Structure–activity relationships in Pd catalysed C–S activation of thioesters

Abstract

Transition metal catalyzed C–S activation has recently become a powerful strategy in organic synthesis, and has shown great potential in petroleum chemistry and protein synthesis. Nonetheless, the inherent structure–activity relationships have been less-well understood, limiting the future development and applications of such protocols. In this study, we carried out a systematic investigation on Pd(0) catalysed C–S activation using density functional theory (DFT) methods. The C–S bond activation of 34 structurally independent thioesters (R¹COSR²) was studied. The correlations between the activation barrier, C–S bond dissociation enthalpy (BDE), the reaction energy and structural parameters of the involving intermediates and transition states were systematically examined.

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1. Introduction

C–S bonds are versatile motifs in natural products and biological/pharmaceutical molecules.^1–7 Particularly, the thioester-containing compounds have shown great potential in organic, petroleum and protein synthesis.^8–27 With the recent progress in transition metal catalysis, the C–S bond activation of thioesters has been successfully achieved. For example, the pioneering studies by Shaver and co-workers showed that C–S bond activation can be realized by chelating Rh(PPh₃)₃Cl with 8-quinoline thioester.²⁴ Recently, the Pd catalysed cross-coupling of thioesters with silylzinc chlorides has been successfully achieved via the C–S bond activation/C–C bond formation strategy.^9,10 Moreover, Liebeskind group recently reported the first Pd catalyzed cross-coupling of alkyl/aryl thioesters with organoboric acids, where ketones were generated as the final products (eqn (1)). The reactions can tolerate different substituents on the thioesters and the yields of these reactions might be up to 93%.^25,26

It is noteworthy that the different types of C–S substrates (such as thioethers and thioesters) might show distinct activities and selectivity in the aforementioned C–S activation reactions.^28–34 For example, in Liebeskind's reactions (eqn (1)), the yield of the ketones varies (52–93%) starting from the different thioesters under the same reaction conditions (Pd-catalyst, Cu(I) carboxylate and boric acid).²⁵ The similar observation has also been frequently noted in other C–S activation reactions. Therefore, the structure–activity correlations of thioesters might be fundamentally important in understanding and predicting the reactivity of the substrates in the C–S activation processes.

According to the previous studies, the oxidative addition of the C–S substrate to the catalytically active Pd center is an essential step in the C–S activation-coupling reactions.^29–34 In addition, the oxidative addition might also act as the rate-determining step of the whole reaction. Nonetheless, the previous studies mainly focus on the overall catalytic cycle for C–S activations of the modelling reactant, whereas the systematic understanding on the distinctions between the different C–S substrates are rarely reported.²⁸ What is more important, little is known about the key structural parameters and the inherent structure–activity relationships therein. To this end, we carried out the systematic studies on elementary C–S activation steps, and the diphosphine ligated Pd(0) (i.e. Pd(PPh₃)₂) mediated C–S activation of the thioesters (Fig. 1) were used as the target system.³⁵

Fig. 1 The selected 34 thioesters in calculations.

2. Results and discussion

2.1 BDE and BDFE of the thioesters 1–34

According to the recent studies, the activation barrier of the transition metal catalysed C–H bond activation might be directly related to the stability of the C(aryl)–[M] (M = Pd) bond or the C–[M]/C–H bond dissociation energy gap (M = Cu) in Pd or Cu-promoted C–H activation of heteroarenes.^36,37 In this regard, we first calculated the C–S bond dissociation enthalpy (BDE) of the selected 34 thioesters (see ESI Fig. S1†). For comparison, the bond dissociation free energy (BDFE) and the entropy change in the bond dissociation processes have also been provided (Table 1).

Table 1 The calculated bond dissociation enthalpy (BDE, kcal mol⁻¹), bond dissociation free energy (BDFE, kcal mol⁻¹) and entropy change (ΔS, cal (mol K)⁻¹) of the C–S bond cleavage process for selected thioesters 1–34

Thioester	1	2	3	4	5	6	7	8	9	10
BDE	76.56	77.25	77.25	76.74	77.38	76.62	77.00	77.19	76.46	76.54
BDFE	63.86	63.63	64.09	65.42	64.79	64.03	63.65	64.24	63.71	63.75
ΔS	42.60	45.69	44.12	37.97	42.25	42.22	44.78	43.44	43.06	42.90

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Thioester	11	12	13	14	15	16	17	18	19	20
BDE	76.08	77.91	77.38	67.04	66.28	64.99	68.92	66.24	62.94	67.39
BDFE	63.55	64.45	63.86	53.70	53.09	52.37	55.64	53.30	49.63	54.39
ΔS	42.02	45.13	44.77	44.73	42.33	44.23	44.53	43.42	44.65	43.59

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Thioester	21	22	23	24	25	26	27	28	29	30
BDE	67.00	64.83	68.04	67.34	66.57	69.24	66.04	67.06	67.95	66.77
BDFE	53.75	51.91	55.09	54.54	54.27	56.24	52.27	54.67	54.59	53.69
ΔS	44.44	43.34	43.43	43.17	41.27	43.61	46.20	41.54	44.81	44.09

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Thioester	31	32	33	34
BDE	65.96	68.69	66.72	66.78
BDFE	52.98	55.51	53.51	53.72
ΔS	43.53	44.19	44.56	44.32

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From the calculation results in Table 1, it can be seen that the BDE values of all thioesters with the alkyl thiol groups (R²) are similar to each other (1–13, 76–78 kcal mol⁻¹). Meanwhile, the BDE values significantly decreased by about 10 kcal mol⁻¹ when the substituents on thiol group (R²) are changed to the aromatic groups (14–34, 62–70 kcal mol⁻¹). The results indicate that the C–S bond strength in the thioester substrates is insensitive to the substituents on the carbonyl group (R¹), while the substituents on the thiol group significantly affect the C–S BDEs. In addition, the C–S BDEs of the thioesters with the aromatic thiol groups show good linear correlations with the substituent constant σ_p, implying that the C–S bond strength is mainly determined by the electronic effect of the thiol groups.³⁸ As shown in Fig. 2, for the ten para-substituted thioesters, the linear correlation coefficient R value is 0.9513, and the slope of the linear correlation is 3.95. The positive correlations indicate that the C–S bond is weakened by the electron donating substituents, while is strengthened by the electron withdrawing group. Note that the positive correlations has also been previously observed in the S–S BDEs of the disulfides,³⁹ and the reason relates to the high instability of the formed electron-deficient radicals.

Fig. 2 The linear correlation plot between BDE of the selected thioesters and the substituent constant (σ_p).

In Table 1, the BDFE shows the same trends with BDE, as the BDFE of the thioesters with the alkyl thiol groups (R²) are all around 64 kcal mol⁻¹ (1–13), while the BDFE of the thioesters with the aromatic thiol groups (R²) are all around 55 kcal mol⁻¹ (14–34). Interestingly, examining the relationship between BDE and BDFE, we noticed the strong linear correlation: BDE = BDFE + 12.98. The linear correlation coefficient R is as high as 0.9963, and the square deviation (SD) is only 0.45 kcal mol⁻¹ for the 34 concerned structures. Note that the similar good correlation between BDE and BDFE were also reported in the previous studies.³⁶ The good linear correlation suggests that the entropy effect in C–S bond dissociation processes is highly alike for different thioesters, and the average entropic change is about 43.5 cal (mol K)⁻¹ (calculated from the intercept of the linear plot in Fig. 3). From the detailed entropy data in Table 1, it can be seen that the variation of different data is about 3 cal (mol K)⁻¹. In other words, the entropy changes of the C–S bond dissociation of different thioesters lie in the range of 43.5 ± 3.0 cal (mol K)⁻¹.

Fig. 3 The linear correlation plot between BDE and BDFE.

2.2 ΔG^≠ and ΔH^≠ for the C–S activation processes

On the basis of the calculation results on the elementary C–S bond dissociation step, we then carried out calculations on the transition states and the products of the C–S activation processes of 1–34. According to our previous theoretical studies, the C–S activation occurs via the oxidative addition process, and thus the three-membered transition states were used for the discussions.²⁸ For clarity reasons, the transition state corresponding to each thioester substrate n (n = 1–34) is named as n-TS, and the product is named as n-P. An illustrative diagram of the C–S activation has been given in Scheme 1.

Scheme 1 The C–S activation of thioesters with Pd(PPh₃)₂.

Similar to the aforementioned discussions on BDE and BDFE, both the activation Gibbs free energy (ΔG^≠) and the activation enthalpy (ΔH^≠) have been listed, and thus the ΔS^≠ could be generated accordingly (Table 2). From the calculation results in Table 2, it can be seen that the activation free energies of most thioesters with the alkyl thiol groups are over 20 kcal mol⁻¹ (1–13, except for 12), while the ΔG^≠ for most thioesters with the aryl thiol groups are below 18 kcal mol⁻¹ (14–34, except for 23–25). Meanwhile, the activation enthalpies of 14–34 are also relatively lower than those of 1–13 (note that the negative activation enthalpies are caused by the algorithm of the theoretical calculations⁴⁰). Nonetheless, unlike the insensitivity of the BDEs on the steric effect of the thioester substrates, the activation barrier of the oxidative addition is critically affected by the bulkiness of the substrates. For example, the change of the methyl carbonyl group to the ethyl carbonyl group results in the slight increase of the activation free energy barrier by about 1.5 kcal mol⁻¹ (1 vs. 4). Meanwhile, changing the methyl thiol group into the iso-propyl thiol group results in the ∼2.3 kcal mol⁻¹ increase of the activation free energy barrier (1 vs. 3). This proposal is also supported by the comparison of 7 vs. 8, and 14 vs. 24 etc. Interestingly, the relative enthalpies also follow the same trend. Indeed, ΔG^≠ shows good linear correlations with ΔH^≠ (Fig. 4), despite the correlation coefficient is relatively lower than the one between BDE and BDFE in Fig. 3. The weaker correlations in activation energies are caused by the relatively complex interactions (C–S bond dissociation, Pd–C bond formation, and Pd–S bond formation) in the transition states. For this reason, the correlation of ΔG^≠ with the C–S BDEs in the thioester substrates is very weak (the linear correlation coefficient R = 0.7954, and the square deviation is 1.56 kcal mol⁻¹ for the 34 molecules, please see ESI† for the linear plots between ΔG^≠ and the C–S BDE of the substrates). For better understanding on the inherent interactions in the C–S activation transition states, the optimized geometries of the representative species are given in Fig. 5 (please see ESI† for more details about the other structures).

Table 2 The C–S bond activation free energy (ΔG^≠, kcal mol⁻¹), enthalpy (ΔH^≠, kcal mol⁻¹), and entropy (ΔS^≠, cal (mol K)⁻¹) for 1–34

Thioester	1	2	3	4	5	6	7	8	9
ΔG^≠	20.08	20.21	22.43	21.60	22.38	20.70	20.14	23.39	20.57
ΔH^≠	3.55	3.85	5.01	3.63	4.91	2.43	2.50	4.14	3.39
ΔS^≠	−55.43	−54.88	−58.42	−60.26	−58.60	−61.28	−59.16	−64.56	−57

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Thioester	10	11	12	13	14	15	16	17	18
ΔG^≠	21.06	20.89	18.48	20.27	16.15	16.71	17.93	14.10	16.97
ΔrH^≠	2.90	2.57	0.64	1.41	−1.64	−0.60	−1.19	−2.69	−1.05
ΔS^≠	−60.92	−61.44	−59.85	−63.83	−59.67	−62.17	−60.04	−56.32	−60.47

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Thioester	19	20	21	22	23	24	25	26	27
ΔG^≠	17.05	17.33	16.36	15.40	19.71	18.68	19.29	15.80	17.59
ΔH^≠	−0.18	−1.32	−0.60	−0.88	1.89	−0.46	−1.34	−2.57	−1.48
ΔS^≠	−57.82	−62.58	−56.90	−54.62	−59.78	−64.18	−69.20	−61.62	−63.95

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Thioester	28	29	30	31	32	33	34
ΔG^≠	15.76	15.84	15.93	16.60	15.60	16.92	15.95
ΔH^≠	−2.57	−2.19	−2.07	−1.69	−2.33	−1.70	−1.66
ΔS^≠	−61.50	−60.49	−60.36	−61.35	−60.16	−62.44	−59.08

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Fig. 4 The linear correlation plot between ΔG^≠ and ΔH^≠ values.

Fig. 5 The optimized structures of 1-TS, 6-TS, 14-TS and 30-TS. The bond lengths are in angstrom.

From Fig. 5, it can be seen that all these transition states correspond to the three-membered ring structures. Comparing the structures with different types of R¹ and R² groups (alkyl or aryl), we found that the Pd–C, C–S and S–Pd bond distances all change a lot. The change of alkyl to aryl in either R¹ or R² causes shortening of the C–S bond distance in the transition state. This behaviour can be interpreted from the following two aspects. First, the aryl substituents increase the electron density between C and S atoms in the thioester group. Second, the steric effect of the aromatic group disfavours the approaching of the Pd(PPh₃)₂ group, leading to the relatively longer Pd–C and Pd–S bond distances. Meanwhile, regarding the relative activation barriers of these transition states, the introduction of the aryl substituents on the thiol group enables the d–π* conjugations between the Pd(d) orbital and the π* orbitals of the aryl group. Therefore, the relative activation energy of the substrate with the aromatic R² group is significantly lower than that of the thioester with the alkyl R² group. In addition, the para-electron-withdrawing group (such as –NO₂) tends to lower the π* orbital, leading to the strengthened d–π* conjugation and the lowered activation barrier (such as 14-TS vs. 17-TS).

2.3 Δ_rH and Δ_rG values

In addition to the above-mentioned results, the enthalpy changes and free energy changes of the oxidation-addition processes were also calculated to investigate the relationship between the Δ_rH (the reaction enthalpy change, Δ_rH = H(n-P) − H(n) − H(PdL₂)) and Δ_rG (the reaction free energy change, Δ_rG = G(n-P) − G(n) − G(PdL₂)). Similar to the discussions on bond dissociation energy and the activation energy, the calculation results in Table 3 also indicate that the C–S activation of the aromatic R² substituted thioesters (14–34) is thermodynamically more facile than the alkyl R² substituted ones (1–13) in both reaction enthalpy and free energy change. The d–π* conjugation might be mainly responsible for the higher stability of the products with the R² aryl substituents. Interestingly, according to the linear correlation between Δ_rG and Δ_rH (Fig. 6), despite the square deviation (SD) is relatively larger than those in Fig. 3 (BDE vs. BDFE) and Fig. 4 (ΔG^≠ vs. ΔH^≠), a good linear correlation coefficient (R = 0.9822) has been gained. In this context, the average entropic change for the oxidative addition of all these examined substrates is −61.4 cal (mol K)⁻¹.

Table 3 The reaction enthalpy (Δ_rH, kcal mol⁻¹), Gibbs free energy (Δ_rG, kcal mol⁻¹) and entropy change (Δ_rS, cal (mol K)⁻¹) of the thioester with Pd(0)L₂

Thioester	1	2	3	4	5	6	7	8	9
ΔrG	17.49	17.20	16.68	18.53	16.99	17.39	17.89	20.48	16.98
ΔrH	1.08	1.19	0.41	0.38	−0.39	0.31	0.43	2.13	0.73
ΔrS	−55.03	−53.71	−54.57	−60.88	−58.29	−57.27	−58.57	−61.51	−54.50

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Thioester	10	11	12	13	14	15	16	17	18
ΔrG	18.30	18.34	16.73	16.59	9.57	10.78	11.76	6.03	11.33
ΔrH	0.77	0.23	−0.98	−1.98	−8.37	−7.66	−6.64	−13.33	−7.56
ΔrS	−58.81	−60.73	−59.41	−62.84	−60.17	−61.85	−61.70	−64.95	−63.36

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Thioester	19	20	21	22	23	24	25	26	27
ΔrG	13.23	9.80	9.83	10.55	12.40	8.38	10.24	4.86	12.49
ΔrH	−6.09	−9.15	−8.32	−6.68	−6.80	−9.37	−8.64	−14.29	−6.76
ΔrS	−64.80	−63.59	−60.88	−57.82	−64.40	−59.52	−63.34	−64.26	−64.57

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Thioester	28	29	30	31	32	33	34
ΔrG	9.89	10.63	10.27	12.40	6.24	11.57	10.85
ΔrH	−9.67	−7.35	−9.49	−6.75	−14.40	−8.87	−8.69
ΔrS	−65.59	−60.29	−66.27	−64.22	−69.21	−68.57	−65.55

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Fig. 6 The linear correlation plots between Δ_rG and Δ_rH values.

From the good linear correlations of BDE vs. BDFE, ΔG^≠ vs. ΔH^≠ and Δ_rG vs. Δ_rH, we noted that the entropic changes in each of these processes show little dependence on the substituents of the substrates. For a better view, the entropic changes in C–S bond dissociation (ΔS, Table 1 and Fig. 3), the C–S activation (ΔS^≠, Table 2 and Fig. 4) and the oxidation-addition reaction processes (Δ_rS, Table 3 and Fig. 6) are listed in Table 4.

Table 4 The entropy changes of the C–S bond cleavage process (ΔS, cal (mol K)⁻¹), C–S bond activation process (ΔS^≠, cal (mol K)⁻¹) and oxidation-addition process (Δ_rS, cal (mol K)⁻¹), respectively. The Pd–S bond dissociation enthalpies (BDE_Pd–S, kcal mol⁻¹) of products are also list

Thioester	1	2	3	4	5	6	7	8	9
ΔS	42.60	45.69	44.12	37.97	42.25	42.22	44.78	43.44	43.06
ΔS^≠	−55.43	−54.88	−58.42	−60.26	−58.60	−61.28	−59.16	−64.56	−57.63
ΔrS	−55.03	−53.71	−54.57	−60.88	−58.29	−57.27	−58.57	−61.51	−54.50
BDEPd–S	53.62	54.20	54.98	54.41	55.82	53.30	53.56	52.05	53.49

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Thioester	10	11	12	13	14	15	16	17	18
ΔS	42.90	42.02	45.13	44.77	44.73	44.23	42.33	44.53	43.42
ΔS^≠	−60.92	−61.44	−59.85	−63.83	−59.67	−60.04	−62.17	−56.32	−60.47
ΔrS	−58.81	−60.73	−59.41	−62.84	−60.17	−61.85	−61.70	−64.95	−63.36
BDEPd–S	52.76	53.73	52.48	56.35	53.55	52.08	49.77	60.39	51.94

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Thioester	19	20	21	22	23	24	25	26	27
ΔS	44.65	43.59	44.44	43.34	43.43	43.17	41.27	43.61	46.20
ΔS^≠	−57.82	−62.58	−56.90	−54.62	−59.78	−64.18	−69.20	−61.62	−63.95
ΔrS	−64.80	−63.59	−60.88	−57.82	−64.40	−59.52	−63.34	−64.26	−64.57
BDEPd–S	47.17	54.68	53.47	49.66	52.98	54.76	53.26	61.58	41.75

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Thioester	28	29	30	31	32	33	34
ΔS	41.54	44.81	44.09	43.53	44.19	44.56	44.32
ΔS^≠	−61.50	−60.49	−60.36	−61.35	−60.16	−62.44	−59.08
ΔrS	−65.59	−60.29	−66.27	−64.22	−69.21	−68.57	−65.55
BDEPd–S	50.72	52.37	53.25	49.71	60.08	52.58	53.23

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Herein, it worth noting that the BDE_Pd–S of the products are about 52.00 kcal mol⁻¹ except for 17-P, 26-P and 32-P (with the para-nitrate substituted aromatic R² groups, Table 4). In 17-P, 26-P and 32-P, the BDEs are relatively higher than those of the other complexes due to the stronger d–π* conjugations.

2.4 The relationships between ΔG^≠ and BDE, Δ_rH, Δ_rG

Based on the above calculation results, the structure–activity relationships in the Pd catalysed C–S activation of thioesters was finally examined. Similar to our previous studies on a series of Cu catalysed C–H activation processes,³⁷ we first examined the relationship between activation free energy and BDE gap of the substrates (i.e. the energy difference between the Pd–S BDE in n-Prod and the C–S BDE in n, n = 1–34). From Fig. 7, it can be seen that almost no linear relationship exists between ΔG^≠ and the BDE gap (R = 0.7718). Therefore, the result is different from that of the Cu catalysed C–H bond activation.^36,37 Nonetheless, as the thioesters can be roughly categorized into two types (regarding to the alkyl or aryl R² groups), the change from alkyl to aryl R² causes both the lower ΔBDEs and the ΔG^≠ values. Meanwhile, the ΔBDEs and the ΔG^≠ thioesters with the NO₂-substituted aromatic thiol groups are relatively lower than the other aromatic thiolesters.

Fig. 7 Relationship between ΔG^≠ and ΔBDE (BDE[Pd–S] − BDE[C–S]).

Finally, the relationships between ΔG^≠ and Δ_rH/Δ_rG were investigated (Fig. 8). Compared to BDEs and BDE gaps, the correlation between Δ_rH or Δ_rG and ΔG^≠ is significantly better. The linear correlation coefficients are 0.8591 and 0.8640, respectively, indicating that the reaction energy (free energy or enthalpy) changes could act as a better reference (than BDEs) in evaluating the activity of the C–S bonds of thioesters. Nonetheless, the standard deviations are both 1.3 kcal mol⁻¹, indicating that these data should be used with caution.

Fig. 8 The linear correlation plots between ΔG^≠ and Δ_rG, Δ_rH, respectively.

3. Conclusions

With the aid of density functional theory (DFT) methods, the C–S activation step of thioesters promoted Pd(0) complex (i.e. Pd(PPh₃)₂) were systematically studied. 34 structurally independent thioesters (R¹C(O)SR²) were chosen as the samples. To investigate the structure–activity relationship, the C–S bond activation free energy (ΔG^≠), C–S bond dissociation enthalpy energy (BDE), the bond dissociation free energy (BDFE), the reaction free energy changes (Δ_rG), and enthalpy changes (Δ_rH) of the oxidation-addition process were examined. Some novel insights into the C–S activation step are gained:

(1) Strong linear correlations have been located for BDE vs. BDFE, ΔG^≠ vs. ΔH^≠ and Δ_rG vs. Δ_rH. Therefore, the entropic changes in C–S bond dissociation (of the thioester substrates) and the C–S activation (in both kinetic and thermodynamic aspects) are insensitive to the substituents on the substrates.

(2) The linear correlation between ΔG^≠ and BDE/BDFE or ΔBDE (BDE[Pd–S] − BDE[C–S]) is very weak. This result is different from that of the transition metal (Pd or Cu) catalysed C–H bond activation. By contrast, ΔG^≠ show a rough linear relationship with the reaction energies (Δ_rG or Δ_rH), implying that the thermodynamic facilities can be roughly used to evaluate the kinetic facilities in the C–S activation processes.

(3) The substituent on the carbonyl group hardly influences the C–S bond strength in the thioester substrates and the C–S activation processes. By contrast, both these two processes are sensitive to the substituents on the thiol group of the thioesters. The aromatic thiol group results in the easier C–S bond dissociations and C–S activations (in both kinetic and thermodynamic aspects) compared to the alkyl thiol group.

4. Calculation methods

According to our recent theoretical studies, M06-2X is a reliable DFT method in predicting the physical chemical parameters (such as pK_a and BDEs) of S-containing molecules and studying the mechanism of the transition metal catalysed C–S activations.^41–43 Therefore, M06-2X method was used for calculations in this study. Meanwhile, the LanL2DZ basis set was used for Pd,^28,44–47 and the standard Pople all electron basis set of 6-31G(d) was used for the other atoms. In accordance with the previous experimental studies,²⁵ several groups of R¹COSR² thioesters (regarding the type of R¹ and R²) were chosen for the discussions. As shown in Fig. 1, the R¹ and R² substituents could be alkyl–alkyl (1–5), aryl–alkyl (6–13), alkyl–aryl (14–29) and aryl–aryl groups (30–34). Note that the solvent effect has also been examined by calculating the single point energies on the gas-phase optimized structures with the SMD model^48,49 and tetrahydrofuran solvent (THF, ε = 7.4257).⁵⁰ The additional calculations show the same trend with the gas phase calculations, and the details are provided in the ESI.†

Throughout this study, the gas-phase calculation results are used for discussions. All these calculations were carried out using the Gaussian 09 program.⁵¹

Acknowledgements

We thank scientific research funds of Anhui University (J01006021) for financial supports, the Shanghai Supercomputer Centre for technical support and National Supercomputing Centre in Shenzhen for providing the computational resources and Gaussian 09 (version D01).

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Footnote

† Electronic supplementary information (ESI) available. See DOI: 10.1039/c6ra12607c

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