organic compounds
(S)-2-(2-Pyrrolidinio)-1H-benzimidazol-3-ium dichloride monohydrate
aOrdered Matter Science Research Center, College of Chemistry and Chemical Engineering, Southeast University, Nanjing 210096, People's Republic of China
*Correspondence e-mail: fudavid88@yahoo.com.cn
In the title compound, C11H15N32+·2Cl−·H2O, one N atom of the imidazole ring and the N atom of the pyrrolidine ring are protonated. The is stabilized by aromatic π–π interactions between the benzene rings of neighbouring benzimidazole systems [centroid–centroid duistance = 3.712 (2) Å]. The is further stabilized by intermolecular N—H⋯Cl, O—H⋯Cl and N—H⋯O hydrogen bonds.
Related literature
For proline derivatives, see: Fu et al. (2007); Aminabhavi et al. (1986). For related structures, see: Dai & Fu (2008a,b); Fu & Ye (2007).
Experimental
Crystal data
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Refinement
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Data collection: CrystalClear (Rigaku, 2005); cell CrystalClear; data reduction: CrystalClear; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 (Farrugia, 1997) and DIAMOND (Brandenburg, 1998); software used to prepare material for publication: SHELXTL (Sheldrick, 2008).
Supporting information
10.1107/S1600536809019084/lx2100sup1.cif
contains datablocks I, global. DOI:Structure factors: contains datablock I. DOI: 10.1107/S1600536809019084/lx2100Isup2.hkl
The homochiral ligand (S)-2-(pyrrolidin-2-yl)-1H-benzimidazole was synthesized by reaction of S-pyrrolidine-2-carboxylic acid and benzene-1,2-diamine according to the procedure described in the literature(Aminabhavi, et al.(1986)). Then (S)-2-(pyrrolidin-2-yl)-1H-benzimidazole (3 mmol) was dissolved in the solution of distilled water (20 ml) and hydrochloric acid (1 ml) and evaporated in the air affording colorless block crystals of this compound suitable for X-ray analysis.
All H atoms attached to C, N and O atoms were fixed geometrically and treated as riding with C—H = 0.93 Å (aromatic), 0.97 Å (methylene) or 0.98 Å (methine) and N—H = 0.90 Å (N3), 0.86 Å (N1, N2) and O—H = 0.85 Å with Uiso(H) = 1.2Ueq(C,N) and Uiso(H) = 1.5Ueq(O). The distances of O1W—H were restrained to 0.85 (1) Å using command DFIX.
Data collection: CrystalClear (Rigaku, 2005); cell
CrystalClear (Rigaku, 2005); data reduction: CrystalClear (Rigaku, 2005); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 (Farrugia, 1997) and DIAMOND (Brandenburg, 1998); software used to prepare material for publication: SHELXTL (Sheldrick, 2008).Fig. 1. A view of the title compound with the atomic numbering scheme. Displacement ellipsoids were drawn at the 30% probability level. | |
Fig. 2. The π–π, N—H···Cl, O—H···Cl and N—H···O interactions (dotted line) in the title compound. Cg denotes the ring centroid of the C1-C6 benzene ring. [Symmetry codes: (i) -x+1, -y+1, -z+1; (ii) x-1, y, z-1; (iii) x, y+1, z; (iv) x, y, z-1; (v) -x, -y+1, -z; (vi) x+1, -y+2, -z+1; (vii) x, y-1, z; (viii) x, y, z+1; (ix) -x+1, -y+1, -z.] |
C11H15N32+·2Cl−·H2O | Z = 2 |
Mr = 278.18 | F(000) = 292 |
Triclinic, P1 | Dx = 1.361 Mg m−3 |
Hall symbol: -P 1 | Mo Kα radiation, λ = 0.71073 Å |
a = 7.493 (2) Å | Cell parameters from 3108 reflections |
b = 9.739 (2) Å | θ = 3.1–27.5° |
c = 9.937 (2) Å | µ = 0.47 mm−1 |
α = 99.23 (3)° | T = 293 K |
β = 95.73 (3)° | Block, colorless |
γ = 106.27 (3)° | 0.35 × 0.30 × 0.15 mm |
V = 679.0 (3) Å3 |
Rigaku Mercury2 diffractometer | 3108 independent reflections |
Radiation source: fine-focus sealed tube | 2310 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.037 |
Detector resolution: 13.6612 pixels mm-1 | θmax = 27.5°, θmin = 3.1° |
CCD profile fitting scans | h = −9→9 |
Absorption correction: multi-scan (CrystalClear; Rigaku, 2005) | k = −12→12 |
Tmin = 0.959, Tmax = 0.982 | l = −12→12 |
7119 measured reflections |
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)] = 0.050 | Hydrogen site location: difference Fourier map |
wR(F2) = 0.120 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.08 | w = 1/[σ2(Fo2) + (0.0354P)2 + 0.3615P] where P = (Fo2 + 2Fc2)/3 |
3108 reflections | (Δ/σ)max < 0.001 |
162 parameters | Δρmax = 0.28 e Å−3 |
2 restraints | Δρmin = −0.24 e Å−3 |
C11H15N32+·2Cl−·H2O | γ = 106.27 (3)° |
Mr = 278.18 | V = 679.0 (3) Å3 |
Triclinic, P1 | Z = 2 |
a = 7.493 (2) Å | Mo Kα radiation |
b = 9.739 (2) Å | µ = 0.47 mm−1 |
c = 9.937 (2) Å | T = 293 K |
α = 99.23 (3)° | 0.35 × 0.30 × 0.15 mm |
β = 95.73 (3)° |
Rigaku Mercury2 diffractometer | 3108 independent reflections |
Absorption correction: multi-scan (CrystalClear; Rigaku, 2005) | 2310 reflections with I > 2σ(I) |
Tmin = 0.959, Tmax = 0.982 | Rint = 0.037 |
7119 measured reflections |
R[F2 > 2σ(F2)] = 0.050 | 2 restraints |
wR(F2) = 0.120 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.08 | Δρmax = 0.28 e Å−3 |
3108 reflections | Δρmin = −0.24 e Å−3 |
162 parameters |
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. |
x | y | z | Uiso*/Ueq | ||
Cl1 | 0.81735 (10) | 0.00616 (8) | 0.30163 (7) | 0.0600 (2) | |
Cl2 | 0.79242 (9) | 0.58762 (8) | 0.97152 (7) | 0.0597 (2) | |
N1 | 0.2136 (3) | 0.5855 (2) | 0.31035 (18) | 0.0390 (4) | |
H1 | 0.2058 | 0.5445 | 0.2257 | 0.047* | |
N2 | 0.2230 (3) | 0.7465 (2) | 0.48963 (18) | 0.0414 (5) | |
H2A | 0.2224 | 0.8269 | 0.5400 | 0.050* | |
N3 | 0.1820 (3) | 0.7775 (2) | 0.11964 (19) | 0.0425 (5) | |
H3A | 0.0823 | 0.7024 | 0.0759 | 0.051* | |
H3B | 0.2875 | 0.7518 | 0.1123 | 0.051* | |
C1 | 0.2450 (3) | 0.6267 (3) | 0.5381 (2) | 0.0405 (5) | |
C2 | 0.2697 (4) | 0.5979 (3) | 0.6704 (3) | 0.0573 (7) | |
H2 | 0.2738 | 0.6666 | 0.7483 | 0.069* | |
C3 | 0.2877 (4) | 0.4640 (4) | 0.6804 (3) | 0.0662 (8) | |
H3 | 0.3058 | 0.4419 | 0.7674 | 0.079* | |
C4 | 0.2798 (4) | 0.3597 (3) | 0.5650 (3) | 0.0628 (8) | |
H4 | 0.2919 | 0.2697 | 0.5766 | 0.075* | |
C5 | 0.2546 (4) | 0.3866 (3) | 0.4338 (3) | 0.0537 (6) | |
H5 | 0.2481 | 0.3169 | 0.3562 | 0.064* | |
C6 | 0.2394 (3) | 0.5228 (2) | 0.4234 (2) | 0.0379 (5) | |
C7 | 0.2029 (3) | 0.7186 (2) | 0.3528 (2) | 0.0364 (5) | |
C8 | 0.1637 (3) | 0.8211 (3) | 0.2668 (2) | 0.0409 (5) | |
H8 | 0.0341 | 0.8225 | 0.2709 | 0.049* | |
C9 | 0.2916 (4) | 0.9767 (3) | 0.3080 (3) | 0.0529 (6) | |
H9A | 0.4185 | 0.9793 | 0.3426 | 0.063* | |
H9B | 0.2454 | 1.0327 | 0.3786 | 0.063* | |
C10 | 0.2868 (6) | 1.0359 (3) | 0.1762 (3) | 0.0755 (9) | |
H10A | 0.2191 | 1.1077 | 0.1822 | 0.091* | |
H10B | 0.4137 | 1.0822 | 0.1609 | 0.091* | |
C11 | 0.1905 (5) | 0.9111 (3) | 0.0618 (3) | 0.0666 (8) | |
H11A | 0.2606 | 0.9135 | −0.0152 | 0.080* | |
H11B | 0.0648 | 0.9134 | 0.0302 | 0.080* | |
O1W | 0.5254 (3) | 0.7671 (3) | 0.0856 (3) | 0.0863 (8) | |
H1A | 0.613 (4) | 0.832 (3) | 0.142 (3) | 0.117 (16)* | |
H1B | 0.572 (5) | 0.707 (3) | 0.043 (3) | 0.102 (13)* |
U11 | U22 | U33 | U12 | U13 | U23 | |
Cl1 | 0.0704 (5) | 0.0589 (4) | 0.0530 (4) | 0.0339 (4) | 0.0092 (3) | −0.0076 (3) |
Cl2 | 0.0536 (4) | 0.0722 (5) | 0.0447 (4) | 0.0234 (3) | 0.0033 (3) | −0.0186 (3) |
N1 | 0.0487 (11) | 0.0378 (10) | 0.0303 (9) | 0.0166 (9) | 0.0067 (8) | −0.0010 (7) |
N2 | 0.0501 (11) | 0.0408 (11) | 0.0331 (10) | 0.0182 (9) | 0.0101 (8) | −0.0037 (8) |
N3 | 0.0439 (11) | 0.0448 (11) | 0.0382 (10) | 0.0161 (9) | 0.0007 (8) | 0.0050 (8) |
C1 | 0.0378 (12) | 0.0459 (13) | 0.0378 (12) | 0.0124 (10) | 0.0106 (9) | 0.0056 (10) |
C2 | 0.0588 (16) | 0.0740 (19) | 0.0380 (13) | 0.0176 (14) | 0.0137 (12) | 0.0085 (13) |
C3 | 0.0662 (19) | 0.086 (2) | 0.0546 (17) | 0.0220 (17) | 0.0159 (14) | 0.0355 (16) |
C4 | 0.0642 (18) | 0.0557 (17) | 0.077 (2) | 0.0197 (14) | 0.0146 (15) | 0.0316 (15) |
C5 | 0.0593 (16) | 0.0436 (14) | 0.0600 (17) | 0.0172 (12) | 0.0119 (13) | 0.0104 (12) |
C6 | 0.0380 (12) | 0.0374 (12) | 0.0381 (12) | 0.0111 (10) | 0.0082 (9) | 0.0052 (9) |
C7 | 0.0357 (11) | 0.0376 (12) | 0.0350 (11) | 0.0123 (9) | 0.0076 (9) | 0.0010 (9) |
C8 | 0.0392 (12) | 0.0445 (13) | 0.0420 (13) | 0.0197 (10) | 0.0086 (10) | 0.0031 (10) |
C9 | 0.0599 (16) | 0.0413 (14) | 0.0550 (16) | 0.0156 (12) | 0.0086 (13) | 0.0021 (11) |
C10 | 0.110 (3) | 0.0456 (16) | 0.069 (2) | 0.0160 (17) | 0.0164 (18) | 0.0150 (14) |
C11 | 0.092 (2) | 0.0606 (18) | 0.0564 (18) | 0.0338 (17) | 0.0045 (16) | 0.0239 (14) |
O1W | 0.0539 (13) | 0.0682 (15) | 0.125 (2) | 0.0221 (12) | 0.0145 (14) | −0.0227 (14) |
N1—C7 | 1.324 (3) | C4—H4 | 0.9300 |
N1—C6 | 1.384 (3) | C5—C6 | 1.381 (3) |
N1—H1 | 0.8600 | C5—H5 | 0.9300 |
N2—C7 | 1.327 (3) | C7—C8 | 1.484 (3) |
N2—C1 | 1.376 (3) | C8—C9 | 1.514 (3) |
N2—H2A | 0.8600 | C8—H8 | 0.9800 |
N3—C8 | 1.487 (3) | C9—C10 | 1.514 (4) |
N3—C11 | 1.492 (3) | C9—H9A | 0.9700 |
N3—H3A | 0.9000 | C9—H9B | 0.9700 |
N3—H3B | 0.9000 | C10—C11 | 1.481 (4) |
C1—C6 | 1.386 (3) | C10—H10A | 0.9700 |
C1—C2 | 1.393 (3) | C10—H10B | 0.9700 |
C2—C3 | 1.366 (4) | C11—H11A | 0.9700 |
C2—H2 | 0.9300 | C11—H11B | 0.9700 |
C3—C4 | 1.389 (4) | O1W—H1A | 0.85 (3) |
C3—H3 | 0.9300 | O1W—H1B | 0.84 (3) |
C4—C5 | 1.375 (4) | ||
C7—N1—C6 | 109.38 (18) | N1—C6—C1 | 105.90 (19) |
C7—N1—H1 | 125.3 | N1—C7—N2 | 108.91 (19) |
C6—N1—H1 | 125.3 | N1—C7—C8 | 127.69 (19) |
C7—N2—C1 | 109.25 (18) | N2—C7—C8 | 123.30 (19) |
C7—N2—H2A | 125.4 | C7—C8—N3 | 112.88 (18) |
C1—N2—H2A | 125.4 | C7—C8—C9 | 115.7 (2) |
C8—N3—C11 | 104.06 (19) | N3—C8—C9 | 103.78 (19) |
C8—N3—H3A | 110.9 | C7—C8—H8 | 108.1 |
C11—N3—H3A | 110.9 | N3—C8—H8 | 108.1 |
C8—N3—H3B | 110.9 | C9—C8—H8 | 108.1 |
C11—N3—H3B | 110.9 | C8—C9—C10 | 104.4 (2) |
H3A—N3—H3B | 109.0 | C8—C9—H9A | 110.9 |
N2—C1—C6 | 106.55 (19) | C10—C9—H9A | 110.9 |
N2—C1—C2 | 132.8 (2) | C8—C9—H9B | 110.9 |
C6—C1—C2 | 120.7 (2) | C10—C9—H9B | 110.9 |
C3—C2—C1 | 116.9 (3) | H9A—C9—H9B | 108.9 |
C3—C2—H2 | 121.6 | C11—C10—C9 | 107.4 (2) |
C1—C2—H2 | 121.6 | C11—C10—H10A | 110.2 |
C2—C3—C4 | 122.2 (3) | C9—C10—H10A | 110.2 |
C2—C3—H3 | 118.9 | C11—C10—H10B | 110.2 |
C4—C3—H3 | 118.9 | C9—C10—H10B | 110.2 |
C5—C4—C3 | 121.5 (3) | H10A—C10—H10B | 108.5 |
C5—C4—H4 | 119.3 | C10—C11—N3 | 105.7 (2) |
C3—C4—H4 | 119.3 | C10—C11—H11A | 110.6 |
C4—C5—C6 | 116.5 (3) | N3—C11—H11A | 110.6 |
C4—C5—H5 | 121.8 | C10—C11—H11B | 110.6 |
C6—C5—H5 | 121.8 | N3—C11—H11B | 110.6 |
C5—C6—N1 | 131.8 (2) | H11A—C11—H11B | 108.7 |
C5—C6—C1 | 122.3 (2) | H1A—O1W—H1B | 109 (4) |
C7—N2—C1—C6 | 0.6 (2) | C6—N1—C7—N2 | 0.8 (2) |
C7—N2—C1—C2 | −179.6 (3) | C6—N1—C7—C8 | −175.7 (2) |
N2—C1—C2—C3 | −179.8 (3) | C1—N2—C7—N1 | −0.9 (3) |
C6—C1—C2—C3 | 0.0 (4) | C1—N2—C7—C8 | 175.8 (2) |
C1—C2—C3—C4 | −0.7 (4) | N1—C7—C8—N3 | −14.5 (3) |
C2—C3—C4—C5 | 0.4 (5) | N2—C7—C8—N3 | 169.4 (2) |
C3—C4—C5—C6 | 0.6 (4) | N1—C7—C8—C9 | −133.8 (2) |
C4—C5—C6—N1 | −180.0 (2) | N2—C7—C8—C9 | 50.1 (3) |
C4—C5—C6—C1 | −1.3 (4) | C11—N3—C8—C7 | −164.9 (2) |
C7—N1—C6—C5 | 178.4 (3) | C11—N3—C8—C9 | −38.9 (2) |
C7—N1—C6—C1 | −0.4 (2) | C7—C8—C9—C10 | 154.4 (2) |
N2—C1—C6—C5 | −179.1 (2) | N3—C8—C9—C10 | 30.1 (3) |
C2—C1—C6—C5 | 1.1 (4) | C8—C9—C10—C11 | −10.2 (3) |
N2—C1—C6—N1 | −0.1 (2) | C9—C10—C11—N3 | −13.5 (4) |
C2—C1—C6—N1 | −180.0 (2) | C8—N3—C11—C10 | 32.6 (3) |
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1···Cl2i | 0.86 | 2.17 | 3.018 (2) | 169 |
N2—H2A···Cl1i | 0.86 | 2.18 | 3.021 (2) | 166 |
N3—H3A···Cl2ii | 0.90 | 2.20 | 3.058 (2) | 158 |
N3—H3B···O1W | 0.90 | 1.80 | 2.656 (3) | 159 |
O1W—H1A···Cl1iii | 0.85 (3) | 2.22 (3) | 3.069 (3) | 174 (4) |
O1W—H1B···Cl2iv | 0.84 (3) | 2.37 (4) | 3.181 (2) | 161 (4) |
Symmetry codes: (i) −x+1, −y+1, −z+1; (ii) x−1, y, z−1; (iii) x, y+1, z; (iv) x, y, z−1. |
Experimental details
Crystal data | |
Chemical formula | C11H15N32+·2Cl−·H2O |
Mr | 278.18 |
Crystal system, space group | Triclinic, P1 |
Temperature (K) | 293 |
a, b, c (Å) | 7.493 (2), 9.739 (2), 9.937 (2) |
α, β, γ (°) | 99.23 (3), 95.73 (3), 106.27 (3) |
V (Å3) | 679.0 (3) |
Z | 2 |
Radiation type | Mo Kα |
µ (mm−1) | 0.47 |
Crystal size (mm) | 0.35 × 0.30 × 0.15 |
Data collection | |
Diffractometer | Rigaku Mercury2 diffractometer |
Absorption correction | Multi-scan (CrystalClear; Rigaku, 2005) |
Tmin, Tmax | 0.959, 0.982 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 7119, 3108, 2310 |
Rint | 0.037 |
(sin θ/λ)max (Å−1) | 0.649 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.050, 0.120, 1.08 |
No. of reflections | 3108 |
No. of parameters | 162 |
No. of restraints | 2 |
H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
Δρmax, Δρmin (e Å−3) | 0.28, −0.24 |
Computer programs: CrystalClear (Rigaku, 2005), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), ORTEP-3 (Farrugia, 1997) and DIAMOND (Brandenburg, 1998), SHELXTL (Sheldrick, 2008).
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1···Cl2i | 0.86 | 2.17 | 3.018 (2) | 169.3 |
N2—H2A···Cl1i | 0.86 | 2.18 | 3.021 (2) | 165.6 |
N3—H3A···Cl2ii | 0.90 | 2.20 | 3.058 (2) | 158.2 |
N3—H3B···O1W | 0.90 | 1.80 | 2.656 (3) | 158.9 |
O1W—H1A···Cl1iii | 0.85 (3) | 2.22 (3) | 3.069 (3) | 174 (4) |
O1W—H1B···Cl2iv | 0.84 (3) | 2.37 (4) | 3.181 (2) | 161 (4) |
Symmetry codes: (i) −x+1, −y+1, −z+1; (ii) x−1, y, z−1; (iii) x, y+1, z; (iv) x, y, z−1. |
Acknowledgements
This work was supported by a start-up grant from Southeast University to Professor Ren-Gen Xiong.
References
Aminabhavi, T. M., Biradar, N. S. & Patil, S. B. (1986). Inorg. Chim. Acta, 125, 125-128. CrossRef CAS Web of Science Google Scholar
Brandenburg, K. (1998). DIAMOND. Crystal Impact GbR, Bonn, Germany. Google Scholar
Dai, W. & Fu, D.-W. (2008a). Acta Cryst. E64, m1016. Web of Science CSD CrossRef IUCr Journals Google Scholar
Dai, W. & Fu, D.-W. (2008b). Acta Cryst. E64, m1017. Web of Science CSD CrossRef IUCr Journals Google Scholar
Farrugia, L. J. (1997). J. Appl. Cryst. 30, 565. CrossRef IUCr Journals Google Scholar
Fu, D.-W., Song, Y.-M., Wang, G.-X., Ye, Q. & Xiong, R.-G. (2007). J. Am. Chem. Soc. 129, 5346–5347. Web of Science CSD CrossRef PubMed CAS Google Scholar
Fu, D.-W. & Ye, H.-Y. (2007). Acta Cryst. E63, m2453. Web of Science CSD CrossRef IUCr Journals Google Scholar
Rigaku (2005). CrystalClear. Rigaku Corporation, Tokyo, Japan. Google Scholar
Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. Web of Science CrossRef CAS IUCr Journals Google Scholar
This is an open-access article distributed under the terms of the Creative Commons Attribution (CC-BY) Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.
Amino acid derivatives provide wide applications in the field of material science, such as ferroelectric, fluorescence and dielectric behaviors. Also,there have been much attention in the preparation of amino acid coordination compound. (Aminabhavi et al., 1986; Dai & Fu 2008a,b; Fu & Ye 2007; Fu, et al. 2007). Here we report the crystal structure of the title compound, (S)-2-(pyrrolidinium-2-yl)-1H-benzimidazol-3-ium dichloride monohydrate (Fig. 1).
The crystal packing (Fig. 2) is stabilized by aromatic π–π interactions between the benzene rings of the neighbouring benzimidazole systems. The Cg···Cgi distance is 3.712 (2) Å (Cg is the centroide of the C1—C6 benzene ring, symmetry code as in Fig. 2). The molecular packing is further stabilized by intermolecular N—H···Cl, O—H···Cl and N—H···O hydrogen bonds (Fig. 2 and Table 1; symmetry code as in Fig. 2).