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DFT study of the dimethyl sulfoxide reduction on silicene
Accepted Manuscript Full Length Article DFT study of the dimethyl sulfoxide reduction on silicene Reyes Garcia-Diaz, Jonathan Guerrero-Sánchez, Héctor Noé FernándezEscamilla, Noboru Takeuchi PII: DOI: Reference:
S0169-4332(18)32870-8 https://doi.org/10.1016/j.apsusc.2018.10.114 APSUSC 40682
To appear in:
Applied Surface Science
Received Date: Revised Date: Accepted Date:
23 July 2018 3 October 2018 13 October 2018
Please cite this article as: R. Garcia-Diaz, J. Guerrero-Sánchez, H. Noé Fernández-Escamilla, N. Takeuchi, DFT study of the dimethyl sulfoxide reduction on silicene, Applied Surface Science (2018), doi: https://doi.org/10.1016/ j.apsusc.2018.10.114
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DFT study of the dimethyl sulfoxide reduction on silicene
Reyes Garcia-Diaza*, Jonathan Guerrero-Sánchezb, Héctor Noé Fernández-Escamillab,c, and Noboru Takeuchib,1
aCONACyT-Facultad
de Ciencias Físico Matemáticas, Universidad Autónoma de Coahuila,
Camporredondo, 25000, Saltillo, Coah, México. bCentro
de Nanociencias y Nanotecnología, Universidad Nacional Autónoma de México,
Apartado Postal 14, 22800, Ensenada, Baja California, México. cFCFM
Facultad de Ciencias Físico Matemáticas, Universidad Autónoma de Nuevo León,
66450, San Nicolás de los Garza, Nuevo León, México. Abstract We have studied the minimum energy pathway for the dimethyl sulfoxide reduction on silicene substrates. Starting with a configuration in which the molecule and the substrate are not interacting, the dimethyl sulfide molecule is physisorbed on the silicene as a first step, until it is finally reduced with the formation of silicene oxide units. As the reaction proceeds, the system gains energy, favoring the reduction of the molecule. The energy barrier for the reaction to proceed forward is 0.20 eV, which is 0.30 eV lower than the energy barrier for desorption. At the maximum coverage of ¼ monolayer, silicene oxide lines are formed. These results pave the way to use silicene as a substrate to reduce dimethyl sulfoxide (a molecule with low dose toxicity) to dimethyl sulfide, an important compound in the global ecosystem cycle. In the final state, the DMS molecule is physisorbed on silicene oxide. Therefore, this reaction is also a viable and efficient mechanism for oxidation of silicene. Key words: Dimethyl sulfide; Minimum energy pathway; Energy barrier; NEB; DFT E-mails:
[email protected]*,
[email protected],
[email protected], [email protected] Declarations of interest: none 1Present
address: Department of Chemistry, University of California, Riverside.
1. Introduction Dimethyl sulfoxide (DMSO) is a highly soluble molecule due to its amphipathic characteristics: a non-bonded electron pair on the almost tetrahedral sulfur atom, and two nonpolar CH3 groups [1]. It is widely used in industrial [2], medical [1, 3], and other applications [4]. However, it has been demonstrated that DMSO is toxic at low concentrations. Also, DMSO (widely used as solvent) inactivates platinum complexes used to treat several kinds of cancer [5]. Therefore, such a hazardous molecule should be handled with care. Moreover, it is desirable to find a replacement for its use [6], and a way to trap/reduce it, once it is generated. On the other hand, dimethyl sulfide (DMS) is a sulfur compound produced by phytoplankton in the sea. It is oxidized in the atmosphere to generate sulfate aerosols that act as cloudcondensation nuclei [7-9]. Therefore, it is an important climate regulator [7]. Also, it has been demonstrated that DMS plays a key role as a signal to facilitate the tritrophic (resource-toresource) mutualism between some sea birds and phytoplankton [10]. DMS is less toxic than DMSO, and it only presents certain odor issues [11]. Therefore, it is interesting to see if it is possible to reduce DMSO into DMS. It is also important to find a material that can be used as a catalyst of this reduction. In this regard, the new promising properties of two dimensional materials could be of use. In particular, silicene, a potential material in the next generation of nanoelectronic devices [12], is a good candidate to carry out this task. Silicene is a 2D buckled honeycomb network constructed of silicon atoms. Its sp2-sp3 mixed hybridization makes it a highly reactive surface. Theoretical studies have shown that silicene is a good sensor for toxic molecules, and greenhouse gases [13, 14]. It can be easily oxidized by dissociation of O2 [15], and it can be transformed from semimetal to metal, or semiconductor by controlling the oxygen functional groups adsorbed
on it [16]. Also, it can be functionalized by self-propagating reactions of organic molecules [17]. In this work we have investigated the reduction reaction of DMSO molecules on silicene via nudged elastic band calculations. Our results show a new reduction mechanism for DMSO driven by silicene, resulting in an ordered silicene oxide substrate, with physisorbed DMS molecules as products.
2. Calculation We have used first principles calculations based on the density functional theory (DFT), as implemented in the Quantum ESPRESSO open source package [18]. The exchangecorrelation (XC) potential has been modeled with the generalized gradient approximation (GGA) as proposed by Perdew-Burke-Ernzerhof (PBE) [19]. We have also considered van der Waals interactions with empirical dispersion corrections (vdw-DF2) to the XC functional [20]. Ultrasoft pseudopotentials were used for all the atomic species. Energy cutoffs of 30 Ry and 240 Ry have been used for the electronic wave functions and charge density, respectively. A Monkhorst-Pack mesh with a gamma centered k-points grid of (661) was used for the Brillouin zone integrations [21]. The atomic structures were fully optimized, taking into account a force and energy criteria: we have defined convergence when forces on each atom were smaller than 1×10-2 eV/Bohr. and the energy differences lower than 1×10-3 eV. Spinpolarized calculations were accounted for all modeled structures. To describe the reaction of reduction of DMSO and further silicene oxidation we have determined the minimum energy pathway (MEP) through nudged elastic band calculations (NEB) [22, 23]. A climbing image scheme was used to guarantee the correct description of the transition state [24]. The allowed error per image to achieve energy minimization was set to 0.05 eV/Å.
3. Results and discussion After fully optimizing the atomic positions of pristine silicene, we have found the following structural parameters: a lattice constant of 3.86 Å, Si-Si bond lengths of 2.29 Å, and a buckling height of 0.51 Å, all of them are in good agreement with previous investigations [14]. To study the reaction, we have started with a system in which the silicene and the DMSO molecule are not interacting. We have used a 4×4 silicene supercell, large enough to avoid inplane molecule self-interactions generated by the periodic conditions. We have used a lattice constant of 25 Å along the z-direction (perpendicular to the silicene). The molecule and the substrate were separated by 10 Å from each other to eliminate any possible interaction. The remaining 15 Å of empty space secure that the molecule does not interact with the image of the substrate generated by the supercell periodic conditions. From now on, this configuration is called zero energy state (ZS). The intermediate step of the reaction is defined when the DMSO is attached to the substrate (see Figure 1). Several molecule orientations were tested and the one with lowest energy was defined as the intermediate state (IS) of the reaction. This is a chemisorbed state with the DMSO molecule on top of a silicon atom, forming a Si-O bond with a bond length of 1.97 Å, larger than the one reported for the SiO tetrahedron (1.62 Å) [25]. The remaining part of the molecule is around 1.47 Å above the oxygen position. Formation of the Si-O bond drives a charge density redistribution, which generates slight alterations on the molecule after chemisorption. The S=O double bond is modified from 1.51 Å to 1.58 Å, while the S-C bond length decreases from 1.86 Å to 1.84 Å, and the C-S-C bond angle increases from 95.72° to 98.22°. Moreover, the distance of the Si (the one bonding with O) to its nearest neighbors
experiences an elongation from 2.29 Å to 2.33 Å. This effect is a result of the charge transfer from the substrate to the oxygen atom of the molecule. Looking at the MEP, we can see that as the molecule approximates to the silicene substrate, at the beginning there is no interaction, but around 5 Å the molecule and the substrate start interacting, as seen in the energy gain (Figure 1). Notice that to reach the intermediate state, there is no energy barrier. Moreover, the IS is more stable than the ZS state by 0.50 eV. To arrive to the final state of the reaction (FS), in which the DMSO is reduced to DMS, the system must overcome an energy barrier of 0.20 eV at the transition state (TS). Such energy barrier is associated to the breaking of the S=O bond, which is weakened due to the Si-O bond formation. Once the molecule is in the IS state, the desorption energy is 0.50 eV, which is 0.3 eV larger than the 0.20 eV needed for the reaction to go forward. Therefore, the formation of DMS is very favorable. Moreover, at the FS, the system is very stable, gaining 2.03 eV with respect to the IS (see Figure 1), corresponding to an exothermic reaction. Once the DMSO has been reduced, the O atom occupies a bridge position (which is the most stable adsorption site for an O atom in silicene), forming silicene oxide units. On the other hand, the DMS molecule is physisorbed, and it is located at around 3 Å above the substrate (see Figure 1). To study the electronic properties of our system, we have calculated the total density of states (DOS) at the ZS, IS and FS, and plotted them in Figure 2 (the zero energy was set to the Fermi level in all cases). In Figure 2 (a) are shown the total DOS of the ZS (black line), the DOS of the DMSO molecule (red line) and silicene DOS (blue line). In the DMSO molecule DOS, the two peaks closer to the Fermi level are due mainly to O p orbitals, indicating that when a charge transfer occurs such orbitals will be probably involved. The DOS of the IS state is shown in Figure 2 (b). Here the main changes in the electronic states are the vanishing of the molecule peaks close to the Fermi level, and the appearance of a new peak at around -4 eV. This effect is a direct consequence of the chemisorption of the
DMSO molecule, and it can be understood by the O-p orbitals sharing charge with the closest silicon atom of the substrate, inducing a charge density redistribution that is confirmed by a shift in the DOS of the DMSO to more negative energies. This can be interpreted as the S=O double bond breaking and the formation of a O-Si bond. We can also see, that the electronic character of silicene at the Fermi level remains almost without any change. Finally, the DOS of the final state is depicted in Figure 2 (c). It is clear that the DMS molecule have localized states away from the Fermi level, at more negative energies, which implies that it does not contribute to the electronic properties of the silicene oxide. It is also important to note that even after formation of the silicene oxide unit, the main electronic characteristics of the system around the Fermi level remain unchanged. In Figure 3 is presented the charge density distribution of the DMSO molecule as the reduction reaction go forward (for the ZS, IS and FS). In the ZS, the charge density is mainly distributed around the molecule, see Figure 3 (a), indicating that there is not interaction with the substrate. Once the molecule is detected by the substrate, its charge density undergoes a slight rearrangement due to the interaction of the oxygen atom with a silicon atom of the substrate (Si-O bond formation), as seen in Figure 3 (b). Once the molecule is reduced, the DMS stabilizes rearranging its charge between the S, C, and H atoms of the molecule. On the other hand, the oxygen atom is adsorbed on a bridge position sharing charge with two silicon atoms of the substrate, as seen in Figure 3 (c). Finally, note that the Si-O bond formation in both IS and FS states is responsible for a slightly elliptical distortion of the charge density around the oxygen atoms, this behavior is expected due to the difference in electronegativities between the oxygen and silicon atoms. Since, as described before, the reduction of a single DMSO molecule is favorable, we systematically have increased the number of DMSO molecules that can react with the silicene substrate (Figure 4). The maximum coverage considered is 1/4 monolayer (ML). At this
coverage, the reduction of the DMSO molecules drives the formation of silicene oxide lines, with a distance between O atoms in a range of 7.68 Å to 7.95 Å. In order to determine the maximum coverage, we have calculated the adsorption energy per molecule (Eads) using the following form: 𝐸𝑎𝑑𝑠 =
𝐸𝑝𝑟𝑜𝑑 ‒ 𝐸𝑠𝑢𝑏𝑠𝑡𝑟𝑎𝑡𝑒 ‒ 𝑁𝑚𝑜𝑙𝐸𝑚𝑜𝑙 𝑁𝑚𝑜𝑙
, (1)
where Eprod, Esubstrate, and Emol stands for the total energy of the FS (with different coverages), the pristine silicene, and the DSMO molecule, respectively. Nmol is the number of DMSO molecules considered in the coverage. According to this definition, Eads<0 indicates that the chemisorption is exothermic and favorable. We have calculated Eads for four different coverages: 1/16 ML, 1/8 ML, 3/16 ML, and 1/4 ML, corresponding to the adsorption of one to four DMSO molecules per supercell. We have obtained the following values: -2.48, -2.29, 1.96, and -1.78 eV/molecule for one, two, three, and four DMSO adsorbed molecules, respectively. Even though Eads raises upon increasing the coverage, in all cases the chemisorption of the molecules is favorable. As silicene oxide sites are formed, adsorption (reaction) sites are missing, leading to an eventual total transformation of silicene into silicone oxide. At this point no more DMSO molecules can be chemisorbed or reduced. Silicene has not been obtained freestanding and it is not stable in air [26, 27]. However, it has been grown in Ag substrates, and it is interesting to study the main stages of the DMSO reduction reaction in a Silicene/Ag(111) superstructure. Such superstructure is formed by a 3×3 Silicene layer on top of an Ag(111) surface with a periodicity of 4×4, as seen in Figure 5a. The substrate induces a rearrangement in the Silicene sheet, depicting a flower-like pattern in a 4×4 superstructure [28-31]. More details on the construction of the model used in this work, distances and STM images of the superstructure can be found in [32]. To carry out the structural optimizations, we have used similar conditions as stated in the methods section and
in [32]. Results demonstrate that the reduction reaction is as favorable as in the case of freestanding Silicene. In this case, the reference energy is the DMSO molecule and the substrate (4x4 superstructure) without interaction. When the molecule interacts with the substrate to form the intermediate state of the reaction (Figure 5b), the adsorption energy is 0.59 eV, a value slightly larger than the one obtained in freestanding Silicene. After adsorption, there is a chemical interaction between Si atoms of the substrate and the O atom of the molecule. The distance between these atoms is 1.96 Å, exactly the same obtained in when interacting with the freestanding sheet. A similar trend is observed in the remaining part of the molecule, where the S=O bond experiences an elongation from 1.51 Å to 1.59 Å, and the S-C bonds (1.85 Å) remain almost unchanged. In the final step of the reduction reaction, this system presents an adsorption energy of -2.69 eV, which in this case is 2.1 eV more stable than the IS, a value similar than the one obtained for the FS in freestanding Silicene. In the FS, the molecule also breaks down forming a Silicene oxide unit, with the DMS molecule adsorbed on the substrate. After carefully analyzing the structure and energetics of the IS and FS states, we expect a reduction reaction as favorable as in the case of freestanding Silicene. This interesting result opens a new route to use this Silicene superstructure as a catalyst for an efficient DMSO reduction.
4. Conclusions In this paper we have proposed a viable and efficient mechanism to reduce the harmful DMSO molecule to DMS, a less toxic molecule with important implications in the climate regulation, by forming well defined silicene oxide patterns and DMS molecules physisorbed on it. This is a process with great energy gain, and low energy barriers, favoring the reduction reaction. Also it was observed that ordered silicene oxide units can be formed during the
DMSO to DMS reduction. This can be useful for silicene bandgap engineering.
Acknowledgements We thank DGAPA-UNAM project IN100516 for partial financial support. NT thanks DGAPAUNAM for a scholarship for a sabbatical leave at University of California, Riverside. RGD thanks CONACyT for cathedra position and support. We thank A. Rodriguez-Guerrero for technical support. Calculations were performed in the DGCTIC-UNAM supercomputing center project LANCAD-UNAM-DGTIC-051.
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Figures
Figure 1. Minimum energy pathway for the DMSO reduction to DMS on silicone, calculated with NEB. The relative energies are in eV. ZS correspond to the starting point where the DMSO molecule and substrate are not interacting, IS stands for the system where chemisorption of DMSO occurs, TS accounts for the transition state, FS is the state where reduction of DMSO has already occurred and the DMS molecule is physisorbed .
Figure 2. Total density of states of the main steps of the reduction reaction: (a) for the molecule and substrate without interaction (ZS), (b) when DMSO is chemisorbed on the substrate (IS), and (c) for silicene oxide unit plus physisorbed DMS molecule (FS). Black lines correspond to the total DOS, the red one to the molecule DOS, and the blue line to the DOS of the substrate.
Figure 3. Charge density distributions of the DMSO molecule in its reduction process on silicene at (a) the zero energy state (ZE), (b) during the chemical interaction between DMSO and silicene (IS), (c) after DMSO is reduced to DMS and silicene oxide unit is formed (FS).
Figure 4. Different number of DMS molecules generated by the reduction of DMSO molecules on silicene. Corresponding to (a) 1/16, (b) 1/8, (c) 3/16 and (d) 1/4 of silicon oxide mono layer coverage.
Figure 5. Top and side view of Silicene (Si) deposited on Ag(111)-4x4 surface: (a) clean system, (b) with DMSO adsorbed and (c) with DMS molecule adsorbed.
Graphical abstract
Highlights: DFT results suggest the dimethyl sulfoxide (MDSO) reduction on silicene as viable. Toxic DMSO can be reduced to dimethyl sulfide (DMS), a harmless substance. Nudged elastic band (NEB) results show a reaction energy barrier of 0.2 eV. This reaction energy is 0.3 eV lower than energy needed for the DMSO desorption. Also a controlled silicene oxidation can take place during the reduction process.
S0169-4332(18)32870-8 https://doi.org/10.1016/j.apsusc.2018.10.114 APSUSC 40682
To appear in:
Applied Surface Science
Received Date: Revised Date: Accepted Date:
23 July 2018 3 October 2018 13 October 2018
Please cite this article as: R. Garcia-Diaz, J. Guerrero-Sánchez, H. Noé Fernández-Escamilla, N. Takeuchi, DFT study of the dimethyl sulfoxide reduction on silicene, Applied Surface Science (2018), doi: https://doi.org/10.1016/ j.apsusc.2018.10.114
This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.
DFT study of the dimethyl sulfoxide reduction on silicene
Reyes Garcia-Diaza*, Jonathan Guerrero-Sánchezb, Héctor Noé Fernández-Escamillab,c, and Noboru Takeuchib,1
aCONACyT-Facultad
de Ciencias Físico Matemáticas, Universidad Autónoma de Coahuila,
Camporredondo, 25000, Saltillo, Coah, México. bCentro
de Nanociencias y Nanotecnología, Universidad Nacional Autónoma de México,
Apartado Postal 14, 22800, Ensenada, Baja California, México. cFCFM
Facultad de Ciencias Físico Matemáticas, Universidad Autónoma de Nuevo León,
66450, San Nicolás de los Garza, Nuevo León, México. Abstract We have studied the minimum energy pathway for the dimethyl sulfoxide reduction on silicene substrates. Starting with a configuration in which the molecule and the substrate are not interacting, the dimethyl sulfide molecule is physisorbed on the silicene as a first step, until it is finally reduced with the formation of silicene oxide units. As the reaction proceeds, the system gains energy, favoring the reduction of the molecule. The energy barrier for the reaction to proceed forward is 0.20 eV, which is 0.30 eV lower than the energy barrier for desorption. At the maximum coverage of ¼ monolayer, silicene oxide lines are formed. These results pave the way to use silicene as a substrate to reduce dimethyl sulfoxide (a molecule with low dose toxicity) to dimethyl sulfide, an important compound in the global ecosystem cycle. In the final state, the DMS molecule is physisorbed on silicene oxide. Therefore, this reaction is also a viable and efficient mechanism for oxidation of silicene. Key words: Dimethyl sulfide; Minimum energy pathway; Energy barrier; NEB; DFT E-mails:
[email protected]*,
[email protected],
[email protected], [email protected] Declarations of interest: none 1Present
address: Department of Chemistry, University of California, Riverside.
1. Introduction Dimethyl sulfoxide (DMSO) is a highly soluble molecule due to its amphipathic characteristics: a non-bonded electron pair on the almost tetrahedral sulfur atom, and two nonpolar CH3 groups [1]. It is widely used in industrial [2], medical [1, 3], and other applications [4]. However, it has been demonstrated that DMSO is toxic at low concentrations. Also, DMSO (widely used as solvent) inactivates platinum complexes used to treat several kinds of cancer [5]. Therefore, such a hazardous molecule should be handled with care. Moreover, it is desirable to find a replacement for its use [6], and a way to trap/reduce it, once it is generated. On the other hand, dimethyl sulfide (DMS) is a sulfur compound produced by phytoplankton in the sea. It is oxidized in the atmosphere to generate sulfate aerosols that act as cloudcondensation nuclei [7-9]. Therefore, it is an important climate regulator [7]. Also, it has been demonstrated that DMS plays a key role as a signal to facilitate the tritrophic (resource-toresource) mutualism between some sea birds and phytoplankton [10]. DMS is less toxic than DMSO, and it only presents certain odor issues [11]. Therefore, it is interesting to see if it is possible to reduce DMSO into DMS. It is also important to find a material that can be used as a catalyst of this reduction. In this regard, the new promising properties of two dimensional materials could be of use. In particular, silicene, a potential material in the next generation of nanoelectronic devices [12], is a good candidate to carry out this task. Silicene is a 2D buckled honeycomb network constructed of silicon atoms. Its sp2-sp3 mixed hybridization makes it a highly reactive surface. Theoretical studies have shown that silicene is a good sensor for toxic molecules, and greenhouse gases [13, 14]. It can be easily oxidized by dissociation of O2 [15], and it can be transformed from semimetal to metal, or semiconductor by controlling the oxygen functional groups adsorbed
on it [16]. Also, it can be functionalized by self-propagating reactions of organic molecules [17]. In this work we have investigated the reduction reaction of DMSO molecules on silicene via nudged elastic band calculations. Our results show a new reduction mechanism for DMSO driven by silicene, resulting in an ordered silicene oxide substrate, with physisorbed DMS molecules as products.
2. Calculation We have used first principles calculations based on the density functional theory (DFT), as implemented in the Quantum ESPRESSO open source package [18]. The exchangecorrelation (XC) potential has been modeled with the generalized gradient approximation (GGA) as proposed by Perdew-Burke-Ernzerhof (PBE) [19]. We have also considered van der Waals interactions with empirical dispersion corrections (vdw-DF2) to the XC functional [20]. Ultrasoft pseudopotentials were used for all the atomic species. Energy cutoffs of 30 Ry and 240 Ry have been used for the electronic wave functions and charge density, respectively. A Monkhorst-Pack mesh with a gamma centered k-points grid of (661) was used for the Brillouin zone integrations [21]. The atomic structures were fully optimized, taking into account a force and energy criteria: we have defined convergence when forces on each atom were smaller than 1×10-2 eV/Bohr. and the energy differences lower than 1×10-3 eV. Spinpolarized calculations were accounted for all modeled structures. To describe the reaction of reduction of DMSO and further silicene oxidation we have determined the minimum energy pathway (MEP) through nudged elastic band calculations (NEB) [22, 23]. A climbing image scheme was used to guarantee the correct description of the transition state [24]. The allowed error per image to achieve energy minimization was set to 0.05 eV/Å.
3. Results and discussion After fully optimizing the atomic positions of pristine silicene, we have found the following structural parameters: a lattice constant of 3.86 Å, Si-Si bond lengths of 2.29 Å, and a buckling height of 0.51 Å, all of them are in good agreement with previous investigations [14]. To study the reaction, we have started with a system in which the silicene and the DMSO molecule are not interacting. We have used a 4×4 silicene supercell, large enough to avoid inplane molecule self-interactions generated by the periodic conditions. We have used a lattice constant of 25 Å along the z-direction (perpendicular to the silicene). The molecule and the substrate were separated by 10 Å from each other to eliminate any possible interaction. The remaining 15 Å of empty space secure that the molecule does not interact with the image of the substrate generated by the supercell periodic conditions. From now on, this configuration is called zero energy state (ZS). The intermediate step of the reaction is defined when the DMSO is attached to the substrate (see Figure 1). Several molecule orientations were tested and the one with lowest energy was defined as the intermediate state (IS) of the reaction. This is a chemisorbed state with the DMSO molecule on top of a silicon atom, forming a Si-O bond with a bond length of 1.97 Å, larger than the one reported for the SiO tetrahedron (1.62 Å) [25]. The remaining part of the molecule is around 1.47 Å above the oxygen position. Formation of the Si-O bond drives a charge density redistribution, which generates slight alterations on the molecule after chemisorption. The S=O double bond is modified from 1.51 Å to 1.58 Å, while the S-C bond length decreases from 1.86 Å to 1.84 Å, and the C-S-C bond angle increases from 95.72° to 98.22°. Moreover, the distance of the Si (the one bonding with O) to its nearest neighbors
experiences an elongation from 2.29 Å to 2.33 Å. This effect is a result of the charge transfer from the substrate to the oxygen atom of the molecule. Looking at the MEP, we can see that as the molecule approximates to the silicene substrate, at the beginning there is no interaction, but around 5 Å the molecule and the substrate start interacting, as seen in the energy gain (Figure 1). Notice that to reach the intermediate state, there is no energy barrier. Moreover, the IS is more stable than the ZS state by 0.50 eV. To arrive to the final state of the reaction (FS), in which the DMSO is reduced to DMS, the system must overcome an energy barrier of 0.20 eV at the transition state (TS). Such energy barrier is associated to the breaking of the S=O bond, which is weakened due to the Si-O bond formation. Once the molecule is in the IS state, the desorption energy is 0.50 eV, which is 0.3 eV larger than the 0.20 eV needed for the reaction to go forward. Therefore, the formation of DMS is very favorable. Moreover, at the FS, the system is very stable, gaining 2.03 eV with respect to the IS (see Figure 1), corresponding to an exothermic reaction. Once the DMSO has been reduced, the O atom occupies a bridge position (which is the most stable adsorption site for an O atom in silicene), forming silicene oxide units. On the other hand, the DMS molecule is physisorbed, and it is located at around 3 Å above the substrate (see Figure 1). To study the electronic properties of our system, we have calculated the total density of states (DOS) at the ZS, IS and FS, and plotted them in Figure 2 (the zero energy was set to the Fermi level in all cases). In Figure 2 (a) are shown the total DOS of the ZS (black line), the DOS of the DMSO molecule (red line) and silicene DOS (blue line). In the DMSO molecule DOS, the two peaks closer to the Fermi level are due mainly to O p orbitals, indicating that when a charge transfer occurs such orbitals will be probably involved. The DOS of the IS state is shown in Figure 2 (b). Here the main changes in the electronic states are the vanishing of the molecule peaks close to the Fermi level, and the appearance of a new peak at around -4 eV. This effect is a direct consequence of the chemisorption of the
DMSO molecule, and it can be understood by the O-p orbitals sharing charge with the closest silicon atom of the substrate, inducing a charge density redistribution that is confirmed by a shift in the DOS of the DMSO to more negative energies. This can be interpreted as the S=O double bond breaking and the formation of a O-Si bond. We can also see, that the electronic character of silicene at the Fermi level remains almost without any change. Finally, the DOS of the final state is depicted in Figure 2 (c). It is clear that the DMS molecule have localized states away from the Fermi level, at more negative energies, which implies that it does not contribute to the electronic properties of the silicene oxide. It is also important to note that even after formation of the silicene oxide unit, the main electronic characteristics of the system around the Fermi level remain unchanged. In Figure 3 is presented the charge density distribution of the DMSO molecule as the reduction reaction go forward (for the ZS, IS and FS). In the ZS, the charge density is mainly distributed around the molecule, see Figure 3 (a), indicating that there is not interaction with the substrate. Once the molecule is detected by the substrate, its charge density undergoes a slight rearrangement due to the interaction of the oxygen atom with a silicon atom of the substrate (Si-O bond formation), as seen in Figure 3 (b). Once the molecule is reduced, the DMS stabilizes rearranging its charge between the S, C, and H atoms of the molecule. On the other hand, the oxygen atom is adsorbed on a bridge position sharing charge with two silicon atoms of the substrate, as seen in Figure 3 (c). Finally, note that the Si-O bond formation in both IS and FS states is responsible for a slightly elliptical distortion of the charge density around the oxygen atoms, this behavior is expected due to the difference in electronegativities between the oxygen and silicon atoms. Since, as described before, the reduction of a single DMSO molecule is favorable, we systematically have increased the number of DMSO molecules that can react with the silicene substrate (Figure 4). The maximum coverage considered is 1/4 monolayer (ML). At this
coverage, the reduction of the DMSO molecules drives the formation of silicene oxide lines, with a distance between O atoms in a range of 7.68 Å to 7.95 Å. In order to determine the maximum coverage, we have calculated the adsorption energy per molecule (Eads) using the following form: 𝐸𝑎𝑑𝑠 =
𝐸𝑝𝑟𝑜𝑑 ‒ 𝐸𝑠𝑢𝑏𝑠𝑡𝑟𝑎𝑡𝑒 ‒ 𝑁𝑚𝑜𝑙𝐸𝑚𝑜𝑙 𝑁𝑚𝑜𝑙
, (1)
where Eprod, Esubstrate, and Emol stands for the total energy of the FS (with different coverages), the pristine silicene, and the DSMO molecule, respectively. Nmol is the number of DMSO molecules considered in the coverage. According to this definition, Eads<0 indicates that the chemisorption is exothermic and favorable. We have calculated Eads for four different coverages: 1/16 ML, 1/8 ML, 3/16 ML, and 1/4 ML, corresponding to the adsorption of one to four DMSO molecules per supercell. We have obtained the following values: -2.48, -2.29, 1.96, and -1.78 eV/molecule for one, two, three, and four DMSO adsorbed molecules, respectively. Even though Eads raises upon increasing the coverage, in all cases the chemisorption of the molecules is favorable. As silicene oxide sites are formed, adsorption (reaction) sites are missing, leading to an eventual total transformation of silicene into silicone oxide. At this point no more DMSO molecules can be chemisorbed or reduced. Silicene has not been obtained freestanding and it is not stable in air [26, 27]. However, it has been grown in Ag substrates, and it is interesting to study the main stages of the DMSO reduction reaction in a Silicene/Ag(111) superstructure. Such superstructure is formed by a 3×3 Silicene layer on top of an Ag(111) surface with a periodicity of 4×4, as seen in Figure 5a. The substrate induces a rearrangement in the Silicene sheet, depicting a flower-like pattern in a 4×4 superstructure [28-31]. More details on the construction of the model used in this work, distances and STM images of the superstructure can be found in [32]. To carry out the structural optimizations, we have used similar conditions as stated in the methods section and
in [32]. Results demonstrate that the reduction reaction is as favorable as in the case of freestanding Silicene. In this case, the reference energy is the DMSO molecule and the substrate (4x4 superstructure) without interaction. When the molecule interacts with the substrate to form the intermediate state of the reaction (Figure 5b), the adsorption energy is 0.59 eV, a value slightly larger than the one obtained in freestanding Silicene. After adsorption, there is a chemical interaction between Si atoms of the substrate and the O atom of the molecule. The distance between these atoms is 1.96 Å, exactly the same obtained in when interacting with the freestanding sheet. A similar trend is observed in the remaining part of the molecule, where the S=O bond experiences an elongation from 1.51 Å to 1.59 Å, and the S-C bonds (1.85 Å) remain almost unchanged. In the final step of the reduction reaction, this system presents an adsorption energy of -2.69 eV, which in this case is 2.1 eV more stable than the IS, a value similar than the one obtained for the FS in freestanding Silicene. In the FS, the molecule also breaks down forming a Silicene oxide unit, with the DMS molecule adsorbed on the substrate. After carefully analyzing the structure and energetics of the IS and FS states, we expect a reduction reaction as favorable as in the case of freestanding Silicene. This interesting result opens a new route to use this Silicene superstructure as a catalyst for an efficient DMSO reduction.
4. Conclusions In this paper we have proposed a viable and efficient mechanism to reduce the harmful DMSO molecule to DMS, a less toxic molecule with important implications in the climate regulation, by forming well defined silicene oxide patterns and DMS molecules physisorbed on it. This is a process with great energy gain, and low energy barriers, favoring the reduction reaction. Also it was observed that ordered silicene oxide units can be formed during the
DMSO to DMS reduction. This can be useful for silicene bandgap engineering.
Acknowledgements We thank DGAPA-UNAM project IN100516 for partial financial support. NT thanks DGAPAUNAM for a scholarship for a sabbatical leave at University of California, Riverside. RGD thanks CONACyT for cathedra position and support. We thank A. Rodriguez-Guerrero for technical support. Calculations were performed in the DGCTIC-UNAM supercomputing center project LANCAD-UNAM-DGTIC-051.
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Figures
Figure 1. Minimum energy pathway for the DMSO reduction to DMS on silicone, calculated with NEB. The relative energies are in eV. ZS correspond to the starting point where the DMSO molecule and substrate are not interacting, IS stands for the system where chemisorption of DMSO occurs, TS accounts for the transition state, FS is the state where reduction of DMSO has already occurred and the DMS molecule is physisorbed .
Figure 2. Total density of states of the main steps of the reduction reaction: (a) for the molecule and substrate without interaction (ZS), (b) when DMSO is chemisorbed on the substrate (IS), and (c) for silicene oxide unit plus physisorbed DMS molecule (FS). Black lines correspond to the total DOS, the red one to the molecule DOS, and the blue line to the DOS of the substrate.
Figure 3. Charge density distributions of the DMSO molecule in its reduction process on silicene at (a) the zero energy state (ZE), (b) during the chemical interaction between DMSO and silicene (IS), (c) after DMSO is reduced to DMS and silicene oxide unit is formed (FS).
Figure 4. Different number of DMS molecules generated by the reduction of DMSO molecules on silicene. Corresponding to (a) 1/16, (b) 1/8, (c) 3/16 and (d) 1/4 of silicon oxide mono layer coverage.
Figure 5. Top and side view of Silicene (Si) deposited on Ag(111)-4x4 surface: (a) clean system, (b) with DMSO adsorbed and (c) with DMS molecule adsorbed.
Graphical abstract
Highlights: DFT results suggest the dimethyl sulfoxide (MDSO) reduction on silicene as viable. Toxic DMSO can be reduced to dimethyl sulfide (DMS), a harmless substance. Nudged elastic band (NEB) results show a reaction energy barrier of 0.2 eV. This reaction energy is 0.3 eV lower than energy needed for the DMSO desorption. Also a controlled silicene oxidation can take place during the reduction process.