supplementary materials


HTML versionpdf versioncif file3d viewstructure factorssupplementary materialsCIF check reportsimilar papers Open access

Acta Cryst. (2009). E65, o2332    [ doi:10.1107/S1600536809034576 ]

1H-Imidazo[4,5-f][1,10]phenanthrolin-7-ium perchlorate monohydrate

S.-M. Shen

Abstract top

In the title crystal structure, C13H9N4+·ClO4-·H2O, cations, anions and water molecules are linked through intermolecular N-H...O, O-H...N and O-H...O hydrogen bonds, forming layers parallel to (001). In addition, there are weak [pi]-[pi] stacking interactions between the layers, involving the cations and with centroid-centroid distances in the range 3.584 (2)-3.662 (2) Å, forming a three-dimensional network.

Comment top

1H-imidazo[4,5-f][1,10]-phenanthroline (IP) is an important derivative of 1,10-phenanthroline that has been used to recognize the secondary structure of DNA in an Ru(II) complex (Xiong et al., 1999). IP is a good molecular building block and has been used to construct some interesting structures (Yu et al., 2009, Liu et al., 2009). In an attempt to form a Zn(II) complex with IP, we adventitiously formed the title compound (I) and its crystal structure is determined herein.

The asymmetric unit of (I) is shown in Fig 1. In the crystal structure N-H···O, O-H···N and O-H···O hydrogen bonds link cations, water molecules and perchlorate anions into a 2-D network (Fig. 2). Details of the hydrogen-bonding geometry are given in Table 1. In addition, there are weak π–π stacking interactions between layers, involving cations with centroid to centroid distances in the range 3.584 (2)-3.662 (2)Å forming a three-dimensional network.

Related literature top

For background to 1H-imidazo[4,5-f][1,10]-phenanthroline and its use as a molecular building block, see: Xiong et al. (1999); Yu et al. (2009); Liu et al. (2009).

Experimental top

IP (0.23 mg,0.1 mmol), Zn(ClO4)2 (0.27 mg, 0.1 mmol), were dissolved in methanol. The mixture was heated and stirred for ten hours under reflux. The resulting solid was then filtered off to give a pure solution which was treated with diethyl ether in a closed vessel. Five weeks later, single crystals were obtained.

Refinement top

All H atoms were visible in difference Fourier maps but were subsequently placed in calculated positions treated as riding with C—H = 0.93, N—H == 0.86Å and with Uiso(H) = 1.2Ueq(C,N). The H atoms of the water molecules were included in the subsequent refinement with O-H = 0.84Å and Uiso(H) = 1.5Ueq(O).

Computing details top

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: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008).

Figures top
[Figure 1] Fig. 1. The asymmetric unit of (I) with displacement ellipdoids drawn at the the 30% probability level. H atoms are shown as spheres of arbitrary radii.
[Figure 2] Fig. 2. Part of the crystal structure of (I). Hydrogen bonds are drawn as dashed lines and π–π stacking interactions are denoted by dashed lines along with labels (A) and (B).
1H-Imidazo[4,5-f][1,10]phenanthrolin-7-ium perchlorate monohydrate top
Crystal data top
C13H9N4+·ClO4−·H2OF(000) = 696
Mr = 338.71Dx = 1.590 Mg m−3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 2521 reflections
a = 11.401 (2) Åθ = 1.8–25.2°
b = 18.475 (3) ŵ = 0.30 mm−1
c = 6.7163 (13) ÅT = 298 K
β = 90.179 (3)°Block, colorless
V = 1414.7 (4) Å30.30 × 0.26 × 0.17 mm
Z = 4
Data collection top
Bruker APEXII area-detector
diffractometer		2534 independent reflections
Radiation source: fine-focus sealed tube1734 reflections with I > 2σ(I)
graphiteRint = 0.031
φ and ω scansθmax = 25.2°, θmin = 1.8°
Absorption correction: multi-scan
(SADABS; Bruker, 2005)		h = −13→11
Tmin = 0.914, Tmax = 0.950k = −21→22
7051 measured reflectionsl = −7→8
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.057Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.197H-atom parameters constrained
S = 1.01 w = 1/[σ2(Fo2) + (0.1261P)2 + 0.1912P]
where P = (Fo2 + 2Fc2)/3
2534 reflections(Δ/σ)max < 0.001
208 parametersΔρmax = 0.41 e Å−3
3 restraintsΔρmin = −0.39 e Å−3
Crystal data top
C13H9N4+·ClO4−·H2OV = 1414.7 (4) Å3
Mr = 338.71Z = 4
Monoclinic, P21/cMo Kα radiation
a = 11.401 (2) ŵ = 0.30 mm−1
b = 18.475 (3) ÅT = 298 K
c = 6.7163 (13) Å0.30 × 0.26 × 0.17 mm
β = 90.179 (3)°
Data collection top
Bruker APEXII area-detector
diffractometer		2534 independent reflections
Absorption correction: multi-scan
(SADABS; Bruker, 2005)		1734 reflections with I > 2σ(I)
Tmin = 0.914, Tmax = 0.950Rint = 0.031
7051 measured reflectionsθmax = 25.2°
Refinement top
R[F2 > 2σ(F2)] = 0.057H-atom parameters constrained
wR(F2) = 0.197Δρmax = 0.41 e Å−3
S = 1.01Δρmin = −0.39 e Å−3
2534 reflectionsAbsolute structure: ?
208 parametersFlack parameter: ?
3 restraintsRogers parameter: ?
Special details top

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. 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 > 2sigma(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 (Å2) top
xyzUiso*/Ueq
N10.7565 (2)0.41426 (15)0.3687 (4)0.0563 (7)
N20.5235 (2)0.38399 (13)0.3439 (4)0.0494 (7)
H2A0.55100.42730.33900.059*
N30.8115 (3)0.14741 (15)0.3782 (4)0.0539 (7)
H3A0.88550.13880.38320.065*
N40.6190 (3)0.12600 (14)0.3669 (4)0.0537 (7)
C10.4079 (3)0.37511 (19)0.3383 (5)0.0583 (9)
H10.35900.41530.33010.070*
C20.3602 (3)0.30690 (19)0.3445 (5)0.0577 (9)
H20.27920.30080.34350.069*
C30.4328 (3)0.24803 (18)0.3521 (4)0.0508 (8)
H30.40110.20160.35270.061*
C40.5552 (2)0.25749 (16)0.3589 (4)0.0423 (7)
C50.5997 (2)0.32858 (16)0.3569 (4)0.0424 (7)
C60.7246 (3)0.34396 (16)0.3670 (4)0.0437 (7)
C70.8053 (3)0.28627 (17)0.3736 (4)0.0463 (7)
C80.9257 (3)0.3041 (2)0.3816 (5)0.0575 (9)
H80.98260.26810.38590.069*
C90.9563 (3)0.3750 (2)0.3827 (5)0.0676 (10)
H91.03500.38800.38830.081*
C100.8704 (3)0.4282 (2)0.3753 (5)0.0656 (10)
H100.89420.47630.37510.079*
C110.7577 (3)0.21528 (16)0.3725 (4)0.0462 (7)
C120.6393 (3)0.20018 (16)0.3648 (4)0.0451 (7)
C130.7259 (3)0.09872 (19)0.3745 (5)0.0584 (9)
H130.74020.04920.37700.070*
Cl10.15290 (7)0.11627 (5)0.40411 (14)0.0643 (4)
O10.2077 (4)0.07296 (19)0.5458 (6)0.1414 (17)
O20.2199 (3)0.1137 (2)0.2286 (6)0.1356 (15)
O30.0402 (2)0.08894 (19)0.3635 (5)0.0990 (10)
O40.1451 (3)0.18729 (16)0.4828 (6)0.1099 (12)
O1W0.4428 (2)0.02582 (13)0.2434 (5)0.0871 (9)
H1WB0.49340.05640.27710.131*
H1WA0.37550.04090.27130.131*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
N10.0558 (17)0.0523 (17)0.0608 (16)−0.0063 (13)−0.0055 (13)0.0023 (12)
N20.0472 (15)0.0436 (15)0.0572 (16)0.0054 (11)−0.0031 (12)0.0011 (11)
N30.0536 (16)0.0575 (17)0.0506 (15)0.0156 (14)0.0007 (12)0.0021 (12)
N40.0655 (18)0.0469 (16)0.0488 (15)0.0036 (13)0.0019 (13)0.0006 (11)
C10.050 (2)0.064 (2)0.061 (2)0.0124 (16)−0.0055 (15)−0.0016 (15)
C20.0421 (17)0.069 (2)0.062 (2)0.0021 (16)−0.0014 (15)−0.0016 (16)
C30.0482 (18)0.057 (2)0.0470 (17)−0.0054 (15)−0.0012 (13)0.0004 (14)
C40.0434 (17)0.0471 (17)0.0364 (15)−0.0003 (13)0.0031 (12)−0.0003 (12)
C50.0421 (16)0.0479 (17)0.0372 (15)0.0035 (13)−0.0024 (12)0.0004 (12)
C60.0469 (17)0.0445 (17)0.0396 (15)−0.0030 (13)−0.0012 (12)0.0032 (11)
C70.0434 (16)0.057 (2)0.0381 (15)0.0013 (14)0.0004 (12)0.0020 (12)
C80.0431 (18)0.071 (2)0.0581 (19)0.0031 (16)−0.0005 (14)0.0023 (16)
C90.044 (2)0.086 (3)0.074 (2)−0.0140 (18)−0.0041 (17)0.0049 (19)
C100.062 (2)0.059 (2)0.076 (2)−0.0161 (18)−0.0063 (18)0.0054 (17)
C110.0507 (18)0.0493 (19)0.0386 (15)0.0098 (14)0.0016 (13)0.0023 (12)
C120.0511 (18)0.0476 (18)0.0366 (15)0.0031 (14)0.0033 (12)0.0001 (12)
C130.078 (2)0.0406 (18)0.0570 (19)0.0052 (18)−0.0009 (17)−0.0016 (14)
Cl10.0453 (5)0.0575 (6)0.0902 (7)0.0079 (4)−0.0048 (4)−0.0043 (4)
O10.157 (4)0.089 (2)0.178 (4)0.033 (2)−0.096 (3)0.005 (2)
O20.100 (3)0.167 (4)0.140 (3)−0.013 (2)0.059 (2)−0.016 (3)
O30.0470 (15)0.117 (2)0.133 (3)−0.0055 (15)−0.0056 (16)−0.028 (2)
O40.107 (3)0.0571 (18)0.166 (3)0.0161 (16)−0.005 (2)−0.0134 (19)
O1W0.0592 (16)0.0560 (16)0.146 (3)−0.0021 (12)0.0052 (16)−0.0208 (15)
Geometric parameters (Å, °) top
N1—C101.324 (4)C5—C61.454 (4)
N1—C61.349 (4)C6—C71.408 (4)
N2—C11.329 (4)C7—C81.413 (4)
N2—C51.345 (4)C7—C111.419 (4)
N2—H2A0.8600C8—C91.355 (5)
N3—C131.327 (4)C8—H80.9300
N3—C111.396 (4)C9—C101.388 (5)
N3—H3A0.8600C9—H90.9300
N4—C131.320 (4)C10—H100.9300
N4—C121.390 (4)C11—C121.379 (4)
C1—C21.373 (5)C13—H130.9300
C1—H10.9300Cl1—O11.390 (3)
C2—C31.367 (5)Cl1—O31.406 (3)
C2—H20.9300Cl1—O21.407 (4)
C3—C41.408 (4)Cl1—O41.417 (3)
C3—H30.9300O1W—H1WB0.8379
C4—C51.408 (4)O1W—H1WA0.8377
C4—C121.429 (4)
C10—N1—C6116.9 (3)C6—C7—C11116.7 (3)
C1—N2—C5123.2 (3)C8—C7—C11126.0 (3)
C1—N2—H2A118.4C9—C8—C7118.4 (3)
C5—N2—H2A118.4C9—C8—H8120.8
C13—N3—C11106.6 (3)C7—C8—H8120.8
C13—N3—H3A126.7C8—C9—C10120.2 (3)
C11—N3—H3A126.7C8—C9—H9119.9
C13—N4—C12102.9 (3)C10—C9—H9119.9
N2—C1—C2120.3 (3)N1—C10—C9123.7 (3)
N2—C1—H1119.8N1—C10—H10118.1
C2—C1—H1119.8C9—C10—H10118.1
C3—C2—C1119.4 (3)C12—C11—N3104.4 (3)
C3—C2—H2120.3C12—C11—C7124.2 (3)
C1—C2—H2120.3N3—C11—C7131.4 (3)
C2—C3—C4120.2 (3)C11—C12—N4111.2 (3)
C2—C3—H3119.9C11—C12—C4120.5 (3)
C4—C3—H3119.9N4—C12—C4128.3 (3)
C3—C4—C5118.2 (3)N4—C13—N3114.9 (3)
C3—C4—C12125.0 (3)N4—C13—H13122.6
C5—C4—C12116.8 (3)N3—C13—H13122.6
N2—C5—C4118.6 (3)O1—Cl1—O3109.5 (2)
N2—C5—C6119.1 (3)O1—Cl1—O2108.1 (3)
C4—C5—C6122.3 (3)O3—Cl1—O2108.9 (2)
N1—C6—C7123.5 (3)O1—Cl1—O4107.8 (2)
N1—C6—C5116.9 (3)O3—Cl1—O4110.2 (2)
C7—C6—C5119.5 (3)O2—Cl1—O4112.2 (2)
C6—C7—C8117.3 (3)H1WB—O1W—H1WA110.3
Hydrogen-bond geometry (Å, °) top
D—H···AD—HH···AD···AD—H···A
N2—H2A···O1Wi0.861.902.713 (4)156
N3—H3A···O3ii0.861.992.825 (4)162
O1W—H1WB···N40.842.022.852 (4)177
O1W—H1WA···O20.842.253.018 (5)154
Symmetry codes: (i) −x+1, y+1/2, −z+1/2; (ii) x+1, y, z.
Table 1
Hydrogen-bond geometry (Å, °) top
D—H···AD—HH···AD···AD—H···A
N2—H2A···O1Wi0.861.902.713 (4)156
N3—H3A···O3ii0.861.992.825 (4)162
O1W—H1WB···N40.842.022.852 (4)177
O1W—H1WA···O20.842.253.018 (5)154
Symmetry codes: (i) −x+1, y+1/2, −z+1/2; (ii) x+1, y, z.
Acknowledgements top

The authors are grateful to the Zhejiang Economic and Trade Polytechnic for financial support.

references
References top

Bruker (2005). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.

Liu, J. Q., Zhang, Y. N., Wang, Y. Y., Jin, J. C., Lermontova, E. K. & Shi, Q. Z. (2009). Dalton Trans. pp. 5365–5378.

Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122.

Xiong, Y., He, X. F., Zhou, X. H., Wu, J. Z., Chen, X. M., Ji, L. N., Li, R. H., Zhou, J. Y. & Yu, K. B. (1999). J. Chem. Soc. Dalton Trans. pp. 19–24.

Yu, J. (2009). Acta Cryst. E65, m618.