Crystal structure of 3-(2-hy­droxy­eth­yl)-2-methyl­sulfanyl-6-nitro-3H-benzimidazol-1-ium chloride monohydrate

The title hydrated salt, C₁₀H₁₂N₃O₃S⁺·Cl⁻·H₂O, forms centrosymmetric (20) dimers through inter­molecular C—H...O hydrogen bonds. These dimers are stacked via N—H...O and O—H...Cl hydrogen bonds involving the water mol­ecules and chloride anions. Offset π–π inter­actions are also present.

Key indicators

• Single-crystal X-ray study
• T = 298 K
• Mean [sigma](C-C) = 0.002 Å
• R factor = 0.037
• wR factor = 0.110
• Data-to-parameter ratio = 21.1

checkCIF/PLATON results

No syntax errors found



Datablock: I


Alert level C
PLAT910_ALERT_3_C Missing # of FCF Reflection(s) Below Theta(Min)          10 Note
PLAT911_ALERT_3_C Missing # FCF Refl Between THmin & STh/L=  0.600         13 Report
PLAT913_ALERT_3_C Missing # of Very Strong Reflections in FCF ....          8 Note

Alert level G
PLAT002_ALERT_2_G Number of Distance or Angle Restraints on AtSite          3 Note
PLAT007_ALERT_5_G Number of Unrefined Donor-H Atoms ..............          2 Report
PLAT172_ALERT_4_G The CIF-Embedded .res File Contains DFIX Records          1 Report
PLAT790_ALERT_4_G Centre of Gravity not Within Unit Cell: Resd.  #          3 Note
              H2 O
PLAT860_ALERT_3_G Number of Least-Squares Restraints .............          2 Note
PLAT912_ALERT_4_G Missing # of FCF Reflections Above STh/L=  0.600         18 Note
PLAT978_ALERT_2_G Number C-C Bonds with Positive Residual Density           6 Note

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

   0 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
   2 ALERT type 2 Indicator that the structure model may be wrong or deficient
   4 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

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Computing details

Data collection: COLLECT (Hooft, 1998); cell refinement: DENZO/SCALEPACK (Otwinowski & Minor, 1997); data reduction: DENZO/SCALEPACK (Otwinowski & Minor, 1997); program(s) used to solve structure: SIR94 (Burla et al., 2005); program(s) used to refine structure: SHELXL2014 (Sheldrick, 2015); molecular graphics: PLATON (Spek, 2009); software used to prepare material for publication: SHELXL2014 (Sheldrick, 2015), publCIF (Westrip, 2010) and WinGX (Farrugia, 2012).

3-(2-Hydroxyethyl)-2-methylsulfanyl-6-nitro-3H-benzimidazol-1-ium chloride monohydrate

Crystal data

C10H12N3O3S^+·Cl^−·H2O	F(000) = 640
Mr = 307.75	Dx = 1.534 Mg m^−3
Monoclinic, P21/c	Melting point: 425 K
Hall symbol: -P 2ybc	Mo Kα radiation, λ = 0.71073 Å
a = 8.8587 (5) Å	Cell parameters from 15850 reflections
b = 22.1427 (8) Å	θ = 4.1–30.1°
c = 7.1657 (2) Å	µ = 0.46 mm^−1
β = 108.497 (3)°	T = 298 K
V = 1332.98 (10) Å^3	Block, yellow
Z = 4	0.30 × 0.15 × 0.10 mm

Data collection

Nonius KappaCCD diffractometer	3030 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tube	Rint = 0.029
Graphite monochromator	θmax = 30.1°, θmin = 4.1°
f and ω scans	h = −12→12
15850 measured reflections	k = −31→31
3856 independent reflections	l = −9→9

Refinement

Refinement on F^2	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: mixed
R[F^2 > 2σ(F^2)] = 0.037	H atoms treated by a mixture of independent and constrained refinement
wR(F^2) = 0.110	w = 1/[σ^2(Fo^2) + (0.0512P)^2 + 0.4116P] where P = (Fo^2 + 2Fc^2)/3
S = 1.06	(Δ/σ)max < 0.001
3856 reflections	Δρmax = 0.29 e Å^−3
183 parameters	Δρmin = −0.24 e Å^−3
2 restraints	Extinction correction: SHELXL2014 (Sheldrick 2015, Fc^*=kFc[1+0.001xFc^2λ^3/sin(2θ)]^-1/4
48 constraints	Extinction coefficient: 0.010 (3)
Primary atom site location: structure-invariant direct methods

Special details

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 > 2σ(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 (Ų)

	x	y	z	Uiso*/Ueq
Cl1	0.13738 (5)	0.08560 (2)	0.42268 (6)	0.05068 (14)
S2	0.57871 (5)	0.21143 (2)	0.26622 (7)	0.04747 (14)
O3	−0.15176 (14)	0.05681 (6)	0.56505 (18)	0.0472 (3)
N4	0.36705 (14)	0.12789 (5)	0.06943 (17)	0.0345 (3)
O5	0.1477 (2)	0.20574 (6)	0.1828 (3)	0.0718 (4)
H5	0.1668	0.1773	0.2603	0.108*
O6	0.45778 (19)	−0.14042 (6)	0.3012 (2)	0.0634 (4)
C7	0.34801 (17)	−0.05387 (6)	0.1321 (2)	0.0342 (3)
O8	0.24519 (18)	−0.14988 (6)	0.0528 (2)	0.0679 (4)
N9	0.56755 (14)	0.08753 (5)	0.29958 (17)	0.0314 (2)
H9	0.6563	0.0838	0.3931	0.038*
C10	0.33709 (16)	0.06625 (6)	0.06760 (19)	0.0313 (3)
C11	0.50505 (17)	0.13941 (6)	0.2131 (2)	0.0333 (3)
N12	0.35085 (17)	−0.11931 (6)	0.1646 (2)	0.0430 (3)
C13	0.46514 (15)	0.04077 (6)	0.21301 (19)	0.0288 (3)
C14	0.1141 (2)	0.18374 (9)	−0.0101 (3)	0.0561 (5)
H14A	0.0477	0.2127	−0.1014	0.067*
H14B	0.0548	0.1463	−0.0229	0.067*
C15	0.21856 (18)	−0.02957 (7)	−0.0142 (2)	0.0395 (3)
H15	0.1372	−0.0546	−0.0881	0.047*
C16	0.47534 (16)	−0.02074 (6)	0.2500 (2)	0.0310 (3)
H16	0.5606	−0.0383	0.3459	0.037*
C17	0.26321 (19)	0.17270 (8)	−0.0631 (2)	0.0443 (4)
H17A	0.2347	0.1583	−0.1977	0.053*
H17B	0.3207	0.2104	−0.0550	0.053*
C18	0.21161 (17)	0.03179 (7)	−0.0491 (2)	0.0390 (3)
H18	0.1269	0.0493	−0.1461	0.047*
C19	0.7761 (2)	0.19682 (8)	0.4278 (3)	0.0560 (5)
H19A	0.7703	0.1756	0.5421	0.084*
H19B	0.8311	0.2344	0.4673	0.084*
H19C	0.8327	0.1727	0.3606	0.084*
H3B	−0.076 (2)	0.0647 (10)	0.524 (3)	0.060 (6)*
H3A	−0.152 (3)	0.0212 (7)	0.573 (4)	0.070 (8)*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
Cl1	0.0492 (2)	0.0521 (3)	0.0514 (2)	−0.00027 (17)	0.01683 (18)	0.00853 (17)
S2	0.0580 (3)	0.02568 (18)	0.0586 (3)	−0.00229 (15)	0.0185 (2)	−0.00067 (15)
O3	0.0382 (6)	0.0495 (7)	0.0520 (7)	0.0023 (5)	0.0116 (5)	0.0069 (5)
N4	0.0362 (6)	0.0320 (6)	0.0354 (6)	0.0051 (4)	0.0116 (5)	0.0048 (4)
O5	0.1054 (13)	0.0430 (7)	0.0891 (11)	0.0073 (7)	0.0620 (10)	0.0007 (7)
O6	0.0788 (10)	0.0336 (6)	0.0715 (9)	−0.0019 (6)	0.0152 (7)	0.0062 (6)
C7	0.0393 (7)	0.0307 (6)	0.0376 (7)	−0.0053 (5)	0.0193 (6)	−0.0049 (5)
O8	0.0661 (9)	0.0436 (7)	0.0917 (11)	−0.0218 (6)	0.0217 (8)	−0.0198 (7)
N9	0.0322 (6)	0.0264 (5)	0.0335 (6)	−0.0009 (4)	0.0075 (4)	−0.0016 (4)
C10	0.0325 (6)	0.0329 (6)	0.0299 (6)	0.0013 (5)	0.0119 (5)	0.0003 (5)
C11	0.0380 (7)	0.0283 (6)	0.0360 (7)	0.0018 (5)	0.0150 (5)	0.0011 (5)
N12	0.0507 (8)	0.0323 (6)	0.0540 (8)	−0.0091 (5)	0.0278 (6)	−0.0085 (6)
C13	0.0276 (6)	0.0301 (6)	0.0296 (6)	−0.0013 (5)	0.0103 (5)	−0.0019 (5)
C14	0.0517 (10)	0.0490 (10)	0.0725 (12)	0.0175 (8)	0.0269 (9)	0.0167 (9)
C15	0.0352 (7)	0.0463 (8)	0.0379 (7)	−0.0097 (6)	0.0129 (6)	−0.0094 (6)
C16	0.0330 (6)	0.0297 (6)	0.0322 (6)	−0.0002 (5)	0.0128 (5)	−0.0003 (5)
C17	0.0451 (8)	0.0437 (8)	0.0447 (8)	0.0122 (7)	0.0151 (7)	0.0151 (7)
C18	0.0317 (7)	0.0491 (8)	0.0335 (7)	0.0004 (6)	0.0066 (5)	−0.0011 (6)
C19	0.0531 (10)	0.0394 (8)	0.0723 (12)	−0.0149 (7)	0.0153 (9)	−0.0057 (8)

Geometric parameters (Å, º)

S2—C11	1.7194 (14)	N9—H9	0.8600
S2—C19	1.794 (2)	C10—C18	1.388 (2)
O3—H3B	0.833 (16)	C10—C13	1.3932 (18)
O3—H3A	0.792 (16)	C13—C16	1.3849 (18)
N4—C11	1.3492 (18)	C14—C17	1.506 (2)
N4—C10	1.3898 (18)	C14—H14A	0.9700
N4—C17	1.4758 (18)	C14—H14B	0.9700
O5—C14	1.405 (3)	C15—C18	1.379 (2)
O5—H5	0.8200	C15—H15	0.9300
O6—N12	1.219 (2)	C16—H16	0.9300
C7—C16	1.3853 (19)	C17—H17A	0.9700
C7—C15	1.393 (2)	C17—H17B	0.9700
C7—N12	1.4667 (19)	C18—H18	0.9300
O8—N12	1.2251 (18)	C19—H19A	0.9600
N9—C11	1.3390 (17)	C19—H19B	0.9600
N9—C13	1.3867 (16)	C19—H19C	0.9600
C11—S2—C19	101.51 (8)	C17—C14—H14A	109.2
H3B—O3—H3A	105 (2)	O5—C14—H14B	109.2
C11—N4—C10	108.48 (11)	C17—C14—H14B	109.2
C11—N4—C17	126.35 (13)	H14A—C14—H14B	107.9
C10—N4—C17	125.16 (12)	C18—C15—C7	119.69 (13)
C14—O5—H5	109.5	C18—C15—H15	120.2
C16—C7—C15	124.82 (13)	C7—C15—H15	120.2
C16—C7—N12	117.17 (13)	C13—C16—C7	114.40 (12)
C15—C7—N12	118.01 (13)	C13—C16—H16	122.8
C11—N9—C13	108.53 (11)	C7—C16—H16	122.8
C11—N9—H9	125.7	N4—C17—C14	111.36 (13)
C13—N9—H9	125.7	N4—C17—H17A	109.4
C18—C10—N4	131.27 (13)	C14—C17—H17A	109.4
C18—C10—C13	122.29 (13)	N4—C17—H17B	109.4
N4—C10—C13	106.44 (11)	C14—C17—H17B	109.4
N9—C11—N4	109.42 (12)	H17A—C17—H17B	108.0
N9—C11—S2	128.39 (11)	C15—C18—C10	116.82 (13)
N4—C11—S2	122.18 (11)	C15—C18—H18	121.6
O6—N12—O8	123.47 (15)	C10—C18—H18	121.6
O6—N12—C7	118.44 (13)	S2—C19—H19A	109.5
O8—N12—C7	118.09 (15)	S2—C19—H19B	109.5
C16—C13—N9	130.92 (12)	H19A—C19—H19B	109.5
C16—C13—C10	121.98 (12)	S2—C19—H19C	109.5
N9—C13—C10	107.10 (11)	H19A—C19—H19C	109.5
O5—C14—C17	112.04 (17)	H19B—C19—H19C	109.5
O5—C14—H14A	109.2
C11—N4—C10—C18	179.32 (14)	C11—N9—C13—C10	0.53 (15)
C17—N4—C10—C18	−0.1 (2)	C18—C10—C13—C16	0.1 (2)
C11—N4—C10—C13	−1.53 (14)	N4—C10—C13—C16	−179.10 (12)
C17—N4—C10—C13	179.07 (13)	C18—C10—C13—N9	179.86 (12)
C13—N9—C11—N4	−1.51 (15)	N4—C10—C13—N9	0.61 (14)
C13—N9—C11—S2	178.15 (11)	C16—C7—C15—C18	−0.1 (2)
C10—N4—C11—N9	1.90 (15)	N12—C7—C15—C18	179.95 (13)
C17—N4—C11—N9	−178.70 (13)	N9—C13—C16—C7	179.86 (13)
C10—N4—C11—S2	−177.78 (10)	C10—C13—C16—C7	−0.51 (19)
C17—N4—C11—S2	1.6 (2)	C15—C7—C16—C13	0.5 (2)
C19—S2—C11—N9	11.50 (16)	N12—C7—C16—C13	−179.58 (12)
C19—S2—C11—N4	−168.88 (13)	C11—N4—C17—C14	−106.73 (18)
C16—C7—N12—O6	5.1 (2)	C10—N4—C17—C14	72.56 (19)
C15—C7—N12—O6	−174.94 (15)	O5—C14—C17—N4	60.0 (2)
C16—C7—N12—O8	−174.90 (14)	C7—C15—C18—C10	−0.2 (2)
C15—C7—N12—O8	5.0 (2)	N4—C10—C18—C15	179.29 (14)
C11—N9—C13—C16	−179.79 (14)	C13—C10—C18—C15	0.3 (2)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
O5—H5···Cl1	0.82	2.40	3.1840 (15)	161
C17—H17B···S2	0.97	2.68	3.1514 (18)	110
O3—H3B···Cl1	0.83 (2)	2.28 (2)	3.1090 (14)	178 (2)
O3—H3A···Cl1^i	0.79 (2)	2.37 (2)	3.1561 (14)	174 (2)
C14—H14B···O8^ii	0.97	2.60	3.189 (2)	119
N9—H9···O3^iii	0.86	1.85	2.6949 (16)	165

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