Tuning Adsorption of Methylamine and Methanethiol on Twisted

Article Cite This: J. Phys. Chem. C 2019, 123, 15273−15283

pubs.acs.org/JPCC

Tuning Adsorption of Methylamine and Methanethiol on TwistedBilayer 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

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S Supporting Information *

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.

1. INTRODUCTION Molecular adsorption is the physical phenomenon inherently associated with functionalization, sensors design, and selfassembly. Nanostructures such as nanoparticles, slabs, and surfaces1−4 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 bonding16,17 or noncovalent 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 © 2019 American Chemical Society

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 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 the Fermi level similar to those of mLG.27 Instead, small angles induce strongly correlated electrons, which generates a new set of interesting and fascinating physical properties: an angledependence of van Hove singularities,28,29 the existence of superconductivity for certain magic angles,30,31 flat bands near the Fermi level,27,32 and 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 Received: March 18, 2019 Revised: May 20, 2019 Published: June 3, 2019 15273

DOI: 10.1021/acs.jpcc.9b02577 J. Phys. Chem. C 2019, 123, 15273−15283

Article

The Journal of Physical Chemistry C

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 distance 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 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 scheme41 is employed with a (11 × 11 × 1) k-grid. Finally, geometrical optimizations were carried out keeping the cell parameters fixed but allowing a structural relaxation up to interatomic forces that were smaller than 0.01 eV/Å in each atom.

of molecule with 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 studying 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. ATOMIC MODELS AND ADSORPTION SITES Here, mLG is simulated by a 6 × 6 supercell containing 72 carbon atoms and a corresponding surface area of ∼189 Å2, as shown in Figure 1a. 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

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 form35 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 have 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, two-dimensional 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 ́ Garcia-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 the Supporting Information to keep continuity in

are a1 = 6 × a0

(

3 2

,

1 2

) and a

2

= 6 × a0

(

3 2

1

)

, − 2 , 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, one of them (the top layer) locating 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 with respect to the bottom one by exactly a C−C bond length and along the binding direction, as is shown in Figure 1b and 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 15274


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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 1c. 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., ΔG = zmax − zmin. As a consequence, dt−b has to be redefined because corrugation is no longer zero. Hence

supercell, now containing 144 carbon atoms but with the same lattice vectors and surface area as 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 with 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, 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

dt−b =

(3, 2)

lattice vectors × a0

(

5 3 2

1 2

,

); (√3,

lattice parameters (Å)

θ (deg)

no. of atoms

area (Å2)

10.718

13.17

76

100

8.866

32.20

52

68

16.125

44.80

172

225

4) (2√3, 1); (3, 1)

(6, 1)

(

) ( , ); ( , ) 3 2

7 3 2

3 2

7 2

,

5 2

13 2

N

∑ (zitop − zibottom) 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. While dt−b = 3.27 Å and ΔGt = ΔGb = 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, 0.012, 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 ΔG 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 metaldoped graphene through the presence of an impurity, while adsorption does not happen on pristine graphene.48−50 Additionally, adsorption on monolayer graphene of saturated organic molecules, like pyridine51,52 and aminotriazines,53 has been reported. Taking into account these previous results, we study the adsorption energy of CH3NH2 and CH3SH

Table 1. Structural Parameters of Unit Cells of (n, m) tbLG (n, m)

1 N

(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 ensure that those molecule−molecule interactions are still negligible. Therefore, these tBLG have a reasonable number of

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 gray, including the 11 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. 15275


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define the following strategy for the three tbLGs studied here. We choose an arbitrary path along each supercell. Along this path, we define 11 equidistant points, testing each one as an adsorption site for both molecules. Finally, the adsorption energy, Eads, is calculated as usual36

molecules on their saturated form (see Figure 3) on mLG, bLG, and tbLG. Amine (−NH2) and thiol (−SH) groups are

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 to 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

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.

Table 2. Eads of CH3NH2 Adsorbed on mLG in Top (T), Bridge (B and B2), and Hollow (H) sitesa

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 Ni54 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. Initially, 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. 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 nonconsecutive carbon atoms (second neighbors). Figure 1a depicts these four adsorption sites in mLG. In A−B stacking, top (t) and hole (h) atoms define new possible adsorption sites (see Figure 1b). 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 1b. 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 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

site

Eads

zN

zC

T B B2 H

0.411 (9.451) 0.412 (9.472) 0.438 (10.078) 0.460 (10.589)

2.966 2.976 2.911 2.851

3.174 3.173 3.228 3.084

a

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.

the adsorption energies of the four sites defined for mLG in the previous section. All these energies are between 0.411 and 0.461 eV, which are much larger than kBT0 ∼ 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 kBT0. As a result of molecular adsorption, mLG is structurally distorted, where a corrugation is found. The corrugation is similar for all adsorption sites with ΔG ∼ 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 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. Now, let us discuss the case of CH3NH2 adsorbed on bLG. Table 3 shows the adsorption energies and the principal structural parameters for the six sites on bLG. First, we found that the adsorption energies are slightly diminished with respect to those in mLG., i.e, now they are in the range 0.380− 15276


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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 defines the direction of the electric dipole moment (red arrow).

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 ΔGt and ΔGb on 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, Respectivelya site Tt Th B Bt Bh H

Eads 0.384 0.379 0.386 0.386 0.403 0.427

(8.839) (8.719) (8.875) (8.870) (9.264) (9.814)

dt−b

ΔGt

ΔGb

zN

zC

3.250 3.247 3.239 3.242 3.244 3.247

0.121 0.133 0.144 0.134 0.135 0.127

0.004 0.006 0.006 0.006 0.005 0.005

2.904 2.857 2.881 2.818 2.819 2.741

3.103 3.014 3.052 3.102 3.037 2.955

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 ΔGt and ΔGba

a

tbLG

site

Eads

dt−b

ΔGt

ΔGb

zN

zC

(3, (3, (3, (3, (6, (6,

H T H T H T

0.450 0.392 0.452 0.401 0.447 0.405

3.333 3.325 3.336 3.323 3.326 3.328

0.120 0.136 0.108 0.147 0.131 0.137

0.040 0.046 0.035 0.035 0.058 0.063

2.840 2.855 2.781 2.861 2.778 2.931

3.061 3.090 3.042 3.030 3.050 3.069

2) 2) 1) 1) 1) 1)

Eads is in eV, and distances in Å.

energies fall into the interval defined by H and T configurations. Figure 5 displays all the calculated adsorption

Eads is in eV (kcal mol−1), and distances are in Å.

a

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 with respect to mLG. Now, corrugation is induced in top (ΔGt) and bottom (ΔGb) layers. Here, ΔGt is 10 times larger than the corrugation in mLG, while ΔGb is almost 2 orders of magnitude smaller than ΔGt, i.e., even smaller than corrugation in mLG; thus, ΔGt > ΔGmLG > ΔGb. As a consequence of corrugation, the distance between graphene layers, dt−b, decreases, such that the larger ΔGt 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 is shown in Tables 2 and 3. From those tables, we observe that the adsorption energy on bLG is smaller with 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. 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 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 11 equidistant adsorption sites, finding that all adsorption

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 given by H and T configurations, respectively. However, the adsorption of CH3SH is different (see text). Values are reported in eV.

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, ΔGb, increases 1 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 ΔGt. Notice that the corresponding three tbLG configurations with 15277


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The Journal of Physical Chemistry C HAE exhibit also the smallest corrugations, ΔGt, 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 1 order of magnitude larger than kBT0 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 largest adsorption energy is in the H configuration. With a second graphene layer in A−B stacking, the adsorption energy decreases with respect to mLG. However, by making a relative angle between top and bottom graphene layers, the adsorption energy increases with respect to those observed in bLG, suggesting a tuning effect. Additionally, the adsorption of the molecule induces corrugation in graphene layers. While corrugations 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 with 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. 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 ΔG 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 with zN and zC reported in Table 2 for CH3NH2. While both zC distances are essentially the same, zS > zN, which

Table 5. Eads of CH3SH Adsorbed on mLG at T, B, B2, and H Configurationsa Eads

case T B B2 H

0.361 0.369 0.380 0.368

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

ΔG

zS

zC

0.048 0.121 0.097 0.112

3.466 3.388 3.383 3.388

3.226 3.168 3.132 3.128

ΔG 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. a

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. On bLG, adsorption energies of CH3SH decrease, and the interval between higher and lower limits is similar to the energy differences found for CH3NH2 (Table 6). Now, we find Table 6. Eads of CH3SH Adsorbed on bLG in Tt, Th, B, Bt, Bh, and H sites; ΔGt and ΔGb Are the Corrugation of Top and Bottom Layers; zS and zC Are the Distance from Graphene to S and C Atoms of CH3SHa case Tt Th B Bt Bh H a

Eads 0.346 0.316 0.340 0.321 0.356 0.338

(7.951) (7.265) (7.811) (7.375) (8.211) (7.777)

dt−b

ΔGt

ΔGb

zS

zC

3.252 3.243 3.255 3.258 3.242 3.245

0.142 0.176 0.128 0.128 0.169 0.170

0.005 0.006 0.005 0.004 0.006 0.005

3.307 3.316 3.394 3.301 3.316 3.314

3.144 3.159 3.205 3.182 3.058 3.132

Eads is in eV (kcal mol−1), and distances are in Å.

that HAE and LAE correspond to Bh and Th configurations. Here, ΔGt, ΔGb, and dt−b are slightly larger than those generated by CH3NH2, and the molecular distances, zS and zC, are slightly reduced with respect to mLG. But comparing both molecules, we found that they are still obeying 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. Following the same methodology used before, we explore different adsorption sites of 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 with respect to bLG, in a similar way that CH3NH2 does, as we have discussed above. It is noteworthy Table 7. HAE and Sites of CH3SH on (3, 2), (3, 1), and (6, 1) tbLG, Interlayer Distance (dt−b), and Corrugations ΔGt and ΔGba

a

15278

tbLG

site

Eads

dt−b

ΔGt

ΔGb

zS

zC

(3, 2) (3, 1) (6, 1)

B2 B2 B2

0.385 0.379 0.390

3.314 3.336 3.328

0.181 0.128 0.148

0.120 0.028 0.112

3.233 3.226 3.323

3.054 3.113 3.063

Energies are in eV, and distances in Å. DOI: 10.1021/acs.jpcc.9b02577 J. Phys. Chem. C 2019, 123, 15273−15283

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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.

that the induced corrugation on the bottom layer, ΔGb, increases notably up to values close to ΔGt. Although this corrugation is also observed in CH3NH2 adsorbed on tbLG, these values are twice as large, so they might be a direct consequence of the interaction between CH3SH and graphene layers, as we will discuss later. Notice that the relative twist angle between the top and bottom layers brings an increase in the adsorption energy of CH3SH with 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 nonsymmetric electronic charge distribution in twistedgraphene structures. Also, the similarity of HAE between tbLGs and mG (see Figure 5) is according to the decoupled regime to which the three tbLGs belong.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 were carried out. 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 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, allowing 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, μ⃗, which points from the functional groups to the methyl radical. From our DFT calculations, we obtained that |μ⃗CH3NH2| = 1.32 D and |μ⃗CH3SH| = 1.44 D, which are similar to that exhibited by other polar molecules, like the

water molecule (|μ⃗H2O| = 1.85 D).56 As we have discussed along herein, upon adsorption either molecule is oriented such that zS > zN, whereas the corresponding methyl positions are almost the same. These molecular orientations imply that μ⃗CH3NH2 has a vertical component pointing outside graphene (up), while μ⃗CH3SH does pointing inside graphene (down), as shown in Figure 4. To explain this difference, we refer to previous works that focused on study of 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 nonlocal 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 orientation (up or down), utterly absent in the far-field limit. They also reported that the up configuration of the dipole is more stable than 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 15279


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Figure 7. Electronic charge redistribution given by the plane average electron density difference, Δρ̅(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.

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. 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 and −0.75 eV that correspond to the horizontal lines in Figures 6a, b, c and 6d, e, f, respectively. At energies lower than −3.0 eV, the electronic band structure of

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 toward the surface, and their wave functions 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 wave function 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 wave functions, 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 15280


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CH3SH show different profile mainly at the interface. Hence, Δρ̅(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 Δρ̅(z), which again could be related to the different pointing direction of the molecular electric dipole moment.

graphene remains undisturbed with respect to pristine graphene arrangement upon CH3NH adsorption, as insets show 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 with 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 with corrugation. Although a direct comparison between the band structure of the molecule adsorbed on 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 to study the charge redistribution at the interface and vacuum region close to the molecule and graphene layers. Such analysis can be made through the notion of the plane average electron density difference, Δρ̅(z), which describes the difference in the electronic charge distribution associated with the mutual interaction of the structures that set up the system with respect isolated structures. First, the plane average electron density, ρ̅(z), of each structure is defined as ρ ̅ (z ) =

1 A

∫SC ρ(x , y , z)dxdy

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 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 kBT0 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 molecularadsorption 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 with 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. On the other 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 number 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.

(3)

where ρ(x, y, z) is the electron density in real space, the integration is over the XY plane, and A correspond to the surface area of the supercell.67 Hence, Δρ̅(z), the difference in the electronic charge distribution, is defined as follows: Δρ ̅ (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 Δρ̅(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 in the same order as those reported for MoS2−G heterostructures.68 First, Δρ̅(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 Δρ̅(z) for CH3NH2, the charge is essentially redistributed in the same way, except for slight variations in the intensity. Instead, the three Δρ̅(z) for

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ASSOCIATED CONTENT

* Supporting Information S

The Supporting Information is available free of charge on the ACS Publications website at DOI: 10.1021/acs.jpcc.9b02577. Comparison between standard and extended basis set, based on the plane average electron density difference, Δρ̅(z), and the notion of ghost orbitals (PDF)

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AUTHOR INFORMATION

Corresponding Author

*E-mail: [email protected]. ORCID

Francisco Hidalgo: 0000-0003-1987-6478 15281


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Cecilia Noguez: 0000-0003-2044-156X Notes

The authors declare no competing financial interest.

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ACKNOWLEDGMENTS The authors are thankful for the computing time granted by LANCAD on the supercomputer Yoltla at LSVP UAMIztapalapa. This work is partially supported by the projects DGAPA-UNAM project PAPIIT IN109618 and UAM-A-CBI2232021. We gratefully acknowledge the SNI-Conacyt-México for the distinction of our membership and the stipend received.

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ABBREVIATIONS DFT density functional theory mLG monolayer graphene bLG bilayer graphene tbLG twisted-bilayer graphene

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