Generation and applications of structure envelopes for porous metal-organic frameworks

The synthesis of polycrystalline, as opposed to single-crystalline, porous materials, such as zeolites and metal-organic frameworks (MOFs), is usually beneficial because the former have shorter synthesis times and higher yields. However, the structural determination of these materials using powder X-ray diffraction (PXRD) data is usually complicated. Recently, several methods for the structural investigation of zeolite polycrystalline materials have been developed, taking advantage of the structural characteristics of zeolites. Nevertheless, these techniques have rarely been applied in the structure determination of a MOF even though, with the electron-density contrast between the metal-containing units and pore regions, the construction of a structure envelope, the surface between high- and low-electron-density regions, should be straightforward for a MOF. Herein an example of such structure solution of MOFs based on PXRD data is presented. To start, a Patterson map was generated from powder diffraction intensities. From this map, structure factor phases for several of the strongest reflections were extracted and a structure envelope (SE) of a MOF was subsequently constructed. This envelope, together with all extracted reflection intensities, was used as input to the SUPERFLIP software and a charge-flipping (CF) structure solution was performed. This structure solution method has been tested on the PXRD data of both activated (solvent removed from the pores; d_min = 0.78 Å) and as-synthesized (d_min = 1.20 Å) samples of HKUST-1. In both cases, our method has led to structure solutions. In fact, charge-flipping calculations using SE provided correct solutions in minutes (6 min for activated and 3 min for as-synthesized samples), while regular charge flipping or charge flipping with histogram matching calculation provided meaningful solutions only after several hours. To confirm the applicability of structure envelopes to low-symmetry MOFs, the structure of monoclinic PCN-200 has been solved via CF+SE calculations.

Computing details

Cell refinement: FULLPROF (Rodriguez-Carvajal, 1993) for HKUST1a, HKUST1syn; TOPAS v.4.2 (Bruker AXS, 2009) for PCN200a. Data reduction: Fit 2D (Hammersley, 1996) for PCN200a. For all compounds, program(s) used to solve structure: SUPERFLIP (Palatinus&Chapuis, 2007); program(s) used to refine structure: Jana 2006 (Petricek, 2006); molecular graphics: Chimera (Pettersen, 2004); software used to prepare material for publication: Jana 2006 (Petricek, 2006).

(HKUST1a)

Crystal data

(C12H4Cu2O10)·(C3)	Dx = 1.032 Mg m^−3
Mr = 471.3	Synchrotron radiation, λ = 0.45875 Å
Cubic, Fm3m	µ = 0.43 mm^−1
Hall symbol: -F 4 2 3	T = 100 K
a = 26.3034 (2) Å	Particle morphology: crystalline powder
V = 18198.6 (3) Å^3	purple
Z = 24	cylinder, 10.0 × 0.9 mm
F(000) = 5568	Specimen preparation: Prepared at 100 K and 101.325 kPa, cooled at 0 K min^−1

Data collection

Diffractometr at 11-BM line	Data collection mode: transmission
Radiation source: synchrotron, synchrotron	Scan method: continuous
PSL DCM Si(111) monochromator	2θmin = 0.751°, 2θmax = 33.999°, 2θstep = 0.001°
Specimen mounting: glass capillary sealted under Ar-atmosphere

Refinement

Rp = 0.090	48 parameters
Rwp = 0.117	4 restraints
Rexp = 0.068	8 constraints
RBragg = 0.082	H-atom parameters constrained
χ^2 = 2.993	Weighting scheme based on measured s.u.'s
49497 data points	(Δ/σ)max = 0.043
Excluded region(s): from 0.499 to 0.750, from 34 to 50.045	Background function: 20 Legendre polynoms
Profile function: Pseudo-Voigt	Preferred orientation correction: March & Dollase

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Ų)

	x	y	z	Uiso*/Ueq	Occ. (<1)
Cu1	0.21612 (5)	0.78388 (5)	0	0.0516 (4)*
O1	0.18783 (13)	0.74203 (12)	−0.04904 (12)	0.0781 (16)*
O2	0.1568 (2)	0.8432 (2)	0	0.0781 (16)*
C1	0.20441 (5)	0.70441 (5)	−0.06992 (6)	0.0781 (16)*
C2	0.18112 (5)	0.68112 (5)	−0.11622 (6)	0.041 (3)*
C3	0.20276 (6)	0.63785 (5)	−0.13785 (5)	0.033 (2)*
H1	0.23101	0.623733	−0.123733	0.0398*
C1s	0.1587 (4)	0.1587 (4)	0.1587 (4)	0.064 (4)*	0.75
C2s	0.3809 (3)	0.5	0.3809 (3)	0.064 (4)*

Geometric parameters (Å, º)

Cu1—Cu1^i	2.5205 (17)	O1—C1	1.213 (4)
Cu1—O1	1.852 (3)	C1—C2	1.494 (2)
Cu1—O1^ii	1.852 (3)	C2—C3	1.394 (2)
Cu1—O1^iii	1.852 (3)	C2—C3^v	1.394 (2)
Cu1—O1^iv	1.852 (3)	C3—H1	0.91
Cu1^i—Cu1—O1	82.18 (11)	Cu1—O1—C1	131.0 (3)
Cu1^i—Cu1—O1^ii	82.18 (11)	O1—C1—O1^vi	112.4 (2)
Cu1^i—Cu1—O1^iii	82.18 (11)	O1—C1—C2	123.8 (2)
Cu1^i—Cu1—O1^iv	82.18 (11)	O1^vi—C1—C2	123.8 (2)
O1—Cu1—O1^ii	164.35 (16)	C1—C2—C3	120.00 (13)
O1—Cu1—O1^iii	88.30 (15)	C1—C2—C3^v	120.00 (13)
O1—Cu1—O1^iv	89.57 (14)	C3—C2—C3^v	120.00 (14)
O1^ii—Cu1—O1^iii	89.57 (14)	C2—C3—C2^vii	120.00 (14)
O1^ii—Cu1—O1^iv	88.30 (15)	C2—C3—H1	120.00
O1^iii—Cu1—O1^iv	164.35 (16)	C2^vii—C3—H1	120.00

Symmetry codes: (i) −x+1/2, −y+3/2, z; (ii) −y+1, −x+1, −z; (iii) x, y, −z; (iv) −y+1, −x+1, z; (v) −z, x+1/2, −y+1/2; (vi) y−1/2, x+1/2, z; (vii) y−1/2, −z+1/2, −x.

(HKUST1syn)

Crystal data

(C12H4Cu2O10)·(C21)	Dx = 1.503 Mg m^−3
Mr = 687.5	Synchrotron radiation, λ = 0.45875 Å
Cubic, Fm3m	µ = 0.45 mm^−1
Hall symbol: -F 4 2 3	T = 100 K
a = 26.3167 (11) Å	Particle morphology: crystalline powder
V = 18226.1 (14) Å^3	blue
Z = 24	cylinder, 10.0 × 0.9 mm
F(000) = 8160	Specimen preparation: Prepared at 100 K and 101.325 kPa, cooled at 0 K min^−1

Data collection

Diffractometr at 11-BM line	Data collection mode: transmission
Radiation source: synchrotron, synchrotron	Scan method: continuous
PSL DCM Si(111) monochromator	2θmin = 1.001°, 2θmax = 21.999°, 2θstep = 0.001°
Specimen mounting: capton capillary

Refinement

Rp = 0.077	44 parameters
Rwp = 0.097	8 restraints
Rexp = 0.059	23 constraints
RBragg = 0.068	H-atom parameters constrained
χ^2 = 2.690	Weighting scheme based on measured s.u.'s
49497 data points	(Δ/σ)max = 0.021
Excluded region(s): from 0.499 to 1.000, from 22 to 50.045	Background function: 12 Legendre polynoms
Profile function: Pseudo-Voigt	Preferred orientation correction: none

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Ų)

	x	y	z	Uiso*/Ueq
Cu1	0.214733 (13)	0.785267 (13)	0	0.0911 (7)*
O1	0.18034 (6)	0.73992 (7)	−0.04856 (6)	0.0911 (7)*
O2	0.15671 (3)	0.84329 (3)	0	0.0911 (7)*
C1	0.20124 (6)	0.70124 (6)	−0.06625 (6)	0.0911 (7)*
C2	0.17793 (6)	0.67793 (6)	−0.11271 (6)	0.0911 (7)*
C3	0.19967 (6)	0.63445 (5)	−0.13445 (5)	0.0911 (7)*
C1s	0.3900 (5)	0.3900 (5)	0.1100 (5)	0.0911 (7)*
C2s	0.5	0.5	0	0.0911 (7)*
C3s	0.4416 (4)	0.4416 (4)	0.0584 (4)	0.0911 (7)*
C4s	0.3003 (3)	0.3003 (3)	0.1997 (3)	0.0911 (7)*
C5s	0.0717 (5)	0.4283 (5)	0.0717 (5)	0.0911 (7)*
C6s	0.25	0.25	0.25	0.0911 (7)*
C7s	0.2285 (10)	0.5	0	0.0911 (7)*
C8s	0	0.5	0	0.0911 (7)*
C9s	0.1690 (9)	0.5	0	0.0911 (7)*
C10s	0.0863 (5)	0.4137 (5)	0.0863 (5)	0.0911 (7)*
C11s	0.3280 (4)	0.3280 (4)	0.1720 (4)	0.0911 (7)*
C12s	0.2185 (4)	0.5808 (3)	0	0.0911 (7)*
C13s	0.4268 (3)	0.4268 (3)	0.1565 (4)	0.0911 (7)*
C14s	0.3446 (9)	0.5	0	0.0911 (7)*
C15s	0.4084 (4)	0.4084 (4)	−0.0916 (4)	0.0911 (7)*
H1	0.228525	0.620028	−0.120000	0.1093*

Geometric parameters (Å, º)

Cu1—Cu1^i	2.6251 (5)	O1—C1	1.247 (2)
Cu1—O1	1.9690 (17)	C1—C2	1.499 (2)
Cu1—O1^ii	1.9690 (17)	C2—C3	1.401 (2)
Cu1—O1^iii	1.9690 (17)	C2—C3^v	1.401 (2)
Cu1—O1^iv	1.9690 (17)	C3—H1	0.93
Cu1^i—Cu1—O1	84.05 (5)	O1—C1—O1^vi	125.50 (16)
Cu1^i—Cu1—O1^ii	84.05 (5)	O1—C1—C2	117.25 (14)
Cu1^i—Cu1—O1^iii	84.05 (5)	O1^vi—C1—C2	117.25 (14)
Cu1^i—Cu1—O1^iv	84.05 (5)	C1—C2—C3	120.00 (13)
O1—Cu1—O1^ii	168.11 (7)	C1—C2—C3^v	120.00 (13)
O1—Cu1—O1^iii	80.94 (7)	C3—C2—C3^v	120.00 (14)
O1—Cu1—O1^iv	97.82 (7)	C2—C3—C2^vii	120.00 (14)
O1^ii—Cu1—O1^iii	97.82 (7)	C2—C3—H1	120.00
O1^ii—Cu1—O1^iv	80.94 (7)	C2^vii—C3—H1	120.00
O1^iii—Cu1—O1^iv	168.11 (7)	C1s^viii—C15s—C3s^viii	180.0 (5)
Cu1—O1—C1	122.29 (13)

Symmetry codes: (i) −x+1/2, −y+3/2, z; (ii) −y+1, −x+1, −z; (iii) x, y, −z; (iv) −y+1, −x+1, z; (v) −z, x+1/2, −y+1/2; (vi) y−1/2, x+1/2, z; (vii) y−1/2, −z+1/2, −x; (viii) y, x, −z.

(PCN200a)

Crystal data

C8.5H7CuN5O2	F(000) = 1104
Mr = 274.7	Dx = 1.639 Mg m^−3
Monoclinic, C2/c	Synchrotron radiation, λ = 0.6065 Å
Hall symbol: -C 2yc	µ = 1.27 mm^−1
a = 28.697 (2) Å	T = 295 K
b = 9.2637 (5) Å	Particle morphology: samll crystalline powder
c = 9.3223 (5) Å	blue
β = 116.087 (4)°	cylinder, 10.0 × 0.9 mm
V = 2225.8 (2) Å^3	Specimen preparation: Prepared at 373 K and 101.325 kPa, cooled at 180 K min^−1
Z = 8

Data collection

Diffractometr at 1-BM line	Specimen mounting: capton capillary with He exchange gas
Radiation source: synchrotron, synchrotron	Data collection mode: transmission
PSL DCM Si(111) monochromator	Scan method: Stationary detector

Refinement

Rp = 0.039	74 parameters
Rwp = 0.055	28 restraints
Rexp = 0.014	43 constraints
RBragg = 0.047	H-atom parameters constrained
χ^2 = 16.565	Weighting scheme based on measured s.u.'s
1903 data points	(Δ/σ)max = 0.018
Excluded region(s): from 1.218 to 1.620, from 24.72 to 25.019	Background function: 12 Legendre polynoms
Profile function: Pseudo-Voigt	Preferred orientation correction: none

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Ų)

	x	y	z	Uiso*/Ueq
Cu1	0.18682 (19)	0.8289 (6)	0.3113 (6)	0.036 (2)*
O1	0.1250 (6)	1.0750 (18)	0.340 (2)	0.062 (4)*
O2	0.1426 (6)	1.177 (2)	0.5772 (18)	0.062 (4)*
N1	0.2178 (5)	1.0042 (18)	0.7372 (14)	0.062 (4)*
N2	0.2550 (4)	0.9029 (19)	0.7914 (13)	0.062 (4)*
N3	0.2522 (4)	0.8284 (14)	0.6666 (17)	0.062 (4)*
N4	0.2139 (5)	0.8802 (17)	0.5343 (14)	0.062 (4)*
N11	0.1415 (3)	0.6590 (9)	0.3297 (12)	0.062 (4)*
C1	0.1493 (3)	1.0864 (14)	0.485 (2)	0.062 (4)*
C2	0.1933 (3)	0.9878 (11)	0.5802 (13)	0.062 (4)*
C11	0.1077 (5)	0.7170 (9)	0.3780 (15)	0.062 (4)*
C12	0.0702 (4)	0.6392 (10)	0.4014 (13)	0.062 (4)*
C13	0.06779 (17)	0.4916 (10)	0.3722 (5)	0.062 (4)*
C14	0.1021 (3)	0.4281 (9)	0.3224 (14)	0.062 (4)*
C15	0.1382 (3)	0.5156 (9)	0.3026 (16)	0.062 (4)*
C16	0.02799 (14)	0.4000 (12)	0.39533 (13)	0.062 (4)*
C17	0	0.3057 (13)	0.25	0.062 (4)*
H11a	0.109707	0.819031	0.397655	0.0747*
H12a	0.046969	0.685455	0.436102	0.0747*
H14a	0.100856	0.326244	0.302152	0.0747*
H15a	0.161855	0.471912	0.268001	0.0747*
H16a	0.003934	0.46015	0.409283	0.0747*
H16b	0.044724	0.341391	0.486102	0.0747*
H17a	0.02337	0.24148	0.23773	0.0747*

Geometric parameters (Å, º)

Cu1—O2^i	1.985 (15)	C11—C12	1.39 (2)
Cu1—N1^i	2.049 (17)	C11—H11a	0.96
Cu1—N4	1.932 (13)	C12—C13	1.391 (13)
Cu1—N11	2.096 (12)	C12—H12a	0.96
O1—C1	1.23 (2)	C13—C14	1.390 (13)
O2—C1	1.27 (3)	C13—C16	1.512 (10)
N1—N2	1.34 (2)	C14—C15	1.391 (15)
N1—C2	1.325 (16)	C14—H14a	0.96
N2—N3	1.32 (2)	C15—H15a	0.96
N3—N4	1.329 (16)	C16—C17	1.512 (10)
N4—C2	1.32 (2)	C16—H16a	0.94
N11—C11	1.347 (19)	C16—H16b	0.94
N11—C15	1.348 (12)	C17—H17a	0.94
C1—C2	1.493 (13)	C17—H17a^ii	0.94
O2^i—Cu1—N1^i	79.1 (7)	C12—C11—H11a	117.7278
O2^i—Cu1—N4	161.7 (8)	C11—C12—C13	117.0 (11)
O2^i—Cu1—N11	87.2 (7)	C11—C12—H12a	121.4957
N1^i—Cu1—N4	98.5 (6)	C13—C12—H12a	121.4961
N1^i—Cu1—N11	166.2 (4)	C12—C13—C14	120.0 (9)
N4—Cu1—N11	93.9 (6)	C12—C13—C16	120.0 (8)
Cu1^iii—O2—C1	120.7 (12)	C14—C13—C16	120.0 (8)
Cu1^iii—N1—N2	142.4 (9)	C13—C14—C15	118.4 (8)
Cu1^iii—N1—C2	111.2 (9)	C13—C14—H14a	120.7761
N2—N1—C2	106.5 (13)	C15—C14—H14a	120.7776
N1—N2—N3	107.6 (10)	N11—C15—C14	123.0 (12)
N2—N3—N4	109.5 (13)	N11—C15—H15a	118.4987
Cu1—N4—N3	133.4 (13)	C14—C15—H15a	118.4991
Cu1—N4—C2	120.6 (9)	C13—C16—C17	109.5 (3)
N3—N4—C2	106.1 (12)	C13—C16—H16a	109.4702
Cu1—N11—C11	107.0 (7)	C13—C16—H16b	109.47
Cu1—N11—C15	136.0 (10)	C17—C16—H16a	109.4722
C11—N11—C15	117.0 (11)	C17—C16—H16b	109.4717
O1—C1—O2	128.4 (13)	H16a—C16—H16b	109.4672
O1—C1—C2	121.6 (15)	C16—C17—C16^ii	109.5 (9)
O2—C1—C2	110.0 (13)	C16—C17—H17a	110.4
N1—C2—N4	110.4 (10)	C16—C17—H17a^ii	112.5 (2)
N1—C2—C1	119.0 (12)	C16^ii—C17—H17a	112.5 (2)
N4—C2—C1	130.6 (11)	C16^ii—C17—H17a^ii	110.4 (2)
N11—C11—C12	124.5 (9)	H17a—C17—H17a^ii	101.5
N11—C11—H11a	117.7259

Symmetry codes: (i) x, −y+2, z−1/2; (ii) −x, y, −z+1/2; (iii) x, −y+2, z+1/2.