DFT investigations of the adsorption and hydrodesulfurization mechanism of thiophene catalyzed by Pd(111) surface

Abstract

The adsorption behavior and the selective hydrodesulfurization mechanism of thiophene on a Pd(111) surface were elucidated by density functional theory (DFT). All the pertinent species of different pathways were gathered to obtain their preferred adsorption sites. The activation energy and reaction energy of each step in different pathways were also calculated. The results show that the adsorption at the hollow site was the most stable when the thiophene was parallel to the Pd(111) surface with a ring plane. In the process of hydrodesulfurization, the heat of reaction was almost negative; therefore, reducing the temperature is helpful for the removal of S atom. The mechanism of direct hydrodesulfurization has a low activation energy, but the reaction has more than one possible product and is difficult to control. The mechanism of indirect hydrodesulfurization was the best fit for the 1,2-cis-hydrogenation process. The most feasible reaction pathway is (1) C₄H₄S + H₂ → α,β-C₄H₆S; (2) α,β-C₄H₆S + H₂ → C₄H₈S; (3) C₄H₈S + H₂ → C₄H₁₀ + S. Among these steps, the formation of C₄H₈S is the rate-determining step.

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1. Introduction

Thiophene is a group of basic constituents contained in fuel oil and is considered to be one of the primary causes of acid rain in the environment.^1–3 With the increasing consumption of fossil based fuel oil, numerous stringent environmental regulations have been applied in many countries to reduce the sulfur levels in fuel oil. As a result, interest in the research of desulfurization of thiophene has increased dramatically.^4–7

At present, on comparison with the non-hydrodesulfurization (NHDS) method for sulfur removal, the method of hydrodesulfurization (HDS) is more mature, effective and economical.^1,8,9 Most of the previous studies focused on the application of precious metal catalysts in the HDS of thiophene, which has superior catalytic activity and milder reaction conditions.^10,11 Among these catalysts, palladium (Pd) nanoparticles are one of the most effective precious metal catalysts, which are characterized by a high degree of dispersion and small average particle size,^12,13 and have been widely applied in the hydrogenation reactions of thiophene. Badano et al.¹⁴ compared the sulfur resistance of different catalysts; the result shows that the Pd catalyst had the highest activity. Vit et al.¹⁵ synthesized Pd/silica–alumina, and the result suggests that the higher acidity and surface area could improve the activities of Pd catalyst in the HDS of thiophene. In addition, they also found that the PdH_x phase most likely served as a storage medium during the hydrogenation reaction.¹⁶ Although there has been extensive experimental research on the hydrogenation reaction of thiophene, there are only a few reports on its adsorption process and hydrogenation mechanism due to the complexity of the experiments and the limitations of the characterization methods.

Density functional theory^17,18 has been widely used to calculate the adsorption energy, structure parameters, activation energy and reaction energy in the process of different reactions. Liao et al.¹⁹ made comparisons among different Mo-catalysts during the C–S cleavage of thiophene in order to find the most active catalyst species. Moreover, by DFT, Zhu et al.^20,21 researched the hydrogenation reaction of thiophene over Pt(110) and Pt(111) surfaces to present the most efficient reaction route. Our previous work²² predicted the most favorable mechanism for thiophene catalyzed on an Au(111) surface, and found that the hydroisomerization process is dominant.

In this work, we studied the adsorption process and hydrogenation mechanism of thiophene on a clean Pd(111) surface by the DFT method using the Dmol³ program package. The properties of different adsorption sites were also elucidated, which include structure parameters and adsorption energy. Furthermore, the possible reaction pathways of thiophene hydrogenation were discussed in detail to discover the primary HDS mechanism. The aim of this work is to provide a better understanding of the structural, energetic, catalytic and selective properties of Pd catalysts for the hydrodesulfurization of thiophene.

2. Computational details

2.1. Calculation methods

The density functional calculations shown in this work were performed with the DMol³ (ref. 23) program package using the Materials Studio 5.5 of Accelrys Inc. The exchange–correlation functional of Perdew and Wang (PW91)^24–26 was used to calculate the electronic structures with the generalized gradient approximation (GGA). The valence electron functions were expanded into a set of numerical atomic orbitals by a double-numerical basis with polarization functions (DNP). The tolerances of energy, force and displacement convergence were 5 × 10⁻⁴ eV, 2 × 10⁻² eV nm⁻¹ and 5 × 10⁻⁴ nm, respectively. The maximum self-consistent field (SCF) cycles were 1000 with a tolerance of 2 × 10⁻⁴ eV, and the k-point was set to 1 × 1 × 1. The transition state (TS) structures were computed using the Complete LST/QST tools²⁷ to investigate the minimum energy pathway for the hydrogenation of thiophene. In addition, each TS was verified by only one imaginary frequency. Throughout the calculations, smearing was employed to accelerate convergence of orbital occupation with a convergence value of 0.002 Ha, and all of the computations were performed with spin-polarization.

2.2. Surface model

In order to establish a good balance among the calculation accuracy, calculation efficiency and the complexity of the thiophene molecule, we modeled the Pd(111) crystal surface to simulate the exposed Pd atoms. The periodical surface was modeled by three-layer slabs with a 4 × 4 unit cell which contains 48 Pd atoms to study the adsorption and the hydrogenation of the thiophene molecular systems, as shown in Fig. 1. Only one thiophene molecule was adsorbed on one side of the slab; in other words, the coverage is 1/16 mono-layer (ML). The vacuum region thickness between the repeated slabs was 1 nm, which was large enough to avoid interactions between different slabs. The layer and the vacuum region could form a unit which was repeated periodically in the space. In the process of geometry optimization and TS search, the upmost two Pd layers were allowed to relax freely, and the bottom layer was frozen. Under the computational conditions mentioned above, the lattice parameter of the Pd(111) surface was calculated to be 0.3893 nm, which is in good agreement with the experimental value of 0.3895 nm.^28,29 These results show that the method of calculation in this paper is reliable.

Fig. 1 The top (left) and side (right) view of Pd(111) surface models (4 × 4).

3. Results and discussion

3.1. Adsorption energies and geometries analysis

Calculations of the adsorption energies of thiophene on Pd(111) surfaces were performed in order to discuss the HDS mechanisms of thiophene on Pd substrates during the initial stage. In the present work, the adsorption energies (E_ads) were calculated using the equation below:

E_ads = E_(A/surface) − (E_A + E_surface)

where, E_(A/surface) is the total energy of the Pd(111) surface with a thiophene molecule on it, E_surface is the energy of the Pd(111) surface without the thiophene molecule and E_A is the energy of the free thiophene molecule. With this definition, E_ads generally has a negative value, and a larger value corresponds to a more stable adsorption on the Pd(111) surface.

According to previous works,^22,30 the thiophene plane would interact with the metal surface through the S atom. In addition, the vertical adsorption sites would be converted to parallel adsorption sites; this implies that the model of parallel adsorption is more stable. As a result, we chose twelve highly symmetric parallel adsorption sites on the Pd(111) surface for calculations, as shown in Fig. 1. These adsorption sites include top (0°, 30°, 60°), hcp (0°, 30°, 60°), fcc (0°, 30°, 60°) and bridge (0°, 30°, 60°) sites. As can be seen in Fig. 1, 0°, 30° and 60° represent the adsorption sites with the symmetry axis rotating 0°, 30° and 60° from the horizontal direction.

The adsorption energies and geometric parameters of different sites were calculated and are listed in Table 1; only those in stable adsorption configurations were summarized. Moreover, the most stable structure of thiophene adsorbed on the Pd(111) surface is shown in Fig. 2. As can be seen from Table 1 and Fig. 2, a thiophene molecule is adsorbed on the Pd(111) surface with an energy of −176 to −186 kJ mol⁻¹, and preferentially adsorbed in a parallel way through the ring plane. Among different initial adsorption sites, the E_ads of the Bri-0° site is −185.3 kJ mol⁻¹, and the distance between the Pd atom and S atom is 0.1461 nm. The maximum of E_ads and the least value of d_Pd–S suggest that the position of Bri-0° is the most stable. During the process of adsorption, the S atom and H atoms of thiophene move upward, and the axial rotation of the ring plane is clockwise. Finally, the S atom of thiophene is transferred to the hollow site and interacted with the Pd(111) surface.

Table 1 Adsorption energies and geometric parameters of a thiophene molecule on a Pd(111) surface^a

Adsorption site	Eads/(kJ mol^−1)	dPd–S nm^−1	Adsorption site	Eads/(kJ mol^−1)	dPd–S nm^−1
a The adsorption positions in Table 1 represent the initial adsorption sites of thiophene.
Top-0°	−176.0	0.1559	Fcc-0°	−182.4	0.1578
Top-30°	−184.6	0.1587	Fcc-30°	−179.8	0.1516
Top-60°	−176.8	0.1560	Fcc-60°	−183.2	0.1562
Hcp-0°	−181.6	0.1542	Bri-0°	−185.3	0.1461
Hcp-30°	−184.7	0.1584	Bri-30°	−184.5	0.1577
Hcp-60°	−182.1	0.1558	Bri-60°	−184.7	0.1551

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Fig. 2 The most stable configurations of thiophene on the Pd(111) surface (A) represented thiophene; (B) represented top view; (C) represented side view.

In order to analyze the structure parameter of the most stable adsorption site of a thiophene molecule on a Pd(111) surface, Table 2 lists the adsorption energy and bond lengths of the thiophene molecule at the initial site of Bri-0°. On comparing the data in Table 2, it can be seen that the calculation of bond length for free thiophene is in good agreement with the experimental values.³⁰ After adsorption, there is an elongation in the range of 0.0013–0.0112 nm for the bond lengths of d₁–d₅, while the energy of thiophene decreases. This phenomena suggests that the adsorption of thiophene on a Pd(111) surface could promote the hydrogenation reaction. In addition, the greatest change in d₁ implies that the H atom is more likely to attack the α-C of thiophene.

Table 2 Adsorption energy and bond lengths of a thiophene molecule on Pd(111) for the most stable adsorption geometry

Model	Eads/(kJ mol^−1)	d1/nm	d2/nm	d3/nm	d4/nm	d5/nm
Thiophene (expt)	—	0.1730	0.1370	0.1420	0.1370	0.1730
Thiophene (calc)	—	0.1729	0.1372	0.1422	0.1372	0.1727
Thiophene/Au(111)	−185.3	0.1841	0.1424	0.1435	0.1482	0.1801
|Δd|	—	0.0112	0.0052	0.0013	0.0110	0.0074

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3.2. Hydrogenation mechanism of thiophene

Based on previous studies,^21,31–35 it is already known that two different competing reaction pathways exist, as can be seen in Fig. 3. The first one is termed as the direct desulfurization (DDS) pathway, which would generate an S atom and butadiene without further hydrogenation. In contrast, the second one is termed as the hydrogenation (HYD) pathway, and the major products are an S atom and n-butane.

Fig. 3 Different reaction pathways for the hydrogenation of thiophene. A, B, C, D, E and F represent mechanisms A, B, C, D, E and F.

Table 3 provides six possible hydrogenation mechanisms of thiophene on a Pd(111) surface. The mechanisms of A–E represent the HYD pathway, and the mechanism of F represents the DDS pathway. Among the hydrogenation mechanisms of A–F, the major difference is the diversity of the hydrogenation position of the α-C and β-C in the thiophene molecule. According to the mechanisms of A–F in Table 3, we optimized the structures of the reactants (IS) and products (FS), and then searched the TS between them. The activation energies and reaction energies at the TS are tabulated in Table 4. Among different hydrogenation mechanisms, the initial step is the coadsorption of thiophene and atomic H, thus we only compared the intermediate steps of the hydrogenation process in Table 3 (Step 1–4).

Table 3 Reaction mechanisms of A–F for the hydrogenation of thiophene on a Pd(111) surface^a

Step	Mechanism A	Mechanism B	Mechanism C
a aα,β represent hydrogenation of α-C or β-C.
1	C4H4S* + H* → α-C4H5S* + *
2	α-C4H5S* + H* → α,β-C4H6S* + *		α-C4H5S* + H* → α,α-C4H6S* + *
3	α,β-C4H6S* + H* → α,β,α-C4H7S* + *	α,β-C4H6S* + H* → α,β,β-C4H7S* + *	α,α-C4H6S* + H* → α,α,β-C4H7S* + *
4	α,β,α-C4H7S* + H* → C4H8S* + *	α,β,β-C4H7S* + H* → C4H8S* + *	α,α,β-C4H7S* + H* → C4H8S* + *
5	C4H8S* + H* → C4H9S* + *
6	C4H9S* + H* → C4H10* + S*

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Step	Mechanism D	Mechanism E	Mechanism F
1	C4H4S* + H* → β-C4H5S* + *		C4H4S* + H* → C4H5S* + *
2	β-C4H5S* + H* → β,α-C4H6S* + *		C4H5S* + H* → C4H6* + S*
3	β,α-C4H6S* + H* → β,α,β-C4H7S* + *	β,α-C4H6S* + H* → β,α,α-C4H7S* + *
4	β,α,β-C4H7S* + H* → C4H8S* + *	β,α,α-C4H7S* + H* → C4H8S* + *
5	C4H8S* + H* → C4H9S* + *
6	C4H9S* + H* → C4H10* + S*

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Table 4 Activation energies (E_a) and reaction energies (ΔE) of elementary reactions on the Pd(111) surface

Intermediates	Reaction	Ea/(kJ mol^−1)	ΔE/(kJ mol^−1)
TS1	C4H4S* + H* → α-C4H5S* + *	41.6	−54.6
TS2	C4H4S* + H* → β-C4H5S* + *	85.6	−50.7
TS3	α-C4H5S* + H* → α,β-C4H6S* + *	142.1	−22.9
TS4	α-C4H5S* + H* → α,α-C4H6S* + *	185.6	21.3
TS5	α,β-C4H6S* + H* → α,β,α-C4H7S* +	124.2	85.3
TS6	α,β-C4H6S* + H* → α,β,β-C4H7S* +	110.1	−36.6
TS7	α,β,β-C4H7S* + H* → C4H8S* + *	229.9	11.3
TS8	C4H8S* + H* → C4H9S* + *	198.8	−37.8
TS9	C4H9S* + H* → C4H10* + S*	169.1	−48.3
TS10	C4H4S* + H* → C4H5S* + *	62.5	−54.6
TS11	C4H5S* + H* → C4H6* + S*	58.6	−90.1

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3.2.1 HYD mechanism of thiophene. At the outset of the HYD reaction, we considered two possible active sites in the thiophene molecule, including the α-C and β-C. The calculated barriers (E_a), the total energy change (ΔE), and the corresponding TS structures for the mechanism of A–E(1) are shown in Fig. 4.

C₄H₄S* + H* → C₄H₅S* (FS1 or FS2)

Fig. 4 The IS, TS, FS, activation energy and reaction energy (kJ mol⁻¹) of mechanisms A–E(1) on the Pd(111) surface A–C(1): E_a = 41.6; ΔE = −54.6 D–E(1): E_a = 85.6; ΔE = −50.7.

For the reaction of C₄H₄S* + H* → α-C₄H₅S* (FS1), we calculated the coadsorption of thiophene and atomic H as IS1. After complete optimization, the thiophene adsorbed with the S atom downwardly bonded to the Pd(111) surface at the original hollow site; moreover, the C₂ and C₃ atoms of thiophene moved upward. The atomic H transferred from the fcc site to the neighboring bridge site. In TS1, the reacted α-C tilted by 38.4° from the horizontal plane, and the atomic H moved to the hcp site with an α-C–H distance of 0.1756 nm. When FS1 formed, the reacted H of α-C continued to tilt upward until it was perpendicular to the Pd(111) surface. Finally, the FS1 was adsorbed at the hollow site through the unreacted double bond of C=C to the surface. The bond length of the reacted α-C–H decreased from 0.2729 nm to 0.1095 nm, and d₁ was elongated to 0.1841 nm. This reaction was exothermic by −54.6 kJ mol⁻¹, and the corresponding E_a was 41.6 kJ mol⁻¹.

For the reaction of C₄H₄S* + H* → β-C₄H₅S* (FS2), the IS of the first step is exactly the same as the IS1. In TS2, the S atom tilted upward slightly, and the atomic H gradually moved away from the surface at the same time. The bond length of the reacted β-C–H decreased from 0.2366 nm in IS1 to 0.1597 nm. When FS2 formed, the reacted H of β-C continued to tilt upward until it was perpendicular to the Pd(111) surface; moreover, the S atom moved upward noticeably. This reaction was exothermic by −50.7 kJ mol⁻¹, and the corresponding E_a was 85.6 kJ mol⁻¹.

As can be seen from Table 4 and Fig. 4, the relative energies of FS1 and FS2 are exothermic with negative values, which indicates that reducing the temperature is helpful for the reaction in step 1. In addition, the formation of FS1 is more favorable because of the comparably lower activation energy of 41.6 kJ mol⁻¹. Therefore, the hydrogenation process of α-C in thiophene occurs more easily in step 1, and this result is in good agreement with the analysis of the structure parameters in Section 3.1.

α-C₄H₅S* + H* → C₄H₆S* (FS3 or FS4)

α-C₄H₅S* is regarded as the dominant product in step 1, and the further hydrogenation process would occur on the basis of α-C₄H₅S*. The E_a, ΔE and the corresponding TS structures for the mechanism of A–C(2) are shown in Fig. 5.

Fig. 5 The IS, TS, FS, activation energy and reaction energy (kJ mol⁻¹) of mechanisms A–C(2) on the Pd(111) surface A–B(2): E_a = 142.1; ΔE = −22.9 C(2): E_a = 185.6; ΔE = 21.3.

For the reaction of α-C₄H₅S* + H* → α,β-C₄H₆S* (FS3), we calculated the coadsorption of α-C₄H₅S and atomic H as IS2. When the reaction occurred, the methylene of α-C₄H₅S tilted upward and other C atoms lay flush with each other. The atomic H got transferred from the fcc site to the neighboring hcp site. In TS3, the reacted β-C–H moved upward, and the atomic H moved close to the ring plane. The product α,β-C₄H₅S* (FS3) was generated after the atomic H reached the reacted β-C and settled at the hollow site through the double bond. The d₁ was elongated to 0.1852 nm. This reaction was exothermic by −22.9 kJ mol⁻¹, and the corresponding E_a was 142.1 kJ mol⁻¹.

For the reaction of α-C₄H₅S* + H* → α,α-C₄H₆S* (FS4), the reactant is the same as in IS2. In TS4, the reacted α-C moved upward, and the atomic H got transferred to the adjacent hcp site in order to move close to the reacted α-C with an α-C–H distance of 0.2200 nm. Additionally, the C₂ and C₃ atoms are electron-rich because of the hydrogenation process of α-C; as a result, the double bond between C₂ and C₃ was formed during the reaction. Once FS4 was produced, the H atoms of α-C retained almost the same structure, both of which had a tilting angle of 109.5°. Finally, the FS4 was adsorbed at the bridge site via the double bond of C₂ and C₃. This reaction was endothermic by 21.3 kJ mol⁻¹, and the corresponding E_a was 185.6 kJ mol⁻¹.

Compared with the calculation results in step 2, the formation of α,β-C₄H₅S* is exothermic, while the formation of α,α-C₄H₅S* is endothermic. The hydrogenation process of C₄H₅S* to α,β-C₄H₅S* seems more liable to take place due to its lower energy barrier (142.1 kJ mol⁻¹). Hence, the α,β-C₄H₅S* species is selected as the species for further hydrogenation below.

α,β-C₄H₆S* + H* → C₄H₇S* (FS5 or FS6)

α,β-C₄H₆S* is considered as the most favorable product in step 2, and the further hydrogenation process of α,β-C₄H₆S leads to α,β,α-C₄H₆S or α,β,β-C₄H₆S. The E_a, ΔE and the corresponding TS structures for the mechanism of A–B(3) are illustrated in Fig. 6.

Fig. 6 The IS, TS, FS, activation energy and reaction energy (kJ mol⁻¹) of mechanisms A–B(3) on the Pd(111) surface A(3): E_a = 124.2; ΔE = 85.3 B(3): E_a = 110.1; ΔE = −36.6.

The reaction of α,β-C₄H₆S* + H* → α,β,α-C₄H₇S* (FS5) starts from the coadsorption of α,β-C₄H₆S and atomic H. In the initial state, the structure of α,β-C₄H₆S remained the same as in FS3, and was located at the hollow site through the double bond. The atomic H got transferred to the adjacent hcp site. In TS5, the atomic H left its hcp site and moved to the adjacent hcp site, and the ring plane rotated anticlockwise to meet the attacking H atom. The forming α-C–H distance decreased from 0.3582 nm to 0.2531 nm. Once FS5 was formed, the S atom moved away from the Pd surface, and the ring plane tilted downwards. The bond length of the reacted α-C–H decreased to 0.1225 nm. This reaction was endothermic by 85.3 kJ mol⁻¹, and the corresponding E_a was 124.2 kJ mol⁻¹.

For the reaction of α,β-C₄H₆S* + H* → α,β,β-C₄H₇S* (FS6), the reactant was the same as what was described in IS3. In TS6, the atomic H got transferred from the hcp site to the neighboring top site. At the same time, the C₂ and C₃ atoms moved upwards. The distance between the atomic H and reacted β-C was decreased to 0.2128 nm from 0.2929 nm. While FS6 was produced, the C₂ and C₃ atoms further moved upward. Subsequently, the β-C–H bond was activated with a distance of 0.1102 nm and d₁ was elongated to 0.1860 nm. This reaction was exothermic by −36.6 kJ mol⁻¹, and the corresponding E_a was 110.1 kJ mol⁻¹.

As can be seen from the data mentioned above, the reactant α,β-C₄H₆S prefers hydrogenation on β-C rather than α-C. The formation of FS5 is endothermic, while the formation of FS6 is exothermic. Furthermore, a low barrier of 110.1 kJ mol⁻¹ as well as a short bond length of 0.1102 nm are present for the β-C–H bond formed in FS6. Therefore, the formation of FS6 from α,β-C₄H₆S is likely to occur.

α,β,β-C₄H₇S* + H* → C₄H₈S* (FS7)

From the previous discussion, the mechanism B is regarded as the most favorable pathway. There is only one possibility for the further hydrogenation of α,β,β-C₄H₆S to form the saturated product of C₄H₈S. The E_a, ΔE, and the corresponding TS structures for the mechanism of B(4) are illustrated in Fig. 7.

Fig. 7 The IS, TS, FS, activation energy and reaction energy (kJ mol⁻¹) of mechanism B(4) on the Pd(111) surface B(4): E_a = 229.9; ΔE = 11.3.

The reaction of α,β,β-C₄H₇S* + H* → α,β,β,α-C₄H₈S* (FS7) began with the coadsorption of α,β,β-C₄H₇S and atomic H, as can be seen in IS4. For IS4 adsorption on the Pd surface, the preferential adsorption site was where the atomic H got transferred to the nearby hcp site, and the α,β,β-C₄H₇S molecule was bound at the hollow site via the S atom, where the adsorption configuration is the same as in FS6. In TS7, the unsaturated α-C moved upward and the atomic H got transferred to the adjacent hollow site in order to form the saturated bond of α-C–H. The distance between the atomic H and unsaturated α-C was decreased from 0.3466 to 0.2011 nm. Once FS7 was adsorbed at the top site through the S atom, the C atoms of the ring plane lay flush with each other parallel to the Pd surface. The d₁ was elongated to 0.1866 nm. This reaction was exothermic by 11.3 kJ mol⁻¹, and the corresponding E_a was 229.9 kJ mol⁻¹.

C₄H₈S* + 2H* → C₄H₁₀* + S* (FS8 and FS9)

In the final step, C₄H₈S* is further hydrogenated to n-butane and an S atom with the help of atomic H. The E_a, ΔE and the corresponding TS structures for the mechanism of B(5–6) are illustrated in Fig. 8.

Fig. 8 The IS, TS, FS, activation energy and reaction energy (kJ mol⁻¹) of mechanisms B(5–6) on the Pd(111) surface B(5): E_a = 198.8; ΔE = −37.8 B(6): E_a = 169.1; ΔE = −48.3.

The reaction of C₄H₈S* + H* → C₄H₉S* (FS8) was exothermic by −37.8 kJ mol⁻¹, with the corresponding E_a of 198.8 kJ mol⁻¹. In the initial state, the C₄H₈S molecule bound at the top site through the S atom, and the atomic H got transferred from the fcc site to the adjacent bridge site. In TS8, the atomic H moved close to the reacted α-C, resulting in a shortening of the distance between the α-C and atomic H from 0.3020 nm to 0.2257 nm. Moreover, one of the C–S bonds broke up, and the S atom moved downward to the Pd surface. The formed FS8 was adsorbed at the hcp site via the S atom and d₅ was elongated to 0.1879 nm; moreover, the distance between the α-C and the atomic H was further reduced to 0.1110 nm to form the bond of α-C–H.

For the reaction C₄H₉S* + H* → C₄H₁₀* + S* (FS9), we calculated the coadsorption of C₄H₉S and atomic H as IS6. After adsorption, the atomic H was located at the original fcc site. The C₃ and C₄ atoms of C₄H₉S tilted upwards, compared with the structure in FS8. From the TS9 shown in Fig. 8, the atomic H was located at the nearby top site with an α-C–H distance of 0.3756 nm; moreover, the S atom was separated from C₄H₉S. Once FS9 was produced, the dissociated S settled at the fcc site, and the C₄H₁₀ molecule was adsorbed on the Pd surface through the H atoms of C₂ and C₄, whose structure was perpendicular to the Pd surface. This phenomenon is similar to previous results reported in the literature.³⁶ This reaction was exothermic by −48.3 kJ mol⁻¹, and the corresponding E_a was 169.1 kJ mol⁻¹.

3.2.2 DDS mechanism of thiophene. Regarding the DDS reaction, the thiophene molecule would react with the atomic H, and then decompose into dissociated S and butadiene. The E_a, ΔE and the corresponding TS structures for the mechanisms of F(1) and F(2) are shown in Fig. 9 and Fig. 10.

C₄H₄S* + H* → C₄H₅S* (FS10)

Fig. 9 The IS, TS, FS, activation energy and reaction energy (kJ mol⁻¹) of mechanism F(1) on the Pd(111) surface F(1): E_a = 62.5; ΔE = −54.6.

Fig. 10 The IS, TS, FS, activation energy and reaction energy (kJ mol⁻¹) of mechanism F(2) on the Pd(111) surface F(2): E_a = 58.6; ΔE = −90.1.

For the reaction of C₄H₄S* + H* → C₄H₅S* (FS10), the configuration of the reactant is the same as described in IS1. In TS10, d₅ decreased from 0.1820 nm to 0.1805 nm. This phenomena caused the d₁ bond to break, which was accompanied by migration of the atomic H to the top site and upward migration of C₃ and C₄. While FS10 was formed, the C₃ atom moved downward, which made the C₁–C₃ atoms parallel to the Pd surface. Finally, FS10 was adsorbed at the hollow site on the Pd surface via the double bond of C₁ and C₂. This reaction was exothermic by −54.6 kJ mol⁻¹, and the corresponding E_a was 62.5 kJ mol⁻¹.

C₄H₅S* + H* → C₄H₆* + S* (FS11)

The reaction C₄H₅S* + H* → C₄H₆S* (FS11) started with the coadsorption of C₄H₄S and atomic H. During the process, the atomic H migrated to the hcp site from the initial fcc site, and the structure of C₄H₅S remained the same as in FS10. Moreover, the d₅ bond was elongated to 0.1843 nm. In TS11, the atomic H moved to the adjacent fcc site to form the bond of α-C–H, leading to the breaking of the C–S bond. Then, the dissociated S got transferred to the hcp site. When FS11 produced, the dissociated S got located at the hcp site, and the molecule of butadiene was parallely adsorbed at bridge sites on the Pd surface through the double bonds of C₁=C₂ and C₃=C₄. This reaction was exothermic by −90.1 kJ mol⁻¹, and the corresponding E_a was 58.6 kJ mol⁻¹.

3.3. Brief summary of the hydrogenation process of thiophene

We have investigated the overall reactions involving the HYD and DDS mechanisms of thiophene. On the basis of the discussed activation energies and reaction energies, the detailed potential energy diagram for the HYD and DDS mechanisms of thiophene on a Pd(111) surface is shown in Fig. 11. As displayed in Fig. 11, the mechanism of DDS has a low energy of activation, but the product of butadiene would continue hydrogenating to produce monoolefine, alkane and so on. As a result, it is indicated that the DDS pathway has more than one possible product and is difficult to control. For the HYD mechanism, it is found that 1,2-cis-hydrogenation is dominant, and the most favourable route for thiophene hydrogenation on the Pd(111) surface is described as follows: C₄H₄S → α-C₄H₆S → α,β-C₄H₆S → α,β,β-C₄H₆S → C₄H₈S → C₄H₉S → C₄H₁₀ + S. This result is in good agreement with the experimental research.³⁷ During the process, the formation of C₄H₈S from α,β,β-C₄H₇S hydrogenation is considered as the rate-limiting step, which has the highest energy barrier.

Fig. 11 Sketch for potential relative energy (E_R) of reaction mechanisms F and B on the Pd(111) surface.

4. Conclusions

In this paper, we have examined the adsorption process and hydrogenation mechanism of thiophene on a Pd(111) surface in detail by performing periodic DFT calculations. Various adsorption modes of the intermediates involved in the reaction were investigated from energetic and geometrical viewpoints, and the hydrogenation mechanism has been clarified.

Our results show that the parallel adsorption of thiophene at the hollow site through the ring plane is the most stable adsorption structure on the Pd(111) surface. After thiophene gets adsorbed, all the bond lengths increase, and the H atom is most liable to attack the α-C of thiophene when the hydrogenation reaction occurs.

No matter what kind of mechanism it follows, the hydrogenation of thiophene is almost exothermic; therefore, reducing the temperature is beneficial for desulfurization. For the DDS mechanism, the reaction has a lower energy of activation as compared with the HDS reaction, but the hydrogenated product has more than one possibility and is difficult to control. For the HDS mechanism, it is found that 1,2-cis-hydrogenation is predominant. During the reaction, the C–S bond length in thiophene increases gradually, while the bond energy of C–S decreases. All of these changes facilitate the cleavage of C–S. The reaction path of HYD is found to proceed as follows: C₄H₄S → α-C₄H₆S → α,β-C₄H₆S → α,β,β-C₄H₆S → C₄H₈S → C₄H₉S → C₄H₁₀ + S. The formation of C₄H₈S is considered as the rate-limiting step, which has the highest energy barrier.

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