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. 2023 Feb 13;8(7):6523–6529. doi: 10.1021/acsomega.2c06888

Impact of Hydrogen Coverage Trend on Methyl Formate Adsorption on MoS2 Surface: A First Principles Study

Samuel E P P Masan †,‡, Febdian Rusydi ‡,¶,*, Wahyu A E Prabowo §,‡, Daniel Elisandro ‡, Wun F Mark-Lee ∥, Nabila A Karim ⊥, Adhitya G Saputro #
PMCID: PMC9948192  PMID: 36844535

Abstract

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Adsorbates coverage plays a crucial role in a catalysis reaction. In hydrodeoxygenation (HDO), which involves high hydrogen pressure, hydrogen coverage on the surface may affect the adsorption of other adsorbates. The HDO is used in green diesel technology to produce clean and renewable energy from organic compounds. This motivates us to study the hydrogen coverage effect on methyl formate adsorption on MoS2 as a model case of the actual HDO. We calculate the methyl formate adsorption energy as a function of hydrogen coverage using density functional theory (DFT) and then comprehensively analyze the physical origin of the results. We find that methyl formate can have several adsorption modes on the surface. The increased hydrogen coverage can stabilize or destabilize these adsorption modes. However, finally, it leads to convergence at high hydrogen coverage. We extrapolated the trend further and concluded that some adsorption modes might not exist at high hydrogen coverage, while others remain.

Introduction

Adsorption on a catalyst surface is an important step in heterogeneous catalysis. If adsorption is too weak, catalysis may not occur. On the other hand, if adsorption is too strong, the final product cannot be achieved. This is the well-known Sabatier principle.1 It has motivated many fundamental studies about adsorption on surfaces.2−5

Moreover, interactions between adsorbates could also influence catalysis. This is commonly known as the coverage effect. On monometallic catalysts, the coverage effect has been intensively studied. Changes in coverage may affect molecule adsorption and later change the reaction rate and selectivity.6−8 On the other hand, the studies on the coverage effect on transition metal dichalcogenide (TMD) materials are limited. The coverage effect on TMD may differ from that on monometallic catalysts. For instance, Huang et al. reported that methyl formate hydrogenolysis rates on a copper-based catalyst have a positive order for hydrogen.9 This means that an increase in hydrogen pressure, which corresponds to an increase in hydrogen coverage, will raise the reaction rate. Interestingly, Wang et al. reported the opposite trend for hydrodeoxygenation (HDO) of p-cresol on MoS2.10

There are several works that discuss the effect of hydrogen coverage on MoS2. For instance, Grønborg et al. studied the hydrogen-induced reshaping and edge activation of MoS2.11 Kronberg et al. studied the hydrogen coverage effect on the hydrogen adsorption on MoS2.12 Rosen et al. studied the MoS2 stability under the reaction condition in which high-pressure H2 and H2S are involved.13 Nevertheless, studies about the hydrogen coverage effect on the adsorption of an oxygenated molecule are still scarce.

In this work, we report the hydrogen coverage effect on the adsorption of the oxygenated molecule on MoS2 using density functional theory (DFT) calculation. We choose methyl formate as the oxygenated molecule since it has the same ester functional group as triglyceride, commonly used as raw material in HDO for green diesel production.14−17 Moreover, several recent works also used methyl formate in triglyceride interesterification for biodiesel production.18,19 We only consider the perfect Mo-edge of MoS2 (see left panel of Figure 1) since adsorption on the other edge (S-edge) is weaker for both hydrogen12 and ester molecules.20 Note that under reaction conditions the perfect Mo-edge may be saturated with sulfur atoms, rendering it unreactive.13 However, this sulfur coverage is not discussed in this work and has yet to be investigated.

Figure 1.

Figure 1

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Mo-edge MoS2 surface (left) and methyl formate molecule (right) used in this work.

Computational Details

We carried out DFT calculations using the Quantum ESPRESSO package.21,22 We modeled the core electrons using Plane Augmented Wave function23 and described the exchange–correlation functional using the generalized gradient approximation Perdew–Burke–Ernzerhof (PBE).24 We also took into account the dispersion correction using Grimme-d2.25 The optimized MoS2 structural parameters given by these models are a0 = 3.188 Å and c0 = 12.332 Å, which are in good agreement with the reported experimental value (a0 = 3.160 Å and c0 = 12.294 Å).26

Other calculation details are reported as follows. To sample the Brillouin zone, we used a 3 × 1 × 1 Monkhorst–Pack k-point grid.27 We chose a 500 eV kinetic energy cutoff (Ecutoff) for the wave function. The rationale for the k-point and Ecutoff values can be found in Figure S1 and Figure S2. We set a 10–6 Ry energy threshold for self-consistent field calculation. We performed the geometry optimization based on the Broyden–Fletcher–Goldfarb–Shanno quasi-Newton algorithm28 until the force was smaller than 10–3 Ry/bohr. Moreover, we analyzed the system’s density of states (DOS) by projecting them into an atomic and molecular orbital. An explanation of the latter is provided by Ravikumar et al.29 We calculated the transition barrier between one atomic environment to another using the climbing image nudged elastic band method.30 Finally, we calculated the atomic charge density using the Bader Charge Analysis package.31

We used the same slab model for Mo-edge MoS2 as in ref (20). The slab consists of 36 S atoms and 18 Mo atoms, forming three layers as shown in the left panel of Figure 1. Only the uppermost layer is relaxed during the geometry optimization, while the other two are fixed in the bulk structure. To prevent the interaction between the periodic boundary condition, we set at least 16 Å vacuum in the z axis after performing a convergence test (see Figure S3). The resulting slab’s dimension is 18.97 Å × 12.30 Å × 21.28 Å. This slab has six Mo-top and six Mo–Mo-bridge sites which are considered the active site in this work.

We used the cis conformer of methyl formate as the initial structure before adsorption (see right panel of Figure 1). This conformer is the most stable one at room temperature.32,33 We also confirmed this by comparing the energy of cis conformer with another stable conformer, i.e., trans. Our DFT calculation shows that the energy of the cis conformer is 0.19 eV lower than that of trans.

We defined the adsorption energy as the energy difference between the adsorbed and isolated atom/molecule. The more negative the value, the stronger the adsorption is. We calculated hydrogen and methyl formate adsorption energy using equations 1 and 2, respectively. In those equations, MF, nH, and surf refer to methyl formate, the number of adsorbed hydrogen atoms, and MoS2, respectively. Moreover, we defined the hydrogen coverage by comparing nH with six Mo-top or six Mo–Mo-bridge sites available on the slab (see equation 3).

graphic file with name ao2c06888_m001.jpg 1
graphic file with name ao2c06888_m002.jpg 2
graphic file with name ao2c06888_m003.jpg 3

Results and Discussion

Hydrogen Adsorption

A single hydrogen atom can be adsorbed on Mo-top and Mo–Mo-bridge sites of Mo-edge MoS2. The adsorption energies on both sites are −0.67 and −1.00 eV, respectively. These adsorption sites may be provided by Inline graphic (on Mo-top) and dxz (on Mo–Mo-bridge) bands of the Mo atoms (see peaks A and C in Figure 2). The Inline graphic peak is located just below the Fermi level, while dxz is about −0.2 eV lower. The difference results in a more stable bonding between the s orbital of the hydrogen atom and the dxz band on Mo–Mo-bridge.2 Moreover, compared to Inline graphic, dxz has a higher electron density near the Fermi level which will be transferred to the adsorbate. These explain why the hydrogen atom prefers to be adsorbed on Mo–Mo-bridge more than on Mo-top. At higher hydrogen coverage (θH > 16.7%), hydrogen atoms tend to be adsorbed on the most stable site, i.e., Mo–Mo-bridge. Some hydrogen atoms can be adsorbed on Mo-top only until 66.67% coverage. More than that, all hydrogen atoms are adsorbed on Mo–Mo-bridge.

Figure 2.

Figure 2

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Top panel: the projected density of states (PDOS) of Mo atom’s d bands on Mo-edge MoS2. The energy in the horizontal axis is relative to the Fermi level. The positive and negative values of PDOS correspond to spin up and down, respectively. There are three d band peaks near the Fermi level (peaks A, B, and, C) which may host adsorption on MoS2. Bottom panel: wave function isosurface at energy levels A, B, and C of the top panel figure. The isovalue is 0.0006. Blue and red colors represent positive and negative phases, respectively. Peaks A and C host hydrogen adsorption, while peaks A, B, and C host methyl formate adsorption.

The geometry of MoS2 is almost unchanged upon hydrogen adsorption on Mo-top, while the opposite is true for hydrogen adsorption on Mo–Mo-bridge. On Mo–Mo-bridge, hydrogen attracts its nearest neighbor Mo atoms causing the Mo–Mo distance to be reduced by 0.38 Å. We argue that this geometrical change is important in the hydrogen-induced MoS2 reshaping observed in scanning tunneling microscopy (STM).11 The geometrical change suggests that some internal bonds of MoS2 are getting stronger while other are getting weaker. The change can trigger the reshaping of MoS2 (for instance, bigger structures decompose into several smaller structures). This process is similar to transition metal surface reconstruction which involved subsurface adsorption of hydrogen and oxygen atoms.34,35

The hydrogen adsorption generally destabilizes as the coverage increases; i.e., the adsorption energy increases (see Figure 3). This trend agrees with a previous study by Kronberg et al. which calculates the average of hydrogen adsorption energy as a function of hydrogen coverage on MoS2.12 However, since adsorption is site-dependent, the trend is not always valid. For instance, we observed that at 33.3% coverage, the trend changed into stabilization when the interatomic distance between the adsorbed hydrogen atoms increased by 3.32 Å (see insets of Figure 3). The change between these two atomic environments depicts a hydrogen diffusion with an energy barrier of 0.16 eV (see Figure S6). This barrier is significantly lower than the diffusion barrier of a single adsorbed hydrogen (θH = 0.16%), which is 0.32 eV. The change in adsorption energy and diffusion barrier show that there should be a repulsive interaction between the adsorbed hydrogen atoms. Our Bader charge analysis suggests that this should come from Coulombic repulsion since hydrogen possesses excess electrons after adsorption (see Table S1).

Figure 3.

Figure 3

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Plot of hydrogen adsorption energy (Eads-H) on Mo–Mo-bridge as a function of hydrogen coverage (θH). For the rectangle marks, we put hydrogen atoms on successive Mo–Mo-bridge sites. For the triangle mark, there is an empty Mo–Mo-bridge site between the two adsorbed hydrogen atoms. The visualization of adsorptions at 33% coverage are shown in the inset.

Methyl Formate Adsorption

There are at least six methyl formate adsorption modes on Mo-edge MoS2 (see Figure 4). The density of states (DOS) analysis reveals that the methyl formate molecular orbital undergoes hybridization in all six adsorption modes (see Figure S4). The hybridization implies that all adsorption modes are chemisorption.

Figure 4.

Figure 4

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Energy level diagram of all methyl formate adsorption modes on Mo-edge MoS2. The ηxμy refers to x number of atoms in adsorbate, which is adsorbed through y number of atoms on the surface. Since there are two η1μ1 modes, we mark the less stable one with * to distinguish them.

Generally, methyl formate adsorption on Mo-top (μ1) is stronger than on Mo–Mo-bridge (μ2). The adsorption energy of η1μ1 is 0.1 eV more negative than that of η1μ2. The same trend is also observed in η2μ1 and η2μ2. This trend is interestingly contradicted by hydrogen, which prefers μ2 than μ1 mode (see section Hydrogen Coverage Effect on Methyl Formate Adsorption). The contradiction arises from the difference in the frontier orbital symmetry between hydrogen and methyl formate. The symmetry of the Highest Occupied Molecular Orbital (HOMO) and the Lowest Unoccupied Molecular Orbital (LUMO) (see Figure 5) allow them to interact strongly with the Mo atom’s dxz and dyz bands (see peaks A and B in Figure 2) via adsorption on Mo-top. On the other hand, there should be only a weak interaction on Mo–Mo-bridge. We provide a schematic to explain the interaction of methyl formate molecular orbitals with Mo d bands in Figure 6.

Figure 5.

Figure 5

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Isosurface of HOMO and LUMO of methyl formate. The isovalue is 0.006. Blue and red colors represent positive and negative phases, respectively.

Figure 6.

Figure 6

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Schematic representation of the interaction between methyl formate HOMO–LUMO and Mo d bands. Gray and white lobes represent positive and negative phases, respectively. Peaks A, B, and C refer to d band peaks in Figure 2. Methyl formate could be strongly adsorbed at Mo-top via interaction between the HOMO and peak A, as well as the LUMO and peak B. Meanwhile, there should be a weak interaction between the HOMO and peak C on Mo–Mo-bridge.

In the η1 modes (η1μ1*, η1μ1, and η1μ2), methyl formate is only adsorbed through its oxygen atoms. These η1 modes are also observed in the other oxygenated molecules that adsorbed on MoS220,36−38 and other transition metal surfaces.39 Adsorptions through the oxygen of the carbonyl group (C=O) are 0.2 eV stronger than that of the ether group (C–O–C). This trend agrees with the adsorption of methyl propionate,38 which is assigned to the higher nucleophilic character of the oxygen of the C=O group.

The η2 and η3 modes involve the adsorption of the C=O group. These adsorptions happen through π back-donation, as shown in Figure 7. The shift of the HOMO and LUMO to the right and left of the Fermi level indicates some electron exchange between methyl formate and MoS2. Methyl formate donates electrons from its HOMO. In return, MoS2 gives a back-donation to methyl formate’s LUMO. The LUMO is mainly formed by the π* orbital of the C=O group (see Figure 5). Back-donation to this π* orbital caused the C=O bond elongation for more than 0.1 Å (see Table S3).

Figure 7.

Figure 7

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Projected density of states (PDOS) of the methyl formate’s HOMO and LUMO, before and after adsorption. The energy level on the horizontal axis is relative to the Fermi level. The positive and negative values of PDOS correspond to spin up and down, respectively.

Hydrogen Coverage Effect on Methyl Formate Adsorption

We note that generally, hydrogen coverage strongly affects methyl formate adsorption energy, as shown in Figure 8. The increased hydrogen coverage either stabilizes or destabilizes methyl formate adsorption. Similar to our discussion in the previous subsection about hydrogen adsorption, we suggest that this effect may come from Coulombic interaction since methyl formate and hydrogen are negatively charged on the MoS2 surface (see Bader charge analysis in Table S1 and Table S2). The rest of this subsection will focus on discussing the trend in Figure 8.

Figure 8.

Figure 8

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To see the effect of hydrogen coverage (θH) on methyl formate adsorption energy (Eads-MF), we put two hydrogen atoms on the right of the adsorbed methyl formate (corresponding to θH = 33.3%) and then the other two on the left (θH = 66.7%), as shown in the upper panel figure. The effect is shown in the lower panel figure.

For η1 modes, increased hydrogen coverage first stabilizes the methyl formate adsorption energy by about −0.4 eV but later slowly destabilizes it. The stabilization happens because the Coulombic interaction with hydrogen forces methyl formate toward a more stable adsorption configuration. For instance, η1μ2 transforms into η1μ1 mode, which is more stable (see Figure S5). This may provide a good explanation for the similar trends reported by Valencia et al.40 for organic compound adsorption on the MoO3 surface.

Compared to η1, hydrogen coverage has a smaller effect on η2 adsorption energy. At 33.3% hydrogen coverage, η2 adsorption energy changes by about ±0.2 eV. It later stabilizes by about −0.2 eV at higher coverage (θH = 66.7%). Geometrically, the stabilization is especially noticeable for the η2μ2 mode, which transforms into η3μ2 (see Figure S5).

Interestingly, the most stable adsorption (η3) is strongly affected by hydrogen coverage. Since it is already in the most stable adsorption state, Coulombic repulsion from the surrounding hydrogen can only destabilize it. The adsorption energy is increased by +0.12 eV at 33.3% coverage and then by +0.31 eV more at 66.7% coverage.

In the time scale of experiments, one adsorption mode may change to another. For the most favorable change, which is η1μ1* into η3μ2, NEB calculations show that the higher the hydrogen coverage, the higher the energy barrier of the change (see Figure S7). For 66.7% hydrogen coverage, the energy barrier (0.38 eV) becomes higher than the η1μ1* desorption energy (0.20 eV). These results imply that, under high hydrogen coverage, it is likely for η1μ1* to desorb than to change to another stabler adsorption mode.

Finding the most stable adsorption mode of methyl formate prior to the investigation of HDO catalytic reaction is crucial. The extrapolation of our results in Figure 8 suggests that the η1 mode leads the methyl formate to desorb under high hydrogen pressure. The desorption decreases the number of methyl formate adsorbed on MoS2, which may lead to the decreasing HDO activity on MoS2 at high hydrogen pressure, as reported by Wang et al.10 While the ester in the η1 mode tends to desorb, the one with η2 and η3 converges to a similar mode in higher hydrogen coverage with an adsorption energy around −1.5 eV. The adsorption energy is strong enough to ensure methyl formate stays on the MoS2 surface for pursuing a further reaction stage.

Conclusions

We used DFT calculations to study the effect of hydrogen coverage on methyl formate adsorption over a perfect Mo-edge MoS2 surface. The Mo-edge has Inline graphic, dxz, and dyz peaks near the Fermi level, providing the adsorption sites on the surface’s Mo-top and Mo–Mo-bridge. Since the symmetry of the frontier orbitals of hydrogen and methyl formate are different, they prefer to interact with different d bands. This results in different preferential adsorption sites of hydrogen and methyl formate; i.e., hydrogen prefers to be adsorbed on Mo–Mo-bridge, while methyl formate prefers Mo-top.

We observed that methyl formate could be adsorbed either in η1, η2, or η3 mode. In the η1 mode, methyl formate adsorbs weakly through its oxygen atoms with the adsorption energy more positive than −0.6 eV. On the other hand, the η2 and η3 modes involve a π back-donation that stabilizes the adsorption at more than −1.0 eV.

Methyl formate and hydrogen receive electrons from MoS2 upon adsorption. These excess electrons caused Coulombic repulsive interaction between the adsorbates. The interaction stabilizes their adsorption at low hydrogen coverage but later destabilizes it at high hydrogen coverage. The destabilization may cause desorption of η1 modes of methyl formate due to its weak adsorption energy. Thus, at high hydrogen coverage, one may expect only η2 or η3 modes to exist on the surface.

Acknowledgments

All Quantum ESPRESSO calculations were performed in “Riven”, the computational facility at the Research Center for Quantum Engineering Design, Universitas Airlangga. The authors thank Prof. Yoshitada Morikawa (Osaka University, Japan) for insightful and valuable discussions. S.E.P.P.M. thanks the Ministry of Education, Culture, Sports, Science, and Technology, Japan, for the Scholarship. S.E.P.P.M. thanks Rizka N. Fadilla (Osaka University, Japan) for the insightful discussions.

Supporting Information Available

The Supporting Information is available free of charge at https://pubs.acs.org/doi/10.1021/acsomega.2c06888.

  • Convergence test for k-point, kinetic energy cutoff, and vacuum height of the slab model; Bader change for the adsorbates; PDOS to the methyl formate’s molecular orbital; optimized geometric parameters of adsorbed methyl formate; visualization of all methyl formate’s adsorption modes in several variations of hydrogen coverage; hydrogen diffusion barriers; and methyl formate μ1η1* into μ3η2 energy barriers (PDF)

Author Contributions

Conceptualization: Febdian Rusydi. Methodology: Febdian Rusydi and Samuel E. P. P. Masan. Validation: Wun F. Mark-Lee, Nabila A. Karim, and Adhitya G. Saputro. Formal Analysis: Samuel E. P. P. Masan, Wahyu A. E. Prabowo, Adhitya G. Saputro, Daniel Elisandro, and Febdian Rusydi. Investigation: Samuel E. P. P. Masan and Daniel Elisandro. Resources: Febdian Rusydi. Writing–original draft preparation: Samuel E. P. P. Masan. Writing–review and editing: Febdian Rusydi and Samuel E. P. P. Masan.

This research is funded by “SATU Joint Research Scheme Universitas Airlangga Tahun 2021” number 1296/UN3.15/PT/2021.

The authors declare no competing financial interest.

Supplementary Material

ao2c06888_si_002.pdf (1.5MB, pdf)

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