tert-Butyl 2-(1H-benzimidazol-1-yl)acetate

Al-Mohammed, N.N.; Alias, Y.; Abdullah, Z.; Khaledi, H.

doi:10.1107/S1600536812002814

organic compounds

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ISSN: 2056-9890

Volume 68| Part 3| March 2012| Page o571

doi:10.1107/S1600536812002814

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tert-Butyl 2-(1H-benzimidazol-1-yl)acetate

Nassir N. Al-Mohammed,^a Yatimah Alias,^a Zanariah Abdullah ^a and Hamid Khaledi ^a ^*

^aDepartment of Chemistry, University of Malaya, 50603 Kuala Lumpur, Malaysia
^*Correspondence e-mail: khaledi@siswa.um.edu.my

(Received 22 January 2012; accepted 23 January 2012; online 4 February 2012)

In the title compound, C₁₃H₁₆N₂O₂, the planes of the benzimidazole ring system and the acetate O—C=O fragment make a dihedral angle of 84.5 (3)°. In the crystal, molecules are connected through C—H⋯N hydrogen bonds to form infinite chains in the [-110] direction.

Related literature

For related structures, see: Al-Mohammed et al. (2012 ); Fu et al. (2009 ); Xu et al. (2008 ).

Experimental

Crystal data

C₁₃H₁₆N₂O₂
M_r = 232.28
Monoclinic, C c
a = 5.4204 (2) Å
b = 11.3319 (4) Å
c = 19.8771 (7) Å
β = 96.609 (3)°
V = 1212.81 (8) Å³
Z = 4
Mo Kα radiation
μ = 0.09 mm⁻¹
T = 100 K
0.19 × 0.13 × 0.04 mm

Data collection

Bruker APEXII CCD diffractometer
Absorption correction: multi-scan (SADABS; Sheldrick, 1996 ) T_min = 0.984, T_max = 0.997
3829 measured reflections
1244 independent reflections
1091 reflections with I > 2σ(I)
R_int = 0.036

Refinement

R[F² > 2σ(F²)] = 0.034
wR(F²) = 0.076
S = 1.04
1244 reflections
157 parameters
2 restraints
H-atom parameters constrained
Δρ_max = 0.17 e Å⁻³
Δρ_min = −0.20 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
C3—H3⋯N2ⁱ	0.95	2.48	3.406 (3)	165
Symmetry code: (i) $[x-{\script{1\over 2}}, y+{\script{1\over 2}}, z]$ .

Data collection: APEX2 (Bruker, 2007 ); cell refinement: APEX2; data reduction: SAINT (Bruker, 2007); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: X-SEED (Barbour, 2001 ); software used to prepare material for publication: SHELXL97 and publCIF (Westrip, 2010 ).

Supporting information

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536812002814/gk2453sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536812002814/gk2453Isup2.hkl

Supporting information file. DOI: 10.1107/S1600536812002814/gk2453Isup3.cml

checkCIF report

Comment top

The title compound is the condensation product of the reaction of benzimidazole with tert-butyl chloroacetate. The benzimidazole ring make a dihedral angle of 84.5 (3)° with the plane passing through the acetate group, C9/O1/O2. This value is comparable to those calculated for some similar structures (Al-Mohammed et al., 2012; Fu et al., 2009; Xu et al., 2008). The crystal packing structure contains chains in [-1 1 0] direction formed by C3—H3···N2 hydrogen bonds between the adjacent molecules. Intramolecular C—H···O hydrogen bonding also occurs.

Related literature top

For related structures, see: Al-Mohammed et al. (2012); Fu et al. (2009); Xu et al. (2008).

Experimental top

Sodium hydroxide (0.5 g, 125 mmol) was added to a solution of benzimidazole (1.48 g, 125 mmol) in DMF (20 ml), followed by addition of tert-butyl chloroacetate (1.82 ml, 127 mmol). The mixture was refluxed for 1 h. The reaction mass was quenched with cold water (50 ml) and extracted by dichloromethane (3 x 25 ml). The combined organic layers was washed with cold water and brine and dried over anhydrous sodium sulfate. The solvent was evaporated under vacuum and the formed amorphous solid was stirred in n-hexane (30 ml) at room temperature. The solid was filtered, washed with hexane (2 x 20 ml), and recrystallized from ethyl acetate to afford colorless crystals of the title compound (melting point = 367–369 K).

Computing details top

Data collection: APEX2 (Bruker, 2007); cell refinement: APEX2 (Bruker, 2007); data reduction: SAINT (Bruker, 2007); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: X-SEED (Barbour, 2001); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008) and publCIF (Westrip, 2010).

Figures top

Fig. 1. The molecular structure of the title compound showing displacement ellipsoids at the 50% probability level. Hydrogen atoms are drawn as spheres of arbitrary radius.

tert-Butyl 2-(1H-benzimidazol-1-yl)acetate top

Crystal data top

C₁₃H₁₆N₂O₂	F(000) = 496
M_r = 232.28	D_x = 1.272 Mg m⁻³
Monoclinic, Cc	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: C -2yc	Cell parameters from 1057 reflections
a = 5.4204 (2) Å	θ = 3.6–26.4°
b = 11.3319 (4) Å	µ = 0.09 mm⁻¹
c = 19.8771 (7) Å	T = 100 K
β = 96.609 (3)°	Tablet, colourless
V = 1212.81 (8) Å³	0.19 × 0.13 × 0.04 mm
Z = 4

Data collection top

Bruker APEXII CCD diffractometer	1244 independent reflections
Radiation source: fine-focus sealed tube	1091 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.036
ϕ and ω scans	θ_max = 26.5°, θ_min = 3.6°
Absorption correction: multi-scan (SADABS; Sheldrick, 1996)	h = −6→6
T_min = 0.984, T_max = 0.997	k = −14→14
3829 measured reflections	l = −24→24

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)] = 0.034	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.076	H-atom parameters constrained
S = 1.04	w = 1/[σ²(F_o²) + (0.0394P)² + 0.180P] where P = (F_o² + 2F_c²)/3
1244 reflections	(Δ/σ)_max < 0.001
157 parameters	Δρ_max = 0.17 e Å⁻³
2 restraints	Δρ_min = −0.20 e Å⁻³

Crystal data top

C₁₃H₁₆N₂O₂	V = 1212.81 (8) Å³
M_r = 232.28	Z = 4
Monoclinic, Cc	Mo Kα radiation
a = 5.4204 (2) Å	µ = 0.09 mm⁻¹
b = 11.3319 (4) Å	T = 100 K
c = 19.8771 (7) Å	0.19 × 0.13 × 0.04 mm
β = 96.609 (3)°

Data collection top

Bruker APEXII CCD diffractometer	1244 independent reflections
Absorption correction: multi-scan (SADABS; Sheldrick, 1996)	1091 reflections with I > 2σ(I)
T_min = 0.984, T_max = 0.997	R_int = 0.036
3829 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.034	2 restraints
wR(F²) = 0.076	H-atom parameters constrained
S = 1.04	Δρ_max = 0.17 e Å⁻³
1244 reflections	Δρ_min = −0.20 e Å⁻³
157 parameters

Special details top

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) top

	x	y	z	U_iso*/U_eq
O1	0.0330 (4)	0.41863 (16)	0.04890 (10)	0.0302 (5)
O2	0.2082 (3)	0.59850 (13)	0.07085 (9)	0.0174 (4)
N1	0.3020 (3)	0.38525 (17)	−0.05825 (10)	0.0193 (5)
N2	0.3571 (4)	0.19170 (18)	−0.07541 (12)	0.0243 (5)
C1	0.4419 (5)	0.2870 (2)	−0.04255 (14)	0.0227 (6)
H1	0.5871	0.2872	−0.0108	0.027*
C2	0.1057 (4)	0.3507 (2)	−0.10483 (12)	0.0183 (5)
C3	−0.0961 (4)	0.4127 (2)	−0.13641 (13)	0.0222 (6)
H3	−0.1195	0.4943	−0.1282	0.027*
C4	−0.2609 (5)	0.3489 (2)	−0.18058 (14)	0.0250 (6)
H4	−0.4014	0.3879	−0.2035	0.030*
C5	−0.2268 (5)	0.2281 (2)	−0.19258 (13)	0.0228 (6)
H5	−0.3446	0.1872	−0.2232	0.027*
C6	−0.0250 (5)	0.1677 (2)	−0.16060 (14)	0.0225 (6)
H6	−0.0019	0.0862	−0.1690	0.027*
C7	0.1446 (4)	0.2301 (2)	−0.11554 (13)	0.0192 (5)
C8	0.3234 (4)	0.4973 (2)	−0.02268 (13)	0.0183 (5)
H8A	0.2671	0.5617	−0.0544	0.022*
H8B	0.4997	0.5119	−0.0056	0.022*
C9	0.1684 (4)	0.4977 (2)	0.03638 (13)	0.0187 (5)
C10	0.0928 (4)	0.6199 (2)	0.13424 (13)	0.0200 (5)
C11	0.1856 (5)	0.5282 (2)	0.18666 (14)	0.0264 (6)
H11A	0.1199	0.4505	0.1722	0.040*
H11B	0.1293	0.5487	0.2303	0.040*
H11C	0.3675	0.5260	0.1914	0.040*
C12	0.1849 (5)	0.7429 (2)	0.15475 (15)	0.0256 (6)
H12A	0.3668	0.7432	0.1612	0.038*
H12B	0.1214	0.7655	0.1971	0.038*
H12C	0.1257	0.7992	0.1191	0.038*
C13	−0.1878 (5)	0.6198 (2)	0.11925 (15)	0.0271 (6)
H13A	−0.2380	0.6743	0.0819	0.041*
H13B	−0.2616	0.6451	0.1596	0.041*
H13C	−0.2454	0.5400	0.1065	0.041*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
O1	0.0402 (11)	0.0241 (10)	0.0279 (11)	−0.0125 (8)	0.0109 (9)	−0.0047 (9)
O2	0.0196 (9)	0.0158 (8)	0.0172 (9)	0.0005 (7)	0.0035 (7)	−0.0026 (7)
N1	0.0221 (11)	0.0165 (10)	0.0191 (12)	0.0029 (8)	0.0013 (9)	−0.0011 (9)
N2	0.0288 (12)	0.0191 (11)	0.0239 (12)	0.0041 (9)	−0.0013 (10)	−0.0012 (10)
C1	0.0253 (14)	0.0225 (13)	0.0196 (13)	0.0059 (11)	0.0001 (11)	−0.0002 (11)
C2	0.0214 (13)	0.0185 (12)	0.0153 (14)	0.0003 (10)	0.0037 (10)	−0.0018 (10)
C3	0.0249 (14)	0.0187 (12)	0.0224 (14)	0.0045 (10)	0.0001 (11)	−0.0023 (11)
C4	0.0273 (14)	0.0250 (14)	0.0221 (15)	0.0067 (11)	0.0008 (12)	−0.0008 (11)
C5	0.0266 (14)	0.0251 (14)	0.0163 (13)	0.0001 (11)	−0.0001 (11)	−0.0051 (11)
C6	0.0317 (15)	0.0164 (12)	0.0197 (14)	0.0010 (10)	0.0045 (11)	−0.0024 (10)
C7	0.0242 (14)	0.0186 (12)	0.0148 (13)	0.0031 (10)	0.0022 (10)	−0.0004 (10)
C8	0.0205 (12)	0.0176 (12)	0.0167 (13)	−0.0013 (10)	0.0019 (10)	−0.0030 (10)
C9	0.0210 (12)	0.0180 (12)	0.0163 (13)	0.0017 (10)	−0.0011 (10)	0.0007 (10)
C10	0.0188 (13)	0.0264 (13)	0.0152 (13)	−0.0015 (10)	0.0036 (10)	−0.0033 (11)
C11	0.0268 (14)	0.0341 (14)	0.0180 (13)	−0.0007 (12)	0.0016 (11)	0.0008 (12)
C12	0.0255 (13)	0.0250 (12)	0.0273 (15)	−0.0010 (11)	0.0071 (11)	−0.0092 (12)
C13	0.0167 (13)	0.0394 (15)	0.0255 (15)	−0.0004 (11)	0.0031 (11)	−0.0029 (13)

Geometric parameters (Å, º) top

O1—C9	1.203 (3)	C6—C7	1.399 (4)
O2—C9	1.336 (3)	C6—H6	0.9500
O2—C10	1.490 (3)	C8—C9	1.520 (3)
N1—C1	1.363 (3)	C8—H8A	0.9900
N1—C2	1.384 (3)	C8—H8B	0.9900
N1—C8	1.451 (3)	C10—C11	1.516 (4)
N2—C1	1.317 (3)	C10—C13	1.516 (3)
N2—C7	1.394 (3)	C10—C12	1.520 (4)
C1—H1	0.9500	C11—H11A	0.9800
C2—C3	1.388 (3)	C11—H11B	0.9800
C2—C7	1.402 (3)	C11—H11C	0.9800
C3—C4	1.383 (4)	C12—H12A	0.9800
C3—H3	0.9500	C12—H12B	0.9800
C4—C5	1.406 (4)	C12—H12C	0.9800
C4—H4	0.9500	C13—H13A	0.9800
C5—C6	1.382 (4)	C13—H13B	0.9800
C5—H5	0.9500	C13—H13C	0.9800

C9—O2—C10	120.91 (18)	C9—C8—H8B	109.4
C1—N1—C2	106.6 (2)	H8A—C8—H8B	108.0
C1—N1—C8	126.3 (2)	O1—C9—O2	126.7 (2)
C2—N1—C8	125.84 (19)	O1—C9—C8	124.2 (2)
C1—N2—C7	104.24 (19)	O2—C9—C8	109.14 (18)
N2—C1—N1	113.8 (2)	O2—C10—C11	109.36 (19)
N2—C1—H1	123.1	O2—C10—C13	110.1 (2)
N1—C1—H1	123.1	C11—C10—C13	112.4 (2)
N1—C2—C3	131.6 (2)	O2—C10—C12	102.64 (19)
N1—C2—C7	105.1 (2)	C11—C10—C12	111.8 (2)
C3—C2—C7	123.3 (2)	C13—C10—C12	110.1 (2)
C4—C3—C2	116.1 (2)	C10—C11—H11A	109.5
C4—C3—H3	121.9	C10—C11—H11B	109.5
C2—C3—H3	121.9	H11A—C11—H11B	109.5
C3—C4—C5	122.0 (2)	C10—C11—H11C	109.5
C3—C4—H4	119.0	H11A—C11—H11C	109.5
C5—C4—H4	119.0	H11B—C11—H11C	109.5
C6—C5—C4	121.1 (2)	C10—C12—H12A	109.5
C6—C5—H5	119.5	C10—C12—H12B	109.5
C4—C5—H5	119.5	H12A—C12—H12B	109.5
C5—C6—C7	118.2 (2)	C10—C12—H12C	109.5
C5—C6—H6	120.9	H12A—C12—H12C	109.5
C7—C6—H6	120.9	H12B—C12—H12C	109.5
N2—C7—C6	130.4 (2)	C10—C13—H13A	109.5
N2—C7—C2	110.3 (2)	C10—C13—H13B	109.5
C6—C7—C2	119.4 (2)	H13A—C13—H13B	109.5
N1—C8—C9	111.03 (18)	C10—C13—H13C	109.5
N1—C8—H8A	109.4	H13A—C13—H13C	109.5
C9—C8—H8A	109.4	H13B—C13—H13C	109.5
N1—C8—H8B	109.4

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
C11—H11A···O1	0.98	2.47	3.033 (3)	116
C13—H13C···O1	0.98	2.42	2.995 (3)	117
C3—H3···N2ⁱ	0.95	2.48	3.406 (3)	165

Symmetry code: (i) x−1/2, y+1/2, z.

Experimental details

Crystal data
Chemical formula	C₁₃H₁₆N₂O₂
M_r	232.28
Crystal system, space group	Monoclinic, Cc
Temperature (K)	100
a, b, c (Å)	5.4204 (2), 11.3319 (4), 19.8771 (7)
β (°)	96.609 (3)
V (Å³)	1212.81 (8)
Z	4
Radiation type	Mo Kα
µ (mm⁻¹)	0.09
Crystal size (mm)	0.19 × 0.13 × 0.04

Data collection
Diffractometer	Bruker APEXII CCD diffractometer
Absorption correction	Multi-scan (SADABS; Sheldrick, 1996)
T_min, T_max	0.984, 0.997
No. of measured, independent and observed [I > 2σ(I)] reflections	3829, 1244, 1091
R_int	0.036
(sin θ/λ)_max (Å⁻¹)	0.627

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.034, 0.076, 1.04
No. of reflections	1244
No. of parameters	157
No. of restraints	2
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.17, −0.20

Computer programs: APEX2 (Bruker, 2007), SAINT (Bruker, 2007), SHELXS97 (Sheldrick, 2008), X-SEED (Barbour, 2001), SHELXL97 (Sheldrick, 2008) and publCIF (Westrip, 2010).

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
C3—H3···N2ⁱ	0.95	2.48	3.406 (3)	164.8

Symmetry code: (i) x−1/2, y+1/2, z.

Acknowledgements

The authors thank the University of Malaya for funding this study (FRGS grant No. FP001/2010 A).

References

Al-Mohammed, N. N., Alias, Y., Abdullah, Z. & Khaledi, H. (2012). Acta Cryst. E68, o445. Web of Science CSD CrossRef IUCr Journals Google Scholar
Barbour, L. J. (2001). J. Supramol. Chem. 1, 189–191. CrossRef CAS Google Scholar
Bruker (2007). APEX2 and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA. Google Scholar
Fu, X. & Xu, G. (2009). Acta Cryst. E65, o1535. Web of Science CSD CrossRef IUCr Journals Google Scholar
Sheldrick, G. M. (1996). SADABS. University of Göttingen, Germany. Google Scholar
Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. Web of Science CrossRef CAS IUCr Journals Google Scholar
Westrip, S. P. (2010). J. Appl. Cryst. 43, 920–925. Web of Science CrossRef CAS IUCr Journals Google Scholar
Xu, G.-H. & Wang, W. (2008). Acta Cryst. E64, o1811. Web of Science CrossRef IUCr Journals Google Scholar