organic compounds
A monoclinic polymorph of 5-[(1H-benzimidazol-1-yl)methyl]benzene-1,3-dicarboxylic acid
aFaculty of Life Science and Chemical Engineering, Huaiyin Institute of Technology, Huaian 223003, People's Republic of China
*Correspondence e-mail: hyitshy@126.com
Crystals of the title compound, C16H12N2O4, were obtained accidentally by the hydrothermal reaction of 5-[(1H-benzo[d]imidazol-1-yl)methyl]isophthalic acid with manganese chloride tetrahydrate in the presence of KOH as alkaline reagent for the deprotonation. A triclinic polymorph of this structure has been reported previously from a similar reaction [Cheng (2011). Acta Cryst. E67, o3299]. The benzimidazole ring system is almost planar, with a maximum deviation from the mean plane of 0.020 (4) Å. The benzimidazole unit and benzene ring are inclined at a dihedral angle of 68.17 (4)°, reflecting the axial rotation of the flexible benzimidazolyl arm. In the crystal, pairs of O—H⋯O hydrogen bonds link adjacent molecules into inversion dimers. O—H⋯N contacts connect these dimers into zigzag chains along [010].
Experimental
Crystal data
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Refinement
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Data collection: APEX2 (Bruker, 2008); cell SAINT (Bruker, 2008); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: DIAMOND (Brandenburg, 2000) and Mercury (Macrae et al., 2008); software used to prepare material for publication: SHELXTL (Sheldrick, 2008).
Supporting information
10.1107/S1600536812041025/sj5265sup1.cif
contains datablocks I, global. DOI:Structure factors: contains datablock I. DOI: 10.1107/S1600536812041025/sj5265Isup2.hkl
Supporting information file. DOI: 10.1107/S1600536812041025/sj5265Isup3.cdx
Supporting information file. DOI: 10.1107/S1600536812041025/sj5265Isup4.cml
A reaction mixture comprising manganese chloride tetrahydrate (23.3 mg, 0.1 mmol), 5-((1H-benzo[d]imidazol-1-yl)methyl)isophthalic acid (29.6 mg, 0.1 mmol) and KOH (11.2 mg, 0.2 mmol) in 10 ml H2O was sealed in a 16 ml Teflon-lined stainless steel container and heated to 453 K for 3 days. After cooling to the room temperature, colorless block like crystals of the title compound were obtained.
Hydrogen atoms of the OH groups were found in difference Fourier maps and their coordinates were allowed to ride on those of the O atoms with Uiso(H) = 1.2Ueq(O). Other hydrogen atoms were included in geometrically idealized positions and constrained to ride on their parent atoms, with C—H = 0.93–0.97 Å and Uiso(H) = 1.2Ueq(C).
Data collection: APEX2 (Bruker, 2008); cell
SAINT (Bruker, 2008); data reduction: SAINT (Bruker, 2008); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: DIAMOND (Brandenburg, 2000) and Mercury (Macrae et al., 2008); software used to prepare material for publication: SHELXTL (Sheldrick, 2008).Fig. 1. : The crystal structure of the title compound showing 30% probability displacement ellipsoids. | |
Fig. 2. Crystal packing of the title compound. |
C16H12N2O4 | F(000) = 616 |
Mr = 296.28 | Dx = 1.465 Mg m−3 |
Monoclinic, P21/c | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: -P 2ybc | Cell parameters from 479 reflections |
a = 7.401 (5) Å | θ = 2.2–18.5° |
b = 16.589 (5) Å | µ = 0.11 mm−1 |
c = 11.762 (4) Å | T = 293 K |
β = 111.53 (3)° | Block, colorless |
V = 1343.3 (11) Å3 | 0.20 × 0.10 × 0.10 mm |
Z = 4 |
Bruker Smart APEXII CCD diffractometer | 2358 independent reflections |
Radiation source: fine-focus sealed tube | 1239 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.072 |
ϕ and ω scans | θmax = 25.0°, θmin = 2.2° |
Absorption correction: multi-scan (SADABS; Sheldrick, 1996) | h = −8→6 |
Tmin = 0.979, Tmax = 0.989 | k = −19→19 |
6722 measured reflections | l = −13→13 |
Refinement on F2 | Secondary atom site location: difference Fourier map |
Least-squares matrix: full | Hydrogen site location: inferred from neighbouring sites |
R[F2 > 2σ(F2)] = 0.056 | H-atom parameters constrained |
wR(F2) = 0.152 | w = 1/[σ2(Fo2) + (0.0659P)2] where P = (Fo2 + 2Fc2)/3 |
S = 0.96 | (Δ/σ)max < 0.001 |
2358 reflections | Δρmax = 0.21 e Å−3 |
200 parameters | Δρmin = −0.22 e Å−3 |
0 restraints | Extinction correction: SHELXL, Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4 |
Primary atom site location: structure-invariant direct methods | Extinction coefficient: 0.0052 (15) |
C16H12N2O4 | V = 1343.3 (11) Å3 |
Mr = 296.28 | Z = 4 |
Monoclinic, P21/c | Mo Kα radiation |
a = 7.401 (5) Å | µ = 0.11 mm−1 |
b = 16.589 (5) Å | T = 293 K |
c = 11.762 (4) Å | 0.20 × 0.10 × 0.10 mm |
β = 111.53 (3)° |
Bruker Smart APEXII CCD diffractometer | 2358 independent reflections |
Absorption correction: multi-scan (SADABS; Sheldrick, 1996) | 1239 reflections with I > 2σ(I) |
Tmin = 0.979, Tmax = 0.989 | Rint = 0.072 |
6722 measured reflections |
R[F2 > 2σ(F2)] = 0.056 | 0 restraints |
wR(F2) = 0.152 | H-atom parameters constrained |
S = 0.96 | Δρmax = 0.21 e Å−3 |
2358 reflections | Δρmin = −0.22 e Å−3 |
200 parameters |
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. |
x | y | z | Uiso*/Ueq | ||
C1 | 0.4929 (4) | 0.81173 (19) | 0.6457 (3) | 0.0337 (8) | |
C2 | 0.3157 (4) | 0.81097 (19) | 0.5499 (3) | 0.0359 (8) | |
H1 | 0.2128 | 0.7828 | 0.5586 | 0.043* | |
C3 | 0.2869 (4) | 0.85118 (19) | 0.4407 (3) | 0.0334 (8) | |
C4 | 0.4398 (4) | 0.89389 (18) | 0.4285 (3) | 0.0322 (8) | |
H2 | 0.4224 | 0.9211 | 0.3561 | 0.039* | |
C5 | 0.6190 (4) | 0.89614 (19) | 0.5242 (3) | 0.0335 (8) | |
C6 | 0.6444 (4) | 0.85508 (19) | 0.6319 (3) | 0.0369 (8) | |
H3 | 0.7645 | 0.8566 | 0.6957 | 0.044* | |
C11 | 0.5228 (4) | 0.7621 (2) | 0.7587 (2) | 0.0393 (9) | |
H7 | 0.4032 | 0.7336 | 0.7480 | 0.047* | |
H6 | 0.6222 | 0.7220 | 0.7666 | 0.047* | |
C12 | 0.7566 (4) | 0.8106 (2) | 0.9604 (3) | 0.0419 (9) | |
H8 | 0.8643 | 0.7849 | 0.9542 | 0.050* | |
C13 | 0.5734 (5) | 0.87902 (19) | 1.0306 (3) | 0.0391 (9) | |
C14 | 0.4574 (4) | 0.85280 (19) | 0.9137 (3) | 0.0359 (8) | |
C15 | 0.2615 (5) | 0.8708 (2) | 0.8615 (3) | 0.0526 (10) | |
H9 | 0.1855 | 0.8535 | 0.7833 | 0.063* | |
C16 | 0.1854 (6) | 0.9155 (2) | 0.9315 (4) | 0.0641 (11) | |
H10 | 0.0545 | 0.9293 | 0.8993 | 0.077* | |
C17 | 0.2977 (6) | 0.9410 (2) | 1.0494 (4) | 0.0616 (11) | |
H11 | 0.2394 | 0.9698 | 1.0945 | 0.074* | |
C18 | 0.4931 (5) | 0.9243 (2) | 1.1002 (3) | 0.0529 (10) | |
H12 | 0.5688 | 0.9424 | 1.1780 | 0.063* | |
C31 | 0.0929 (5) | 0.8454 (2) | 0.3395 (3) | 0.0421 (9) | |
C51 | 0.7854 (5) | 0.9411 (2) | 0.5135 (3) | 0.0393 (8) | |
N1 | 0.7629 (4) | 0.85258 (17) | 1.0568 (2) | 0.0451 (8) | |
N2 | 0.5798 (3) | 0.80875 (16) | 0.8720 (2) | 0.0363 (7) | |
O1 | 0.0865 (3) | 0.87513 (17) | 0.23681 (19) | 0.0661 (8) | |
H4 | −0.0285 | 0.8693 | 0.1880 | 0.079* | |
O2 | −0.0442 (3) | 0.81489 (18) | 0.3545 (2) | 0.0756 (9) | |
O3 | 0.7501 (3) | 0.97884 (14) | 0.41101 (19) | 0.0493 (7) | |
H5 | 0.8528 | 1.0018 | 0.4151 | 0.059* | |
O4 | 0.9450 (3) | 0.94199 (15) | 0.5985 (2) | 0.0584 (8) |
U11 | U22 | U33 | U12 | U13 | U23 | |
C1 | 0.0290 (18) | 0.043 (2) | 0.0258 (17) | −0.0006 (16) | 0.0059 (15) | 0.0014 (15) |
C2 | 0.0313 (18) | 0.041 (2) | 0.0351 (18) | −0.0055 (15) | 0.0113 (15) | −0.0018 (16) |
C3 | 0.0288 (18) | 0.040 (2) | 0.0296 (17) | 0.0005 (15) | 0.0088 (14) | 0.0001 (16) |
C4 | 0.0318 (18) | 0.037 (2) | 0.0259 (16) | −0.0018 (15) | 0.0086 (15) | −0.0012 (15) |
C5 | 0.0295 (18) | 0.040 (2) | 0.0282 (17) | −0.0039 (15) | 0.0077 (15) | −0.0017 (15) |
C6 | 0.0283 (19) | 0.047 (2) | 0.0283 (17) | −0.0037 (16) | 0.0022 (15) | −0.0040 (16) |
C11 | 0.0355 (19) | 0.046 (2) | 0.0304 (17) | −0.0040 (16) | 0.0052 (15) | 0.0010 (17) |
C12 | 0.033 (2) | 0.054 (2) | 0.0341 (19) | 0.0039 (17) | 0.0064 (16) | 0.0062 (18) |
C13 | 0.037 (2) | 0.047 (2) | 0.0307 (18) | −0.0021 (17) | 0.0093 (16) | 0.0076 (17) |
C14 | 0.0298 (19) | 0.044 (2) | 0.0327 (18) | −0.0008 (16) | 0.0096 (15) | 0.0020 (16) |
C15 | 0.040 (2) | 0.067 (3) | 0.049 (2) | −0.0017 (19) | 0.0143 (19) | 0.007 (2) |
C16 | 0.048 (2) | 0.076 (3) | 0.074 (3) | 0.008 (2) | 0.029 (2) | 0.012 (2) |
C17 | 0.063 (3) | 0.065 (3) | 0.071 (3) | 0.014 (2) | 0.042 (2) | 0.008 (2) |
C18 | 0.070 (3) | 0.054 (3) | 0.039 (2) | −0.003 (2) | 0.026 (2) | −0.0002 (18) |
C31 | 0.033 (2) | 0.052 (2) | 0.034 (2) | −0.0013 (17) | 0.0048 (17) | 0.0042 (18) |
C51 | 0.035 (2) | 0.050 (2) | 0.0307 (18) | −0.0049 (17) | 0.0092 (17) | −0.0014 (17) |
N1 | 0.0376 (17) | 0.059 (2) | 0.0304 (15) | 0.0002 (14) | 0.0031 (13) | 0.0004 (15) |
N2 | 0.0275 (15) | 0.0483 (18) | 0.0257 (14) | −0.0005 (13) | 0.0011 (12) | 0.0013 (13) |
O1 | 0.0401 (15) | 0.115 (2) | 0.0312 (13) | −0.0222 (14) | −0.0014 (12) | 0.0127 (15) |
O2 | 0.0357 (15) | 0.123 (3) | 0.0534 (16) | −0.0303 (15) | −0.0005 (13) | 0.0262 (16) |
O3 | 0.0402 (14) | 0.0641 (17) | 0.0421 (14) | −0.0163 (12) | 0.0134 (11) | 0.0060 (13) |
O4 | 0.0310 (14) | 0.088 (2) | 0.0449 (14) | −0.0173 (13) | 0.0008 (12) | 0.0130 (14) |
C1—C2 | 1.380 (4) | C13—N1 | 1.392 (4) |
C1—C6 | 1.390 (4) | C13—C18 | 1.394 (4) |
C1—C11 | 1.510 (4) | C13—C14 | 1.397 (4) |
C2—C3 | 1.393 (4) | C14—C15 | 1.384 (4) |
C2—H1 | 0.9300 | C14—N2 | 1.386 (4) |
C3—C4 | 1.386 (4) | C15—C16 | 1.374 (5) |
C3—C31 | 1.494 (4) | C15—H9 | 0.9300 |
C4—C5 | 1.390 (4) | C16—C17 | 1.395 (5) |
C4—H2 | 0.9300 | C16—H10 | 0.9300 |
C5—C6 | 1.389 (4) | C17—C18 | 1.375 (5) |
C5—C51 | 1.484 (4) | C17—H11 | 0.9300 |
C6—H3 | 0.9300 | C18—H12 | 0.9300 |
C11—N2 | 1.463 (4) | C31—O2 | 1.203 (4) |
C11—H7 | 0.9700 | C31—O1 | 1.289 (4) |
C11—H6 | 0.9700 | C51—O4 | 1.236 (3) |
C12—N1 | 1.317 (4) | C51—O3 | 1.297 (3) |
C12—N2 | 1.340 (4) | O1—H4 | 0.8397 |
C12—H8 | 0.9300 | O3—H5 | 0.8356 |
C2—C1—C6 | 118.4 (3) | C18—C13—C14 | 120.4 (3) |
C2—C1—C11 | 120.1 (3) | C15—C14—N2 | 132.1 (3) |
C6—C1—C11 | 121.4 (3) | C15—C14—C13 | 122.3 (3) |
C1—C2—C3 | 121.7 (3) | N2—C14—C13 | 105.5 (3) |
C1—C2—H1 | 119.1 | C16—C15—C14 | 116.3 (3) |
C3—C2—H1 | 119.1 | C16—C15—H9 | 121.8 |
C4—C3—C2 | 119.1 (3) | C14—C15—H9 | 121.8 |
C4—C3—C31 | 122.2 (3) | C15—C16—C17 | 122.3 (4) |
C2—C3—C31 | 118.8 (3) | C15—C16—H10 | 118.9 |
C3—C4—C5 | 120.2 (3) | C17—C16—H10 | 118.9 |
C3—C4—H2 | 119.9 | C18—C17—C16 | 121.2 (4) |
C5—C4—H2 | 119.9 | C18—C17—H11 | 119.4 |
C6—C5—C4 | 119.6 (3) | C16—C17—H11 | 119.4 |
C6—C5—C51 | 119.1 (3) | C17—C18—C13 | 117.4 (3) |
C4—C5—C51 | 121.3 (3) | C17—C18—H12 | 121.3 |
C5—C6—C1 | 121.0 (3) | C13—C18—H12 | 121.3 |
C5—C6—H3 | 119.5 | O2—C31—O1 | 123.7 (3) |
C1—C6—H3 | 119.5 | O2—C31—C3 | 121.7 (3) |
N2—C11—C1 | 114.4 (3) | O1—C31—C3 | 114.6 (3) |
N2—C11—H7 | 108.7 | O4—C51—O3 | 123.6 (3) |
C1—C11—H7 | 108.7 | O4—C51—C5 | 120.9 (3) |
N2—C11—H6 | 108.7 | O3—C51—C5 | 115.6 (3) |
C1—C11—H6 | 108.7 | C12—N1—C13 | 105.2 (3) |
H7—C11—H6 | 107.6 | C12—N2—C14 | 107.0 (3) |
N1—C12—N2 | 113.4 (3) | C12—N2—C11 | 126.3 (3) |
N1—C12—H8 | 123.3 | C14—N2—C11 | 126.4 (3) |
N2—C12—H8 | 123.3 | C31—O1—H4 | 106.1 |
N1—C13—C18 | 130.7 (3) | C51—O3—H5 | 107.3 |
N1—C13—C14 | 109.0 (3) | ||
C6—C1—C2—C3 | 1.0 (5) | C16—C17—C18—C13 | −1.7 (5) |
C11—C1—C2—C3 | −175.2 (3) | N1—C13—C18—C17 | −179.7 (3) |
C1—C2—C3—C4 | −0.8 (5) | C14—C13—C18—C17 | 0.4 (5) |
C1—C2—C3—C31 | 178.0 (3) | C4—C3—C31—O2 | −172.8 (3) |
C2—C3—C4—C5 | 0.1 (5) | C2—C3—C31—O2 | 8.5 (5) |
C31—C3—C4—C5 | −178.6 (3) | C4—C3—C31—O1 | 7.6 (5) |
C3—C4—C5—C6 | 0.3 (4) | C2—C3—C31—O1 | −171.1 (3) |
C3—C4—C5—C51 | 179.7 (3) | C6—C5—C51—O4 | 0.3 (5) |
C4—C5—C6—C1 | −0.1 (5) | C4—C5—C51—O4 | −179.2 (3) |
C51—C5—C6—C1 | −179.6 (3) | C6—C5—C51—O3 | −179.1 (3) |
C2—C1—C6—C5 | −0.5 (5) | C4—C5—C51—O3 | 1.5 (4) |
C11—C1—C6—C5 | 175.6 (3) | N2—C12—N1—C13 | 1.3 (4) |
C2—C1—C11—N2 | −121.4 (3) | C18—C13—N1—C12 | 178.4 (3) |
C6—C1—C11—N2 | 62.6 (4) | C14—C13—N1—C12 | −1.7 (4) |
N1—C13—C14—C15 | −179.2 (3) | N1—C12—N2—C14 | −0.5 (4) |
C18—C13—C14—C15 | 0.7 (5) | N1—C12—N2—C11 | −174.7 (3) |
N1—C13—C14—N2 | 1.4 (3) | C15—C14—N2—C12 | −179.9 (3) |
C18—C13—C14—N2 | −178.7 (3) | C13—C14—N2—C12 | −0.6 (3) |
N2—C14—C15—C16 | 178.6 (3) | C15—C14—N2—C11 | −5.7 (5) |
C13—C14—C15—C16 | −0.6 (5) | C13—C14—N2—C11 | 173.6 (3) |
C14—C15—C16—C17 | −0.7 (5) | C1—C11—N2—C12 | −106.8 (3) |
C15—C16—C17—C18 | 1.9 (6) | C1—C11—N2—C14 | 80.2 (4) |
D—H···A | D—H | H···A | D···A | D—H···A |
O3—H5···O4i | 0.84 | 1.82 | 2.649 (3) | 171 |
O1—H4···N1ii | 0.84 | 1.76 | 2.576 (4) | 164 |
Symmetry codes: (i) −x+2, −y+2, −z+1; (ii) x−1, y, z−1. |
Experimental details
Crystal data | |
Chemical formula | C16H12N2O4 |
Mr | 296.28 |
Crystal system, space group | Monoclinic, P21/c |
Temperature (K) | 293 |
a, b, c (Å) | 7.401 (5), 16.589 (5), 11.762 (4) |
β (°) | 111.53 (3) |
V (Å3) | 1343.3 (11) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 0.11 |
Crystal size (mm) | 0.20 × 0.10 × 0.10 |
Data collection | |
Diffractometer | Bruker Smart APEXII CCD diffractometer |
Absorption correction | Multi-scan (SADABS; Sheldrick, 1996) |
Tmin, Tmax | 0.979, 0.989 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 6722, 2358, 1239 |
Rint | 0.072 |
(sin θ/λ)max (Å−1) | 0.595 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.056, 0.152, 0.96 |
No. of reflections | 2358 |
No. of parameters | 200 |
H-atom treatment | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 0.21, −0.22 |
Computer programs: APEX2 (Bruker, 2008), SAINT (Bruker, 2008), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), DIAMOND (Brandenburg, 2000) and Mercury (Macrae et al., 2008), SHELXTL (Sheldrick, 2008).
D—H···A | D—H | H···A | D···A | D—H···A |
O3—H5···O4i | 0.84 | 1.82 | 2.649 (3) | 171.4 |
O1—H4···N1ii | 0.84 | 1.76 | 2.576 (4) | 164.1 |
Symmetry codes: (i) −x+2, −y+2, −z+1; (ii) x−1, y, z−1. |
References
Brandenburg, K. (2000). DIAMOND. Crystal Impact GbR, Bonn, Germany. Google Scholar
Bruker (2008). APEX2 and SAINT. Bruker AXS Inc., Madison, wisconsin, USA. Google Scholar
Cheng, X.-C. (2011). Acta Cryst. E67, o3299. Web of Science CSD CrossRef IUCr Journals Google Scholar
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. Web of Science CrossRef CAS 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
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5-((1H-benzo[d]imidazol-1-yl)methyl)isophthalic acid (H2L), is usually regarded as an excellent candidate for use as a building block in molecular self-assembly engineerings due to its variable conformations and coordination modes. During an attempt to assemble a coordination polymer, we accidentally obtained some single crystals of the title compound, C16H12N2O4, as a result of the hydrothermal reaction of 5-((1H-benzo[d]imidazol-1-yl)methyl)isophthalic acid with manganese chloride tetrahydrate at 453 K in the presence of KOH as alkaline reagent for the deprotonation. A triclinic polymorph of this structure has been reported previously (Cheng, 2011) from a very similar hydrothermal reaction involving manganese bromide. The bond distances and angles in that molecule are reasonably similar to those reported here. As shown in Fig. 1, the asymmetric unit consists of only one H2L molecule. Interestingly, though crystallizing from alkaline solution, the H2L retains the intact carboxylic acid groups in the crystal structure. The flexible benzimidazolyl arm is apt to rotate axially. As a result, the benzimidazolyl ring and central benzene rings are inclined at a dihedral angle of 68.17 °.
In the crystal structure O3–H5..O4 hydrogen bonds, Table 1, link adjacent molecules into inversion dimers. O1—H4···N1 contacts connect these dimers into zig-zag chains in the 010 plane, Fig. 2.