Crystal structure and DFT study of 2-(pyren-1-yl)-1H-benzimidazole

Faizi, M.S.H.; Dege, N.; Malinkin, S.

doi:10.1107/S2056989017010271

Crystal structure and DFT study of 2-(pyren-1-yl)-1H-benzimidazole

The title compound was prepared from an equimolar mixuture of o-phenylenediamine and pyrene-1-carboxaldehyde. We report herein on its crystal structure and a density functional theory (DFT) study.

Keywords: crystal structure; pyrene-1-carbaldehyde; o-phenylenediamine; benzimidazole; N—H

N hydrogen bonding; C—H

π interactions; DFT.

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Supporting information

	Crystallographic Information File (CIF) https://doi.org/10.1107/S2056989017010271/su5378sup1.cif Contains datablocks I, Global
	Structure factor file (CIF format) https://doi.org/10.1107/S2056989017010271/su5378Isup2.hkl Contains datablock I
	Chemical Markup Language (CML) file https://doi.org/10.1107/S2056989017010271/su5378Isup3.cml Supplementary material

CCDC reference: 1547858

checkCIF report

Key indicators

Single-crystal X-ray study
T = 273 K
Mean (C-C) = 0.003 Å
R factor = 0.049
wR factor = 0.113
Data-to-parameter ratio = 13.0

checkCIF/PLATON results

No syntax errors found



Alert level C
PLAT906_ALERT_3_C Large K value in the Analysis of Variance ......      3.639 Check

Alert level G
PLAT013_ALERT_1_G N.O.K. _shelx_hkl_checksum found in CIF ........     Please Check
PLAT063_ALERT_4_G Crystal Size Likely too Large for Beam Size ....       0.65 mm
PLAT199_ALERT_1_G Reported _cell_measurement_temperature ..... (K)        273 Check
PLAT200_ALERT_1_G Reported   _diffrn_ambient_temperature ..... (K)        273 Check
PLAT910_ALERT_3_G Missing # of FCF Reflection(s) Below Theta(Min)           2 Note
PLAT978_ALERT_2_G Number C-C Bonds with Positive Residual Density.          2 Note

   0 ALERT level A = Most likely a serious problem - resolve or explain
   0 ALERT level B = A potentially serious problem, consider carefully
   1 ALERT level C = Check. Ensure it is not caused by an omission or oversight
   6 ALERT level G = General information/check it is not something unexpected

   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
   2 ALERT type 3 Indicator that the structure quality may be low
   1 ALERT type 4 Improvement, methodology, query or suggestion
   0 ALERT type 5 Informative message, check

Computing details top

Data collection: APEX2 (Bruker, 2005); data reduction: SAINT (Bruker, 2005); program(s) used to solve structure: SHELXT2014 (Sheldrick, 2015a); program(s) used to refine structure: SHELXL2016 (Sheldrick, 2015b); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXL2016 (Sheldrick, 2015b) and PLATON (Spek, 2009).

2-(Pyren-1-yl)-1H-benzimidazole top

Crystal data top

C₂₃H₁₄N₂	D_x = 1.386 Mg m⁻³
M_r = 318.36	Mo Kα radiation, λ = 0.71073 Å
Orthorhombic, Pbca	Cell parameters from 1528 reflections
a = 8.7344 (8) Å	θ = 2.4–16.1°
b = 9.5967 (9) Å	µ = 0.08 mm⁻¹
c = 36.410 (3) Å	T = 273 K
V = 3052.0 (5) Å³	Prism, colorless
Z = 8	0.65 × 0.43 × 0.32 mm
F(000) = 1328

Data collection top

Bruker APEXII CCD area detector diffractometer	1951 reflections with I > 2σ(I)
Radiation source: sealed tube	R_int = 0.103
Graphite monochromator	θ_max = 26.0°, θ_min = 2.6°
phi and ω scans	h = −10→10
36046 measured reflections	k = −11→11
2986 independent reflections	l = −44→44

Refinement top

Refinement on F²	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F² > 2σ(F²)] = 0.049	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.113	H atoms treated by a mixture of independent and constrained refinement
S = 1.03	w = 1/[σ²(F_o²) + (0.0467P)² + 1.2809P] where P = (F_o² + 2F_c²)/3
2986 reflections	(Δ/σ)_max < 0.001
230 parameters	Δρ_max = 0.19 e Å⁻³
0 restraints	Δρ_min = −0.26 e Å⁻³

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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å²) top

	x	y	z	U_iso*/U_eq
N1	0.15929 (18)	0.66443 (16)	0.32741 (4)	0.0190 (4)
N2	0.21591 (19)	0.89171 (17)	0.32393 (5)	0.0195 (4)
C23	0.0470 (2)	0.73209 (19)	0.30713 (5)	0.0176 (5)
C17	0.2581 (2)	0.7637 (2)	0.33673 (5)	0.0190 (5)
C16	0.4042 (2)	0.74213 (19)	0.35556 (5)	0.0195 (5)
C18	0.0808 (2)	0.8748 (2)	0.30499 (5)	0.0179 (4)
C1	0.4229 (2)	0.6448 (2)	0.38432 (5)	0.0193 (5)
C12	0.5724 (2)	0.6212 (2)	0.39850 (5)	0.0199 (5)
C11	0.6999 (2)	0.6952 (2)	0.38411 (5)	0.0210 (5)
C19	−0.0099 (2)	0.9680 (2)	0.28557 (5)	0.0214 (5)
H19	0.012157	1.062811	0.284937	0.026*
C20	−0.1341 (2)	0.9132 (2)	0.26728 (5)	0.0235 (5)
H20	−0.195476	0.971887	0.253275	0.028*
C13	0.5956 (2)	0.5241 (2)	0.42759 (5)	0.0220 (5)
C2	0.2978 (2)	0.5706 (2)	0.40072 (6)	0.0235 (5)
H2	0.198943	0.585875	0.392152	0.028*
C8	0.7452 (2)	0.4990 (2)	0.44151 (5)	0.0252 (5)
C14	0.6749 (2)	0.7950 (2)	0.35696 (6)	0.0239 (5)
H14	0.756769	0.847263	0.348192	0.029*
C4	0.4691 (2)	0.4519 (2)	0.44303 (6)	0.0253 (5)
C15	0.5309 (2)	0.8170 (2)	0.34299 (6)	0.0231 (5)
H15	0.517365	0.883532	0.324701	0.028*
C22	−0.0814 (2)	0.6796 (2)	0.28931 (5)	0.0224 (5)
H22	−0.106657	0.585627	0.290863	0.027*
C21	−0.1703 (2)	0.7709 (2)	0.26926 (5)	0.0247 (5)
H21	−0.255742	0.737591	0.256826	0.030*
C10	0.8497 (2)	0.6653 (2)	0.39798 (6)	0.0273 (5)
H10	0.933899	0.711258	0.388120	0.033*
C9	0.8707 (2)	0.5716 (2)	0.42512 (6)	0.0292 (5)
H9	0.969483	0.553670	0.433385	0.035*
C3	0.3207 (2)	0.4788 (2)	0.42841 (6)	0.0271 (5)
H3	0.236939	0.431824	0.438185	0.033*
C7	0.7635 (3)	0.4060 (2)	0.47055 (6)	0.0311 (6)
H7	0.860961	0.389193	0.479795	0.037*
C5	0.4941 (3)	0.3609 (2)	0.47218 (6)	0.0318 (6)
H5	0.411550	0.314383	0.482643	0.038*
C6	0.6397 (3)	0.3386 (2)	0.48582 (6)	0.0357 (6)
H6	0.654109	0.277746	0.505401	0.043*
H1A	0.271 (2)	0.975 (2)	0.3280 (6)	0.033 (6)*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
N1	0.0191 (9)	0.0153 (9)	0.0225 (9)	0.0003 (7)	−0.0016 (8)	0.0003 (8)
N2	0.0203 (10)	0.0129 (9)	0.0253 (9)	−0.0010 (8)	−0.0014 (8)	0.0010 (7)
C23	0.0207 (11)	0.0152 (10)	0.0170 (10)	0.0012 (8)	0.0014 (9)	0.0013 (8)
C17	0.0198 (11)	0.0168 (11)	0.0205 (10)	0.0007 (9)	0.0039 (10)	0.0006 (8)
C16	0.0200 (11)	0.0158 (10)	0.0227 (11)	0.0009 (9)	0.0000 (10)	−0.0016 (8)
C18	0.0177 (11)	0.0180 (10)	0.0181 (10)	0.0013 (8)	0.0016 (9)	−0.0006 (8)
C1	0.0201 (11)	0.0167 (11)	0.0210 (11)	0.0009 (9)	0.0014 (9)	−0.0029 (9)
C12	0.0208 (11)	0.0187 (11)	0.0202 (10)	0.0009 (9)	0.0008 (9)	−0.0029 (9)
C11	0.0201 (11)	0.0205 (11)	0.0224 (11)	0.0009 (9)	0.0002 (9)	−0.0035 (9)
C19	0.0258 (12)	0.0151 (10)	0.0234 (11)	0.0019 (9)	0.0021 (10)	0.0015 (9)
C20	0.0254 (12)	0.0232 (12)	0.0221 (11)	0.0076 (9)	−0.0011 (10)	0.0011 (9)
C13	0.0228 (12)	0.0220 (11)	0.0213 (11)	0.0038 (9)	−0.0002 (10)	−0.0012 (9)
C2	0.0200 (12)	0.0235 (11)	0.0270 (12)	0.0024 (9)	−0.0002 (10)	0.0027 (10)
C8	0.0246 (12)	0.0265 (12)	0.0246 (11)	0.0052 (9)	−0.0009 (10)	0.0005 (9)
C14	0.0212 (12)	0.0218 (11)	0.0288 (12)	−0.0035 (9)	0.0036 (10)	0.0010 (9)
C4	0.0260 (12)	0.0237 (12)	0.0263 (12)	0.0027 (10)	0.0006 (10)	0.0027 (9)
C15	0.0260 (12)	0.0174 (11)	0.0259 (11)	0.0005 (9)	−0.0005 (10)	0.0036 (9)
C22	0.0253 (12)	0.0154 (11)	0.0267 (11)	−0.0014 (9)	−0.0005 (10)	−0.0022 (9)
C21	0.0240 (12)	0.0246 (12)	0.0256 (12)	0.0009 (9)	−0.0043 (10)	−0.0032 (9)
C10	0.0208 (12)	0.0316 (13)	0.0296 (12)	−0.0013 (10)	0.0027 (10)	0.0018 (10)
C9	0.0183 (12)	0.0361 (14)	0.0333 (13)	0.0056 (10)	−0.0041 (10)	−0.0008 (11)
C3	0.0209 (12)	0.0287 (12)	0.0317 (12)	−0.0023 (10)	0.0046 (10)	0.0075 (10)
C7	0.0259 (13)	0.0351 (13)	0.0325 (12)	0.0066 (10)	−0.0054 (11)	0.0050 (10)
C5	0.0289 (13)	0.0341 (14)	0.0326 (13)	0.0015 (11)	0.0033 (11)	0.0102 (10)
C6	0.0367 (14)	0.0382 (14)	0.0322 (13)	0.0097 (11)	−0.0022 (12)	0.0143 (11)

Geometric parameters (Å, º) top

N1—C17	1.330 (2)	C13—C8	1.423 (3)
N1—C23	1.389 (2)	C2—C3	1.354 (3)
N2—C17	1.364 (2)	C2—H2	0.9300
N2—C18	1.376 (2)	C8—C7	1.392 (3)
N2—H1A	0.94 (2)	C8—C9	1.429 (3)
C23—C22	1.390 (3)	C14—C15	1.373 (3)
C23—C18	1.403 (3)	C14—H14	0.9300
C17—C16	1.463 (3)	C4—C5	1.391 (3)
C16—C15	1.397 (3)	C4—C3	1.425 (3)
C16—C1	1.412 (3)	C15—H15	0.9300
C18—C19	1.389 (3)	C22—C21	1.380 (3)
C1—C12	1.422 (3)	C22—H22	0.9300
C1—C2	1.434 (3)	C21—H21	0.9300
C12—C11	1.421 (3)	C10—C9	1.349 (3)
C12—C13	1.426 (3)	C10—H10	0.9300
C11—C14	1.393 (3)	C9—H9	0.9300
C11—C10	1.431 (3)	C3—H3	0.9300
C19—C20	1.377 (3)	C7—C6	1.378 (3)
C19—H19	0.9300	C7—H7	0.9300
C20—C21	1.403 (3)	C5—C6	1.381 (3)
C20—H20	0.9300	C5—H5	0.9300
C13—C4	1.420 (3)	C6—H6	0.9300

C17—N1—C23	105.01 (16)	C7—C8—C13	118.9 (2)
C17—N2—C18	107.25 (16)	C7—C8—C9	122.8 (2)
C17—N2—H1A	124.7 (13)	C13—C8—C9	118.26 (18)
C18—N2—H1A	128.1 (13)	C15—C14—C11	120.81 (19)
N1—C23—C22	130.42 (18)	C15—C14—H14	119.6
N1—C23—C18	109.72 (17)	C11—C14—H14	119.6
C22—C23—C18	119.84 (18)	C5—C4—C13	119.1 (2)
N1—C17—N2	112.48 (17)	C5—C4—C3	122.8 (2)
N1—C17—C16	125.73 (17)	C13—C4—C3	118.12 (18)
N2—C17—C16	121.57 (17)	C14—C15—C16	121.67 (19)
C15—C16—C1	119.46 (18)	C14—C15—H15	119.2
C15—C16—C17	117.66 (17)	C16—C15—H15	119.2
C1—C16—C17	122.80 (18)	C21—C22—C23	118.06 (19)
N2—C18—C19	131.90 (18)	C21—C22—H22	121.0
N2—C18—C23	105.54 (16)	C23—C22—H22	121.0
C19—C18—C23	122.51 (18)	C22—C21—C20	121.24 (19)
C16—C1—C12	118.71 (18)	C22—C21—H21	119.4
C16—C1—C2	123.31 (19)	C20—C21—H21	119.4
C12—C1—C2	117.96 (18)	C9—C10—C11	121.1 (2)
C11—C12—C1	120.40 (18)	C9—C10—H10	119.4
C11—C12—C13	119.29 (18)	C11—C10—H10	119.4
C1—C12—C13	120.30 (18)	C10—C9—C8	121.8 (2)
C14—C11—C12	118.83 (18)	C10—C9—H9	119.1
C14—C11—C10	122.10 (19)	C8—C9—H9	119.1
C12—C11—C10	119.07 (18)	C2—C3—C4	122.0 (2)
C20—C19—C18	116.68 (19)	C2—C3—H3	119.0
C20—C19—H19	121.7	C4—C3—H3	119.0
C18—C19—H19	121.7	C6—C7—C8	121.2 (2)
C19—C20—C21	121.62 (19)	C6—C7—H7	119.4
C19—C20—H20	119.2	C8—C7—H7	119.4
C21—C20—H20	119.2	C6—C5—C4	121.1 (2)
C4—C13—C8	119.43 (18)	C6—C5—H5	119.5
C4—C13—C12	120.17 (18)	C4—C5—H5	119.5
C8—C13—C12	120.40 (19)	C7—C6—C5	120.3 (2)
C3—C2—C1	121.41 (19)	C7—C6—H6	119.9
C3—C2—H2	119.3	C5—C6—H6	119.9
C1—C2—H2	119.3

Hydrogen-bond geometry (Å, º) top

Cg1, Cg6 and Cg7 are the centroids of rings N1/N2/C17/C18/C23, C18-C23 and N1/N2/C17-C23.

D—H···A	D—H	H···A	D···A	D—H···A
N2—H1A···N1ⁱ	0.94 (2)	1.92 (2)	2.838 (2)	164 (2)
C14—H14···Cg6ⁱⁱ	0.93	2.83	3.537 (2)	134
C21—H21···Cg1ⁱⁱⁱ	0.93	2.95	3.605 (2)	129
C21—H21···Cg7ⁱⁱⁱ	0.93	2.84	3.618 (2)	142

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

Comparison of selected geometric data for (I) (Å, °) from X-ray and calculated (DFT) data top

Bonds	X-ray	B3LYP/6–311G(d,p)
C17—N2	1.364 (2)	1.365
C18—N2	1.376 (2)	1.375
C17—N1	1.330 (2)	1.329
C23—N1	1.389 (2)	1.389
C17—C16	1.463 (3)	1.462
C16—C17—N2	121.57 (17)	121.51
C16—C17—N1	125.73 (17)	125.82
N1—C17—N2	112.48 (17)	112.44

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