research communications
A redetermination from the original data of the
of 2-amino-4,6-dimethoxypyrimidin-1-ium 4-aminobenzoateaInstitute of Physics of the Czech Academy of Sciences, Na Slovance 2, 182 21 Praha 8, Czech Republic
*Correspondence e-mail: fabry@fzu.cz
The title structure, C6H9.5N3O20.5+·C7H6.5NO20.5−, which might be named schematically as 2-amino-4,6-dimethoxypyrimidine-(μ2-hydrogen)-4-aminobenzoate to indicate a bridging H atom, has been redetermined from the data published by Thanigaimani, Muthiah & 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 hydroxy 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.
Keywords: crystal structure; redetermination; hydrogen bonding; symmetric hydrogen bonds; refinement constraints; refinement restraints.
CCDC reference: 1465363
1. 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 et al. (2006) have been found; the pertinent CSD refcode is IFACUO.
of 2-amino-4,6-dimethoxypyrimidine–4-aminobenzoic acid (1/1) by ThanigaimaniThe 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
can be improved.2. 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 [Uiso(Hprimary amine) = 1.2Ueq(Nprimary amine) while Uiso(H4) = 1.5Ueq(O4)].
The improved 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 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 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 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).
byIn the recalculated a 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].
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–H4In a broader sense, the present redetermination emphasizes the importance of careful examination of the difference electron-density maps during structure determinations.
3. 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 R23(7) (Fig. 3) is shown in Fig. 2 of the article by Thanigaimani et al. (2006) and described there as R22(6).
In the present article, the graph-set motif R23(7) includes the atoms O4—H4o4⋯N1—C6—O2⋯H4ai—N4i or O4⋯H4n1—N1—C6—O2⋯H4ai—N4i on a local scale [Fig. 3; symmetry code (i): −x + 1, y − , −z + ].
4. Database survey
The et al. (2006) has been included in the Cambridge Structural Database (Groom & Allen, 2014) under the refcode IFACUO.
by Thanigaimani5. Synthesis and crystallization
The preparation of the title compound has been described by Thanigaimani et al. (2006).
6. Refinement
Crystal data, data collection and structure . 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 Uiso(Haryl) = 1.2Ueq(Caryl) while the methyl hydrogens were constrained by the constraints Cmethyl—Hmethyl = 0.96 Å and Uiso(Hmethyl) = 1.5Ueq(Cmethyl). The hydrogen atoms of the primary amine group N2 were constrained by Uiso(HN2) = 1.2Ueq(N2). The displacement parameters of the hydroxyl hydrogen H4O4 and of the secondary amine H4N1 were constrained by Uiso(H4O4) = 1.5Ueq(O4) and Uiso(H4N1) = 1.5Ueq(N1) while their positional parameters were refined freely.
details are summarized in Table 2
|
The model with the
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.Supporting information
CCDC reference: 1465363
https://doi.org/10.1107/S2056989016004321/su5289sup1.cif
contains datablocks global, I. DOI:Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2056989016004321/su5289Isup2.hkl
Supporting information file. DOI: https://doi.org/10.1107/S2056989016004321/su5289Isup3.smi
Data collection: DENZO (Otwinowski & Minor, 1997) and COLLECT (Hooft, 1998); cell
DENZO (Otwinowski & Minor, 1997) and COLLECT (Hooft, 1998); data reduction: DENZO (Otwinowski & Minor, 1997) and COLLECT (Hooft, 1998); 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).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[F > 3σ(F)] = 0.037 | H atoms treated by a mixture of independent and constrained refinement |
wR(F) = 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) |
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) −x+1, −y+2, −z; (ii) −x+1, y+1/2, −z+1/2; (iii) −x, −y+1, −z; (iv) −x+2, y+1/2, −z+1/2. |
Acknowledgements
The author expresses gratitude for the support provided by Project NPU I - LO1603 of the Ministry of Education of the Czech Republic. Discussions with Dr Radek Cibulka and Igor Linhart from the Chemical University in Prague are gratefully acknowledged.
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