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

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 π–π inter­actions [inter­centroid distance = 3.880 (2) Å] involving neighbouring benzimidazole rings. There are no other significant inter­molecular inter­actions present.

Key indicators

• Single-crystal X-ray study
• T = 296 K
• Mean [sigma](C-C) = 0.006 Å
• R factor = 0.083
• wR factor = 0.226
• Data-to-parameter ratio = 18.7

checkCIF/PLATON results

No syntax errors found



Alert level C
PLAT094_ALERT_2_C Ratio of Maximum / Minimum Residual Density ....       2.31 Report
PLAT220_ALERT_2_C Non-Solvent Resd 1   C   Ueq(max)/Ueq(min) Range        4.1 Ratio
PLAT222_ALERT_3_C Non-Solvent Resd 1   H Uiso(max)/Uiso(min) Range        4.4 Ratio
PLAT230_ALERT_2_C Hirshfeld Test Diff for    O3     --  C13     ..        6.5 s.u.
PLAT234_ALERT_4_C Large Hirshfeld Difference O3     --  C16     ..       0.18 Ang.
PLAT242_ALERT_2_C Low    'MainMol' Ueq as Compared to Neighbors of        C12 Check
PLAT242_ALERT_2_C Low    'MainMol' Ueq as Compared to Neighbors of        C14 Check
PLAT340_ALERT_3_C Low Bond Precision on  C-C Bonds ...............    0.00573 Ang.
PLAT906_ALERT_3_C Large K value in the Analysis of Variance ......     16.375 Check
PLAT906_ALERT_3_C Large K value in the Analysis of Variance ......      3.156 Check
PLAT911_ALERT_3_C Missing # FCF Refl Between THmin & STh/L=  0.600          2 Report

Alert level G
PLAT380_ALERT_4_G Incorrectly? Oriented X(sp2)-Methyl Moiety .....        C15 Check
PLAT912_ALERT_4_G Missing # of FCF Reflections Above STh/L=  0.600         24 Note
PLAT933_ALERT_2_G Number of OMIT records in Embedded RES .........          2 Note
PLAT961_ALERT_5_G Dataset Contains no Negative Intensities .......     Please Check
PLAT978_ALERT_2_G Number C-C Bonds with Positive Residual Density           4 Note

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

   0 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
   7 ALERT type 2 Indicator that the structure model may be wrong or deficient
   5 ALERT type 3 Indicator that the structure quality may be low
   3 ALERT type 4 Improvement, methodology, query or suggestion
   1 ALERT type 5 Informative message, check

---

Computing details

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

Crystal data

C20H21N3O3S	F(000) = 808
Mr = 383.46	Dx = 1.309 Mg m^−3
Monoclinic, P21/c	Mo Kα radiation, λ = 0.71073 Å
a = 4.5974 (3) Å	Cell parameters from 6538 reflections
b = 30.675 (2) Å	θ = 2.5–25.3°
c = 13.8090 (9) Å	µ = 0.19 mm^−1
β = 91.961 (1)°	T = 296 K
V = 1946.3 (2) Å^3	Rod, colourless
Z = 4	0.32 × 0.12 × 0.06 mm

Data collection

Bruker SMART APEX CCD diffractometer	4617 independent reflections
Radiation source: fine-focus sealed tube	3504 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.039
Detector resolution: 8.3333 pixels mm^-1	θmax = 28.0°, θmin = 1.3°
φ and ω scans	h = −6→6
Absorption correction: multi-scan (TWINABS; Sheldrick, 2009)	k = −40→40
Tmin = 0.82, Tmax = 0.99	l = −18→18
35690 measured reflections

Refinement

Refinement on F^2	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F^2 > 2σ(F^2)] = 0.083	Hydrogen site location: inferred from neighbouring sites
wR(F^2) = 0.226	H-atom parameters constrained
S = 1.10	w = 1/[σ^2(Fo^2) + (0.0777P)^2 + 2.7928P] where P = (Fo^2 + 2Fc^2)/3
4617 reflections	(Δ/σ)max = 0.001
247 parameters	Δρmax = 0.85 e Å^−3
0 restraints	Δρmin = −0.37 e Å^−3

Special details

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 (Ų)

	x	y	z	Uiso*/Ueq
S1	0.28987 (19)	0.62771 (3)	0.18681 (7)	0.0520 (3)
O1	1.0846 (7)	0.41553 (9)	0.1427 (2)	0.0689 (8)
O2	0.2040 (6)	0.64395 (9)	0.2825 (2)	0.0639 (7)
O3	0.4997 (10)	0.82164 (13)	0.1892 (4)	0.1150 (14)
N1	0.5178 (7)	0.55192 (10)	0.1319 (2)	0.0503 (7)
N2	0.6805 (6)	0.56988 (9)	0.28267 (19)	0.0440 (6)
N3	0.2691 (10)	0.70843 (12)	0.0456 (3)	0.0814 (12)
C1	0.8087 (7)	0.53035 (10)	0.2602 (2)	0.0429 (7)
C2	1.0008 (8)	0.50354 (12)	0.3125 (3)	0.0509 (8)
H2	1.0697	0.5108	0.3745	0.061*
C3	1.0830 (8)	0.46594 (12)	0.2678 (3)	0.0553 (9)
H3	1.2108	0.4471	0.3005	0.066*
C4	0.9807 (8)	0.45486 (11)	0.1741 (3)	0.0506 (8)
C5	0.7951 (8)	0.48130 (11)	0.1215 (3)	0.0503 (8)
H5	0.7302	0.4741	0.0590	0.060*
C6	0.7077 (7)	0.51995 (10)	0.1669 (2)	0.0430 (7)
C7	0.9808 (13)	0.40132 (16)	0.0497 (3)	0.0821 (14)
H7A	1.0581	0.4198	0.0007	0.123*
H7B	0.7721	0.4027	0.0463	0.123*
H7C	1.0423	0.3718	0.0392	0.123*
C8	0.5114 (7)	0.58028 (11)	0.2024 (2)	0.0457 (7)
C9	0.5748 (8)	0.66390 (12)	0.1477 (3)	0.0566 (9)
H9A	0.7239	0.6669	0.1987	0.068*
H9B	0.6641	0.6520	0.0908	0.068*
C10	0.4424 (8)	0.70796 (12)	0.1243 (3)	0.0521 (8)
C11	0.1534 (12)	0.74665 (16)	0.0195 (3)	0.0826 (14)
H11	0.0277	0.7468	−0.0347	0.099*
C12	0.2018 (11)	0.78517 (14)	0.0647 (3)	0.0683 (11)
C13	0.3896 (13)	0.78359 (14)	0.1456 (4)	0.0778 (13)
C14	0.5068 (10)	0.74393 (13)	0.1791 (3)	0.0622 (10)
C15	0.0700 (16)	0.82688 (18)	0.0263 (5)	0.109 (2)
H15A	0.1288	0.8506	0.0678	0.164*
H15B	0.1355	0.8321	−0.0379	0.164*
H15C	−0.1383	0.8245	0.0246	0.164*
C16	0.319 (2)	0.8389 (3)	0.2528 (7)	0.176 (4)
H16A	0.3030	0.8697	0.2419	0.265*
H16B	0.3940	0.8337	0.3175	0.265*
H16C	0.1305	0.8257	0.2446	0.265*
C17	0.7023 (16)	0.7420 (2)	0.2694 (5)	0.111 (2)
H17A	0.7778	0.7706	0.2835	0.166*
H17B	0.8606	0.7224	0.2591	0.166*
H17C	0.5925	0.7320	0.3229	0.166*
C18	0.7213 (8)	0.59296 (11)	0.3743 (2)	0.0496 (8)
H18A	0.6533	0.6227	0.3662	0.060*
H18B	0.9274	0.5940	0.3916	0.060*
C19	0.5667 (8)	0.57253 (12)	0.4531 (3)	0.0513 (8)
C20	0.4465 (11)	0.55728 (16)	0.5172 (3)	0.0753 (13)
H20	0.3500	0.5450	0.5687	0.090*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
S1	0.0460 (5)	0.0502 (5)	0.0595 (5)	0.0078 (4)	−0.0018 (4)	0.0003 (4)
O1	0.088 (2)	0.0551 (16)	0.0633 (17)	0.0187 (14)	−0.0071 (15)	−0.0094 (13)
O2	0.0613 (16)	0.0595 (16)	0.0722 (18)	0.0094 (13)	0.0213 (14)	−0.0005 (13)
O3	0.120 (3)	0.079 (3)	0.146 (4)	0.000 (2)	0.010 (3)	−0.014 (3)
N1	0.0529 (16)	0.0496 (16)	0.0480 (16)	0.0043 (13)	−0.0043 (13)	0.0003 (13)
N2	0.0474 (15)	0.0406 (14)	0.0437 (14)	−0.0018 (11)	−0.0016 (12)	−0.0024 (11)
N3	0.116 (3)	0.059 (2)	0.068 (2)	0.019 (2)	−0.025 (2)	−0.0048 (18)
C1	0.0421 (16)	0.0386 (16)	0.0480 (17)	−0.0029 (13)	0.0011 (13)	−0.0025 (13)
C2	0.056 (2)	0.0500 (19)	0.0454 (18)	0.0000 (15)	−0.0103 (15)	0.0005 (15)
C3	0.056 (2)	0.0497 (19)	0.059 (2)	0.0065 (16)	−0.0081 (17)	0.0052 (17)
C4	0.054 (2)	0.0419 (17)	0.056 (2)	0.0033 (15)	0.0037 (16)	−0.0010 (15)
C5	0.059 (2)	0.0494 (19)	0.0428 (18)	−0.0024 (16)	−0.0006 (15)	−0.0043 (15)
C6	0.0439 (17)	0.0418 (16)	0.0432 (17)	−0.0022 (13)	−0.0009 (13)	0.0015 (13)
C7	0.117 (4)	0.067 (3)	0.063 (3)	0.016 (3)	0.008 (3)	−0.018 (2)
C8	0.0440 (17)	0.0443 (17)	0.0487 (18)	0.0003 (13)	0.0014 (14)	0.0026 (14)
C9	0.051 (2)	0.054 (2)	0.065 (2)	0.0122 (16)	0.0132 (17)	0.0119 (18)
C10	0.0516 (19)	0.0509 (19)	0.054 (2)	0.0090 (15)	0.0078 (16)	0.0132 (16)
C11	0.110 (4)	0.071 (3)	0.065 (3)	0.016 (3)	−0.027 (3)	0.013 (2)
C12	0.083 (3)	0.056 (2)	0.066 (3)	0.014 (2)	0.008 (2)	0.021 (2)
C13	0.107 (4)	0.047 (2)	0.078 (3)	0.007 (2)	−0.003 (3)	−0.001 (2)
C14	0.074 (3)	0.053 (2)	0.059 (2)	0.0034 (19)	−0.0019 (19)	0.0034 (18)
C15	0.139 (5)	0.074 (3)	0.116 (5)	0.034 (3)	0.003 (4)	0.039 (3)
C16	0.181 (9)	0.200 (10)	0.151 (8)	0.091 (8)	0.044 (7)	−0.020 (7)
C17	0.141 (6)	0.088 (4)	0.100 (4)	0.012 (4)	−0.055 (4)	−0.009 (3)
C18	0.057 (2)	0.0431 (17)	0.0486 (19)	−0.0085 (15)	−0.0021 (15)	−0.0081 (14)
C19	0.056 (2)	0.052 (2)	0.0453 (19)	−0.0034 (16)	−0.0049 (16)	−0.0048 (15)
C20	0.089 (3)	0.085 (3)	0.052 (2)	−0.020 (3)	0.001 (2)	−0.001 (2)

Geometric parameters (Å, º)

S1—O2	1.478 (3)	C7—H7C	0.9600
S1—C8	1.785 (3)	C9—C10	1.513 (5)
S1—C9	1.813 (4)	C9—H9A	0.9700
O1—C4	1.374 (4)	C9—H9B	0.9700
O1—C7	1.423 (5)	C10—C14	1.365 (6)
O3—C16	1.338 (8)	C11—C12	1.351 (6)
O3—C13	1.400 (6)	C11—H11	0.9300
N1—C8	1.307 (4)	C12—C13	1.390 (7)
N1—C6	1.389 (4)	C12—C15	1.504 (6)
N2—C8	1.370 (4)	C13—C14	1.402 (6)
N2—C1	1.388 (4)	C14—C17	1.514 (6)
N2—C18	1.456 (4)	C15—H15A	0.9600
N3—C10	1.325 (5)	C15—H15B	0.9600
N3—C11	1.332 (5)	C15—H15C	0.9600
C1—C2	1.391 (5)	C16—H16A	0.9600
C1—C6	1.392 (5)	C16—H16B	0.9600
C2—C3	1.368 (5)	C16—H16C	0.9600
C2—H2	0.9300	C17—H17A	0.9600
C3—C4	1.402 (5)	C17—H17B	0.9600
C3—H3	0.9300	C17—H17C	0.9600
C4—C5	1.368 (5)	C18—C19	1.461 (5)
C5—C6	1.407 (5)	C18—H18A	0.9700
C5—H5	0.9300	C18—H18B	0.9700
C7—H7A	0.9600	C19—C20	1.158 (6)
C7—H7B	0.9600	C20—H20	0.9300
O2—S1—C8	109.63 (17)	H9A—C9—H9B	108.3
O2—S1—C9	106.11 (18)	N3—C10—C14	124.0 (3)
C8—S1—C9	96.88 (16)	N3—C10—C9	114.3 (4)
C4—O1—C7	116.4 (3)	C14—C10—C9	121.7 (4)
C16—O3—C13	112.9 (7)	N3—C11—C12	126.0 (4)
C8—N1—C6	103.9 (3)	N3—C11—H11	117.0
C8—N2—C1	104.8 (3)	C12—C11—H11	117.0
C8—N2—C18	130.0 (3)	C11—C12—C13	115.4 (4)
C1—N2—C18	125.1 (3)	C11—C12—C15	121.6 (5)
C10—N3—C11	117.0 (4)	C13—C12—C15	123.0 (5)
N2—C1—C2	131.9 (3)	C12—C13—O3	121.5 (4)
N2—C1—C6	106.0 (3)	C12—C13—C14	121.1 (4)
C2—C1—C6	122.1 (3)	O3—C13—C14	116.9 (5)
C3—C2—C1	116.4 (3)	C10—C14—C13	116.5 (4)
C3—C2—H2	121.8	C10—C14—C17	122.5 (4)
C1—C2—H2	121.8	C13—C14—C17	121.0 (4)
C2—C3—C4	122.1 (3)	C12—C15—H15A	109.5
C2—C3—H3	118.9	C12—C15—H15B	109.5
C4—C3—H3	118.9	H15A—C15—H15B	109.5
C5—C4—O1	124.7 (3)	C12—C15—H15C	109.5
C5—C4—C3	122.0 (3)	H15A—C15—H15C	109.5
O1—C4—C3	113.3 (3)	H15B—C15—H15C	109.5
C4—C5—C6	116.4 (3)	O3—C16—H16A	109.5
C4—C5—H5	121.8	O3—C16—H16B	109.5
C6—C5—H5	121.8	H16A—C16—H16B	109.5
N1—C6—C1	110.3 (3)	O3—C16—H16C	109.5
N1—C6—C5	128.7 (3)	H16A—C16—H16C	109.5
C1—C6—C5	121.0 (3)	H16B—C16—H16C	109.5
O1—C7—H7A	109.5	C14—C17—H17A	109.5
O1—C7—H7B	109.5	C14—C17—H17B	109.5
H7A—C7—H7B	109.5	H17A—C17—H17B	109.5
O1—C7—H7C	109.5	C14—C17—H17C	109.5
H7A—C7—H7C	109.5	H17A—C17—H17C	109.5
H7B—C7—H7C	109.5	H17B—C17—H17C	109.5
N1—C8—N2	114.9 (3)	N2—C18—C19	112.8 (3)
N1—C8—S1	118.7 (3)	N2—C18—H18A	109.0
N2—C8—S1	126.4 (3)	C19—C18—H18A	109.0
C10—C9—S1	108.8 (3)	N2—C18—H18B	109.0
C10—C9—H9A	109.9	C19—C18—H18B	109.0
S1—C9—H9A	109.9	H18A—C18—H18B	107.8
C10—C9—H9B	109.9	C20—C19—C18	178.1 (4)
S1—C9—H9B	109.9	C19—C20—H20	180.0
C8—N2—C1—C2	−179.8 (4)	C9—S1—C8—N1	−96.1 (3)
C18—N2—C1—C2	−1.1 (6)	O2—S1—C8—N2	−25.8 (4)
C8—N2—C1—C6	0.4 (3)	C9—S1—C8—N2	84.0 (3)
C18—N2—C1—C6	179.1 (3)	O2—S1—C9—C10	−69.6 (3)
N2—C1—C2—C3	179.4 (4)	C8—S1—C9—C10	177.6 (3)
C6—C1—C2—C3	−0.8 (5)	C11—N3—C10—C14	0.1 (7)
C1—C2—C3—C4	0.2 (6)	C11—N3—C10—C9	−178.0 (4)
C7—O1—C4—C5	−2.2 (6)	S1—C9—C10—N3	−69.5 (4)
C7—O1—C4—C3	177.6 (4)	S1—C9—C10—C14	112.3 (4)
C2—C3—C4—C5	0.8 (6)	C10—N3—C11—C12	1.6 (9)
C2—C3—C4—O1	−179.0 (4)	N3—C11—C12—C13	−0.3 (9)
O1—C4—C5—C6	178.7 (3)	N3—C11—C12—C15	177.1 (6)
C3—C4—C5—C6	−1.1 (5)	C11—C12—C13—O3	168.6 (5)
C8—N1—C6—C1	0.6 (4)	C15—C12—C13—O3	−8.8 (8)
C8—N1—C6—C5	179.6 (3)	C11—C12—C13—C14	−2.8 (8)
N2—C1—C6—N1	−0.6 (4)	C15—C12—C13—C14	179.8 (5)
C2—C1—C6—N1	179.5 (3)	C16—O3—C13—C12	84.8 (8)
N2—C1—C6—C5	−179.7 (3)	C16—O3—C13—C14	−103.5 (7)
C2—C1—C6—C5	0.5 (5)	N3—C10—C14—C13	−3.0 (7)
C4—C5—C6—N1	−178.4 (3)	C9—C10—C14—C13	175.0 (4)
C4—C5—C6—C1	0.5 (5)	N3—C10—C14—C17	179.1 (5)
C6—N1—C8—N2	−0.4 (4)	C9—C10—C14—C17	−3.0 (7)
C6—N1—C8—S1	179.7 (2)	C12—C13—C14—C10	4.3 (7)
C1—N2—C8—N1	0.0 (4)	O3—C13—C14—C10	−167.4 (4)
C18—N2—C8—N1	−178.6 (3)	C12—C13—C14—C17	−177.7 (5)
C1—N2—C8—S1	179.9 (2)	O3—C13—C14—C17	10.6 (8)
C18—N2—C8—S1	1.3 (5)	C8—N2—C18—C19	104.5 (4)
O2—S1—C8—N1	154.0 (3)	C1—N2—C18—C19	−73.8 (4)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
C9—H9A···O2^i	0.97	2.56	3.441 (5)	152

Symmetry code: (i) x+1, y, z.