First-Principles Molecular Dynamics Analysis of Ligand-Free Suzuki

Article pubs.acs.org/JPCC

First-Principles Molecular Dynamics Analysis of Ligand-Free Suzuki− Miyaura Cross-Coupling in Water: Transmetalation and Reductive Elimination Teruo Hirakawa,*,† Yuta Uramoto,† Susumu Yanagisawa,‡ Takashi Ikeda,§ Kouji Inagaki,†,∥ and Yoshitada Morikawa*,†,∥,⊥ †

Department of Precision Science and Technology, Graduate School of Engineering, Osaka University, 2-1, Yamada-oka, Suita, Osaka 565-0871, Japan ‡ Department of Physics and Earth Sciences, Faculty of Science, University of the Ryukyus, 1 Senbaru, Nishihara, Okinawa 903-0213, Japan § Synchrotron Radiation Research Center, Quantum Beam Science Research Directorate, National Institutes for Quantum and Radiological Science and Technology (QST), 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan ∥ Elements Strategy Initiative for Catalysts and Batteries (ESICB), Kyoto University, Katsura, Kyoto 615-8520, Japan ⊥ Research Center for Ultra-Precision Science and Technology, Graduate School of Engineering, Osaka University, 2-1, Yamada-oka, Suita, Osaka 565-0871, Japan S Supporting Information *

ABSTRACT: We investigated the transmetalation step of the Suzuki−Miyaura cross coupling reaction (SMR) catalyzed by ligand-free Pd atom or Pd-X− (X = Cl or Br) using first-principles molecular dynamics simulations with an explicit solvent model. When starting from the single Pd atom, the halogen anion bound to the Pd was not replaced by organoboronate species and instead remained bound to the Pd throughout the transmetalation step. However, when starting from the Pd-X− catalyst, one of the two halogen anions was released from the first coordination sphere of the Pd during transmetalation. Therefore, the products after the transmetalation starting with either the single Pd atom or the PdX− were the same. We concluded that Pd-X− is the active species of the ligand-free Pd catalyst for the SMR. The overall activation free energies for transmetalation and reductive elimination were relatively low, estimated to be at most, 8.1 kcal/mol for X = Br and 8.4 kcal/mol for X = Cl, respectively, leading to the efficient turnover of the SMR. We ascribe the origin for the suppression of the catalytic reactivity of the ligand-free SMR for PhCl to the larger activation barrier in the oxidative addition step, which causes the aggregation of Pd catalysts.

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INTRODUCTION The Suzuki−Miyaura cross coupling reaction (SMR) is one of the most useful catalytic reactions in synthetic chemistry.1−8 In the SMR, an sp2−sp2 C−C bond of a biaryl is formed with high selectivity between an organic electrophile (R1-X) and an organometallic nucleophile ([R2-B(OH)3]−) in the presence of a palladium catalyst and a base under mild conditions. The reaction consists of three steps, namely, oxidative addition, transmetalation, and reductive elimination (see Figure 1 for the reaction in which both R1 and R2 are Ph). In the conventional SMR, a phosphine-ligated Pd complex is typically used and thoroughly investigated to improve the stability and the reactivity of the Pd catalyst.1−29 Recently, as a remarkable improvement that has attracted enormous interest, a phosphine-ligand-free SMR in water was developed to improve the catalytic turn over number (TON), which can reach 399000/Pd when PhBr as one of the reactants and the © XXXX American Chemical Society

palladium-containing perovskites as the Pd-catalyst resource are used.30−33 Furthermore, Arisawa et al. reported a higher TON of up to 2760000/Pd using sulfur-modified Au-supported Pd (SAPd).34,35 Note that when aryl chloride is used instead, the catalytic reactivities of the ligand-free Pd catalysts are as low as those with phosphine ligands in the conventional SMR.30 For rational designing of new catalysts, it is necessary to clarify the reaction mechanism and important factors controlling the reactivity of the catalysts of interest. The reactive form of the Pd catalysts in the phosphine-ligand-free SMR is still under debate. Andrews et al. showed that catalytically ractive Pd species dissolved from the palladiumcontaining perovskite into the water solvent.31 Reetz et al. and de Vries et al. proposed the leaching mechanism of the reactive Received: July 15, 2017

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DOI: 10.1021/acs.jpcc.7b06972 J. Phys. Chem. C XXXX, XXX, XXX−XXX

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The Journal of Physical Chemistry C

Figure 2. Relationship between pathways A and B of the transmetalation step.

boronic acid to form an organoboronate, while pathway B is initiated by substituting an OH− for the halogen atom X in the coordination of the Pd catalyst. Pathway A has been theoretically supported by the Maseras group,12,13,53 whereas pathway B has been supported by both experiments using kinetic analysis and theoretical research.54−57 The Maseras group claimed that while pathway A and pathway B are competitive, the former has lower energy barriers than the latter by approximately 8 kcal/mol.27 Therefore, the boronate pathway (A) is faster. They also attempted to reproduce experimental observations using kinetic analysis and claimed that their theoretical report is consistent with the experimental observations. Here, we examine the reaction mechanism of the transmetalation in the phosphine-ligand-free SMR to clarify the reactivity of a single Pd atom catalyst and a Pd-X− catalyst when PhBr and PhCl are used as the reactants. The single Pd atom catalyst is assumed as the simplest model for the ligand-free Pd catalyst. In this study, we also assumed that the pathway A is the most favorable pathway for transmetalation. It is important to compare the pathways A and B on an equal footing using the same methodologies. There is, however, some difficulty in choosing reaction coordinates for the pathway B in water solvent and therefore, we leave this issue for our future work. In the ligand-free SMR, water molecules can be directly bound to the Pd catalyst as a supporting ligand, which affects the catalytic activity of the Pd catalyst. Therefore, we adopted an explicit solvent model to accurately evaluate the effects of both the ligand and the solvent. We also investigated the reactivity of the reductive elimination, following transmetalation.

Figure 1. General cycle of the SMR, where PhX and PhB(OH)2 are the two reactants, X is a halogen atom, and Ph−Ph is the product. PhB(OH)2 becomes [PhB(OH)3]− in alkaline solutions.

Pd(0) catalyst, in which Pd atoms or clusters are extracted from palladium nanoparticles during the oxidative addition of PhX (X = Cl, I) to the catalyst for the ligand-free Heck reaction.36,37 de Vries and co-workers38 investigated the structure of the ligand-free Pd catalyst for Heck reaction using electrospray ionization mass spectrometry (ES-MS) and extended X-ray absorption fine structure (EXAFS) analysis. They identified [PhPdX2]− (X = I or Cl) as an intermediate, suggesting that a halogen anion X− (X = I or Cl) is ligated to the Pd catalyst as a supporting ligand, as originally proposed by Amatore and Jutand for phosphine-ligated Pd catalysts.39 We recently investigated the oxidative addition step of PhX to a ligand-free single Pd atom catalyst and a single-atom catalyst with a halogen anion, Pd-X− (X = Br or Cl), using firstprinciples molecular dynamics (FPMD) simulations in which water molecules were explicitly taken into account.40 The activation free energy for the oxidative addition of PhBr to a single Pd catalyst or Pd−Br− catalyst was calculated to be 3.4− 5.1 kcal/mol, indicating that the reaction proceeds quite readily in mild conditions. After the oxidative addition, a PhPdBr complex or a [PhPdBr2]− complex is formed. We also showed that after forming these complexes, the aggregation of Pd is suppressed. These properties are likely the origin of the high TON of the Pd catalysts. On the other hand, when PhCl is used as the reactant, the activation free energy was calculated to be 8.4−8.5 kcal/mol, indicating that the lifetime of the η2 complex of Pd, which is formed before the oxidative addition, should be much longer than that of PhBr. Furthermore, we showed that if the Pd catalysts remain in the form of η2 complexes, aggregation is not suppressed, indicating that, for PhCl, Pd single-atom catalysts may suffer from catalyst aggregation. Although in the SMR the rate-determining step is often considered to be oxidative addition or substitution of phosphine ligand by PhX,4,21,41−43 some studies have reported that the rate-determining step is transmetalation.32,44−52 Therefore, transmetalation is an important reaction, which has attracted much interest and several researchers have attempted to clarify the mechanism for the conventional SMR with phosphine-ligated catalysts.12,13,24,46,53−57 Transmetalation is the most complicated step among the three steps of the SMR, and two competitive pathways have been discussed, namely, the boronate mechanism (pathway A) and the palladium-hydroxo mechanism (pathway B; see Figure 2).24,46 Pathway A is initated by an OH−, binding to the

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METHODS All electronic structure calculations for FPMD were based on density functional theory (DFT) within the generalized gradient approximation (GGA-PBE), as implemented in the STATE-Senri code.58 We used ultrasoft pseudopotentials and a plane-wave basis set with cutoff energies of 25 and 225 Ry for the wave functions and charge densities, respectively. We performed FPMD simulations of the transmetalation step in the phosphine-ligand-free, palladium-catalyzed SMR in water. Only Γ point was used for the Brillouin zone sampling. Constanttemperature simulations were performed with a time step of 0.75 fs. We used the mass of deuterium for all H atoms in the system. A Nosé−Hoover chain with a chain length of eight was used, and the temperature target was set to 400 K. Because GGA-PBE tends to overstructure liquid water, the target temperature was set approximately 60 K higher than that in the experiments to mimic the real dynamics of water. The supercell size used in all calculations was 14.21 Å × 14.21 Å × 14.21 Å, and the three-dimensional periodic boundary condition was B


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The Journal of Physical Chemistry C imposed. In the supercell, 96 water molecules were included at the density of 1.0 g/mL. To accurately estimate the free energy barriers for transmetalation and reductive elimination in water, we used the blue moon ensemble (BME) method with constrained MD, in which the mean force was evaluated as a function of an arbitrary reaction coordinate ξ = ξ(r).59,60 The definition of the constraint for each elementary reaction step is given in the Results. We took 2000−4000 steps (total time: 1.5 ps -3.0 ps) for equilibration and then sampled over 5000 MD steps (total time: 3.75 ps) for taking the average of the constraint force. After we took sampling for one ξ value, we moved to the next by decreasing or increasing slightly ξ value depending on the reaction being considered. In calculations of the free energy profiles with the constrained MD, the error was estimated by the method of Jacucci and Rahman, using the concept of the correlation length between those samples.61,62 The coordination number of Pd with respect to the water oxygen CNPd−OW and the boronate oxygen CNPd−OB are defined as N

CNPd − Oi =

∑ i=1

dPd − Oi 8

( ) 1−( ) 1−

d0

dPd − Oi 16 d0

where dPd−Oi is the distance between Pd atom and Oi atom; d0 = 2.6; N is the number of the O atom belonging to the water molecules or the O atom belonging to the boronate molecule in the system, respectively. All structures for static calculations were fully optimized with the PBEPBE and the hybrid B3LYP density functionals as implemented in Gaussian09.63−67 We employed the same computational conditions as those of Braga’s calculations.13 For Pd and Br atoms we used LANL2DZ basis set, which describes the inner and outer electrons using an effective core potential and double-ζ basis set, respectively. For Br, d-polarization functions (exponent 0.4280) are included.68 For H, B, C, O, and P, 6-31+G(d) basis set is used.69 Diffuse function is also added for Br. Solvent effects were introduced by using the polarizable continuum model (PCM) solvation model on gas phase optimized geometries.

Figure 3. Relative free-energy profiles for the formation of an η2 consisting of [PhPdX] and [PhB(OH)3]− in water calculated from FPMD-based BME sampling. The upper panels: snapshots of the reaction process in water. The orange double-headed arrows represent the constrained coordinate ξ = d1. Atom colors are black for Pd, cyan for Br, gray for C, pink for B, red for O, and white for H. The lower panel: the free-energy profiles (upper graph) and CNPd−OW and CNPd−OB (middle and lower graphs for X = Br and for X = Cl, respectively). The solid red and black lines in the upper graph represent the free-energy profiles for X = Br and for X = Cl, respectively. Dashed maroon and green (magenta and blue) lines in the middle graph represent CNPd−OW (CNPd−OB) for X = Br and X = Cl, respectively. The vertical bars are the standard deviation of the estimated free energies and the coordination numbers, respectively.

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groups of [PhB(OH)3]− (upper-middle panel of Figure 3), and then, finally, a η2 complex is formed (upper-right panel of Figure 3). As shown in the lower panel of Figure 3, the process is practically barrierless and significantly exothermic, which is in good agreement with the results of the theoretical research by the Braga group.13 In contrast to transmetalation with phosphine-ligated Pd catalysts, however, the halogen anion is not replaced with the boronate anion, and instead, the H2O molecule bound to Pd is released from the Pd coordination sphere. Therefore, the halogen anion remains bound to the Pd atom in the ligand-free single Pd atom catalyst during transmetalation. To understand why the H2O molecule, rather than the halogen anion, is released from the Pd catalyst, we calculated the Br− anion dissociation process starting from the final state of Figure 3 in water. As Br−−Pd bond length increases, one water molecule approaches to Pd, substituting for Br−. In the process, it was found that the dissociation of the Br− anion into water is strongly endothermic by 17 kcal/mol, as shown in Figure 4. The energy surface is uphill, meaning the reverse

RESULTS Binding Process of PhPdX with [PhB(OH)3]−. According to our previous study, PhPdX is formed after the oxidative addition of PhX to a single Pd atom catalyst. Therefore, for the initial step of transmetalation, we investigated the binding of PhPdX with [PhB(OH)3]− to form an η2-complex in the water solvent. In the simulation of this step, we placed PhPdX, [PhB(OH)3]−, and 82 H2O molecules with a positive background charge in the simulation box, and we chose the bond length between the Pd atom and the first CAr carbon atom in the benzene ring of [PhB(OH)3]− (d1, shown in the upper-left panel of Figure 3) as ξ. As shown in the upper-left panel of Figure 3, PhPdX in water takes a square planar form, namely, PhPdX(H2O)2, where two H2O molecules are coordinated to the Pd atom and the phenyl group and the halogen atom are located in a cis position to each other because of the strong trans-influence of the two substituents. As PhPdX and [PhB(OH)3]− approach each other, one of the H2O molecules bound to Pd is replaced with one of the hydroxyl C


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isomers of PhPdBr(H2O)2, which are formed after the oxidative addition of PhBr. In these calculations, we did not use explicit water solvent but instead calculated these complexes in water PCM by using Gaussian. We notice that PBEPBE in the Gaussian corresponds to GGA-PBE. Structure 1A is the initial state in the binding process by using BME. 1B, an isomer of 1A is less stable by 6.8 kcal/mol in PBEPBE (5.9 kcal/mol in B3LYP) due to the stronger trans-influence of the phenyl group than that of H2O, indicating that isomer 1B is unlikely to form.70 Furthermore, in isomer 1A, the halogen atom is located trans to H2O and, therefore, it is not released easily because the trans-influence of H2O is much lower than that of the phosphine ligand. Indeed, we calculated the binding of [PhB(OH)3]− to the isomer 1A (1A to 1E in Figure 5), followed by the release of the Br anion from the Pd coordination sphere (1E to 1D in Figure 5). Our calculation clearly shows that the release of the Br anion from 1E is disfavored. In addition, the water molecule which is originally bound to the Pd atom is easily released into the water solvent (1A to 1X in Figure 5). The relative energies using the B3LYP shown by red are a bit different from those of the PBEPBE shown by black. The main conclusions, however, are not altered by the choice of the functional as discussed above. Binding Process of [PhPdX2]− with [PhB(OH)3]−. Next, we investigated the binding process of [PhPdX2]− to [PhB(OH)3]−, as the initial state of the transmetalation in the halogen-anion-ligated Pd atom catalyst. To simulate this process, we placed [PhPdX2]−, [PhB(OH)3]−, and 81 H2O molecules with positive background charges (+2e) in the simulation box. Although the background uniform charge is often used as a simple model to mimic the effect of counterions, inclusion of explicit counterions may affect the results. In the present study, however, we take this method and we present the results within this model because inclusion of explicit counterions makes the modeling of the reactions very complicated and significantly longer sampling of MD simulations are necessary. As ξ, we chose the distance difference of ξ = d3 − d4, where d3 is the bond length between the Pd atom and the first CAr atom in the benzene ring of

Figure 4. Relative free-energy profiles for the Br− dissociation from the Pd complex in water. The upper panel shows snapshots of the process. The constrained coordinate ξ is defined as ξ = d2, where d2 is the bond length between the Br atom and the Pd atom, shown with orange double-headed arrows. The lower panel shows the free-energy profiles (upper graph) and CNPd−OW (middle graph). The solid red line in the upper graph represents the free energy profile of the Br− dissociation from the Pd complex in water, where one H2O molecule replaces the Br− anion.

reaction occurs easily. Therefore, the dissociation of the Br− anion cannot be the major reaction path. This means the H2O molecule, rather than the halogen anion, is released from the Pd catalyst in the binding process of PhPdX with [PhB(OH)3]−. We also calculated the relative energies of the intermediate species in the transmetalation step to understand why the H2O molecule, rather than the halogen anion is released in this process. Figure 5 shows the relative stability of two different

Figure 5. Relative energy profiles for the binding process of PhPdBr(H2O)2 to [PhB(OH)3]−. Energy of each structure relative to isomer 1A are shown in kcal/mol. The black and red values are calculated with PBEPBE and B3LYP, respectively. The solid blue arrows represent the coupling with the [PhB(OH)3]− along with the H2O dissociation. The solid green arrow represents isomerization from 1A. The solid purple arrow represents water molecule dissociation from the Pd atom. The solid red arrows represent Br− anion dissociation from the Pd atom. D


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Figure 6. Relative free-energy profiles for the binding of [PhPdX2]− with [PhB(OH)3]− in water. The upper panels: snapshots of the process. The constrained coordinate ξ is defined as ξ = d3 − d4, where d3 and d4 are shown by orange and green double-headed arrows, respectively. The lowerright panel: the free-energy profiles and the number of H2O (boronate) molecules coordinated to the Pd atom. The solid red and black lines in the upper graph represent the free-energy profiles for X = Br and for X = Cl, respectively. The dashed maroon (magenta) line in the middle graph represents CNPd−OW (CNPd−OB), the number of H2O (boronate) molecules coordinated to the Pd atom for X = Br, whereas the dashed green (blue) line in the lower graph represents for X = Cl, respectively. The lower-left panel: the profiles of bond lengths d3 and d4 during the reaction processes. The red and black dots represent the trajectories of d3 and d4 along the reaction coordinate for X = Br and X = Cl, respectively. The vertical and horizontal bars are the standard deviation of the estimated free energies, the coordination numbers, and the bond lengths, respectively.

[PhB(OH)3]− and d4 is the bond length between the Pd atom and one of the two Br atoms (see Figure 6). As shown in Figure 6, as the two anions ([PhPdX2]− and [PhB(OH)3]−) approach each other, the H2O molecule bound to Pd is replaced with one of the hydroxyl groups from [PhB(OH)3]− (IS0 in Figure 6) without any free energy barrier, similar to the process observed in the binding of [PhPdX] with [PhB(OH)3]−. The transition from the initial state to IS0 is exothermic, which is consistent with a theoretical study on the SMR with a phosphine-ligated Pd catalyst using the polarizable continuum solvent model.53 After the formation of the IS0 state, however, one of the two Br anions is dissociated from Pd and replaced with the Ph group of [PhB(OH)3]−, forming an η2 complex (IS1 in Figure 6). The activation free energy, which corresponds to the free energy difference between IS0 and TS1, is 3.3 kcal/mol for X = Br and 8.4 kcal/mol for X = Cl, indicating that the halogen anion dissociates at this reaction temperature. In the final structure of this process (IS1), the Pd center is tetracoordinated and forms a square planar complex chelated by the boronate anion. This structure is the same as the final structure of the first transmetalation step in the case of PhPdX (upper-right panel of Figure 3). Although the present process includes the bond formation of two negatively charged anions, namely, [PhPdX2]− and [PhB(OH)3]−, the free-energy profile shows a rather low activation barrier. One of the possible reasons for this result is that the water solvent can screen the electrostatic potential

quite efficiently because of its large dielectric constant. Another possible reason is that the two anions are already located close enough to each other due to the high concentration of anions in aqueous solutions. In the present computational model, the [PhPdX2]− and [PhB(OH)3]− anions along with 81 H2O molecules are included in the simulation box. This corresponds to approximately 0.58 mol/L [PhB(OH)3]−, which is similar to the concentration in experimental reactions reported in the literature.31,32 We also calculated the relative energies of the intermediate species in the transmetalation step to understand how the energy state differs between the explicit solvent model and the PCM solvent model. Figure 7 shows the relative stability of two different isomers of [PhPdBr2(H2O)]−, which are formed after the oxidative addition of PhBr. In these calculations, we calculated these complexes in the water PCM by using the Gaussian, where we employed the same computational conditions as those of Figure 5. Structure 2A is the initial state in the binding process by using BME. 2B, an isomer of 2A, is less stable by 5.0 kcal/mol using PBEPBE (4.7 kcal/mol using B3LYP) due to the stronger trans-influence of the phenyl group than that of H2O, indicating that isomer 2B is unlikely to be formed.70 2B may be converted easily to 2A in water solvent because a water molecule originally binding to the Pd atom is dissociated easily into the water solvent. We calculated the binding of [PhB(OH)3]− to the isomer 2A (2A to 2C in Figure 7), followed by the release of one of the two Br anions from the Pd coordination sphere (2C to 2D in Figure 7). Our calculation E


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Figure 8. Relative free-energy profiles for the formation of B(OH)3 from the η2 complex consisting of [PhPdX2]− and [PhB(OH)3]− in water calculated from the FPMD-based BME sampling. The upper panels: snapshots of the reaction process in water. The orange doubleheaded arrows represent the constrained coordinate ξ = d5, the bond length between the B atom and C1, the first carbon atom of the phenyl boronate. The lower panel: The solid red (black) line represents the free energy profile for X = Br (for X = Cl). The dashed maroon (magenta) line represents θ∠C1PdB for X = Br (for X = Cl). The dashed blue (green) line represents dPd−C1 for X = Br (for X = Cl). The vertical bars are the standard deviation of the estimated free energies, the angles and the bond lengths, respectively.

Figure 7. Relative energy profiles for the binding of [PhPdBr2(H2O)]− to [PhB(OH)3]−. Energy of each structure relative to isomer 2A are shown in kcal/mol. The black and red values are calculated with PBEPBE and B3LYP, respectively. The solid blue arrows represent the coupling with the [PhB(OH)3]−, replacing the H2O. The solid green arrow represents isomerization from the original structure. The solid red arrows represent Br− anion dissociation from the Pd atom.

by the Gaussian clearly shows that the release of the Br anion from 2C is disfavored, whereas that of the BME calculation ((ii) to (iv) in Figure 6) is favored. 2C in the PCM is more stable than 2A by 13.4 kcal/mol, whereas this energy difference is calculated to be 2.4 kcal/mol by using BME, as seen in Figure 6, indicating that the binding energy between the anionic Pd complex and the anionic boronate is overestimated by the PCM. This discrepancy indicates the limitation of the PCM to describe the binding process of ions in water solvent, because the PCM cannot account for chemical interactions between solvent molecules and an ionic solute molecule.71−76 Phenyl-Boric Acid Bond Dissociation. After the formation of the [PhPdXPhB(OH)3]− complex (IS1), the boric acid (B(OH)3) remains bound to both the Pd through one of the three oxygen atoms and to the phenyl group. In the next step, the bond between the C atom of the phenyl ring and the B atom of the boric acid should break and a σ-bond between Pd and the first C atom of the benzene ring should form. To simulate this process, we placed the final complex, [PhPdXPhB(OH)3]− and 82 H2O molecules with a positive background charge in the simulation box and imposed the constraint ξ = d5, where d5 is the bond length between the boron atom and the carbon atom of the benzene ring (see upper-left panel of Figure 8). Figure 8 shows the free-energy profile of this process. We found that in the range of 1.7 ≤ ξ = d5 ≤ 3.5, the B−CAr bond is broken to generate a Pd−CAr σ-bond and B(OH)3 is formed through a transition state with a relative free energy of 8.1 kcal/ mol when X = Br and 7.1 kcal/mol when X = Cl. This process is exothermic, and the reaction energy is −10.7 kcal/mol when X = Br and −16.0 kcal/mol when X = Cl. Although B(OH)3 is formed, an O atom from one of its hydroxyl groups is still

bound to the palladium atom. The palladium metal center is bound to an O atom from boric acid, two phenyl groups and a halogen anion X−, forming a square planar complex as the second stable intermediate of the transmetalation step (IS2 in Figure 8). Loss of B(OH)3. After the transmetalation, the boric acid is bound to the Pd atom. We investigated the boric acid dissociation from the Pd complex, [Ph2PdBrB(OH)3]− (release of the B(OH)3). To simulate this process, we placed [Ph2PdBrB(OH)3]− and 82 H2O molecules with a positive background charge in the simulation box and imposed the constraint ξ = d6, where d6 is the bond length between the boron atom and the Pd atom (see upper-left panel of Figure 9). Figure 9 shows the free-energy profile of this process. We found that in the range of 2.5 ≤ ξ = d6 ≤ 6.7, the B−CAr bond is broken to generate a Pd−CAr σ-bond and B(OH)3 is released through a transition state with a relative free energy of 2.4 kcal/ mol, and the final state (IS3) is a little more stable than the initial state (IS2) by 3.0 kcal/mol. After this process, B(OH)3 is replaced with one water molecule, indicating that the exchange between B(OH)3 and a water molecule is rather easy. As the final step, the palladium metal center is coordinated by one water molecule, two phenyl groups, and a halogen anion Br−, still forming a square planar complex (the right upper panel in Figure 9). We did not investigate this process for the case of X = Cl. We, however, expect that the process should occur as easily as the case of X = Br. Reductive Elimination. As the final step in the catalytic process of the SMR, we investigated the reductive elimination F


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Figure 9. Relative free-energy profiles for the release of B(OH)3 from the four-coordinated Pd complex. The upper panels: snapshots of the reaction process in water. The orange double-headed arrows represent the constrained coordinate ξ = d6, the bond length between the Pd atom and the B atom of the boric acid for BME sampling. The lower panel: The solid red line represents the free energy profile of the B(OH)3 dissociation from the Pd complex in water, where one H2O molecule binds instead of the boric acid. The dashed maroon (magenta) line represents CNPd−OW (CNPd−OB), the number of H2O (boric acid) molecules coordinated to the Pd atom. The vertical bars are the standard deviation of the estimated free energies and the coordination numbers, respectively.

step. The final state of the transmetalation step, namely, the [PhPdXPh(H2O)]− complex (IS3), was taken as the initial structure for reductive elimination. To simulate the reductive elimination step, we placed the [PhPdXPh(H2O)]− complex and 85 H2O molecules with a positive background charge in a unit cell. We imposed the constraint ξ = θ1, where θ1 is the angle ∠C1PdC′1, where the C1, C′1 are the two first carbon atoms of the two benzene rings that are directly bound to the central Pd atom (see upper-left panel of Figure 10). Initially, the palladium complex has a square planar structure composed of two Pd−CAr bonds with η1 coordination, where the two phenyl groups are cis from each other. As shown in Figure 10, the tetra-coordinated palladium center is transformed to a tricoordinated, trigonal planar structure when one H2O molecule is released from the palladium catalyst into the water solvent. The process is exothermic, and the reaction energy is −20.9 kcal/mol when X = Br and −23.8 kcal/mol when X = Cl. To see the change of the oxidation state of Pd in the reductive elimination process, we also calculated atomic orbital local density of states (AO LDOS) for (i), (ii), and (iv). In the beginning of the reductive elimination process, Pd takes the square planar form of complex as shown in the upper-left panel of Figure 11, which is denoted by (i) IS3. In this complex, Pd is coordinated by two phenyl groups, one halogen anion and one water molecule. Therefore, dx2−y2 orbital hybridize with those ligands strongly and is pushed up above the Fermi level as antibonding orbital, which is clearly seen in the lower panel of Figure 11. In the intermediate state (denoted by (ii) in Figure 11), Pd forms tricoordinated complex, coordinated by two phenyl groups and one halogen anion. In

Figure 10. Relative free-energy profiles for the reductive elimination in water from the four - coordinated palladium complex. The upper panels: snapshots of the reaction process in water. The orange doubleheaded arrows represent the constrained coordinate ξ = θ1 is the angle of ∠C1PdC1′ for BME sampling, where C1 (C1′ ) is the first carbon atom belonging to one (the other) of the benzene rings. The lower panel: the solid red (black) line represents the free energy profile of the reductive elimination for X = Br (X = Cl). The dashed maroon, green, and orange lines represent dC1−C′1, the bond length between C1 and C′1, dPd−C1, the bond length between Pd and C1, and dPd−C′1, the bond length between Pd−C1′ , respectively, for X = Br. The dashed magenta, brown, and blue lines represent dC1−C′1, dPd−C1, and dPd−C′1 for X = Cl in the same way, respectively. The light green (purple) line represents CNPd−Ow, the number of H2O molecules coordinated to the Pd atom for X = Br (X = Cl). The vertical bars are the standard deviation of the estimated free energies, the bond lengths, and the coordination numbers, respectively.

this complex, Pd dxy orbital hybridize with those ligands strongly, and is pushed up above the Fermi level as an antibonding level (see in the lower panel of Figure 11). In the final state (denoted by (iv) in Figure 11), Pd is coordinated by two ligands, namely, biphenyl and one halogen anion. The hybridization between Pd and those ligands is rather weak, and no significant peak except s + p orbitals are observed in the empty state in the lower panel of Figure 11. These results clearly indicate that the oxidation state of Pd is +2 in the cases of (i) and (ii), while that of (iv) is 0. G


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by a leaching mechanism, in which Pd atoms or clusters are extracted by the reactants.36,37,77−79 In our recent work, we investigated the oxidative addition of Ph-X to a single Pd atom catalyst or Pd catalyst with a bound halogen anion (PdX−; X = Cl or Br) in aqueous solution using FPMD simulations and found that the activation barriers are similar for both types of catalysts.40 Therefore, both a single Pd atom and PdX− are possible candidates for the reactive species in the ligand-free SMR. Next, we investigated the transmetalation step for the two catalysts. It has been reported that for conventional phosphine-ligated Pd catalysts, there are two competing paths for transmetalation, and the preferable path is the boronate pathway A, in which OH− is bound to boronic acid to form an organoboronate. Then, the organoboronate attacks the aryland halogen-bound Pd catalyst produced in the oxidative addition step and is substituted for the halogen, as shown in Figure 1. For the single Pd atom catalyst, however, the halogen anion is not released when the organoboronate binds to the Pd catalyst (see Figure 3). On the other hand, for the PdX− catalyst, one of the two halogen anions is released upon binding of the organoboronate to the Pd catalyst (see Figure 6). The same products are produced from transmetalation with the single Pd atom catalyst and the PdX− catalyst, and therefore, even though single-atom catalysts exist in solution at the beginning of the reaction, they become PdX− after one cycle of the SMR. Therefore, we conclude that PdX− should be the reactive species during the ligand-free SMR in aqueous solution. Figure 12 shows the overall relative free-energy profiles of transmetalation and reductive elimination for the PdX − catalysts in aqueous solution. For the BME calculations, we confirmed that geometric parameters shown in Figures 4, 8, and

Figure 11. Upper panels: snapshots of (i) IS3, (ii), and (iv). Final states shown in Figure 10. The black x, y, and z axes represent the directions of the super cell, respectively. The lower panel: the upper, middle, and lower graphs represent AO LDOS of (i), (ii), and (iv), respectively. Each line is identified by colors as follow; s + p orbital (black), dz2 (red), dx2−y2 (green), dxy (blue), dyz (magenta), and dxz (maroon).

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DISCUSSION The Pd catalyst in the ligand-free SMR can be prepared from an aqueous palladium source, namely, PdCl2 in aq. HCl,32,33 or from solid sources, such as Pd-containing perovskite oxides,30,31 or Pd clusters.34,35 Even with solid catalysts, it is well accepted that the catalytically active Pd species is dissolved into solution

Figure 12. Relative free-energy profiles of transmetalation and reductive elimination for the PdX− catalysts in aqueous solution (red solid line: X = Br; black solid line: X = Cl). The free energies relative to the state “IS0” are shown in kcal/mol. For TS3 and IS3 for X = Cl, as indicated by dashed black line, we use the same value as these values for X = Br. H



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10 varied smoothly along the reaction coordinate, whereas the coordination number of oxygen of water around the Pd shown in Figures 3, 4, and 9 may have hysteresis. The hysteresis observed in these simulations, however, should not affect the free energy profiles, because the Pd−O bond strength is rather weak, as indicated in Figure 5. In the case of PhBr, the largest free energy barrier is 8.1 kcal/ mol from IS1 to TS2, while in the case of PhCl, the largest barrier is 8.4 kcal/mol from IS0 to TS1. The largest barrier for PhCl is slightly larger than that for PhBr by only 0.3 kcal/mol, which is probably within the error of our calculations. The largest barriers of 8.1−8.4 kcal/mol suggest that the transmetalation process should proceed quite smoothly at 70 °C and the difference in the catalytic reactivity of the ligand-free Pd catalyst for PhBr and PhCl seems small. In our previous study on the oxidative addition of PhX to PdX− catalyst, we obtained the free energy barriers of 5.1 and 8.4 kcal/mol for X = Br and Cl, respectively.40 Therefore, the largest activation barrier for the oxidative addition process is smaller than that of the transmetalation step in the case of PhBr, while those for the two steps are quite similar in the case of PhCl. As discussed in our previous study, however, the larger activation barrier for PhCl in the oxidative addition step makes much longer lifetime of the η2 complex before the oxidative addition step for PhCl. This may cause the aggregation of Pd catalysts, leading to the significant suppression of the catalytic reactivity in the case of PhCl. Therefore, we think that the oxidative addition should be the rate-datermining step for PhCl.

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Article

ASSOCIATED CONTENT

S Supporting Information *

The Supporting Information is available free of charge on the ACS Publications website at DOI: 10.1021/acs.jpcc.7b06972.

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Additional supporting figures and tables (PDF).

AUTHOR INFORMATION

Corresponding Authors

*E-mail: [email protected]. *E-mail: [email protected]. Phone: +81(0)6 68797288. Fax: +81(0)6 68797290. ORCID

Takashi Ikeda: 0000-0001-5037-624X Yoshitada Morikawa: 0000-0003-4895-4121 Notes

The authors declare no competing financial interest.

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ACKNOWLEDGMENTS We would like to thank Prof. Nobuaki Kambe, Prof. Takanori Iwasaki, Prof. Mitsuhiro Arisawa, and Dr. Daiju Matsumura and Dr. Yasuo Nishihata for valuable discussions. The present study was partly supported by Grants-in-Aid for Scientific Research on Innovative Areas 3D Active-Site Science (Nos. 26105010 and 26105011) and Scientific Research (C) (No. 26410014) from the Japan Society for the Promotion of Science (JSPS), the Elements Strategy Initiative for Catalysts and Batteries (ESICB) supported by the Ministry of Education, Culture, Sports, Science, and Technology, Japan (MEXT), and the JSPS Core-to-Core Program (Type A) “Advanced Research Networks: Computational Materials Design on Green Energy.” The numerical calculations were performed using the facilities of the Supercomputer Center, Institute for Solid State Physics, the University of Tokyo, and computational resources of the HPCI system were provided by Nagoya University, the University of Tokyo, and Tohoku University through the HPCI System Research Project (Project ID: hp130112, hp140166, and hp150201).

CONCLUSION

To clarify the reaction mechanism and the reactive species of the ligand-free Pd catalyst in the SMR, we investigated the transmetalation step for a single Pd atom catalyst and a halogen-anion-bound Pd (Pd-X−, X = Cl or Br) catalyst in water solvent by using FPMD simulations with an explicit solvent model. We found that when starting from a single Pd atom catalyst, the halogen anion bound to the Pd catalyst is not replaced by the organoboronate species but instead remains bound to the Pd catalyst throughout the transmetalation step, which is in strong contrast to the conventional SMR with a phosphine-ligated Pd catalyst. The stability of the Pd-X bond during transmetalation is due to the weak trans-influence of H2O compared with that of the phosphine ligands. When starting from the Pd-X− catalyst, one of the two halogen anions is released from the first-coordination sphere of the Pd catalyst during the transmetalation step, and therefore, after transmetalation, the products are the same from the reactions starting from the single Pd atom catalyst or the Pd-X− catalyst. The overall activation free energies are, at most, 8.1 kcal/mol for X = Br and 8.4 kcal/mol for X = Cl, respectively, leading to high TON of the SMR cycle. Thus, we conclude that Pd-X− is the active species of the ligand-free Pd catalyst for the SMR. By considering the free-energy profile for the transmetalation step obtained in the present study together with that for the oxidative addition step reported in our previous study, we ascribe the origin for the suppression of the catalytic reactivity of the ligand-free SMR for PhCl to the larger activation barrier in the oxidative addition step, which causes the aggregation of Pd catalysts.

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First-Principles Molecular Dynamics Analysis of Ligand-Free Suzuki

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