4-Amino­benzoic acid 4-methyl­pyridine/4-methyl­pyridinium 4-amino­benzoate 0.58/0.42: a redetermination from the original data

Fábry, J.

doi:10.1107/S2056989017013226

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ISSN: 2056-9890

Volume 73| Part 10| October 2017| Pages 1508-1512

https://doi.org/10.1107/S2056989017013226

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4-Aminobenzoic acid 4-methylpyridine/4-methylpyridinium 4-aminobenzoate 0.58/0.42: a redetermination from the original data

Jan Fábry ^a ^*

^aInst. of Physics of the Czech Academy of Sciences, Na Slovance 2, 182 21 Praha 8, Czech Republic
^*Correspondence e-mail: fabry@fzu.cz

Edited by H. Stoeckli-Evans, University of Neuchâtel, Switzerland (Received 5 September 2017; accepted 14 September 2017; online 19 September 2017)

The title structure, 4-aminobenzoic acid 4-methylpyridine/4-methylpyridinium 4-aminobenzoate 0.58/0.42, 0.58(C₆H₇N·C₇H₇NO₂)·0.42(C₆H₈N⁺·C₇H₆NO₂⁻), has been redetermined from the data published by Kumar et al. (2015 ). Acta Cryst. E71, o125-o126. The improvement of the present redetermination consists in the introduction of disorder of the methyl group over two positions as well as in the correction of the positional parameters of the hydrogen atoms that are involved in the O—H⋯N or N—H⋯O hydrogen bonds. After the correction, the hydroxyl hydrogen atom turned out to be disordered over two positions about the centre of the O⋯N bond, which is relatively long [2.642 (2) Å], while the H atoms of the primary amine group account more realistically for the hydrogen-bond pattern after the removal of the positional constraints. All the O—H⋯N or N—H⋯O hydrogen bonds which are present in the title structure are of moderate strength.

Keywords: crystal structure; redetermination; hydrogen bonding; symmetric hydrogen bonds; refinement constraints.

CCDC reference: 1574686

1. Chemical context

Crystal structures that contain hydroxyl, secondary and primary amine groups are sometimes determined incorrectly because of an assumed geometry of these groups from which the applied constraints or restraints were inferred. In such cases, the correct geometry is missed as it is not verified by inspection of the difference electron-density maps. Thus a considerable number of structures could have been determined more correctly – cf. Figs. 1 and 2 in Fábry et al. (2014 ). The inclusion of such structures causes bias in crystallographic databases such as the Cambridge Crystallographic Database (CSD; Groom et al., 2016 ).

Figure 1
View of the constituent molecules of the title structure (top: the original determination (Kumar et al., 2015

); bottom: present redetermination). Displacement ellipsoids are depicted at the 50% probability level.

Figure 2
A section of the difference electron-density map for the redetermined title structure without the atoms H1x and H1y. A build-up of the electron density between the atom O1 (red) and N2ⁱⁱⁱ (blue) [symmetry codes: (iii) x + 1, y, z + 1] is shown; the larger and the smaller peaks correspond to the electron density of 0.12 and 0.11 e A⁻³, respectively. These peaks were assigned to the respective positions of H1x and H1yⁱⁱⁱ. The positive and negative electron densities are indicated by continuous and dashed lines, respectively. The increment of the electron density between neighbouring contours is 0.01 e Å⁻³. Atom C7 is indicated by a gray circle.

In the course of recalculation of suspect structures that were retrieved from the CSD, the structure determination of the title structure by Kumar et al. (2015), CSD refcode WOYPEH, became a candidate for a checking recalculation. The reason was that the primary amine group centered on N1 was constrained to be coplanar to the attached phenyl group with distances N1—H1a and N1—H1b constrained to be equal to 0.86 Å with U_iso(H_{primary/secondary amine}) = 1.2U_eq(N_{primary/secondary amine}).

The hydroxyl hydrogen atom H1 was also suspect because the O—H bond length was reported to be restrained to the value 0.82 Å [the estimated standard deviation/elasticity (Müller et al., 2006 ) was not given in the original article]. However, the distance reported by Kumar et al. (2015) is 0.836 (10) Å, which indicated that the bridging hydrogen atom might have been situated towards the centre of the pertinent O1⋯N2 hydrogen bond. Recalculation with JANA2006 (Petříček et al., 2014 ) revealed hydrogen atom H1 to be disordered over two positions about the centre of the O1⋯N1 hydrogen bond in almost equal proportions, 0.58(7) (H1x) and 0.42(7) (H1y) (Figs. 1 and 2). This is different from the situation reported in the original article (Kumar et al., 2015). Moreover, inspection of the difference electron-density maps has also revealed quite a smeared electron density pertinent to the methyl hydrogen atoms (Fig. 3).

Figure 3
A section of the difference electron-density map for the redetermined title structure without the methyl H atoms. The positions of both methyl-hydrogen triplets are indicated by yellow circles of a different hue. The positive and negative electron densities are indicated by continuous and dashed lines, respectively. The increment of electron density between the neighbouring contours is 0.01 e Å⁻³.

2. Structural commentary

Table 1 lists the hydrogen bonds in the structure which are shown in Fig. 4. All the hydrogen bonds are of moderate strength (Gilli & Gilli, 2009 ). However, the hydrogen bond O1—H1x⋯N2ⁱⁱⁱ/O1⋯H1yⁱⁱⁱ—N2ⁱⁱⁱ [2.642 (2) Å; symmetry code: (iii) x + 1, y, z + 1] is quite long for an O⋯N hydrogen bond with a disordered bridging hydrogen atom, i.e. for a hydrogen atom the substantial part of its electron density is situated along the connecting line between the donor/acceptor atoms as happens in O1—H1x⋯N2ⁱⁱⁱ/O1⋯H1yⁱⁱⁱ—N2ⁱⁱⁱ of the title structure (Fig. 2). This O1⋯N2ⁱⁱⁱ hydrogen bond is even longer than the O3⋯N1 hydrogen bond with a disordered bridging hydrogen atom that was observed in a recently determined structure 2,4,6-triaminopyrimidinium(1+)_x hydrogen trioxofluorophosphate(1−)_x monohydrate/2,4,6-triaminopyrimidinium(2+)_(1–x) trioxofluorophosphate(2−)_(1–x) monohydrate, where x = 0.73, at room temperature (Matulková et al., 2017 ). The latter O⋯N hydrogen bond measured to be 2.5822 (16) Å and is ranked among the longest known O⋯N hydrogen bonds with a disordered bridging hydrogen atom.

Table 1
Hydrogen bonds (Å, °) in the redetermined structure as well as in the determintion by Kumar et al. (2015). Some of the atoms in the original article were transformed

Bond	D—H	H⋯A	D⋯A	D—H⋯A
This determination:
N1—H1a⋯O2ⁱ	0.88 (2)	2.22 (3)	3.051 (3)	158 (3)
N1—H1b⋯O2ⁱⁱ	0.99 (3)	2.04 (3)	3.028 (3)	179 (2)
O1—H1x⋯N2ⁱⁱⁱ	1.0154 (14)	1.6303 (18)	2.642 (2)	173.65 (11)
N2—H1y⋯O1ⁱ	1.0719 (18)	1.5740 (14)	2.642 (2)	173.55 (12)

Determination by
Kumar et al. (2015):
N1—H1a⋯O2ⁱ	0.86	2.32	3.049 (3)	142
N1—H1b⋯O2ⁱⁱ	0.86	2.17	3.031 (3)	174
O1—H1⋯N2ⁱⁱ	0.84 (1)	1.81 (1)	2.644 (3)	177 (4)
Symmetry codes: (i) x − 1, y, z − 1; (ii) x − 1, −y, z − $[{1\over 2}]$ ; (iii) x + 1, y, z + 1.

Figure 4
A section of the title structure. Symmetry codes (i): −x + 1, y, z − 1; (ii): −x + 1, −y, z − $[{1\over 2}]$ ; (iii): x + 1, y, z + 1; (iv): −x + 2, −y, z − $[{3\over 2}]$ (v): x − 2, y, z − 1. Applied colours for the atoms: grey – C and H, blue – N, O – red; applied colours for the bonds: black – covalent bonds, dashed orange – hydrogen bonds.

On the other hand, the tendency for a hydrogen atom to be situated just between the donor and acceptor atoms has been observed for strong hydrogen bonds, especially of the type O⋯H⋯O (Gilli & Gilli, 2009). Such bonds tend to occur in the structures where the difference ΔpK_a = pK_a(base) − pK_a(acid) is close to 0 (Gilli et al., 2009 ). The difference ΔpK_a is correlated with the occurrence of structures where the base and acid components are not ionized, thus forming a co-crystal (ΔpK_a < 0), or ionized, forming a salt (ΔpK_a > 3; Childs et al., 2007 ). It is difficult to predict the form in which the acid and the base are present for 0 < ΔpK_a < 3.

In the case of the title structure, pK_a of 4-methylpyridine and of 4-aminobenzoic acid are equal to 5.99 (CRC Handbook of Chemistry and Physics, 2009 ) and 2.38 (Kortüm et al., 1961 ), respectively. Thus ΔpK_a = 3.61 for the title structure, which means that the salt form should be slightly more probable for the present structure.

The primary amine group centered on N1 was originally constrained to be coplanar with the attached phenyl ring while the N1—H1a and N1—H1b distances were both constrained to 0.86 Å.

The difference electron-density map in the plane of the methyl hydrogen atoms that were excluded from the structure for the sake of this checking calculation (Fig. 4) shows that the methyl group can be better modelled by a disorder over two positions with equal occupancies. The disordered positions of the methyl group are related by a rotation of 60.19 (5)° about the C10—C13 bond.

Table 1, which also compares the values of the hydrogen-bond pattern in the title and the original structures (Kumar et al., 2015), emphasizes the importance of a careful examination of the difference electron-density maps during structure determinations. It serves as an example of the bias that is caused by unsubstantiated constraints of the primary amine groups as well as by constraints or restraints imposed on the hydroxyl groups.

3. Supramolecular features

The strongest hydrogen bond O1—H1x⋯N2ⁱⁱⁱ/O1⋯H1yⁱⁱⁱ—N2ⁱⁱⁱ; symmetry code: (iii) x + 1, y, z + 1] with a bridging hydrogen atom disordered over two positions (H1x and H1yⁱⁱⁱ) forms a finite D(3) pattern (Etter et al., 1990 ) on a local scale (Figs. 1 and 4).

The primary amine group, which is centered on atom N2, is involved in the hydrogen-bond pattern with a pair of symmetry-equivalent O2 atoms. It forms an R₄²(20) graph-set motif, shown in Fig. 4, in which two 4-aminobenzoic acid/aminobenzoate molecules with the symmetry codes (i) and (ii) are involved [symmetry codes: (i) −x + 1, y, z − 1; (ii) −x + 1, −y, z − $[{1\over 2}]$ ] as well as the atoms of the primary amine groups H1a--N1–H1b and atom O2^iv [symmetry code: (iv) −x + 2, −y, z − $[{3\over 2}]$ ].

4. Database survey

The structure determination by Kumar et al. (2015) is included in the Cambridge Structural Database (Groom et al., 2016) under refcode WOYPEH.

5. Synthesis and crystallization

The preparation of the title crystals was described by Kumar et al. (2015).

6. Refinement

Table 2 lists the details regarding the crystal data, data collection and the refinement [some pieces of information were taken from the downloaded CIF of the original article by Kumar et al. (2015)]. The refinement was carried out on the data for which the 826 Friedel pairs were not merged. Since the structure is composed of light atoms only and the applied radiation was Mo Kα the absolute structure could not be determined.

Table 2
Experimental details

Crystal data
Chemical formula	0.58(C₆H₇N·C₇H₇NO₂)·0.42(C₆H₈N⁺·C₇H₆NO₂⁻)
M_r	230.3
Crystal system, space group	Monoclinic, Pc
Temperature (K)	295
a, b, c (Å)	7.5970 (7), 11.6665 (12), 7.6754 (8)
β (°)	114.200 (3)
V (Å³)	620.49 (11)
Z	2
Radiation type	Mo Kα
μ (mm⁻¹)	0.09
Crystal size (mm)	0.28 × 0.24 × 0.20

Data collection
Diffractometer	Bruker Kappa APEXII CCD
Absorption correction	Multi-scan (SADABS; Krause et al., 2015 )
T_min, T_max	0.977, 0.983
No. of measured, independent and observed [I > 3σ(I)] reflections	10064, 2144, 1330
R_int	0.030
(sin θ/λ)_max (Å⁻¹)	0.632

Refinement
R[F > 3σ(F)], wR(F), S	0.031, 0.067, 1.29
No. of reflections	2144
No. of parameters	162
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
Δρ_max, Δρ_min (e Å⁻³)	0.08, −0.08
Absolute structure	826 of Friedel pairs used in the refinement
Computer programs: APEX2 and SAINT (Bruker, 2000 ), SHELXS97 (Sheldrick, 2008 ), JANA2006 (Petříček et al., 2014), PLATON (Spek, 2009 ) and DIAMOND (Brandenburg & Putz, 2005 ).

All hydrogen atoms were discernible in the difference electron-density map. The aryl hydrogens were constrained by the constraints C_aryl—H_aryl = 0.93 Å and U_iso(H_aryl) = 1.2U_eq(C_aryl). The positional parameters of the primary amine hydrogen atoms H1a and H1b were refined freely while their displacement parameters were constrained by U_iso(H_N1) = 1.2U_eq(N1).

The positional parameters of the bridging hydrogen atoms, H1x and H1y, were determined from difference electron-density maps (Fig. 2) and fixed in the subsequent refinement. Their isotropic displacement parameters were set equal and their occupational parameters were refined under the condition that the sum of their occupancies was equal to 1.

The electron density in the plane of the methyl hydrogen atoms, which was centered on atom C13, was found to be quite smeared (Fig. 3). It was modelled by a disorder over two positions with equal occupancies. The rotation between both triplets of the methyl hydrogen atoms is 60.19 (5)°. In order to account for this model, dummy atoms C10a and C13a, both with occupancies equal to 0, were introduced into the structure; their atomic parameters were otherwise constrained to be equal to those of atoms C10 and C13, respectively. The methyl hydrogen atoms were constrained by distance constraints C_methyl—H_methyl = 0.96 Å with U_iso(H_methyl) = 1.5U_eq(C_methyl).

It is worthwhile mentioning that the recalculation of the original model with JANA2006 (Petříček et al., 2014) in order to reproduce the original constraints and restraints converged with difficulty {Δ[last step of the parameter(i)]/σ(i) < 0.6}. The indicators of the refinement of such a model were substantially higher: R_obs = 0.0503, Rw_obs = 0.1035, R_all = 0.0930, Rw_all = 0.1119. The condition for the observed diffractions was I/σ(I) > 3, cf. Table 2 for indicators of the refinement for the redetermined structure.

Supporting information

CCDC reference: 1574686

Crystal structure: contains datablocks global, I. DOI: https://doi.org/10.1107/S2056989017013226/su5390sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2056989017013226/su5390Isup2.hkl

Supporting information file. DOI: https://doi.org/10.1107/S2056989017013226/su5390Isup3.cml

checkCIF report

Computing details top

Data collection: APEX2 (Bruker, 2000); cell refinement: SAINT (Bruker, 2000); data reduction: SAINT (Bruker, 2000); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: JANA2006 (Petříček et al., 2014); molecular graphics: PLATON (Spek, 2009), DIAMOND (Brandenburg & Putz, 2005) and JANA2006 (Petříček et al., 2014); software used to prepare material for publication: JANA2006 (Petříček et al., 2014).

4-Aminobenzoic acid 4-methylpyridine/4-methylpyridinium 4-aminobenzoate 0.58/0.42 top

Crystal data top

0.58(C₆H₇N·C₇H₇NO₂)·0.42(C₆H₈N⁺·C₇H₆NO₂⁻)	F(000) = 244
M_r = 230.3	D_x = 1.233 Mg m⁻³
Monoclinic, Pc	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P -2yc	Cell parameters from 2749 reflections
a = 7.5970 (7) Å	θ = 3.4–21.8°
b = 11.6665 (12) Å	µ = 0.09 mm⁻¹
c = 7.6754 (8) Å	T = 295 K
β = 114.200 (3)°	Block, colourless
V = 620.49 (11) Å³	0.28 × 0.24 × 0.20 mm
Z = 2

Data collection top

Bruker Kappa APEXII CCD diffractometer	2144 independent reflections
Radiation source: fine-focus sealed tube	1330 reflections with I > 3σ(I)
Graphite monochromator	R_int = 0.030
ω and φ scan	θ_max = 26.7°, θ_min = 3.4°
Absorption correction: multi-scan (SADABS; Krause et al., 2015)	h = −9→8
T_min = 0.977, T_max = 0.983	k = −14→14
10064 measured reflections	l = −9→9

Refinement top

Refinement on F²	3 constraints
R[F > 3σ(F)] = 0.031	H atoms treated by a mixture of independent and constrained refinement
wR(F) = 0.067	Weighting scheme based on measured s.u.'s w = 1/(σ²(I) + 0.0004I²)
S = 1.29	(Δ/σ)_max = 0.035
2144 reflections	Δρ_max = 0.08 e Å⁻³
162 parameters	Δρ_min = −0.08 e Å⁻³
0 restraints	Absolute structure: 826 of Friedel pairs used in the refinement

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å²) top

	x	y	z	U_iso*/U_eq	Occ. (<1)
C1	0.3688 (3)	0.10370 (17)	0.7142 (3)	0.0567 (10)
C2	0.4435 (3)	0.20303 (17)	0.6720 (3)	0.0579 (10)
H2	0.367077	0.247318	0.567618	0.0694*
C3	0.6269 (3)	0.23627 (16)	0.7816 (3)	0.0548 (10)
H3	0.673456	0.303544	0.750858	0.0658*
C4	0.7464 (3)	0.17333 (18)	0.9371 (3)	0.0495 (8)
C5	0.6731 (3)	0.07378 (17)	0.9790 (3)	0.0590 (11)
H5	0.75078	0.029552	1.08292	0.0708*
C6	0.4893 (3)	0.03939 (18)	0.8710 (3)	0.0619 (11)
H6	0.443281	−0.027955	0.902126	0.0743*
C7	0.9412 (3)	0.21074 (18)	1.0589 (3)	0.0586 (11)
C8	0.4371 (3)	0.45466 (19)	0.3179 (3)	0.0722 (12)
H8	0.357015	0.51507	0.317318	0.0867*
C9	0.6296 (3)	0.4649 (2)	0.4249 (3)	0.0692 (12)
H9	0.677992	0.53111	0.495943	0.083*
C10	0.7528 (3)	0.3785 (2)	0.4289 (3)	0.0634 (11)
C11	0.6709 (3)	0.2837 (2)	0.3229 (3)	0.0713 (12)
H11	0.748112	0.222191	0.321632	0.0856*
C12	0.4763 (4)	0.2786 (2)	0.2188 (3)	0.0758 (13)
H12	0.424395	0.212877	0.147656	0.0909*
C13	0.9662 (3)	0.3868 (2)	0.5459 (4)	0.0953 (14)
H13a	1.011616	0.460296	0.525995	0.143*	0.5
H13b	1.030779	0.32749	0.507907	0.143*	0.5
H13c	0.99267	0.377834	0.678664	0.143*	0.5
N1	0.1826 (3)	0.0714 (2)	0.6077 (3)	0.0816 (11)
H1b	0.139 (4)	−0.003 (2)	0.635 (4)	0.0979*
H1a	0.119 (4)	0.104 (2)	0.496 (4)	0.0979*
N2	0.3581 (3)	0.36282 (17)	0.2143 (3)	0.0708 (9)
O1	0.9925 (2)	0.30981 (13)	1.0111 (2)	0.0797 (7)
O2	1.0511 (2)	0.15736 (13)	1.1982 (2)	0.0771 (7)
H1x	1.131103	0.335566	1.084979	0.131 (10)*	0.58 (6)
H1y	0.211109	0.33646	0.138026	0.131 (10)*	0.42 (6)
H13d	1.03067	0.399497	0.463082	0.143*	0.5
H13e	0.992562	0.449433	0.634092	0.143*	0.5
H13f	1.011833	0.316689	0.615392	0.143*	0.5

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
C1	0.0553 (15)	0.0586 (14)	0.0525 (14)	−0.0083 (13)	0.0185 (12)	−0.0083 (13)
C2	0.0593 (15)	0.0554 (13)	0.0484 (14)	0.0003 (11)	0.0115 (12)	0.0089 (11)
C3	0.0577 (14)	0.0525 (12)	0.0501 (14)	−0.0059 (11)	0.0179 (12)	0.0043 (11)
C4	0.0520 (12)	0.0483 (11)	0.0419 (12)	0.0043 (11)	0.0128 (10)	0.0032 (11)
C5	0.0675 (16)	0.0517 (14)	0.0475 (15)	0.0003 (12)	0.0131 (12)	0.0050 (11)
C6	0.0771 (18)	0.0505 (12)	0.0573 (15)	−0.0072 (12)	0.0269 (13)	0.0066 (12)
C7	0.0565 (16)	0.0533 (13)	0.0587 (15)	0.0028 (12)	0.0161 (13)	−0.0033 (13)
C8	0.0642 (16)	0.0608 (15)	0.0795 (18)	0.0030 (13)	0.0172 (14)	0.0014 (14)
C9	0.0671 (17)	0.0606 (15)	0.0677 (18)	−0.0086 (13)	0.0153 (13)	−0.0042 (12)
C10	0.0580 (16)	0.0743 (16)	0.0565 (15)	−0.0046 (14)	0.0219 (12)	0.0051 (14)
C11	0.0654 (16)	0.0736 (16)	0.0778 (19)	0.0022 (13)	0.0324 (15)	−0.0068 (14)
C12	0.0759 (18)	0.0752 (17)	0.0718 (19)	−0.0131 (15)	0.0257 (15)	−0.0155 (14)
C13	0.0599 (16)	0.108 (2)	0.102 (2)	−0.0065 (14)	0.0170 (14)	0.0027 (19)
N1	0.0661 (15)	0.0866 (17)	0.0751 (16)	−0.0152 (12)	0.0116 (13)	0.0095 (13)
N2	0.0563 (12)	0.0707 (13)	0.0739 (14)	−0.0070 (12)	0.0150 (10)	−0.0029 (11)
O1	0.0619 (10)	0.0671 (10)	0.0852 (12)	−0.0117 (8)	0.0050 (8)	0.0129 (9)
O2	0.0678 (11)	0.0708 (9)	0.0650 (11)	0.0061 (8)	−0.0011 (9)	0.0100 (8)

Geometric parameters (Å, º) top

C1—C2	1.386 (3)	C10—C13	1.500 (3)
C1—C6	1.395 (3)	C11—H11	0.9299
C1—N1	1.365 (3)	C11—C12	1.363 (3)
C2—H2	0.93	C12—H12	0.93
C2—C3	1.356 (3)	C12—N2	1.322 (3)
C3—H3	0.93	C13—H13a	0.96
C3—C4	1.378 (3)	C13—H13b	0.9599
C4—C5	1.382 (3)	C13—H13c	0.96
C4—C7	1.456 (3)	C13—H13d	0.96
C5—H5	0.93	C13—H13e	0.96
C5—C6	1.360 (3)	C13—H13f	0.96
C6—H6	0.93	N1—H1b	0.99 (3)
C7—O1	1.319 (3)	N1—H1a	0.88 (2)
C7—O2	1.223 (2)	H1b—H1a	1.61 (4)
C8—H8	0.9301	N2—H1xⁱ	1.6303 (18)
C8—C9	1.357 (3)	N2—H1y	1.0719 (18)
C8—N2	1.322 (3)	O1—H1x	1.0154 (14)
C9—H9	0.93	O1—H1yⁱⁱ	1.5740 (14)
C9—C10	1.367 (3)	H1x—H1yⁱⁱ	0.5766 (1)
C10—C11	1.362 (3)

C2—C1—C6	117.69 (18)	C10—C11—H11	119.8
C2—C1—N1	120.94 (18)	C10—C11—C12	120.4 (2)
C6—C1—N1	121.4 (2)	H11—C11—C12	119.79
C1—C2—H2	119.68	C11—C12—H12	118.53
C1—C2—C3	120.63 (17)	C11—C12—N2	123.0 (2)
H2—C2—C3	119.69	H12—C12—N2	118.52
C2—C3—H3	119.02	C10—C13—H13a	109.47
C2—C3—C4	122.0 (2)	C10—C13—H13b	109.47
H3—C3—C4	119.02	C10—C13—H13c	109.47
C3—C4—C5	117.65 (18)	C10—C13—H13d	109.47
C3—C4—C7	122.1 (2)	C10—C13—H13e	109.47
C5—C4—C7	120.19 (17)	C10—C13—H13f	109.47
C4—C5—H5	119.43	H13a—C13—H13b	109.48
C4—C5—C6	121.16 (18)	H13a—C13—H13c	109.47
H5—C5—C6	119.42	H13b—C13—H13c	109.47
C1—C6—C5	120.9 (2)	H13d—C13—H13e	109.48
C1—C6—H6	119.54	H13d—C13—H13f	109.47
C5—C6—H6	119.54	H13e—C13—H13f	109.47
C4—C7—O1	114.98 (17)	C1—N1—H1b	118.1 (13)
C4—C7—O2	124.0 (2)	C1—N1—H1a	119.1 (18)
O1—C7—O2	121.05 (18)	H1b—N1—H1a	120 (2)
H8—C8—C9	118.46	C8—N2—C12	116.79 (19)
H8—C8—N2	118.46	C8—N2—H1xⁱ	129.06 (19)
C9—C8—N2	123.1 (2)	C8—N2—H1y	132.5 (2)
C8—C9—H9	119.78	C12—N2—H1xⁱ	114.12 (16)
C8—C9—C10	120.4 (2)	C12—N2—H1y	110.21 (19)
H9—C9—C10	119.79	C7—O1—H1x	117.45 (14)
C9—C10—C11	116.3 (2)	N2ⁱⁱ—H1x—O1	173.65 (11)
C9—C10—C13	121.8 (2)	N2—H1y—O1ⁱ	173.55 (12)
C11—C10—C13	121.8 (2)

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

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1b···O2ⁱⁱⁱ	0.99 (3)	2.04 (3)	3.028 (3)	179 (2)
N1—H1a···O2ⁱ	0.88 (2)	2.22 (3)	3.051 (3)	158 (3)
O1—H1x···N2ⁱⁱ	1.0154 (14)	1.6303 (18)	2.642 (2)	173.65 (11)
N2—H1y···O1ⁱ	1.0719 (18)	1.5740 (14)	2.642 (2)	173.55 (12)

Symmetry codes: (i) x−1, y, z−1; (ii) x+1, y, z+1; (iii) x−1, −y, z−1/2.

Hydrogen bonds (Å, °) in the redetermined structure as well as in the determintion by Kumar et al. (2015). (Some of the atoms in the original article were transformed.) top

Bond	D—H	H···A	D···A	D—H···A
This determination:
N1—H1a···O2ⁱ	0.88 (2)	2.22 (3)	3.051 (3)	158 (3)
N1—H1b···O2ⁱⁱ	0.99 (3)	2.04 (3)	3.028 (3)	179 (2)
O1—H1x···N2ⁱⁱⁱ	1.0154 (14)	1.6303 (18)	2.642 (2)	173.65 (11)
N2—H1y···O1ⁱ	1.0719 (18)	1.5740 (14)	2.642 (2)	173.55 (12)

Determination by Kumar et al. (2015):
N1—H1a···O2ⁱ	0.86	2.32	3.049 (3)	142
N1—H1b···O2ⁱⁱ	0.86	2.17	3.031 (3)	174
O1—H1···N2ⁱⁱ	0.84 (1)	1.81 (1)	2.644 (3)	177 (4)

Symmetry codes: (i) x - 1, y, z - 1; (ii) x - 1, -y, z - 1/2; (iii) x + 1, y, z + 1.

Funding information

The author expresses gratitude for the support provided by Project NPU I – LO1603 of the Ministry of Education of the Czech Republic to the Institute of Physics of the Academy of Sciences of the Czech Republic).

References

Brandenburg, K. & Putz, H. (2005). DIAMOND. Crystal Impact GbR, Postfach 1251, D-53002 Bonn, Germany.
Bruker (2000). APEX2 and SAINT. Bruker AXS Inc., Madison, Wisconsin. USA.
Childs, S. L., Stahly, G. P. & Park, A. (2007). Mol. Pharm. 4, 323–338. Web of Science CSD CrossRef PubMed CAS
CRC Handbook of Chemistry and Physics (2009). 90th Edition 2009–2010 edited by D. R. Lide. Boca Raton, London, New York: CRC Press.
Etter, M. C., MacDonald, J. C. & Bernstein, J. (1990). Acta Cryst. B46, 256–262. CrossRef CAS Web of Science IUCr Journals
Fábry, J., Dušek, M., Vaněk, P., Rafalovskyi, I., Hlinka, J. & Urban, J. (2014). Acta Cryst. C70, 1153–1160. Web of Science CSD CrossRef IUCr Journals
Gilli, G. & Gilli, P. (2009). The Nature of the Hydrogen Bond, pp. 61 and 71. New York: Oxford University Press.
Gilli, P., Pretto, L., Bertolasi, V. & Gilli, G. (2009). Acc. Chem. Res. 34, 34–44.
Groom, C. R., Bruno, I. J., Lightfoot, M. P. & Ward, S. C. (2016). Acta Cryst. B72, 171–179. Web of Science CSD CrossRef IUCr Journals
Kortüm, G. F. A., Andrussow, K. & Vogel, W. (1961). Dissociation Constants of Organic Acids in Aqueous Solution. London: International Union of Pure and Applied Chemistry, Butterworths.
Krause, L., Herbst-Irmer, R., Sheldrick, G. M. & Stalke, D. (2015). J. Appl. Cryst. 48, 3–10. Web of Science CSD CrossRef CAS IUCr Journals
Kumar, M. K., Pandi, P., Sudhahar, S., Chakkaravarthi, G. & Kumar, R. M. (2015). Acta Cryst. E71, o125–o126. CSD CrossRef IUCr Journals
Matulková, I., Fábry, J., Němec, I., Císařová, I. & Vaněk, P. (2017). Submitted to Acta Cryst. B.
Müller, P., Herbst-Irmer, R., Spek, A. L., Schneider, T. R. & Sawaya, M. R. (2006). Crystal Refinement. A Crystallographer's Guide to SHELXL, pp. 16. New York: Oxford University Press.
Petříček, V., Dušek, M. & Palatinus, L. (2014). Z. Kristallogr. 229, 345–352.
Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. Web of Science CrossRef IUCr Journals
Spek, A. L. (2009). Acta Cryst. D65, 148–155. Web of Science CrossRef CAS IUCr Journals

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