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Acta Crystallogr Sect E Struct Rep Online. 2009 October 1; 65(Pt 10): o2332.
Published online 2009 September 5. doi:  10.1107/S1600536809034576
PMCID: PMC2970354

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

Abstract

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 π–π 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.

Related literature

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

An external file that holds a picture, illustration, etc.
Object name is e-65-o2332-scheme1.jpg

Experimental

Crystal data

  • C13H9N4 +·ClO4 ·H2O
  • M r = 338.71
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-65-o2332-efi1.jpg
  • a = 11.401 (2) Å
  • b = 18.475 (3) Å
  • c = 6.7163 (13) Å
  • β = 90.179 (3)°
  • V = 1414.7 (4) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 0.30 mm−1
  • T = 298 K
  • 0.30 × 0.26 × 0.17 mm

Data collection

  • Bruker APEXII area-detector diffractometer
  • Absorption correction: multi-scan (SADABS; Bruker, 2005 [triangle]) T min = 0.914, T max = 0.950
  • 7051 measured reflections
  • 2534 independent reflections
  • 1734 reflections with I > 2σ(I)
  • R int = 0.031

Refinement

  • R[F 2 > 2σ(F 2)] = 0.057
  • wR(F 2) = 0.197
  • S = 1.01
  • 2534 reflections
  • 208 parameters
  • 3 restraints
  • H-atom parameters constrained
  • Δρmax = 0.41 e Å−3
  • Δρmin = −0.39 e Å−3

Data collection: APEX2 (Bruker, 2005 [triangle]); cell refinement: SAINT (Bruker, 2005 [triangle]); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 [triangle]); molecular graphics: SHELXTL (Sheldrick, 2008 [triangle]); software used to prepare material for publication: SHELXL97.

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536809034576/lh2890sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536809034576/lh2890Isup2.hkl

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

Acknowledgments

The author is grateful to the Zhejiang Economic and Trade Polytechnic for financial support.

supplementary crystallographic information

Comment

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.

Experimental

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

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).

Figures

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.
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).

Crystal data

C13H9N4+·ClO4·H2OF(000) = 696
Mr = 338.71Dx = 1.590 Mg m3
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 mm1
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

Bruker APEXII area-detector diffractometer2534 independent reflections
Radiation source: fine-focus sealed tube1734 reflections with I > 2σ(I)
graphiteRint = 0.031
[var phi] 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

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 = 1.01w = 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 Å3
3 restraintsΔρmin = −0.39 e Å3

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. 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)

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)

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, °)

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, °)

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.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: LH2890).

References

  • 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. [PubMed]
  • Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. [PubMed]
  • 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. [PMC free article] [PubMed]

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