3a,11b-Dihydr­oxy-2-oxo-2,3,3a,11b-tetra­hydro-1H-imidazo[4,5-f][1,10]phenanthrolin-7-ium chloride

In the crystal structure of the title compound, C₁₃H₁₁N₄O₃⁺·Cl⁻, the dihedral angle between the two pyridine rings is 9.72 (9) Å. Ions are linked via N—H...Cl, O—H...Cl and O—H...O hydrogen bonds, forming a three-dimensional framework.

Key indicators

• Single-crystal X-ray study
• T = 293 K
• Mean [sigma](C-C) = 0.002 Å
• R factor = 0.037
• wR factor = 0.103
• Data-to-parameter ratio = 11.9

checkCIF/PLATON results

No syntax errors found



Alert level C
PLAT420_ALERT_2_C D-H Without Acceptor       N3     -   H3A    ...          ?
PLAT066_ALERT_1_C Predicted and Reported Transmissions Identical .          ?
PLAT480_ALERT_4_C Long H...A H-Bond Reported H3A    ..  O2      ..       2.65 Ang.

Alert level G
PLAT199_ALERT_1_G Check the Reported _cell_measurement_temperature        293 K
PLAT200_ALERT_1_G Check the Reported _diffrn_ambient_temperature .        293 K
PLAT793_ALERT_4_G Check the Absolute Configuration of C5     .....          R
PLAT793_ALERT_4_G Check the Absolute Configuration of C7     .....          S

   0 ALERT level A = In general: serious problem
   0 ALERT level B = Potentially serious problem
   3 ALERT level C = Check and explain
   4 ALERT level G = General alerts; check

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

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S1. Comment

Recent year, we used different alkyl-substituted glycolurils as the building blocks to synthesize the partially alkyl substituted cucurbit[n]urils (Zhao et al., 2004; Zheng et al., 2005). In this work, we further report the crystal structure of a phenanthroline-substituted semi-glycoluril.

In the title compound (I), (Fig. 1), consists of organic cations, Cl^- anions. The dihedral angle between two pyridine rings is 9.72 (9) Å. Molecules are linked via N—H···Cl, O—H···Cl and O—H···O hydrogen bonds forming a three-dimensional framework. (Table 1).

Related literature

For general background, see: Zhao et al.,(2004); Zheng et al.,(2005).

S2. Experimental

1,10-Phenanthroline-5,6-dione (3.00 g,14.29 mmol) and carbamide (15.00 g, 250 mmol) were dissolved in acetic acid glacial (120 mL) and hydrochloric acid (5 mL) at room temperature. There was a lot of deposit after the mixture were stirred 5 h. Filtrate, solid was washed by ethanol, drying, gained white powder 2.46 g [yield: 63%].

S3. Refinement

H atoms were placed in calculated positions with C—H = 0.93, N—H = 0.86 and O—H = 0.82 Å and refined as riding, with U_iso(H) = 1.2-1.5U_eq.

Computing details

Data collection: APEX2 (Bruker, 2005); cell refinement: SAINT (Bruker, 2005); data reduction: SAINT (Bruker, 2005); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 for Windows (Farrugia, 1997); software used to prepare material for publication: WinGX (Farrugia, 1999).

Figures

Fig. 1. The molecular structure of (I) showing the atom-labelling scheme. Displacement ellipsoids are drawn at the 50% probability level.

3a,11b-Dihydroxy-2-oxo-2,3,3a,11b-tetrahydro-1H- imidazo[4,5-f][1,10]phenanthrolin-7-ium chloride

Crystal data

C13H11N4O3^+·Cl^−	F(000) = 632
Mr = 306.71	Dx = 1.585 Mg m^−3
Monoclinic, P21/c	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybc	Cell parameters from 2261 reflections
a = 7.9420 (13) Å	θ = 2.0–25.0°
b = 20.352 (3) Å	µ = 0.31 mm^−1
c = 8.2972 (14) Å	T = 293 K
β = 106.620 (5)°	Prism, colourless
V = 1285.1 (4) Å^3	0.31 × 0.22 × 0.19 mm
Z = 4

Data collection

Bruker APEXII CCD area-detector diffractometer	2261 independent reflections
Radiation source: fine-focus sealed tube	2094 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.022
ϕ and ω scans	θmax = 25.0°, θmin = 2.0°
Absorption correction: multi-scan (SADABS; Bruker, 2005)	h = −8→9
Tmin = 0.909, Tmax = 0.943	k = −24→24
13480 measured reflections	l = −9→8

Refinement

Refinement on F^2	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F^2 > 2σ(F^2)] = 0.037	Hydrogen site location: inferred from neighbouring sites
wR(F^2) = 0.103	H-atom parameters constrained
S = 1.05	w = 1/[σ^2(Fo^2) + (0.0589P)^2 + 0.7326P] where P = (Fo^2 + 2Fc^2)/3
2261 reflections	(Δ/σ)max = 0.001
190 parameters	Δρmax = 0.48 e Å^−3
0 restraints	Δρmin = −0.52 e Å^−3

Special details

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

Refinement. Refinement of F² against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F², conventional R-factors R are based on F, with F set to zero for negative F². The threshold expression of F² > σ(F²) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F² are statistically about twice as large as those based on F, and R- factors based on ALL data will be even larger.

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

	x	y	z	Uiso*/Ueq
C1	−0.0113 (3)	0.58542 (11)	0.2547 (3)	0.0409 (5)
H1	−0.0891	0.5658	0.1616	0.049*
C2	−0.0166 (3)	0.65219 (11)	0.2779 (3)	0.0446 (5)
H2	−0.0982	0.6781	0.2015	0.054*
C3	0.1010 (2)	0.68003 (10)	0.4159 (3)	0.0376 (5)
H3	0.0960	0.7249	0.4352	0.045*
C4	0.2275 (2)	0.64158 (9)	0.5271 (2)	0.0280 (4)
C5	0.3591 (2)	0.67304 (8)	0.6779 (2)	0.0288 (4)
C6	0.6083 (2)	0.70941 (8)	0.6106 (2)	0.0286 (4)
C7	0.5217 (2)	0.62729 (8)	0.7653 (2)	0.0265 (4)
C8	0.4878 (2)	0.55393 (8)	0.7408 (2)	0.0250 (4)
C9	0.6001 (2)	0.50849 (9)	0.8421 (2)	0.0311 (4)
H9	0.6963	0.5226	0.9282	0.037*
C10	0.5678 (2)	0.44209 (9)	0.8141 (2)	0.0325 (4)
H10	0.6423	0.4111	0.8805	0.039*
C11	0.4231 (3)	0.42256 (9)	0.6860 (2)	0.0327 (4)
H11	0.4009	0.3778	0.6693	0.039*
C12	0.3479 (2)	0.52914 (8)	0.6134 (2)	0.0258 (4)
C13	0.2261 (2)	0.57459 (8)	0.5007 (2)	0.0261 (4)
N1	0.10578 (19)	0.54886 (8)	0.36612 (19)	0.0314 (4)
H1A	0.1046	0.5070	0.3516	0.038*
N2	0.3139 (2)	0.46487 (7)	0.58529 (19)	0.0315 (4)
N3	0.44790 (19)	0.72802 (7)	0.6258 (2)	0.0337 (4)
H3A	0.4054	0.7671	0.6071	0.040*
N4	0.64752 (19)	0.64940 (7)	0.68046 (18)	0.0284 (3)
H4	0.7373	0.6268	0.6752	0.034*
O1	0.70045 (17)	0.74179 (6)	0.54285 (17)	0.0374 (3)
O2	0.26989 (17)	0.69570 (7)	0.79061 (17)	0.0389 (3)
H2A	0.2216	0.6647	0.8224	0.058*
O3	0.58135 (18)	0.63742 (6)	0.93855 (15)	0.0355 (3)
H3B	0.6013	0.6766	0.9577	0.053*
Cl1	0.03122 (6)	0.58193 (2)	0.83116 (6)	0.03931 (18)

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
C1	0.0294 (10)	0.0529 (13)	0.0332 (10)	−0.0040 (9)	−0.0026 (8)	0.0010 (9)
C2	0.0330 (10)	0.0466 (12)	0.0450 (12)	0.0029 (9)	−0.0037 (9)	0.0121 (10)
C3	0.0304 (10)	0.0314 (10)	0.0473 (12)	0.0010 (8)	0.0053 (8)	0.0062 (8)
C4	0.0242 (9)	0.0289 (9)	0.0305 (9)	−0.0007 (7)	0.0073 (7)	0.0014 (7)
C5	0.0289 (9)	0.0228 (8)	0.0336 (10)	−0.0010 (7)	0.0071 (7)	−0.0031 (7)
C6	0.0302 (9)	0.0226 (8)	0.0285 (9)	−0.0043 (7)	0.0014 (7)	−0.0017 (7)
C7	0.0274 (9)	0.0252 (9)	0.0239 (8)	−0.0032 (7)	0.0028 (7)	−0.0008 (7)
C8	0.0270 (8)	0.0242 (9)	0.0239 (8)	−0.0019 (7)	0.0074 (7)	0.0005 (6)
C9	0.0308 (9)	0.0313 (9)	0.0282 (9)	−0.0021 (7)	0.0037 (7)	0.0017 (7)
C10	0.0357 (10)	0.0285 (9)	0.0331 (10)	0.0041 (8)	0.0099 (8)	0.0067 (8)
C11	0.0402 (10)	0.0225 (9)	0.0369 (10)	−0.0016 (7)	0.0133 (8)	0.0001 (7)
C12	0.0266 (8)	0.0247 (8)	0.0270 (9)	−0.0017 (7)	0.0092 (7)	−0.0021 (7)
C13	0.0230 (8)	0.0296 (9)	0.0255 (9)	−0.0025 (7)	0.0065 (7)	−0.0014 (7)
N1	0.0281 (8)	0.0325 (8)	0.0305 (8)	−0.0031 (6)	0.0031 (6)	−0.0043 (6)
N2	0.0337 (8)	0.0258 (8)	0.0328 (8)	−0.0031 (6)	0.0061 (6)	−0.0036 (6)
N3	0.0296 (8)	0.0197 (7)	0.0488 (10)	0.0004 (6)	0.0065 (7)	0.0035 (7)
N4	0.0258 (7)	0.0233 (7)	0.0348 (8)	0.0006 (6)	0.0064 (6)	0.0037 (6)
O1	0.0358 (7)	0.0304 (7)	0.0443 (8)	−0.0045 (6)	0.0088 (6)	0.0097 (6)
O2	0.0381 (7)	0.0349 (7)	0.0468 (8)	−0.0022 (6)	0.0172 (6)	−0.0118 (6)
O3	0.0482 (8)	0.0293 (7)	0.0239 (7)	−0.0074 (6)	0.0021 (6)	−0.0027 (5)
Cl1	0.0309 (3)	0.0414 (3)	0.0425 (3)	−0.00238 (18)	0.0053 (2)	−0.0005 (2)

Geometric parameters (Å, º)

C1—N1	1.335 (3)	C7—C8	1.520 (2)
C1—C2	1.375 (3)	C8—C9	1.388 (2)
C1—H1	0.9300	C8—C12	1.391 (2)
C2—C3	1.376 (3)	C9—C10	1.383 (3)
C2—H2	0.9300	C9—H9	0.9300
C3—C4	1.394 (3)	C10—C11	1.382 (3)
C3—H3	0.9300	C10—H10	0.9300
C4—C13	1.380 (2)	C11—N2	1.333 (2)
C4—C5	1.523 (2)	C11—H11	0.9300
C5—O2	1.403 (2)	C12—N2	1.342 (2)
C5—N3	1.453 (2)	C12—C13	1.466 (2)
C5—C7	1.589 (2)	C13—N1	1.350 (2)
C6—O1	1.233 (2)	N1—H1A	0.8600
C6—N4	1.350 (2)	N3—H3A	0.8600
C6—N3	1.369 (2)	N4—H4	0.8600
C7—O3	1.394 (2)	O2—H2A	0.8200
C7—N4	1.449 (2)	O3—H3B	0.8200
N1—C1—C2	119.82 (18)	C12—C8—C7	122.01 (15)
N1—C1—H1	120.1	C10—C9—C8	119.56 (17)
C2—C1—H1	120.1	C10—C9—H9	120.2
C1—C2—C3	118.87 (19)	C8—C9—H9	120.2
C1—C2—H2	120.6	C11—C10—C9	118.93 (17)
C3—C2—H2	120.6	C11—C10—H10	120.5
C2—C3—C4	120.59 (19)	C9—C10—H10	120.5
C2—C3—H3	119.7	N2—C11—C10	123.04 (16)
C4—C3—H3	119.7	N2—C11—H11	118.5
C13—C4—C3	118.54 (17)	C10—C11—H11	118.5
C13—C4—C5	121.21 (16)	N2—C12—C8	124.23 (16)
C3—C4—C5	120.21 (16)	N2—C12—C13	116.16 (15)
O2—C5—N3	109.01 (14)	C8—C12—C13	119.61 (15)
O2—C5—C4	109.09 (14)	N1—C13—C4	119.09 (16)
N3—C5—C4	110.92 (15)	N1—C13—C12	117.68 (15)
O2—C5—C7	112.82 (15)	C4—C13—C12	123.23 (16)
N3—C5—C7	100.76 (13)	C1—N1—C13	122.99 (17)
C4—C5—C7	113.94 (14)	C1—N1—H1A	118.5
O1—C6—N4	125.80 (17)	C13—N1—H1A	118.5
O1—C6—N3	125.70 (16)	C11—N2—C12	117.26 (16)
N4—C6—N3	108.49 (15)	C6—N3—C5	110.99 (14)
O3—C7—N4	112.13 (14)	C6—N3—H3A	124.5
O3—C7—C8	106.15 (13)	C5—N3—H3A	124.5
N4—C7—C8	111.12 (14)	C6—N4—C7	112.54 (15)
O3—C7—C5	112.10 (14)	C6—N4—H4	123.7
N4—C7—C5	100.35 (13)	C7—N4—H4	123.7
C8—C7—C5	115.14 (14)	C5—O2—H2A	109.5
C9—C8—C12	116.98 (16)	C7—O3—H3B	109.5
C9—C8—C7	120.98 (15)
N1—C1—C2—C3	0.5 (3)	C9—C8—C12—N2	1.3 (3)
C1—C2—C3—C4	2.3 (3)	C7—C8—C12—N2	179.10 (16)
C2—C3—C4—C13	−3.4 (3)	C9—C8—C12—C13	−179.17 (16)
C2—C3—C4—C5	178.93 (18)	C7—C8—C12—C13	−1.4 (2)
C13—C4—C5—O2	−110.16 (18)	C3—C4—C13—N1	1.7 (3)
C3—C4—C5—O2	67.4 (2)	C5—C4—C13—N1	179.35 (15)
C13—C4—C5—N3	129.75 (17)	C3—C4—C13—C12	−177.36 (17)
C3—C4—C5—N3	−52.7 (2)	C5—C4—C13—C12	0.3 (3)
C13—C4—C5—C7	16.9 (2)	N2—C12—C13—N1	−8.7 (2)
C3—C4—C5—C7	−165.51 (16)	C8—C12—C13—N1	171.79 (15)
O2—C5—C7—O3	−21.6 (2)	N2—C12—C13—C4	170.44 (16)
N3—C5—C7—O3	94.51 (16)	C8—C12—C13—C4	−9.1 (3)
C4—C5—C7—O3	−146.68 (15)	C2—C1—N1—C13	−2.3 (3)
O2—C5—C7—N4	−140.73 (14)	C4—C13—N1—C1	1.1 (3)
N3—C5—C7—N4	−24.66 (16)	C12—C13—N1—C1	−179.75 (17)
C4—C5—C7—N4	94.16 (16)	C10—C11—N2—C12	−0.7 (3)
O2—C5—C7—C8	99.91 (17)	C8—C12—N2—C11	−0.6 (3)
N3—C5—C7—C8	−144.01 (14)	C13—C12—N2—C11	179.89 (16)
C4—C5—C7—C8	−25.2 (2)	O1—C6—N3—C5	167.40 (17)
O3—C7—C8—C9	−39.1 (2)	N4—C6—N3—C5	−12.0 (2)
N4—C7—C8—C9	83.02 (19)	O2—C5—N3—C6	142.10 (15)
C5—C7—C8—C9	−163.78 (16)	C4—C5—N3—C6	−97.76 (17)
O3—C7—C8—C12	143.18 (16)	C7—C5—N3—C6	23.22 (18)
N4—C7—C8—C12	−94.67 (19)	O1—C6—N4—C7	173.90 (17)
C5—C7—C8—C12	18.5 (2)	N3—C6—N4—C7	−6.7 (2)
C12—C8—C9—C10	−0.8 (3)	O3—C7—N4—C6	−98.97 (17)
C7—C8—C9—C10	−178.56 (16)	C8—C7—N4—C6	142.41 (15)
C8—C9—C10—C11	−0.4 (3)	C5—C7—N4—C6	20.17 (17)
C9—C10—C11—N2	1.2 (3)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1A···Cl1^i	0.86	2.41	3.1512 (17)	145
N3—H3A···O2^ii	0.86	2.65	3.146 (2)	118
N4—H4···Cl1^iii	0.86	2.50	3.2490 (16)	147
O2—H2A···Cl1	0.82	2.28	3.0712 (15)	163
O3—H3B···O1^iv	0.82	1.89	2.6867 (18)	165

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