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Acta Crystallographica Section E

Structure Reports Online

ISSN 1600-5368

Hydrogen bonding in 1

H

-naphth[2,3-

d

]imidazole

Robert T. Stibrany, Harvey J. Schugar and Joseph A. Potenza*

Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, New Jersey 08854, USA

Correspondence e-mail: potenza@rutchem.rutgers.edu

Key indicators

Single-crystal X-ray study T= 295 K

Mean(C±C) = 0.007 AÊ Rfactor = 0.046 wRfactor = 0.110 Data-to-parameter ratio = 6.1

For details of how these key indicators were automatically derived from the article, see http://journals.iucr.org/e.

#2004 International Union of Crystallography Printed in Great Britain ± all rights reserved

The title compound, C11H8N2, contains two essentially planar

molecules (AandB) in the asymmetric unit. Molecules of type Bexhibit ±stacking and form in®nite zigzag chains along theaaxis.AandBmolecules are linked by NamineÐH Nimine

hydrogen bonds and form polymeric ±A±B±A±B± criss-crossed chains approximately along the [110] and [110] directions. TheAmolecules show little evidence ofstacking and, in addition to the hydrogen bonds, appear to be held in the crystal structure primarily by CÐH interactions. The geometric parameters of molecules AandBagree well with each other and, where comparisons are appropriate, with those of a naphthimidazolium cation.

Comment

The title compound, (I), C11H8N2, whose structure we report

here, was prepared as a synthetic intermediate for part of a project designed to extend our exploration of the chemistry of bisimidazoles and bisbenzimidazoles to bisnaphthimidazoles. Previously, we have utilized species containing bisimidazoles as agents to study electron self-exchange (Knappet al., 1990), whilst species containing bisbenzimidazoles have been shown to behave as catalysts (Patilet al., 2003; Stibranyet al., 2003; Stibrany, 2001), as geometrically constraining ligands (Stibranyet al., 2004) and as proton sponges (Stibranyet al., 2002).

The structure contains two approximately planar molecules of (I) in the asymmetric unit (Fig. 1). A search of the Cambridge Structural Database (Version 5.24; Allen, 2002) reveals only one entry, the salt 2-methylnaphthimidazolium chloride dihydrate, (II) (REFCODE GEYMAY; Zhan et al., 1988), for a species containing the naphthimidazole substructure. Consequently, the present structure appears to

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provide the ®rst example of a neutral naphthimidazole char-acterized structurally by X-ray diffraction techniques.

Metric parameters for the cation (II) and for the two unique molecules in (I), labeled AandB, respectively, for the mol-ecules containing N11 and N21, compare favorably in general (Fig. 2); in particular, in all three molecules, the pattern of long and short CÐC distances is maintained. Variation in CÐC bond lengths of the magnitude reported here is consistent with

variations observed for a variety of polycyclic aromatic hydrocarbons (Li & Jiang, 1995). As expected, the cation exhibits more nearly equal CÐNimineand CÐNaminedistances

than do the neutral molecules, consistent with greater electron delocalization over the N1ÐC2ÐN3fragment in (II), resulting

from protonation at the Niminesite.

In the crystal structure, moleculesBof (I) are arranged with their planes approximately parallel to thec axis, while mol-eculesAappear more nearly face on (Fig. 3); bothAandB molecules related bya-glide plane symmetry operations form columns along the a axis. When viewed along the c axis (Fig. 4a), theBmolecules appear as zigzag chains propagating in theadirection, within which a given molecule exhibits 17 unique interatomic contacts of between 3.445 (7) and 3.782 (7) AÊ with its neighbors (Table 2), all within the range (3.3±3.8 AÊ; Janiak, 2000) generally accepted to indicate ±

interactions. A view of a portion of the zigzag chain, showing the ring overlap explicitly, is given in Fig. 4(b). MoleculesA and B are linked by strong NamineÐH Nimine hydrogen

bonds (Table 1) to form polymeric ±A±B±A±B± criss-crossed chains parallel to the [110] and [110] directions (Fig. 5). In contrast to molecules B, molecules A show little, if any, evidence ofstacking and, in addition to the hydrogen bonds, appear to be held in the crystal structure primarily by CÐ H interactions with adjacent A- and B-type molecules. Different parameters have been used in the literature to describe CÐH interactions involving aromatic rings (Desiraju & Steiner, 1999). For Table 3, we have used one of these, the H C distances in the CÐH Caromaticfragments,

with a cutoff of 3.25 AÊ, to summarize these interactions in the present structure.

Experimental

The title compound was prepared by following a published procedure (Frieset al., 1935). Crystals were obtained by slow evaporation of a concentrated solution of (I) in dry dimethyl sulfoxide (m.p. 519 K, decomposed).

organic papers

Acta Cryst.(2004). E60, o1648±o1651 Robert T. Stibranyet al. C11H8N2

o1649

Figure 2

Bond distances (AÊ) in moleculesAandBof (I), and in (II).

Figure 3

Projection, along thebaxis, of the structure.Bmolecules are seen edge-on.

Figure 1

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Crystal data C11H8N2

Mr= 168.19 Monoclinic,Ia a= 9.4503 (6) AÊ

b= 16.3882 (8) AÊ

c= 11.4770 (9) AÊ

= 110.502 (4)

V= 1664.90 (19) AÊ3

Z= 8

Dx= 1.342 Mg mÿ3 MoKradiation Cell parameters from 730

re¯ections

= 2.3±20.8

= 0.08 mmÿ1

T= 295 (2) K Plate, pale yellow 0.470.220.02 mm

Data collection

Bruker SMART APEX CCD area-detector diffractometer

'and!scans

Absorption correction: multi-scan

(SADABS; Blessing, 1995)

Tmin= 0.778,Tmax= 1.00 5846 measured re¯ections

1480 independent re¯ections 1145 re¯ections withI> 2(I)

Rint= 0.052

max= 25.1

h=ÿ11!10

k=ÿ19!19

l=ÿ13!13

Re®nement Re®nement onF2

R[F2> 2(F2)] = 0.046

wR(F2) = 0.110

S= 1.00 1480 re¯ections 243 parameters

H atoms treated by a mixture of independent and constrained re®nement

w= 1/[2(F

o2) + (0.0653P)2] whereP= (Fo2+ 2Fc2)/3 (/)max< 0.001

max= 0.14 e AÊÿ3 min=ÿ0.13 e AÊÿ3

Table 1

Hydrogen-bonding geometry (AÊ,).

DÐH A DÐH H A D A DÐH A

N11ÐH11 N23i 0.83 (5) 2.12 (5) 2.888 (5) 155 (5) N21ÐH21 N13 0.85 (5) 2.13 (5) 2.919 (5) 154 (5)

Symmetry code: (i)1

2‡x;12‡y;12‡z.

Table 2

Interatomic N C and C C distances (AÊ) for molecules of typeB, which lie within the range generally accepted for±interactions.

N21 C25ii 3.562 (6) C22 C26aii 3.596 (7)

N21 C26ii 3.515 (6) C22 C27ii 3.673 (7)

N21 C27ii 3.734 (7) C23 C25aii 3.714 (7)

N23 C26ii 3.752 (6) C23 C25bii 3.618 (7)

N23 C26aii 3.445 (7) C23 C26bii 3.659 (7) N23 C26bii 3.637 (6) C24 C25bii 3.523 (8)

C21 C25ii 3.486 (6) C27 C25ii 3.782 (7)

C21 C25aii 3.588 (6) C27 C25aii 3.655 (7) C22 C26ii 3.465 (7)

Symmetry code: (ii)x‡1 2;ÿy;z.

Table 3

Interatomic C H distances less than 3.25 AÊ between anAmolecule and its nearest neighbors.

C11 H24 3.10i C15a H25a 2.95vii

C11 H25b 2.94ii C15b H25a 2.75vii

C11 H16a 3.24iii C16 H27 3.20viii

C12 H15b 3.12iv C16a H25a 3.06vii

C12 H17 3.04iii C16a H26a 3.15ix

C12 H26b 3.22v C16a H27 2.95ix

C13 H15a 3.04vi C16b H25a 2.81vii

C13 H16a 2.90iii C16b H26a 3.15ix

C13 H25b 3.20ii C17 H24 3.15i

C14 H15a 3.22vi C17 H25b 3.20ii

C15 H25a 3.23vii C17 H26b 3.16ii

C15a H22 3.10viii

Symmetry codes: (i)x‡1

2;y‡12;z‡12; (ii) x‡1;y;z‡1; (iii)x;ÿy‡12;ÿ12‡z; (iv) x‡1;y;z; (v) x‡1;ÿy‡1

2;z‡12; (vi) x‡12;ÿy;z; (vii) x‡12;ÿy;z‡1; (viii) xÿ1

2;ÿy;z; (ix)x;ÿy‡12;z‡12.

The structure was originally re®ned in space groupCc, with= 116.801 (4), but was converted toIato reduce correlation amongx

-andz-related parameters. The NamineH atoms, which are involved in hydrogen bonding, were re®ned isotropically; the remaining H atoms

Figure 5

View, along thecaxis, of the imidazole fragments of (I).

Figure 4

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were positioned geometrically and treated as riding, with Csp2ÐH distances set to 0.93 AÊ and Uiso(H) = 1.2Ueq(C). In the absence of anomalous dispersion effects, Friedel pairs were merged.

Data collection: SMART-WNT/2000 (Bruker, 2000); cell re®ne-ment: SAINT-Plus (Bruker, 2000); data reduction: SAINT-Plus; program(s) used to solve structure: SHELXS97 (Sheldrick, 1990); program(s) used to re®ne structure:SHELXL97 (Sheldrick, 1997); molecular graphics: ORTEPIII (Burnett & Johnson, 1996) and ORTEP-32 (Farrugia, 1997); software used to prepare material for publication:SHELXTL(Bruker, 2000).

References

Allen, F. H. (2002).Acta Cryst.B58, 380±388. Blessing, R. H. (1995).Acta Cryst.A51, 33±38.

Bruker (2000).SHELXTL(Version 6.10),SAINT-Plus(Version 6.02) and

SMART-WNT/2000 (Version 5.622). Bruker AXS Inc., Madison, Wisconsin,

USA.

Burnett, M. N. & Johnson, C. K. (1996).ORTEPIII Report ORNL-6895. Oak Ridge National Laboratory, Tennessee, USA.

Desiraju, G. R. & Steiner, T. (1999). The Weak Hydrogen Bond, IUCr Monographs on Crystallography, No. 9, p. 131. Oxford University Press. Farrugia, L. J. (1997).J. Appl. Cryst.30, 565.

Fries, K., Walter, R. & Schilling, K. (1935). Anal. Chem. 516, 248± 285.

Janiak, C. (2000).J. Chem. Soc. Dalton Trans.pp. 3885±3896.

Knapp, S., Keenan, T. P., Zhang, X., Fikar, R., Potenza, J. A. & Schugar, H. J. (1990).J. Am. Chem. Soc.112, 3452±3464.

Li, S. & Jiang, Y. (1995).J. Am. Chem. Soc.117, 8401±8406.

Patil, A. O., Zushma, S., Stibrany, R. T., Rucker, S. P. & Wheeler, L. M. (2003).

J. Polym. Sci. Part A Polym. Chem.41, 2095±2106.

Sheldrick, G. M. (1990).Acta Cryst.A46, 467±473.

Sheldrick, G. M. (1997).SHELXL97. University of GoÈttingen, Germany. Stibrany, R. T. (2001). US Patent 6 180 788.

Stibrany, R. T., Lobanov, M. V., Schugar, H. J. & Potenza, J. A. (2004).Inorg.

Chem.43, 1472±1480.

Stibrany, R. T., Schugar, H. J. & Potenza, J. A. (2002).Acta Cryst.E58, o1142± o1144.

Stibrany, R. T., Schulz, D. N., Kacker, S., Patil, A. O., Baugh, L. S., Rucker, S. P., Zushma, S., Berluche, E. & Sissano, J. A. (2003).Macromolecules,36, 8584± 8586.

Zhan, Y., Luo, Y., Barton, R. J. & Robertson, B. E. (1988).Acta Cryst.C44, 1049±1051.

organic papers

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sup-1

Acta Cryst. (2004). E60, o1648–o1651

supporting information

Acta Cryst. (2004). E60, o1648–o1651 [https://doi.org/10.1107/S1600536804019555]

Hydrogen bonding in 1

H

-naphth[2,3-

d

]imidazole

Robert T. Stibrany, Harvey J. Schugar and Joseph A. Potenza

1H–napth[2,3-d]imidazole

Crystal data C11H8N2

Mr = 168.19

Monoclinic, Ia Hall symbol: I -2ya a = 9.4503 (6) Å b = 16.3882 (8) Å c = 11.4770 (9) Å β = 110.502 (4)° V = 1664.90 (19) Å3

Z = 8

F(000) = 704 Dx = 1.342 Mg m−3

Mo radiation, λ = 0.71073 Å Cell parameters from 730 reflections θ = 2.3–20.8°

µ = 0.08 mm−1

T = 295 K Plate, pale yellow 0.47 × 0.22 × 0.02 mm

Data collection

Bruker SMART APEX CCD area-detector diffractometer

Radiation source: fine-focus sealed tube Graphite monochromator

φ and ω scans

Absorption correction: multi-scan (SADABS; Blessing 1995) Tmin = 0.778, Tmax = 1.00

5846 measured reflections 1480 independent reflections 1145 reflections with I > 2σ(I) Rint = 0.052

θmax = 25.1°, θmin = 3.8°

h = −11→10 k = −19→19 l = −13→13

Refinement Refinement on F2

Least-squares matrix: full R[F2 > 2σ(F2)] = 0.046

wR(F2) = 0.110

S = 1.00 1480 reflections 243 parameters 2 restraints

Primary atom site location: structure-invariant direct methods

Secondary atom site location: difference Fourier map

Hydrogen site location: inferred from neighbouring sites

H atoms treated by a mixture of independent and constrained refinement

w = 1/[σ2(F

o2) + (0.0653P)2]

where P = (Fo2 + 2Fc2)/3

(Δ/σ)max < 0.001

Δρmax = 0.14 e Å−3

Δρmin = −0.13 e Å−3

Special details

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supporting information

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Acta Cryst. (2004). E60, o1648–o1651

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 (Å2)

x y z Uiso*/Ueq

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Acta Cryst. (2004). E60, o1648–o1651

H27 0.3250 0.1195 0.4103 0.057* H21 0.543 (6) 0.010 (3) 0.552 (4) 0.071 (16)*

Atomic displacement parameters (Å2)

U11 U22 U33 U12 U13 U23

N11 0.044 (2) 0.039 (2) 0.0478 (19) −0.0121 (17) 0.0060 (16) −0.0105 (17) N13 0.053 (2) 0.041 (2) 0.0464 (17) −0.0035 (18) 0.0119 (16) −0.0088 (16) C11 0.043 (2) 0.027 (2) 0.038 (2) 0.0010 (18) 0.0050 (18) 0.0029 (16) C12 0.048 (2) 0.050 (3) 0.046 (2) −0.005 (2) 0.0170 (18) −0.003 (2) C13 0.043 (2) 0.033 (2) 0.0338 (18) 0.0022 (18) 0.0022 (17) 0.0014 (15) C14 0.048 (3) 0.038 (2) 0.039 (2) −0.009 (2) 0.0030 (17) −0.0051 (18) C15 0.043 (2) 0.045 (2) 0.0372 (18) 0.006 (2) 0.0042 (16) 0.0081 (18) C15A 0.045 (3) 0.059 (3) 0.051 (2) −0.002 (2) 0.009 (2) 0.006 (2) C15B 0.050 (3) 0.063 (3) 0.067 (3) 0.005 (3) 0.018 (2) 0.016 (3) C16 0.052 (2) 0.037 (2) 0.0363 (18) 0.004 (2) 0.0087 (17) 0.0019 (17) C16A 0.073 (3) 0.037 (2) 0.050 (2) 0.011 (2) 0.022 (2) 0.0023 (19) C16B 0.075 (4) 0.057 (3) 0.069 (3) 0.020 (3) 0.040 (3) 0.019 (2) C17 0.053 (3) 0.032 (2) 0.042 (2) −0.001 (2) 0.0042 (18) −0.0027 (18) N21 0.045 (2) 0.045 (2) 0.0471 (19) −0.0099 (18) 0.0080 (16) −0.0148 (17) N23 0.054 (2) 0.042 (2) 0.0468 (18) −0.0066 (17) 0.0103 (16) −0.0059 (16) C21 0.044 (3) 0.043 (2) 0.040 (2) −0.007 (2) 0.011 (2) −0.0076 (19) C22 0.049 (2) 0.047 (3) 0.041 (2) 0.004 (2) 0.0107 (18) −0.0022 (19) C23 0.045 (2) 0.037 (2) 0.0387 (19) −0.0041 (19) 0.0132 (17) −0.0057 (18) C24 0.051 (3) 0.036 (2) 0.050 (2) −0.0134 (19) 0.015 (2) −0.0082 (18) C25 0.047 (2) 0.047 (3) 0.042 (2) −0.009 (2) 0.0190 (19) −0.0058 (19) C25A 0.053 (3) 0.054 (3) 0.050 (2) −0.008 (2) 0.013 (2) −0.004 (2) C25B 0.057 (3) 0.067 (3) 0.049 (2) 0.011 (3) 0.008 (2) 0.004 (2) C26 0.052 (3) 0.047 (3) 0.041 (2) −0.001 (2) 0.022 (2) −0.0044 (19) C26A 0.070 (3) 0.042 (3) 0.060 (2) 0.000 (2) 0.032 (2) −0.005 (2) C26B 0.071 (3) 0.049 (3) 0.055 (2) 0.010 (3) 0.017 (2) 0.004 (2) C27 0.053 (3) 0.040 (3) 0.048 (2) −0.010 (2) 0.017 (2) −0.009 (2)

Geometric parameters (Å, º)

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supporting information

sup-4

Acta Cryst. (2004). E60, o1648–o1651

C15A—C15B 1.341 (7) C25A—C25B 1.346 (6) C15A—H15A 0.9300 C25A—H25A 0.9300 C15B—C16B 1.409 (7) C25B—C26B 1.395 (7) C15B—H15B 0.9300 C25B—H25B 0.9300 C16—C17 1.402 (6) C26—C27 1.404 (6) C16—C16A 1.431 (6) C26—C26A 1.416 (7) C16A—C16B 1.356 (7) C26A—C26B 1.362 (6) C16A—H16A 0.9300 C26A—H26A 0.9300 C16B—H16B 0.9300 C26B—H26B 0.9300 C17—H17 0.9300 C27—H27 0.9300

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Acta Cryst. (2004). E60, o1648–o1651

C12—N11—C11—C17 179.1 (4) C22—N21—C21—C27 −178.4 (4) C12—N11—C11—C13 0.9 (4) C22—N21—C21—C23 0.6 (4) C13—N13—C12—N11 0.2 (4) C23—N23—C22—N21 0.1 (5) C11—N11—C12—N13 −0.7 (5) C21—N21—C22—N23 −0.4 (5) C12—N13—C13—C14 179.9 (4) C22—N23—C23—C24 177.7 (4) C12—N13—C13—C11 0.4 (4) C22—N23—C23—C21 0.3 (4) C17—C11—C13—C14 1.2 (5) C27—C21—C23—C24 0.8 (6) N11—C11—C13—C14 179.6 (3) N21—C21—C23—C24 −178.3 (4) C17—C11—C13—N13 −179.2 (3) C27—C21—C23—N23 178.5 (4) N11—C11—C13—N13 −0.8 (4) N21—C21—C23—N23 −0.6 (4) N13—C13—C14—C15 179.9 (4) N23—C23—C24—C25 −177.6 (4) C11—C13—C14—C15 −0.6 (5) C21—C23—C24—C25 −0.5 (6) C13—C14—C15—C15A 179.5 (4) C23—C24—C25—C25A 180.0 (4) C13—C14—C15—C16 −0.5 (5) C23—C24—C25—C26 −0.6 (5) C14—C15—C15A—C15B 180.0 (4) C24—C25—C25A—C25B −179.8 (4) C16—C15—C15A—C15B 0.0 (6) C26—C25—C25A—C25B 0.7 (6) C15—C15A—C15B—C16B 0.1 (7) C25—C25A—C25B—C26B −1.4 (7) C14—C15—C16—C17 1.1 (5) C24—C25—C26—C27 1.3 (5) C15A—C15—C16—C17 −178.9 (4) C25A—C25—C26—C27 −179.3 (4) C14—C15—C16—C16A −179.1 (3) C24—C25—C26—C26A −179.2 (4) C15A—C15—C16—C16A 0.9 (5) C25A—C25—C26—C26A 0.3 (5) C17—C16—C16A—C16B 177.9 (4) C27—C26—C26A—C26B 179.0 (4) C15—C16—C16A—C16B −1.8 (5) C25—C26—C26A—C26B −0.6 (6) C16—C16A—C16B—C15B 1.9 (6) C26—C26A—C26B—C25B −0.1 (7) C15A—C15B—C16B—C16A −1.0 (7) C25A—C25B—C26B—C26A 1.1 (7) N11—C11—C17—C16 −178.5 (4) N21—C21—C27—C26 178.7 (4) C13—C11—C17—C16 −0.6 (5) C23—C21—C27—C26 −0.1 (6) C15—C16—C17—C11 −0.5 (5) C26A—C26—C27—C21 179.6 (4) C16A—C16—C17—C11 179.7 (4) C25—C26—C27—C21 −0.9 (5)

Hydrogen-bond geometry (Å, º)

D—H···A D—H H···A D···A D—H···A N11—H11···N23i 0.83 (5) 2.12 (5) 2.888 (5) 155 (5)

N21—H21···N13 0.85 (5) 2.13 (5) 2.919 (5) 154 (5)

References

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