A redetermination from the original data of the crystal structure of 2-amino-4,6-di-meth-oxy-pyrimidin-1-ium 4-amino-benzoate.

The title structure, C6H9.5N3O2 (0.5+)·C7H6.5NO2 (0.5-), which might be named schematically as 2-amino-4,6-di-meth-oxy-pyrimidine-(μ2-hydrogen)-4-amino-benzoate to indicate a bridging H atom, has been redetermined from the data published by Thanigaimani, Mu-thiah & Lynch [Acta Cryst. (2006), E62, o2976-o2978]. The improvement of the present redetermination consists in a released geometry of the primary amine groups, which were originally assumed to be planar, as well as in a redetermination of the position of the hy-droxy H atom. This H atom, whose parameters were originally constrained, turns out to be situated about the centre of the O⋯N hydrogen bond in two disordered positions with occupancies of 0.5 each.

Chemical context

Structures which contain hydroxyl, secondary and primary amine groups are often 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 Structural Database (CSD; Groom & Allen, 2014 ▸).

In the course of recalculation of suspect structures which were retrieved from the CSD, defects in the structure determination of 2-amino-4,6-di­meth­oxy­pyrimidine–4-amino­benzoic acid (1/1) by Thanigaimani et al. (2006 ▸) have been found; the pertinent CSD refcode is IFACUO.

The defects in the original structure concern positional parameters both of the hydroxyl and the primary amine hydrogen atoms, which follow from unsubstanti­ated constraints of these hydrogen atoms. This means that the amine groups were assumed to be planar while the disorder regarding atom H4 was neglected because atom H4 was forced to be situated at atom O4.

The aim of the present article is to demonstrate how the original structure determination can be improved.

Structural commentary

The structure of the title compound has been described by Thanigaimani et al. (2006 ▸) as 2-amino-4,6-di­meth­oxy­pyrimidine/4-amino­benzoic acid (1/1). In that article, the amine groups (centred on atoms N2 and N4) were assumed to be planar and were refined with distance constraints of N—H = 0.86 Å. For the hydroxyl group O4—H4, atom H4 was refined with a distance constraint of O4—H4 = 0.82 Å [U iso(Hprimary amine) = 1.2U eq(Nprimary amine) while U iso(H4) = 1.5U eq(O4)].

The improved refinement by JANA2006 (Petříček et al., 2014 ▸) yielded a non-planar geometry of the primary amine groups and a considerably different position for the hydrogen atom H4. This atom turns out to be disordered over two positions at about the centre of the hydrogen bond O4⋯N1 (Fig. 1 ▸). Thus, the title structure can be envisaged as an example of a structure with a symmetric hydrogen bond where the bridging hydrogen atom is disordered over two positions (see: for example Olovsson et al., 2002 ▸). One of these positions is closer to atom N1 while the other is closer to atom O4, and correspondingly they were labelled as H4n1 and H4o4. Each of the occupancies of H4n1 and H4o4 turned out to be equal to 0.5 within the inter­val given by the refined standard uncertainties; cf. the section of the electron density map in Fig. 2 ▸. The pKa of the conjugate acid to 2-amino-4,6-di­meth­oxy­pyrimidine is equal to 3.36 (Baldwin & van den Broek, 1975 ▸), while pKa1 and pKa2 of 4-amino­benzoic acid are equal to 2.50 and 4.87, respectively (CRC Handbook of Chemistry and Physics, 2009 ▸). pKa1 refers to the deprotonation of the hydrogen carboxyl­ate into the carboxyl­ate group, while pKa2 refers to the deprotonation of the ammonium group into the primary amine group in the solution (cf. pKa for benzoic acid and aniline are equal to 4.20 and 4.87, respectively; CRC Handbook of Chemistry and Physics, 2009 ▸). Thus, 2-amino-4,6-di­meth­oxy­pyrimidine is a weaker acid while 4-amino­benzoic acid is a weaker base. These values favour the formation of the salt rather than of the co-crystal. Since differences in the dissociation constants are relatively mild, the hydrogen atom is situated about the centre of the hydrogen bond N1⋯O4 and the structure in the solid state can be envisaged as a mixture of a co-crystal 2-amino-4,6-di­meth­oxy­pyrimidine–4-amino­benzoic acid (1:1) with a salt 2-amino-4,6-di­meth­oxy­pyrimidin-1-ium 4-amino­benzoate in a 1:1 proportion. Alternatively – as has been stated above – it can be assumed to be a structure with a disordered bridging hydrogen involved in a symmetric hydrogen bond (Olovsson et al., 2002 ▸).

Figure 1

View of the constituent mol­ecules of the title structure after the improved refinement. The displacement ellipsoids are depicted at the 50% probability level. The occupancies of atoms H4N1 and H4O4 are each equal to 0.5.

Figure 2

A section of the difference electron-density map for the present redetermined title structure, which shows the build-up of the electron density between the atom O4 (red) and N1 (blue). Positive and negative electron densities are indicated by continuous and dashed lines, respectively. The increment of electron density between neighbouring contours is 0.05 e Å−3 (JANA2006; Petříček et al., 2014 ▸).

In the recalculated structure determination, the deviation from planarity of the primary amine groups (including the C atoms to which they are attached) is larger for the one that is centred on N4 [C12–N4–H4a 115.4 (9), C12–N4–H4a 114.5 (9), H4a–N4–H4b 119.5 (13)°] than on N2 [C2–N2–H2a 119.5 (8), C2–N2–H2b 119.7 (8), H2a–N2–H2b 120.7 (12)°]. This is in agreement with the longer bond length for C12—N4 [1.3786 (17) Å] compared to C2—N2 [1.3253 (16) Å].

In a broader sense, the present redetermination emphasizes the importance of careful examination of the difference electron-density maps during structure determinations.

Supra­molecular features

The details of the hydrogen bonding and the N—H⋯π-electron ring inter­action involving N4—H4b are given in Table 1 ▸. The graph-set motifs (Etter et al., 1990 ▸) were described by Thanigaimani et al. (2006 ▸) for the title structure. The graph-set motif (7) (Fig. 3 ▸) is shown in Fig. 2 ▸ of the article by Thanigaimani et al. (2006 ▸) and described there as (6).

Table 1

Hydrogen-bond geometry (Å, °)

Cg1 is the centroid of the C9–C14 ring.

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N1—H4N1⋯O4	0.86 (3)	1.78 (3)	2.6459 (14)	176 (2)
O4—H4O4⋯N1	0.89 (3)	1.77 (3)	2.6459 (14)	170 (3)
N2—H2A⋯O3	0.92 (1)	1.91 (1)	2.8163 (14)	172 (1)
N2—H2B⋯O3i	0.88 (1)	2.04 (1)	2.8544 (14)	154 (1)
N4—H4A⋯O4ii	0.92 (2)	2.27 (2)	3.1625 (15)	164 (1)
C7—H7B⋯O2iii	0.96	2.59	3.4571 (15)	150
N4—H4b⋯Cg1iv	0.89 (2)	2.724 (15)	3.5472 (14)	154.7 (12)

Symmetry codes: (i) ; (ii) ; (iii) ; (iv) .

Figure 3

The section of the title structure which shows the graph-set motifs R(7)3 2 O4—H4O4⋯N1—C6—O2⋯H4a i⋯N4i and O4⋯H4N1—N1—C6—O2⋯H4a i⋯N4i [symmetry code: (i) −x + 1, y − , −z + ; colour code for atoms: grey – C and H, blue – N; red – O; colour code for bonds: black: covalent bonds, dashed orange: H⋯hydrogen-bond acceptor; blue O2—N4: inclusion into the graph-set motif R(7)3 2].

In the present article, the graph-set motif (7) includes the atoms O4—H4o4⋯N1—C6—O2⋯H4a i—N4i or O4⋯H4n1—N1—C6—O2⋯H4a i—N4i on a local scale [Fig. 3 ▸; symmetry code (i): −x + 1, y − , −z + ].

Database survey

The structure determination by Thanigaimani et al. (2006 ▸) has been included in the Cambridge Structural Database (Groom & Allen, 2014 ▸) under the refcode IFACUO.

Synthesis and crystallization

The preparation of the title compound has been described by Thanigaimani et al. (2006 ▸).

Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2 ▸. All the hydrogen atoms were discernible in the difference electron-density map. The aryl hydrogen atoms were constrained by the constraints Car­yl—Har­yl = 0.93 Å and U iso(Har­yl) = 1.2U eq(Car­yl) while the methyl hydrogens were constrained by the constraints Cmeth­yl—Hmeth­yl = 0.96 Å and U iso(Hmeth­yl) = 1.5U eq(Cmeth­yl). The hydrogen atoms of the primary amine group N2 were constrained by U iso(HN2) = 1.2U eq(N2). The displacement parameters of the hydroxyl hydrogen H4O4 and of the secondary amine H4N1 were constrained by U iso(H4O4) = 1.5U eq(O4) and U iso(H4N1) = 1.5U eq(N1) while their positional parameters were refined freely.

Table 2

Experimental details

Crystal data
Chemical formula	C6H9.5N3O2 0.5+·C7H6.5NO2 0.5−
M r	292.30
Crystal system, space group	Monoclinic, P21/c
Temperature (K)	293
a, b, c (Å)	6.6358 (4), 7.5560 (5), 27.4226 (16)
β (°)	94.418 (2)
V (Å3)	1370.89 (15)
Z	4
Radiation type	Mo Kα
μ (mm−1)	0.11
Crystal size (mm)	0.44 × 0.32 × 0.08
Data collection
Diffractometer	Bruker–Nonius KappaCCD area-detector
No. of measured, independent and observed [I > 3σ(I)] reflections	14577, 3130, 2302
R int	0.032
(sin θ/λ)max (Å−1)	0.651
Refinement
R[F 2 > 3σ(F 2)], wR(F 2), S	0.037, 0.084, 1.91
No. of reflections	3130
No. of parameters	208
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å−3)	0.21, −0.23

Computer programs: DENZO (Otwinowski & Minor, 1997 ▸), COLLECT (Hooft, 1998 ▸), SHELXS97 (Sheldrick, 2008 ▸), PLATON (Spek, 2009 ▸), DIAMOND (Brandenburg & Putz, 2005 ▸) and JANA2006 (Petříček et al., 2014 ▸).

The model with the refinement of the occupational factors of H4N1 and H4O4 under the condition that the sum of these occupational factors should equal to 1 resulted in the values 0.499 (25) and 0.501 (25), respectively. Therefore the occupational parameters were set to 0.5 in the final model and not further refined.

Crystal structure: contains datablock(s) global, I. DOI: 10.1107/S2056989016004321/su5289sup1.cif

Structure factors: contains datablock(s) I. DOI: 10.1107/S2056989016004321/su5289Isup2.hkl

Click here for additional data file.

Supporting information file. DOI: 10.1107/S2056989016004321/su5289Isup3.smi

CCDC reference: 1465363

Additional supporting information: crystallographic information; 3D view; checkCIF report

C6H9.5N3O20.5+·C7H6.5NO20.5−−	F(000) = 616
Mr = 292.30	Dx = 1.416 Mg m−3
Monoclinic, P21/c	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybc	Cell parameters from 50 reflections
a = 6.6358 (4) Å	θ = 3.5–27.5°
b = 7.5560 (5) Å	µ = 0.11 mm−1
c = 27.4226 (16) Å	T = 293 K
β = 94.418 (2)°	Block, colourless
V = 1370.89 (15) Å3	0.44 × 0.32 × 0.08 mm
Z = 4

Bruker–Nonius KappaCCD area-detector diffractometer	2302 reflections with I > 3σ(I)
Radiation source: Bruker–Nonius FR591 rotating anode	Rint = 0.032
Graphite monochromator	θmax = 27.5°, θmin = 3.5°
φ and ω scans	h = −8→8
14577 measured reflections	k = −9→9
3130 independent reflections	l = −35→35

Refinement on F2	50 constraints
R[F2 > 2σ(F2)] = 0.037	H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.084	Weighting scheme based on measured s.u.'s w = 1/(σ2(I) + 0.0004I2)
S = 1.91	(Δ/σ)max = 0.021
3130 reflections	Δρmax = 0.21 e Å−3
208 parameters	Δρmin = −0.23 e Å−3
0 restraints

Refinement. This part differs from the original article by Thanigaimani et al. (2006). It also differs from the refinement by Thanigaimani et al. (2006) by a different threshold for the consideration of the observed diffractions: F2 > 3σ(F2) has been used as criterion for observed diffractions by JANA2006 which was used for the calculation of the corrected structural model.

	x	y	z	Uiso*/Ueq	Occ. (<1)
O1	−0.31928 (12)	0.65273 (11)	−0.06555 (3)	0.0245 (3)
O2	−0.10295 (12)	0.62305 (10)	0.10293 (3)	0.0220 (3)
N1	0.08195 (15)	0.75282 (13)	0.04894 (4)	0.0190 (3)
N2	0.29136 (17)	0.87608 (15)	−0.00426 (4)	0.0257 (4)
N3	−0.01303 (15)	0.76827 (13)	−0.03671 (3)	0.0195 (3)
C2	0.11662 (18)	0.79867 (15)	0.00265 (4)	0.0187 (4)
C4	−0.18261 (18)	0.68662 (15)	−0.02786 (4)	0.0194 (4)
C5	−0.23220 (18)	0.62937 (15)	0.01815 (4)	0.0201 (4)
C6	−0.09140 (18)	0.66647 (15)	0.05581 (4)	0.0186 (4)
C7	−0.26609 (18)	0.70054 (18)	−0.11374 (4)	0.0261 (4)
C8	−0.26910 (18)	0.51184 (16)	0.11446 (4)	0.0244 (4)
O3	0.54244 (13)	0.93439 (11)	0.08178 (3)	0.0263 (3)
O4	0.31630 (13)	0.82158 (12)	0.12916 (3)	0.0258 (3)
N4	0.9485 (2)	1.16699 (16)	0.28973 (4)	0.0366 (4)
C9	0.60450 (18)	0.96745 (15)	0.16726 (4)	0.0198 (4)
C10	0.5334 (2)	0.95948 (16)	0.21374 (5)	0.0252 (4)
C11	0.6456 (2)	1.02612 (16)	0.25407 (5)	0.0286 (4)
C12	0.8340 (2)	1.10412 (16)	0.24933 (4)	0.0251 (4)
C13	0.90630 (19)	1.11079 (16)	0.20281 (5)	0.0254 (4)
C14	0.79433 (19)	1.04458 (15)	0.16262 (5)	0.0227 (4)
C15	0.48369 (18)	0.90491 (15)	0.12288 (4)	0.0202 (4)
H2a	0.3827 (19)	0.8954 (17)	0.0219 (5)	0.0308*
H2b	0.3152 (19)	0.9139 (17)	−0.0336 (5)	0.0308*
H5	−0.352188	0.570355	0.022827	0.0241*
H7a	−0.38336	0.691873	−0.13641	0.0391*
H7b	−0.163259	0.621794	−0.123627	0.0391*
H7c	−0.216204	0.819832	−0.113329	0.0391*
H8a	−0.266284	0.403993	0.096019	0.0365*
H8b	−0.257451	0.484961	0.148775	0.0365*
H8c	−0.394276	0.572471	0.106262	0.0365*
H4a	0.878 (2)	1.1906 (19)	0.3166 (6)	0.0439*
H4b	1.050 (2)	1.237 (2)	0.2829 (5)	0.0439*
H10	0.408167	0.908373	0.217631	0.0302*
H11	0.595299	1.019027	0.284732	0.0344*
H13	1.032145	1.160827	0.198977	0.0305*
H14	0.845086	1.051013	0.131987	0.0273*
H4N1	0.157 (5)	0.771 (4)	0.0756 (12)	0.0285*	0.5
H4O4	0.251 (5)	0.797 (4)	0.1004 (12)	0.0387*	0.5

	U11	U22	U33	U12	U13	U23
O1	0.0216 (5)	0.0332 (5)	0.0179 (5)	−0.0044 (4)	−0.0040 (4)	0.0017 (4)
O2	0.0211 (5)	0.0274 (5)	0.0173 (5)	−0.0059 (4)	0.0009 (4)	0.0032 (4)
N1	0.0188 (6)	0.0218 (6)	0.0161 (5)	−0.0025 (5)	0.0004 (4)	−0.0001 (4)
N2	0.0232 (6)	0.0371 (7)	0.0165 (6)	−0.0107 (5)	−0.0004 (5)	0.0015 (5)
N3	0.0190 (6)	0.0212 (5)	0.0179 (5)	−0.0008 (4)	−0.0012 (4)	−0.0006 (4)
C2	0.0203 (7)	0.0184 (6)	0.0173 (6)	−0.0003 (5)	0.0008 (5)	−0.0010 (5)
C4	0.0188 (7)	0.0188 (6)	0.0201 (6)	0.0027 (5)	−0.0026 (5)	−0.0015 (5)
C5	0.0178 (7)	0.0212 (6)	0.0211 (7)	−0.0029 (5)	0.0000 (5)	0.0002 (5)
C6	0.0212 (7)	0.0171 (6)	0.0175 (6)	0.0015 (5)	0.0024 (5)	0.0007 (5)
C7	0.0260 (7)	0.0347 (8)	0.0169 (7)	0.0014 (6)	−0.0024 (6)	0.0022 (5)
C8	0.0228 (7)	0.0268 (7)	0.0239 (7)	−0.0055 (6)	0.0043 (6)	0.0043 (5)
O3	0.0258 (5)	0.0358 (5)	0.0172 (5)	−0.0057 (4)	0.0016 (4)	−0.0019 (4)
O4	0.0243 (5)	0.0324 (5)	0.0204 (5)	−0.0089 (4)	−0.0002 (4)	0.0003 (4)
N4	0.0480 (8)	0.0393 (7)	0.0209 (6)	−0.0112 (6)	−0.0072 (6)	−0.0028 (5)
C9	0.0236 (7)	0.0177 (6)	0.0176 (6)	0.0004 (5)	−0.0009 (5)	0.0006 (5)
C10	0.0294 (8)	0.0246 (7)	0.0214 (7)	−0.0043 (6)	0.0017 (6)	0.0008 (5)
C11	0.0400 (9)	0.0287 (7)	0.0171 (7)	−0.0048 (6)	0.0017 (6)	0.0005 (5)
C12	0.0341 (8)	0.0189 (6)	0.0207 (7)	0.0012 (6)	−0.0076 (6)	−0.0002 (5)
C13	0.0239 (7)	0.0261 (7)	0.0255 (7)	−0.0033 (6)	−0.0031 (6)	0.0001 (5)
C14	0.0252 (7)	0.0240 (7)	0.0189 (7)	0.0016 (6)	0.0004 (6)	0.0002 (5)
C15	0.0211 (7)	0.0196 (6)	0.0199 (7)	0.0019 (5)	0.0017 (5)	0.0010 (5)

O1—C4	1.3462 (14)	O4—H4O4	0.89 (3)
O1—C7	1.4400 (14)	N4—C12	1.3786 (17)
O2—C6	1.3411 (14)	N4—H4a	0.918 (15)
O2—C8	1.4405 (15)	N4—H4b	0.886 (15)
N1—C2	1.3525 (16)	C9—C10	1.3940 (17)
N1—C6	1.3483 (16)	C9—C14	1.4026 (17)
N1—H4N1	0.86 (3)	C9—C15	1.4821 (16)
N2—C2	1.3253 (16)	C10—C11	1.3799 (17)
N2—H2a	0.914 (13)	C10—H10	0.93
N2—H2b	0.880 (14)	C11—C12	1.3973 (19)
N3—C2	1.3472 (15)	C11—H11	0.93
N3—C4	1.3221 (15)	C12—C13	1.3980 (18)
C4—C5	1.3969 (17)	C13—C14	1.3751 (17)
C5—C6	1.3672 (16)	C13—H13	0.93
C5—H5	0.93	C14—H14	0.93
C7—H7a	0.96	H2a—H2b	1.559 (19)
C7—H7b	0.96	H7a—H7b	1.5677
C7—H7c	0.96	H7a—H7c	1.5677
C8—H8a	0.96	H7b—H7c	1.5677
C8—H8b	0.96	H8a—H8b	1.5677
C8—H8c	0.96	H8a—H8c	1.5677
O3—C15	1.2409 (15)	H8b—H8c	1.5677
O4—C15	1.2998 (15)	H4a—H4b	1.56 (2)
C4—O1—C7	117.31 (9)	H8a—C8—H8b	109.47
C6—O2—C8	117.11 (8)	H8a—C8—H8c	109.47
C2—N1—C6	117.63 (10)	H8b—C8—H8c	109.47
C2—N1—H4N1	129 (2)	C15—O4—H4O4	110 (2)
C6—N1—H4N1	114 (2)	C12—N4—H4a	115.4 (9)
C2—N2—H2a	119.5 (8)	C12—N4—H4b	114.5 (9)
C2—N2—H2b	119.7 (8)	H4a—N4—H4b	119.5 (13)
H2a—N2—H2b	120.7 (12)	C10—C9—C14	118.07 (11)
C2—N3—C4	115.62 (10)	C10—C9—C15	122.49 (11)
N1—C2—N2	117.46 (11)	C14—C9—C15	119.39 (11)
N1—C2—N3	124.33 (11)	C9—C10—C11	121.15 (12)
N2—C2—N3	118.20 (11)	C9—C10—H10	119.43
O1—C4—N3	118.71 (10)	C11—C10—H10	119.43
O1—C4—C5	116.29 (10)	C10—C11—C12	120.73 (12)
N3—C4—C5	125.00 (10)	C10—C11—H11	119.64
C4—C5—C6	115.08 (11)	C12—C11—H11	119.64
C4—C5—H5	122.46	N4—C12—C11	120.82 (12)
C6—C5—H5	122.46	N4—C12—C13	120.96 (12)
O2—C6—N1	111.45 (10)	C11—C12—C13	118.18 (11)
O2—C6—C5	126.24 (11)	C12—C13—C14	121.08 (12)
N1—C6—C5	122.31 (11)	C12—C13—H13	119.46
O1—C7—H7a	109.47	C14—C13—H13	119.46
O1—C7—H7b	109.47	C9—C14—C13	120.80 (12)
O1—C7—H7c	109.47	C9—C14—H14	119.6
H7a—C7—H7b	109.47	C13—C14—H14	119.6
H7a—C7—H7c	109.47	O3—C15—O4	122.60 (11)
H7b—C7—H7c	109.47	O3—C15—C9	120.04 (11)
O2—C8—H8a	109.47	O4—C15—C9	117.35 (11)
O2—C8—H8b	109.47	N1—H4N1—H4O4	171 (5)
O2—C8—H8c	109.47	O4—H4O4—H4N1	165 (5)

D—H···A	D—H	H···A	D···A	D—H···A
N1—H4N1···O4	0.86 (3)	1.78 (3)	2.6459 (14)	176 (2)
O4—H4O4···N1	0.89 (3)	1.77 (3)	2.6459 (14)	170 (3)
N2—H2A···O3	0.92 (1)	1.91 (1)	2.8163 (14)	172 (1)
N2—H2B···O3i	0.88 (1)	2.04 (1)	2.8544 (14)	154 (1)
N4—H4A···O4ii	0.92 (2)	2.27 (2)	3.1625 (15)	164 (1)
C7—H7B···O2iii	0.96	2.59	3.4571 (15)	150
N4—H4b···Cg1iv	0.89 (2)	2.724 (15)	3.5472 (14)	154.7 (12)