B-IncStrDB

Superspace description of the structure of the composite crystal urea/n-octane at room temperature

Authors:

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

Journal:

Acta Crystallographica, Section B 57 378-385 (2001)

DOI:

https://doi.org/10.1107/S0108768100020218

B-IncStrDB ID: NYm9l2peHwb Entry date: 2021-12-21 Last revision: 2024-01-02

octano1

Chemical data

Common Name: octane+urea inclusion compound [ Help ]

Formula moiety: C6 O6 N12 H24+0.893(C8 H18) [ Help ]

Structural Formula Sum: C13.144 O6 N12 H40.074 [ Help ]

Formula weight: 462.35 Da [ Help ]

Crystallographic data and experimental details

a: 8.226(4) Å [ Help ]

b: 8.226(4) Å [ Help ]

c: 11.019(4) Å [ Help ]

α: 90 ° [ Help ]

β: 90 ° [ Help ]

γ: 120 ° [ Help ]

Volume: 645.7(4) Å³ [ Help ]

Z: 6 [ Help ]

Cell measurement temperature: 293 K [ Help ]

Cell determination reflection Nb.: 608 [ Help ]

θ(max) for cell determination: 26.08 ° [ Help ]

θ(min) for cell determination: 2.86 ° [ Help ]

λ for cell measurement: 0.71073 Å [ Help ]

Modulation dimension: 1 [ Help ]

Measured independent wave vectors: (Show/hide table) [ 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: octane [ 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: hexagonal [ Help ]

Superspace group name (ITC): P6122(00γ) [ Help ]

Symmetry operations of the superspace group: (Show/hide table) [ Help ]

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

Absorption correction type: none [ Help ]

Minimum transmission factor: 1.000 [ Help ]

Maximum transmission factor: 1.000 [ Help ]

μ: 0.09 mm^-1 [ Help ]

Experimental remarks: Data were recorded at 293K using the Stoe Imaging Plate system. The φ-range was 0-200° with an increment of 2°. Exposure timeper frame was 3 min and the distance of the imaging plate was 70mm. For integration a dynamic profile function was used (Minimum profile diameter= 15 pixels; Maximum profile diameter= 19 pixels.) [ Help ]

Refinement details

h(min): 1 [ Help ]

h(max): 10 [ Help ]

k(min): -8 [ Help ]

k(max): 0 [ Help ]

l(min): 0 [ Help ]

l(max): 12 [ Help ]

m1(min): 0 [ Help ]

m1(max): 0 [ Help ]

Intense reflections threshold: 3σ [ Help ]

Total nb. of reflections: 418 [ Help ]

Nb. of observed reflections: 278 [ Help ]

Refinement based on: F [ Help ]

Weighting scheme: sigma [ Help ]

Weighting scheme remarks: w=1/(σ²(F)+0.0001F²) [ Help ]

R(obs): 0.0551 [ Help ]

wR(obs): 0.0627 [ Help ]

R(all): 0.0807 [ Help ]

wR(all): 0.0633 [ Help ]

Nb. of reflections: 418 [ Help ]

Nb. of parameters: 28 [ Help ]

S(all): 3.14 [ Help ]

S(obs): 2.54 [ Help ]

Δ/σ(max): 0.0108 [ Help ]

Δ/σ(mean): 0.0031 [ Help ]

Δρ(max): 1.27 e_Å^-3 [ Help ]

Δρ(min): -0.19 e_Å^-3 [ Help ]

Extinction method: none [ Help ]

Refinement remarks: Guest molecules were located using three dummy atoms marked with DA in the atom list [ Help ]

Structural Information

Average Structure: (Show/hide table) [ Help ]

Atom site label	Site description	Atom symbol	Subsystem	Symmetry multiplicity	Occupancy	x	y	z	Uiso/equiv
O	.	O	1	2	1	0.6404(2)	0.3202(1)	0.083333	0.0375(8)
C	.	C	1	2	1	0.8164(4)	0.4082(2)	0.083333	0.035(1)
N	.	N	1	1	1	0.9128(3)	0.4340(3)	0.1854(2)	0.049(1)
Uh1	.	H	1	1	1	0.858(3)	0.392(3)	0.245(2)	0.043(5)
Uh2	.	H	1	1	1	1.029(3)	0.481(3)	0.187(2)	0.043(5)
Centera	DA	C	2	12	0	0	0	0	0.037995
Xa	DA	C	2	2	0	0.121566	0	0	0.037995
Ya	DA	C	2	6	0	0	0	0.081674	0.037995
Cg1a	.	C	2	1	0.166667	-0.052638	0	0.050025	0.166954
H11a	.	H	2	1	0.166667	-0.06551	0.114544	0.050025	0.166954
H12a	.	H	2	1	0.166667	-0.180053	-0.114544	0.050025	0.166954
Cg2a	.	C	2	1	0.166667	0.052638	0	0.150076	0.166954
H21a	.	H	2	1	0.166667	0.180053	0.114544	0.150076	0.166954
H22a	.	H	2	1	0.166667	0.06551	-0.114544	0.150076	0.166954
Cg3a	.	C	2	1	0.166667	-0.052638	0	0.250127	0.166954
H31a	.	H	2	1	0.166667	-0.06551	0.114544	0.250127	0.166954
H32a	.	H	2	1	0.166667	-0.180053	-0.114544	0.250127	0.166954
Cg4a	.	C	2	1	0.166667	0.052638	0	0.350178	0.166954
H41a	.	H	2	1	0.166667	0.180053	0.114544	0.350178	0.166954
H42a	.	H	2	1	0.166667	0.06551	-0.114544	0.350178	0.166954
H43a	.	H	2	1	0.166667	0.122781	0	0.416824	0.166954

ADP components: (Show/hide table) [ Help ]

Atom site label	U11	U22	U33	U12	U13	U23
O	0.033(1)	0.0464(9)	0.028(1)	0.0167(6)	0	-0.0020(8)
C	0.045(2)	0.036(1)	0.028(2)	0.0223(9)	0	-0.006(1)
N	0.036(1)	0.075(2)	0.027(1)	0.021(1)	-0.001(1)	0.005(1)
Cg1a	0.100431	0.100431	0.3	0.050216	0	0
H11a	0.100431	0.100431	0.3	0.050216	0	0
H12a	0.100431	0.100431	0.3	0.050216	0	0
Cg2a	0.100431	0.100431	0.3	0.050216	0	0
H21a	0.100431	0.100431	0.3	0.050216	0	0
H22a	0.100431	0.100431	0.3	0.050216	0	0
Cg3a	0.100431	0.100431	0.3	0.050216	0	0
H31a	0.100431	0.100431	0.3	0.050216	0	0
H32a	0.100431	0.100431	0.3	0.050216	0	0
Cg4a	0.100431	0.100431	0.3	0.050216	0	0
H41a	0.100431	0.100431	0.3	0.050216	0	0
H42a	0.100431	0.100431	0.3	0.050216	0	0
H43a	0.100431	0.100431	0.3	0.050216	0	0

Fourier Wave Vectors (explicit: q_x,q_y,q_z or coefficients: q_1,q_2,...): (Show/hide table) [ Help ]

Wave vector code	q_x	q_y	q_z
1	0.00000	0.00000	0.89300

Definition of the displacive (translational) Fourier series: (Show/hide table) [ Help ]

Modulation code	Atom site label	Displacement axis	Wave vector code
Cex1	Centera	x	1
Cey1	Centera	y	1
Cez1	Centera	z	1
Xax1	Xa	x	1
Xay1	Xa	y	1
Xaz1	Xa	z	1
Yax1	Ya	x	1
Yay1	Ya	y	1
Yaz1	Ya	z	1
Cg1ax1	Cg1a	x	1
Cg1ay1	Cg1a	y	1
Cg1az1	Cg1a	z	1
H11ax1	H11a	x	1
H11ay1	H11a	y	1
H11az1	H11a	z	1
H12ax1	H12a	x	1
H12ay1	H12a	y	1
H12az1	H12a	z	1
Cg2ax1	Cg2a	x	1
Cg2ay1	Cg2a	y	1
Cg2az1	Cg2a	z	1
H21ax1	H21a	x	1
H21ay1	H21a	y	1
H21az1	H21a	z	1
H22ax1	H22a	x	1
H22ay1	H22a	y	1
H22az1	H22a	z	1
Cg3ax1	Cg3a	x	1
Cg3ay1	Cg3a	y	1
Cg3az1	Cg3a	z	1
H31ax1	H31a	x	1
H31ay1	H31a	y	1
H31az1	H31a	z	1
H32ax1	H32a	x	1
H32ay1	H32a	y	1
H32az1	H32a	z	1
Cg4ax1	Cg4a	x	1
Cg4ay1	Cg4a	y	1
Cg4az1	Cg4a	z	1
H41ax1	H41a	x	1
H41ay1	H41a	y	1
H41az1	H41a	z	1
H42ax1	H42a	x	1
H42ay1	H42a	y	1
H42az1	H42a	z	1
H43ax1	H43a	x	1
H43ay1	H43a	y	1
H43az1	H43a	z	1

Displacive (translational) Fourier coefficients: (Show/hide table) [ Help ]

Modulation code	Cosine coefficient	Sine coefficient
Cex1	-0.0376(16)	-0.02169(94)
Cey1	0	-0.0434(19)
Cez1	0	0
Xax1	-0.0376(16)	-0.02169(94)
Xay1	0	-0.0434(19)
Xaz1	0	0
Yax1	-0.0376(16)	-0.02169(94)
Yay1	0	-0.0434(19)
Yaz1	0	0
Cg1ax1	-0.0376(16)	-0.02169(94)
Cg1ay1	0	-0.0434(19)
Cg1az1	0	0
H11ax1	-0.0376(16)	-0.02169(94)
H11ay1	0	-0.0434(19)
H11az1	0	0
H12ax1	-0.0376(16)	-0.02169(94)
H12ay1	0	-0.0434(19)
H12az1	0	0
Cg2ax1	-0.0376(16)	-0.02169(94)
Cg2ay1	0	-0.0434(19)
Cg2az1	0	0
H21ax1	-0.0376(16)	-0.02169(94)
H21ay1	0	-0.0434(19)
H21az1	0	0
H22ax1	-0.0376(16)	-0.02169(94)
H22ay1	0	-0.0434(19)
H22az1	0	0
Cg3ax1	-0.0376(16)	-0.02169(94)
Cg3ay1	0	-0.0434(19)
Cg3az1	0	0
H31ax1	-0.0376(16)	-0.02169(94)
H31ay1	0	-0.0434(19)
H31az1	0	0
H32ax1	-0.0376(16)	-0.02169(94)
H32ay1	0	-0.0434(19)
H32az1	0	0
Cg4ax1	-0.0376(16)	-0.02169(94)
Cg4ay1	0	-0.0434(19)
Cg4az1	0	0
H41ax1	-0.0376(16)	-0.02169(94)
H41ay1	0	-0.0434(19)
H41az1	0	0
H42ax1	-0.0376(16)	-0.02169(94)
H42ay1	0	-0.0434(19)
H42az1	0	0
H43ax1	-0.0376(16)	-0.02169(94)
H43ay1	0	-0.0434(19)
H43az1	0	0