S1

Supplementary Information

Confined Pyrolysis within Metal-Organic Frameworks to Form Uniform

Ru3 Clusters for Efficient Oxidation of Alcohols

Shufang Ji,†,○ Yuanjun Chen,

†,○ Qiang Fu,‡,○ Yifeng Chen,§ Juncai Dong,‖ Wenxing

Chen,† Zhi Li,

† Yu Wang,⊥ Lin Gu,

# Wei He,§ Chen Chen,

† Qing Peng,

† Yu Huang,

†, ∇

Xiangfeng Duan,∇ Dingsheng Wang,†* Claudia Draxl,

‡ Yadong Li

†*

†Department of Chemistry, Tsinghua University, Beijing 100084, China,

‡Institut für Physik and IRIS Adlershof, Humboldt-Universität zu Berlin, Berlin 12489, Germany,

§School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China,

‖Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of

Sciences, Beijing 100049, China,

⊥Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of

Sciences, Shanghai 201204, China,

#Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of

Sciences, Beijing 100190, China,

∇Department of Materials Science & Engineering, University of California, Los Angeles, California

90095, United States.

Address correspondence to wangdingsheng@mail.tsinghua.edu.cn; ydli@mail.tsinghua.edu.cn.

Table of Contents

1. Experimental Section..............................................................................................................................S2-6

2. Supporting Figures and Tables........................................................................................................S6-22

S2

3. Characterization and Selected H NMR Spectra of Products.......................................S23-30

4. Reference........................................................................................................................................................S31

1. Experimental Section

Reagents

Triruthenium dodecacarbonyl (99%, Acros), ruthenium(III) 2,4-pentanedionate (Ru 24%, Alfa Aesar),

2-methylimidazole (97%, Acros), zinc nitrate hexahydrate (98%, Alfa Aesar), 2-aminobenzyl alcohol

(98%, Alfa Aesar), ruthenium (III) nitrosyl nitrate (Ru 31%, Alfa Aesar), H2O2 (32%, Alfa Aesar), poly

(N-vinyl-2-pyrrolidone) (PVP, MW=10000, Alfa Aesar) were used without any further purification and

were analytical grade.

Synthesis of Ru3(CO)12 @ZIF-8

In a typical synthesis of Ru3(CO)12@ZIF-8, Ru3(CO)12 (19.2 mg, 0.03 mmol) and Zn(NO3)2•6H2O (238

mg, 0.8 mmol) were dissolved in the mixture of THF (2 mL) and MeOH (4 mL) under ultrasound at

60°C for 1h to form a clear solution in flask A. Then, a solution of 2-methylinidazole (263 mg, 3.2

mmol) in the mixture of DMF (1.2 mL) and MeOH (0.8 mL) was added to flask A. The resulting

solution was transferred into 10ml Teflon-lined stainless-steel autoclaves and then was placed into a

constant temperature oven at 120 °C for 4 h. When it finished and cooled to room temperature, the

product was separated by centrifugation at 9500 rpm for 6 min and washed subsequently with THF for

three times, then washed with methanol for twice and finally dried under vacuum at 80 °C for 12 h.

Synthesis of Ru(acac)3@ZIF-8 and ZIF-8

In a typical synthesis of Ru(acac)3@ZIF-8, Ru(acac)3 (20 mg, 0.05 mmol) and Zn(NO3)2•6 H2O (238

mg, 0.8 mmol) were dissolved in MeOH (6 mL) under ultrasound in flask B. Then, a solution of

2-methylinidazole (263 mg, 3.2 mmol) in the mixture of DMF (1.2 mL) and MeOH (0.8 mL) was added

to B. The sealed vessel was placed into a constant temperature oven at 120 °C for 4 h. When it finished,

S3

the product was separated by centrifugation at 10000 rpm for 5 min and washed subsequently with

methanol until a colorless solution and finally dried under vacuum at 80 °C for 12 h. ZIF-8 was

prepared with the same synthesis condition of Ru(acac)3@ZIF-8 except Ru(acac)3 was not added.

Synthesis of Ru3/CN, Ru1/CN or CN

The as-prepared powder of Ru3(CO)12@ZIF-8, Ru(acac)3@ZIF-8 or ZIF-8 were transferred into a

ceramic boat and then placed into a tube furnace maintaining 800°C for 3 h under flowing mixture of 5%

H2/Ar atmosphere with a heating rate of 5 oC min

-1, respectively. When it finished and cooled to room

temperature, the final powders, Ru3/CN, Ru1/CN or CN, were collected respectively. The Ru loading of

Ru3/CN and Ru1/CN catalysts are 0.10 wt% and 0.23 wt% determined by ICP-AES analysis,

respectively. The as-prepared catalysts are without any treatment for further use.

Synthesis of Ru NPs/CN

Ru nanoparticles (2.5 nm) were synthesized using a reported method1. PVP (0.0112 mmol, 112 mg) and

Ru(NO)(NO3)3 (0.112 mmol, 35.5 mg) were dissolved in 100 mL of ethylene glycol (EG) under

ultrasound and stirring. The mixture solution was heated at 198 oC and refluxed under air atmosphere

for 3 h. Ru nanoparticles were collected and washed by an ethanol-acetone mixture. Then, the product

and 100 mg CN were dispersed in 15 mL ethanol with stirring overnight. After that, the suspension was

separated and dried in a vacuum oven at 60 °C for 12 h. The Ru loading of prepared Ru NPs/CN

catalyst is 1.1 wt% determined by ICP-AES analysis.

Characterizations

XRD data of samples was determined using a Rigaku RU-200b X-ray powder diffractometer (XRD)

with Cu Kα radiation (λ = 1.5406 Å). TEM images were performed on a Hitachi H-800 TEM operated

at 100 kV. The high-angle annular-dark-field scanning transmission electron microscopy

(HAADF-STEM) images were performed on using a Titan 80-300 STEM operated at 300 kV, equipped

S4

with a probe spherical aberration corrector. The Ru concentrations of the samples were conducted on the

inductively coupled plasma atomic emission spectroscopy (ICP-AES). The X-ray photoelectron

spectroscopy (XPS) data was carried out at the Catalysis and Surface Science End station at the BL11U

beamline of National Synchrotron Radiation Laboratory (NSRL) in Hefei, China. 1H-NMR was

recorded on a Bruker AscendTM

400 spectrometers. 1H-NMR were recorded on a Bruker Ascend

TM 400

spectrometers. Chemical shifts (in ppm) were referenced to internal solvent peaks (1H) or an external

TMS (10% in CDCl3). At the end of the catalytic run the reaction mixture was subjected to ISQ GC-MS

with a ECD detector (ThermoTrace GC Ultra) using a capillary column (TR-5MS, from Thermo

Scientific, length 30 m, i.d. 0.25 mm, film 0.25 μm), and the extent of conversion was calculated on the

basis of the ratio of areas of starting material and product as an external standard. The

Autosorb-IQ2-MP Brunauer-Emmett-Teller (BET) measurement was carried out. Mass spectra of

samples were carried out by time-of-flight secondary ion mass spectrometry 5 (TOF-SIMS) (ION-TOF

GmbH, Münster, Germany) with a 30 keV Bi3++

liquid metal ion gun (LMIG) in a high mass resolution

(HMR) mode.

XAFS measurements and analysis details

X-ray absorption find structure (XAFS) spectra (Ru K-edge) were collected at BL14W1 station in

Shanghai Synchrotron Radiation Facility (SSRF). The storage rings of SSRF were operated at 3.5 GeV

with a maximum current of 250 mA. Using Si (311) double-crystal monochromator, the data collection

was carried out in transmission mode using ionization chamber for Ru foil, RuO2, RuCl3, and Ru3(CO)12,

and in fluorescence excitation mode using a 7 element Ge detector for Ru3/CN and Ru1/CN. All spectra

were collected in ambient conditions. The acquired EXAFS data were processed according to the

standard procedures using the ATHENA module implemented in the IFEFFIT software packages. The

k2-weighted EXAFS spectra were obtained by subtracting the post-edge background from the overall

absorption and then normalizing with respect to the edge-jump step. Subsequently, k2-weighted χ(k)

data of Ru K-edge were Fourier transformed to real (R) space using a hanning windows (dk=1.0 Å-1

) to

S5

separate the EXAFS contributions from different coordination shells. To obtain the quantitative

structural parameters around central atoms, least-squares curve parameter fitting was performed using

the ARTEMIS module of IFEFFIT software packages. The following EXAFS equation was used:

]2sin[]

2exp[]2exp[

22

2

2

kkkk

kk

jj

j

jj

j

joj

RR

kRFSN

S02 is the amplitude reduction factor, Fj(k) is the effective curved-wave backscattering amplitude, Nj is

the number of neighbors in the jth

atomic shell, Rj is the distance between the X-ray absorbing central

atom and the atoms in the jth

atomic shell (backscatterer), λ is the mean free path in Å, ϕ j(k) is the phase

shift (including the phase shift for each shell and the total central atom phase shift), σj is the

Debye-Waller parameter of the jth

atomic shell (variation of distances around the average Rj). The

functions Fj(k), λ and ϕ j(k) were calculated with the ab initio code FEFF8.2.

Catalysis testing

A mixture of 2-aminobenzyl alcohol (0.5 mmol, 1.0 equiv.), Ru species catalysts ( Ru 0.001 equiv.;

Ru3/CN, 50 mg; Ru1/CN, 22 mg; Ru NPs, 4.6 mg; respectively), H2O2 (250 μL, 2.0 equiv.) and MeCN

(2 mL) in a 10 mL round-bottomed flask was heated at 80 oC and vigorously stirred (800 rpm) for 3

hours. Aliquots were taken at specific time for determination of component concentrations by GC-MS.

After completion of reaction, reaction mixture was extracted with ethyl acetate (3×5ml) and the

combined organic layer dried over anhydrous MgSO4. The yield was determined by GC using tridecane

as an internal standard. Then the mixture was concentrated under reduced pressure and the product was

purified by silica gel column chromatography. The active sites of the catalysts were measured by

ICP-AES experiments. The TOFs were calculated using the following equation:

TOF =Substrate oxidized (mol)

N active sites(mol) ∙ time(h) in [molecules per active site per h]

Computational details

All calculations were performed by the projector augmented wave (PAW) approach2 utilizing the Vienna

ab initio simulation package (VASP)3. Effects of spin-polarization were considered for systems

containing Ru1 and Ru3 clusters, which were embedded into a 6×6 graphene unit cell. A plane-wave

S6

energy cutoff of 400 eV was used. Exchange-correlation interactions were described by the PBE

functional4, and for adsorptions of 2-aminobenzyl alcohol molecules, the Grimme’ DFT-D2 correction

was included to account for van der Waals (vdW) interactions5. The first Brillouin zone was sampled

using a 3×3×1 Monkhorst-Pack grid6. The atomic coordinates were relaxed until the maximum residual

force is less than 0.02 eV/Å. A dipole correction to the energies was applied along the vertical direction

in order to eliminate spurious interaction between the periodic images. Bader charge analysis was

carried out according to Henkelman and coworkers with core charges included in the partitions7.

Visualization of optimized structures was carried out with the program VESTA8.

2. Supporting Figures and Tables

Figure S1. XRD patterns of the as-prepared Ru3/CN (pink) and CN (blue) samples by annealing

Ru3(CO)12@ZIF-8 (red) and ZIF-8 (black) at 800°C for 3h with a 5% H2/Ar atmosphere, respectively.

S7

Figure S2. The IR spectra of the as-prepared ZIF-8 (green), Ru3(CO)12 (blue), Ru3(CO)12@ZIF-8 (pink)

and Ru3/CN (red), respectively, indicating that Ru3(CO)12 molecules had been encapsulated by cages of

ZIF-8 and carbonyl was removed followed by a thermal treatment at 800°C for 3h with a 5% H2/Ar

atmosphere.

Figure S3. XPS spectra of Ru3/CN for the C 1s (a) and N 1s (b) regions, respectively. The N spectrum

reveals the coexistence of graphitic N at 401.5 eV, pyrrolic N at 400.5 eV and pyridinic N at 398.5 eV,

which act as anchoring points to stabilize Ru3 clusters.

S8

Figure S4. Pore size distribution for Ru3/CN (0.368 nm) and Ru3(CO)12@ZIF-8 (0.628 nm).

Figure S5. (a) HRTEM magnified image of Ru3/CN (inset: HRTEM image of Ru3/CN), (b)

Aberration-corrected HRTEM image of Ru3 /CN. Distorted graphite structures were observed on the

edge of Ru3/CN.

S9

Figure S6. The wavelet transform for the k2-weighted Ru K-edge EXAFS signal for the first

coordination shell of Ru foil. The colour in the contour figure indicates the moduli of the Morlet wavelet

transform.

Figure S7. The TOF-SIMS spectrum around m/z 305.7 signals of Ru3(CO)12, Ru3/CN and CN in

positive ion mode. The obvious fragment signal in Ru3/CN was detected at m/z 305.73 in positive ion

mode, which was consistent with observation of [Ru3]+ (cluster of peak at 305.73) from Ru3(CO)12

precursor. In addition, the m/z 305.73 signal ([Ru3]+) of CN sample was not detected. The results were a

powerful proof to further confirm the presence of Ru3 cluster species in Ru3/CN sample.

S10

Figure S8. The corresponding EXAFS k space fitting curve (red) and the experimental one (black) of

Ru3/CN.

Figure S9. The corresponding EXAFS R space fitting curve (red) and the experimental one (black

cycles) of Ru foil.

S11

Figure S10. The corresponding EXAFS R space fitting curve (red) and the experimental one (black

cycles) of RuO2.

Figure S11. The XRD pattern of Ru3/CN after reaction.

S12

Figure S12. (a) The TEM image and (b) The HAADF-STEM and corresponding element mapping

images showing the distribution of Ru (red), C (blue), and N (green) of Ru3/CN after reaction.

Figure S13. The aberration-corrected HAADF-STEM image of Ru3/CN after reaction. Ru3 clusters

were marked by yellow circles.

S13

Figure S14. The experimental Ru K-edge XANES spectra of Ru3 /CN catalyst before (black line) and

after reaction (red line).

Figure S15. The EXAFS Fourier transformed (FT) k2-weightedχ(k)-function spectra of the Ru3/CN

catalyst before (black line) and after reaction (red line).

S14

Figure S16. The TEM image of Ru1/CN.

Figure S17. The HAADF-STEM image of Ru1/CN.

S15

Figure S18. The corresponding element mapping images of Ru1/CN, showing the distribution of Ru

(red), N (blue), and C (green).

Figure S19. (a,b,c)Aberration-corrected HAADF-STEM images of Ru1/CN, showing several isolated

bright dots (marked red cycles), corresponding to Ru atoms.

S16

Figure S20. XRD patterns of Ru1/CN (blue) by annealing Ru(acac)3@ZIF-8 (red) at 800°C for 3h with

5% H2/Ar, and ZIF-8 (black), respectively.

Figure S21. XPS spectra of Ru1/CN for the C 1s (a) and N 1s (b) regions, respectively. The N 1s

spectrum revealed the coexistence of graphitic N at 401.5 eV, pyrrolic N at 400.3 eV and pyridinic N at

398.5 eV, which acted as anchoring points to stabilize single-atom Ru.

S17

Figure S22. The experimental Ru K-edge XANES spectra of Ru1/CN and references, which show the

energy absorption threshold value of Ru1/CN is higher than that of Ru foil and lower than that of RuO2,

indicating that Ru1 single atom carries positive charge.

Figure S23. The EXAFS Fourier transformed (FT) k

2-weightedχ(k)-function spectra of the Ru1/CN and

references. The FT-EXAFS spectrum of the Ru1/CN shows a main peak at about 1.5 Å (without phase

correction) corresponding to the first shell of Ru-N scattering, and the Ru–Ru peak at about 2.4 Å was

S18

not detected.

Figure S24. The corresponding EXAFS k space fitting curve (red) and the experimental one (black) of

Ru1/CN.

Figure S25. The corresponding EXAFS R space fitting curves of Ru1/CN.

S19

Figure S26. Embedded RuN4 model used to simulate Ru1/CN. The gray, blue, and teal spheres

represent carbon, nitrogen, and ruthenium atoms, respectively.

S20

Figure S27. (a) The TEM image of Ru NPs. The size of Ru NPs is about 2.5 nm. (b) The TEM image of

Ru NPs/CN. (c, d) The enlarged TEM images of Ru NPs/CN.

Table S1. Structure parameters of Ru3/CN, Ru1/CN, Ru foil and RuO2 bulk extracted from the EXAFS

fitting. (S02=0.85)

a

sample path N R(Å) ΔE0 (eV)

σ2 (10

-3

Å2)

R factor

(%)

Ru3/CN

Ru-N 2.2±0.7 1.99±0.02 -2.3±0.9 7.4±1.2

0.02 Ru-Ru 1.6±0.5 2.53±0.02 5.8±0.6 15.0±0.9

Ru-C 2.4±0.6 3.18±0.02 7.2±1.1 8.6±0.8

Ru1/CN Ru-N 3.1±0.6 2.09±0.02 9.4±4.7 5.5±2.5 0.01

Ru foila

Ru-Ru 6* 2.67±0.02 -5.7±0.9 4.2±0.6

0.01

Ru-Ru 6* 2.72±0.02 3.7±0.5 1.8±0.6

RuO2b

Ru-O 2* 1.90±0.02 3.3±0.5 -13.6±1.0

0.01

Ru-O 4* 2.02±0.02 3.7±0.5 4.8±1.0

Ru-Ru 2* 3.10±0.02 5.2±0.6 -7.7±1.2

Ru-Ru 8* 3.47±0.02 5.5±0.6 3.2±0.5

aN is the coordination number; R is distance between absorber and backscatter atoms; σ

2 is

Debye-Waller factor (a measure of thermal and static disorder in absorber-scatterer distances); ΔE0 is

edge-energy shift (the difference between the zero kinetic energy value of the sample and that of the

theoretical model). R factor (%) indicates the goodness of the fit. Error bounds (accuracies) that

characterize the structural parameters obtained by EXAFS spectroscopy were estimated as N ± 20%; R

± 1%; σ2

± 20%; ΔE0 ± 20%. S02 was fixed to 0.85 as determined from Fe foil fitting. * is fixed

coordination number (N) according to the crystal structure. b Fiting range: 4.0≤ k (/Å) ≤ 15.4 Å

-1 and 1.6

S21

R ≤ R (Å) ≤ 3.0 Å. c Fiting range: 2.0 ≤ k (/Å) ≤ 14.2 Å

-1 and 0.7 ≤ R (Å) ≤3.9 Å.

Table S2. Structural parameters of bond length (R) and coordination number (N) from computational

simulations. a

Sample Bond N R(Å)

Ru3/CN

Ru-N 2 2.01±0.05

Ru-Ru 2 2.42±0.13

Ru1/CN Ru-N 4 1.96±0.01

Ru foil Ru-Ru 12 2.68±0.03

aN is the coordination number; R is the corresponding bond length. Ru-N coordination numbers are

slightly underestimated, which we assign to the quasi-two-dimensional structure of the simulation

model compared with the experimental three-dimensional CN architecture.

Table S3. Products and yields of products from the oxidation of primary alcohols catalyzed by Ru3/CNa

CHO

MeO

CHO

Br

CHO

HO

CHO

O2N

CHO CHO

Br

CHO

OH

N CHOCHO

2a

99% (99%)

R OH R H

O

1 2a-i

2b

97% (98%)

2c

96% (99%)

2d

97% (98%)

2e, 18 h

92% (98%)

2f

96% (99%)

2g

95% (97%)

2h, 18 h

93% (99%)

2i, 18 h

94% (98%)

Cat. Ru3/CN

H2O2, MeCN, 80oC, 12h

S22

aReaction conditions: primary alcohols (denoted as 1) (0.5 mmol, 1.0 eq), Ru3/CN (50 mg, 0.001 eq),

H2O2 (250 uL, 2.0 eq) and MeCN (2mL) were mixted and heated at 80oC for 12-18 hours. The products

of excessive oxidation were not detected even extending the reaction time. The yield of the products

(denoted as 2a-i) was determined by GC using tridecane as an internal standard. The GC yields were

listed in parentheses.

Table S4. ICP-AES analysis.

entry catalyst

Ru atomic wt% by

ICP-AES

(Ru)

1 Ru3/CN 0.10

2 Ru1/CN 0.23

3 Ru NPs/CN 1.1

S23

3. Characterization of Products and Selected H NMR Spectra

2-Aminobenzaldehyde

1H-NMR (400 MHz, CDCl3): δ = 9.86 (s, 1H), 7.49-7.47 (m, 1H), 7.33-7.29 (m, 1H), 6.76-6.73 (m, 1H),

6.64 (d, J=8.0Hz, 1H), 6.1 (brs, 2H). 9

2a. 4-Methylbenzaldehyde

1H-NMR (400 MHz, CDCl3): δ = 9.96 (s, 1H), 7.77 (d, J=8.0Hz, 2H), 7.32 (d, J=8.0Hz, 2H), 2.44 (s,

3H). 9

2b. 4-Methoxybenzaldehyde

1H-NMR (400 MHz, CDCl3): δ = 9.88 (s, 1H), 7.83 (d, J=8.0Hz, 2H), 6.99 (d, J=8.0Hz, 2H), 3.89 (s,

3H). 9

2c. 4-Bromobenzaldehyde

1H-NMR (400 MHz, CDCl3): δ = 9.98 (s, 1H), 7.74 (d, J=8.0Hz, 2H), 7.68 (d, J=8.0Hz, 2H).

9

S24

2d. 4-Hydroxybenzaldehyde

1H-NMR (400 MHz, CDCl3): δ = 9.86 (s, 1H), 7.84-7.80 (m, 2H), 6.99-6.96 (m, 2H), 6.25 (s, 1H).

9

2e. 4-Nitrobenzaldehyde

1H-NMR (400 MHz, CDCl3): δ = 10.16 (s, 1H), 8.39 (d, J=8.0Hz, 2H), 8.09-8.06 (m, 2H).

9

2f. 2-Bromobenzaldehyde

1H-NMR (400 MHz, CDCl3): δ = 10.37 (s, 1H), 7.93-7.90 (m, 1H), 7.66-7.63 (m, 1H), 7.47-7.41 (m,

2H). 9

2g. 2-Hydroxybenzaldehyde

1H-NMR (400 MHz, CDCl3): δ = 10.02 (s, 1H), 9.90 (s, 1H), 7.57-7.51 (m, 2H), 7.04-6.98 (m, 2H).

9

2h. Cinnamaldehyde

1H-NMR (400 MHz, CDCl3): δ = 9.70 (d, J=8.0Hz, 1H), 7.59-7.56 (m, 2H), 7.51-7.41 (m, 4H),

6.76-6.70 (m, 1H).10

S25

2i. Picolinaldehyde

1H-NMR (400 MHz, CDCl3): δ = 10.07 (d, J=4.0Hz, 1H), 8.78 (d, J=4.0Hz, 1H), 7.97-7.95 (m, 1H),

7.89-7.86 (m, 1H), 7.54-7.50 (m, 1H).11

S26

S27

S28

S29

S30

S31

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