Supporting information
Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536810014583/bt5240sup1.cif | |
Structure factor file (CIF format) https://doi.org/10.1107/S1600536810014583/bt5240Isup2.hkl |
CCDC reference: 778070
Key indicators
- Single-crystal X-ray study
- T = 200 K
- Mean (C-C) = 0.002 Å
- Disorder in main residue
- R factor = 0.054
- wR factor = 0.160
- Data-to-parameter ratio = 24.0
checkCIF/PLATON results
No syntax errors found
Alert level A PLAT113_ALERT_2_A ADDSYM Suggests Possible Pseudo/New Space-group. P21/m
Author Response: The structure neither solves nor refines in P21/m. This is thus due to pseudo-symmetry. |
Alert level B PLAT110_ALERT_2_B ADDSYM Detects Potential Lattice Centering or Halving . ? PLAT112_ALERT_2_B ADDSYM Detects Additional (Pseudo) Symm. Elem... Z PLAT910_ALERT_3_B Missing # of FCF Reflections Below Th(Min) ..... 18
Alert level C PLAT250_ALERT_2_C Large U3/U1 Ratio for Average U(i,j) Tensor .... 2.73 PLAT250_ALERT_2_C Large U3/U1 Ratio for Average U(i,j) Tensor .... 2.06 PLAT432_ALERT_2_C Short Inter X...Y Contact C1B .. C3A .. 3.15 Ang. PLAT432_ALERT_2_C Short Inter X...Y Contact C1B .. C3A .. 3.18 Ang. PLAT911_ALERT_3_C Missing # FCF Refl Between THmin & STh/L= 0.600 18 PLAT913_ALERT_3_C Missing # of Very Strong Reflections in FCF .... 1 PLAT042_ALERT_1_C Calc. and Reported MoietyFormula Strings Differ ? PLAT480_ALERT_4_C Long H...A H-Bond Reported H2BA .. O62A .. 2.62 Ang. PLAT912_ALERT_4_C Missing # of FCF Reflections Above STh/L= 0.600 424
Alert level G PLAT301_ALERT_3_G Note: Main Residue Disorder ................... 7.00 Perc. PLAT860_ALERT_3_G Note: Number of Least-Squares Restraints ....... 24 PLAT720_ALERT_4_G Number of Unusual/Non-Standard Labels .......... 12 PLAT779_ALERT_4_G Suspect or Irrelevant (Bond) Angle in CIF ...... 43.10 Deg. O62B -N6A -O62A 1.555 1.555 1.555 PLAT779_ALERT_4_G Suspect or Irrelevant (Bond) Angle in CIF ...... 42.40 Deg. O61B -N6A -O61A 1.555 1.555 1.555
1 ALERT level A = In general: serious problem 3 ALERT level B = Potentially serious problem 9 ALERT level C = Check and explain 5 ALERT level G = General alerts; check 1 ALERT type 1 CIF construction/syntax error, inconsistent or missing data 7 ALERT type 2 Indicator that the structure model may be wrong or deficient 5 ALERT type 3 Indicator that the structure quality may be low 5 ALERT type 4 Improvement, methodology, query or suggestion 0 ALERT type 5 Informative message, check
4-Methoxy-6-methylpyrimidin-2-amine (1.39 g, 0.01 mol) was dissolved in 25 ml of ethanol. Picric acid (2.29 g, 0.01 mol) was dissolved in 15 ml of water. Both the solutions were mixed and to this, 5 ml of 5M HCl was added and stirred for few minutes. The formed complex was filtered and dried. Good quality crystals were grown from ethanol solution by slow evaporation (m. p.: 399 K). Composition: Found (Calculated): C: 39.09 (39.14); H: 3.24 (3.28); N: 22.77% (22.82%).
All of the H atoms were placed in their calculated positions and then refined using the riding model with C—H = 0.95-0.98 Å, N—H = 0.88 Å, and with Uiso(H) = 1.18-1.52Ueq(C,N).
The synthesis of imidazo[1,2-a]pyrimidines has been widely investigated and is one of the most common strategies in the use of 2-aminopyrimidine as the starting material (Katritzky et al., 2003). Recently, the hydrogen-bonding patterns in 2-amino-4,6-dimethylpyrimidinium picrate has been reported (Subashini et al., 2006). In continuation of our work on picrates of biologically important molecules, we have prepared a new picrate of 2-amino-4-methoxy-6-methylpyrimidine, [C6H10N3 O]+, [C6H2N3O7]- and its crystal structure is reported.
The title compound,(I), C12H12N6O8, crystallizes as a salt with one C6H10N3 O+, C6H2N3O7- , cation-anion pair in the asymmetric unit (Fig. 1). The dihedral angle between the mean planes of the benzene and pyridine rings is 3.10°. In the cation the methoxy group is almost coplanar with the pyridine ring [C6B-O1B-C5B-N3B torsion angle = -0.63 (19)°]. Bond distances and angles in both the cation and anion are in normal ranges (Allen, 2002). The p [torsion angle C3A-C4A-N4A-O41A = 1.17 (18)°] and one o [torsion angle C1A-C2A-N2A-O21A = 1.83 (19)°] nitro group in the anion are nearly coplanar with the benzene ring. The other disordered o nitro group containing the predomoinate oxygen atom (occupancy = 0.868 (6)) is twisted -29.0 (2)\5 from the mean plane of the benzene ring. Bifurcated intramolecular donor, N1B, [O1A [N1B—H1BB···O21A. & N1B—H1BB···O1A] and acceptor, O1A, [N1B—H1BB···O1A & N2B—H2BA···O1A] hydrogen bonds and a weak C3B—H3BB···O62A(0.868 (6)) hydrogen bond interaction (Table 2) between the cation and anion produces a network of infinite O—H···O—H···O—H chains along the c axis in the [101] plane which helps to establish crystal packing (Fig. 2).
A density functional theory (DFT) geometry optimization molecular orbital calculation (Schmidt & Polik, 2007) was performed on the independent cation-anion pair (C6H10N3 O+, C6H2N3O7- ) within the asymmetric unit with the B3LYP 6-31-G(d) basis set (Hehre et al., 1986). Starting geometries were taken from X-ray refinement data. The dihedral angle between the mean planes of the benzene and pyridine rings increases to 28.10°. In the anion, the mean planes of the two o-nitro groups become twisted by 23.14° and 24.20°, respectively, from the mean plane of the benzene ring. The mean plane of the p-nitro group remains planar to the benzene ring. The mean plane of the methoxy group in the cation also remains planar to the pyridine ring. These observations suggest that the bifurcated N—H···(O,O) donor and acceptor hydrogen bonds and weak C—H···O intermolecular interactions play a significant role in crystal stability.
For the synthesis of imidazo[1,2-a]pyrimidines, see: Katritzky et al. (2003). For related structures, see: Ferguson et al. (1984); Glidewell et al. (2003); Narayana et al. (2008); Scheinbeim & Schempp, (1976); Schlueter et al. (2006); Subashini et al. (2006). For density functional theory, see: Hehre et al. (1986); Schmidt & Polik (2007).
Data collection: CrysAlis PRO (Oxford Diffraction, 2007); cell refinement: CrysAlis RED (Oxford Diffraction, 2007); data reduction: CrysAlis RED (Oxford Diffraction, 2007); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97) (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL (Sheldrick, 2008) and PLATON (Spek, 2009).
C6H10N3O+·C6H2N3O7− | F(000) = 760 |
Mr = 368.28 | Dx = 1.616 Mg m−3 |
Monoclinic, P21/c | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: -P 2ybc | Cell parameters from 3951 reflections |
a = 8.9442 (3) Å | θ = 4.6–34.8° |
b = 6.2793 (3) Å | µ = 0.14 mm−1 |
c = 27.0354 (8) Å | T = 200 K |
β = 94.471 (3)° | Prism, yellow |
V = 1513.78 (10) Å3 | 0.52 × 0.46 × 0.35 mm |
Z = 4 |
Oxford Diffraction Gemini diffractometer | 6133 independent reflections |
Radiation source: fine-focus sealed tube | 3107 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.031 |
Detector resolution: 10.5081 pixels mm-1 | θmax = 34.9°, θmin = 4.6° |
φ and ω scans | h = −11→14 |
Absorption correction: multi-scan (CrysAlis RED; Oxford Diffraction, 2007) | k = −9→9 |
Tmin = 0.986, Tmax = 1.000 | l = −42→43 |
15870 measured reflections |
Refinement on F2 | Primary atom site location: structure-invariant direct methods |
Least-squares matrix: full | Secondary atom site location: difference Fourier map |
R[F2 > 2σ(F2)] = 0.054 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.160 | H-atom parameters constrained |
S = 0.94 | w = 1/[σ2(Fo2) + (0.0847P)2] where P = (Fo2 + 2Fc2)/3 |
6133 reflections | (Δ/σ)max < 0.001 |
256 parameters | Δρmax = 0.43 e Å−3 |
24 restraints | Δρmin = −0.29 e Å−3 |
C6H10N3O+·C6H2N3O7− | V = 1513.78 (10) Å3 |
Mr = 368.28 | Z = 4 |
Monoclinic, P21/c | Mo Kα radiation |
a = 8.9442 (3) Å | µ = 0.14 mm−1 |
b = 6.2793 (3) Å | T = 200 K |
c = 27.0354 (8) Å | 0.52 × 0.46 × 0.35 mm |
β = 94.471 (3)° |
Oxford Diffraction Gemini diffractometer | 6133 independent reflections |
Absorption correction: multi-scan (CrysAlis RED; Oxford Diffraction, 2007) | 3107 reflections with I > 2σ(I) |
Tmin = 0.986, Tmax = 1.000 | Rint = 0.031 |
15870 measured reflections |
R[F2 > 2σ(F2)] = 0.054 | 24 restraints |
wR(F2) = 0.160 | H-atom parameters constrained |
S = 0.94 | Δρmax = 0.43 e Å−3 |
6133 reflections | Δρmin = −0.29 e Å−3 |
256 parameters |
Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds 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 | Occ. (<1) | |
O1A | 0.55766 (10) | 0.25342 (17) | 0.27447 (3) | 0.0282 (2) | |
O21A | 0.30234 (11) | 0.2803 (2) | 0.21683 (4) | 0.0407 (3) | |
O22A | 0.31232 (12) | 0.2676 (2) | 0.13799 (4) | 0.0545 (4) | |
O41A | 0.75641 (11) | 0.24825 (17) | 0.05802 (3) | 0.0317 (2) | |
O42A | 0.97162 (12) | 0.2438 (2) | 0.09966 (4) | 0.0505 (4) | |
O61A | 1.00309 (15) | 0.1699 (4) | 0.27556 (5) | 0.0322 (5) | 0.868 (6) |
O62A | 0.83577 (17) | 0.3370 (5) | 0.31386 (5) | 0.0433 (6) | 0.868 (6) |
O61B | 1.0068 (10) | 0.311 (3) | 0.2751 (3) | 0.040 (3) | 0.132 (6) |
O62B | 0.8309 (11) | 0.195 (3) | 0.3157 (3) | 0.038 (3) | 0.132 (6) |
O1B | 0.28372 (11) | 0.24739 (17) | 0.49248 (3) | 0.0326 (2) | |
N2A | 0.37356 (11) | 0.26925 (19) | 0.18027 (4) | 0.0241 (2) | |
N4A | 0.83482 (12) | 0.24677 (19) | 0.09742 (4) | 0.0251 (2) | |
N6A | 0.87761 (11) | 0.25092 (18) | 0.27698 (4) | 0.0222 (2) | |
N1B | 0.30287 (11) | 0.25263 (17) | 0.32338 (3) | 0.0193 (2) | |
H1BA | 0.2044 | 0.2490 | 0.3191 | 0.023* | |
H1BB | 0.3568 | 0.2555 | 0.2975 | 0.023* | |
N2B | 0.52320 (11) | 0.25912 (18) | 0.37421 (3) | 0.0194 (2) | |
H2BA | 0.5741 | 0.2630 | 0.3477 | 0.023* | |
N3B | 0.28659 (11) | 0.24940 (18) | 0.40787 (3) | 0.0209 (2) | |
C1A | 0.61812 (12) | 0.2561 (2) | 0.23423 (4) | 0.0173 (2) | |
C2A | 0.53717 (12) | 0.2594 (2) | 0.18562 (4) | 0.0175 (2) | |
C3A | 0.60696 (13) | 0.2561 (2) | 0.14188 (4) | 0.0183 (2) | |
H3AA | 0.5490 | 0.2588 | 0.1109 | 0.022* | |
C4A | 0.76183 (13) | 0.2487 (2) | 0.14336 (4) | 0.0184 (2) | |
C5A | 0.85022 (12) | 0.2451 (2) | 0.18818 (4) | 0.0186 (2) | |
H5AA | 0.9565 | 0.2389 | 0.1888 | 0.022* | |
C6A | 0.77977 (12) | 0.2506 (2) | 0.23132 (4) | 0.0173 (2) | |
C1B | 0.36982 (12) | 0.2538 (2) | 0.36869 (4) | 0.0169 (2) | |
C2B | 0.59876 (14) | 0.2586 (2) | 0.42009 (4) | 0.0243 (3) | |
C3B | 0.76596 (15) | 0.2631 (3) | 0.42302 (5) | 0.0375 (4) | |
H3BA | 0.8052 | 0.2642 | 0.4579 | 0.056* | |
H3BB | 0.7996 | 0.3914 | 0.4065 | 0.056* | |
H3BC | 0.8030 | 0.1366 | 0.4066 | 0.056* | |
C4B | 0.51754 (14) | 0.2534 (3) | 0.46052 (5) | 0.0300 (3) | |
H4BA | 0.5652 | 0.2521 | 0.4932 | 0.036* | |
C5B | 0.35982 (14) | 0.2501 (2) | 0.45220 (4) | 0.0235 (3) | |
C6B | 0.12228 (16) | 0.2460 (3) | 0.48535 (5) | 0.0344 (3) | |
H6BA | 0.0799 | 0.2454 | 0.5177 | 0.052* | |
H6BB | 0.0891 | 0.1184 | 0.4667 | 0.052* | |
H6BC | 0.0880 | 0.3732 | 0.4668 | 0.052* |
U11 | U22 | U33 | U12 | U13 | U23 | |
O1A | 0.0188 (4) | 0.0497 (7) | 0.0167 (4) | 0.0001 (4) | 0.0047 (3) | 0.0008 (4) |
O21A | 0.0198 (4) | 0.0763 (9) | 0.0263 (5) | 0.0020 (5) | 0.0042 (4) | −0.0057 (5) |
O22A | 0.0213 (5) | 0.1159 (13) | 0.0248 (5) | −0.0006 (6) | −0.0071 (4) | 0.0054 (6) |
O41A | 0.0354 (5) | 0.0456 (6) | 0.0138 (4) | −0.0003 (5) | −0.0010 (3) | 0.0000 (4) |
O42A | 0.0219 (5) | 0.1061 (12) | 0.0246 (5) | 0.0017 (6) | 0.0091 (4) | 0.0009 (6) |
O61A | 0.0179 (6) | 0.0502 (13) | 0.0273 (6) | 0.0077 (7) | −0.0054 (4) | −0.0034 (7) |
O62A | 0.0343 (7) | 0.0769 (18) | 0.0180 (6) | 0.0094 (9) | −0.0035 (5) | −0.0166 (8) |
O61B | 0.021 (4) | 0.077 (9) | 0.023 (4) | −0.006 (5) | −0.005 (3) | 0.002 (5) |
O62B | 0.023 (4) | 0.069 (8) | 0.022 (4) | −0.009 (5) | 0.001 (3) | 0.008 (4) |
O1B | 0.0272 (5) | 0.0534 (7) | 0.0183 (4) | −0.0004 (5) | 0.0076 (3) | 0.0000 (4) |
N2A | 0.0153 (4) | 0.0341 (7) | 0.0226 (5) | −0.0017 (5) | −0.0001 (4) | 0.0013 (5) |
N4A | 0.0252 (5) | 0.0352 (6) | 0.0153 (4) | −0.0001 (5) | 0.0031 (4) | 0.0001 (5) |
N6A | 0.0180 (4) | 0.0324 (6) | 0.0157 (4) | −0.0022 (5) | −0.0016 (3) | 0.0014 (5) |
N1B | 0.0148 (4) | 0.0265 (5) | 0.0163 (4) | 0.0003 (5) | −0.0002 (3) | −0.0010 (4) |
N2B | 0.0152 (4) | 0.0278 (6) | 0.0152 (4) | −0.0004 (5) | 0.0001 (3) | 0.0002 (4) |
N3B | 0.0180 (4) | 0.0273 (6) | 0.0177 (4) | 0.0012 (5) | 0.0025 (3) | 0.0001 (4) |
C1A | 0.0162 (5) | 0.0202 (6) | 0.0155 (4) | 0.0003 (5) | 0.0019 (4) | −0.0006 (5) |
C2A | 0.0143 (4) | 0.0208 (6) | 0.0171 (5) | −0.0007 (5) | −0.0005 (4) | −0.0006 (5) |
C3A | 0.0196 (5) | 0.0191 (6) | 0.0158 (4) | −0.0012 (5) | −0.0011 (4) | 0.0003 (5) |
C4A | 0.0196 (5) | 0.0229 (6) | 0.0129 (4) | 0.0003 (5) | 0.0031 (4) | 0.0006 (5) |
C5A | 0.0159 (5) | 0.0229 (6) | 0.0168 (5) | −0.0005 (5) | 0.0007 (4) | 0.0007 (5) |
C6A | 0.0163 (5) | 0.0218 (6) | 0.0134 (4) | 0.0010 (5) | −0.0014 (3) | 0.0004 (5) |
C1B | 0.0154 (5) | 0.0172 (5) | 0.0181 (5) | 0.0001 (5) | 0.0008 (4) | −0.0002 (5) |
C2B | 0.0170 (5) | 0.0354 (7) | 0.0200 (5) | −0.0001 (6) | −0.0023 (4) | 0.0009 (5) |
C3B | 0.0174 (5) | 0.0706 (12) | 0.0235 (6) | −0.0024 (7) | −0.0037 (4) | 0.0003 (7) |
C4B | 0.0225 (6) | 0.0505 (9) | 0.0164 (5) | −0.0006 (7) | −0.0022 (4) | −0.0003 (6) |
C5B | 0.0227 (5) | 0.0320 (7) | 0.0162 (5) | −0.0005 (6) | 0.0039 (4) | 0.0009 (5) |
C6B | 0.0252 (6) | 0.0494 (9) | 0.0302 (6) | −0.0014 (7) | 0.0124 (5) | −0.0013 (7) |
O1A—C1A | 1.2523 (13) | N3B—C5B | 1.3204 (15) |
O21A—N2A | 1.2190 (13) | N3B—C1B | 1.3416 (14) |
O22A—N2A | 1.2284 (14) | C1A—C2A | 1.4503 (15) |
O41A—N4A | 1.2287 (13) | C1A—C6A | 1.4545 (16) |
O42A—N4A | 1.2205 (14) | C2A—C3A | 1.3797 (15) |
O61A—N6A | 1.2357 (17) | C3A—C4A | 1.3834 (16) |
O62A—N6A | 1.2182 (17) | C3A—H3AA | 0.9500 |
O61B—N6A | 1.221 (10) | C4A—C5A | 1.3944 (15) |
O62B—N6A | 1.210 (9) | C5A—C6A | 1.3685 (15) |
O1B—C5B | 1.3283 (14) | C5A—H5AA | 0.9500 |
O1B—C6B | 1.4418 (17) | C2B—C4B | 1.3593 (17) |
N2A—C2A | 1.4605 (14) | C2B—C3B | 1.4916 (18) |
N4A—C4A | 1.4477 (14) | C3B—H3BA | 0.9800 |
N6A—C6A | 1.4565 (14) | C3B—H3BB | 0.9800 |
N1B—C1B | 1.3210 (14) | C3B—H3BC | 0.9800 |
N1B—H1BA | 0.8800 | C4B—C5B | 1.4112 (18) |
N1B—H1BB | 0.8800 | C4B—H4BA | 0.9500 |
N2B—C2B | 1.3654 (15) | C6B—H6BA | 0.9800 |
N2B—C1B | 1.3687 (14) | C6B—H6BB | 0.9800 |
N2B—H2BA | 0.8800 | C6B—H6BC | 0.9800 |
C5B—O1B—C6B | 117.54 (10) | C3A—C4A—C5A | 121.63 (10) |
O21A—N2A—O22A | 122.12 (11) | C3A—C4A—N4A | 119.53 (10) |
O21A—N2A—C2A | 120.33 (10) | C5A—C4A—N4A | 118.84 (10) |
O22A—N2A—C2A | 117.55 (10) | C6A—C5A—C4A | 118.20 (10) |
O42A—N4A—O41A | 123.06 (10) | C6A—C5A—H5AA | 120.9 |
O42A—N4A—C4A | 118.35 (10) | C4A—C5A—H5AA | 120.9 |
O41A—N4A—C4A | 118.59 (10) | C5A—C6A—C1A | 124.91 (10) |
O62B—N6A—O62A | 43.1 (8) | C5A—C6A—N6A | 115.86 (10) |
O62B—N6A—O61B | 121.1 (6) | C1A—C6A—N6A | 119.22 (9) |
O62A—N6A—O61B | 104.4 (6) | N1B—C1B—N3B | 119.52 (10) |
O62B—N6A—O61A | 106.5 (6) | N1B—C1B—N2B | 118.64 (9) |
O62A—N6A—O61A | 123.08 (13) | N3B—C1B—N2B | 121.84 (10) |
O61B—N6A—O61A | 42.4 (9) | C4B—C2B—N2B | 118.22 (11) |
O62B—N6A—C6A | 120.6 (5) | C4B—C2B—C3B | 123.65 (11) |
O62A—N6A—C6A | 119.45 (12) | N2B—C2B—C3B | 118.13 (11) |
O61B—N6A—C6A | 118.3 (4) | C2B—C3B—H3BA | 109.5 |
O61A—N6A—C6A | 117.40 (10) | C2B—C3B—H3BB | 109.5 |
C1B—N1B—H1BA | 120.0 | H3BA—C3B—H3BB | 109.5 |
C1B—N1B—H1BB | 120.0 | C2B—C3B—H3BC | 109.5 |
H1BA—N1B—H1BB | 120.0 | H3BA—C3B—H3BC | 109.5 |
C2B—N2B—C1B | 121.33 (9) | H3BB—C3B—H3BC | 109.5 |
C2B—N2B—H2BA | 119.3 | C2B—C4B—C5B | 117.54 (11) |
C1B—N2B—H2BA | 119.3 | C2B—C4B—H4BA | 121.2 |
C5B—N3B—C1B | 116.75 (10) | C5B—C4B—H4BA | 121.2 |
O1A—C1A—C2A | 124.65 (10) | N3B—C5B—O1B | 119.64 (11) |
O1A—C1A—C6A | 123.03 (10) | N3B—C5B—C4B | 124.31 (10) |
C2A—C1A—C6A | 112.30 (9) | O1B—C5B—C4B | 116.05 (11) |
C3A—C2A—C1A | 123.31 (10) | O1B—C6B—H6BA | 109.5 |
C3A—C2A—N2A | 115.63 (10) | O1B—C6B—H6BB | 109.5 |
C1A—C2A—N2A | 121.06 (9) | H6BA—C6B—H6BB | 109.5 |
C2A—C3A—C4A | 119.64 (10) | O1B—C6B—H6BC | 109.5 |
C2A—C3A—H3AA | 120.2 | H6BA—C6B—H6BC | 109.5 |
C4A—C3A—H3AA | 120.2 | H6BB—C6B—H6BC | 109.5 |
O1A—C1A—C2A—C3A | −178.06 (12) | C2A—C1A—C6A—N6A | 178.84 (11) |
C6A—C1A—C2A—C3A | 0.43 (19) | O62B—N6A—C6A—C5A | −158.8 (10) |
O1A—C1A—C2A—N2A | 2.7 (2) | O62A—N6A—C6A—C5A | 151.0 (2) |
C6A—C1A—C2A—N2A | −178.78 (11) | O61B—N6A—C6A—C5A | 22.2 (11) |
O21A—N2A—C2A—C3A | −177.43 (13) | O61A—N6A—C6A—C5A | −26.1 (2) |
O22A—N2A—C2A—C3A | 2.02 (18) | O62B—N6A—C6A—C1A | 21.3 (10) |
O21A—N2A—C2A—C1A | 1.83 (19) | O62A—N6A—C6A—C1A | −29.0 (2) |
O22A—N2A—C2A—C1A | −178.72 (13) | O61B—N6A—C6A—C1A | −157.8 (11) |
C1A—C2A—C3A—C4A | 0.2 (2) | O61A—N6A—C6A—C1A | 153.92 (16) |
N2A—C2A—C3A—C4A | 179.42 (12) | C5B—N3B—C1B—N1B | 179.78 (12) |
C2A—C3A—C4A—C5A | −0.2 (2) | C5B—N3B—C1B—N2B | −0.12 (19) |
C2A—C3A—C4A—N4A | −179.57 (12) | C2B—N2B—C1B—N1B | −179.40 (12) |
O42A—N4A—C4A—C3A | 178.82 (13) | C2B—N2B—C1B—N3B | 0.5 (2) |
O41A—N4A—C4A—C3A | −1.17 (19) | C1B—N2B—C2B—C4B | −0.2 (2) |
O42A—N4A—C4A—C5A | −0.59 (19) | C1B—N2B—C2B—C3B | 179.57 (13) |
O41A—N4A—C4A—C5A | 179.42 (13) | N2B—C2B—C4B—C5B | −0.3 (2) |
C3A—C4A—C5A—C6A | −0.5 (2) | C3B—C2B—C4B—C5B | 179.86 (15) |
N4A—C4A—C5A—C6A | 178.91 (12) | C1B—N3B—C5B—O1B | 179.54 (12) |
C4A—C5A—C6A—C1A | 1.2 (2) | C1B—N3B—C5B—C4B | −0.5 (2) |
C4A—C5A—C6A—N6A | −178.78 (12) | C6B—O1B—C5B—N3B | −0.6 (2) |
O1A—C1A—C6A—C5A | 177.37 (13) | C6B—O1B—C5B—C4B | 179.43 (14) |
C2A—C1A—C6A—C5A | −1.14 (19) | C2B—C4B—C5B—N3B | 0.8 (2) |
O1A—C1A—C6A—N6A | −2.6 (2) | C2B—C4B—C5B—O1B | −179.30 (14) |
D—H···A | D—H | H···A | D···A | D—H···A |
N1B—H1BA···O61Bi | 0.88 | 2.09 | 2.883 (10) | 150 |
N1B—H1BA···O61Ai | 0.88 | 2.13 | 2.9309 (17) | 151 |
N1B—H1BB···O1A | 0.88 | 1.95 | 2.7223 (13) | 146 |
N1B—H1BB···O21A | 0.88 | 2.20 | 2.8855 (14) | 134 |
N2B—H2BA···O1A | 0.88 | 1.97 | 2.7380 (12) | 145 |
N2B—H2BA···O62B | 0.88 | 2.55 | 3.303 (10) | 144 |
N2B—H2BA···O62A | 0.88 | 2.62 | 3.381 (2) | 145 |
Symmetry code: (i) x−1, y, z. |
Experimental details
Crystal data | |
Chemical formula | C6H10N3O+·C6H2N3O7− |
Mr | 368.28 |
Crystal system, space group | Monoclinic, P21/c |
Temperature (K) | 200 |
a, b, c (Å) | 8.9442 (3), 6.2793 (3), 27.0354 (8) |
β (°) | 94.471 (3) |
V (Å3) | 1513.78 (10) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 0.14 |
Crystal size (mm) | 0.52 × 0.46 × 0.35 |
Data collection | |
Diffractometer | Oxford Diffraction Gemini |
Absorption correction | Multi-scan (CrysAlis RED; Oxford Diffraction, 2007) |
Tmin, Tmax | 0.986, 1.000 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 15870, 6133, 3107 |
Rint | 0.031 |
(sin θ/λ)max (Å−1) | 0.805 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.054, 0.160, 0.94 |
No. of reflections | 6133 |
No. of parameters | 256 |
No. of restraints | 24 |
H-atom treatment | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 0.43, −0.29 |
Computer programs: CrysAlis PRO (Oxford Diffraction, 2007), CrysAlis RED (Oxford Diffraction, 2007), SHELXS97 (Sheldrick, 2008), SHELXL97) (Sheldrick, 2008), SHELXTL (Sheldrick, 2008) and PLATON (Spek, 2009).
D—H···A | D—H | H···A | D···A | D—H···A |
N1B—H1BA···O61Bi | 0.88 | 2.09 | 2.883 (10) | 149.9 |
N1B—H1BA···O61Ai | 0.88 | 2.13 | 2.9309 (17) | 150.8 |
N1B—H1BB···O1A | 0.88 | 1.95 | 2.7223 (13) | 146.2 |
N1B—H1BB···O21A | 0.88 | 2.20 | 2.8855 (14) | 134.1 |
N2B—H2BA···O1A | 0.88 | 1.97 | 2.7380 (12) | 144.5 |
N2B—H2BA···O62B | 0.88 | 2.55 | 3.303 (10) | 143.9 |
N2B—H2BA···O62A | 0.88 | 2.62 | 3.381 (2) | 145.4 |
Symmetry code: (i) x−1, y, z. |
The synthesis of imidazo[1,2-a]pyrimidines has been widely investigated and is one of the most common strategies in the use of 2-aminopyrimidine as the starting material (Katritzky et al., 2003). Recently, the hydrogen-bonding patterns in 2-amino-4,6-dimethylpyrimidinium picrate has been reported (Subashini et al., 2006). In continuation of our work on picrates of biologically important molecules, we have prepared a new picrate of 2-amino-4-methoxy-6-methylpyrimidine, [C6H10N3 O]+, [C6H2N3O7]- and its crystal structure is reported.
The title compound,(I), C12H12N6O8, crystallizes as a salt with one C6H10N3 O+, C6H2N3O7- , cation-anion pair in the asymmetric unit (Fig. 1). The dihedral angle between the mean planes of the benzene and pyridine rings is 3.10°. In the cation the methoxy group is almost coplanar with the pyridine ring [C6B-O1B-C5B-N3B torsion angle = -0.63 (19)°]. Bond distances and angles in both the cation and anion are in normal ranges (Allen, 2002). The p [torsion angle C3A-C4A-N4A-O41A = 1.17 (18)°] and one o [torsion angle C1A-C2A-N2A-O21A = 1.83 (19)°] nitro group in the anion are nearly coplanar with the benzene ring. The other disordered o nitro group containing the predomoinate oxygen atom (occupancy = 0.868 (6)) is twisted -29.0 (2)\5 from the mean plane of the benzene ring. Bifurcated intramolecular donor, N1B, [O1A [N1B—H1BB···O21A. & N1B—H1BB···O1A] and acceptor, O1A, [N1B—H1BB···O1A & N2B—H2BA···O1A] hydrogen bonds and a weak C3B—H3BB···O62A(0.868 (6)) hydrogen bond interaction (Table 2) between the cation and anion produces a network of infinite O—H···O—H···O—H chains along the c axis in the [101] plane which helps to establish crystal packing (Fig. 2).
A density functional theory (DFT) geometry optimization molecular orbital calculation (Schmidt & Polik, 2007) was performed on the independent cation-anion pair (C6H10N3 O+, C6H2N3O7- ) within the asymmetric unit with the B3LYP 6-31-G(d) basis set (Hehre et al., 1986). Starting geometries were taken from X-ray refinement data. The dihedral angle between the mean planes of the benzene and pyridine rings increases to 28.10°. In the anion, the mean planes of the two o-nitro groups become twisted by 23.14° and 24.20°, respectively, from the mean plane of the benzene ring. The mean plane of the p-nitro group remains planar to the benzene ring. The mean plane of the methoxy group in the cation also remains planar to the pyridine ring. These observations suggest that the bifurcated N—H···(O,O) donor and acceptor hydrogen bonds and weak C—H···O intermolecular interactions play a significant role in crystal stability.