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Acta Crystallogr Sect E Struct Rep Online. 2008 September 1; 64(Pt 9): o1750.
Published online 2008 August 13. doi:  10.1107/S1600536808025154
PMCID: PMC2960689

N-(Imidazol-1-ylmeth­yl)phthalimide

Abstract

The title compound [systematic name: 2-(imidazol-1-ylmeth­yl)isoindole-1,3-dione], C12H9N3O2, was prepared by reaction of N-(bromo­meth­yl)phthalimide and imidazole in chloro­form solution. The crystal structure is stabilized by weak inter­molecular C—H(...)π inter­actions and inter­molecular π–π inter­actions with centroid–centroid distances in the range 3.6469 (8)–3.8831 (9) Å.

Related literature

For related literature, see: Brooks & Davidson (1960 [triangle]); Zhao et al. (2000 [triangle]); Barszcz et al. (2004 [triangle]); Jian et al. (2004 [triangle]).

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Object name is e-64-o1750-scheme1.jpg

Experimental

Crystal data

  • C12H9N3O2
  • M r = 227.22
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-64-o1750-efi1.jpg
  • a = 7.9905 (6) Å
  • b = 19.8096 (15) Å
  • c = 6.9229 (5) Å
  • β = 105.5540 (10)°
  • V = 1055.69 (14) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 0.10 mm−1
  • T = 273 (2) K
  • 0.2 × 0.15 × 0.15 mm

Data collection

  • Bruker SMART CCD area-detector diffractometer
  • Absorption correction: none
  • 6792 measured reflections
  • 2556 independent reflections
  • 1868 reflections with I > 2σ(I)
  • R int = 0.027

Refinement

  • R[F 2 > 2σ(F 2)] = 0.039
  • wR(F 2) = 0.101
  • S = 1.03
  • 2556 reflections
  • 155 parameters
  • H-atom parameters constrained
  • Δρmax = 0.24 e Å−3
  • Δρmin = −0.15 e Å−3

Data collection: SMART (Bruker, 1997 [triangle]); cell refinement: SAINT (Bruker, 1997 [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: SHELXTL.

Table 1
Selected interatomic distances (Å)
Table 2
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536808025154/at2605sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536808025154/at2605Isup2.hkl

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

supplementary crystallographic information

Comment

The imidazole and its derivatives are of considerable interest as the ligands in many biological systems in which they provide the potential binding site for metal ions (Brooks et al., 1960). In our search for new ligands of this type, we have synthesized the title compound (I), and describe its structure here.

In the crystal structure of (I) (Fig. 1), the C═O bond lengths are 1.2030 (15) and 1.2026 (15) Å. The C—N bond lengths are in agreement with those observed before (Zhao et al., 2000). The dihedral angles formed by the N1/N2/C1-C3 and N3/C5/C6/C11/C12 rings, with the C6-C12 ring, are 70.95 (7) ang 0.44 (7)°, respectively.

The crystal structure is stabilized by weak intermolecular C—H···π interactions and intermolecular π–π interactions with centroid-to-centroid distances of 3.6469 (8)–3.8831 (9) Å (Table 1). The crystal packing of the title compound is shown in Fig. 2, viewed down the a axis.

Experimental

N-bromomethyl phthalic imidine 7.2 g (0.03 mol) and imidazole 2.04 g (0.03 mol) were dissolved in 20 ml chloroform. The solution was cooled to 283 K. Then, 3 g (0.03 mol) triethylamine was added dropwise via cannula into the well stirred solution.The reaction mixture was stirred at 283 K for 6 h. Then the solution was continued to stir at room temperature about 17 h. 20 ml water was added into the solution, the organic phase was seperated and dryed with anhydrous potassium carbonate. The colourless organic phase was evaporated. The title compound is afforded in 65% yield. The colourless crystals of suitable for X-ray determination were obtained from anhydrous ethanol at room temperature after two days.

Refinement

H atoms were fixed geometrically and allowed to ride on their parent atoms, with C—H distance of 0.93 Å, respectively, and with Uiso=1.2Ueq of the parent atoms.

Figures

Fig. 1.
The molecular structure and atom-labeling scheme for (I), with displacement ellipsoids drawn at the 50% probability level.
Fig. 2.
The crystal packing of (I), viewed down the a axis.

Crystal data

C12H9N3O2F000 = 472
Mr = 227.22Dx = 1.430 Mg m3
Monoclinic, P21/cMo Kα radiation λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 2256 reflections
a = 7.9905 (6) Åθ = 2.1–28.3º
b = 19.8096 (15) ŵ = 0.10 mm1
c = 6.9229 (5) ÅT = 273 (2) K
β = 105.5540 (10)ºBar, colourless
V = 1055.69 (14) Å30.2 × 0.15 × 0.15 mm
Z = 4

Data collection

Bruker SMART CCD area-detector diffractometer1868 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tubeRint = 0.027
Monochromator: graphiteθmax = 28.3º
T = 293(2) Kθmin = 2.1º
[var phi] and ω scansh = −7→10
Absorption correction: nonek = −25→26
6792 measured reflectionsl = −8→9
2556 independent reflections

Refinement

Refinement on F2Hydrogen site location: inferred from neighbouring sites
Least-squares matrix: fullH-atom parameters constrained
R[F2 > 2σ(F2)] = 0.039  w = 1/[σ2(Fo2) + (0.0428P)2 + 0.1392P] where P = (Fo2 + 2Fc2)/3
wR(F2) = 0.101(Δ/σ)max < 0.001
S = 1.03Δρmax = 0.24 e Å3
2556 reflectionsΔρmin = −0.15 e Å3
155 parametersExtinction correction: SHELXL97 (Sheldrick, 2008), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
Primary atom site location: structure-invariant direct methodsExtinction coefficient: 0.008 (2)
Secondary atom site location: difference Fourier map

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 (Å2)

xyzUiso*/Ueq
O10.38144 (13)0.59386 (5)0.45690 (16)0.0582 (3)
O20.88708 (13)0.71264 (5)0.64832 (19)0.0713 (3)
N10.79858 (19)0.51519 (6)0.1175 (2)0.0656 (4)
N20.80767 (14)0.55831 (5)0.41391 (16)0.0424 (3)
N30.65627 (13)0.63862 (5)0.56497 (15)0.0407 (3)
C10.7178 (2)0.52112 (7)0.2578 (2)0.0535 (4)
H1B0.61030.50180.25050.064*
C20.9506 (2)0.55038 (7)0.1900 (3)0.0604 (4)
H2A1.03670.55500.12340.073*
C30.95804 (18)0.57721 (7)0.3700 (2)0.0518 (4)
H3A1.04720.60330.44880.062*
C40.75385 (19)0.57605 (6)0.5912 (2)0.0471 (3)
H4A0.85580.58060.70420.057*
H4B0.68270.54000.62160.057*
C50.47554 (17)0.64220 (6)0.49665 (18)0.0402 (3)
C60.43317 (15)0.71539 (6)0.48572 (17)0.0382 (3)
C70.27516 (18)0.74781 (7)0.4294 (2)0.0510 (3)
H7A0.17170.72370.39000.061*
C80.2764 (2)0.81774 (8)0.4338 (2)0.0582 (4)
H8A0.17150.84100.39800.070*
C90.4295 (2)0.85355 (7)0.4899 (2)0.0540 (4)
H9A0.42590.90050.49110.065*
C100.58863 (18)0.82107 (7)0.54462 (18)0.0476 (3)
H10A0.69220.84520.58170.057*
C110.58717 (16)0.75136 (6)0.54189 (17)0.0387 (3)
C120.73314 (17)0.70263 (6)0.59332 (19)0.0441 (3)

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
O10.0538 (6)0.0424 (6)0.0806 (8)−0.0112 (4)0.0217 (5)−0.0014 (5)
O20.0410 (6)0.0627 (7)0.1006 (9)−0.0031 (5)0.0027 (6)−0.0102 (6)
N10.0894 (10)0.0504 (7)0.0696 (9)−0.0025 (7)0.0429 (8)−0.0105 (6)
N20.0453 (6)0.0332 (5)0.0525 (6)0.0058 (4)0.0200 (5)0.0031 (5)
N30.0417 (6)0.0354 (6)0.0464 (6)0.0046 (4)0.0141 (5)−0.0016 (4)
C10.0633 (9)0.0393 (7)0.0639 (9)−0.0074 (6)0.0273 (7)−0.0080 (6)
C20.0676 (10)0.0490 (8)0.0787 (11)0.0133 (7)0.0439 (9)0.0093 (8)
C30.0412 (8)0.0447 (7)0.0723 (10)0.0066 (6)0.0200 (7)0.0079 (7)
C40.0543 (8)0.0416 (7)0.0480 (7)0.0114 (6)0.0184 (6)0.0063 (6)
C50.0440 (7)0.0390 (7)0.0411 (7)−0.0014 (5)0.0173 (5)0.0002 (5)
C60.0425 (7)0.0377 (6)0.0353 (6)0.0014 (5)0.0122 (5)−0.0005 (5)
C70.0437 (8)0.0503 (8)0.0565 (8)0.0053 (6)0.0090 (6)−0.0003 (6)
C80.0590 (9)0.0540 (9)0.0558 (9)0.0200 (7)0.0054 (7)0.0026 (7)
C90.0767 (11)0.0362 (7)0.0453 (7)0.0095 (7)0.0095 (7)0.0013 (6)
C100.0610 (9)0.0378 (7)0.0421 (7)−0.0048 (6)0.0109 (6)−0.0034 (5)
C110.0448 (7)0.0378 (7)0.0339 (6)0.0002 (5)0.0111 (5)−0.0029 (5)
C120.0428 (7)0.0439 (7)0.0444 (7)−0.0018 (6)0.0095 (6)−0.0055 (5)

Geometric parameters (Å, °)

O1—C51.2030 (15)C4—H4A0.9700
O2—C121.2026 (15)C4—H4B0.9700
N1—C11.3075 (18)C5—C61.4861 (17)
N1—C21.373 (2)C6—C71.3764 (18)
N2—C11.3455 (17)C6—C111.3843 (17)
N2—C31.3683 (16)C7—C81.386 (2)
N2—C41.4487 (16)C7—H7A0.9300
N3—C51.3957 (17)C8—C91.377 (2)
N3—C121.3996 (16)C8—H8A0.9300
N3—C41.4496 (15)C9—C101.3845 (19)
C1—H1B0.9300C9—H9A0.9300
C2—C31.341 (2)C10—C111.3810 (18)
C2—H2A0.9300C10—H10A0.9300
C3—H3A0.9300C11—C121.4820 (18)
Cg1···Cg1i3.8831 (9)Cg3···Cg2iii3.6985 (8)
Cg2···Cg3ii3.6985 (8)Cg3···Cg3ii3.7214 (8)
Cg2···Cg3iii3.6469 (8)Cg3···Cg3iii3.7214 (8)
Cg3···Cg2ii3.6469 (8)
C1—N1—C2104.28 (13)O1—C5—C6130.18 (13)
C1—N2—C3106.40 (12)N3—C5—C6105.53 (10)
C1—N2—C4126.73 (12)C7—C6—C11121.21 (12)
C3—N2—C4126.86 (12)C7—C6—C5130.44 (12)
C5—N3—C12112.14 (10)C11—C6—C5108.34 (11)
C5—N3—C4123.97 (11)C6—C7—C8117.36 (13)
C12—N3—C4123.78 (11)C6—C7—H7A121.3
N1—C1—N2112.51 (13)C8—C7—H7A121.3
N1—C1—H1B123.7C9—C8—C7121.47 (13)
N2—C1—H1B123.7C9—C8—H8A119.3
C3—C2—N1110.84 (13)C7—C8—H8A119.3
C3—C2—H2A124.6C8—C9—C10121.27 (13)
N1—C2—H2A124.6C8—C9—H9A119.4
C2—C3—N2105.96 (13)C10—C9—H9A119.4
C2—C3—H3A127.0C11—C10—C9117.21 (13)
N2—C3—H3A127.0C11—C10—H10A121.4
N2—C4—N3111.91 (10)C9—C10—H10A121.4
N2—C4—H4A109.2C10—C11—C6121.47 (12)
N3—C4—H4A109.2C10—C11—C12130.15 (12)
N2—C4—H4B109.2C6—C11—C12108.38 (11)
N3—C4—H4B109.2O2—C12—N3124.54 (12)
H4A—C4—H4B107.9O2—C12—C11129.87 (13)
O1—C5—N3124.30 (12)N3—C12—C11105.59 (11)

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

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
C10—H10A···Cg1iv0.932.943.6105 (15)130

Symmetry codes: (iv) −x+1, y−1/2, −z+1/2.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: AT2605).

References

  • Barszcz, B., Glowiak, T., Jezierska, J. & Tomkiewicz, A. (2004). Polyhedron, 23, 1309–1316.
  • Brooks, P. & Davidson, N. (1960). J. Am. Chem. Soc.82, 2118–2123.
  • Bruker (1997). SMART and SAINT Bruker AXS Inc., Madison, Wisconsin, USA.
  • Jian, F.-F., Xiao, H.-L., Qin, Y.-Q. & Xu, L.-Z. (2004). Acta Cryst. C60, o492–o493. [PubMed]
  • Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. [PubMed]
  • Zhao, P. S., Jian, F. F., Lu, L. D., Yang, X. J. & Wang, X. (2000). Chinese J. Inorg. Chem.16, 964–968.

Articles from Acta Crystallographica Section E: Structure Reports Online are provided here courtesy of International Union of Crystallography