Synthesis and crystal structure of 2,9-di­amino-5,6,11,12-tetra­hydro­dibenzo[a,e]cyclo­octene

Successful separation of cis- and trans-di­amino­dibenzo­cyclo­octane (DADBCO) allows the crystal structure solution of cis-DADBCO.

Key indicators

Structure: I

• Single-crystal X-ray study
• T = 100 K
• Mean [sigma](C-C) = 0.005 Å
• R factor = 0.046
• wR factor = 0.106
• Data-to-parameter ratio = 11.9

checkCIF/PLATON results

No syntax errors found



Alert level C
STRVA01_ALERT_4_C           Flack test results are meaningless.
           From the CIF: _refine_ls_abs_structure_Flack    0.300
           From the CIF: _refine_ls_abs_structure_Flack_su    1.200

Author Response: the absolute strucure was not determined due to the absence of heavy atoms

THETM01_ALERT_3_C  The value of sine(theta_max)/wavelength is less than 0.590
            Calculated sin(theta_max)/wavelength =    0.5879

Author Response: The value is 0.5879

PLAT089_ALERT_3_C Poor Data / Parameter Ratio (Zmax < 18) ........       6.63 Note
PLAT340_ALERT_3_C Low Bond Precision on  C-C Bonds ...............    0.00517 Ang.
PLAT420_ALERT_2_C D-H Bond Without Acceptor  N1       --H1A      .     Please Check

Author Response: N1--H2A 2.458A | N2--H1B 2.456A

PLAT420_ALERT_2_C D-H Bond Without Acceptor  N2       --H2B      .     Please Check

Author Response: N1--H2A 2.458A | N2--H1B 2.456A

PLAT911_ALERT_3_C Missing FCF Refl Between Thmin & STh/L=    0.588          5 Report
                2  0  0,   3  3  0,   0  4  0,   1  4  0,   2  5  7,

Author Response: data collected as triclinic, crystal is weakly diffracting and has needle morphology

Alert level G
PLAT002_ALERT_2_G Number of Distance or Angle Restraints on AtSite          3 Note
PLAT003_ALERT_2_G Number of Uiso or Uij Restrained non-H Atoms ...         18 Report
PLAT007_ALERT_5_G Number of Unrefined Donor-H Atoms ..............          2 Report
              H2A   H2B
PLAT032_ALERT_4_G Std. Uncertainty on Flack Parameter Value High .      1.200 Report
PLAT172_ALERT_4_G The CIF-Embedded .res File Contains DFIX Records          3 Report
PLAT177_ALERT_4_G The CIF-Embedded .res File Contains DELU Records          1 Report
PLAT178_ALERT_4_G The CIF-Embedded .res File Contains SIMU Records          1 Report
PLAT795_ALERT_4_G C-Atom in CIF Coordinate List Out-of-Sequence ..        C21 Note
PLAT860_ALERT_3_G Number of Least-Squares Restraints .............        172 Note
PLAT909_ALERT_3_G Percentage of I>2sig(I) Data at Theta(Max) Still        72% Note
PLAT916_ALERT_2_G Hooft y and Flack x Parameter Values Differ by .       0.60 Check
PLAT933_ALERT_2_G Number of HKL-OMIT Records in Embedded .res File          8 Note
                2  0  0,   0  4  0,   1  2 -6,   3  3  0,   1  4  0,   2  0 -2,
                4 21  3,   2  5  7,
PLAT969_ALERT_5_G The 'Henn et al.' R-Factor-gap value ...........       2.74 Note
              Predicted wR2: Based on SigI   2  3.88 or SHELX Weight 10.28       
PLAT978_ALERT_2_G Number C-C Bonds with Positive Residual Density.          0 Info

   0 ALERT level A = Most likely a serious problem - resolve or explain
   0 ALERT level B = A potentially serious problem, consider carefully
   7 ALERT level C = Check. Ensure it is not caused by an omission or oversight
  14 ALERT level G = General information/check it is not something unexpected

   0 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
   7 ALERT type 2 Indicator that the structure model may be wrong or deficient
   6 ALERT type 3 Indicator that the structure quality may be low
   6 ALERT type 4 Improvement, methodology, query or suggestion
   2 ALERT type 5 Informative message, check

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Computing details

2,9-Diamino-5,6,11,12-tetrahydrodibenzo[a,e][8]annulene

Crystal data

C16H18N2	Dx = 1.293 Mg m^−3
Mr = 238.32	Cu Kα radiation, λ = 1.54178 Å
Orthorhombic, Pna21	Cell parameters from 8510 reflections
a = 8.8641 (3) Å	θ = 4.0–73.6°
b = 22.0075 (6) Å	µ = 0.59 mm^−1
c = 6.2771 (2) Å	T = 100 K
V = 1224.52 (7) Å^3	Needle, clear light green
Z = 4	0.1 × 0.1 × 0.01 mm
F(000) = 512

Data collection

Bruker APEXII CCD diffractometer	1781 reflections with I > 2σ(I)
φ and ω scans	Rint = 0.118
Absorption correction: multi-scan (SADABS; Krause et al., 2015)	θmax = 65.0°, θmin = 4.0°
Tmin = 0.459, Tmax = 0.754	h = −10→10
39813 measured reflections	k = −25→25
2060 independent reflections	l = −6→7

Refinement

Refinement on F^2	Hydrogen site location: mixed
Least-squares matrix: full	H atoms treated by a mixture of independent and constrained refinement
R[F^2 > 2σ(F^2)] = 0.046	w = 1/[σ^2(Fo^2) + (0.0353P)^2 + 0.9951P] where P = (Fo^2 + 2Fc^2)/3
wR(F^2) = 0.106	(Δ/σ)max < 0.001
S = 1.08	Δρmax = 0.18 e Å^−3
2060 reflections	Δρmin = −0.22 e Å^−3
173 parameters	Absolute structure: Refined as an inversion twin
172 restraints	Absolute structure parameter: 0.3 (12)
Primary atom site location: shelXT

Special details

Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes.

Refinement. Refined as a 2-component inversion twin.

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

	x	y	z	Uiso*/Ueq
N1	0.8644 (4)	0.33304 (16)	0.4674 (6)	0.0276 (8)
H1A	0.855 (5)	0.325 (2)	0.332 (4)	0.058 (18)*
H1B	0.950 (4)	0.321 (2)	0.516 (7)	0.052 (16)*
N2	0.3459 (4)	0.76938 (14)	0.2091 (6)	0.0295 (9)
H2A	0.293746	0.748604	0.114219	0.035*
H2B	0.284518	0.793724	0.279538	0.035*
C11	0.7832 (4)	0.43707 (17)	0.3906 (6)	0.0205 (9)
H11	0.750058	0.424326	0.253757	0.025*
C12	0.7645 (4)	0.49766 (16)	0.4496 (6)	0.0181 (8)
C13	0.8118 (4)	0.51680 (17)	0.6518 (6)	0.0186 (8)
C14	0.8763 (4)	0.47369 (16)	0.7896 (7)	0.0211 (8)
H14	0.908901	0.485974	0.927203	0.025*
C15	0.8932 (4)	0.41367 (17)	0.7284 (7)	0.0228 (9)
H15	0.935284	0.385279	0.825644	0.027*
C16	0.8497 (4)	0.39431 (17)	0.5276 (7)	0.0217 (9)
C31	0.6953 (4)	0.54170 (17)	0.2940 (6)	0.0195 (8)
H31A	0.692418	0.522457	0.151541	0.023*
H31B	0.760925	0.577985	0.284019	0.023*
C32	0.5330 (4)	0.56256 (16)	0.3539 (6)	0.0192 (8)
H32A	0.467057	0.556422	0.228475	0.023*
H32B	0.495208	0.535789	0.468896	0.023*
C33	0.7993 (4)	0.58216 (16)	0.7233 (7)	0.0214 (8)
H33A	0.836432	0.608605	0.606980	0.026*
H33B	0.866689	0.588157	0.847236	0.026*
C34	0.6377 (4)	0.60340 (17)	0.7861 (6)	0.0217 (8)
H34A	0.572848	0.567063	0.802213	0.026*
H34B	0.642990	0.623702	0.926614	0.026*
C21	0.4468 (4)	0.66922 (16)	0.2906 (7)	0.0205 (8)
H21	0.418445	0.656557	0.151499	0.025*
C22	0.5171 (4)	0.62758 (17)	0.4262 (6)	0.0182 (8)
C23	0.5629 (4)	0.64650 (17)	0.6289 (6)	0.0213 (8)
C24	0.5334 (5)	0.70611 (17)	0.6907 (7)	0.0269 (9)
H24	0.564002	0.719258	0.828207	0.032*
C25	0.4600 (5)	0.74720 (19)	0.5557 (7)	0.0287 (10)
H25	0.439745	0.787438	0.602401	0.034*
C26	0.4170 (4)	0.72879 (17)	0.3533 (7)	0.0235 (9)

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
N1	0.0259 (19)	0.0224 (18)	0.034 (2)	0.0023 (15)	0.0022 (17)	−0.0011 (16)
N2	0.0270 (18)	0.0243 (18)	0.037 (2)	0.0035 (14)	−0.0119 (16)	0.0037 (15)
C11	0.0109 (18)	0.026 (2)	0.025 (2)	−0.0010 (15)	−0.0004 (15)	0.0018 (16)
C12	0.0108 (17)	0.0217 (19)	0.022 (2)	0.0020 (15)	0.0000 (16)	0.0021 (16)
C13	0.0106 (17)	0.0234 (18)	0.022 (2)	0.0013 (15)	0.0018 (16)	−0.0004 (16)
C14	0.0129 (17)	0.027 (2)	0.023 (2)	−0.0011 (15)	0.0004 (16)	0.0019 (17)
C15	0.0153 (18)	0.027 (2)	0.026 (2)	0.0022 (16)	0.0008 (17)	0.0042 (18)
C16	0.0179 (19)	0.0185 (19)	0.029 (2)	0.0003 (15)	0.0041 (17)	0.0010 (17)
C31	0.0152 (18)	0.0242 (19)	0.019 (2)	0.0001 (15)	−0.0003 (16)	−0.0019 (16)
C32	0.0140 (17)	0.0197 (19)	0.024 (2)	−0.0009 (14)	−0.0024 (16)	−0.0010 (15)
C33	0.0175 (18)	0.0240 (19)	0.023 (2)	−0.0017 (15)	0.0000 (17)	−0.0019 (16)
C34	0.0232 (19)	0.0210 (18)	0.021 (2)	0.0029 (16)	−0.0043 (17)	−0.0023 (16)
C21	0.0157 (18)	0.0207 (18)	0.025 (2)	−0.0007 (15)	−0.0031 (17)	0.0004 (16)
C22	0.0141 (18)	0.0189 (19)	0.022 (2)	−0.0010 (14)	0.0011 (16)	0.0018 (15)
C23	0.0186 (19)	0.0215 (19)	0.024 (2)	0.0000 (15)	−0.0030 (17)	−0.0006 (16)
C24	0.031 (2)	0.023 (2)	0.027 (2)	0.0030 (18)	−0.0071 (17)	−0.0039 (18)
C25	0.032 (2)	0.022 (2)	0.032 (3)	0.0022 (18)	−0.0055 (19)	−0.0045 (18)
C26	0.0185 (19)	0.0217 (19)	0.030 (2)	−0.0010 (16)	−0.0073 (17)	0.0034 (17)

Geometric parameters (Å, º)

N1—H1A	0.87 (2)	C31—C32	1.556 (5)
N1—H1B	0.86 (2)	C32—H32A	0.9900
N1—C16	1.406 (5)	C32—H32B	0.9900
N2—H2A	0.8817	C32—C22	1.508 (5)
N2—H2B	0.8824	C33—H33A	0.9900
N2—C26	1.419 (5)	C33—H33B	0.9900
C11—H11	0.9500	C33—C34	1.557 (5)
C11—C12	1.394 (5)	C34—H34A	0.9900
C11—C16	1.404 (5)	C34—H34B	0.9900
C12—C13	1.401 (5)	C34—C23	1.520 (5)
C12—C31	1.506 (5)	C21—H21	0.9500
C13—C14	1.406 (5)	C21—C22	1.398 (5)
C13—C33	1.511 (5)	C21—C26	1.394 (5)
C14—H14	0.9500	C22—C23	1.399 (6)
C14—C15	1.384 (5)	C23—C24	1.393 (5)
C15—H15	0.9500	C24—H24	0.9500
C15—C16	1.385 (6)	C24—C25	1.400 (6)
C31—H31A	0.9900	C25—H25	0.9500
C31—H31B	0.9900	C25—C26	1.387 (6)
H1A—N1—H1B	111 (4)	C22—C32—C31	116.1 (3)
C16—N1—H1A	116 (3)	C22—C32—H32A	108.3
C16—N1—H1B	107 (3)	C22—C32—H32B	108.3
H2A—N2—H2B	109.3	C13—C33—H33A	108.4
C26—N2—H2A	109.7	C13—C33—H33B	108.4
C26—N2—H2B	109.6	C13—C33—C34	115.4 (3)
C12—C11—H11	119.1	H33A—C33—H33B	107.5
C12—C11—C16	121.9 (4)	C34—C33—H33A	108.4
C16—C11—H11	119.1	C34—C33—H33B	108.4
C11—C12—C13	119.5 (4)	C33—C34—H34A	108.5
C11—C12—C31	119.5 (4)	C33—C34—H34B	108.5
C13—C12—C31	121.0 (3)	H34A—C34—H34B	107.5
C12—C13—C14	118.4 (4)	C23—C34—C33	115.1 (3)
C12—C13—C33	122.2 (3)	C23—C34—H34A	108.5
C14—C13—C33	119.3 (3)	C23—C34—H34B	108.5
C13—C14—H14	119.4	C22—C21—H21	119.0
C15—C14—C13	121.1 (4)	C26—C21—H21	119.0
C15—C14—H14	119.4	C26—C21—C22	121.9 (4)
C14—C15—H15	119.5	C21—C22—C32	118.7 (3)
C14—C15—C16	121.1 (4)	C21—C22—C23	119.2 (3)
C16—C15—H15	119.5	C23—C22—C32	121.9 (3)
C11—C16—N1	121.1 (4)	C22—C23—C34	122.1 (3)
C15—C16—N1	120.9 (4)	C24—C23—C34	119.3 (4)
C15—C16—C11	117.9 (3)	C24—C23—C22	118.6 (4)
C12—C31—H31A	108.7	C23—C24—H24	119.1
C12—C31—H31B	108.7	C23—C24—C25	121.8 (4)
C12—C31—C32	114.2 (3)	C25—C24—H24	119.1
H31A—C31—H31B	107.6	C24—C25—H25	120.2
C32—C31—H31A	108.7	C26—C25—C24	119.6 (4)
C32—C31—H31B	108.7	C26—C25—H25	120.2
C31—C32—H32A	108.3	C21—C26—N2	119.7 (4)
C31—C32—H32B	108.3	C25—C26—N2	121.5 (4)
H32A—C32—H32B	107.4	C25—C26—C21	118.8 (4)
C11—C12—C13—C14	−0.3 (5)	C31—C32—C22—C21	108.3 (4)
C11—C12—C13—C33	178.1 (3)	C31—C32—C22—C23	−75.3 (4)
C11—C12—C31—C32	108.7 (4)	C32—C22—C23—C34	2.6 (5)
C12—C11—C16—N1	178.4 (3)	C32—C22—C23—C24	−174.8 (4)
C12—C11—C16—C15	1.8 (5)	C33—C13—C14—C15	−178.4 (3)
C12—C13—C14—C15	0.0 (5)	C33—C34—C23—C22	68.8 (5)
C12—C13—C33—C34	76.1 (5)	C33—C34—C23—C24	−113.8 (4)
C12—C31—C32—C22	109.5 (4)	C34—C23—C24—C25	−177.7 (4)
C13—C12—C31—C32	−71.9 (4)	C21—C22—C23—C34	179.0 (3)
C13—C14—C15—C16	1.3 (5)	C21—C22—C23—C24	1.6 (5)
C13—C33—C34—C23	−107.9 (4)	C22—C21—C26—N2	179.7 (3)
C14—C13—C33—C34	−105.6 (4)	C22—C21—C26—C25	0.7 (6)
C14—C15—C16—N1	−178.8 (3)	C22—C23—C24—C25	−0.2 (6)
C14—C15—C16—C11	−2.1 (5)	C23—C24—C25—C26	−1.0 (6)
C16—C11—C12—C13	−0.6 (5)	C24—C25—C26—N2	−178.3 (4)
C16—C11—C12—C31	178.8 (3)	C24—C25—C26—C21	0.7 (6)
C31—C12—C13—C14	−179.7 (3)	C26—C21—C22—C32	174.7 (3)
C31—C12—C13—C33	−1.3 (5)	C26—C21—C22—C23	−1.9 (5)

Hydrogen-bond geometry (Å, º)

Cg1 and Cg2 are the centroids of rings C11–C16 and C21–C26, respectively.

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1B···N2^i	0.86 (4)	2.46 (4)	3.295 (5)	165 (4)
N2—H2A···N1^ii	0.88	2.46	3.295 (5)	159
N2—H2B···Cg2^iii	0.88	2.96	3.742 (4)	149
C14—H14···Cg1^iv	0.95	2.84	3.572 (4)	135
C32—H32A···Cg1^ii	0.99	2.78	3.640 (4)	145

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