organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

Journal logoIUCrDATA
ISSN: 2414-3146

5-Meth­­oxy-2-{[(4-meth­­oxy-3,5-di­methyl­pyridin-2-yl)meth­yl)]sulfin­yl}-1-(prop-2-yn-1-yl)-1H-benzimidazole

CROSSMARK_Color_square_no_text.svg

aLaboratoire de Chimie Organique Hétérocyclique, URAC 21, Pôle de Compétence Pharmacochimie, Av. Ibn Battouta, BP 1014, Faculté des Sciences, Université Mohammed V, Rabat, Morocco, bMedicinal Chemistry Laboratory, Faculty of Medicine and Pharmacy, Mohammed V University in Rabat, 10170 Rabat, Morocco, and cDepartment of Chemistry, Tulane University, New Orleans, LA 70118, USA
*Correspondence e-mail: youness.chimie14@gmail.com

Edited by H. Stoeckli-Evans, University of Neuchâtel, Switzerland (Received 22 October 2016; accepted 22 October 2016; online 28 October 2016)

In the title omeprazole derivative, C20H21N3O3S, the benzimidazole ring is inclined to the pyridine ring by 21.21 (8)°. In the crystal, neighbouring mol­ecules are linked by C—H⋯O hydrogen bonds, forming chains along the a-axis direction. Within the chains, there are offset ππ inter­actions [inter­centroid distance = 3.880 (2) Å] involving neighbouring benzimidazole rings. There are no other significant inter­molecular inter­actions present.

3D view (loading...)
[Scheme 3D1]
Chemical scheme
[Scheme 1]

Structure description

Omeprazoles (Fig. 1[link]) are a class of Proton Pump Inhibitors (PPIs) that inhibit the pump by irreversibly binding to cysteines in the pump. The irreversibility of the covalent bond results in inhibition of acid secretion until more enzymes are synthesized, viz. inhibition of enzymes H+, K+ ATPase (Hydrogen–Potassium Adenosine Triphosphates) at the secretory surface of the gastric parietal cells. This effect leads to inhibition of both basal and stimulated acid secretion, irrespective of the stimulus, for more than 24 h (Sachs et al., 1976[Sachs, G., Chang, H. H., Rabon, E., Schackman, R., Lewin, M. & Saccomani, G. (1976). J. Biol. Chem. 251, 7690-7698.]; Dibona et al., 1979[Dibona, D. R., Ito, S., Berglindh, T. & Sachs, G. (1979). Proc. Natl Acad. Sci. 76, 6689-6693.]; Fellenius et al., 1981[Fellenius, E., Berglindh, T. & Sachs, G. (1981). Nature, 290, 156-161.]).

[Figure 1]
Figure 1
The structure of omeprazole.

In the title compound (Fig. 2[link]), the benzimidazole moiety (N1/N2/C1–C6/C8) is planar (r.m.s. deviation = 0.008 Å) and it is inclined to the substituted pyridine ring (N1/C10–C14) by 21.21 (18)°.

[Figure 2]
Figure 2
The mol­ecular structure of the title compound, showing the atom labelling and 25% probability displacement ellipsoids.

In the crystal, neighbouring mol­ecules are linked by C—H⋯O hydrogen bonds, forming chains along the a-axis direction (Table 1[link] and Figs. 3[link] and 4[link]). Within the chains, there are offset ππ inter­actions present involving neighbouring benzimidazole rings [Cg1⋯Cg3(x − 1, y, z) = 3.880 (2) Å; Cg1 and Cg3 are the centroids of rings N1/N2/C1/C6/C8 and C1–C6, inter­planar distance = 3.620 (1) Å, slippage = 1.408 Å]. There are no other significant inter­molecular inter­actions present.

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
C9—H9A⋯O2i 0.97 2.56 3.441 (5) 152
Symmetry code: (i) x+1, y, z.
[Figure 3]
Figure 3
A partial view along the c axis of the crystal packing of the title compound, with the C—H⋯O hydrogen bonds (Table 1[link]) shown as dashed lines.
[Figure 4]
Figure 4
A view along the a axis of the crystal packing of the title compound, with the C—H⋯O hydrogen bonds (Table 1[link]) shown as dashed lines.

Synthesis and crystallization

To a solution of 5-meth­oxy-2-[(4-meth­oxy-3,5-di­methyl­pyri­din-2-yl)methyl­sulfin­yl]-1H-benzimidazole (0.5 g, 1.45 mmol) in N,N-di­methyl­formamide (15 ml) was added potassium carbonate (0.2 g, 1.21 mmol), propargyl bromide (0.1 ml, 1.21 mmol) and a catalytic amount of tetra-n-butyl­ammonium bromide. The reaction mixture was stirred for 12 h. The solution was then concentrated to dryness under reduced pressure and the residue extracted with di­chloro­methane. The precipitate formed by cooling was filtered and crystallized from ethanol to give colourless rod-like crystals of the title compound (yield 76%).

Refinement

Crystal and refinement data are presented in Table 2[link]. Trial refinements with both single- and two-component data files indicated the former to provide a better refinement.

Table 2
Experimental details

Crystal data
Chemical formula C20H21N3O3S
Mr 383.46
Crystal system, space group Monoclinic, P21/c
Temperature (K) 296
a, b, c (Å) 4.5974 (3), 30.675 (2), 13.8090 (9)
β (°) 91.961 (1)
V3) 1946.3 (2)
Z 4
Radiation type Mo Kα
μ (mm−1) 0.19
Crystal size (mm) 0.32 × 0.12 × 0.06
 
Data collection
Diffractometer Bruker SMART APEX CCD
Absorption correction Multi-scan (TWINABS; Sheldrick, 2009[Sheldrick, G. M. (2009). TWINABS. University of Göttingen, Göttingen, Germany.])
Tmin, Tmax 0.82, 0.99
No. of measured, independent and observed [I > 2σ(I)] reflections 35690, 4617, 3504
Rint 0.039
(sin θ/λ)max−1) 0.659
 
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.083, 0.226, 1.10
No. of reflections 4617
No. of parameters 247
H-atom treatment H-atom parameters constrained
Δρmax, Δρmin (e Å−3) 0.85, −0.37
Computer programs: APEX3 and SAINT (Bruker, 2016[Bruker (2016). APEX3, SADABS and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]), SHELXT (Sheldrick, 2015a[Sheldrick, G. M. (2015a). Acta Cryst. A71, 3-8.]), SHELXL2014 (Sheldrick, 2015b[Sheldrick, G. M. (2015b). Acta Cryst. C71, 3-8.]), DIAMOND (Brandenburg & Putz, 2012[Brandenburg, K. & Putz, H. (2012). DIAMOND. Crystal Impact GbR, Bonn, Germany.]), Mercury (Macrae et al., 2008[Macrae, C. F., Bruno, I. J., Chisholm, J. A., Edgington, P. R., McCabe, P., Pidcock, E., Rodriguez-Monge, L., Taylor, R., van de Streek, J. & Wood, P. A. (2008). J. Appl. Cryst. 41, 466-470.]) and SHELXTL (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]).

Structural data


Computing details top

Data collection: APEX3 (Bruker, 2016); cell refinement: SAINT (Bruker, 2016); data reduction: SAINT (Bruker, 2016); program(s) used to solve structure: SHELXT (Sheldrick, 2015a); program(s) used to refine structure: SHELXL2014 (Sheldrick, 2015b); molecular graphics: DIAMOND (Brandenburg & Putz, 2012) and Mercry (Macrae et al., 2008); software used to prepare material for publication: SHELXTL (Sheldrick, 2008).

5-Methoxy-2-{[(4-methoxy-3,5-dimethylpyridin-2-yl)methyl)]sulfinyl}-1-(prop-2-yn-1-yl)-1H-benzimidazole top
Crystal data top
C20H21N3O3SF(000) = 808
Mr = 383.46Dx = 1.309 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
a = 4.5974 (3) ÅCell parameters from 6538 reflections
b = 30.675 (2) Åθ = 2.5–25.3°
c = 13.8090 (9) ŵ = 0.19 mm1
β = 91.961 (1)°T = 296 K
V = 1946.3 (2) Å3Rod, colourless
Z = 40.32 × 0.12 × 0.06 mm
Data collection top
Bruker SMART APEX CCD
diffractometer
4617 independent reflections
Radiation source: fine-focus sealed tube3504 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.039
Detector resolution: 8.3333 pixels mm-1θmax = 28.0°, θmin = 1.3°
φ and ω scansh = 66
Absorption correction: multi-scan
(TWINABS; Sheldrick, 2009)
k = 4040
Tmin = 0.82, Tmax = 0.99l = 1818
35690 measured reflections
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.083Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.226H-atom parameters constrained
S = 1.10 w = 1/[σ2(Fo2) + (0.0777P)2 + 2.7928P]
where P = (Fo2 + 2Fc2)/3
4617 reflections(Δ/σ)max = 0.001
247 parametersΔρmax = 0.85 e Å3
0 restraintsΔρmin = 0.37 e Å3
Special details top

Experimental. The diffraction data were collected in three sets of 363 frames (0.5° width in ω) at φ = 0, 120 and 240°. A scan time of 70 sec/frame was used. Analysis of 1608 reflections having I/σ(I) > 12 and chosen from the full data set with CELL_NOW (Sheldrick, 2008) showed the crystal to belong to the monoclinic system and to consist of two components, the minor one likely a parasite on the main crystal. The raw data were processed using the multi-component version of SAINT under control of the two-component orientation file generated by CELL_NOW.

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.

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 > 2sigma(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. H-atoms attached to carbon were placed in calculated positions (C—H = 0.95 - 1.00 Å). All were included as riding contributions with isotropic displacement parameters 1.2 - 1.5 times those of the attached atoms. Trial refinements with both single- and two-component data files indicated the former to provide a better refinement.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
S10.28987 (19)0.62771 (3)0.18681 (7)0.0520 (3)
O11.0846 (7)0.41553 (9)0.1427 (2)0.0689 (8)
O20.2040 (6)0.64395 (9)0.2825 (2)0.0639 (7)
O30.4997 (10)0.82164 (13)0.1892 (4)0.1150 (14)
N10.5178 (7)0.55192 (10)0.1319 (2)0.0503 (7)
N20.6805 (6)0.56988 (9)0.28267 (19)0.0440 (6)
N30.2691 (10)0.70843 (12)0.0456 (3)0.0814 (12)
C10.8087 (7)0.53035 (10)0.2602 (2)0.0429 (7)
C21.0008 (8)0.50354 (12)0.3125 (3)0.0509 (8)
H21.06970.51080.37450.061*
C31.0830 (8)0.46594 (12)0.2678 (3)0.0553 (9)
H31.21080.44710.30050.066*
C40.9807 (8)0.45486 (11)0.1741 (3)0.0506 (8)
C50.7951 (8)0.48130 (11)0.1215 (3)0.0503 (8)
H50.73020.47410.05900.060*
C60.7077 (7)0.51995 (10)0.1669 (2)0.0430 (7)
C70.9808 (13)0.40132 (16)0.0497 (3)0.0821 (14)
H7A1.05810.41980.00070.123*
H7B0.77210.40270.04630.123*
H7C1.04230.37180.03920.123*
C80.5114 (7)0.58028 (11)0.2024 (2)0.0457 (7)
C90.5748 (8)0.66390 (12)0.1477 (3)0.0566 (9)
H9A0.72390.66690.19870.068*
H9B0.66410.65200.09080.068*
C100.4424 (8)0.70796 (12)0.1243 (3)0.0521 (8)
C110.1534 (12)0.74665 (16)0.0195 (3)0.0826 (14)
H110.02770.74680.03470.099*
C120.2018 (11)0.78517 (14)0.0647 (3)0.0683 (11)
C130.3896 (13)0.78359 (14)0.1456 (4)0.0778 (13)
C140.5068 (10)0.74393 (13)0.1791 (3)0.0622 (10)
C150.0700 (16)0.82688 (18)0.0263 (5)0.109 (2)
H15A0.12880.85060.06780.164*
H15B0.13550.83210.03790.164*
H15C0.13830.82450.02460.164*
C160.319 (2)0.8389 (3)0.2528 (7)0.176 (4)
H16A0.30300.86970.24190.265*
H16B0.39400.83370.31750.265*
H16C0.13050.82570.24460.265*
C170.7023 (16)0.7420 (2)0.2694 (5)0.111 (2)
H17A0.77780.77060.28350.166*
H17B0.86060.72240.25910.166*
H17C0.59250.73200.32290.166*
C180.7213 (8)0.59296 (11)0.3743 (2)0.0496 (8)
H18A0.65330.62270.36620.060*
H18B0.92740.59400.39160.060*
C190.5667 (8)0.57253 (12)0.4531 (3)0.0513 (8)
C200.4465 (11)0.55728 (16)0.5172 (3)0.0753 (13)
H200.35000.54500.56870.090*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
S10.0460 (5)0.0502 (5)0.0595 (5)0.0078 (4)0.0018 (4)0.0003 (4)
O10.088 (2)0.0551 (16)0.0633 (17)0.0187 (14)0.0071 (15)0.0094 (13)
O20.0613 (16)0.0595 (16)0.0722 (18)0.0094 (13)0.0213 (14)0.0005 (13)
O30.120 (3)0.079 (3)0.146 (4)0.000 (2)0.010 (3)0.014 (3)
N10.0529 (16)0.0496 (16)0.0480 (16)0.0043 (13)0.0043 (13)0.0003 (13)
N20.0474 (15)0.0406 (14)0.0437 (14)0.0018 (11)0.0016 (12)0.0024 (11)
N30.116 (3)0.059 (2)0.068 (2)0.019 (2)0.025 (2)0.0048 (18)
C10.0421 (16)0.0386 (16)0.0480 (17)0.0029 (13)0.0011 (13)0.0025 (13)
C20.056 (2)0.0500 (19)0.0454 (18)0.0000 (15)0.0103 (15)0.0005 (15)
C30.056 (2)0.0497 (19)0.059 (2)0.0065 (16)0.0081 (17)0.0052 (17)
C40.054 (2)0.0419 (17)0.056 (2)0.0033 (15)0.0037 (16)0.0010 (15)
C50.059 (2)0.0494 (19)0.0428 (18)0.0024 (16)0.0006 (15)0.0043 (15)
C60.0439 (17)0.0418 (16)0.0432 (17)0.0022 (13)0.0009 (13)0.0015 (13)
C70.117 (4)0.067 (3)0.063 (3)0.016 (3)0.008 (3)0.018 (2)
C80.0440 (17)0.0443 (17)0.0487 (18)0.0003 (13)0.0014 (14)0.0026 (14)
C90.051 (2)0.054 (2)0.065 (2)0.0122 (16)0.0132 (17)0.0119 (18)
C100.0516 (19)0.0509 (19)0.054 (2)0.0090 (15)0.0078 (16)0.0132 (16)
C110.110 (4)0.071 (3)0.065 (3)0.016 (3)0.027 (3)0.013 (2)
C120.083 (3)0.056 (2)0.066 (3)0.014 (2)0.008 (2)0.021 (2)
C130.107 (4)0.047 (2)0.078 (3)0.007 (2)0.003 (3)0.001 (2)
C140.074 (3)0.053 (2)0.059 (2)0.0034 (19)0.0019 (19)0.0034 (18)
C150.139 (5)0.074 (3)0.116 (5)0.034 (3)0.003 (4)0.039 (3)
C160.181 (9)0.200 (10)0.151 (8)0.091 (8)0.044 (7)0.020 (7)
C170.141 (6)0.088 (4)0.100 (4)0.012 (4)0.055 (4)0.009 (3)
C180.057 (2)0.0431 (17)0.0486 (19)0.0085 (15)0.0021 (15)0.0081 (14)
C190.056 (2)0.052 (2)0.0453 (19)0.0034 (16)0.0049 (16)0.0048 (15)
C200.089 (3)0.085 (3)0.052 (2)0.020 (3)0.001 (2)0.001 (2)
Geometric parameters (Å, º) top
S1—O21.478 (3)C7—H7C0.9600
S1—C81.785 (3)C9—C101.513 (5)
S1—C91.813 (4)C9—H9A0.9700
O1—C41.374 (4)C9—H9B0.9700
O1—C71.423 (5)C10—C141.365 (6)
O3—C161.338 (8)C11—C121.351 (6)
O3—C131.400 (6)C11—H110.9300
N1—C81.307 (4)C12—C131.390 (7)
N1—C61.389 (4)C12—C151.504 (6)
N2—C81.370 (4)C13—C141.402 (6)
N2—C11.388 (4)C14—C171.514 (6)
N2—C181.456 (4)C15—H15A0.9600
N3—C101.325 (5)C15—H15B0.9600
N3—C111.332 (5)C15—H15C0.9600
C1—C21.391 (5)C16—H16A0.9600
C1—C61.392 (5)C16—H16B0.9600
C2—C31.368 (5)C16—H16C0.9600
C2—H20.9300C17—H17A0.9600
C3—C41.402 (5)C17—H17B0.9600
C3—H30.9300C17—H17C0.9600
C4—C51.368 (5)C18—C191.461 (5)
C5—C61.407 (5)C18—H18A0.9700
C5—H50.9300C18—H18B0.9700
C7—H7A0.9600C19—C201.158 (6)
C7—H7B0.9600C20—H200.9300
O2—S1—C8109.63 (17)H9A—C9—H9B108.3
O2—S1—C9106.11 (18)N3—C10—C14124.0 (3)
C8—S1—C996.88 (16)N3—C10—C9114.3 (4)
C4—O1—C7116.4 (3)C14—C10—C9121.7 (4)
C16—O3—C13112.9 (7)N3—C11—C12126.0 (4)
C8—N1—C6103.9 (3)N3—C11—H11117.0
C8—N2—C1104.8 (3)C12—C11—H11117.0
C8—N2—C18130.0 (3)C11—C12—C13115.4 (4)
C1—N2—C18125.1 (3)C11—C12—C15121.6 (5)
C10—N3—C11117.0 (4)C13—C12—C15123.0 (5)
N2—C1—C2131.9 (3)C12—C13—O3121.5 (4)
N2—C1—C6106.0 (3)C12—C13—C14121.1 (4)
C2—C1—C6122.1 (3)O3—C13—C14116.9 (5)
C3—C2—C1116.4 (3)C10—C14—C13116.5 (4)
C3—C2—H2121.8C10—C14—C17122.5 (4)
C1—C2—H2121.8C13—C14—C17121.0 (4)
C2—C3—C4122.1 (3)C12—C15—H15A109.5
C2—C3—H3118.9C12—C15—H15B109.5
C4—C3—H3118.9H15A—C15—H15B109.5
C5—C4—O1124.7 (3)C12—C15—H15C109.5
C5—C4—C3122.0 (3)H15A—C15—H15C109.5
O1—C4—C3113.3 (3)H15B—C15—H15C109.5
C4—C5—C6116.4 (3)O3—C16—H16A109.5
C4—C5—H5121.8O3—C16—H16B109.5
C6—C5—H5121.8H16A—C16—H16B109.5
N1—C6—C1110.3 (3)O3—C16—H16C109.5
N1—C6—C5128.7 (3)H16A—C16—H16C109.5
C1—C6—C5121.0 (3)H16B—C16—H16C109.5
O1—C7—H7A109.5C14—C17—H17A109.5
O1—C7—H7B109.5C14—C17—H17B109.5
H7A—C7—H7B109.5H17A—C17—H17B109.5
O1—C7—H7C109.5C14—C17—H17C109.5
H7A—C7—H7C109.5H17A—C17—H17C109.5
H7B—C7—H7C109.5H17B—C17—H17C109.5
N1—C8—N2114.9 (3)N2—C18—C19112.8 (3)
N1—C8—S1118.7 (3)N2—C18—H18A109.0
N2—C8—S1126.4 (3)C19—C18—H18A109.0
C10—C9—S1108.8 (3)N2—C18—H18B109.0
C10—C9—H9A109.9C19—C18—H18B109.0
S1—C9—H9A109.9H18A—C18—H18B107.8
C10—C9—H9B109.9C20—C19—C18178.1 (4)
S1—C9—H9B109.9C19—C20—H20180.0
C8—N2—C1—C2179.8 (4)C9—S1—C8—N196.1 (3)
C18—N2—C1—C21.1 (6)O2—S1—C8—N225.8 (4)
C8—N2—C1—C60.4 (3)C9—S1—C8—N284.0 (3)
C18—N2—C1—C6179.1 (3)O2—S1—C9—C1069.6 (3)
N2—C1—C2—C3179.4 (4)C8—S1—C9—C10177.6 (3)
C6—C1—C2—C30.8 (5)C11—N3—C10—C140.1 (7)
C1—C2—C3—C40.2 (6)C11—N3—C10—C9178.0 (4)
C7—O1—C4—C52.2 (6)S1—C9—C10—N369.5 (4)
C7—O1—C4—C3177.6 (4)S1—C9—C10—C14112.3 (4)
C2—C3—C4—C50.8 (6)C10—N3—C11—C121.6 (9)
C2—C3—C4—O1179.0 (4)N3—C11—C12—C130.3 (9)
O1—C4—C5—C6178.7 (3)N3—C11—C12—C15177.1 (6)
C3—C4—C5—C61.1 (5)C11—C12—C13—O3168.6 (5)
C8—N1—C6—C10.6 (4)C15—C12—C13—O38.8 (8)
C8—N1—C6—C5179.6 (3)C11—C12—C13—C142.8 (8)
N2—C1—C6—N10.6 (4)C15—C12—C13—C14179.8 (5)
C2—C1—C6—N1179.5 (3)C16—O3—C13—C1284.8 (8)
N2—C1—C6—C5179.7 (3)C16—O3—C13—C14103.5 (7)
C2—C1—C6—C50.5 (5)N3—C10—C14—C133.0 (7)
C4—C5—C6—N1178.4 (3)C9—C10—C14—C13175.0 (4)
C4—C5—C6—C10.5 (5)N3—C10—C14—C17179.1 (5)
C6—N1—C8—N20.4 (4)C9—C10—C14—C173.0 (7)
C6—N1—C8—S1179.7 (2)C12—C13—C14—C104.3 (7)
C1—N2—C8—N10.0 (4)O3—C13—C14—C10167.4 (4)
C18—N2—C8—N1178.6 (3)C12—C13—C14—C17177.7 (5)
C1—N2—C8—S1179.9 (2)O3—C13—C14—C1710.6 (8)
C18—N2—C8—S11.3 (5)C8—N2—C18—C19104.5 (4)
O2—S1—C8—N1154.0 (3)C1—N2—C18—C1973.8 (4)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C9—H9A···O2i0.972.563.441 (5)152
Symmetry code: (i) x+1, y, z.
 

Acknowledgements

JTM thanks Tulane University for support of the Tulane Crystallography Laboratory.

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