Ab Initio Molecular Dynamic Simulations on Pd Clusters Confined in

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Ab initio Molecular Dynamic Simulations on Pd Clusters Confined in UiO-66-NH 2

De-Li Chen, Shengnan Wu, Pengyong Yang, Sihui He, Li Dou, and Fang-Fang Wang J. Phys. Chem. C, Just Accepted Manuscript • DOI: 10.1021/acs.jpcc.7b00957 • Publication Date (Web): 23 Mar 2017 Downloaded from http://pubs.acs.org on April 7, 2017

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The Journal of Physical Chemistry

Ab initio Molecular Dynamic Simulations on Pd Clusters Confined in UiO-66-NH2 De-Li Chen,1 Shengnan Wu,1 Pengyong Yang,1 Sihui He,2 Li Dou,1 Fang-Fang Wang2* 1

Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Zhejiang Normal

University, 321004 Jinhua, China 2

College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, China

E-mail: [email protected]

1

ACS Paragon Plus Environment


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Abstract Thermodynamically stable metal organic framework (MOF), UiO-66-NH2, have experimentally been demonstrated as ideal platform to isolate metal clusters within its nanocages, however, the electronic structures and the dynamics of the encapsulated metal clusters are still unclear. Ab initio molecular dynamics simulations combined with density functional theory based methods were employed to search the stable structures of Pdn@UiO-66-NH2 composites, and their electronic properties were analyzed in detail. We found that the thermodynamics of the composites are highly correlated with charge transfer between Pdn cluster and UiO-66-NH2 framework, as well as the deformation energy of the framework. In addition, both ab initio molecular dynamics simulations and density functional theory calculations show that the small Pd clusters can easily diffuse into the tetrahedral cage of UiO-66-NH2 from the octahedral cage through the window connecting these two types of cages, with a small energy barrier.

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1. Introduction In the past decade, metal organic frameworks (MOFs) have attracted great interests in many fields, such as gas storage, gas separation, and catalysis, due to their high tuning flexibilities of metal nodes and organic ligands.1-11 Recently, the MOFs based composites have received increasingly attention because of their potential applications in catalysis.11-22 Highly ordered nanometer-sized nanocages in MOFs make them possible as ideal platforms to disperse metal nanoparticles, forming new heterogeneous catalysts with high catalytic activities for many important reactions.23-26 Noble metal nanoparticles (MNP) such as Au, Pd, and Pt have been successfully introduced into the zirconium based UiO-66 and its derivatives,23-25,27-29 possessing excellent thermodynamic and chemical stabilities not typically found in common MOFs, and thus being considered as promising materials for industrial applications. For example, Au nanoparticles were successfully introduced into UiO-66 forming an oxidation catalyst, exhibiting a very high selectivity towards the ketone.28 With amine functionalized UiO-66-NH2 as the platform, small Pd nanoparticles were well dispersed inside the cavities, and the obtained catalysts exhibited excellent performance on the hydrodeoxygenation of vanillin in water25 and one-pot tandem oxidation-acetalization reaction23; Pt nanoclusters confined inside the cavities of UiO-66-NH2 was also developed with a very high Pt loading of 10.7 wt%, and the catalyst show both high selectivity to cinnamyl alcohol and high conversion of cinnamaldehyde. Many progresses have been made on the synthesis of MNP@MOFs, however, the electronic structures of MNP confined in the materials remain unclear, which is very important to gain deep insight into the microscopic 3



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properties of the composites towards catalytic reactions. Density functional theory (DFT) based methods have been widely used to study structures, stabilities, and catalytic activities of the isolated MNP and the MNP coated on the surface of metal oxide. In contrast, there are only limited studies have been reported for the prediction of structures and stabilities of metal cluster encapsulated MOFs. Vilhelmsen et al.30,31 employed DFT method combined with genetic algorithm to search stable structures of Pd and Au clusters encapsulated MOFs such as MOF-74 and UiO-66. Based on the over hundred number of isomers obtained, they further studied the mobility of metal cluster within the MOF-74 by linking the configurations at various positions in the cages. In these studies, although the obtained final configuration may not be the global minima, these theoretical predictions are very important since with the obtained reasonable configuration it is possible to study the electronic properties of MNP@MOFs. Furthermore, the obtained reasonable configurations of MNP@MOFs allow us to study the specific reaction mechanism and thus it helps us to design better catalysts to improve the catalytic properties. Since the number of possible configurations for the MNP@MOFs composites is huge, it is almost impossible to search the global minima for a given Pdn@UiO-66-NH2 system. Thus, in this study, we aimed to search reasonable configuration for the system rather than find the global minima. It is well known that the Ab initio molecular dynamics (AIMD) simulations together with annealing simulation algorithm have been successfully proved to search global minima for isolated metal cluster,32,33 and thus it is reasonable to use this technique to locate reasonable configuration for the Pdn@UiO-66-NH2. Comparing to the traditional DFT methods, the AIMD method additionally allows us to gain microscopic insights into the dynamics of the encapsulated 4


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metal cluster for their diffusion between the nanocages, the catalytic reactions confined in the nanocages, as well as the prediction of defects inside the frameworks. In the following, we will first present the results obtained by the AIMD simulations combined with annealing algorithm and DFT method, with which the stable structures for all of the Pdn@UiO-66-NH2 with n up to 32 were found; Secondly, the electronic structures were then analyzed to reveal the stabilities of the Pdn@UiO-66-NH2 composites; Thirdly, the dynamics of small Pdn clusters were analyzed to reveal the mechanism of the aggregation of small metal clusters into large metal clusters. 2. Theoretical Methods The DFT calculations were carried out to compute the 3-dimensional structure of Pd encapsulated UiO-66-NH2 composites, where the primitive cell of dehydrated UiO-66-NH2 containing 120 atoms34 was adopted to represent the periodic structure, allowing us to study the confinement effect of the nanopores on the encapsulation of metal clusters. The reliability of the model based on 1 primitive cell of UiO-66-NH2 was confirmed by comparing the interaction energies between the models of 1 and 2 primitive cells, of which the details will be discussed in section 3.2. We utilized a plane wave basis set as implemented in the Vienna Ab-initio Simulation Package (VASP)35-38 within the projected augmented wave (PAW)39 method, and the generalized gradient approximation functional of Perdew-Burke-Ernzerhof (PBE)40 was used to describe the exchange-correlation functional. A kinetic energy cutoff of 300 eV in the plane wave basis set was used for the expensive AIMD simulations. The final configurations from AIMD simulations were further optimized using a higher kinetic energy cutoff of 400 eV to make sure a local minima was found. During the AIMD simulations, only gamma point was used to sample the Brillouin zone. All of the optimized structures were relaxed until the absolute force on each atom is smaller than 5



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0.03 eV/Å. All of the AIMD simulations with annealing technique were performed from a high temperature of 700 K to 300 K, where a time step of 2 fs was used to accelerate the simulations and the mass of hydrogen atoms were set to 3,41,42 thus the vibration of H could be reduced. The Climbing image nudged elastic band (NEB) method43 was employed to search the transition states. The PBE functional has been successfully employed to study the structures of MOFs and the interaction between metal cluster (such as Pd) and MOFs.30,31,44,45 In this study, the optimized cubic unit cell from PBE functional (a = 20.67 Å) with energy cutoff of 400 eV well reproduce the experimental structure (a = 20.70 Å) of UiO-66,34 and the optimized amine functionalized UiO-66-NH2 has a very similar crystal structure with a = 20.64 Å. In addition, the computed cohesive energy of Pd metal of 3.73 eV using PBE functional with energy cutoff of 400 eV is only slightly smaller than the experimental value of 3.89 eV.46 Therefore, the PBE functional used in this study should give reasonable prediction of the structures and interaction energies of Pdn@UiO-66-NH2 systems. 3. Results and Discussions 3.1 Stable structures of Pdn@UiO-66-NH2 composites In this study, only the perfect UiO-66-NH2 material was selected as the platforms for encapsulating Pdn clusters, although it has been suggested that the defect sites in UiO-66 and its analogues based catalysts may play an important role in their high catalytic activities.13,47 There are two types of cages in perfect UiO-66-NH2 materials, i.e., the large octahedronal cage A and the small tetrahedral cage B, with a ratio of 1:2, as shown in Fig. 1(A). The two cages are connected by a window with the diameter estimated to be 7.0 Å, as shown in Fig. 1(B), where the 6


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size of the circle was represented by the six C atoms from the three benzene rings.

Fig 1. The optimized crystal structure of (A) UiO-66-NH2, with 1:2 octahedral and tetrahedral cages, which are connected by a window (B) with diameter of 7.0 Å. The C, H, N, O, Zr atoms are represented by gray, white, blue, red, and cyan balls, respectively. We started from searching the favorable adsorption sites for small Pdn (n = 1, 2, 4) clusters confined in the cages of UiO-66-NH2. Several starting configurations were built in both cage A and cage B and then simulated using AIMD with NVT ensemble, as well as annealing simulations. The AIMD simulations with NVT emsemble were carried out at a temperature of 700 K to facilitate the search of thermodynamically stable structures for Pdn@UiO-66-NH2 with a total simulation time up to 40 ps. The annealing simulations were performed for the systems with temperature from 700 K to 300 K. All of the final configurations obtained from the AIMD simulations were then optimized using PBE functional. Note that, during all of the AIMD simulations in this study, the framework was carefully checked to avoid any collapse. For n = 1-4, we found that the AIMD simulations with annealing technique have a higher efficiency locating a lower energy structure compared to the AIMD simulations with NVT emsemble. The computational results show that the small Pdn (n = 1 - 4 ) cluster strongly bind to the window site, i.e., the Pd atoms form bonds with the C atoms from benzene ring and N atom from amine group. The stable structure of Pd1@UiO-66-NH2 is shown in Fig. 2 (A), where the Pd atom binds to two C atoms (from benzene 7



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ring) and one N atom from the neighboring organic linker, with distance of 2.10, 2.26, and 2.26 Å, respectively. Similarly, each Pd atom in the Pd2 dimer bind to C atoms from benzene rings (see Fig. 2 (B)), with Pd-C distance between 2.12 to 2.33 Å. Since the Pd2 dimer (dPd-Pd = 2.77 Å) was also computed to be loaded at the window site, the amine group also makes contribution to the stabilization of Pd2 dimer, with Pd-N distance of 2.27 Å. Note that the amine group on the organic linker sites in the octahedral cage, and thus it has no contribution to the binding of metal cluster when the metal cluster is completely encapsulated inside the tetrahedral cage. Indeed, different from the Pd atom and its dimer, the Pd4 cluster was found to be completed confined in the tetrahedral cage forming a tetrahedral-like shape, with three Pd atoms binding to the three organic linkers, as shown in Fig. 2 (C). The six Pd-C bond distances are between 2.17 to 2.21 Å, close to those in Pd1@UiO-66-NH2 and Pd2@UiO-66-NH2; the six Pd-Pd bond lengths are from 2.60 to 2.72 Å, slightly smaller than that (2.77 Å) of Pd dimer, indicating the Pd-Pd bonds in Pd4@UiO-66-NH2 are stronger. In summary, the calculations indicate that the small Pd clusters are energetically more favorable located at the window sites and the tetrahedral cage, by forming strong binding between Pd atoms and C atoms from the organic linkers. Therefore, it is expected that the small Pd clusters in the tetrahedral cage become the anchors for binding the diffused Pd atom or small Pd clusters in the UiO-66-NH2 nanopores and aggregate into large clusters or nanoparticles.

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Fig 2. The stable configurations of Pd1@UiO-66-NH2, Pd2@UiO-66-NH2, and Pd4@UiO-66-NH2, as well as the bond lengths for some important bonds (unit: Å). The Pd atoms are represented by blue balls and the definition of other atoms are the same to Fig. 1. Note that only part of the atoms in the frameworks are represented by balls and sticks for clarity while the other atoms are shown in lines. The same computational approach was used to search stable structures of large Pdn (n = 8, 12, 16, 20, 24, 28, 32) clusters encapsulated UiO-66-NH2 composite. Starting from a smaller Pd4m@UiO-66-NH2 (m = 1 – 7), we build a larger cluster Pdm+1 by creating single Pd atom at each window site (4 window sites in total) in the tetrahedral cage encapsulating the Pdm cluster, and the obtained initial structures were simulated by AIMD with annealing technique and finally optimized with PBE functional. The AIMD simulation trajectories show that all of the single atoms placed at the window site diffuse into the tetrahedral cage rather than the octehedral cage, and then aggregate into larger Pd cluster. The obtained stable structures of Pdn@UiO-66-NH2 (n = 8, 12, 16, 20, 24, 28 and 32) are shown in Fig. 3. The small Pdn cluster is completely confined inside the tetrhedral cage, and the pore is gradually filled with Pd atoms as the cluster size increases. After the pore is fully filled with Pd cluster, the window sites are finally also occupied with Pd atoms. In Pd28@UiO-66-NH2, each window site has three Pd atoms, forming small (111) surface, 9



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as shown in Fig. 4 (A). With the encapsulation of Pd28 cluster, the tetrahedral cage expands and and the window size increases from 7.0 to 7.3 Å. The 4 Pd atoms at the core of the Pd28 cluster have coordination number of 12 that is the same to the Pd metal, the 12 Pd atoms at the window sites have coordination number of 5, and the other 12 Pd atoms have coordinated atoms of 7. This structure of the encapsulated Pd28 is the same to the structure of stable Pd28@UiO-66, computed using DFT combined with genetic algorithm by Vilhelmsen and Sholl,31 which suggests the approach used in this study is able to reproduce the same thermodynamically stable structure. Due to the limited size of the tetrahedral cage, additinoal Pd atoms beyond n of 28 should only be located in the neighboring octehedral cage. Indeed, the core of Pd32@UiO-66-NH2 is the same to Pd28@UiO-66-NH2 and the additional 4 Pd atoms are evenly distributed at the four window site surrounding the tetrahedral cage, with each Pd atom binding to the 3 Pd atoms at the window site. Note that theses 4 Pd atoms are actually located at the octehedral cage rather than the tetrahedral cage. The electronic properties of the Pdn@UiO-66-NH2 are discussed in the next section.

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Fig 3. The stable configurations for Pdn encapsulated UiO-66-NH2, where the Pd atoms are represented by blue balls while all of the atoms in framework are shown in lines.

Fig 4. (A) The computed Pd28@UiO-66-NH2 configuration with 4 (111) Pd surfaces at each window site and (B) the size of window. 3.2 Electronic structures and charge transfer in Pdn@UiO-66-NH2 The binding energy of a metal cluster to a support was usually computed to understand the mutual interaction between the guest and host systems, but not reflect the aggregation of a cluster from single metal atom. In this study, we tried to gain insight into the thermodynamic stability of differently sized Pd clusters encapsulated UiO-66-NH2, thus it is necessary to have a 11



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different reference energy.31 Based on the stable structures of Pdn@UiO-66-NH2 (n = 2 – 32), we calculated the binding energy per Pd atom for size dependent metal clusters, EPd(N):

EPd ( N ) = Et ot − EMOF − n × Eat om where Etot, EMOF, Eatom represent the energy of Pdn@UiO-66-NH2, UiO-66-NH2, and single Pd atom, respectively. The EPd(N) value for each configuration is plotted in Fig. 5. The value is monotonously decreased from -2.35 eV (n = 4) to -2.98 eV (n = 28), and then increase to -2.95 eV (n = 32). To confirm the reliability of 1 primitive cell model, a model of 2 primitive cell was built to encapsulate Pd28 cluster and the computed EPd(28) value is -2.99 eV, very close to the value of -2.98 eV using 1 primitive cell model, indicating the model based on 1 primitive cell is reasonable. The large difference between the EPd(N) values and the computed cohesive energy (3.73 eV) of Pd metal is not surprising since the coordination number of the Pd atom in metal is 12, while the coordination number of the Pd atoms in the small Pdn clusters encapsulted in UiO-66-NH2 is much smaller. Take Pd28@UiO-66-NH2 for example, the average coordination number is only 6.9, much smaller than 12. The trend of EPd(N) values well explain the evolution of the pore filling with Pdn cluter. The average coordination number of Pd atom becomes larger as the size of Pd cluster increases, resulting to stronger Pd-Pd interaction. When the number of Pd atoms reach 28, each window site has three Pd atoms that bind to the three organic ligands, forming strong Pd-C bonding. The decrease of EPd(N) value from Pd28 to Pd32 can be explained by the fact that the additional 4 Pd atoms are in the octahedral cage and only bind to the 3 Pd atoms at the window site with a small coordination number of 3.

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-2.3 -2.4 -2.5 EPd(N) /eV

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-2.6 -2.7 -2.8 -2.9 -3.0 -3.1

4

8

12

16

20

24

28

32

N (Number of Pd Atoms)

Fig 5. Adsorption energy per Pd atom confined in cage A of UiO-66-NH2 framework, where the structures are obtained from AIMD simulations. To better understand the stabilities of the Pdn@UiO-66-NH2 composites, we calculated the charge transfer between the metal cluster and the framework. Interestingly, we found that more electron is transferred from metal cluster to framework as the size of Pd cluster grows. As shown in Table 1, there is only 0.20 electron transferred from the Pd4 metal cluster to the framework, and the transferred electron monotonically reaches 1.33 for the thermodynamically most stable Pd28@UiO-66-NH2, and then decreases to 0.89 electron for Pd32@UiO-66-NH2. The values of charge transfer from the metal cluster to the framework monotonically increases, of which the trend is the same to the increased values of EPd(N) until the metal atoms reach 28. To gain further insight into the charge transfer betwee the host and the guest, the population of the atomic charges of metal cluster were analyzed in details. Take Pd4@UiO-66-NH2 (see structure in Fig. 2(C)) for example, the atomic charges for the 3 Pd atoms coordinated to the aromatic ring are 0.10, 0.10, and 0.07 |e|, respectively, while the other Pd atom coordinated to the 3 Pd atoms is negative, -0.07 |e|. This suggests that the Pd metal atoms tends to lose electrons to the aromatic 13



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ring forming strong interactions between the encapsulated metal cluster and the framework of UiO-66-NH2. Similar charge population for other Pdn@UiO-66-NH2 systems were found, i.e., the Pd atoms coordinated to the aromatic ring lose electron of about 0.07 to 0.12 |e|, while the other Pd atoms gain electron. Consequently, the coordinated number of aromatic rings for metal cluster increases as the size of metal cluster grows, and thus the total value of charge transfer becomes larger, leading to stronger mutual interaction between the encapsulated Pd cluster and the framework. However, the Pd32@UiO-66-NH2 does not follow the same trend. Comparing to the value of 1.32 |e| in Pd28@UiO-66-NH2, the charge transfer between the Pd32 metal cluster and the framework decreases to 0.89 |e|. Further analyses of the population indicate that the 4 Pd atoms located in the octehedral cage of Pd32@UiO-66-NH2 gain relatively large value of -0.88 |e| in total, while the other 28 Pd atoms (confined in the tetrahedral cage) have a total charge of 1.77 |e|. In addition, we computed the decomposition energy of the framework in each Pdn@UiO-66-NH2 to analyze the impact of the encapsulated metal cluster on the stability of UiO-66-NH2. The decomposition energy of the framework was calculated as the energy difference between the optimized UiO-66-NH2 framework and the structure obtained from the Pdn@UiO-66-NH2 after removing Pdn cluster. Table 1 shows that the decomposition energy for Pd4@UiO-66-NH2 is only about 0.43 eV, suggesting that the tetrahedral cage was only slightly distorted mainly due to the binding between Pd4 cluster and framework (see structure in Fig. 2). As the metal cluster size grows, the decomposition energy gradually increases as expected (see Table 1). The decomposition energy for Pd28@UiO-66-NH2 was calculated to be 5.46 eV, and the value further increases to 5.59 eV for Pd32@UiO-66-NH2. This trend is different from the total 14


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value of charge transfer as a function of metal atoms. However, the total charge of the 28 Pd atoms confined in the tetrahedral cage of Pd32@UiO-66-NH2 is 1.77 |e|, which follows the same trend of the decomposition energy. In summary, the thermodynamical stability of Pdn@UiO-66-NH2 are mainly determined by the interplay of two factors, i.e., interaction between the metal cluster and the framework and the deformation energy of UiO-66-NH2 framework. As the cluster size grows, the interaction between the Pd metal cluster and the framework is stronger, while the increased deformation energy has negative impact on the stability of the composites. The charge transfer from metal cluster to the framework could be considered as an indication of the thermodynamical stability of the system. Overall, the Pd28@UiO-66-NH2 configuration could be used as a prototypical model for investigating the reaction mechanism of specific reactions confined in the nanocages. The tetrahedral cages are connected with octahedral cages, and thus the 4 naked (111) surfaces at the window site could be the main adsorption sites for the reactants and the actives sites for specific reactions.

Table 1. The deformation energy and the charge transfer from metal cluster to UiO-66-NH2 framework computed based on the stable structures of Pdn@UiO-66-NH2. Deformation

Charge of Pdn

energy (eV)

cluster (|e|)

4

0.43

0.20

8

2.13

0.48

12

2.38

0.79 15



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16

2.95

0.98

20

3.09

1.21

24

4.19

1.32

28

5.46

1.33

32

5.59

0.89

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3.3 Diffusion of Pdn clusters confined in nanocages Many

experiments

have

shown

that

the

Pd

nanoparticles

encapsulated

in

amine-functionalized UiO-66 were very well dispersed and the size of the nanoparticles are small both before and after they were employed as catalysts in specific reactions. However, it remains unclear how the Pdn nanoparticles (or clusters) diffuse within the nanocages, which is the key to understand the formation of Pdn@UiO-66-NH2. Therefore, we carried out AIMD simulations to obtain the diffusion trajectory of Pd4 cluster from octahedral cage to tetrahedral cage, and then climbing NEB method was used to compute the diffusion barriers.

Fig. 6 The 4 snapshots from the trajectory of AIMD simulation for the Pd4@UiO-66-NH2 16


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system with simulation time t of (A) 0.00 ps, (B) 7.752 ps, (C) 8.40 ps, and (D) 40.00 ps.

The AIMD simulations with annealing technique were performed for the Pd4@UiO-66-NH2 system with a total simulation time of 40 ps, where the initial position of Pd4 cluster was placed at the center of octahedral cage, as shown in Fig. 6 (A). The trajectory of the AIMD simulations shows that the Pd4 cluster initially diffuse to the window site and then gradually moves into the tetrahedral cage within about 9 ps. Several snapshots were recorded and shown in Fig. 6. The structure of Pd4 cluster has a tetrahedral shape at simulation time of 7.52 ps, and during the period of diffusion from octahedral to tetrahedral cage the Pd4 structure changes to a 2D shape (see Fig. 6 (C)), and finally the structure changes back to a tetrahedral shape. To obtain deep insight into the structure transition of Pd4 cluster, the climbing NEB calculations were performed to estimate the energy barriers. Four snapshots were selected from the AIMD simulations and were used to compute the diffusion path. Our calculations indicate that all of the energy barriers are less than 0.33 eV, which are small enough for the diffusion of Pd4 metal cluster. In addition, analyses of the relative energies of different configurations shown in Fig. 7 indicate that this process is energetically favorable. Consequently, the diffusion of small metal cluster such as Pd4 from octahedral cage to tetrahedral cage is both thermodynamically and dynamically favorable. It is worthwhile to mention that it is the narrow window force the transition of Pd4 cluster from 3D structure to 2D planar structure and finally back to 3D shape. In another word, the metal cluster would have a structural transition when passing the window site. Therefore, it is highly plausible that the large Pd metal cluster should overcome a higher energy barrier in order to transit from octahedral cage to tetrahedral cage. 17



0.2

Relative Energy (eV)

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0.0 -0.2 7.52 ps -0.4 -0.6

8.40 ps

-0.8 -1.0

8.04 ps

0

5

8.80 ps

10

15

20

25

Reaction Coordinate (Angstrom) Fig. 7 The computed diffusion path for the Pd4 metal cluster from the octahedral cage to the tetrahedral cage in UiO-66-NH2, during the AIMD simulation time period from 7.52 ps to 8.80 ps. The snapshots at different simulation time (7.52, 8.04, 8.40, and 8.80 ps) from the AIMD simulations were fully relaxed using PBE functional and the other images were computed using Climbing image NEB method.

4. Conclusions The AIMD simulations combined with DFT calculations have been performed to search thermodynamically stable configurations for the Pd cluster encapsulated UiO-66-NH2 systems with the number of Pd atoms up to 32. The results show that the Pd28@UiO-66-NH2 model was found to be the thermodynamically most stable structure among the systems we investigated, of which the stability was illustrated as the interplay of the binding energy of the confined Pd cluster and the deformation energy of UiO-66-NH2 framework. Bader charge analyses show that the framework continuously obtained electron from the Pd cluster as its size increases until the number of Pd atoms reach 28. In addition, the diffusion of small Pd4 cluster between the 18


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octahedral and tetrahedral cages were studied and it was found that the energy barrier is small, indicating that the small Pd cluster should easily diffuse within the pores and aggregate into a larger size cluster. Our calculations indicate that the method we used in this study could be used to search the reasonable model for Pdn@UiO-66-NH2, which should also be applied to other similar systems, i.e., single metal cluster encapsulated MOFs and binary metal cluster encapsulated MOFs. With the reasonable MNP@MOFs, it is plausible to study the reaction mechanism of specific catalytic reactions, which have been attracted great attention recently by many

experimental

research

groups.

The

investigation

of

the

hydrogenation

of

2,3,5-Trimethylbenzoquinone using the Pd28@UiO-66-NH2 model have been performed to illustrate the experiment by our group and cooperators,48 which will be published elsewhere.

Acknowledgements F.-F.W. and D.-L.C gratefully acknowledge the support from the Zhejiang Provincial Natural Science Foundation of China (LQ14B030001, LY17B060001) and the National Natural Science Foundation of China (21403198, 21303165).

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TOC GRAPHIC

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The optimized crystal structure of (A) UiO-66-NH2, with 1:2 octahedral and tetrahedral cages, which are connected by a window (B) with diameter of 7.0 Å. The C, H, N, O, Zr atoms are represented by gray, white, blue, red, and cyan balls, respectively. 99x34mm (300 x 300 DPI)


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The stable configurations of Pd1@UiO-66-NH2, Pd2@UiO-66-NH2, and Pd4@UiO-66-NH2, as well as the bond lengths for some important bonds (unit: Å). The Pd atoms are represented by green balls and the definition of other atoms are the same to Fig. 1. Note that only part of the atoms in the frameworks are represented by balls and sticks for clarity while the other atoms are shown in lines. 99x38mm (300 x 300 DPI)



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The stable configurations for Pdn encapsulated UiO-66-NH2, where the Pd atoms are represented by green balls while all of the atoms in framework are shown in lines. 99x87mm (300 x 300 DPI)


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(A) The computed Pd28@UiO-66-NH2 configuration with 4 (111) Pd surfaces at each window site and (B) the size of window. 99x31mm (300 x 300 DPI)



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Adsorption energy per Pd atom confined in cage A of UiO-66-NH2 framework, where the structures are obtained from AIMD simulations. 82x57mm (300 x 300 DPI)


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The 4 snapshots from the trajectory of AIMD simulation for the Pd4@UiO-66-NH2 system with simulation time t of (A) 0.00 ps, (B) 7.752 ps, (C) 8.40 ps, and (D) 40.00 ps. 99x91mm (300 x 300 DPI)



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Ab Initio Molecular Dynamic Simulations on Pd Clusters Confined in

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