Adsorption of Organic Molecules on the Hydrogenated Germanene: A

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Adsorption of Organic Molecules on the Hydrogenated Germanene: A DFT Study Pamela Rubio-Pereda, and Noboru Takeuchi J. Phys. Chem. C, Just Accepted Manuscript • DOI: 10.1021/acs.jpcc.5b08370 • Publication Date (Web): 24 Nov 2015 Downloaded from http://pubs.acs.org on November 29, 2015

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The Journal of Physical Chemistry

Adsorption of Organic Molecules on the Hydrogenated Germanene: A DFT Study

Pamela Rubio-Pereda a, Noboru Takeuchi b,* a

Centro de Investigación Científica y de Educación Superior de Ensenada 3918, Código Postal 22860, Ensenada, Baja California, México b

Centro de Nanociencias y Nanotecnología, Universidad Nacional Autónoma de México, Apartado postal 14, Código Postal 22800, Ensenada, Baja California, México

a

[email protected]; b [email protected]

* Corresponding author at: Centro de Nanociencias y Nanotecnología, Universidad Nacional Autónoma de México, Apartado postal 14, Código Postal 22800, Ensenada, Baja California, México Tel.: +52 646 161 60 41. E-mail address: [email protected]

Author Contributions: The manuscript was written through contributions of all authors. All authors have given approval to the final version of the manuscript

ACS Paragon Plus Environment

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ABSTRACT

Graphene-like group IV semiconductors such as silicene and germanene may be organic functionalized to supply the necessary tools for the manipulations at a molecular level that the microelectronic industry will demand within the following years. In particular, the organic functionalization with molecules containing unsaturated C−C bonds by means of a radical initiated reaction on hydrogenated surfaces constitutes a favorable route for the attachment of organic layers. In this work we have evaluated the organic functionalization of the hydrogenated germanene (H-germanene) with acetylene, ethylene and styrene and compared these results with previous calculations made by us of the adsorption on the hydrogenated graphene surface (Hgraphene) and on the hydrogenated silicene surface (H-silicene). Results towards organic functionalization from H-germanene and H-graphene are markedly different. On the Hgermanene the adsorption of acetylene and ethylene is energetically favorable while the adsorption of styrene, despite being energetically favorable, leads to a final state whose structure configuration does not favor a chain reaction. On the other hand, adsorption of these molecules on the H-graphene is less likely to occur with acetylene and ethylene, while for styrene it is not energetically favorable. These variations in surface reactivity between H-graphene and Hgermanene are attributed to the larger lattice constant of H-germanene, and differences in the electronegativity of C, Ge and H atoms.


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I. Introduction Graphene-like group IV semiconductors, such as silicene and gemanene, have electronic and mechanical properties comparable to those of graphene. By chemical modification, it is possible to tune the band structure, use the resulting materials for charge storage, chemical and biological sensing, or even to make new two dimensional composite materials. Therefore, the organic functionalization of silicene and germanene may have applications in electronic devices, such as in flexible, large area, or transparent electronics, or to fabricate sensors that could be used for food monitoring, as biosensors, or in explosive detection, for example. Furthermore, the organic functionalization could be an option to supply the necessary tools for the manipulations at a molecular level that the microelectronic industry will demand within the following years.1-3 Despite plenty of research activity around graphene, there are still some important challenges to overcome: the ability to grow graphene over large areas and its integration in the semiconductor electronic industry by retooling its processes to work with carbon-based nanostructures is one of them. Nevertheless, the discovery of extremely high carrier mobility, thermal conductivity and mechanical strength in graphene has led to the study of other two-dimensional (2D) materials that may as well present these advantageous properties not observed in their parent 3D structures.4 In this regard, graphene-like group IV semiconductors made of silicon and germanium, the most important and ubiquitous materials of the current era, are being investigated. Silicene the two-dimensional version of silicon, firstly achieved experimentally by epitaxial growth of silicon atoms on silver substrates,5–12 has demonstrated better surface reactivity compared to graphene for organic functionalization.13-14 On the other hand, germanium, the material of 1940s transistors, is an important semiconductor material vastly used in the current silicon-based semiconductor industry and unlike graphene, it offers a much more


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favored compatibility for the integration of its 2D version, germanene, into silicon-based nanoelectronics, by exploiting traditional silicon manufacturing methods as much as possible1516

. The idea of the 2D version of germanium was conceived even before the first samples of

graphene could be obtained.17 It is found that Ge atoms forms a bilayer structure, similar to the one formed by Ge atoms in the ideally terminated Ge(111) surface.18 The structure of germanene is stable with a free standing form characterized by a low buckling configuration of 0.64 Å due to the simultaneous presence of sp2 and sp3 hybrid orbitals. The equilibrium lattice constant is of 3.97 Å with a Ge-Ge bond length of 2.38 Å. Furthermore, recent theoretical works have pointed out that germanene constitutes a semimetal with linearly crossing bands at the Fermi level like graphene.19-22 Among the possible ways to organic functionalize these 2D materials a particularly proven approach is a radical-initiated reaction of terminally unsaturated molecules with hydrogenterminated surfaces.23-26 Using topotactic synthesis Jiang et al. found that “group IV fully hydrogenated graphene analogues can be synthesized in gram-scale quantities and in thin films via the topotactic deintercalation of layered Zintl phase precursors”.15 With the topotactic deintercalation epitaxially grown Zintl phases on Si/Ge substrates can be isolated via manual exfoliation into few layers and single layers. The organic functionalization with molecules that contain C−C unsaturated bonds constitutes a possible route to fabricate organic layer/germanene interfaces. In organic chemistry, unsaturated molecules form part of a very well-studied functional group with a number of reactions that are well-known.27-29 One possibility is a radical-initiated chain reaction, previously shown for graphene and silicene:13-14 the attachment of these molecules on the fully hydrogenated


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germanene should begin with a hydrogen (H) vacancy that will lead to the formation of a germanium dangling bond with a single spin-unpaired electron which is very reactive. Experimentally, H vacancies can be created by removing H atoms with a Scanning Tunneling Microscope (STM) tip or by irradiating sections of the surface sample with ultra violet (UV) light. An incoming molecule should bind to the surface at the H vacancy site, giving rise to a surface-bound organic group with a carbon-centered radical. The highly reactive carbon radical then should abstract a H atom from a neighboring Ge−H group to produce a new germanium dangling bond on the surface where another molecule can attach. This process is repeated, leading to a surface chain reaction in a controlled manner. This kind of reactions have been studied theoretically and experimentally on the H-Si[111] and H-Si[001] surfaces.23-26, 30-34 In this work we report the adsorption of acetylene, ethylene and styrene molecules on the hydrogenated germanene by applying density functional theory. Furthermore, we compare these results with the adsorption of these molecules on hydrogenated graphene.13 We found that on the H-germanene the adsorption of acetylene and ethylene proceeds with low energy barriers favoring a chain radical initiated reaction while the adsorption of styrene despite being energetically favorable, leads to a final state whose atomic configuration does not favor a chain reaction. On the other hand, adsorption of these molecules on the H-graphene resulted energetically less favorable.13 These differences in surface reactivity are attributed to the size of the honeycomb net and electronegativity distributions. The larger hexagonal lattice parameter of H-germanene compared with H-graphene favors the adsorption of these particular organic molecules. We present and discuss these results in the rest of the paper which is organized as follows: in section II we describe the methods, in section III we present the results and discussion of our calculations, and in section IV we conclude the paper.


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II. Theoretical Method We have performed periodic density functional theory (DFT) using the quantum espresso package35 where the electronic states are expanded in plane waves with kinetic-energy cutoffs of 30 and 240 Ry for the wave function and charge density, respectively. Electron-ion interactions are treated within the pseudopotential method. 36 Exchange and correlation energies are modeled according to the generalized gradient approximation (GGA) with the Perdew-Burke-Ernzerhof (PBE) gradient corrected functional.

37

The van der Waals interactions are included in the

exchange-correlation PBE functional with empirical dispersion corrections of Grimme (DFT-D2 functional).

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Binding energies were calculated with a Monkhorst-Pack mesh39 of 2x2x1

differing by no more than 0.05 eV compared with larger Monkhorst-Pack meshes of 4x4x1 and 6x6x1. Finally, since the systems we are studying have a spin-unpaired electron, the calculations are spin unrestricted.

Substrate and molecules To optimize the germanene structure, as well as the consecutive steps of hydrogenation addition reactions of acetylene, ethylene and styrene, we have used a 5×4 unit cell, with 40 Ge atoms (Figure 1a). With the hydrogenation of the germanene structure (H-germanene), the resultant buckling configuration is of 0.73 Å, which is 0.09 Å larger than the buckling configuration for pristine germanene, and the Ge-Ge bond length is enlarged by 0.08 Å. The vacuum size between adjacent H-germanene images is always larger than 20 Å. The shortest distance in the plane along the Minimum Energy Path (MEP) between two adjacent molecules of acetylene, ethylene and styrene is 14.11 Å, 11.56 Å and 9.03 Å, respectively.


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In previous calculations of the functionalization of hydrogenated silicon surfaces31-34, and hydrogenated silicene14, using the string method, it was found that the path from the intermediate to the final state, involves the breaking of the H-Si bond and the formation of a new C-H bond. Therefore, in this paper we have used this C-H distance as the reaction coordinate by imposing a distance constraint between the highly reactive carbon centered radical (C*) and the hydrogen atom to be abstracted (H*) (Figure 1b). Binding energies were calculated in the context of SCF and damped ionic dynamics. For each reaction, we have used a large number of atomic configurations (up to 24 images) between the intermediate and the final state, this is not only a large number but also the number of configurations is denser close to the transition state so we do not miss it. Furthermore, we have imposed strict conditions for convergence such as when forces on atoms are less than 1x10-3 a. u. and total energy for ionic minimization between two consecutive steps is less than 1x10-6 a.u. With this protocol, the relaxation of a set of images along an initial pathway between two local minima can be successfully achieved.

Figure 1. (a) H-germanene surface simulation with a 5x4 supercell and (b) for the acetylene case, the location of the highly reactive carbon centered radical (C*) and the hydrogen atom to be abstracted (H*).

III. Results


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Minimum energy paths (MEP) and adsorption structures are studied for the addition reactions of acetylene, ethylene and styrene on H-germanene. First of all, an initial state is represented by the non-interacting system of H-germanene with one hydrogen vacancy (please refer to Figure S1 available in the supporting information). Initial states are characterized with a value of 0.0 eV in the MEP. For each addition reaction, we first study the adsorption structure of the organic molecule attached to an isolated germanium dangling bond in the H-germanene surface, this state is known as the intermediate state (IS). Then, we distinguish between IS, containing a C centered radical, and final structures after hydrogen abstraction, known as final states (FS). The highest potential energy in the MEP, connecting the IS with the FS, is known as the transition state (TS). The difference in energy between the TS and IS is the energy barrier height. At the TS, the reaction can proceed to form products or go backwards to the reactants depending on the energy barrier height and its energy value compared with the non-interacting initial state (surface with a vacancy and an isolated organic molecule). To find the TS, which is a maximum along the MEP, is equivalent to find the maximum along a given degree of freedom such as the distance between the highly reactive carbon centered radical (C*) and the hydrogen atom to be abstracted (H*). We present results of the addition reaction for each kind of molecule and finally a comparison of surface reactivity between H-germanene and H-graphene tested previously in ref 13.

a. Addition reaction of acetylene The MEP for this reaction is shown in Figure 2a. The adsorption of acetylene occurs straightforward, with the IS configuration located at -0.76 eV (Figure 2c), the FS at -2.06 eV (Figure 2e) and the TS at -0.61 eV (Figure 2d). The energy barrier for this reaction is 0.15 eV releasing in the process 1.30 eV of energy, known as the heat of adsorption (∆HA), where in this


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case is negative (see Table 1). Different from the acetylene reactions with H-graphene13 and Hsilicene14 where the transition state is characterized by the hydrogen bond breaking, in the addition reactions with H-germanene the transition state is characterized by the sagging of the Hgermanene sheet (Figure 2b). Unlike the H-graphene and H-silicene systems, the H-germanene has a wider honeycomb net due to the larger atomic radius of Ge atoms (125 pm) in comparison with C (70 pm) and Si (110 pm) atoms. A wider honeycomb net increases the distance between the highly reactive carbon centered radical (C*) and the hydrogen (H) atom to be abstracted (H*). Therefore, the originally buckled H-germanene system needs to bend in order to reduce the distance by a magnitude of 1.33 Å between the C* and the H* (Figure 2b). This step defines the TS of the reaction. The H abstraction takes place further below the reaction coordinate in the MEP as can be seen in Figure 2a.


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Figure 2. For the addition reaction of acetylene on H-germanene: (a) minimum energy path profile; (b) sagging of the H-germanene sheet present at the transition state (TS) depicted in black lines on top of the intermediate state (IS) depicted in gray lines; from (c) to (e) atomic configurations for the intermediate, hydrogen bond breaking and final states. Germanium, carbon and hydrogen atoms are represented by yellow, gray and blue spheres respectively. Atomic configuration for the IS, H bond breaking and FS are shown in Figures 2c-e. After acetylene is attached where the H vacancy was located, a C* is created at the organic molecule with a single spin-unpaired electron that is distributed in space located mainly at the C* as can be seen in Figure 3a. During the H bond breaking, the single spin-unpaired electron distributes itself around the C* and the neighboring Ge atom (Figure 3c). Finally, when the H abstraction process is completed, a new H vacancy is created with a single spin-unpaired electron located entirely at the vacancy (Figure 3e).

Table 1. Comparison of energies in eV for initial, intermediate, transition and final states and the energy barrier and heat of adsorption (∆HA) in the addition reactions of acetylene, ethylene and styrene on H-germanene.

molecule

initial

intermediate

transition

energy

final

state

state

state

barrier

state

∆HA (eV)

(eV)

(eV)

(eV)

(eV)

(eV)

acetylene

0.0

-0.76

-0.61

0.15

-2.06

-1.30

ethylene

0.0

-0.65

-0.32

0.33

-1.51

-0.86

styrene

0.0

-1.07

-0.55

0.52

-1.65

-0.58


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Through a population analysis with the Löwdin method40 we have studied the change in the valence electron population for each atom in the system. These changes are calculated between the atoms within the presented system (Löwdin method) and the individual neutral atoms. The results of these analyses are represented pictorially in Figures 3b,d,f for the IS, H bond breaking and FS, respectively. We have used a blue-white-red scale: atoms whose valence electron population increased/decreased the most are shown in red/blue; atoms whose valence electron population did not change are shown in white. As H atoms are more electronegative compared with Ge atoms, in Figure 3b H atoms appear in a whitish color while Ge atoms appear in a bluish color, this is to say that there is a transfer in valence electron population from the less electronegative Ge atoms to the more electronegative H atoms. Different from the H-germanene, the H atoms of acetylene (Figure 3b) appear with a bluish color and the C atoms with a reddish to clear red color indicating that the transfer in valence electron population occurs from the H atoms to the much more electronegative C atoms. This difference in electronegativity creates a partial charge distribution that enables the adsorption of acetylene on H-germanene. Furthermore, in Figure 3b the carbon atom which is bonded to a Ge atom exhibits a greater increment in electron population than the C* does. This increment comes from the Ge atom located below which in turn appears with a blueish color. At the H bond breaking (Figure 3d), the valence electron population of H* starts to decrease; part of it is being transferred to the valence electron population of C*. Finally, the FS in Figure 3f shows both C atoms with almost an equal gain in valence electron population after the hydrogen abstraction. On the other hand, the charge of the Ge atom at the H vacancy is increased compared with neighboring Ge-H


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groups, since this Ge atom is in fact not bonded with a H atom that could diminish its valence electron population.

Figure 3. For the addition reaction of acetylene on H-germanene: total spin density isosurfaces σ(rԦ) = ρ↑(rԦ) −ρ↓(rԦ)

and changes in the valence electron population for the intermediate state (IS)

(a) and (b), H bond breaking (c) and (d), and the final state (FS) (e) and (f). Germanium, carbon and hydrogen atoms are represented by yellow, gray and blue spheres respectively. The change in valence electron population is depicted in a blue-white-red color bar normalized scale; atoms whose electron population increased/decreased the most are shown in red/blue color; atoms whose valence electron population did not change are shown in white color. For each state, color


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intensity is in accordance with data normalization to the largest gain or lost in valence electron population.

As mentioned before, during the H abstraction process, there is a deformation of the Hgermanene. To quantify this behavior, we define a “sheet angle” as the angle formed by the atom that sinks the most with two other unperturbed equivalent Ge atoms (Figure S2). In this way the angle of the ideal H-germanene sheet is 180° as shown in Table 2, where we have summarized this and other structural parameters along the MEP. The triple C-C bond of acetylene with a length of 1.21 Å is gradually enlarged to the characteristic length of a double C-C bond of 1.34 Å. At the IS the separation distance between C* and H* is originally of 3.17 Å and at the FS this distance is reduced to 1.11 Å which is the characteristic length of a C-H bond. On the other hand, the C-Ge bond remains pretty much constant along the reaction coordinate just stretching a little bit during the TS and H bond breaking where the angle of the H-germanene sheet reaches a minimum value of 170.9°. When the H abstraction process has already taken place, the Hgermanene sheet recovers the shape of an almost completely flat surface with an angle very close to 180°. Finally, by measuring the angle that the C-C bond of acetylene makes with the horizontal (CC-hor.angle), we can see that during the TS and H bond breaking, the acetylene molecule is leaned towards the H-germanene sheet to finally end at a slightly greater angle of 34.4° compared with the angle that it had before the H abstraction process took place (30.2°). Since the honeycomb net of the H-germanene is greater than the H-silicene’s, steric effects between two adjacent attached molecules should be smaller, and a chain reaction could be favorable, with the starting atomic configuration being the one shown in Figure 3e, with one molecule attached and a newly created H vacancy next to it. Further calculations corroborate this


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assumption since the total energy for the adsorption of two acetylene molecules is -2.07 eV/molecule which is 0.01 eV below the energy of adsorption for one molecule (please refer to Figure S3 for the schematic atomic configuration).

Table 2. Calculated bond lengths (Å) and bond angles (deg) for the different states involved during the addition reactions of acetylene, ethylene and styrene on H-germanene.

acetylene

Ethylene

Styrene

bond and angle

initial

intermediate

transition

H bond

type

state

state

state

breaking

C-C

1.21

1.31

1.31

1.32

1.34

C*-H

>10

3.17

1.84

1.64

1.11

C-Ge

-

1.98

2.00

2.00

1.96

CC-hor.angle

0

30.2

23.8

24.4

34.4

sheet angle

180

177.9

170.9

172.2

178.7

C-C

1.33

1.46

1.49

1.50

1.53

C*-H

>10

3.05

1.75

1.56

1.11

C-Ge

-

2.05

2.03

2.01

1.99

CC-hor.angle

0

20.6

20.2

20.3

26.4

sheet angle

180

177.0

171.1

172.1

179.1

C-C

1.35

1.45

1.48

1.50

1.53

C*-H

>10

3.34

1.69

1.59

1.11

C-Ge

-

2.06

2.05

2.04

2.00

CC-hor.angle

0

26.9

21.6

24.9

28.8

0

31.5

33.3

40.0

3.5

180

175.6

168.9

172.4

178.8

final state

phenylhorizontal angle sheet angle


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b. Addition reaction of Ethylene The MEP for the addition reaction of ethylene is shown in Figure 4a. Unlike acetylene, the adsorption of ethylene, despite being energetically favorable, exhibits a larger energy barrier of 0.33 eV and a smaller value of the heat of adsorption (-0.86 eV, as shown in Table 1). The IS has an energy value of -0.65 eV (Figure 4c), which is 0.11 eV above the IS for acetylene and the energy of the FS is -1.51 eV (Figure 4e), 0.55 eV higher than in the case of acetylene. The TS is located 0.32 eV below the zero energy value (Figure 4d) and, similar to the adsorption of acetylene, the TS corresponds to the maximum bending of the H-germanene sheet (Figure 4b). With this bending, the distance between the C* and the H* was reduced by a magnitude of 1.30 Å. As in the previous case, the breaking of the H-Ge bond takes place further below the reaction coordinate in the MEP. The differences between the acetylene and ethylene reactions can be attributed to the larger size of the ethylene molecule. Nonetheless, as in the case of acetylene, the addition reaction of ethylene is energetically favorable. The total energy for the adsorption of two ethylene molecules is -1.48 eV/molecule which is 0.03 eV above the energy of adsorption for one molecule (Figure S3). This indicates that the energy loss due to steric effects for the adsorption of a second molecule is in fact small.


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Figure 4. For the addition reaction of ethylene on H-germanene: (a) minimum energy path profile; (b) sagging of the H-germanene sheet present at the transition state (TS) depicted in black lines on top of the intermediate state (IS) depicted in gray lines; from (c) to (e) atomic configurations for the intermediate, hydrogen bond breaking and final states. Germanium, carbon and hydrogen atoms are represented by yellow, gray and blue spheres respectively.

Atomic configurations for the IS, H bond breaking and FS are shown in Figures 4c-e. For the H abstraction process to occur, the C*, with its two H atoms, rotates in order to accommodate the incoming H* atom (Figure 4d). Total spin density surfaces are shown in Figures 5a,c,e for the IS, H bond breaking and FS, respectively. The spread of the single spin-unpaired electron and the behavior of the valence electron population occur, as expected, similar to the acetylene case.


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Figure 5. For the addition reaction of ethylene on H-germanene: total spin density isosurfaces σ(rԦ) = ρ↑(rԦ) −ρ↓(rԦ)

and the change in the valence electron population for the intermediate state

(IS) (a) and (b), H bond breaking (c) and (d), and the final state (FS) (e) and (f). Germanium, carbon and hydrogen atoms are represented by yellow, gray and blue spheres respectively. The change in valence electron population is depicted in a blue-white-red color bar normalized scale; atoms whose valence electron population increased/decreased the most are shown in red/blue color; atoms whose valence electron population did not change are shown in white color. For each state, color intensity is in accordance with data normalization to the largest gain or lost in valence electron population.


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Finally, an analysis of the structural parameters is summarized in Table 2. Along the reaction coordinate, the double C-C bond of ethylene with an initial length of 1.33 Å is gradually enlarged to the characteristic length of a single C-C bond of 1.53 Å. The separation distance between the C* and the H atom to be abstracted was reduced from its original value of 3.05 Å at the IS, to a final value of 1.11 Å at the FS, which is the characteristic length of a C-H bond. On the other hand, the C-Ge bond length steadily decreases from 2.05 Å to 1.99 Å. In general, the CGe bond lengths are larger than in the adsorption of acetylene. At the FS, the C-Ge bond length is 1.99 Å, larger by 0.03 Å than in the acetylene case (1.96 Å). This difference may be due to a favorable interaction between ethylene and the buckled H-germanene system as can be seen in Figure 4c, with the ethylene molecule bending towards the surface, and increasing the C-Ge length. This favorable interaction may be attributed to the larger size of the honeycomb net of Hgermanene which in turn reduces the presence of steric effects and allows the coupling between the organic molecule and the buckled system. As a consequence, the CC-horizontal angles in ethylene are lower than in acetylene as shown in Table 2 and the H-Germanene sheet bends at the TS with an angle of 171.1° which is slightly greater than in acetylene.

Addition reaction of Styrene In this section, we consider the addition reaction of styrene on H-germanene. In this particular case, due to the larger size of the styrene molecule and the resulting increase in the number of degrees of freedom compared with the previous cases, the determination of the MEP is more difficult. Left side of Figure 6a shows the MEP for the addition reaction of styrene up to a pseudo-final state known as F*S located at -1.25 eV, where the phenyl group forms a non-zero


18

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angle with the surface (Figures 6d and 7d) and the single spin-unpaired electron appears at the newly created H-vacancy (Figure 9e). Unlike previous cases of acetylene and ethylene, the IS is much more stable with an energy value of 1.07 eV below the zero energy value (Figures 6b and 7b). This enhanced stability is attributed to a resonance effect where the single spin-unpaired electron is distributed along the phenyl group which is known as an electron withdrawing group (EWG) (Figure 9a). The TS corresponds again to the maximum bending of the H-germanene sheet as shown in Figure 7a and it has an energy value of -0.55 eV. The TS gives rise to an energy barrier of 0.52 eV, higher compared with acetylene and ethylene cases, however, not high enough to prevent the abstraction of the H atom.


19


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Page 20 of 43

Figure 6. For the addition reaction of styrene on H-germanene: (a) minimum energy path profile; from (b) to (g) side views of the atomic configurations for the intermediate state (b), the hydrogen bond breaking (c), the pseudo-final state (d), the first (e) and second (f) polar rotation, and the final state with the azimuthal rotation (g). Germanium, carbon and hydrogen atoms are represented by yellow, gray and blue spheres respectively. When the H abstraction process is completed and the reaction has reached the F*S, there is a subsequent movement of the phenyl ring of the styrene molecule which results in a FS


20

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significantly different from those obtained with the adsorption of this same molecule on the Hgraphene13 and H-silicene14 surfaces. From the entire MEP shown in Figure 6a, after reaching the F*S, the phenyl ring makes two subsequent rotations that bring him closer to the H-germanene surface: firstly, it rotates in a plane parallel to the surface (Figures 6e-f and 7e-f) with no energy barrier; secondly, it rotates in a plane perpendicular to the surface to finally couple face-to-face with it at 1.65 eV below the zero energy value (Figures 6g and 7g). From the IS to the FS, the adsorption of styrene releases 0.58 eV of energy (∆HA), which is the smallest of the three cases we have studied. This coupling between the phenyl ring and the surface at the newly created Hvacancy (Figure 9e) stops any possibility for a chain reaction to occur (Figure 9g).


21


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Figure 7. For the addition reaction of styrene on H-germanene: (a) sagging of the H-germanene sheet present at the transition state (TS) depicted in black lines on top of the intermediate state (IS) depicted in gray lines; from (b) to (g) top views of the atomic configurations for the intermediate state (b), the hydrogen bond breaking (c), the pseudo-final state (d), the first (e) and second (f) polar rotation, and the final state with the azimuthal rotation (g). Germanium, carbon and hydrogen atoms are represented by yellow, gray and blue spheres respectively.


22

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It is worth mentioning that the coupling between styrene and the H-germanene surface did not occur with the H-silicene surface due to its reduced honeycomb size net that does not allow the positioning of the phenyl ring at the newly created H vacancy due to steric effects between the molecule and H atoms of the surface (Figure 8). The minimum distance between the H atoms of the H-silicene surface and the molecule at the FS is of 2.73 Å and with the H-germanene surface at the F*S is of 3.22 Å. On the other hand, with the addition reaction of styrene on the Hgraphene surface, the adsorption was not favorable due to similar electronegativity distributions between both systems and the even smaller honeycomb net of H-graphene13.

Figure 8. Atomic configurations with total spin density isosurfaces for the final states (FS) of the addition reaction of styrene on H-silicene (a) and H-germanene (b).

At the FS, electronic charge is transferred from the H-vacancy towards the EWG (Figure 9f,h), giving as a result a zero total spin density (Figure 9g). The electrophilicity of the EWG decreases the valence electron population of the Ge atom by 0.05 electrons. With regard to the change in the valence electron population, the left column of Figure 9 clearly shows the changes in partial charges distribution between the organic molecule and the H-germanene which in turn causes the favorable coupling between both molecules.


23


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Figure 9. For the addition reaction of styrene on H-germanene: total spin density isosurfaces σ(rԦ) = ρ↑(rԦ) −ρ↓(rԦ)

and the change in the valence electron population for the intermediate state (IS)

(a) and (b), the H bond breaking (c) and (d), the pseudo-final state (F*S) (e) and (f), and the final state (FS) (g) and (h). Germanium, carbon and hydrogen atoms are represented by yellow, gray and blue spheres respectively. The change in valence electron population is depicted in a blue-


24

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white-red

color

bar

normalized

scale;

atoms

whose

valence

electron

population

increased/decreased the most are shown in red/blue color; atoms whose valence electron population did not change are shown in white color. For each state, color intensity is in accordance with data normalization to the largest gain or lost in valence electron population. We finally discuss the structural parameters of the most important states during the reaction with styrene (see Table 2). Along the reaction coordinate, the double C-C bond of styrene with an initial length of 1.35 Å is enlarged to the characteristic length of a single C-C bond of 1.53 Å as a result of the H abstraction process. The separation distance between the C* and the H atom to be abstracted was reduced from its original value of 3.34 Å at the IS, to a final value of 1.11 Å at the FS. As in previous cases, at the TS the H-Germanene sheet is bent, with and angle of 168.9° reducing the distance between the C* and the H* by a magnitude of 1.65 Å, which stand for the lowest angle and the largest distance in all three cases (please refer to Table S1 for a detailed comparison). As in the ethylene case, the C-Ge bond length for styrene is steadily reduced, going from 2.06 Å to 2.00 Å, however the C-Ge bond lengths are larger than in the acetylene case. For example, at the FS, the C-Ge bond length is 2.00 Å. Again, a larger C-Ge bond length may be traced to a favorable interaction between the phenyl group of styrene and the buckled H-germanene system (Figure 7f,g). The CC-horizontal angle is 26.9° at the IS and once the H abstraction process has taken place is increased to 28.8°. Nonetheless, the most notorious change for styrene along the reaction coordinate is the variation in the angle between the phenyl group and the H-germanene surface (phenyl-horizontal angle). At the IS the phenyl-horizontal angle is 31.5° and while the H abstraction is taking place this angle increases up to 40.0° in order to diminish steric effects


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Page 26 of 43

between the phenyl group and the H atom being transferred. After rotations in the polar and azimuthal planes, the phenyl group ends face-to-face with the surface with an angle of 3.5°.

c. Comparison with H-graphene In table 3 we show the energetics for the addition reactions of acetylene, ethylene and styrene on H-germanene and H-graphene. If we compare the results of H-graphene with those of Hgermanene, we see that the IS for acetylene and ethylene are energetically more favorable for Hgraphene; however the FS were not as stable as those of H-germanene with a difference of 0.32 eV for the acetylene case and of 0.60 eV for the ethylene case. On the other hand, energy barriers in both cases are of similar height for each kind of molecule. For the adsorption of styrene, which is favorable for H-germanene, on H-graphene is not probable to occur since the FS is less stable than the IS. These differences in surface reactivity with H-graphene are due to its smaller lattice parameter and the higher electronegativity of carbon with respect to germanium. As a consequence, there is repulsion between the organic molecules and H-graphene, since they both exhibit a similar charge distribution pattern of partial positive charges at the periphery (please refer to Figure S4). In summary, results are very different and reveal that the energetics for organic molecular functionalization with H-germanene are better than with H-graphene.

Table 3. Comparison of energies in eV for intermediate and final states in the addition reactions of acetylene, ethylene and styrene on H-germanene and H-graphene.

system

molecule

intermediate

transition

energy

final

∆HA

state

state

barrier

state

(eV)


26

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(eV)

(eV)

(eV)

(eV)

-0.76

-0.61

0.15

-2.06

-1.30

H-graphene

-1.17

-1.00

0.17

-1.74

-0.57

H-germanene

-0.65

-0.32

0.33

-1.51

-0.86

-0.75

-0.50

0.26

-0.91

-0.16

-1.07

-0.55

0.52

-1.65

-0.58

-0.45

-

-

0.0

+0.45

H-germanene acetylene a

ethylene a

H-graphene

H-germanene styrene H-graphenea a

Theoretical results for H-graphene are taken from ref 13.

IV. Conclusions By applying density functional theory, we have studied the organic functionalization, following a radical initiated reaction mechanism, of H-germanene with molecules containing unsaturated C−C bonds such as acetylene, ethylene and styrene and compare these results with the surface reactivity of H-graphene tested in ref 11. Different from the organic functionalization of H-graphene and H-silicene, at the transition state, the H-germanene surface is strongly bent in order to reduce the separation distance between the highly reactive carbon centered radical and the H atom to be abstracted. The addition reactions of acetylene, ethylene and styrene on H-germanene were energetically favorable with especially low energy barriers for the acetylene and ethylene cases. For styrene, due to the larger size of the H-germanene honeycomb net and the difference in electronegativity between C and Ge atoms, the phenyl group ends located face-to-face with the surface at the Hvacancy, preventing any possibility for a chain reaction to occur. On the other hand, for


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Page 28 of 43

acetylene and ethylene, all conditions are present for a chain reaction to proceed. Nonetheless, competing reactions, such as polymerization cannot be discarded. In comparison with H-graphene, H-germanene offers a surface reactivity more favorable to the addition reactions of acetylene and ethylene with energetically more stable final states. Overall, the organic functionalization of H-germanene, with acetylene and ethylene, may be a more favorable route, than with H-graphene, to provide the necessary tools for molecular level manipulations.

Acknowledgments We thank financial support from Conacyt Project 164485 and DGAPA project IN100516. Calculations were performed in the DGCTIC-UNAM supercomputing center; project SC15-1IR-15.

Supporting Information Available: Atomic configuration, spin density isosurface and change in the valence electron population for the hydrogen vacancy at the partially hydrogenated germanene surface. Schematic illustration of the sagging of the H-germanene sheet. Schematic structures for the adsorption of a second molecule of acetylene and ethylene on the H-germanene surface. Change in the valence electron population for the styrene/H-graphene and styrene/Hgermanene systems at the intermediate state. For each system, bending angles (deg) of the Hgermanene sheet and distance reductions (Å) between the highly reactive carbon radical (C*) and the hydrogen atom to be abstracted (H*) at the transition state (TS). Tables with the numerical


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analysis for the change in the valence electron population for each reaction and state. This material is available free of charge via the Internet at http://pubs.acs.org.

References (1) Claridge, A. S.; Liao, W.-S.; Thomas, J. C.; Zhao, Y.; Cao, H. H.; Cheunkar, S.; Serino, A. C.; Andrews, A. M.; Weiss, P. S. From the Bottom Up: Dimensional Control and Characterization in Molecular Monolayers. Chem. Soc. Rev. 2013, 42, 2725−2745. (2) Teplyakov, A.V.; Bent, S. F. Semiconductor Surface Functionalization for Advances in Electronics, Energy Conversion, and Dynamic Systems. J. Vac. Sci. Technol. A 2013, 31, 050810, 1-12. (3) Bent, S. F. Organic Functionalization of Group IV Semiconductor Surfaces: Principles, Examples, Applications, and Prospects. Surf. Sci. 2002, 500, 879−903. (4) Avouris, P. Graphene: Electronic and Photonic Properties and Devices. Nano Lett. 2010, 10, 4285−4294. (5) Lin, C.-L.; Arafune, R.; Kawahara, K.; Tsukahara, N.; Minamitani, E.; Kim, Y.; Takagi, N.; Kawai, M. Structure of Silicene Grown on Ag(111). Appl. Phys. Exp. 2012, 5, 045802, 1-3. (6) Nakano, H.; Mitsuoka, T.; Harada, M.; Horibuchi, K.; Nozaki, H.; Takahashi, N.; Nonaka, T.; Seno, Y.; Nakamura, H. Soft Synthesis of Single-crystal Silicon Monolayer Sheets. Angew. Chem. 2006, 45, 6303-6306. (7) Okamoto, H.; Kumai, Y.; Sugiyama, Y.; Mitsuoka, T.; Nakanishi, K.; Ohta, T.; Nozaki, H.; Yamaguchi, S.; Shirai, S.; Nakano, H. Silicon Nanosheets and Their Self-Assembled Regular Stacking Structure. J. Am. Chem. Soc. 2010, 132, 2710-2718. (8) Sugiyama, Y.; Okamoto, H.; Mitsuoka, T.; Morikawa, T.; Nakanishi, K.; Ohta, T.; Nakano, H. Synthesis and Optical Properties of Monolayer Organosilicon Nanosheets. J. Am. Chem. Soc. 2010, 132, 5946-5947. (9) Leandri, C.; Le Lay, G.; Aufray, B.; Girardeaux, C.; Avila, J.; Davila, M. E.; Asensio, M. C.; Ottaviani, C.; Cricenti, A. Self-aligned Silicon Quantum Wires on Ag(110). Surf. Sci. 2005, 574, L9-L15.


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(10) Lalmi, B.; Oughaddou, H.; Enriquez, H.; Kara, A.; Vizzini, S.; Ealet, B.; Aufray, B. Epitaxial Growth of a Silicene Sheet. Appl. Phys. Lett. 2010, 97, 223109 (2pp). (11) Martín-Gago, J. A.; Fasel, R.; Hayoz, J.; Agostino, R. G.; Naumovi, D.; Aebi, P.; Schlapbach, L. Surface Atomic Structure of c(2x2)-Si on Cu(110). Phys. Rev. B 1997, 55, 12896-12898. (12) Leandri, C.; Saifi, H.; Guillermet, O.; Aufray, B. Silicon Thin Films Deposited on Ag(001): Growth and Temperature Behavior. App. Surf. Sci. 2001, 177, 303-306. (13) Rubio-Pereda, P.; Takeuchi, N. Density Functional Theory Study of the Organic Functionalization of Hydrogenated Graphene. J. Phys. Chem. C. 2013, 117, 18738−18745. (14) Rubio-Pereda, P.; Takeuchi, N. Density Functional Theory Study of the Organic Functionalization of Hydrogenated Silicene. J. Chem. Phys. 2013, 138, 194702. (15) Jiang, S.; Arguilla, M. Q.; Cultrara, N. D.; Goldberger, J. E. Covalently-Controlled Properties by Design in Group IV Graphane Analogues. Acc. Chem. Res. 2015, 48, 144−151. (16) Dimoulas, A. Silicene and Germanene: Silicon and Germanium in the “Flatland”. Microelectron. Eng. 2015, 131, 68−78. (17) Takeda, K.; Shiraishi, K. Theoretical Possibility of Stage Corrugation in Si and Ge Analogs of Graphite. Phys. Rev. B 1994, 50, 14916-14922. (18) Takeuchi, N.; Selloni, A.; Tosatti, E. Adatom Diffusion and Disordering at the Ge (111)-c (2× 8)–(1× 1) Surface Transition. Phys. Rev. B 1994, 49, 10757-10760. (19) Pang, Q.; Zhang, C. – L.; Li, L.; Fu, Z. – Q.; Wei, X. – M.; Song, Y. – L. Adsorption of Alkali Metal Atoms on Germanene: A First-principles Study. App. Surf. Sci. 2014, 314, 15-20. (20) Cahangirov, S.; Topsakal, M.; Aktürk, E.; Sahin, H.; Ciraci, S. Two- and one-dimensional Honeycomb Structures of Silicon and Germanium, Phys. Rev. Lett. 2009, 102, 236804, 1-4.


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(21) Pang, Q.; Zhang, Y.; Zhang, J.-M.; Ji, V.; Xu, K.-W. Electronic and Magnetic Properties of Pristine and Chemically Functionalized Germanene Nanoribbons, Nanoscale 2011, 3, 4330–4338. (22) Garcia, J.C.; De Lima, D.B.; Assali, L.V.C.; Justo, J.F. Group IV Graphene- and Graphane-like Nanosheets. J. Phys. Chem. C 2011, 115, 13242–13246. (23) Linford, M. R.; Chidsey, C. E. D. Alkyl Monolayers Covalently Bonded to Silicon Surfaces J. Am. Chem. Soc. 1993, 115, 12631-12632. (24) Lopinski, G. P.; Wayner, D. D.M.; Wolkow, R. A. Self-Directed Growth of Molecular Nanostructures on Silicon. Nature 2000, 406, 48-51. (25) Hosssain, Md. Z.; Kato, H. S.; Kawai, M. Controlled Fabrication of 1D Molecular Lines Across the Dimer Rows on the Si(100)-(2 × 1)-H Surface Through the Radical Chain Reaction. J. Am. Chem. Soc. 2005, 127, 1503015031. (26) Hosssain, Md. Z.; Kato, H. S.; Kawai, M. Fabrication of Interconnected 1D Molecular Lines Along and Across the Dimer Rows on the Si(100)-(2 × 1)-H Surface Through the Radical Chain Reaction. J. Phys. Chem. B 2005, 109, 23129-23133. (27) Wassermann, A. Diels−Alder Reactions: Organic Background and Physico-Chemical Aspect; Elsevier: New York, 1965. (28) Gill, G. B.; Willis, M. R. Pericyclic Reactions; Chapman and Hall: London, 1974. (29) Carruthers, W. Cycloaddition Reactions in Organic Synthesis; Pergamon Press: New York, 1990. (30) Kang, J. K.; Musgrave, C. B. J. A Quantum Chemical Study of the Self-Directed Growth Mechanism of Styrene and Propylene Molecular Nanowires on the Silicon (100) 2 × 1 Surface. J. Chem. Phys. 2002, 116, 9907−9913. (31) Takeuchi, N.; Kanai, Y.; Selloni, A. Suface Reaction of Alkynes and Alkenes with H-Si(100): A Density Functional Theory Study. J. Am. Chem. Soc. 2004, 126, 15890−15896.


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(32) Takeuchi, N.; Selloni, A. Density Functional Theory Study of One-Dimensional Growth of Styrene on the Hydrogen-Terminated Si(001)-(3 × 1) Surface. J. Phys. Chem. B 2005, 109, 11967−11972. (33) Takeuchi, N.; Kanai, Y.; Selloni, A. Surface Radical Chain Reaction Revisited: Comparative Investigation of Styrene and 2,4-Dimethyl-Styrene on Hydrogenated Si(001) Surface from Density Functional Theory Calculations. J. Phys. Chem. C 2010, 114, 3981−3986. (34) Kanai, Y.; Takeuchi, N.; Car, R.; Selloni, A. Role of Molecular Conjugation in the Surface Radical Reaction of Aldehydes With H-Si (111): First Principles Study, J. Phys. Chem. B 2005, 109, 18889-18894 (35) Giannozzi, P.; Baroni, S.; Bonini, N.; Calandra, M.; Car, R.; Cavazzoni, C.; Ceresoli, D.; Chiarotti, G. L.; Cococcioni, M.; Dabo, I. et al. QUANTUM ESPRESSO: a Modular and Open-Source Software Project for Quantum Simulations of Materials. J. Phys. Condens. Matter. 2009, 21, 395502, 1-19. (36) Laasonen, K.; Pasquarello, A.; Car, R.; Lee, C.; Vanderbilt, D. Molecular-Dynamics with Vanderbilt Ultrasoft Pseudopotentials. Phys. Rev. B. 1993, 47, 10142-10153. (37) Perdew, J. P.; Burke, K.; Ernzerholf, M. Generalized Gradient Approximation Made Simple. Phys. Rev. Lett. 1996, 77, 3865-3868. (38) Grimme, S. Semiempirical GGA-Type Density Functional Constructed with a Long-Range Dispersion Correction. J. Comput. Chem. 2006, 27, 1787-1799. (39) Monkhorst, H. J.; Pack, J. D. Special Points for Brillouin-zone Integrations. Phys. Rev. B 1976, 13, 51885192. (40) Jensen, F. Introduction to Computational Chemistry; John Wiley & Sons: Chichester, 2003.


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Table of Contents (TOC)/Abstract Graphic


33

The Journal of Physical Chemistry Page 34 of 43 4

3 1 2 2 C* H* 4 5 Plus Environment 31 2ACS3 Paragon 4 5 5x4 supercell b) C* and H* disposition a) 6 Po wderCell 2 .0

Adsorption Energy (eV)

b) Minimum EnergyThe Profile a) Page 35 of 43 Journal of Physical ChemistryTS at -0.61 eV 1 2 3 4 5 6 7 8 9 10 11 12 13 c) 14 15 16 17 18 19 20 21 22 23

0.0

TS

-0.3 IS -0.6 -0.9 -1.2

H bond rupture

-1.5 -1.8

FS

-2.1 3.3 3.0 2.7 2.4 2.1 1.8 1.5 1.2

distance C*-H (Å) IS at -0.76 eV

d) H bond rupture at -0.75 eV e)


FS at -2.06 eV

Acetylene

The Journal of Physical Chemistry Page 36 of 43

Total spin density Change in valence isosurfaces electron population 1 2a) 3 4 5 6 7 8 9 10 11 c) 12 13 14 15 16 17 18 19 20 e) 21 22 23 24 25 26 27

b)

d)

f)


Reaction Energy (eV)

b) Minimum EnergyThe Profile a) Page 37 of 43 Journal of Physical ChemistryTS at -0.32 eV 1 2 3 4 5 6 7 8 9 10 11 12 13 c) 14 15 16 17 18 19 20 21 22 23

0.0 -0.3

TS

IS

-0.6

H bond rupture

-0.9 -1.2

FS

-1.5 -1.8 -2.1 3.3 3.0 2.7 2.4 2.1 1.8 1.5 1.2 c

distance C*-H (Å) b

IS at -0.65 eV

a

d) H bond rupture at -0.47 eV e)


FS at -1.51 eV

Ethylene


Total spin density Change in valence isosurfaces electron population 1 2a) 3 4 5 6 7 8 9 10 11 c) 12 13 14 15 16 17 18 19 20 e) 21 22 23 24 25 26 27

b)

d)

f)


Minimum EnergyChemistry Profile The Journal of Physical

1 2 3 4 5 6 7 8 9 10 11 12 13 14b) 15 16 17 18 19 20 21 22 23 24 25 26e) 27 28 29 30 31 32 33 34 35

Reaction Energy (eV)

Page 39 of 43a) 0.0

TS

-0.3 -0.6

IS

F*S

-0.9

H bond rupture

-1.2 -1.5 -1.8

Polar rotation

Azimuthal rotation

-2.1 3.3 3.0 2.7 2.4 2.1 1.8 1.5 1.2

distance C*-H (Å) IS at -1.07 eV

First polar rotation

40 35 30 25 20 15 10

5

FS

0

phenyl angle (°)

c) H bond rupture at -0.61 eV

d)

F*S at -1.25 eV

f)

g)

FS at -1.65 eV

Second polar rotation


a) at -0.55 Chemistry eV The JournalTS of Physical 1 2 3 4 5 6 7 8 9 10 11 12 13 b) 14 15 16 17 18 19 20 21 22 23 24 e) 25 26 27 28 29 30 31 32 33 34 35

Page 40 of 43

PowderCell 2.0

Powd erCell 2.0

IS at -1.07 eV

First polar rotation

c) H bond rupture at -0.61 eV d)

f)

Second polar rotation


g)

F*S at -1.25 eV

FS at -1.65 eV

b) Chemistry a)PageThe 41 of Journal 43 of Physical 1 2 3 ACS Paragon Plus Environment 4 5 Styrene/H-silicene Styrene/H-germanene 6

Styrene


Total spin density Change in valence isosurfaces electron population 1 2a) 3 4 5 6 7 8 9 10 11 c) 12 13 14 15 16 17 18 19 20 e) 21 22 23 24 25 26 27 28 29 30 g) 31 32 33 34 35 36 37

b)

d)

f)

h)


HJournal Page 43 The of 43 Hof Physical Chemistry CC

1 2 3 4 5 6 7

Acetylene molecule Ge


Adsorption of Organic Molecules on the Hydrogenated Germanene: A

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