Supplementary Information X-ray Snapshot Observation of Palladium ...
Supplementary Information X-ray Snapshot Observation of Palladium-Mediated Bromination in a Porous Complex
Aromatic
Koki Ikemoto1, Yasuhide Inokuma1, Kari Rissanen2 and Makoto Fujita1* 1
Department of Applied Chemistry, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan. 2
Department of Chemistry, NanoScience Center, University of Jyväskylä, P.O. Box 35, 40014 Jyväskylä, Finland.
Table of Contents Materials and Methods
S2–S8
X-ray Crystallographic Analysis
S9–S13
Figure S1. 1H NMR spectrum obtained by digestion of solvent-exchanged crystal 1•3 S14 Figure S2. 1H NMR spectrum obtained after X-ray observation of product 5
S14
Figure S3. Time-dependent X-ray diffraction data in the reaction
S15
Figure S4. Time-dependent IR spectra in the reaction
S16
Figure S5. Raman spectra
S17
Figure S6. Multiple C–H•••I interactions in the crystal structure of 1•4
S18
Figure S7. Columnar stacking in the crystal structure of 1•4
S18
Figure S8. Putative reaction mechanism
S19
References
S20
S1
Material and Methods Reagents and equipment Solvents and reagents were of reagent grade and purchased from TCI Co., Ltd., WAKO Pure Chemical Industries Ltd., and Sigma-Aldrich Co. recrystallized from hot water.
N–bromosuccinimide (NBS) was
All other reagents and solvents were used as obtained.
Dibenzo[f,h]quinolone and sodium methylxanthate were prepared according to the reported procedure1,2.
Silica gel column chromatography was performed on Wakogel C-300 (WAKO
Pure Chemical Industries Ltd.).
1
H and 13C NMR spectra were recorded on a Bruker DRX-500
equipped with 5 mm BBO gradient probe and on a Bruker AV-500 equipped with TCI gradient CryoProbe.
All NMR spectra data were collected at 300 K, and chemical shift values reported
here are with respect to an internal tetramethylsilane (TMS) standard.
Data are reported as
follows: chemical shift, multiplicity (s = singlet, d = doublet, t = triplet, q = quartet, m = multiplet), coupling constant in hertz (Hz), and integration.
IR measurements were carried out
as KBr pellets using a DIGILAB FTS-7000 instrument for organic molecules.
ATR-IR spectra
were measured on a DIGILAB FTS-7000 instrument with SPECAC golden gate single reflection diamond ATR accessory for network crystals.
Elemental analyses were performed
on the CE-440F CHN/O/S Elemental Analyzer (Exeter Analytical, Inc.).
High resolution mass
spectra were recorded on Bruker maXis or microTOF II spectrometer equipped with ESI probe or APPI probe.
Atomic absorption spectroscopy was performed on HITACHI Z-2000 series
polarized Zeeman Atomic Absorption Spectrophotometer. JASCO NRS-5100 with 785 nm excitation.
Raman spectra were recorded on
Single crystal X-ray diffraction data were
collected on a BRUKER APEX-II CCD rotating anode diffractometer equipped with focusing mirrors with MoKα (λ = 0.71073 Å) radiation under cryogenic conditions, which are controlled with a cryostat system equipped with a N2 generator (Japan Thermal Eng. Co., Ltd.).
S2
Synthesis
of
dibenzo[f,h]quinolinyl j
g
Me
m
O
f
k
Pd Me
a
c
A
mixture of
dibnezo[f,h]quinoline (642 mg, 2.80 mmol) in 200 mL of MeOH was refluxed for 24 h.
The resulting precipitate was
collected and washed with 10 mL of MeOH.
O
N d
acetylacetonate:
palladium(II) acetylacetonate (609 mg, 2.00 mmol) and
i h
e
palladium(II)
b
l
The yellow
solid was suspended in 35 × 2 mL of CH2Cl2 and centrifuged at 3000 ppm for 15 min, then the supernatant was filtered
through a disk filter with 0.20 µm pore size (25HP020AN, ADVANTEC).
The combined
filtrate was concentrated in vacuo to afford the title compound as as a yellow crystal (519 mg, 60%).
IR (KBr) 1580 (s), 1514 (s), 1427 (w), 1389 (m), 1263 (w), 753 (m) cm-1; 1H NMR
(CDCl3, 500 MHz) δ 8.93 (d, J = 5.0 Hz, 1H, Ha), 8.84 (d, J = 8.0 Hz, 1H, Hc), 8.60 (d, J = 8.0 Hz, 1H, Hd or Hg), 8.49 (d, J = 8.0 Hz, 1H, Hh), 8.18 (d, J = 8.0 Hz, 1H, Hd or Hg), 7.74 (d, J = 8.0 Hz, 1H, Hj), 7.71 (t, J = 8.0 Hz, 1H, He or Hf), 7.66 (t, J = 8.0 Hz, 1H, Hi), 7.55 (d, J = 8.0 Hz, 1H, He or Hf), 7.51 (dd, J = 8.0, 5.0 Hz, 1H, Hb), 5.46 (s, 1H, Hk), 2.17 (s, 1H, Hl or Hm), 2.12 (s, 1H, Hl or Hm);
13
C NMR (CDCl3, 125 MHz) δ 188.4 (Cq, CO), 186.9 (Cq, CO), 156.6
(Cq), 152,2 (Cq), 147.2 (CH), 139.9 (Cq), 132.3 (CH), 131.4 (Cq), 131.1 (Cq), 129.6 (CH), 128.9 (CH), 128.6 (CH), 127.7 (Cq), 127.3 (CH), 125.6 (Cq), 124.0 (CH), 123.6 (CH), 121.2 (CH), 118.1 (CH), 100.8 (CH), 28.3 (CH3), 27.8 (CH3);
Elemental analysis (%); Calcd for
C22H17NO2Pd: C 60.91, H 3.95, N 3.23; found: C 60.91, H 3.74, N 3.25; m/z: calcd for C22H17NO2Pd ([M+H]+) 434.0376, found 434.0384.
S3
HRMS (ESI-TOF)
Synthesis of dibenzo[f,h]quinolinyl palladium(II) methylxanthate (3): To a solution of dibenzo[f,h]quinolinyl palladium(II) acetylacetonate (86.8
i h
j
mg, 0.20 mmol) in 27 mL of CHCl3 was added a solution of
g S
f
OMe
Pd e
S
N d
a
c b
k
sodium methylxanthate (27.3 mg, 0.21 mmol) in 3.5 mL of MeOH dropwise. at r.t..
The reaction mixture was stirred for 12 h
Solvent was evaporated in vacuo, and the resulting
solid was suspended in 27 mL of CHCl3.
insoluble was removed by filtration and the filtrate was concentrated in vacuo. solid was washed with 10 mL of MeOH and collected by filtration. obtained as yellow powder (49.9 mg, 56%).
The white The resulting
The title compound was
IR (KBr) 1443 (m), 1240 (s), 1171 (m), 1038 (m),
750 (m) cm-1; 1H NMR (CDCl3, 500 MHz) δ 8.96 (d, J = 8.5 Hz, 1H, Hc), 8.71 (d, J = 5.0 Hz, 1H, Ha), 8.64 (d, J = 8.0 Hz, 1H, Hd or Hg), 8.55 (d, J = 8.0 Hz, 1H, Hd or Hg), 8.26 (d, J = 8.0 Hz, 1H, Hh), 7.76 (t, J = 8.0 Hz, 1H, He or Hf), 7.71 (t, J = 8.0 Hz, 1H, He or Hf), 7.56 (dd, J = 8.5, 5.0 Hz, 1H, Hb), 7.52 (t, J = 7.5 Hz, 1H, Hi), 7.37 (d, J = 7.0 Hz, 1H, Hj), 4.33 (s, 1H); 13C NMR (CDCl3, 125 MHz) δ 234.8 (Cq), 156.1 (Cq), 154.2 (Cq), 149.8 (CH), 140.7 (Cq), 133.0 (CH), 132.7 (CH), 132.0 (Cq), 131.2 (Cq), 129.6 (CH), 128.8 (CH), 127.5 (Cq), 127.4 (CH), 126.1 (Cq), 123.9 (CH), 123.5 (CH), 122.0 (CH), 118.5 (CH), 58.7 (CH3);
Elemental analysis
(%); Calcd for C19H13NOPdS2: C 51.65, H 2.97, N 3.17; found: C 51.63, H 3.08, N 3.05:
S4
Synthesis
of
as-synthesized
network
complex
1•3:
Onto
a
solution
of
2,4,6-tris(4-pyridyl)-1,3,5-triazine (2) (6.3 mg, 0.02 mmol) and dibenzo[f,h]quinolinyl palladium(II) methylxanthate (3) (13.3 mg, 0.03 mmol) in nitrobenzene/methanol (4.0 mL/1.0 mL) was carefully layered 0.50 mL of methanol, and subsequently 0.50 mL of methanol solution of ZnI2 (9.6 mg, 0.03 mmol) in a test tube (inner diameter 1 cm, height 10 cm). mixture was allowed to stand for 1 week at room temperature.
The
Resulting brown precipitate at
the bottom of the test tube was removed by a pipette and yellow crystals, which formed at the interface between the metal layer and the ligand layer, were collected and washed with nitrobenzene to give 1•3 in 34% yield (8.5 mg) based on 2 (The isolation yield of the complex is calculated as an averaged value of 5 batches.).
Elemental analysis (%); Calcd for
{[(ZnI2)3(2)2•(3)]•(C6H5NO2)4}n: C 37.70, H 2.28, N 9.46; found: C 38.06, H 2.01, N 9.48;
IR
(ATR) 1619 (w), 1575 (w), 1514 (s), 1375 (m), 1343 (s), 1315 (w), 1236 (m), 1059 (m), 1026 (m), 851 (w), 797 (m), 760 (w), 702 (s), 669 (s), 655 (s) cm-1.
Solvent replacement procedure of 1•3: As-synthesized network complex of 1•3 was immersed in acetonitrile (4 mL toward 10 mg of complex) and was allowed to stand at r.t. for 1 d, then the supernatant was removed by decantation. 3 of acetonitrile. by filtration.
This protocol was repeated three times with 4 mL ×
The crystals were directly used for the following reactions without collection
Elemental analysis (%); Calcd for {[(ZnI2)3(2)2•(3)]•(CH3CN)1}n: C 33.15, H
1.95, N 9.50; found: C 32.78, H 1.69, N 9.19;
IR (ATR) 1619 (w), 1574 (w), 1514 (s), 1371
(s), 1314 (w), 1239 (m), 1059 (m), 1026 (m), 801 (s), 759 (m), 655 (s) cm-1.
X-ray observation of 12-bromodibenzo[f,h]quinoline (5) within network crystal 1: The crystals 1•3 (8 mg, containing 0.004 mmol of 3), whose crystalline solvent in the pores was replaced with acetonitrile using the above-mentioned procedure, were transferred into a test tube (inner diameter 1 cm, height 10 cm) containing 4.0 mL of 0.025 M acetonitrile solution of N-bromosuccinimide (17.8 mg, 0.10 mmol).
The test tube was wrapped in aluminum foil and
the mixture was allowed to stand at r.t. for 1 d.
One of the resulting crystals were picked up
and directly measured by X-ray diffraction at 90 K.
Exclusive formation of
1
12-bromodibenzo[f,h]quinolone (5) was also confirmed by H NMR after the digestion of the crystals with DMSO-d6 (Figure S1). {[(ZnI2)3(2)2•(5)]}n: IR (ATR) 1619 (w), 1575 (w), 1516 (s), 1423 (w), 1372 (s), 1314 (w), 1058 (m), 1028 (m), 805 (s), 759 (m), 656 (s) cm-1.
S5
Isolation of 12-bromodibenzo[f,h]quinoline (5):
as-synthesized network 1•3 (132 mg, 0.058 mmol) was subjected to the
i h
j
solvent replacement with acetonitrile and the reaction with 0.025 M
g f
Br
e
The resulting crystals were The reaction
mixture was neutralized with 5 M NaOH aq. until pH became ca. 7 and
a
c
acetonitrile solution of NBS for 1 d.
collected and digested with 20 mL of 5 M HCl aq.
N d
According to the procedure above,
b
extracted with dichloromethane (20 × 2 mL).
Organic layer was
combined and washed with 20 mL of saturated NaCl aq., dried over Na2SO4, concentrated and purified by silica gel column chromatography using dichloromethane/hexane (1/1) as the eluent, to afford 5 as brown powder (8.8 mg, 49% yield).
IR (KBr) 1587 (w), 1558 (m), 1423 (m),
1395 (m), 1009 (m), 799 (m), 750 (s), 642 (m) cm-1;
1
H NMR (CDCl3, 500 MHz) δ 9.03 (dd, J
a
= 4.0, 1.5 Hz, 1H, H ), 8.86 (dd, J = 8.0, 1.5 Hz, 1H, Hc), 8.63 (d, J = 8.0 Hz, 1H, Hh), 8.60 (m, 1H, Hd or Hg), 8.53 (m, 1H, Hd or Hg), 8.09 (d, J = 7.5 Hz, 1H, Hj), 7.69–7.67 (m, 2H, He and Hf), 7.61 (dd, J = 8.0, 4.0 Hz, 1H, Hb), 7.50 (t, J = 8.0 Hz, 1H, Hi) ;
13
C NMR (CDCl3, 125
MHz) δ 145.5 (CH), 144.6 (Cq), 135.0 (CH), 133.2 (Cq), 129.4 (CH), 128.3 (Cq), 127.9 (Cq), 127.4 (CH), 127.2 (Cq), 127.1 (CH), 126.9 (CH), 124.2 (Cq), 122.8 (CH), 122.0 (CH), 121.4 (CH), 121.3 (CH), 119.4 (Cq);
Elemental analysis (%); Calcd for C17H10BrN: C 66.26, H 3.27,
N 4.55; found: C 66.09, H 3.10, N 4.51;
HRMS (ESI-TOF) m/z: calcd for C17H10BrN
([M+H]+) 308.0069, found 308.0060.
Time-dependent X-ray diffraction analysis: Time-dependent X-ray diffraction analysis in the reaction was carried out separately with 7 batches.
Crystals 1•3 (8 mg, containing 0.004 mmol
of 3), whose crystalline solvent in the pores was replaced with acetonitrile using the above-mentioned procedure, were transferred to test tubes (inner diameter 1 cm, height 10 cm) containing 4.0 mL of 0.025 M acetonitrile solution of N-bromosuccinimide (17.8 mg, 0.10 mmol).
The test tubes were wrapped in aluminum foil and the mixture was allowed to stand at
r.t. for 3 h.
The resulting crystals were picked up from a batch and directly analyzed by X-ray
diffraction at 90 K (Figure S3) and ATR-IR spectroscopy (Figure S4).
For the other 6 bathes,
the reaction supernatant was respectively replaced with 4.0 mL of fresh acetonitrile in order to wash away residual Br species in the pores.
X-ray diffraction data were collected at 15 min, 1
h, 2 h, 6 h, and 15 h after the wash by picking up a single crystal from each batches.
S6
Control
experiment
of
the
reaction
between
sodium
methylxanthate
and
N-bromosuccinimide: Our X-ray snapshot observation indicated that N-bromosuccinimide, usually known as bromo cation synthon, generated bromo anion in the reaction.
Indeed, the formation of bromo anion
was confirmed by the fact that the addition of AgNO3 after the reaction in acetonitrile afforded pale yellow precipitation of AgBr.
We can conclude that oxidation reaction of xanthate ligand
feeded bromo anion by performing the following experiment:
Br
S NaS
OMe
N
O
+
S
O CH3CN r.t., 10 min
NBS (1.0 eq.)
MeO
S S
S
OMe
+
NaBr
6 50% yield
To a solution of sodium methylxanthate (650.8 mg, 5.0 mmol) in 150 mL of acetonitrile was added N-bromosuccinimide (890.0 mg, 5.0 mmol) portion-wise, and the mixture was stirred for 10 min.
The resulting precipitate was collected by filtration, washed with 20 mL of
acetonitrile and dried in vacuo to afford 409 mg of pale yellow powder, in which powder X-ray diffraction exhibited peaks derived only from NaBr.
The filtrate was concentrated in vacuo
and purified by silica gel chromatography using dichloromethane/hexane (1/2) as the eluent to afford disulfide 6 as yellow oil (267 mg, 50% yield). 1
The formation of compound 6 was
13
confirmed by GC-MS, H and C NMR spectra, which match the reported values3.
Br S MeO
S S
S
+
O
N
AgNO3 (5.0 eq.)
O CH3CN r.t., 1 d
OMe
6
NBS (5.0 eq.)
AgBr
To a solution of disulfide 6 (103 mg, 0.48 mmol) in 15 mL of acetonitrile was added N-bromosuccinimide (428 mg, 2.4 mmol) portion-wise, and the mixture was stirred for 1 d.
1
H
NMR analysis in CDCl3 showed as least 6 peaks in MeO region, suggesting the formation of complicated mixture.
Addition of AgNO3 (408 mg, 2.4 mmol) into the reaction solution
caused precipitate, which was collected by filtration, washed with 5 mL of acetonitrile.
333
mg of pale yellow powder was obtained and characterized as AgBr by powder X-ray diffraction.
S7
Control experiment of the reaction between Pd complex 3 and N-bromosuccinimide in solution: Br N
O S
(NBS)
Br
OMe
Pd N
O
S
CDCl 3/CD3CN
N
r.t., 4 h 5
3
77% NMR yield
To a solution of Pd complex 3 (8.84 mg, 0.02 mmol) in CDCl3 3.0 mL and a few drops of CD3CN was added N-bromosuccinimide (3.56 mg, 0.02 mmol) portion-wise, and the mixture was stirred for 4 h.
1
H NMR study of the solution showed the complete disappearance of 3
and the formation of 5 in 77% NMR yield.
S8
X-ray Crystallographic Analysis The data collections were done using a Bruker Apex-II CCD rotating anode diffractometer with focusing mirrors with Mo-Kα (λ = 0.71073 Å) radiation.
Bruker APEX2 software4 was used
for the data collections and CrysAlisPro5 for the data processing.
The structures were solved
by charge flipping with SUPERFLIP6 and refined by full-matrix least-squares methods using SHELXL-20137 within the OLEX28 suite of programs.
Empirical absorption correction using
spherical harmonics, implemented in SCALE3 ABSPACK scaling algorithm within the CrysAlisPro software. atom model.
All C-H hydrogen positions were calculated and refined using a riding
In all structures, the framework atoms was first located and refined (no disorder
of the framework was observed) after which in each case the guest (3, 4 and 5) was clearly visible in the difference electron density map.
However the refinements of the guest with full
occupancy resulted in larger than expected temperature factors coupled with one (1•3 and 1•5) or two (1•4) large additional electron density peaks.
Careful refinements with minimal
restraints and constraints (see below) revealed the guest to be slightly disordered in plane of the guest, 90:10 for 1•3, 80:20 for 1•4 and 95:5 for 1•5.
The extra residual electron density peaks
were identified to belong to the minor disorder component and in a case of 1•3 was assigned as Pd, in 1•4 as Pd and Br and in 1•5 as Br atoms.
Only the heavy atoms of the minor component
of the disordered guest could be reliably located and taken into the final refinements.
In the
structure 1•3 altogether 13 restraints (DFIX) and one constraint (EADP) were applied to the three solvent nitrobenzene molecules (with occupancies 1/2, 1/3, 1/3), two EDAP constraints had to be used to equalize the guest 3 carbon atoms.
Due to the quite low quality of the data
for 1•4, the following restraints and constraints had to be applied: three DFIX and one EADP for the solvent acetonitrile; due to the positional disorder and uneven thermal movement of the guest 4 atoms in the final anisotropic refinement, they were constrained to have the same thermal movement using one general EDAP to 23 atoms, in addition two EADP’s were used for the minor component Pd and Br. the guest 5 was applied.
For the 1•5, one EDAP constraint equalizing two carbons for
A few bad reflections were omitted from the final refinements: 12 for
1•3, 9 for 1•4 and 4 reflections for 1•5.
As the crystal lattice in each three structures contains
large voids filled with a lot of scattered electron density which could not be modeled chemically, after locating and modeling any chemically reasonable solvent molecule(s), the remaining electron density was flattened out using the solvent masking protocol inside OLEX2 resulting in a decrease in the final R value, reported below as Rmask and Runmask.
S9
Crystal data for 1•3: M = 2134.09, yellow prism, 0.13 × 0.05 × 0.05 mm3, Orthorhombic, space group Pbca, a = 27.8747(4) Å, b = 13.78762(17) Å, c = 45.4150(5) Å, V = 17454.1(4) Å3, Z = 8, Dc = 1.624 g/cm3, F000 = 8074, µ = 3.226 mm-1, T = 90.0(1) K, 2θmax = 50.10°, 15455 reflections used, 12970 with Io > 2σ(Io), Rint = 0.0445, 839 parameters, 13 restraints, GoF = 1.043, Rmask = 0.0616 [Io > 2σ(Io)], wRmask= 0.1917 (all reflections), 3.574 < ∆ρ < –2.115 e/Å3. [Runmask = 0.0676 [Io > 2σ(Io)], wRunmask= 0.2190 (all reflections)] CCDC deposit number: 967379
Response to A and B level checkcif alerts: Alert level A PLAT307_ALERT_2_A Isolated Metal Atom (Unusual !) ................
2σ(I), 1011 parameters, 1.47 < θ < 27.27°, final R factors R1 = 0.0754, wR2 = 0.2143. The SQUEEZE program in PLATON was used for analysis to remove the disordered solvent densities in the pore.
Disordered model (a) 59% occupancy
(b) 41% occupancy
Two component disordered model in the crystal structure of 1•3 after the solvent exchange with acetonitrile.
ORTEP diagrams are drawn at 30% probability level.
S11
Crystal data for 1•4: M = 2024.99, yellow prism, 0.08 × 0.06 × 0.06 mm3, Orthorhombic, space group Pbca, a = 27.6775(9) Å, b = 13.7981(3) Å, c = 44.3415(11) Å, V = 16933.9(8) Å3, Z = 8, Dc = 1.583 g/cm3, F000 = 7554, µ= 3.743 mm-1, T = 90.0(1) K, 2θmax = 50.10°, 14996 reflections used, 7541 with Io > 2σ(Io), Rint = 0.1949, 510 parameters, 3 restraints, GoF = 1.249, R = 0.1278 [Io > 2σ(Io)], wR= 0.3870 (all reflections), 3.201 < ∆ρ < –3.235 e/Å3.
[Runmask =
0.1638 [Io > 2σ(Io)], wRunmask= 0.4782 (all reflections)] CCDC deposit number: 967380
Response to A and B level checkcif alerts: Alert level A PLAT308_ALERT_2_A Single Bonded Metal Atom (Unusual !) ...........
0.35
Weighted R factor given
0.389
Crystal system given = orthorhombic PLAT019_ALERT_1_B Check _diffrn_measured_fraction_theta_full/_max
0.974
PLAT084_ALERT_3_B High wR2 Value (i.e. > 0.25) ...................
0.39
PLAT242_ALERT_2_B Low
Ueq as Compared to Neighbors for .....
Zn4 Check
PLAT250_ALERT_2_B Large U3/U1 Ratio for Average U(i,j) Tensor ....
4.3 Note
PLAT972_ALERT_2_B Large Calcd. Non-Metal Negative Residual Density
-3.32 eA-3
PLAT972_ALERT_2_B Large Calcd. Non-Metal Negative Residual Density
-2.96 eA-3
Response:
1. – 5. The B level alerts result in from weakly diffracting crystal and low quality of the data 6. and 7. Probably due to difficulties in/inefficient absorption correction
S12
Crystal data for 1•5: M = 1878.94, yellow prism, 0.15 × 0.14 × 0.14 mm3, Orthorhombic, space group Pbca, a = 27.5504(3) Å, b = 13.83530(19) Å, c = 44.5398(6) Å, V = 16977.2(4) Å3, Z = 8, Dc = 1.470 g/cm3, F000 = 7040, µ= 3.526 mm-1, T = 90.0(1) K, 2θmax = 50.0°, 14965 reflections used, 12615 with Io > 2σ(Io), Rint = 0.0357, 683 parameters, 0 restraints, GoF = 1.050, R = 0.0825 [Io > 2σ(Io)], wR= 0.2791 (all reflections), 4.325 < ∆ρ < –2.199 e/Å3.
[Runmask =
0.1242 [Io > 2σ(Io)], wRunmask= 0.4251 (all reflections)] CCDC deposit number: 967381
Alert level A PLAT973_ALERT_2_A Large Calcd. Positive Residual Density on
Response:
Probably due to difficulties in/inefficient absorption correction
S13
Zn13
2.25 eA-3
*
* a d&g
b e&f
c
j
h
i *
*
* i h
10
9.5
9
8.5
8
7.5
7
j
g
ppm
k
S
f
k
OMe
Pd
e
S
N
d
a
c b
10
9
8
7
6
5
4
3
2
1
0
ppm
Figure S1. 1H NMR spectrum (500 MHz, DMSO-d6, 300 K) obtained by the digestion of the solvent-exchanged crystal 1•3.
Asterisks correspond to peaks derived from ligand 2 and
solvent.
i g
h
j
f
Br
e d c
*
*
N a
b&d&g
b
c
9.5
a
9
h d&g
j
8.5
i
8
7.5
ppm
Figure S2. 1H NMR spectrum of the reaction mixture obtained by digestion of the crystals after X-ray observation of 5 (500 MHz, DMSO-d6, 300 K). from ligand 2.
S14
Asterisks correspond to peaks derived
(a) before the wash (0.60σ)
(b) before the wash (0.95σ)
unassignable electron density
(c) 15 min after the wash
unassignable electron density
site 1
site 1
(e) 2 h after the wash
(d) 1 h after the wash
site 1
(f)
6 h after the wash
Me N
Pd
N Br
4
site 1
(g) 15 h after the wash
Pd–Br
C–Br
Pd–Br
(h) final state N Br
5
C–Br
Pd–Br
C–Br
Figure S3. Electron density maps (Fo) obtained by time-dependent X-ray diffradtion in the reaction.
(a), (b) Electron density maps (Fo) before the wash.
The same data are contoured at
different σ levels, namely 0.60σ level for (a) and 0.95σ level for (b), respectively. Unassignable electron densitiy in the pores hampered precise identification of the resulting intermediate at this stage.
(c)–(g) Electron density maps (Fo) obtained at 15 min, 1 h, 2 h, 6 h,
and 15 h after the wash.
After the wash, the strong electron densities in the pores disappeared
and electron density at the coordination site of Pd trans to the nitrogen donor (indicated as site 1) gradually increased and reached maximum after 2 h.
Crystallographic refinement of data in
(e) showed the formation of intermediate 4, which gradually converted product 5 as time passed. (h) Electron density maps (Fo) in the final state.
All maps are depicted within 2.5 Å-thick slice
of the cartridge molecules and contoured at the same absolute 0.95σ level unless otherwise mentioned.
S15
C O streching of CO2
C N streching of free CH 3CN
transmittance
0 min
1h
3h
8h
CH 3CN–Pd 2500
2450
2400
2350
2300
2250
2200
wavenumber (cm -1)
Figure S4. Time-dependent ATR-IR spectra in the reaction.
A transient peak at 2326 cm-1,
which is attributable to the CN stretching in CH3CN-Pd structure, is emphasized with a red rectangle.
S16
intensity (a.u.) 250
200
150
100
Raman Shift (cm -1)
in the reaction (2 h after the wash)
before the reaction
1800
1600
1400
1200
1000
800
600
400
200
Raman Shift (cm-1)
Figure S5. Raman spectra of a single crystal 1 with 785 nm excitation.
One was obtained
before the reaction (black) and the other was obtained after the incubation of NBS for 3 h, followed by the wash for 2 h (red).
The inset is a magnified view of the region of Pd-Br bond.
S17
(a)
(b)
N
N
I
N
N
I
Zn
N
C Pd Br
N N
N
H C
C H 3.14 Å I H
N
N 3.27 Å
Zn
I
Figure S6. Multiple C–H•••I interactions between methyl group of the coordinating acetonitrile and ZnI2 in the crystal structure of 1•4. Figure 3b.
(a) Sideview of the pore in the crystal structure of
(b) ChemDraw representation at the inserted circle in (a).
(a)
(b)
Pd (green)
Pd (green)
Figure S7. Columnar structure between 2 and 4 in the crystal structure of 1•4. (b) topview.
(a) Sideview.
Apical positions of Pd are covered with ligand 2, making the formation of high
oxidation state Pd complexes unrealistic in the network crystal.
S18
CH3CN
Br N C
II
Pd
S S
OCH3
N
+ O
N
O
C (NBS)
3
S 1/2
N C
H 3CO
II
Pd
NCCH3 X
X = CH 3CN or Br or O
N
O
S S
N
S
OCH3 NBS
= C
oxidized S compounds + n Br X
N C
N
Br
5
C Pd 0
II
Pd
NCCH3 Br
4
(eluted out into the solution)
Figure S8. A putative reaction mechanism. NBS oxidizes CH3OCS2- to generate Br- and (CH3OCS2)2.
This redox reaction (CH3OCS2Na to (CH3OCS2)2) was independently confirmed
in a solution experiment.
(See control experiment in page S7)
A Pd(II)/Pd(0) catalytic cycle
can be proposed for the aromatic bromination by assuming the reoxidation of Pd(0) with NBS (i. e., Pd(0) + “Br+” --> Pd(II) + “Br-“).
S19
References 1.
Nagao, I.; Shimizu, M.; Hiyama, T. Angew. Chem. Int. Ed. 2009, 48, 7573–7576.
2.
Ma, H.; Wang, G.; Yee, G. T.; Petersen, J. L.; Jensen, M. P. Inorg. Chim. Acta 2009, 362, 4563–4569.
3.
Schroll, A. L.; Eastep, S. J.; Barany, G. J. Org. Chem. 1990, 55, 1475–1479.
4.
Bruker (2007), APEX2, Bruker AXS Inc., Madison, Wisconsin, USA.
5.
Agilent (2011), CrysAlis PRO, Agilent Technologies UK Ltd, Yarnton, England.
6.
Palatinus, L.; Chapuis, G. J. Appl. Cryst. 2007, 40, 786–790.
7.
Sheldrick, G. M. Acta Cryst. 2008, A64, 112–122.
8.
Dolomanov, O. V.; Bourhis, L. J.; Gildea, R. J.; Howard, J. a. K.; Puschmann, H. J. Appl. Cryst. 2009, 42, 339–341.
S20
Aromatic
Koki Ikemoto1, Yasuhide Inokuma1, Kari Rissanen2 and Makoto Fujita1* 1
Department of Applied Chemistry, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan. 2
Department of Chemistry, NanoScience Center, University of Jyväskylä, P.O. Box 35, 40014 Jyväskylä, Finland.
Table of Contents Materials and Methods
S2–S8
X-ray Crystallographic Analysis
S9–S13
Figure S1. 1H NMR spectrum obtained by digestion of solvent-exchanged crystal 1•3 S14 Figure S2. 1H NMR spectrum obtained after X-ray observation of product 5
S14
Figure S3. Time-dependent X-ray diffraction data in the reaction
S15
Figure S4. Time-dependent IR spectra in the reaction
S16
Figure S5. Raman spectra
S17
Figure S6. Multiple C–H•••I interactions in the crystal structure of 1•4
S18
Figure S7. Columnar stacking in the crystal structure of 1•4
S18
Figure S8. Putative reaction mechanism
S19
References
S20
S1
Material and Methods Reagents and equipment Solvents and reagents were of reagent grade and purchased from TCI Co., Ltd., WAKO Pure Chemical Industries Ltd., and Sigma-Aldrich Co. recrystallized from hot water.
N–bromosuccinimide (NBS) was
All other reagents and solvents were used as obtained.
Dibenzo[f,h]quinolone and sodium methylxanthate were prepared according to the reported procedure1,2.
Silica gel column chromatography was performed on Wakogel C-300 (WAKO
Pure Chemical Industries Ltd.).
1
H and 13C NMR spectra were recorded on a Bruker DRX-500
equipped with 5 mm BBO gradient probe and on a Bruker AV-500 equipped with TCI gradient CryoProbe.
All NMR spectra data were collected at 300 K, and chemical shift values reported
here are with respect to an internal tetramethylsilane (TMS) standard.
Data are reported as
follows: chemical shift, multiplicity (s = singlet, d = doublet, t = triplet, q = quartet, m = multiplet), coupling constant in hertz (Hz), and integration.
IR measurements were carried out
as KBr pellets using a DIGILAB FTS-7000 instrument for organic molecules.
ATR-IR spectra
were measured on a DIGILAB FTS-7000 instrument with SPECAC golden gate single reflection diamond ATR accessory for network crystals.
Elemental analyses were performed
on the CE-440F CHN/O/S Elemental Analyzer (Exeter Analytical, Inc.).
High resolution mass
spectra were recorded on Bruker maXis or microTOF II spectrometer equipped with ESI probe or APPI probe.
Atomic absorption spectroscopy was performed on HITACHI Z-2000 series
polarized Zeeman Atomic Absorption Spectrophotometer. JASCO NRS-5100 with 785 nm excitation.
Raman spectra were recorded on
Single crystal X-ray diffraction data were
collected on a BRUKER APEX-II CCD rotating anode diffractometer equipped with focusing mirrors with MoKα (λ = 0.71073 Å) radiation under cryogenic conditions, which are controlled with a cryostat system equipped with a N2 generator (Japan Thermal Eng. Co., Ltd.).
S2
Synthesis
of
dibenzo[f,h]quinolinyl j
g
Me
m
O
f
k
Pd Me
a
c
A
mixture of
dibnezo[f,h]quinoline (642 mg, 2.80 mmol) in 200 mL of MeOH was refluxed for 24 h.
The resulting precipitate was
collected and washed with 10 mL of MeOH.
O
N d
acetylacetonate:
palladium(II) acetylacetonate (609 mg, 2.00 mmol) and
i h
e
palladium(II)
b
l
The yellow
solid was suspended in 35 × 2 mL of CH2Cl2 and centrifuged at 3000 ppm for 15 min, then the supernatant was filtered
through a disk filter with 0.20 µm pore size (25HP020AN, ADVANTEC).
The combined
filtrate was concentrated in vacuo to afford the title compound as as a yellow crystal (519 mg, 60%).
IR (KBr) 1580 (s), 1514 (s), 1427 (w), 1389 (m), 1263 (w), 753 (m) cm-1; 1H NMR
(CDCl3, 500 MHz) δ 8.93 (d, J = 5.0 Hz, 1H, Ha), 8.84 (d, J = 8.0 Hz, 1H, Hc), 8.60 (d, J = 8.0 Hz, 1H, Hd or Hg), 8.49 (d, J = 8.0 Hz, 1H, Hh), 8.18 (d, J = 8.0 Hz, 1H, Hd or Hg), 7.74 (d, J = 8.0 Hz, 1H, Hj), 7.71 (t, J = 8.0 Hz, 1H, He or Hf), 7.66 (t, J = 8.0 Hz, 1H, Hi), 7.55 (d, J = 8.0 Hz, 1H, He or Hf), 7.51 (dd, J = 8.0, 5.0 Hz, 1H, Hb), 5.46 (s, 1H, Hk), 2.17 (s, 1H, Hl or Hm), 2.12 (s, 1H, Hl or Hm);
13
C NMR (CDCl3, 125 MHz) δ 188.4 (Cq, CO), 186.9 (Cq, CO), 156.6
(Cq), 152,2 (Cq), 147.2 (CH), 139.9 (Cq), 132.3 (CH), 131.4 (Cq), 131.1 (Cq), 129.6 (CH), 128.9 (CH), 128.6 (CH), 127.7 (Cq), 127.3 (CH), 125.6 (Cq), 124.0 (CH), 123.6 (CH), 121.2 (CH), 118.1 (CH), 100.8 (CH), 28.3 (CH3), 27.8 (CH3);
Elemental analysis (%); Calcd for
C22H17NO2Pd: C 60.91, H 3.95, N 3.23; found: C 60.91, H 3.74, N 3.25; m/z: calcd for C22H17NO2Pd ([M+H]+) 434.0376, found 434.0384.
S3
HRMS (ESI-TOF)
Synthesis of dibenzo[f,h]quinolinyl palladium(II) methylxanthate (3): To a solution of dibenzo[f,h]quinolinyl palladium(II) acetylacetonate (86.8
i h
j
mg, 0.20 mmol) in 27 mL of CHCl3 was added a solution of
g S
f
OMe
Pd e
S
N d
a
c b
k
sodium methylxanthate (27.3 mg, 0.21 mmol) in 3.5 mL of MeOH dropwise. at r.t..
The reaction mixture was stirred for 12 h
Solvent was evaporated in vacuo, and the resulting
solid was suspended in 27 mL of CHCl3.
insoluble was removed by filtration and the filtrate was concentrated in vacuo. solid was washed with 10 mL of MeOH and collected by filtration. obtained as yellow powder (49.9 mg, 56%).
The white The resulting
The title compound was
IR (KBr) 1443 (m), 1240 (s), 1171 (m), 1038 (m),
750 (m) cm-1; 1H NMR (CDCl3, 500 MHz) δ 8.96 (d, J = 8.5 Hz, 1H, Hc), 8.71 (d, J = 5.0 Hz, 1H, Ha), 8.64 (d, J = 8.0 Hz, 1H, Hd or Hg), 8.55 (d, J = 8.0 Hz, 1H, Hd or Hg), 8.26 (d, J = 8.0 Hz, 1H, Hh), 7.76 (t, J = 8.0 Hz, 1H, He or Hf), 7.71 (t, J = 8.0 Hz, 1H, He or Hf), 7.56 (dd, J = 8.5, 5.0 Hz, 1H, Hb), 7.52 (t, J = 7.5 Hz, 1H, Hi), 7.37 (d, J = 7.0 Hz, 1H, Hj), 4.33 (s, 1H); 13C NMR (CDCl3, 125 MHz) δ 234.8 (Cq), 156.1 (Cq), 154.2 (Cq), 149.8 (CH), 140.7 (Cq), 133.0 (CH), 132.7 (CH), 132.0 (Cq), 131.2 (Cq), 129.6 (CH), 128.8 (CH), 127.5 (Cq), 127.4 (CH), 126.1 (Cq), 123.9 (CH), 123.5 (CH), 122.0 (CH), 118.5 (CH), 58.7 (CH3);
Elemental analysis
(%); Calcd for C19H13NOPdS2: C 51.65, H 2.97, N 3.17; found: C 51.63, H 3.08, N 3.05:
S4
Synthesis
of
as-synthesized
network
complex
1•3:
Onto
a
solution
of
2,4,6-tris(4-pyridyl)-1,3,5-triazine (2) (6.3 mg, 0.02 mmol) and dibenzo[f,h]quinolinyl palladium(II) methylxanthate (3) (13.3 mg, 0.03 mmol) in nitrobenzene/methanol (4.0 mL/1.0 mL) was carefully layered 0.50 mL of methanol, and subsequently 0.50 mL of methanol solution of ZnI2 (9.6 mg, 0.03 mmol) in a test tube (inner diameter 1 cm, height 10 cm). mixture was allowed to stand for 1 week at room temperature.
The
Resulting brown precipitate at
the bottom of the test tube was removed by a pipette and yellow crystals, which formed at the interface between the metal layer and the ligand layer, were collected and washed with nitrobenzene to give 1•3 in 34% yield (8.5 mg) based on 2 (The isolation yield of the complex is calculated as an averaged value of 5 batches.).
Elemental analysis (%); Calcd for
{[(ZnI2)3(2)2•(3)]•(C6H5NO2)4}n: C 37.70, H 2.28, N 9.46; found: C 38.06, H 2.01, N 9.48;
IR
(ATR) 1619 (w), 1575 (w), 1514 (s), 1375 (m), 1343 (s), 1315 (w), 1236 (m), 1059 (m), 1026 (m), 851 (w), 797 (m), 760 (w), 702 (s), 669 (s), 655 (s) cm-1.
Solvent replacement procedure of 1•3: As-synthesized network complex of 1•3 was immersed in acetonitrile (4 mL toward 10 mg of complex) and was allowed to stand at r.t. for 1 d, then the supernatant was removed by decantation. 3 of acetonitrile. by filtration.
This protocol was repeated three times with 4 mL ×
The crystals were directly used for the following reactions without collection
Elemental analysis (%); Calcd for {[(ZnI2)3(2)2•(3)]•(CH3CN)1}n: C 33.15, H
1.95, N 9.50; found: C 32.78, H 1.69, N 9.19;
IR (ATR) 1619 (w), 1574 (w), 1514 (s), 1371
(s), 1314 (w), 1239 (m), 1059 (m), 1026 (m), 801 (s), 759 (m), 655 (s) cm-1.
X-ray observation of 12-bromodibenzo[f,h]quinoline (5) within network crystal 1: The crystals 1•3 (8 mg, containing 0.004 mmol of 3), whose crystalline solvent in the pores was replaced with acetonitrile using the above-mentioned procedure, were transferred into a test tube (inner diameter 1 cm, height 10 cm) containing 4.0 mL of 0.025 M acetonitrile solution of N-bromosuccinimide (17.8 mg, 0.10 mmol).
The test tube was wrapped in aluminum foil and
the mixture was allowed to stand at r.t. for 1 d.
One of the resulting crystals were picked up
and directly measured by X-ray diffraction at 90 K.
Exclusive formation of
1
12-bromodibenzo[f,h]quinolone (5) was also confirmed by H NMR after the digestion of the crystals with DMSO-d6 (Figure S1). {[(ZnI2)3(2)2•(5)]}n: IR (ATR) 1619 (w), 1575 (w), 1516 (s), 1423 (w), 1372 (s), 1314 (w), 1058 (m), 1028 (m), 805 (s), 759 (m), 656 (s) cm-1.
S5
Isolation of 12-bromodibenzo[f,h]quinoline (5):
as-synthesized network 1•3 (132 mg, 0.058 mmol) was subjected to the
i h
j
solvent replacement with acetonitrile and the reaction with 0.025 M
g f
Br
e
The resulting crystals were The reaction
mixture was neutralized with 5 M NaOH aq. until pH became ca. 7 and
a
c
acetonitrile solution of NBS for 1 d.
collected and digested with 20 mL of 5 M HCl aq.
N d
According to the procedure above,
b
extracted with dichloromethane (20 × 2 mL).
Organic layer was
combined and washed with 20 mL of saturated NaCl aq., dried over Na2SO4, concentrated and purified by silica gel column chromatography using dichloromethane/hexane (1/1) as the eluent, to afford 5 as brown powder (8.8 mg, 49% yield).
IR (KBr) 1587 (w), 1558 (m), 1423 (m),
1395 (m), 1009 (m), 799 (m), 750 (s), 642 (m) cm-1;
1
H NMR (CDCl3, 500 MHz) δ 9.03 (dd, J
a
= 4.0, 1.5 Hz, 1H, H ), 8.86 (dd, J = 8.0, 1.5 Hz, 1H, Hc), 8.63 (d, J = 8.0 Hz, 1H, Hh), 8.60 (m, 1H, Hd or Hg), 8.53 (m, 1H, Hd or Hg), 8.09 (d, J = 7.5 Hz, 1H, Hj), 7.69–7.67 (m, 2H, He and Hf), 7.61 (dd, J = 8.0, 4.0 Hz, 1H, Hb), 7.50 (t, J = 8.0 Hz, 1H, Hi) ;
13
C NMR (CDCl3, 125
MHz) δ 145.5 (CH), 144.6 (Cq), 135.0 (CH), 133.2 (Cq), 129.4 (CH), 128.3 (Cq), 127.9 (Cq), 127.4 (CH), 127.2 (Cq), 127.1 (CH), 126.9 (CH), 124.2 (Cq), 122.8 (CH), 122.0 (CH), 121.4 (CH), 121.3 (CH), 119.4 (Cq);
Elemental analysis (%); Calcd for C17H10BrN: C 66.26, H 3.27,
N 4.55; found: C 66.09, H 3.10, N 4.51;
HRMS (ESI-TOF) m/z: calcd for C17H10BrN
([M+H]+) 308.0069, found 308.0060.
Time-dependent X-ray diffraction analysis: Time-dependent X-ray diffraction analysis in the reaction was carried out separately with 7 batches.
Crystals 1•3 (8 mg, containing 0.004 mmol
of 3), whose crystalline solvent in the pores was replaced with acetonitrile using the above-mentioned procedure, were transferred to test tubes (inner diameter 1 cm, height 10 cm) containing 4.0 mL of 0.025 M acetonitrile solution of N-bromosuccinimide (17.8 mg, 0.10 mmol).
The test tubes were wrapped in aluminum foil and the mixture was allowed to stand at
r.t. for 3 h.
The resulting crystals were picked up from a batch and directly analyzed by X-ray
diffraction at 90 K (Figure S3) and ATR-IR spectroscopy (Figure S4).
For the other 6 bathes,
the reaction supernatant was respectively replaced with 4.0 mL of fresh acetonitrile in order to wash away residual Br species in the pores.
X-ray diffraction data were collected at 15 min, 1
h, 2 h, 6 h, and 15 h after the wash by picking up a single crystal from each batches.
S6
Control
experiment
of
the
reaction
between
sodium
methylxanthate
and
N-bromosuccinimide: Our X-ray snapshot observation indicated that N-bromosuccinimide, usually known as bromo cation synthon, generated bromo anion in the reaction.
Indeed, the formation of bromo anion
was confirmed by the fact that the addition of AgNO3 after the reaction in acetonitrile afforded pale yellow precipitation of AgBr.
We can conclude that oxidation reaction of xanthate ligand
feeded bromo anion by performing the following experiment:
Br
S NaS
OMe
N
O
+
S
O CH3CN r.t., 10 min
NBS (1.0 eq.)
MeO
S S
S
OMe
+
NaBr
6 50% yield
To a solution of sodium methylxanthate (650.8 mg, 5.0 mmol) in 150 mL of acetonitrile was added N-bromosuccinimide (890.0 mg, 5.0 mmol) portion-wise, and the mixture was stirred for 10 min.
The resulting precipitate was collected by filtration, washed with 20 mL of
acetonitrile and dried in vacuo to afford 409 mg of pale yellow powder, in which powder X-ray diffraction exhibited peaks derived only from NaBr.
The filtrate was concentrated in vacuo
and purified by silica gel chromatography using dichloromethane/hexane (1/2) as the eluent to afford disulfide 6 as yellow oil (267 mg, 50% yield). 1
The formation of compound 6 was
13
confirmed by GC-MS, H and C NMR spectra, which match the reported values3.
Br S MeO
S S
S
+
O
N
AgNO3 (5.0 eq.)
O CH3CN r.t., 1 d
OMe
6
NBS (5.0 eq.)
AgBr
To a solution of disulfide 6 (103 mg, 0.48 mmol) in 15 mL of acetonitrile was added N-bromosuccinimide (428 mg, 2.4 mmol) portion-wise, and the mixture was stirred for 1 d.
1
H
NMR analysis in CDCl3 showed as least 6 peaks in MeO region, suggesting the formation of complicated mixture.
Addition of AgNO3 (408 mg, 2.4 mmol) into the reaction solution
caused precipitate, which was collected by filtration, washed with 5 mL of acetonitrile.
333
mg of pale yellow powder was obtained and characterized as AgBr by powder X-ray diffraction.
S7
Control experiment of the reaction between Pd complex 3 and N-bromosuccinimide in solution: Br N
O S
(NBS)
Br
OMe
Pd N
O
S
CDCl 3/CD3CN
N
r.t., 4 h 5
3
77% NMR yield
To a solution of Pd complex 3 (8.84 mg, 0.02 mmol) in CDCl3 3.0 mL and a few drops of CD3CN was added N-bromosuccinimide (3.56 mg, 0.02 mmol) portion-wise, and the mixture was stirred for 4 h.
1
H NMR study of the solution showed the complete disappearance of 3
and the formation of 5 in 77% NMR yield.
S8
X-ray Crystallographic Analysis The data collections were done using a Bruker Apex-II CCD rotating anode diffractometer with focusing mirrors with Mo-Kα (λ = 0.71073 Å) radiation.
Bruker APEX2 software4 was used
for the data collections and CrysAlisPro5 for the data processing.
The structures were solved
by charge flipping with SUPERFLIP6 and refined by full-matrix least-squares methods using SHELXL-20137 within the OLEX28 suite of programs.
Empirical absorption correction using
spherical harmonics, implemented in SCALE3 ABSPACK scaling algorithm within the CrysAlisPro software. atom model.
All C-H hydrogen positions were calculated and refined using a riding
In all structures, the framework atoms was first located and refined (no disorder
of the framework was observed) after which in each case the guest (3, 4 and 5) was clearly visible in the difference electron density map.
However the refinements of the guest with full
occupancy resulted in larger than expected temperature factors coupled with one (1•3 and 1•5) or two (1•4) large additional electron density peaks.
Careful refinements with minimal
restraints and constraints (see below) revealed the guest to be slightly disordered in plane of the guest, 90:10 for 1•3, 80:20 for 1•4 and 95:5 for 1•5.
The extra residual electron density peaks
were identified to belong to the minor disorder component and in a case of 1•3 was assigned as Pd, in 1•4 as Pd and Br and in 1•5 as Br atoms.
Only the heavy atoms of the minor component
of the disordered guest could be reliably located and taken into the final refinements.
In the
structure 1•3 altogether 13 restraints (DFIX) and one constraint (EADP) were applied to the three solvent nitrobenzene molecules (with occupancies 1/2, 1/3, 1/3), two EDAP constraints had to be used to equalize the guest 3 carbon atoms.
Due to the quite low quality of the data
for 1•4, the following restraints and constraints had to be applied: three DFIX and one EADP for the solvent acetonitrile; due to the positional disorder and uneven thermal movement of the guest 4 atoms in the final anisotropic refinement, they were constrained to have the same thermal movement using one general EDAP to 23 atoms, in addition two EADP’s were used for the minor component Pd and Br. the guest 5 was applied.
For the 1•5, one EDAP constraint equalizing two carbons for
A few bad reflections were omitted from the final refinements: 12 for
1•3, 9 for 1•4 and 4 reflections for 1•5.
As the crystal lattice in each three structures contains
large voids filled with a lot of scattered electron density which could not be modeled chemically, after locating and modeling any chemically reasonable solvent molecule(s), the remaining electron density was flattened out using the solvent masking protocol inside OLEX2 resulting in a decrease in the final R value, reported below as Rmask and Runmask.
S9
Crystal data for 1•3: M = 2134.09, yellow prism, 0.13 × 0.05 × 0.05 mm3, Orthorhombic, space group Pbca, a = 27.8747(4) Å, b = 13.78762(17) Å, c = 45.4150(5) Å, V = 17454.1(4) Å3, Z = 8, Dc = 1.624 g/cm3, F000 = 8074, µ = 3.226 mm-1, T = 90.0(1) K, 2θmax = 50.10°, 15455 reflections used, 12970 with Io > 2σ(Io), Rint = 0.0445, 839 parameters, 13 restraints, GoF = 1.043, Rmask = 0.0616 [Io > 2σ(Io)], wRmask= 0.1917 (all reflections), 3.574 < ∆ρ < –2.115 e/Å3. [Runmask = 0.0676 [Io > 2σ(Io)], wRunmask= 0.2190 (all reflections)] CCDC deposit number: 967379
Response to A and B level checkcif alerts: Alert level A PLAT307_ALERT_2_A Isolated Metal Atom (Unusual !) ................
2σ(I), 1011 parameters, 1.47 < θ < 27.27°, final R factors R1 = 0.0754, wR2 = 0.2143. The SQUEEZE program in PLATON was used for analysis to remove the disordered solvent densities in the pore.
Disordered model (a) 59% occupancy
(b) 41% occupancy
Two component disordered model in the crystal structure of 1•3 after the solvent exchange with acetonitrile.
ORTEP diagrams are drawn at 30% probability level.
S11
Crystal data for 1•4: M = 2024.99, yellow prism, 0.08 × 0.06 × 0.06 mm3, Orthorhombic, space group Pbca, a = 27.6775(9) Å, b = 13.7981(3) Å, c = 44.3415(11) Å, V = 16933.9(8) Å3, Z = 8, Dc = 1.583 g/cm3, F000 = 7554, µ= 3.743 mm-1, T = 90.0(1) K, 2θmax = 50.10°, 14996 reflections used, 7541 with Io > 2σ(Io), Rint = 0.1949, 510 parameters, 3 restraints, GoF = 1.249, R = 0.1278 [Io > 2σ(Io)], wR= 0.3870 (all reflections), 3.201 < ∆ρ < –3.235 e/Å3.
[Runmask =
0.1638 [Io > 2σ(Io)], wRunmask= 0.4782 (all reflections)] CCDC deposit number: 967380
Response to A and B level checkcif alerts: Alert level A PLAT308_ALERT_2_A Single Bonded Metal Atom (Unusual !) ...........
0.35
Weighted R factor given
0.389
Crystal system given = orthorhombic PLAT019_ALERT_1_B Check _diffrn_measured_fraction_theta_full/_max
0.974
PLAT084_ALERT_3_B High wR2 Value (i.e. > 0.25) ...................
0.39
PLAT242_ALERT_2_B Low
Ueq as Compared to Neighbors for .....
Zn4 Check
PLAT250_ALERT_2_B Large U3/U1 Ratio for Average U(i,j) Tensor ....
4.3 Note
PLAT972_ALERT_2_B Large Calcd. Non-Metal Negative Residual Density
-3.32 eA-3
PLAT972_ALERT_2_B Large Calcd. Non-Metal Negative Residual Density
-2.96 eA-3
Response:
1. – 5. The B level alerts result in from weakly diffracting crystal and low quality of the data 6. and 7. Probably due to difficulties in/inefficient absorption correction
S12
Crystal data for 1•5: M = 1878.94, yellow prism, 0.15 × 0.14 × 0.14 mm3, Orthorhombic, space group Pbca, a = 27.5504(3) Å, b = 13.83530(19) Å, c = 44.5398(6) Å, V = 16977.2(4) Å3, Z = 8, Dc = 1.470 g/cm3, F000 = 7040, µ= 3.526 mm-1, T = 90.0(1) K, 2θmax = 50.0°, 14965 reflections used, 12615 with Io > 2σ(Io), Rint = 0.0357, 683 parameters, 0 restraints, GoF = 1.050, R = 0.0825 [Io > 2σ(Io)], wR= 0.2791 (all reflections), 4.325 < ∆ρ < –2.199 e/Å3.
[Runmask =
0.1242 [Io > 2σ(Io)], wRunmask= 0.4251 (all reflections)] CCDC deposit number: 967381
Alert level A PLAT973_ALERT_2_A Large Calcd. Positive Residual Density on
Response:
Probably due to difficulties in/inefficient absorption correction
S13
Zn13
2.25 eA-3
*
* a d&g
b e&f
c
j
h
i *
*
* i h
10
9.5
9
8.5
8
7.5
7
j
g
ppm
k
S
f
k
OMe
Pd
e
S
N
d
a
c b
10
9
8
7
6
5
4
3
2
1
0
ppm
Figure S1. 1H NMR spectrum (500 MHz, DMSO-d6, 300 K) obtained by the digestion of the solvent-exchanged crystal 1•3.
Asterisks correspond to peaks derived from ligand 2 and
solvent.
i g
h
j
f
Br
e d c
*
*
N a
b&d&g
b
c
9.5
a
9
h d&g
j
8.5
i
8
7.5
ppm
Figure S2. 1H NMR spectrum of the reaction mixture obtained by digestion of the crystals after X-ray observation of 5 (500 MHz, DMSO-d6, 300 K). from ligand 2.
S14
Asterisks correspond to peaks derived
(a) before the wash (0.60σ)
(b) before the wash (0.95σ)
unassignable electron density
(c) 15 min after the wash
unassignable electron density
site 1
site 1
(e) 2 h after the wash
(d) 1 h after the wash
site 1
(f)
6 h after the wash
Me N
Pd
N Br
4
site 1
(g) 15 h after the wash
Pd–Br
C–Br
Pd–Br
(h) final state N Br
5
C–Br
Pd–Br
C–Br
Figure S3. Electron density maps (Fo) obtained by time-dependent X-ray diffradtion in the reaction.
(a), (b) Electron density maps (Fo) before the wash.
The same data are contoured at
different σ levels, namely 0.60σ level for (a) and 0.95σ level for (b), respectively. Unassignable electron densitiy in the pores hampered precise identification of the resulting intermediate at this stage.
(c)–(g) Electron density maps (Fo) obtained at 15 min, 1 h, 2 h, 6 h,
and 15 h after the wash.
After the wash, the strong electron densities in the pores disappeared
and electron density at the coordination site of Pd trans to the nitrogen donor (indicated as site 1) gradually increased and reached maximum after 2 h.
Crystallographic refinement of data in
(e) showed the formation of intermediate 4, which gradually converted product 5 as time passed. (h) Electron density maps (Fo) in the final state.
All maps are depicted within 2.5 Å-thick slice
of the cartridge molecules and contoured at the same absolute 0.95σ level unless otherwise mentioned.
S15
C O streching of CO2
C N streching of free CH 3CN
transmittance
0 min
1h
3h
8h
CH 3CN–Pd 2500
2450
2400
2350
2300
2250
2200
wavenumber (cm -1)
Figure S4. Time-dependent ATR-IR spectra in the reaction.
A transient peak at 2326 cm-1,
which is attributable to the CN stretching in CH3CN-Pd structure, is emphasized with a red rectangle.
S16
intensity (a.u.) 250
200
150
100
Raman Shift (cm -1)
in the reaction (2 h after the wash)
before the reaction
1800
1600
1400
1200
1000
800
600
400
200
Raman Shift (cm-1)
Figure S5. Raman spectra of a single crystal 1 with 785 nm excitation.
One was obtained
before the reaction (black) and the other was obtained after the incubation of NBS for 3 h, followed by the wash for 2 h (red).
The inset is a magnified view of the region of Pd-Br bond.
S17
(a)
(b)
N
N
I
N
N
I
Zn
N
C Pd Br
N N
N
H C
C H 3.14 Å I H
N
N 3.27 Å
Zn
I
Figure S6. Multiple C–H•••I interactions between methyl group of the coordinating acetonitrile and ZnI2 in the crystal structure of 1•4. Figure 3b.
(a) Sideview of the pore in the crystal structure of
(b) ChemDraw representation at the inserted circle in (a).
(a)
(b)
Pd (green)
Pd (green)
Figure S7. Columnar structure between 2 and 4 in the crystal structure of 1•4. (b) topview.
(a) Sideview.
Apical positions of Pd are covered with ligand 2, making the formation of high
oxidation state Pd complexes unrealistic in the network crystal.
S18
CH3CN
Br N C
II
Pd
S S
OCH3
N
+ O
N
O
C (NBS)
3
S 1/2
N C
H 3CO
II
Pd
NCCH3 X
X = CH 3CN or Br or O
N
O
S S
N
S
OCH3 NBS
= C
oxidized S compounds + n Br X
N C
N
Br
5
C Pd 0
II
Pd
NCCH3 Br
4
(eluted out into the solution)
Figure S8. A putative reaction mechanism. NBS oxidizes CH3OCS2- to generate Br- and (CH3OCS2)2.
This redox reaction (CH3OCS2Na to (CH3OCS2)2) was independently confirmed
in a solution experiment.
(See control experiment in page S7)
A Pd(II)/Pd(0) catalytic cycle
can be proposed for the aromatic bromination by assuming the reoxidation of Pd(0) with NBS (i. e., Pd(0) + “Br+” --> Pd(II) + “Br-“).
S19
References 1.
Nagao, I.; Shimizu, M.; Hiyama, T. Angew. Chem. Int. Ed. 2009, 48, 7573–7576.
2.
Ma, H.; Wang, G.; Yee, G. T.; Petersen, J. L.; Jensen, M. P. Inorg. Chim. Acta 2009, 362, 4563–4569.
3.
Schroll, A. L.; Eastep, S. J.; Barany, G. J. Org. Chem. 1990, 55, 1475–1479.
4.
Bruker (2007), APEX2, Bruker AXS Inc., Madison, Wisconsin, USA.
5.
Agilent (2011), CrysAlis PRO, Agilent Technologies UK Ltd, Yarnton, England.
6.
Palatinus, L.; Chapuis, G. J. Appl. Cryst. 2007, 40, 786–790.
7.
Sheldrick, G. M. Acta Cryst. 2008, A64, 112–122.
8.
Dolomanov, O. V.; Bourhis, L. J.; Gildea, R. J.; Howard, J. a. K.; Puschmann, H. J. Appl. Cryst. 2009, 42, 339–341.
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