1-(2-Morpholinoethyl)-1H-benz­imidazole

In the title compound, C₁₃H₁₇N₃O, the benz­imidazole ring is connected by an ethyl­ene group to the morpholine ring, which has a chair conformation.

Key indicators

• Single-crystal X-ray study
• T = 293 K
• R factor = 0.031
• wR factor = 0.075
• Data-to-parameter ratio = 11.1

checkCIF/PLATON results

No syntax errors found



Alert level C
STRVA01_ALERT_4_C           Flack parameter is too small
           From the CIF: _refine_ls_abs_structure_Flack  -10.000
           From the CIF: _refine_ls_abs_structure_Flack_su   10.000
PLAT032_ALERT_4_C Std Uncertainty in Flack Parameter too High ....      10.00
PLAT033_ALERT_2_C Flack Parameter Value Deviates from Zero .......     -10.00
PLAT066_ALERT_1_C Predicted and Reported Transmissions Identical .          ?

Alert level G
REFLT03_ALERT_4_G Please check that the estimate of the number of Friedel pairs is
            correct. If it is not, please give the correct count in the
            _publ_section_exptl_refinement section of the submitted CIF.
           From the CIF: _diffrn_reflns_theta_max           28.96
           From the CIF: _reflns_number_total               1721
           Count of symmetry unique reflns         1743
           Completeness (_total/calc)             98.74%
           TEST3: Check Friedels for noncentro structure
           Estimate of Friedel pairs measured         0
           Fraction of Friedel pairs measured     0.000
           Are heavy atom types Z>Si present         no

   0 ALERT level A = In general: serious problem
   0 ALERT level B = Potentially serious problem
   4 ALERT level C = Check and explain
   1 ALERT level G = General alerts; check

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

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Computing details

Data collection: X-AREA (Stoe & Cie, 2002); cell refinement: X-AREA; data reduction: X-RED32 (Stoe & Cie, 2002); program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: ORTEPIII (Farrugia, 1997); software used to prepare material for publication: WinGX (Farrugia, 1999).

1-(2-Morpholinoethhyl)benzimidazole

Crystal data

C13H17N3O	F(000) = 248
Mr = 231.30	Dx = 1.243 Mg m^−3
Monoclinic, P21	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2yb	Cell parameters from 5862 reflections
a = 6.3949 (7) Å	θ = 2.3–29.0°
b = 8.7222 (7) Å	µ = 0.08 mm^−1
c = 11.0868 (12) Å	T = 293 K
β = 92.345 (9)°	Prism, colorless
V = 617.88 (11) Å^3	0.56 × 0.45 × 0.29 mm
Z = 2

Data collection

STOE IPDS II diffractometer	1282 reflections with I > 2σ(I)
Radiation source: sealed X-ray tube, 12 x 0.4 mm long-fine focus	Rint = 0.032
Plane graphite monochromator	θmax = 29.0°, θmin = 3.0°
Detector resolution: 6.67 pixels mm^-1	h = −8→8
rotation method scans	k = −11→11
5862 measured reflections	l = 0→14
1721 independent reflections

Refinement

Refinement on F^2	Hydrogen site location: inferred from neighbouring sites
Least-squares matrix: full	H-atom parameters not refined
R[F^2 > 2σ(F^2)] = 0.031	w = 1/[σ^2(Fo^2) + (0.043P)^2] where P = (Fo^2 + 2Fc^2)/3
wR(F^2) = 0.075	(Δ/σ)max < 0.001
S = 0.89	Δρmax = 0.14 e Å^−3
1721 reflections	Δρmin = −0.11 e Å^−3
155 parameters	Extinction correction: shelxl, FC^*=KFC[1+0.001XFC^2Λ^3/SIN(2Θ)]^-1/4
1 restraint	Extinction coefficient: 0.090 (8)
Primary atom site location: structure-invariant direct methods	Absolute structure: Flack H.D. (1983), Acta Cryst. A39, 876-881
Secondary atom site location: difference Fourier map	Absolute structure parameter: −10 (10)

Special details

Geometry. Bond distances, angles etc. have been calculated using the rounded fractional coordinates. All su's are estimated from the variances of the (full) variance-covariance matrix. The cell e.s.d.'s are taken into account in the estimation of distances, angles and torsion angles

Refinement. Refinement on F^{2 for ALL reflections except those flagged by the user for potential systematic errors. Weighted R-factors wR and all goodnesses of fit S are based on F}2, conventional R-factors R are based on F, with F set to zero for negative F^{2. The observed criterion of F}2 > σ(F^{2) is used only for calculating -R-factor-obs etc. and is not relevant to the choice of reflections for refinement. R-factors based on F}2 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 (Ų)

	x	y	z	Uiso*/Ueq
O1	0.3334 (2)	0.19432 (19)	0.96858 (13)	0.0649 (5)
N1	1.2248 (2)	0.0268 (2)	0.44317 (14)	0.0535 (5)
N2	0.9024 (2)	0.01707 (17)	0.51502 (12)	0.0430 (4)
N3	0.5095 (2)	0.11827 (16)	0.74370 (12)	0.0416 (4)
C1	1.1092 (3)	−0.0093 (2)	0.53380 (17)	0.0518 (6)
C2	0.8796 (2)	0.0790 (2)	0.40029 (14)	0.0383 (5)
C3	0.7060 (3)	0.1304 (2)	0.33417 (15)	0.0435 (5)
C4	0.7399 (3)	0.1857 (2)	0.22039 (16)	0.0496 (6)
C5	0.9398 (3)	0.1876 (3)	0.17431 (16)	0.0523 (6)
C6	1.1111 (3)	0.1359 (2)	0.24000 (15)	0.0489 (6)
C7	1.0810 (2)	0.0817 (2)	0.35674 (15)	0.0413 (5)
C8	0.7373 (3)	−0.0082 (2)	0.59989 (16)	0.0477 (6)
C9	0.6672 (3)	0.1409 (2)	0.65393 (16)	0.0467 (6)
C10	0.6005 (3)	0.0664 (2)	0.85912 (16)	0.0518 (6)
C11	0.4345 (4)	0.0528 (3)	0.95016 (17)	0.0627 (8)
C12	0.2407 (4)	0.2436 (3)	0.8578 (2)	0.0685 (8)
C13	0.3985 (3)	0.2615 (3)	0.76244 (18)	0.0560 (7)
H1	1.16530	−0.05000	0.60560	0.0620*
H3	0.57290	0.12770	0.36490	0.0520*
H4	0.62740	0.22270	0.17320	0.0600*
H5	0.95690	0.22500	0.09680	0.0630*
H6	1.24340	0.13670	0.20810	0.0590*
H8A	0.78840	−0.07600	0.66390	0.0570*
H8B	0.61890	−0.05760	0.55840	0.0570*
H9A	0.78740	0.19260	0.69150	0.0560*
H9B	0.61020	0.20650	0.59010	0.0560*
H10A	0.70650	0.13870	0.88780	0.0620*
H10B	0.66720	−0.03230	0.84890	0.0620*
H11A	0.33180	−0.02260	0.92260	0.0750*
H11B	0.49740	0.01720	1.02620	0.0750*
H12A	0.17120	0.34100	0.86960	0.0820*
H12B	0.13550	0.16980	0.83070	0.0820*
H13A	0.32820	0.29310	0.68730	0.0670*
H13B	0.49800	0.34080	0.78650	0.0670*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
O1	0.0847 (10)	0.0643 (9)	0.0473 (8)	0.0011 (8)	0.0221 (7)	−0.0102 (7)
N1	0.0449 (8)	0.0693 (11)	0.0466 (9)	0.0100 (8)	0.0046 (7)	0.0010 (8)
N2	0.0455 (8)	0.0465 (8)	0.0376 (7)	0.0054 (7)	0.0089 (6)	0.0051 (6)
N3	0.0467 (7)	0.0447 (8)	0.0337 (7)	0.0047 (6)	0.0066 (6)	0.0022 (6)
C1	0.0512 (10)	0.0600 (12)	0.0439 (10)	0.0161 (9)	−0.0002 (8)	0.0040 (9)
C2	0.0423 (8)	0.0377 (8)	0.0353 (8)	−0.0016 (7)	0.0049 (6)	−0.0027 (7)
C3	0.0389 (8)	0.0477 (9)	0.0440 (9)	−0.0030 (7)	0.0023 (7)	−0.0018 (8)
C4	0.0506 (10)	0.0557 (10)	0.0418 (9)	−0.0022 (9)	−0.0070 (8)	0.0038 (9)
C5	0.0599 (10)	0.0605 (11)	0.0366 (9)	−0.0123 (10)	0.0042 (8)	0.0014 (8)
C6	0.0459 (9)	0.0596 (11)	0.0419 (10)	−0.0100 (9)	0.0120 (8)	−0.0054 (9)
C7	0.0380 (8)	0.0463 (9)	0.0397 (9)	0.0002 (8)	0.0041 (7)	−0.0050 (7)
C8	0.0570 (10)	0.0449 (10)	0.0421 (10)	0.0012 (8)	0.0132 (8)	0.0047 (8)
C9	0.0563 (10)	0.0429 (10)	0.0418 (9)	0.0005 (8)	0.0117 (8)	0.0028 (8)
C10	0.0590 (11)	0.0570 (11)	0.0394 (9)	0.0060 (9)	0.0014 (8)	0.0046 (9)
C11	0.0887 (15)	0.0614 (14)	0.0387 (10)	0.0034 (12)	0.0127 (10)	0.0042 (9)
C12	0.0648 (12)	0.0730 (14)	0.0691 (15)	0.0167 (11)	0.0189 (11)	−0.0071 (12)
C13	0.0669 (12)	0.0546 (11)	0.0468 (12)	0.0166 (10)	0.0080 (9)	0.0044 (9)

Geometric parameters (Å, º)

O1—C11	1.412 (3)	C12—C13	1.499 (3)
O1—C12	1.409 (3)	C1—H1	0.9301
N1—C1	1.310 (2)	C3—H3	0.9300
N1—C7	1.386 (2)	C4—H4	0.9299
N2—C1	1.350 (2)	C5—H5	0.9298
N2—C2	1.384 (2)	C6—H6	0.9303
N2—C8	1.459 (2)	C8—H8A	0.9701
N3—C9	1.459 (2)	C8—H8B	0.9706
N3—C10	1.456 (2)	C9—H9A	0.9703
N3—C13	1.456 (3)	C9—H9B	0.9695
C2—C3	1.380 (2)	C10—H10A	0.9699
C2—C7	1.3940 (19)	C10—H10B	0.9695
C3—C4	1.376 (2)	C11—H11A	0.9699
C4—C5	1.396 (3)	C11—H11B	0.9701
C5—C6	1.367 (3)	C12—H12A	0.9701
C6—C7	1.399 (2)	C12—H12B	0.9699
C8—C9	1.508 (3)	C13—H13A	0.9703
C10—C11	1.499 (3)	C13—H13B	0.9698
O1···N3	2.856 (2)	H4···H11B^viii	2.5395
O1···C6^i	3.418 (2)	H4···H11A^vi	2.4807
O1···H4^ii	2.8972	H5···O1^v	2.8582
O1···H5^i	2.8582	H6···O1^v	2.7858
O1···H6^i	2.7858	H8A···C10	2.8078
N3···O1	2.856 (2)	H8A···H1	2.5310
N1···H3^iii	2.5770	H8A···H10B	2.2545
N1···H8B^iii	2.8744	H8A···C6^ix	2.7940
C3···C9	3.565 (2)	H8B···N1^x	2.8744
C3···C13^iv	3.448 (3)	H8B···C3	3.0484
C6···O1^v	3.418 (2)	H9A···H10A	2.3059
C9···C3	3.565 (2)	H9A···H13B	2.5228
C13···C3^vi	3.448 (3)	H9B···C2	2.9883
C2···H13A^iv	2.9701	H9B···C3	3.0015
C2···H9B	2.9883	H9B···H3	2.5912
C3···H8B	3.0484	H9B···H13A	2.2678
C3···H1^vii	2.9747	H9B···H13B	2.5993
C3···H13A^iv	2.9590	H10A···H9A	2.3059
C3···H9B	3.0015	H10A···H13B	2.4544
C4···H11A^vi	3.0228	H10B···C8	2.8228
C4···H1^vii	3.0509	H10B···H8A	2.2545
C4···H11B^viii	2.9878	H11A···C13	3.0882
C6···H8A^vii	2.7940	H11A···H12B	2.3077
C8···H10B	2.8228	H11A···C4^iv	3.0228
C8···H3	3.0123	H11A···H4^iv	2.4807
C10···H8A	2.8078	H11B···C4^ii	2.9878
C11···H4^ii	3.0956	H11B···H4^ii	2.5395
C13···H11A	3.0882	H11B···H13B^xi	2.5836
H1···H8A	2.5310	H12B···H11A	2.3077
H1···C3^ix	2.9747	H13A···H9B	2.2678
H1···C4^ix	3.0509	H13A···C2^vi	2.9701
H3···N1^x	2.5770	H13A···C3^vi	2.9590
H3···C8	3.0123	H13B···H9A	2.5228
H3···H9B	2.5912	H13B···H9B	2.5993
H4···O1^viii	2.8972	H13B···H10A	2.4544
H4···C11^viii	3.0956	H13B···H11B^xii	2.5836
C11—O1—C12	108.63 (16)	C5—C6—H6	121.09
C1—N1—C7	103.54 (13)	C7—C6—H6	121.07
C1—N2—C2	105.90 (13)	N2—C8—H8A	109.44
C1—N2—C8	127.21 (15)	N2—C8—H8B	109.41
C2—N2—C8	126.85 (13)	C9—C8—H8A	109.38
C9—N3—C10	112.27 (13)	C9—C8—H8B	109.41
C9—N3—C13	109.63 (14)	H8A—C8—H8B	108.00
C10—N3—C13	108.72 (14)	N3—C9—H9A	109.12
N1—C1—N2	114.88 (16)	N3—C9—H9B	109.15
N2—C2—C3	131.85 (14)	C8—C9—H9A	109.16
N2—C2—C7	105.12 (13)	C8—C9—H9B	109.15
C3—C2—C7	123.03 (15)	H9A—C9—H9B	107.86
C2—C3—C4	116.58 (17)	N3—C10—H10A	109.57
C3—C4—C5	121.38 (18)	N3—C10—H10B	109.58
C4—C5—C6	121.80 (17)	C11—C10—H10A	109.60
C5—C6—C7	117.84 (16)	C11—C10—H10B	109.60
N1—C7—C2	110.55 (14)	H10A—C10—H10B	108.10
N1—C7—C6	130.09 (14)	O1—C11—H11A	109.28
C2—C7—C6	119.36 (15)	O1—C11—H11B	109.27
N2—C8—C9	111.14 (15)	C10—C11—H11A	109.30
N3—C9—C8	112.30 (14)	C10—C11—H11B	109.30
N3—C10—C11	110.35 (16)	H11A—C11—H11B	107.94
O1—C11—C10	111.67 (18)	O1—C12—H12A	109.17
O1—C12—C13	112.03 (19)	O1—C12—H12B	109.23
N3—C13—C12	110.94 (19)	C13—C12—H12A	109.22
N1—C1—H1	122.56	C13—C12—H12B	109.21
N2—C1—H1	122.56	H12A—C12—H12B	107.89
C2—C3—H3	121.71	N3—C13—H13A	109.43
C4—C3—H3	121.71	N3—C13—H13B	109.45
C3—C4—H4	119.35	C12—C13—H13A	109.48
C5—C4—H4	119.27	C12—C13—H13B	109.47
C4—C5—H5	119.11	H13A—C13—H13B	108.02
C6—C5—H5	119.09
C11—O1—C12—C13	−58.7 (2)	C13—N3—C10—C11	55.5 (2)
C12—O1—C11—C10	59.7 (2)	C9—N3—C13—C12	−177.82 (16)
C1—N1—C7—C6	−179.19 (19)	N2—C2—C3—C4	−179.78 (18)
C1—N1—C7—C2	1.0 (2)	N2—C2—C7—N1	−1.5 (2)
C7—N1—C1—N2	−0.1 (2)	C3—C2—C7—C6	−1.3 (3)
C8—N2—C2—C3	−1.1 (3)	C3—C2—C7—N1	178.56 (17)
C2—N2—C8—C9	−73.7 (2)	N2—C2—C7—C6	178.67 (15)
C2—N2—C1—N1	−0.8 (2)	C7—C2—C3—C4	0.1 (3)
C8—N2—C1—N1	−178.46 (16)	C2—C3—C4—C5	0.8 (3)
C1—N2—C2—C3	−178.71 (19)	C3—C4—C5—C6	−0.5 (3)
C1—N2—C2—C7	1.37 (18)	C4—C5—C6—C7	−0.7 (3)
C8—N2—C2—C7	179.01 (16)	C5—C6—C7—N1	−178.3 (2)
C1—N2—C8—C9	103.5 (2)	C5—C6—C7—C2	1.5 (3)
C10—N3—C13—C12	−54.8 (2)	N2—C8—C9—N3	−177.12 (14)
C10—N3—C9—C8	78.05 (18)	N3—C10—C11—O1	−59.5 (2)
C13—N3—C9—C8	−161.00 (15)	O1—C12—C13—N3	57.8 (2)
C9—N3—C10—C11	177.00 (16)

Symmetry codes: (i) x−1, y, z+1; (ii) x, y, z+1; (iii) x+1, y, z; (iv) −x+1, y−1/2, −z+1; (v) x+1, y, z−1; (vi) −x+1, y+1/2, −z+1; (vii) −x+2, y+1/2, −z+1; (viii) x, y, z−1; (ix) −x+2, y−1/2, −z+1; (x) x−1, y, z; (xi) −x+1, y−1/2, −z+2; (xii) −x+1, y+1/2, −z+2.

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
C3—H3···N1^x	0.93	2.58	3.471 (2)	161

Symmetry code: (x) x−1, y, z.