Supporting information
Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536807047447/lw2035sup1.cif | |
Structure factor file (CIF format) https://doi.org/10.1107/S1600536807047447/lw2035Isup2.hkl |
CCDC reference: 609700
A hot methanolic solution (20 ml) of 2-amino-4,6-dimethoxy pyrimidine (38 mg, Aldrich) and phthalic acid (41 mg, Loba chemie) was warmed for half an hour over a water bath. The mixture was cooled slowly and kept at room temperature. After a few days colourless plate-like crystals were obtained.
All H atoms were positioned geometrically and were refined using a riding model. The C—H, O—H and N—H bond lengths are 0.93–0.96, 0.82 and 0.86 Å, respectively [Uiso (H)=1.2 Ueq(parent atom)].
Aminopyrimidine-carboxylate interactions are of fundamental important since they are involved in protein-nucleic acids recognition and protein-drug binding (Hunt et al., 1980; Baker & Santi, 1965). The adducts of carboxylic acid with 2-amino heterocylic ring system have a graph-set motif [R22(8)] (Lynch & Jones, 2004). This motif is very robust in aminopyrimidine- carboxylic acid/ carboxylate systems. The crystal structures of aminopyrimidine derivatives (Schwalbe & Williams, 1982), aminopyrimidine carboxylates (Muthiah et al., 2006) and cocrystals (Chinnakali et al., 1999) have been reported. The crystal structure of 2-amino-4,6-dimethoxy pyrimidine (Low et al., 2002) and 2-amino-4,6-dimethoxypyrimidine-4-aminobenzoic acid (1/1) (Thanigaimani et al., 2006) have also been reported. The crystal structure of phthalic acid (Van Schalkwyk, 1954) is known. The present study investigates the hydrogen bonding patterns in 2-amino-4,6-dimethoxy pyrimidine: phthalic acid (1/1) cocrystal(I).
The asymmetric unit (Fig 1) contains one 2-amino-4,6-dimethoxypyrimidine molecule and one phthalic acid molecule, which are linked by N—H···O and O—H···N intermolecular hydrogen bonds involving the nitrogen (N1) atom and 2-amino (NH2) group of the pyrimidine ring and carboxyl oxygen atoms (O3 and O4) to form a eight membered ring motif of graph-set notation of [R22(8)] (Etter, 1990; Bernstein et al., 1995). The another nitrogen atom (N3) and 2-amino (NH2) group of the pyrimidine ring also interact with carboxyl oxygen atoms (O5 and O6) to form a similar eight membered ring motif, generating a helical chain (made up of alternating pyrimidine and phthalic acid molecules) along the b axis (Fig 2). This chain is interpenetrated by a centrosymmetrically related chain (Fig 3) to which it is linked by π-π stacking of pyrimidines with a perpendicular separation of 3.332 Å, a centroid-centroid distance of 3.6424 (7) Å, ring offset of 1.471 Å and a slip angle (the angle between the centroid vector and the normal to the plane) of 23.81° These are typical aromatic stacking values (Hunter, 1994).
For related literature, see: Baker & Santi (1965); Bernstein et al. (1995); Chinnakali et al. (1999); Etter (1990); Hunt et al. (1980); Hunter (1994); Low et al. (2002); Lynch & Jones (2004); Muthiah et al. (2006); Schwalbe & Williams (1982); Thanigaimani et al. (2006); Van Schalkwyk (1954).
Data collection: DENZO (Otwinowski & Minor, 1997) and COLLECT (Hooft, 1998); cell refinement: 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, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: PLATON (Spek, 2003); software used to prepare material for publication: PLATON (Spek, 2003).
C6H9N3O2·C8H6O4 | F(000) = 672 |
Mr = 321.29 | Dx = 1.461 Mg m−3 |
Monoclinic, P21/c | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: -P 2ybc | Cell parameters from 25 reflections |
a = 11.2175 (3) Å | θ = 2.9–27.5° |
b = 7.3323 (2) Å | µ = 0.12 mm−1 |
c = 17.7651 (4) Å | T = 120 K |
β = 90.776 (2)° | Plate, colourless |
V = 1461.05 (6) Å3 | 0.50 × 0.40 × 0.25 mm |
Z = 4 |
Bruker–Nonius KappaCCD area-detector diffractometer | 2748 reflections with I > 2σ(I) |
Radiation source: Bruker–Nonius FR591 rotating anode | Rint = 0.029 |
Graphite monochromator | θmax = 27.5°, θmin = 3.5° |
φ and ω scans | h = −14→14 |
17905 measured reflections | k = −9→9 |
3328 independent reflections | l = −23→23 |
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)] = 0.041 | H-atom parameters constrained |
wR(F2) = 0.114 | w = 1/[σ2(Fo2) + (0.062P)2 + 0.4007P] where P = (Fo2 + 2Fc2)/3 |
S = 1.08 | (Δ/σ)max < 0.001 |
3328 reflections | Δρmax = 0.33 e Å−3 |
211 parameters | Δρmin = −0.30 e Å−3 |
0 restraints | Extinction correction: SHELXL97 (Sheldrick, 1997), FC*=KFC[1+0.001XFC2Λ3/SIN(2Θ)]-1/4 |
Primary atom site location: structure-invariant direct methods | Extinction coefficient: 0.034 (4) |
C6H9N3O2·C8H6O4 | V = 1461.05 (6) Å3 |
Mr = 321.29 | Z = 4 |
Monoclinic, P21/c | Mo Kα radiation |
a = 11.2175 (3) Å | µ = 0.12 mm−1 |
b = 7.3323 (2) Å | T = 120 K |
c = 17.7651 (4) Å | 0.50 × 0.40 × 0.25 mm |
β = 90.776 (2)° |
Bruker–Nonius KappaCCD area-detector diffractometer | 2748 reflections with I > 2σ(I) |
17905 measured reflections | Rint = 0.029 |
3328 independent reflections |
R[F2 > 2σ(F2)] = 0.041 | 0 restraints |
wR(F2) = 0.114 | H-atom parameters constrained |
S = 1.08 | Δρmax = 0.33 e Å−3 |
3328 reflections | Δρmin = −0.30 e Å−3 |
211 parameters |
Geometry. Bond distances, angles etc. have been calculated using the rounded fractional coordinates. All su's are estimated from the variances of the (full) variance-covariance matrix. The cell e.s.d.'s are taken into account in the estimation of distances, angles and torsion angles |
Refinement. Refinement on F2 for ALL reflections except those flagged by the user for potential systematic errors. Weighted R-factors wR and all goodnesses of fit S are based on F2, conventional R-factors R are based on F, with F set to zero for negative F2. The observed criterion of F2 > σ(F2) is used only for calculating -R-factor-obs 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 | ||
O1 | 1.33166 (8) | 0.41207 (13) | −0.01434 (5) | 0.0234 (3) | |
O2 | 0.94377 (8) | 0.19097 (15) | −0.08929 (5) | 0.0270 (3) | |
N1 | 0.99024 (9) | 0.26729 (16) | 0.02820 (6) | 0.0207 (3) | |
N2 | 1.03481 (10) | 0.33885 (18) | 0.15133 (6) | 0.0275 (4) | |
N3 | 1.18347 (9) | 0.37441 (15) | 0.06527 (6) | 0.0206 (3) | |
C2 | 1.07043 (11) | 0.32599 (18) | 0.08002 (7) | 0.0202 (4) | |
C4 | 1.21785 (11) | 0.35975 (17) | −0.00621 (7) | 0.0190 (3) | |
C5 | 1.14427 (11) | 0.29757 (18) | −0.06394 (7) | 0.0205 (3) | |
C6 | 1.02900 (11) | 0.25317 (18) | −0.04249 (7) | 0.0203 (4) | |
C7 | 1.38345 (12) | 0.39831 (19) | −0.08761 (7) | 0.0248 (4) | |
C8 | 0.97333 (13) | 0.1688 (2) | −0.16733 (7) | 0.0313 (5) | |
O3 | 0.76763 (8) | 0.15122 (14) | 0.05538 (5) | 0.0255 (3) | |
O4 | 0.79349 (9) | 0.23059 (17) | 0.17615 (5) | 0.0361 (4) | |
O5 | 0.76904 (9) | −0.13437 (16) | 0.24381 (5) | 0.0335 (3) | |
O6 | 0.65842 (8) | −0.00257 (14) | 0.33283 (5) | 0.0266 (3) | |
C9 | 0.61256 (11) | 0.08770 (17) | 0.13920 (7) | 0.0189 (3) | |
C10 | 0.58606 (11) | 0.00391 (17) | 0.20794 (7) | 0.0191 (3) | |
C11 | 0.47029 (11) | −0.05260 (19) | 0.22163 (8) | 0.0246 (4) | |
C12 | 0.38160 (12) | −0.0300 (2) | 0.16694 (9) | 0.0293 (4) | |
C13 | 0.40797 (12) | 0.0508 (2) | 0.09912 (8) | 0.0283 (4) | |
C14 | 0.52267 (11) | 0.11137 (19) | 0.08528 (7) | 0.0230 (4) | |
C15 | 0.73442 (11) | 0.16274 (18) | 0.12583 (7) | 0.0202 (4) | |
C16 | 0.68190 (11) | −0.04810 (18) | 0.26337 (7) | 0.0206 (4) | |
H2A | 1.08350 | 0.37690 | 0.18570 | 0.0330* | |
H2B | 0.96320 | 0.30910 | 0.16290 | 0.0330* | |
H5 | 1.16990 | 0.28630 | −0.11330 | 0.0250* | |
H7A | 1.46440 | 0.44060 | −0.08530 | 0.0370* | |
H7B | 1.33860 | 0.47170 | −0.12260 | 0.0370* | |
H7C | 1.38200 | 0.27340 | −0.10380 | 0.0370* | |
H8A | 0.90510 | 0.12350 | −0.19460 | 0.0470* | |
H8B | 1.03790 | 0.08370 | −0.17160 | 0.0470* | |
H8C | 0.99670 | 0.28430 | −0.18780 | 0.0470* | |
H3 | 0.83520 | 0.19250 | 0.05140 | 0.0380* | |
H6 | 0.71170 | −0.04000 | 0.36090 | 0.0400* | |
H11 | 0.45190 | −0.10580 | 0.26760 | 0.0300* | |
H12 | 0.30440 | −0.06950 | 0.17610 | 0.0350* | |
H13 | 0.34860 | 0.06480 | 0.06250 | 0.0340* | |
H14 | 0.53960 | 0.16800 | 0.03980 | 0.0280* |
U11 | U22 | U33 | U12 | U13 | U23 | |
O1 | 0.0198 (4) | 0.0317 (5) | 0.0188 (4) | −0.0030 (4) | 0.0051 (3) | −0.0006 (4) |
O2 | 0.0199 (5) | 0.0452 (6) | 0.0160 (4) | −0.0030 (4) | 0.0022 (3) | −0.0057 (4) |
N1 | 0.0188 (5) | 0.0277 (6) | 0.0156 (5) | −0.0002 (4) | 0.0027 (4) | 0.0000 (4) |
N2 | 0.0186 (5) | 0.0486 (8) | 0.0155 (5) | −0.0066 (5) | 0.0037 (4) | −0.0022 (5) |
N3 | 0.0189 (5) | 0.0263 (6) | 0.0165 (5) | −0.0003 (4) | 0.0022 (4) | 0.0002 (4) |
C2 | 0.0193 (6) | 0.0232 (7) | 0.0181 (6) | 0.0013 (5) | 0.0015 (5) | 0.0014 (5) |
C4 | 0.0187 (6) | 0.0196 (6) | 0.0188 (6) | 0.0025 (5) | 0.0035 (5) | 0.0022 (5) |
C5 | 0.0224 (6) | 0.0247 (7) | 0.0145 (5) | 0.0017 (5) | 0.0037 (5) | 0.0003 (5) |
C6 | 0.0209 (6) | 0.0228 (7) | 0.0173 (6) | 0.0027 (5) | 0.0007 (5) | 0.0002 (5) |
C7 | 0.0242 (7) | 0.0273 (7) | 0.0231 (6) | −0.0019 (5) | 0.0099 (5) | −0.0009 (6) |
C8 | 0.0248 (7) | 0.0522 (10) | 0.0170 (6) | −0.0034 (6) | 0.0021 (5) | −0.0083 (6) |
O3 | 0.0210 (5) | 0.0382 (6) | 0.0174 (5) | −0.0054 (4) | 0.0041 (4) | −0.0006 (4) |
O4 | 0.0277 (5) | 0.0595 (8) | 0.0212 (5) | −0.0182 (5) | 0.0044 (4) | −0.0079 (5) |
O5 | 0.0236 (5) | 0.0565 (7) | 0.0204 (5) | 0.0149 (5) | 0.0017 (4) | −0.0024 (5) |
O6 | 0.0273 (5) | 0.0363 (6) | 0.0162 (4) | 0.0104 (4) | 0.0020 (4) | −0.0001 (4) |
C9 | 0.0197 (6) | 0.0190 (6) | 0.0180 (6) | 0.0009 (5) | 0.0011 (5) | −0.0018 (5) |
C10 | 0.0192 (6) | 0.0185 (6) | 0.0198 (6) | 0.0023 (5) | 0.0030 (5) | −0.0011 (5) |
C11 | 0.0225 (6) | 0.0233 (7) | 0.0282 (7) | 0.0008 (5) | 0.0071 (5) | 0.0016 (6) |
C12 | 0.0164 (6) | 0.0305 (8) | 0.0411 (8) | −0.0022 (5) | 0.0036 (6) | −0.0023 (6) |
C13 | 0.0218 (7) | 0.0295 (8) | 0.0334 (8) | 0.0043 (5) | −0.0062 (5) | −0.0011 (6) |
C14 | 0.0242 (6) | 0.0225 (7) | 0.0223 (6) | 0.0021 (5) | −0.0017 (5) | 0.0008 (5) |
C15 | 0.0208 (6) | 0.0225 (7) | 0.0173 (6) | 0.0011 (5) | 0.0024 (5) | 0.0028 (5) |
C16 | 0.0201 (6) | 0.0238 (7) | 0.0180 (6) | −0.0001 (5) | 0.0039 (5) | 0.0016 (5) |
O1—C4 | 1.3427 (15) | C5—H5 | 0.9300 |
O1—C7 | 1.4361 (15) | C7—H7B | 0.9600 |
O2—C6 | 1.3386 (16) | C7—H7A | 0.9600 |
O2—C8 | 1.4391 (15) | C7—H7C | 0.9600 |
O3—C15 | 1.3134 (15) | C8—H8C | 0.9600 |
O4—C15 | 1.2123 (16) | C8—H8A | 0.9600 |
O5—C16 | 1.2188 (16) | C8—H8B | 0.9600 |
O6—C16 | 1.3086 (15) | C9—C10 | 1.4025 (18) |
O3—H3 | 0.8200 | C9—C15 | 1.4955 (18) |
O6—H6 | 0.8200 | C9—C14 | 1.3922 (18) |
N1—C2 | 1.3489 (16) | C10—C16 | 1.4974 (18) |
N1—C6 | 1.3385 (16) | C10—C11 | 1.3878 (18) |
N2—C2 | 1.3368 (16) | C11—C12 | 1.391 (2) |
N3—C4 | 1.3364 (16) | C12—C13 | 1.378 (2) |
N3—C2 | 1.3460 (16) | C13—C14 | 1.3863 (18) |
N2—H2B | 0.8600 | C11—H11 | 0.9300 |
N2—H2A | 0.8600 | C12—H12 | 0.9300 |
C4—C5 | 1.3849 (18) | C13—H13 | 0.9300 |
C5—C6 | 1.3916 (18) | C14—H14 | 0.9300 |
O3···N1 | 2.6881 (14) | C13···H14v | 3.0100 |
O4···C16 | 2.8629 (17) | C14···H14v | 3.1000 |
O4···N2 | 2.8609 (15) | C14···H7Cii | 3.0300 |
O4···O5 | 2.9479 (16) | C15···H7Bvi | 2.8000 |
O5···O4 | 2.9479 (16) | C15···H2B | 2.8500 |
O5···N2i | 2.8704 (15) | C16···H2Ai | 2.8300 |
O5···C8ii | 3.2199 (17) | H2A···C16iii | 2.8300 |
O5···C15 | 3.0443 (17) | H2A···O5iii | 2.0600 |
O6···N3i | 2.6738 (14) | H2A···H6iii | 2.5300 |
O1···H6iii | 2.8000 | H2A···C8vii | 2.9200 |
O1···H13iv | 2.8900 | H2B···O4 | 2.0100 |
O2···H3 | 2.8000 | H2B···C8vii | 3.0200 |
O3···H14 | 2.5700 | H2B···H3 | 2.5800 |
O3···H13v | 2.9200 | H2B···C15 | 2.8500 |
O4···H7Bvi | 2.8000 | H3···C2 | 2.8500 |
O4···H2B | 2.0100 | H3···N1 | 1.8700 |
O4···H8Avii | 2.8100 | H3···O2 | 2.8000 |
O5···H2Ai | 2.0600 | H3···C6 | 2.7900 |
O5···H8Bii | 2.5600 | H3···H2B | 2.5800 |
O5···H5ii | 2.6700 | H5···C7 | 2.5700 |
O6···H11 | 2.6900 | H5···O5ii | 2.6700 |
O6···H7Aviii | 2.6700 | H5···H8C | 2.3400 |
N1···O3 | 2.6881 (14) | H5···C8 | 2.5400 |
N2···O5iii | 2.8704 (15) | H5···H7B | 2.3400 |
N2···O4 | 2.8609 (15) | H5···H7C | 2.3800 |
N2···C8vii | 3.3041 (17) | H5···H8B | 2.3300 |
N3···O6iii | 2.6738 (14) | H6···C4i | 2.7900 |
N3···C16iii | 3.4273 (16) | H6···H2Ai | 2.5300 |
N1···H3 | 1.8700 | H6···C2i | 2.8200 |
N2···H8Cvi | 2.8600 | H6···N3i | 1.8600 |
N3···H6iii | 1.8600 | H6···O1i | 2.8000 |
N3···H13iv | 2.9300 | H7A···O6xii | 2.6700 |
C2···C6vi | 3.3452 (19) | H7B···C5 | 2.7400 |
C6···C2vi | 3.3452 (19) | H7B···C15vi | 2.8000 |
C7···C15vi | 3.5417 (19) | H7B···H11xii | 2.5400 |
C8···O5ii | 3.2199 (17) | H7B···O4vi | 2.8000 |
C8···N2ix | 3.3041 (17) | H7B···H5 | 2.3400 |
C10···C11x | 3.5441 (19) | H7C···H5 | 2.3800 |
C11···C10xi | 3.5441 (19) | H7C···C9ii | 2.7200 |
C13···C14v | 3.5805 (19) | H7C···C14ii | 3.0300 |
C14···C14v | 3.4735 (18) | H7C···C10ii | 2.7800 |
C14···C13v | 3.5805 (19) | H7C···C5 | 2.7700 |
C15···O5 | 3.0443 (17) | H8A···H12v | 2.4100 |
C15···C7vi | 3.5417 (19) | H8A···O4ix | 2.8100 |
C16···O4 | 2.8629 (17) | H8B···H5 | 2.3300 |
C16···N3i | 3.4273 (16) | H8B···O5ii | 2.5600 |
C2···H6iii | 2.8200 | H8B···C5 | 2.7300 |
C2···H3 | 2.8500 | H8C···N2vi | 2.8600 |
C4···H6iii | 2.7900 | H8C···C5 | 2.7400 |
C4···H13iv | 2.8800 | H8C···H5 | 2.3400 |
C5···H7C | 2.7700 | H11···O6 | 2.6900 |
C5···H8B | 2.7300 | H11···C9xi | 2.8900 |
C5···H8C | 2.7400 | H11···C10xi | 2.9300 |
C5···H7B | 2.7400 | H11···C7viii | 3.0900 |
C6···H3 | 2.7900 | H11···H7Bviii | 2.5400 |
C7···H11xii | 3.0900 | H12···H8Av | 2.4100 |
C7···H5 | 2.5700 | H13···O1xiii | 2.8900 |
C8···H2Bix | 3.0200 | H13···N3xiii | 2.9300 |
C8···H2Aix | 2.9200 | H13···C4xiii | 2.8800 |
C8···H5 | 2.5400 | H13···O3v | 2.9200 |
C9···H7Cii | 2.7200 | H14···O3 | 2.5700 |
C9···H11x | 2.8900 | H14···C13v | 3.0100 |
C10···H7Cii | 2.7800 | H14···C14v | 3.1000 |
C10···H11x | 2.9300 | ||
C4—O1—C7 | 118.31 (10) | H8A—C8—H8C | 110.00 |
C6—O2—C8 | 117.70 (10) | H8B—C8—H8C | 109.00 |
C15—O3—H3 | 109.00 | O2—C8—H8A | 109.00 |
C16—O6—H6 | 109.00 | O2—C8—H8B | 109.00 |
C2—N1—C6 | 116.29 (11) | C10—C9—C14 | 119.58 (11) |
C2—N3—C4 | 116.65 (11) | C14—C9—C15 | 120.00 (11) |
C2—N2—H2B | 120.00 | C10—C9—C15 | 120.29 (11) |
H2A—N2—H2B | 120.00 | C9—C10—C16 | 121.70 (11) |
C2—N2—H2A | 120.00 | C11—C10—C16 | 118.29 (11) |
N1—C2—N3 | 124.93 (11) | C9—C10—C11 | 119.56 (12) |
N2—C2—N3 | 117.41 (11) | C10—C11—C12 | 120.28 (13) |
N1—C2—N2 | 117.65 (11) | C11—C12—C13 | 120.12 (13) |
O1—C4—C5 | 124.92 (11) | C12—C13—C14 | 120.23 (13) |
N3—C4—C5 | 123.60 (11) | C9—C14—C13 | 120.22 (12) |
O1—C4—N3 | 111.49 (11) | O3—C15—C9 | 113.54 (11) |
C4—C5—C6 | 114.89 (11) | O4—C15—C9 | 121.70 (11) |
O2—C6—C5 | 124.62 (11) | O3—C15—O4 | 124.74 (12) |
N1—C6—C5 | 123.62 (11) | O6—C16—C10 | 113.78 (11) |
O2—C6—N1 | 111.76 (11) | O5—C16—O6 | 125.01 (12) |
C4—C5—H5 | 123.00 | O5—C16—C10 | 121.07 (11) |
C6—C5—H5 | 123.00 | C10—C11—H11 | 120.00 |
O1—C7—H7B | 109.00 | C12—C11—H11 | 120.00 |
O1—C7—H7C | 109.00 | C11—C12—H12 | 120.00 |
H7A—C7—H7C | 109.00 | C13—C12—H12 | 120.00 |
H7B—C7—H7C | 110.00 | C12—C13—H13 | 120.00 |
H7A—C7—H7B | 110.00 | C14—C13—H13 | 120.00 |
O1—C7—H7A | 109.00 | C9—C14—H14 | 120.00 |
O2—C8—H8C | 109.00 | C13—C14—H14 | 120.00 |
H8A—C8—H8B | 109.00 | ||
C7—O1—C4—N3 | 177.86 (11) | C15—C9—C10—C11 | 175.14 (12) |
C7—O1—C4—C5 | −1.95 (18) | C15—C9—C10—C16 | −12.75 (18) |
C8—O2—C6—N1 | −179.91 (11) | C10—C9—C14—C13 | −0.7 (2) |
C8—O2—C6—C5 | −0.14 (19) | C15—C9—C14—C13 | −176.50 (12) |
C6—N1—C2—N2 | −179.02 (12) | C10—C9—C15—O3 | 147.33 (12) |
C6—N1—C2—N3 | 1.7 (2) | C10—C9—C15—O4 | −34.25 (19) |
C2—N1—C6—O2 | 178.89 (11) | C14—C9—C15—O3 | −36.88 (17) |
C2—N1—C6—C5 | −0.89 (19) | C14—C9—C15—O4 | 141.55 (14) |
C4—N3—C2—N1 | −1.06 (19) | C9—C10—C11—C12 | 1.4 (2) |
C4—N3—C2—N2 | 179.63 (12) | C16—C10—C11—C12 | −170.97 (13) |
C2—N3—C4—O1 | 179.80 (11) | C9—C10—C16—O5 | −49.60 (19) |
C2—N3—C4—C5 | −0.39 (19) | C9—C10—C16—O6 | 134.45 (13) |
O1—C4—C5—C6 | −179.18 (12) | C11—C10—C16—O5 | 122.61 (15) |
N3—C4—C5—C6 | 1.04 (19) | C11—C10—C16—O6 | −53.35 (16) |
C4—C5—C6—O2 | 179.89 (12) | C10—C11—C12—C13 | −0.8 (2) |
C4—C5—C6—N1 | −0.36 (19) | C11—C12—C13—C14 | −0.6 (2) |
C14—C9—C10—C11 | −0.67 (19) | C12—C13—C14—C9 | 1.3 (2) |
C14—C9—C10—C16 | 171.44 (12) |
Symmetry codes: (i) −x+2, y−1/2, −z+1/2; (ii) −x+2, −y, −z; (iii) −x+2, y+1/2, −z+1/2; (iv) x+1, y, z; (v) −x+1, −y, −z; (vi) −x+2, −y+1, −z; (vii) x, −y+1/2, z+1/2; (viii) x−1, −y+1/2, z+1/2; (ix) x, −y+1/2, z−1/2; (x) −x+1, y+1/2, −z+1/2; (xi) −x+1, y−1/2, −z+1/2; (xii) x+1, −y+1/2, z−1/2; (xiii) x−1, y, z. |
D—H···A | D—H | H···A | D···A | D—H···A |
N2—H2A···O5iii | 0.86 | 2.06 | 2.8704 (15) | 156 |
N2—H2B···O4 | 0.86 | 2.01 | 2.8609 (15) | 173 |
O3—H3···N1 | 0.82 | 1.87 | 2.6881 (14) | 171 |
O6—H6···N3i | 0.82 | 1.86 | 2.6738 (14) | 172 |
C8—H8B···O5ii | 0.96 | 2.56 | 3.2199 (17) | 126 |
Symmetry codes: (i) −x+2, y−1/2, −z+1/2; (ii) −x+2, −y, −z; (iii) −x+2, y+1/2, −z+1/2. |
Experimental details
Crystal data | |
Chemical formula | C6H9N3O2·C8H6O4 |
Mr | 321.29 |
Crystal system, space group | Monoclinic, P21/c |
Temperature (K) | 120 |
a, b, c (Å) | 11.2175 (3), 7.3323 (2), 17.7651 (4) |
β (°) | 90.776 (2) |
V (Å3) | 1461.05 (6) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 0.12 |
Crystal size (mm) | 0.50 × 0.40 × 0.25 |
Data collection | |
Diffractometer | Bruker–Nonius KappaCCD area-detector |
Absorption correction | – |
No. of measured, independent and observed [I > 2σ(I)] reflections | 17905, 3328, 2748 |
Rint | 0.029 |
(sin θ/λ)max (Å−1) | 0.650 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.041, 0.114, 1.08 |
No. of reflections | 3328 |
No. of parameters | 211 |
H-atom treatment | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 0.33, −0.30 |
Computer programs: DENZO (Otwinowski & Minor, 1997) and COLLECT (Hooft, 1998), SHELXS97 (Sheldrick, 1997), SHELXL97 (Sheldrick, 1997), PLATON (Spek, 2003).
O1—C4 | 1.3427 (15) | O6—C16 | 1.3086 (15) |
O1—C7 | 1.4361 (15) | N1—C2 | 1.3489 (16) |
O2—C6 | 1.3386 (16) | N1—C6 | 1.3385 (16) |
O2—C8 | 1.4391 (15) | N2—C2 | 1.3368 (16) |
O3—C15 | 1.3134 (15) | N3—C4 | 1.3364 (16) |
O4—C15 | 1.2123 (16) | N3—C2 | 1.3460 (16) |
O5—C16 | 1.2188 (16) | ||
C4—O1—C7 | 118.31 (10) | O2—C6—C5 | 124.62 (11) |
C6—O2—C8 | 117.70 (10) | N1—C6—C5 | 123.62 (11) |
C2—N1—C6 | 116.29 (11) | O2—C6—N1 | 111.76 (11) |
C2—N3—C4 | 116.65 (11) | O3—C15—C9 | 113.54 (11) |
N1—C2—N3 | 124.93 (11) | O4—C15—C9 | 121.70 (11) |
N2—C2—N3 | 117.41 (11) | O3—C15—O4 | 124.74 (12) |
N1—C2—N2 | 117.65 (11) | O6—C16—C10 | 113.78 (11) |
O1—C4—C5 | 124.92 (11) | O5—C16—O6 | 125.01 (12) |
N3—C4—C5 | 123.60 (11) | O5—C16—C10 | 121.07 (11) |
O1—C4—N3 | 111.49 (11) |
D—H···A | D—H | H···A | D···A | D—H···A |
N2—H2A···O5i | 0.8600 | 2.0600 | 2.8704 (15) | 156.00 |
N2—H2B···O4 | 0.8600 | 2.0100 | 2.8609 (15) | 173.00 |
O3—H3···N1 | 0.8200 | 1.8700 | 2.6881 (14) | 171.00 |
O6—H6···N3ii | 0.8200 | 1.8600 | 2.6738 (14) | 172.00 |
C8—H8B···O5iii | 0.9600 | 2.5600 | 3.2199 (17) | 126.00 |
Symmetry codes: (i) −x+2, y+1/2, −z+1/2; (ii) −x+2, y−1/2, −z+1/2; (iii) −x+2, −y, −z. |
Aminopyrimidine-carboxylate interactions are of fundamental important since they are involved in protein-nucleic acids recognition and protein-drug binding (Hunt et al., 1980; Baker & Santi, 1965). The adducts of carboxylic acid with 2-amino heterocylic ring system have a graph-set motif [R22(8)] (Lynch & Jones, 2004). This motif is very robust in aminopyrimidine- carboxylic acid/ carboxylate systems. The crystal structures of aminopyrimidine derivatives (Schwalbe & Williams, 1982), aminopyrimidine carboxylates (Muthiah et al., 2006) and cocrystals (Chinnakali et al., 1999) have been reported. The crystal structure of 2-amino-4,6-dimethoxy pyrimidine (Low et al., 2002) and 2-amino-4,6-dimethoxypyrimidine-4-aminobenzoic acid (1/1) (Thanigaimani et al., 2006) have also been reported. The crystal structure of phthalic acid (Van Schalkwyk, 1954) is known. The present study investigates the hydrogen bonding patterns in 2-amino-4,6-dimethoxy pyrimidine: phthalic acid (1/1) cocrystal(I).
The asymmetric unit (Fig 1) contains one 2-amino-4,6-dimethoxypyrimidine molecule and one phthalic acid molecule, which are linked by N—H···O and O—H···N intermolecular hydrogen bonds involving the nitrogen (N1) atom and 2-amino (NH2) group of the pyrimidine ring and carboxyl oxygen atoms (O3 and O4) to form a eight membered ring motif of graph-set notation of [R22(8)] (Etter, 1990; Bernstein et al., 1995). The another nitrogen atom (N3) and 2-amino (NH2) group of the pyrimidine ring also interact with carboxyl oxygen atoms (O5 and O6) to form a similar eight membered ring motif, generating a helical chain (made up of alternating pyrimidine and phthalic acid molecules) along the b axis (Fig 2). This chain is interpenetrated by a centrosymmetrically related chain (Fig 3) to which it is linked by π-π stacking of pyrimidines with a perpendicular separation of 3.332 Å, a centroid-centroid distance of 3.6424 (7) Å, ring offset of 1.471 Å and a slip angle (the angle between the centroid vector and the normal to the plane) of 23.81° These are typical aromatic stacking values (Hunter, 1994).