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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; dmin = 0.78 Å) and as-synthesized (dmin = 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.

Supporting information

cif

Crystallographic Information File (CIF) https://doi.org/10.1107/S0021889812050935/fs5026sup1.cif
Contains datablocks global, HKUST1a, HKUST1syn, PCN200a

pdf

Portable Document Format (PDF) file https://doi.org/10.1107/S0021889812050935/fs5026sup2.pdf
Supplementary figures and information

CCDC references: 855255; 943008; 943009

Computing details top

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) top
Crystal data top
(C12H4Cu2O10)·(C3)Dx = 1.032 Mg m3
Mr = 471.3Synchrotron radiation, λ = 0.45875 Å
Cubic, Fm3mµ = 0.43 mm1
Hall symbol: -F 4 2 3T = 100 K
a = 26.3034 (2) ÅParticle morphology: crystalline powder
V = 18198.6 (3) Å3purple
Z = 24cylinder, 10.0 × 0.9 mm
F(000) = 5568Specimen preparation: Prepared at 100 K and 101.325 kPa, cooled at 0 K min1
Data collection top
Diffractometr at 11-BM lineData collection mode: transmission
Radiation source: synchrotron, synchrotronScan method: continuous
PSL DCM Si(111) monochromator2θmin = 0.751°, 2θmax = 33.999°, 2θstep = 0.001°
Specimen mounting: glass capillary sealted under Ar-atmosphere
Refinement top
Rp = 0.09048 parameters
Rwp = 0.1174 restraints
Rexp = 0.0688 constraints
RBragg = 0.082H-atom parameters constrained
χ2 = 2.993Weighting 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 50.045Background function: 20 Legendre polynoms
Profile function: Pseudo-VoigtPreferred orientation correction: March & Dollase
Crystal data top
(C12H4Cu2O10)·(C3)Z = 24
Mr = 471.3Synchrotron radiation, λ = 0.45875 Å
Cubic, Fm3mµ = 0.43 mm1
a = 26.3034 (2) ÅT = 100 K
V = 18198.6 (3) Å3cylinder, 10.0 × 0.9 mm
Data collection top
Diffractometr at 11-BM lineScan method: continuous
Specimen mounting: glass capillary sealted under Ar-atmosphere2θmin = 0.751°, 2θmax = 33.999°, 2θstep = 0.001°
Data collection mode: transmission
Refinement top
Rp = 0.09049497 data points
Rwp = 0.11748 parameters
Rexp = 0.0684 restraints
RBragg = 0.082H-atom parameters constrained
χ2 = 2.993
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/UeqOcc. (<1)
Cu10.21612 (5)0.78388 (5)00.0516 (4)*
O10.18783 (13)0.74203 (12)0.04904 (12)0.0781 (16)*
O20.1568 (2)0.8432 (2)00.0781 (16)*
C10.20441 (5)0.70441 (5)0.06992 (6)0.0781 (16)*
C20.18112 (5)0.68112 (5)0.11622 (6)0.041 (3)*
C30.20276 (6)0.63785 (5)0.13785 (5)0.033 (2)*
H10.231010.6237330.1237330.0398*
C1s0.1587 (4)0.1587 (4)0.1587 (4)0.064 (4)*0.75
C2s0.3809 (3)0.50.3809 (3)0.064 (4)*
Geometric parameters (Å, º) top
Cu1—Cu1i2.5205 (17)O1—C11.213 (4)
Cu1—O11.852 (3)C1—C21.494 (2)
Cu1—O1ii1.852 (3)C2—C31.394 (2)
Cu1—O1iii1.852 (3)C2—C3v1.394 (2)
Cu1—O1iv1.852 (3)C3—H10.91
Cu1i—Cu1—O182.18 (11)Cu1—O1—C1131.0 (3)
Cu1i—Cu1—O1ii82.18 (11)O1—C1—O1vi112.4 (2)
Cu1i—Cu1—O1iii82.18 (11)O1—C1—C2123.8 (2)
Cu1i—Cu1—O1iv82.18 (11)O1vi—C1—C2123.8 (2)
O1—Cu1—O1ii164.35 (16)C1—C2—C3120.00 (13)
O1—Cu1—O1iii88.30 (15)C1—C2—C3v120.00 (13)
O1—Cu1—O1iv89.57 (14)C3—C2—C3v120.00 (14)
O1ii—Cu1—O1iii89.57 (14)C2—C3—C2vii120.00 (14)
O1ii—Cu1—O1iv88.30 (15)C2—C3—H1120.00
O1iii—Cu1—O1iv164.35 (16)C2vii—C3—H1120.00
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) y1/2, x+1/2, z; (vii) y1/2, z+1/2, x.
(HKUST1syn) top
Crystal data top
(C12H4Cu2O10)·(C21)Dx = 1.503 Mg m3
Mr = 687.5Synchrotron radiation, λ = 0.45875 Å
Cubic, Fm3mµ = 0.45 mm1
Hall symbol: -F 4 2 3T = 100 K
a = 26.3167 (11) ÅParticle morphology: crystalline powder
V = 18226.1 (14) Å3blue
Z = 24cylinder, 10.0 × 0.9 mm
F(000) = 8160Specimen preparation: Prepared at 100 K and 101.325 kPa, cooled at 0 K min1
Data collection top
Diffractometr at 11-BM lineData collection mode: transmission
Radiation source: synchrotron, synchrotronScan method: continuous
PSL DCM Si(111) monochromator2θmin = 1.001°, 2θmax = 21.999°, 2θstep = 0.001°
Specimen mounting: capton capillary
Refinement top
Rp = 0.07744 parameters
Rwp = 0.0978 restraints
Rexp = 0.05923 constraints
RBragg = 0.068H-atom parameters constrained
χ2 = 2.690Weighting 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 50.045Background function: 12 Legendre polynoms
Profile function: Pseudo-VoigtPreferred orientation correction: none
Crystal data top
(C12H4Cu2O10)·(C21)Z = 24
Mr = 687.5Synchrotron radiation, λ = 0.45875 Å
Cubic, Fm3mµ = 0.45 mm1
a = 26.3167 (11) ÅT = 100 K
V = 18226.1 (14) Å3cylinder, 10.0 × 0.9 mm
Data collection top
Diffractometr at 11-BM lineScan method: continuous
Specimen mounting: capton capillary2θmin = 1.001°, 2θmax = 21.999°, 2θstep = 0.001°
Data collection mode: transmission
Refinement top
Rp = 0.07749497 data points
Rwp = 0.09744 parameters
Rexp = 0.0598 restraints
RBragg = 0.068H-atom parameters constrained
χ2 = 2.690
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
Cu10.214733 (13)0.785267 (13)00.0911 (7)*
O10.18034 (6)0.73992 (7)0.04856 (6)0.0911 (7)*
O20.15671 (3)0.84329 (3)00.0911 (7)*
C10.20124 (6)0.70124 (6)0.06625 (6)0.0911 (7)*
C20.17793 (6)0.67793 (6)0.11271 (6)0.0911 (7)*
C30.19967 (6)0.63445 (5)0.13445 (5)0.0911 (7)*
C1s0.3900 (5)0.3900 (5)0.1100 (5)0.0911 (7)*
C2s0.50.500.0911 (7)*
C3s0.4416 (4)0.4416 (4)0.0584 (4)0.0911 (7)*
C4s0.3003 (3)0.3003 (3)0.1997 (3)0.0911 (7)*
C5s0.0717 (5)0.4283 (5)0.0717 (5)0.0911 (7)*
C6s0.250.250.250.0911 (7)*
C7s0.2285 (10)0.500.0911 (7)*
C8s00.500.0911 (7)*
C9s0.1690 (9)0.500.0911 (7)*
C10s0.0863 (5)0.4137 (5)0.0863 (5)0.0911 (7)*
C11s0.3280 (4)0.3280 (4)0.1720 (4)0.0911 (7)*
C12s0.2185 (4)0.5808 (3)00.0911 (7)*
C13s0.4268 (3)0.4268 (3)0.1565 (4)0.0911 (7)*
C14s0.3446 (9)0.500.0911 (7)*
C15s0.4084 (4)0.4084 (4)0.0916 (4)0.0911 (7)*
H10.2285250.6200280.1200000.1093*
Geometric parameters (Å, º) top
Cu1—Cu1i2.6251 (5)O1—C11.247 (2)
Cu1—O11.9690 (17)C1—C21.499 (2)
Cu1—O1ii1.9690 (17)C2—C31.401 (2)
Cu1—O1iii1.9690 (17)C2—C3v1.401 (2)
Cu1—O1iv1.9690 (17)C3—H10.93
Cu1i—Cu1—O184.05 (5)O1—C1—O1vi125.50 (16)
Cu1i—Cu1—O1ii84.05 (5)O1—C1—C2117.25 (14)
Cu1i—Cu1—O1iii84.05 (5)O1vi—C1—C2117.25 (14)
Cu1i—Cu1—O1iv84.05 (5)C1—C2—C3120.00 (13)
O1—Cu1—O1ii168.11 (7)C1—C2—C3v120.00 (13)
O1—Cu1—O1iii80.94 (7)C3—C2—C3v120.00 (14)
O1—Cu1—O1iv97.82 (7)C2—C3—C2vii120.00 (14)
O1ii—Cu1—O1iii97.82 (7)C2—C3—H1120.00
O1ii—Cu1—O1iv80.94 (7)C2vii—C3—H1120.00
O1iii—Cu1—O1iv168.11 (7)C1sviii—C15s—C3sviii180.0 (5)
Cu1—O1—C1122.29 (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) y1/2, x+1/2, z; (vii) y1/2, z+1/2, x; (viii) y, x, z.
(PCN200a) top
Crystal data top
C8.5H7CuN5O2F(000) = 1104
Mr = 274.7Dx = 1.639 Mg m3
Monoclinic, C2/cSynchrotron radiation, λ = 0.6065 Å
Hall symbol: -C 2ycµ = 1.27 mm1
a = 28.697 (2) ÅT = 295 K
b = 9.2637 (5) ÅParticle morphology: samll crystalline powder
c = 9.3223 (5) Åblue
β = 116.087 (4)°cylinder, 10.0 × 0.9 mm
V = 2225.8 (2) Å3Specimen preparation: Prepared at 373 K and 101.325 kPa, cooled at 180 K min1
Z = 8
Data collection top
Diffractometr at 1-BM lineSpecimen mounting: capton capillary with He exchange gas
Radiation source: synchrotron, synchrotronData collection mode: transmission
PSL DCM Si(111) monochromatorScan method: Stationary detector
Refinement top
Rp = 0.03974 parameters
Rwp = 0.05528 restraints
Rexp = 0.01443 constraints
RBragg = 0.047H-atom parameters constrained
χ2 = 16.565Weighting 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 25.019Background function: 12 Legendre polynoms
Profile function: Pseudo-VoigtPreferred orientation correction: none
Crystal data top
C8.5H7CuN5O2V = 2225.8 (2) Å3
Mr = 274.7Z = 8
Monoclinic, C2/cSynchrotron radiation, λ = 0.6065 Å
a = 28.697 (2) ŵ = 1.27 mm1
b = 9.2637 (5) ÅT = 295 K
c = 9.3223 (5) Åcylinder, 10.0 × 0.9 mm
β = 116.087 (4)°
Data collection top
Diffractometr at 1-BM lineData collection mode: transmission
Specimen mounting: capton capillary with He exchange gasScan method: Stationary detector
Refinement top
Rp = 0.0391903 data points
Rwp = 0.05574 parameters
Rexp = 0.01428 restraints
RBragg = 0.047H-atom parameters constrained
χ2 = 16.565
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
Cu10.18682 (19)0.8289 (6)0.3113 (6)0.036 (2)*
O10.1250 (6)1.0750 (18)0.340 (2)0.062 (4)*
O20.1426 (6)1.177 (2)0.5772 (18)0.062 (4)*
N10.2178 (5)1.0042 (18)0.7372 (14)0.062 (4)*
N20.2550 (4)0.9029 (19)0.7914 (13)0.062 (4)*
N30.2522 (4)0.8284 (14)0.6666 (17)0.062 (4)*
N40.2139 (5)0.8802 (17)0.5343 (14)0.062 (4)*
N110.1415 (3)0.6590 (9)0.3297 (12)0.062 (4)*
C10.1493 (3)1.0864 (14)0.485 (2)0.062 (4)*
C20.1933 (3)0.9878 (11)0.5802 (13)0.062 (4)*
C110.1077 (5)0.7170 (9)0.3780 (15)0.062 (4)*
C120.0702 (4)0.6392 (10)0.4014 (13)0.062 (4)*
C130.06779 (17)0.4916 (10)0.3722 (5)0.062 (4)*
C140.1021 (3)0.4281 (9)0.3224 (14)0.062 (4)*
C150.1382 (3)0.5156 (9)0.3026 (16)0.062 (4)*
C160.02799 (14)0.4000 (12)0.39533 (13)0.062 (4)*
C1700.3057 (13)0.250.062 (4)*
H11a0.1097070.8190310.3976550.0747*
H12a0.0469690.6854550.4361020.0747*
H14a0.1008560.3262440.3021520.0747*
H15a0.1618550.4719120.2680010.0747*
H16a0.0039340.460150.4092830.0747*
H16b0.0447240.3413910.4861020.0747*
H17a0.023370.241480.237730.0747*
Geometric parameters (Å, º) top
Cu1—O2i1.985 (15)C11—C121.39 (2)
Cu1—N1i2.049 (17)C11—H11a0.96
Cu1—N41.932 (13)C12—C131.391 (13)
Cu1—N112.096 (12)C12—H12a0.96
O1—C11.23 (2)C13—C141.390 (13)
O2—C11.27 (3)C13—C161.512 (10)
N1—N21.34 (2)C14—C151.391 (15)
N1—C21.325 (16)C14—H14a0.96
N2—N31.32 (2)C15—H15a0.96
N3—N41.329 (16)C16—C171.512 (10)
N4—C21.32 (2)C16—H16a0.94
N11—C111.347 (19)C16—H16b0.94
N11—C151.348 (12)C17—H17a0.94
C1—C21.493 (13)C17—H17aii0.94
O2i—Cu1—N1i79.1 (7)C12—C11—H11a117.7278
O2i—Cu1—N4161.7 (8)C11—C12—C13117.0 (11)
O2i—Cu1—N1187.2 (7)C11—C12—H12a121.4957
N1i—Cu1—N498.5 (6)C13—C12—H12a121.4961
N1i—Cu1—N11166.2 (4)C12—C13—C14120.0 (9)
N4—Cu1—N1193.9 (6)C12—C13—C16120.0 (8)
Cu1iii—O2—C1120.7 (12)C14—C13—C16120.0 (8)
Cu1iii—N1—N2142.4 (9)C13—C14—C15118.4 (8)
Cu1iii—N1—C2111.2 (9)C13—C14—H14a120.7761
N2—N1—C2106.5 (13)C15—C14—H14a120.7776
N1—N2—N3107.6 (10)N11—C15—C14123.0 (12)
N2—N3—N4109.5 (13)N11—C15—H15a118.4987
Cu1—N4—N3133.4 (13)C14—C15—H15a118.4991
Cu1—N4—C2120.6 (9)C13—C16—C17109.5 (3)
N3—N4—C2106.1 (12)C13—C16—H16a109.4702
Cu1—N11—C11107.0 (7)C13—C16—H16b109.47
Cu1—N11—C15136.0 (10)C17—C16—H16a109.4722
C11—N11—C15117.0 (11)C17—C16—H16b109.4717
O1—C1—O2128.4 (13)H16a—C16—H16b109.4672
O1—C1—C2121.6 (15)C16—C17—C16ii109.5 (9)
O2—C1—C2110.0 (13)C16—C17—H17a110.4
N1—C2—N4110.4 (10)C16—C17—H17aii112.5 (2)
N1—C2—C1119.0 (12)C16ii—C17—H17a112.5 (2)
N4—C2—C1130.6 (11)C16ii—C17—H17aii110.4 (2)
N11—C11—C12124.5 (9)H17a—C17—H17aii101.5
N11—C11—H11a117.7259
Symmetry codes: (i) x, y+2, z1/2; (ii) x, y, z+1/2; (iii) x, y+2, z+1/2.

Experimental details

(HKUST1a)(HKUST1syn)(PCN200a)
Crystal data
Chemical formula(C12H4Cu2O10)·(C3)(C12H4Cu2O10)·(C21)C8.5H7CuN5O2
Mr471.3687.5274.7
Crystal system, space groupCubic, Fm3mCubic, Fm3mMonoclinic, C2/c
Temperature (K)100100295
a, b, c (Å)26.3034 (2), 26.3034 (2), 26.3034 (2)26.3167 (11), 26.3167 (11), 26.3167 (11)28.697 (2), 9.2637 (5), 9.3223 (5)
α, β, γ (°)90, 90, 9090, 90, 9090, 116.087 (4), 90
V3)18198.6 (3)18226.1 (14)2225.8 (2)
Z24248
Radiation typeSynchrotron, λ = 0.45875 ÅSynchrotron, λ = 0.45875 ÅSynchrotron, λ = 0.6065 Å
µ (mm1)0.430.451.27
Specimen shape, size (mm)Cylinder, 10.0 × 0.9Cylinder, 10.0 × 0.9Cylinder, 10.0 × 0.9
Data collection
DiffractometerDiffractometr at 11-BM lineDiffractometr at 11-BM lineDiffractometr at 1-BM line
Specimen mountingGlass capillary sealted under Ar-atmosphereCapton capillaryCapton capillary with He exchange gas
Data collection modeTransmissionTransmissionTransmission
Scan methodContinuousContinuousStationary detector
2θ values (°)2θmin = 0.751 2θmax = 33.999 2θstep = 0.0012θmin = 1.001 2θmax = 21.999 2θstep = 0.0012θfixed = ?
Refinement
R factors and goodness of fitRp = 0.090, Rwp = 0.117, Rexp = 0.068, RBragg = 0.082, χ2 = 2.993Rp = 0.077, Rwp = 0.097, Rexp = 0.059, RBragg = 0.068, χ2 = 2.690Rp = 0.039, Rwp = 0.055, Rexp = 0.014, RBragg = 0.047, χ2 = 16.565
No. of data points49497494971903
No. of parameters484474
No. of restraints4828
H-atom treatmentH-atom parameters constrainedH-atom parameters constrainedH-atom parameters constrained

Computer programs: FULLPROF (Rodriguez-Carvajal, 1993), TOPAS v.4.2 (Bruker AXS, 2009), Fit 2D (Hammersley, 1996), SUPERFLIP (Palatinus&Chapuis, 2007), Jana 2006 (Petricek, 2006), Chimera (Pettersen, 2004).

 

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