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Average structure of the composite crystal urea/octanedioic acid at room temperature within the superspace formalism

Authors:

Peral, I.; Madariaga, G.; Petricek, V.; Breczewski, T.

Journal:

Acta Crystallographica, Section B 57 386-393 (2001)

DOI:

https://doi.org/10.1107/S0108768101002166

B-IncStrDB ID: u9Y6RGuOZp1 Entry date: 2021-12-21 Last revision: 2023-09-03

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Chemical data

Common Name: octanedioic acid+urea inclusion compound [ Help ]

Formula moiety: C6 O6 N12 H24+0.893(C8 O4 H14) [ Help ]

Structural Formula Sum: C13.144 O9.572 N12 H36.502 [ Help ]

Formula weight: 515.4 Da [ Help ]

Crystallographic data and experimental details

a: 14.185(6) Å [ Help ]

b: 14.185(6) Å [ Help ]

c: 10.978(1) Å [ Help ]

α: 90 ° [ Help ]

β: 90 ° [ Help ]

γ: 120 ° [ Help ]

Volume: 1913(1) Å3 [ Help ]

Z: 18 [ Help ]

Modulation dimension: 1 [ Help ]

Measured independent wave vectors: [ Help ]

Wave vector id q_x q_y q_z
1 0.00000 0.00000 0.89300

Number of subsystems: 2 [ Help ]

Subsystem code: 1 [ Help ]

Subsystem description: 1st subsystem: urea [ Help ]

W matrix:

1.0 0.0 0.0 0.0
0.0 1.0 0.0 0.0
0.0 0.0 1.0 0.0
0.0 0.0 0.0 1.0

Subsystem code: 2 [ Help ]

Subsystem description: 2nd subsystem: octanedioic acid [ Help ]

W matrix:

1.0 0.0 0.0 0.0
0.0 1.0 0.0 0.0
0.0 0.0 0.0 1.0
0.0 0.0 1.0 0.0

Crystal system: trigonal [ Help ]

Superspace group name: X3121(00γ) [ Help ]

Symmetry operations of the superspace group: [ Help ]

Operation code Operation in algebraic form
1 x1,x2,x3,x4
2 -x2,x1-x2,1/3+x3,x4
3 x2,x1,1/3-x3,-x4
4 -x1+x2,-x1,2/3+x3,x4
5 -x1,-x1+x2,2/3-x3,-x4
6 x1-x2,-x2,-x3,-x4
7 1/3+x1,2/3+x2,x3,2/3+x4
8 1/3-x2,2/3+x1-x2,1/3+x3,2/3+x4
9 1/3+x2,2/3+x1,1/3-x3,2/3-x4
10 1/3-x1+x2,2/3-x1,2/3+x3,2/3+x4
11 1/3-x1,2/3-x1+x2,2/3-x3,2/3-x4
12 1/3+x1-x2,2/3-x2,-x3,2/3-x4
13 2/3+x1,1/3+x2,x3,1/3+x4
14 2/3-x2,1/3+x1-x2,1/3+x3,1/3+x4
15 2/3+x2,1/3+x1,1/3-x3,1/3-x4
16 2/3-x1+x2,1/3-x1,2/3+x3,1/3+x4
17 2/3-x1,1/3-x1+x2,2/3-x3,1/3-x4
18 2/3+x1-x2,1/3-x2,-x3,1/3-x4

Absorption correction type: none [ Help ]

Minimum transmission factor: 1.000 [ Help ]

Maximum transmission factor: 1.000 [ Help ]

μ: 0.291 mm-1 [ Help ]

Refinement details

h(min): -17 [ Help ]

h(max): 8 [ Help ]

k(min): 0 [ Help ]

k(max): 17 [ Help ]

l(min): 0 [ Help ]

l(max): 13 [ Help ]

m1(min): -2 [ Help ]

m1(max): 2 [ Help ]

Intense reflections threshold: 3σ [ Help ]

Total nb. of reflections: 2146 [ Help ]

Nb. of observed reflections: 1017 [ Help ]

Refinement based on: F [ Help ]

Weighting scheme: sigma [ Help ]

Weighting scheme remarks: w=1/(σ2(F)+0.000004F2) [ Help ]

R(obs): 0.0591 [ Help ]

wR(obs): 0.0594 [ Help ]

R(all): 0.2089 [ Help ]

wR(all): 0.0601 [ Help ]

Nb. of reflections: 2146 [ Help ]

Nb. of parameters: 62 [ Help ]

S(all): 8.84 [ Help ]

S(obs): 6.05 [ Help ]

Δ/σ(max): 0.1756 [ Help ]

Δ/σ(mean): 0.0366 [ Help ]

Δρ(max): 0.53 e_Å-3 [ Help ]

Δρ(min): -1.10 e_Å-3 [ Help ]

Extinction method: none [ Help ]

Structural Information

Average Structure: [ Help ]

Atom site label Atom symbol Subsystem Symmetry multiplicity Occupancy x y z Uiso/equiv
O(a) O 1 2 1 0.3237(1) 0 0 0.0342(8)
O(b) O 1 2 1 0.3132(1) 0.3132(1) 0.166667 0.0352(9)
C(a) C 1 2 1 0.4121(2) 0 0 0.037(1)
C(b) C 1 2 1 0.4025(2) 0.4025(2) 0.166667 0.032(1)
N(a) N 1 1 1 0.4510(2) -0.0166(2) 0.0989(2) 0.046(1)
N(b) N 1 1 1 0.4608(1) 0.4449(2) 0.2740(1) 0.0436(8)
H(1a) H 1 1 1 0.4229(9) -0.0384(9) 0.1831(5) 0.040(2)
H(1b) H 1 1 1 0.4231(9) 0.3922(7) 0.3408(8) 0.040(2)
H(2a) H 1 1 1 0.5283(5) -0.003(1) 0.099(1) 0.040(2)
H(2b) H 1 1 1 0.5390(4) 0.5032(6) 0.275(1) 0.040(2)
C(4a) C 2 1 0.083333 0.050(1) 0.0171(7) -0.18(1) 0.056(4)
C(3a) C 2 1 0.083333 0.002(1) -0.0410(7) -0.28(1) 0.056(4)
C(2a) C 2 1 0.083333 0.078(1) 0.0166(7) -0.38(1) 0.056(4)
C(1a) C 2 1 0.083333 0.030(1) -0.0277(7) -0.49(1) 0.056(4)
O(11a) O 2 1 0.083333 -0.062(1) -0.1052(7) -0.50(1) 0.056(4)
O(21a) O 2 1 0.083333 0.098(1) 0.0256(7) -0.57(1) 0.056(4)
H(14a) H 2 1 0.083333 0.065(1) 0.1007(7) -0.18(1) 0.056(4)
H(24a) H 2 1 0.083333 0.130(1) 0.0231(7) -0.16(1) 0.056(4)
H(13a) H 2 1 0.083333 -0.016(1) -0.1261(7) -0.28(1) 0.056(4)
H(23a) H 2 1 0.083333 -0.076(1) -0.0441(7) -0.30(1) 0.056(4)
H(12a) H 2 1 0.083333 0.103(1) 0.1033(7) -0.38(1) 0.056(4)
H(22a) H 2 1 0.083333 0.154(1) 0.0137(7) -0.37(1) 0.056(4)
H(11a) H 2 1 0.083333 0.063(1) -0.0041(7) -0.64(1) 0.056(4)
C(5a) C 2 1 0.083333 -0.023(1) -0.0390(7) -0.08(1) 0.056(4)
C(6a) C 2 1 0.083333 0.026(1) 0.0191(7) 0.03(1) 0.056(4)
C(7a) C 2 1 0.083333 -0.050(1) -0.0384(7) 0.12(1) 0.056(4)
C(8a) C 2 1 0.083333 -0.002(1) 0.0058(7) 0.23(1) 0.056(4)
O(18a) O 2 1 0.083333 0.090(1) 0.0833(7) 0.25(1) 0.056(4)
O(28a) O 2 1 0.083333 -0.070(1) -0.0475(7) 0.31(1) 0.056(4)
H(15a) H 2 1 0.083333 -0.037(1) -0.1226(7) -0.07(1) 0.056(4)
H(25a) H 2 1 0.083333 -0.102(1) -0.0450(7) -0.09(1) 0.056(4)
H(16a) H 2 1 0.083333 0.044(1) 0.1042(7) 0.02(1) 0.056(4)
H(26a) H 2 1 0.083333 0.104(1) 0.0222(7) 0.04(1) 0.056(4)
H(17a) H 2 1 0.083333 -0.075(1) -0.1252(7) 0.12(1) 0.056(4)
H(27a) H 2 1 0.083333 -0.126(1) -0.0356(7) 0.12(1) 0.056(4)
H(18a) H 2 1 0.083333 -0.035(1) -0.0178(7) 0.39(1) 0.056(4)
C(4b) C 2 1 0.083333 0.059(2) 0.020(2) 0.121607 0.056(4)
C(3b) C 2 1 0.083333 -0.002(2) -0.019(2) 0.01418 0.056(4)
C(2b) C 2 1 0.083333 0.075(2) 0.003(2) -0.080953 0.056(4)
C(1b) C 2 1 0.083333 0.022(2) -0.020(2) -0.191048 0.056(4)
O(11b) O 2 1 0.083333 -0.076(2) -0.057(2) -0.205053 0.056(4)
O(21b) O 2 1 0.083333 0.092(2) 0.002(2) -0.271661 0.056(4)
H(14b) H 2 1 0.083333 0.116(2) 0.108(2) 0.116084 0.056(4)
H(24b) H 2 1 0.083333 0.109(2) -0.019(2) 0.134431 0.056(4)
H(13b) H 2 1 0.083333 -0.062(2) -0.107(2) 0.01832 0.056(4)
H(23b) H 2 1 0.083333 -0.049(2) 0.022(2) -0.000215 0.056(4)
H(12b) H 2 1 0.083333 0.140(2) 0.089(2) -0.082401 0.056(4)
H(22b) H 2 1 0.083333 0.117(2) -0.044(2) -0.074565 0.056(4)
H(11b) H 2 1 0.083333 0.054(2) -0.012(2) -0.344498 0.056(4)
C(5b) C 2 1 0.083333 -0.015(2) -0.003(2) 0.21931 0.056(4)
C(6b) C 2 1 0.083333 0.046(2) 0.036(2) 0.326737 0.056(4)
C(7b) C 2 1 0.083333 -0.031(2) 0.014(2) 0.42187 0.056(4)
C(8b) C 2 1 0.083333 0.022(2) 0.037(2) 0.531964 0.056(4)
O(18b) O 2 1 0.083333 0.120(2) 0.073(2) 0.54597 0.056(4)
O(28b) O 2 1 0.083333 -0.047(2) 0.015(2) 0.612578 0.056(4)
H(15b) H 2 1 0.083333 -0.072(2) -0.091(2) 0.224833 0.056(4)
H(25b) H 2 1 0.083333 -0.065(2) 0.036(2) 0.206486 0.056(4)
H(16b) H 2 1 0.083333 0.106(2) 0.124(2) 0.322597 0.056(4)
H(26b) H 2 1 0.083333 0.093(2) -0.005(2) 0.341132 0.056(4)
H(17b) H 2 1 0.083333 -0.095(2) -0.072(2) 0.423318 0.056(4)
H(27b) H 2 1 0.083333 -0.073(2) 0.061(2) 0.415482 0.056(4)
H(18b) H 2 1 0.083333 -0.010(2) 0.028(2) 0.685415 0.056(4)

ADP components: [ Help ]

Atom site label U11 U22 U33 U12 U13 U23
O(a) 0.0282(7) 0.068(1) 0.020(1) 0.0340(6) -0.0018(4) -0.0036(9)
O(b) 0.046(1) 0.046(1) 0.021(1) 0.028(1) 0.0009(5) -0.0009(5)
C(a) 0.039(1) 0.041(2) 0.033(2) 0.0206(8) 0.0015(7) 0.003(1)
C(b) 0.041(1) 0.041(1) 0.021(2) 0.025(2) 0.0053(7) -0.0053(7)
N(a) 0.060(1) 0.064(1) 0.0174(9) 0.034(1) 0.0090(9) 0.0110(8)
N(b) 0.0348(9) 0.045(1) 0.020(1) -0.0033(8) -0.0035(8) -0.0136(9)