which means facing the folding problem associated supercell calculations. The band structure obtained in a supercell can hide essential physical properties in the 2D Brillouin zone associated with the molecular-surface interaction. 64–66 Despite the lack of evidence of charge transfer between molecule and graphene layers, it is worthy of study the charge redistribution at the interface and vacuum region close around the molecule and graphene layers. Such analysis can be made through the notion of the plane average electron density difference, ∆ρ(z), which describes the difference in the electronic charge distribution associated with the mutual interaction of the structures that set up the system respect isolated structures. Firstly, the plane average electron density, ρ(z), of each structure is defined as 1 ρ(z) = A

Z ρ(x, y, z)dxdy;

(3)

SC

where ρ(x, y, z) is the electron density in real space, the integration is over the XY plane 21



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and A correspond to the surface area of the supercell. 67 Hence, ∆ρ(z), the difference in the electronic charge distribution is defined as follows:

∆ρ(z) = ρ(z)S − ρ(z)M − ρ(z)G ,

(4)

where the S, M and G subindexes denoting graphene layers plus molecular structures, the isolated molecule, and graphene structures, respectively. Figure 7 depicts ∆ρ(z) for the HAE of CH3NH2 (left in red) and CH3SH (right in blue) adsorbed on mLG (top row), bLG (middle row) and (6, 1) tbLG. Notice that intensities of the density profile are on the same order than those reported for MoS2 G heterostructures. 68 Firstly, ∆ρ(z) extends in the vacuum region going across the bottom layer and beyond molecules. It is observed that CH3NH2 generates a larger electron accumulation at the interface than CH3SH does. Beside, while CH3NH2 exhibits a charge accumulation in the vacuum region close to the bottom layer, there is an electron charge depletion for CH3SH cases. This opposite behavior of the charge redistribution around the bottom layer could be explained by the pointing direction of the molecular electric dipole moment. Comparing the three ∆ρ(z) for CH3NH2, the charge is essentially redistributed in the same way, except for slight variations in the intensity. Instead, the three ∆ρ(z) for CH3SH show different profile mainly at the interface. Hence, ∆ρ(z) of CH3SH appears more sensitive to the electronic charge distribution of graphene structures than the density profile of CH3NH2. Furthermore, we conclude that the higher Eads shown by CH3NH2 on graphene structures are involved with larger charge redistribution ∆ρ(z), which again could be related to the different pointing direction of the molecular electric dipole moment.

5. Conclusion Along this work we have studied the adsorption of the methylamine and methanethiol on the monolayer, A-B stacked bilayer and twisted-bilayer graphene. Although methylamine and 22


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Figure 7: Electronic charge redistribution given by the plane average electron density difference, ∆ρ(z) for HAE configurations. Left hand corresponds to CH3NH2 (red line) and right hand to CH3SH (blue line) on mLG (top row), bLG (middle row) and (6, 1) tbLG (bottom row). Positions of graphene layers and molecules are approximated.

23



methanethiol are constituted by different functional groups, they exhibit similar behaviors upon adsorption on graphene structures. For instance, both molecules are physisorbed with energies larger than kB T0 at room temperature. Largest adsorption energies are observed for monolayer case. In the A-B stacking, adsorption energies always decrease; but for tbLG, they increase to values close to the monolayer case according to the decoupling of the two layers expected for these twist angles, suggesting a molecular-adsorption tunning effect. Additionally, the methylamine is adsorbed with larger energies than methanethiol, and the final molecular orientation shows that the amine group is closer to the graphene layer than the thiol group is. Graphene layers become corrugated due to their interaction with the molecule. Such corrugation is larger for the top layer when the methanethiol is adsorbed, inducing slight deviations of the electronic band structures at low energies. However, around the Fermi level, the band structures remain unperturbed respect to pristine graphene structures. Although our calculations show that there is not any charge transfer between graphene layers and molecules, a charge redistribution is observed at the interface and the vacuum region, close to the bottom layer and molecules. We observe that the pointing direction of the electric dipole moment of the molecule plays a relevant role in the adsorption energy, corrugation on graphene layers, and electronic charge redistribution as well. In another hand, it is interesting to study molecule adsorption on tbLGs with small twist angles, where electrons of graphene layers are strongly correlated and a vast of fascinating phenomena occur. However, the main limitation is the computational effort required for these large unit cells. We hope this work stimulates future studies related to the molecule adsorption and the relative angle in tbLG, with possible applications in sensor design and functionalized graphene as well.

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Acknowledgement The authors thank the computing time granted by LANCAD on the supercomputer Yoltla at LSVP UAM-Iztapalapa. This work is partially supported by the projects DGAPA-UNAM project PAPIIT IN109618 and UAM-A-CBI-2232021. We gratefully acknowledge the SNIConacyt-México for the distinction of our membership and the stipend received.

Supporting Information Available The following files are available free of charge. • Tunning-the-adsorption-SI.pdf: Comparison between standard and extended basis set. It is based on the plane average electron density difference, ∆ρ(z), and the notion of ghost orbitals.

References 1. Gan, T.; Hu, S. Electrochemical Sensors Based on Graphene Materials. Microchim. Acta 2011, 175, 1. 2. Strano, M. S.; Dyke, C. A.; Usrey, M. L.; Barone, P. W.; Allen, M. J.; Shan, H.; Kittrell, C.; Hauge, R. H.; Tour, J. M.; Smalley, R. E. Electronic Structure Control of Single-Walled Carbon Nanotube Functionalization. Science 2003, 301, 1519–1522. 3. Sperling, R. A.; Parak, W. J. Surface Modification, Functionalization and Bioconjugation of Colloidal Inorganic Nanoparticles. Philos. T. R. Soc. A 2010, 368, 1333–1383. 4. Barth, J. V. Molecular Architectonic on Metal Surfaces. Annu. Rev. Phys. Chem. 2007, 58, 375–407.

25



5. Lei, S.; Wang, X.; Li, B.; Kang, J.; He, Y.; George, A.; Ge, L.; Gong, Y.; Dong, P.; Jin, Z. et al. Surface Functionalization of Two-Dimensional Metal Chalcogenides by Lewis Acid–Base Chemistry. Nat. Nanotechnol. 2016, 11, 465–472. 6. Schedin, F.; Geim, A. K.; Morozov, S. V.; Hill, E. W.; Blake, P.; Katsnelson, M. I.; Novoselov, K. S. Detection of Individual Gas Molecules Adsorbed on Graphene. Nat. Mater. 2007, 6, 652–655. 7. Georgakilas, V.; Tiwari, J. N.; Kemp, K. C.; Perman, J. A.; Bourlinos, A. B.; Kim, K. S.; Zboril, R. Noncovalent Functionalization of Graphene and Graphene Oxide for Energy Materials, Biosensing, Catalytic, and Biomedical Applications. Chem. Rev. 2016, 116, 5464–5519. 8. Butler, S. Z.; Hollen, S. M.; Cao, L.; Cui, Y.; Gupta, J. A.; Gutiérrez, H. R.; Heinz, T. F.; Hong, S. S.; Huang, J.; Ismach, A. F. et al. Progress, Challenges, and Opportunities in Two-Dimensional Materials Beyond Graphene. ACS Nano 2013, 7, 2898–2926. 9. Allen, M. J.; Tung, V. C.; Kaner, R. B. Honeycomb Carbon: A Review of Graphene. Chem. Rev. 2010, 110, 132–145. 10. Chung, C.; Kim, Y.-K.; Shin, D.; Ryoo, S.-R.; Hong, B. H.; Min, D.-H. Biomedical Applications of Graphene and Graphene Oxide. Accounts Chem. Res. 2013, 46, 2211– 2224. 11. Ioniţă, M.; Vlăsceanu, G. M.; Watzlawek, A. A.; Voicu, S. I.; Burns, J. S.; Iovu, H. Graphene and Functionalized Graphene: Extraordinary Prospects for Nanobiocomposite Materials. Compos. Part B: Eng. 2017, 121, 34 – 57, Bio-inspired Nano-engineered Materials. 12. Wang, S.; Goh, B. M.; Manga, K. K.; Bao, Q.; Yang, P.; Loh, K. P. Graphene as Atomic Template and Structural Scaffold in the Synthesis of Graphene-Organic Hybrid Wire with Photovoltaic Properties. ACS Nano 2010, 4, 6180–6186. 26


Page 26 of 34

Page 27 of 34 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


13. Machado, B. F.; Serp, P. Graphene-Based Materials for Catalysis. Catal. Sci. Technol. 2012, 2, 54–75. 14. Kuila, T.; Bose, S.; Mishra, A. K.; Khanra, P.; Kim, N. H.; Lee, J. H. Chemical Functionalization of Graphene and its Applications. Prog. Mat. Sci. 2012, 57, 1061 – 1105. 15. Georgakilas, V.; Otyepka, M.; Bourlinos, A. B.; Chandra, V.; Kim, N.; Kemp, K. C.; Hobza, P.; Zboril, R.; Kim, K. S. Functionalization of Graphene: Covalent and NonCovalent Approaches, Derivatives and Applications. Chem. Rev. 2012, 112, 6156–6214. 16. Sinitskii, A.; Dimiev, A.; Corley, D. A.; Fursina, A. A.; Kosynkin, D. V.; Tour, J. M. Kinetics of Diazonium Functionalization of Chemically Converted Graphene Nanoribbons. ACS Nano 2010, 4, 1949–1954. 17. Niyogi, S.; Bekyarova, E.; Itkis, M. E.; Zhang, H.; Shepperd, K.; Hicks, J.; Sprinkle, M.; Berger, C.; Lau, C. N.; deHeer, W. A. et al. Spectroscopy of Covalently Functionalized Graphene. Nano Lett. 2010, 10, 4061–4066. 18. Lu, Y. H.; Chen, W.; Feng, Y. P.; He, P. M. Tuning the Electronic Structure of Graphene by an Organic Molecule. J. Phys. Chem. B 2009, 113, 2–5. 19. Shen, H.; Zhang, L.; Liu, M.; Zhang, Z. Biomedical Applications of Graphene. Theranostics 2012, 2, 283–294. 20. Singh, M.; Holzinger, M.; Tabrizian, M.; Winters, S.; Berner, N. C.; Cosnier, S.; Duesberg, G. S. Noncovalently Functionalized Monolayer Graphene for Sensitivity Enhancement of Surface Plasmon Resonance Immunosensors. J. Am. Chem. Soc. 2015, 137, 2800–2803. 21. Nilsson, J.; Neto, A. H. C.; Guinea, F.; Peres, N. M. R. Electronic Properties of Graphene Multilayers. Phys. Rev. Lett. 2006, 97, 266801.

27



22. McCann, E.; Koshino, M. The Electronic Properties of Bilayer Graphene. Rep. Prog. Phys. 2013, 76, 056503. 23. Rozhkov, A.; Sboychakov, A.; Rakhmanov, A.; Nori, F. Electronic Properties of Graphene-Based Bilayer Systems. Phys. Rep. 2016, 648, 1 – 104. 24. Ohta, T.; Bostwick, A.; Seyller, T.; Horn, K.; Rotenberg, E. Controlling the Electronic Structure of Bilayer Graphene. Science 2006, 313, 951–954. 25. Boukhvalov, D. W.; Katsnelson, M. I. Tuning the Gap in Bilayer Graphene Using Chemical Functionalization: Density Functional Calculations. Phys. Rev. B 2008, 78, 085413. 26. Lopes dos Santos, J. M. B.; Peres, N. M. R.; Castro Neto, A. H. Graphene Bilayer with a Twist: Electronic Structure. Phys. Rev. Lett. 2007, 99, 256802. 27. Uchida, K.; Furuya, S.; Iwata, J.-I.; Oshiyama, A. Atomic Corrugation and Electron Localization due to Moiré Patterns in Twisted Bilayer Graphenes. Phys. Rev. B 2014, 90, 155451. 28. Li, G.; Luican, A.; Lopes dos Santos, J. M. B.; Castro Neto, A. H.; Reina, A.; Kong, J.; Andrei, E. Y. Observation of Van Hove singularities in twisted graphene layers. Nat. Phys. 2009, 6, 109–113. 29. Yan, W.; Liu, M.; Dou, R.-F.; Meng, L.; Feng, L.; Chu, Z.-D.; Zhang, Y.; Liu, Z.; Nie, J.-C.; He, L. Angle-Dependent van Hove Singularities in a Slightly Twisted Graphene Bilayer. Phys. Rev. Lett. 2012, 109, 126801. 30. Tarnopolsky, G.; Kruchkov, A. J.; Vishwanath, A. Origin of Magic Angles in Twisted Bilayer Graphene. Phys. Rev. Lett. 2019, 122, 106405. 31. Yankowitz, M.; Chen, S.; Polshyn, H.; Zhang, Y.; Watanabe, K.; Taniguchi, T.; Graf, D.; Young, A. F.; Dean, C. R. Tuning Superconductivity in Twisted Bilayer Graphene. Science 2019, 363, 1059–1064. 28


Page 28 of 34

Page 29 of 34 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


32. Bistritzer, R.; MacDonald, A. H. Moiré Bands in Twisted Double-Layer Graphene. P. Natl. Acad. Sci. 2011, 108, 12233–12237. 33. Ohta, T.; Robinson, J. T.; Feibelman, P. J.; Bostwick, A.; Rotenberg, E.; Beechem, T. E. Evidence for Interlayer Coupling and Moiré Periodic Potentials in Twisted Bilayer Graphene. Phys. Rev. Lett. 2012, 109, 186807. 34. Soler, J. M.; Artacho, E.; Gale, J. D.; García, A.; Junquera, J.; Ordejón, P.; SánchezPortal, D. The SIESTA Method for Ab Initio Order- N Materials Simulation. J. Phys.: Condens. Matter 2002, 14, 2745. 35. Perdew, J. P.; Zunger, A. Self-Interaction Correction to Density-Functional Approximations for Many-Electron Systems. Phys. Rev. B 1981, 23, 5048–5079. 36. Ma, Y.; Dai, Y.; Guo, M.; Niu, C.; Huang, B. Graphene Adhesion on MoS2 Monolayer: An Ab Initio Study. Nanoscale 2011, 3, 3883–3887. 37. Ma, Y.; Dai, Y.; Wei, W.; Niu, C.; Yu, L.; Huang, B. First-Principles Study of the Graphene@MoSe2 Heterobilayers. J. Phys. Chem. C 2011, 115, 20237–20241. 38. Junquera, J.; Paz, O.; Sánchez-Portal, D.; Artacho, E. Numerical Atomic Orbitals for Linear-Scaling Calculations. Phys. Rev. B 2001, 64, 235111. 39. García-Gil, S.; García, A.; Lorente, N.; Ordejón, P. Optimal Strictly Localized Basis Sets for Noble Metal Surfaces. Phys. Rev. B 2009, 79, 075441. 40. Bengtsson, L. Dipole Correction for Surface Supercell Calculations. Phys. Rev. B 1999, 59, 12301–12304. 41. Monkhorst, H. J.; Pack, J. D. Special Points for Brillouin-Zone Integrations. Phys. Rev. B 1976, 13, 5188–5192. 42. Castro Neto, A. H.; Guinea, F.; Peres, N. M. R.; Novoselov, K. S.; Geim, A. K. The Electronic Properties of Graphene. Rev. Mod. Phys. 2009, 81, 109–162. 29



43. Liu, Z.; Suenaga, K.; Harris, P. J. F.; Iijima, S. Open and Closed Edges of Graphene Layers. Phys. Rev. Lett. 2009, 102, 015501. 44. Lee, J.-K.; Lee, S.-C.; Ahn, J.-P.; Kim, S.-C.; Wilson, J. I. B.; John, P. The Growth of AA Graphite on (111) Diamond. J. Chem. Phys. 2008, 129, 234709. 45. Rode, J. C.; Zhai, D.; Belke, C.; Hong, S. J.; Schmidt, H.; Sandler, N.; Haug, R. J. Linking Interlayer Twist Angle to Geometrical Parameters of Self-Assembled Folded Graphene Structures. 2D Mater. 2019, 6, 015021. 46. Kim, C.-J.; Sánchez-Castillo, A.; Ziegler, Z.; Ogawa, Y.; Noguez, C.; Park, J. Chiral Atomically Thin Films. Nat. Nanotechnol. 2016, 11, 520. 47. Mele, E. J. Commensuration and Interlayer Coherence in Twisted Bilayer Graphene. Phys. Rev. B 2010, 81, 161405. 48. Zhang, Z.; Jia, H.; Ma, F.; Han, P.; Liu, X.; Xu, B. First Principle Study of Cysteine Molecule on Intrinsic and Au-Doped Graphene Surface as a Chemosensor Device. J. Mol. Model. 2011, 17, 649–655. 49. Ma, F.; Zhang, Z.; Jia, H.; Liu, X.; Hao, Y.; Xu, B. Adsorption of Cysteine Molecule on Intrinsic and Pt-Doped Graphene: A First-Principle Study. J. Mol. Struc.: THEOCHEM 2010, 955, 134 – 139. 50. Luo, H.; Li, H.; Fu, Q.; Chu, Y.; Cao, X.; Sun, C.; Yuan, X.; Liu, L. Density Functional Theory Study on the Interactions of L-cysteine with Graphene: Adsorption Stability and Magnetism. Nanotechnology 2013, 24, 495702. 51. Kong, X.; Chen, Q. The Positive Influence of Boron-Doped Graphene with Pyridine as a Probe Molecule on SERS: a Density Functional Theory Study. J. Mater. Chem. 2012, 22, 15336–15341.

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52. Voloshina, E.; Mollenhauer, D.; Chiappisi, L.; Paulus, B. Theoretical Study on the Adsorption of Pyridine Derivatives on Graphene. Chem. Phys. Lett. 2011, 510, 220 – 223. 53. Wuest, J. D.; Rochefort, A. Strong Adsorption of Aminotriazines on Graphene. Chem. Commun. 2010, 46, 2923–2925. 54. Hu, L.; Hu, X.; Wu, X.; Du, C.; Dai, Y.; Deng, J. Density Functional Calculation of Transition Metal Adatom Adsorption on Graphene. Physica B 2010, 405, 3337 – 3341. 55. Leenaerts, O.; Partoens, B.; Peeters, F. M. Adsorption of H20, NH3, CO, NO2 and NO on Graphene: A First-Principles Study. Phys. Rev. B 2008, 77, 125416. 56. Fernández-Torre, D.; Kupiainen, O.; Pyykkö, P.; Halonen, L. Long-Range Interactions between Polar Molecules and Metallic Surfaces: A Comparison of Classical and Density Functional Theory based Models. Chem. Phys. Lett. 2009, 471, 239 – 243. 57. Kokalj, A. Electrostatic Model for Treating Long-Range Lateral Interactions between Polar Molecules Adsorbed on Metal Surfaces. Phys. Rev. B 2011, 84, 045418. 58. Gabovich, A.; Gun’ko, V.; Klymenko, V.; Voitenko, A. Role of Dipole Image Forces in Molecular Adsorption. Eur. Phys. J. B 2012, 85, 284. 59. Gabovich, A. M.; Li, M. S.; Szymczak, H.; Voitenko, A. I. Image Forces for a Point-Like Dipole Near a Plane Metal Surface: An Account of the Spatial Dispersion of Dielectric Permittivity. Surf. Sci. 2012, 606, 510 – 515. 60. Holmström, S.; Holloway, S. The Interaction of a Dipole with a Metal Surface. Surf. Sci. Lett. 1986, 173, L647–L654. 61. Ibach, H. Physics of Surfaces and Interfaces; Springer: Jülich, Germany, 2006. 62. Bagus, P. S.; Staemmler, V.; Wöll, C. Exchangelike Effects for Closed-Shell Adsorbates: Interface Dipole and Work Function. Phys. Rev. Lett. 2002, 89, 096104. 31



63. Khomyakov, P. A.; Giovannetti, G.; Rusu, P. C.; Brocks, G.; van den Brink, J.; Kelly, P. J. First-Principles Study of the Interaction and Charge Transfer between Graphene and Metals. Phys. Rev. B 2009, 79, 195425. 64. Deretzis, I.,; Calogero, G.,; Angilella, G. G. N.,; La Magna, A., Role of Basis Sets on the Unfolding of Supercell Band Structures: From Tight-Binding to Density Functional Theory. EPL 2014, 107, 27006. 65. Le, N. B.; Huan, T. D.; Woods, L. M. Interlayer Interactions in van der Waals Heterostructures: Electron and Phonon Properties. ACS Appl. Mater. Inter. 2016, 8, 6286– 6292. 66. Sánchez-Ochoa, F.; Hidalgo, F.; Pruneda, J. M.; Noguez, C. Strong modulation in the electronic structure of twisted graphene on WS2. In preparation 67. Junquera, J.; Cohen, M. H.; Rabe, K. M. Nanoscale Smoothing and the Analysis of Interfacial Charge and Dipolar Densities. J. Phys.: Condens. Matter 2007, 19, 213203. 68. Jin, C.; Rasmussen, F. A.; Thygesen, K. S. Tuning the Schottky Barrier at the Graphene/MoS2 Interface by Electron Doping: Density Functional Theory and ManyBody Calculations. J. Phys. Chem. C 2015, 119, 19928–19933.

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Tuning Adsorption of Methylamine and Methanethiol on Twisted

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