organic compounds
4-Amino-2,8-dimethyl-6H-pyrimido[1,2-a][1,3,5]triazin-6-one1
aDepartment of Pharmacy, Faculty of Science, National University of Singapore, 18 Science Drive 4, Singapore 117543, Singapore, and bDepartment of Chemistry, Faculty of Science, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore
*Correspondence e-mail: dolzhenkoav@gmail.com
In the title compound, C8H9N5O, the mean planes through the pyrimidine and triazine rings form a dihedral angle of 2.83 (16)°. The amino group adopts a trigonal-planar configuration and forms an intramolecular resonance-assisted N—H⋯O=C hydrogen bond with the carbonyl group. In the crystal, molecules are linked via intermolecular N—H⋯N hydrogen bonds into chains of C22(6)[R22(6)] motif. The molecules form two types of sheet parallel to (201) and (01), respectively.
Related literature
For reviews on the synthesis and biological activity of fused 1,3,5-triazines see: Dolzhenko et al. (2006, 2008a). For the synthesis and structural and biological investigations of pyrimido[1,2-a][1,3,5]triazines and their benzo-fused analogues, see Agasimundin et al. (1985); Dolzhenko et al. (2008b, 2009a,b). For the graph-set analysis of hydrogen bonding, see: Bernstein et al. (1995).
Experimental
Crystal data
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Refinement
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Data collection: SMART (Bruker, 2001); cell SAINT (Bruker, 2001); data reduction: SAINT; 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.
Supporting information
https://doi.org/10.1107/S1600536810027522/ez2220sup1.cif
contains datablocks I, global. DOI:Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S1600536810027522/ez2220Isup2.hkl
The title compound was prepared by the cyclocondensation of 4-methyl-6-oxo-1,6-dihydropyrimidin-2-yl guanidine with triethyl orthoacetate. The details of the synthesis will be published elsewhere. Single crystals suitable for crystallographic analysis were grown by recrystallization from ethyl acetate.
All the H atoms attached to the carbon atoms were constrained in a riding motion approximation [0.95 Å for Caryl—H and 0.98 Å for methyl groups; Uiso(H) =1.2Ueq(Caryl) and Uiso(H) = 1.5Ueq(Cmethyl)] while the N-bound H atoms were located in a difference map and refined freely. In the absence of significant
effects 706 Friedel pairs have been merged.Fused 1,3,5-triazines have been shown to possess a range of biological activities (Dolzhenko et al., 2006; Dolzhenko et al., 2008a). However, data on the synthesis and structure of pyrimido[1,2-a][1,3,5]triazines are limited (Agasimundin et al., 1985; Dolzhenko et al., 2009b). In continuation of our work on the synthesis, structural and biological investigation of pyrimido[1,2-a][1,3,5]triazines and their benzofused analogues (Dolzhenko et al., 2008b; Dolzhenko et al., 2009a,b), we report herein the molecular and crystal structures of 4-amino-2,8-dimethyl-pyrimido[1,2-a][1,3,5]triazin-6(5H)-one (Fig. 1 and 2).
The molecule of 4-amino-2,8-dimethyl-pyrimido[1,2-a][1,3,5]triazin-6(5H)-one is essentially planar with 0.0524 r.m.s. deviation for non-hydrogen atoms. The dihedral angle between the mean planes through the pyrimidine and triazine rings is 2.83 (16)°. The C—N bond distances at the bridgehead nitrogen atom viz. C2—N3 [1.4199 (37) Å], C3—N3 [1.4113 (36) Å] and C6—N3 [1.4488 (37) Å] are larger than typical values.The amino group adopts a trigonal planar configuration with atom N5 deviating by 0.0375 (229) Å from the C2/H51/H52 mean plane. The significantly shortened C2—N5 bond length [1.3114 (39) Å, the shortest C—N bond distance in the molecule] indicates a high degree of π-electron delocalization of the N5 atom with the heterocyclic system. The carbonyl group C6═O1 further extends this delocalization by resonance assisted N—H···O═C hydrogen bonding (Table 1).
In the crystal, the amino group acts as a hydrogen donor for intermolecular N—H···N hydrogen bonding with the nitrogen atoms N1 and N4 (Fig. 2), thereby forming extended chains with the C22(6)[R22(6)] hydrogen bond pattern (Bernstein et al., 1995). The chains are organized in two types of sheets parallel to (201) and (201) planes, respectively.
For reviews on the synthesis and biological activity of fused 1,3,5-triazines see: Dolzhenko et al. (2006, 2008a). For the synthesis and structural and biological investigations of pyrimido[1,2-a][1,3,5]triazines and their benzo-fused analogues, see Agasimundin et al. (1985); Dolzhenko et al. (2008b, 2009a,b). For the graph-set analysis of hydrogen bonding, see: Bernstein et al. (1995).
Data collection: SMART (Bruker, 2001); cell
SAINT (Bruker, 2001); data reduction: SAINT (Bruker, 2001); 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).C8H9N5O | Dx = 1.496 Mg m−3 |
Mr = 191.20 | Melting point: 545 K |
Orthorhombic, Pna21 | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: P 2c -2n | Cell parameters from 614 reflections |
a = 11.1369 (19) Å | θ = 2.8–26.8° |
b = 18.913 (3) Å | µ = 0.11 mm−1 |
c = 4.0311 (7) Å | T = 100 K |
V = 849.1 (3) Å3 | Needle, colourless |
Z = 4 | 0.60 × 0.08 × 0.06 mm |
F(000) = 400 |
Bruker SMART APEX CCD diffractometer | 1119 independent reflections |
Radiation source: fine-focus sealed tube | 1019 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.050 |
φ and ω scans | θmax = 27.5°, θmin = 2.2° |
Absorption correction: multi-scan (SADABS; Sheldrick, 2001) | h = −13→14 |
Tmin = 0.938, Tmax = 0.994 | k = −24→22 |
5774 measured reflections | l = −5→4 |
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)] = 0.053 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.117 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.15 | w = 1/[σ2(Fo2) + (0.053P)2 + 0.4545P] where P = (Fo2 + 2Fc2)/3 |
1119 reflections | (Δ/σ)max < 0.001 |
137 parameters | Δρmax = 0.33 e Å−3 |
1 restraint | Δρmin = −0.25 e Å−3 |
C8H9N5O | V = 849.1 (3) Å3 |
Mr = 191.20 | Z = 4 |
Orthorhombic, Pna21 | Mo Kα radiation |
a = 11.1369 (19) Å | µ = 0.11 mm−1 |
b = 18.913 (3) Å | T = 100 K |
c = 4.0311 (7) Å | 0.60 × 0.08 × 0.06 mm |
Bruker SMART APEX CCD diffractometer | 1119 independent reflections |
Absorption correction: multi-scan (SADABS; Sheldrick, 2001) | 1019 reflections with I > 2σ(I) |
Tmin = 0.938, Tmax = 0.994 | Rint = 0.050 |
5774 measured reflections |
R[F2 > 2σ(F2)] = 0.053 | 1 restraint |
wR(F2) = 0.117 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.15 | Δρmax = 0.33 e Å−3 |
1119 reflections | Δρmin = −0.25 e Å−3 |
137 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 | ||
O1 | 0.61240 (19) | 0.88225 (11) | −0.2411 (7) | 0.0229 (6) | |
N1 | 0.3706 (2) | 0.71578 (13) | 0.3214 (8) | 0.0145 (6) | |
N2 | 0.5341 (2) | 0.67258 (13) | −0.0011 (7) | 0.0137 (6) | |
N3 | 0.4963 (2) | 0.79702 (13) | 0.0265 (7) | 0.0119 (5) | |
N4 | 0.3255 (2) | 0.83294 (13) | 0.3415 (7) | 0.0138 (6) | |
N5 | 0.6531 (2) | 0.74865 (15) | −0.2904 (7) | 0.0154 (6) | |
H51 | 0.673 (3) | 0.793 (2) | −0.326 (11) | 0.018 (9)* | |
H52 | 0.689 (3) | 0.7098 (19) | −0.349 (11) | 0.019 (9)* | |
C1 | 0.4393 (3) | 0.66472 (15) | 0.2008 (8) | 0.0134 (6) | |
C2 | 0.5625 (2) | 0.73778 (15) | −0.0888 (8) | 0.0128 (6) | |
C3 | 0.3965 (2) | 0.78262 (15) | 0.2314 (8) | 0.0121 (6) | |
C4 | 0.3465 (2) | 0.90073 (15) | 0.2475 (9) | 0.0139 (6) | |
C5 | 0.4418 (3) | 0.91978 (16) | 0.0552 (8) | 0.0147 (6) | |
H5 | 0.4531 | 0.9683 | 0.0019 | 0.018* | |
C6 | 0.5246 (3) | 0.86906 (15) | −0.0674 (8) | 0.0155 (7) | |
C7 | 0.4091 (3) | 0.59100 (15) | 0.3046 (10) | 0.0191 (7) | |
H7A | 0.4559 | 0.5784 | 0.5017 | 0.029* | |
H7B | 0.4282 | 0.5582 | 0.1239 | 0.029* | |
H7C | 0.3232 | 0.5880 | 0.3562 | 0.029* | |
C8 | 0.2543 (3) | 0.95324 (15) | 0.3617 (9) | 0.0182 (7) | |
H8A | 0.1796 | 0.9460 | 0.2381 | 0.027* | |
H8B | 0.2840 | 1.0013 | 0.3224 | 0.027* | |
H8C | 0.2392 | 0.9467 | 0.5992 | 0.027* |
U11 | U22 | U33 | U12 | U13 | U23 | |
O1 | 0.0225 (11) | 0.0152 (11) | 0.0310 (14) | −0.0048 (8) | 0.0116 (12) | 0.0017 (11) |
N1 | 0.0125 (11) | 0.0128 (12) | 0.0183 (14) | −0.0008 (9) | 0.0027 (11) | 0.0007 (11) |
N2 | 0.0132 (11) | 0.0131 (13) | 0.0149 (13) | −0.0011 (9) | −0.0009 (11) | −0.0029 (11) |
N3 | 0.0101 (10) | 0.0113 (12) | 0.0144 (13) | −0.0013 (8) | 0.0024 (10) | −0.0011 (10) |
N4 | 0.0116 (10) | 0.0137 (12) | 0.0162 (13) | −0.0004 (9) | 0.0017 (11) | −0.0011 (11) |
N5 | 0.0139 (12) | 0.0123 (13) | 0.0200 (15) | 0.0017 (10) | 0.0064 (12) | −0.0007 (12) |
C1 | 0.0124 (12) | 0.0152 (14) | 0.0126 (15) | −0.0014 (11) | −0.0034 (12) | −0.0002 (13) |
C2 | 0.0101 (12) | 0.0167 (15) | 0.0114 (14) | 0.0023 (11) | −0.0002 (12) | −0.0034 (13) |
C3 | 0.0108 (12) | 0.0161 (14) | 0.0096 (14) | −0.0022 (10) | 0.0013 (12) | −0.0003 (13) |
C4 | 0.0142 (13) | 0.0136 (14) | 0.0139 (15) | −0.0001 (10) | −0.0048 (12) | −0.0030 (14) |
C5 | 0.0190 (14) | 0.0085 (14) | 0.0165 (16) | −0.0027 (11) | −0.0031 (13) | −0.0007 (12) |
C6 | 0.0156 (13) | 0.0122 (15) | 0.0187 (17) | −0.0050 (11) | −0.0018 (13) | 0.0009 (13) |
C7 | 0.0215 (14) | 0.0126 (14) | 0.0232 (18) | −0.0004 (11) | 0.0046 (15) | 0.0005 (13) |
C8 | 0.0182 (13) | 0.0154 (15) | 0.0209 (16) | 0.0021 (11) | 0.0018 (13) | −0.0010 (14) |
O1—C6 | 1.228 (4) | N5—H52 | 0.87 (4) |
N1—C1 | 1.324 (4) | C1—C7 | 1.494 (4) |
N1—C3 | 1.346 (4) | C4—C5 | 1.363 (4) |
N2—C2 | 1.321 (4) | C4—C8 | 1.501 (4) |
N2—C1 | 1.342 (4) | C5—C6 | 1.420 (4) |
N3—C3 | 1.411 (4) | C5—H5 | 0.9500 |
N3—C2 | 1.420 (4) | C7—H7A | 0.9800 |
N3—C6 | 1.449 (4) | C7—H7B | 0.9800 |
N4—C3 | 1.314 (4) | C7—H7C | 0.9800 |
N4—C4 | 1.357 (4) | C8—H8A | 0.9800 |
N5—C2 | 1.311 (4) | C8—H8B | 0.9800 |
N5—H51 | 0.89 (4) | C8—H8C | 0.9800 |
C1—N1—C3 | 117.5 (3) | C5—C4—C8 | 122.2 (3) |
C2—N2—C1 | 117.0 (2) | C4—C5—C6 | 121.7 (3) |
C3—N3—C2 | 116.6 (2) | C4—C5—H5 | 119.2 |
C3—N3—C6 | 120.4 (2) | C6—C5—H5 | 119.2 |
C2—N3—C6 | 122.9 (2) | O1—C6—C5 | 125.3 (3) |
C3—N4—C4 | 119.1 (3) | O1—C6—N3 | 120.9 (3) |
C2—N5—H51 | 116 (2) | C5—C6—N3 | 113.8 (3) |
C2—N5—H52 | 113 (2) | C1—C7—H7A | 109.5 |
H51—N5—H52 | 130 (3) | C1—C7—H7B | 109.5 |
N1—C1—N2 | 126.6 (3) | H7A—C7—H7B | 109.5 |
N1—C1—C7 | 116.6 (3) | C1—C7—H7C | 109.5 |
N2—C1—C7 | 116.8 (3) | H7A—C7—H7C | 109.5 |
N5—C2—N2 | 119.7 (3) | H7B—C7—H7C | 109.5 |
N5—C2—N3 | 118.6 (3) | C4—C8—H8A | 109.5 |
N2—C2—N3 | 121.6 (3) | C4—C8—H8B | 109.5 |
N4—C3—N1 | 117.4 (3) | H8A—C8—H8B | 109.5 |
N4—C3—N3 | 122.1 (3) | C4—C8—H8C | 109.5 |
N1—C3—N3 | 120.5 (3) | H8A—C8—H8C | 109.5 |
N4—C4—C5 | 122.9 (3) | H8B—C8—H8C | 109.5 |
N4—C4—C8 | 114.9 (3) | ||
C3—N1—C1—N2 | 0.9 (5) | C2—N3—C3—N4 | −177.1 (3) |
C3—N1—C1—C7 | 179.8 (3) | C6—N3—C3—N4 | 0.7 (4) |
C2—N2—C1—N1 | 0.2 (5) | C2—N3—C3—N1 | 2.8 (4) |
C2—N2—C1—C7 | −178.8 (3) | C6—N3—C3—N1 | −179.4 (3) |
C1—N2—C2—N5 | −178.8 (3) | C3—N4—C4—C5 | −3.2 (5) |
C1—N2—C2—N3 | 0.4 (4) | C3—N4—C4—C8 | 174.9 (3) |
C3—N3—C2—N5 | 177.4 (3) | N4—C4—C5—C6 | 1.6 (5) |
C6—N3—C2—N5 | −0.3 (4) | C8—C4—C5—C6 | −176.3 (3) |
C3—N3—C2—N2 | −1.8 (4) | C4—C5—C6—O1 | −179.9 (3) |
C6—N3—C2—N2 | −179.5 (3) | C4—C5—C6—N3 | 1.0 (4) |
C4—N4—C3—N1 | −177.9 (3) | C3—N3—C6—O1 | 178.8 (3) |
C4—N4—C3—N3 | 2.0 (4) | C2—N3—C6—O1 | −3.6 (4) |
C1—N1—C3—N4 | 177.5 (3) | C3—N3—C6—C5 | −2.1 (4) |
C1—N1—C3—N3 | −2.4 (4) | C2—N3—C6—C5 | 175.5 (3) |
D—H···A | D—H | H···A | D···A | D—H···A |
N5—H51···O1 | 0.89 (4) | 1.84 (4) | 2.575 (3) | 139 (3) |
N5—H51···N1i | 0.89 (4) | 2.63 (4) | 2.961 (4) | 103 (3) |
N5—H52···N4i | 0.87 (4) | 2.12 (4) | 2.876 (4) | 144 (3) |
Symmetry code: (i) x+1/2, −y+3/2, z−1. |
Experimental details
Crystal data | |
Chemical formula | C8H9N5O |
Mr | 191.20 |
Crystal system, space group | Orthorhombic, Pna21 |
Temperature (K) | 100 |
a, b, c (Å) | 11.1369 (19), 18.913 (3), 4.0311 (7) |
V (Å3) | 849.1 (3) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 0.11 |
Crystal size (mm) | 0.60 × 0.08 × 0.06 |
Data collection | |
Diffractometer | Bruker SMART APEX CCD |
Absorption correction | Multi-scan (SADABS; Sheldrick, 2001) |
Tmin, Tmax | 0.938, 0.994 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 5774, 1119, 1019 |
Rint | 0.050 |
(sin θ/λ)max (Å−1) | 0.649 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.053, 0.117, 1.15 |
No. of reflections | 1119 |
No. of parameters | 137 |
No. of restraints | 1 |
H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
Δρmax, Δρmin (e Å−3) | 0.33, −0.25 |
Computer programs: SMART (Bruker, 2001), SAINT (Bruker, 2001), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), SHELXTL (Sheldrick, 2008).
D—H···A | D—H | H···A | D···A | D—H···A |
N5—H51···O1 | 0.89 (4) | 1.84 (4) | 2.575 (3) | 139 (3) |
N5—H51···N1i | 0.89 (4) | 2.63 (4) | 2.961 (4) | 103 (3) |
N5—H52···N4i | 0.87 (4) | 2.12 (4) | 2.876 (4) | 144 (3) |
Symmetry code: (i) x+1/2, −y+3/2, z−1. |
Acknowledgements
This work was supported by the National Medical Research Council, Singapore (grant No. NMRC/NIG/0020/2008).
References
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This is an open-access article distributed under the terms of the Creative Commons Attribution (CC-BY) Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.
Fused 1,3,5-triazines have been shown to possess a range of biological activities (Dolzhenko et al., 2006; Dolzhenko et al., 2008a). However, data on the synthesis and structure of pyrimido[1,2-a][1,3,5]triazines are limited (Agasimundin et al., 1985; Dolzhenko et al., 2009b). In continuation of our work on the synthesis, structural and biological investigation of pyrimido[1,2-a][1,3,5]triazines and their benzofused analogues (Dolzhenko et al., 2008b; Dolzhenko et al., 2009a,b), we report herein the molecular and crystal structures of 4-amino-2,8-dimethyl-pyrimido[1,2-a][1,3,5]triazin-6(5H)-one (Fig. 1 and 2).
The molecule of 4-amino-2,8-dimethyl-pyrimido[1,2-a][1,3,5]triazin-6(5H)-one is essentially planar with 0.0524 r.m.s. deviation for non-hydrogen atoms. The dihedral angle between the mean planes through the pyrimidine and triazine rings is 2.83 (16)°. The C—N bond distances at the bridgehead nitrogen atom viz. C2—N3 [1.4199 (37) Å], C3—N3 [1.4113 (36) Å] and C6—N3 [1.4488 (37) Å] are larger than typical values.The amino group adopts a trigonal planar configuration with atom N5 deviating by 0.0375 (229) Å from the C2/H51/H52 mean plane. The significantly shortened C2—N5 bond length [1.3114 (39) Å, the shortest C—N bond distance in the molecule] indicates a high degree of π-electron delocalization of the N5 atom with the heterocyclic system. The carbonyl group C6═O1 further extends this delocalization by resonance assisted N—H···O═C hydrogen bonding (Table 1).
In the crystal, the amino group acts as a hydrogen donor for intermolecular N—H···N hydrogen bonding with the nitrogen atoms N1 and N4 (Fig. 2), thereby forming extended chains with the C22(6)[R22(6)] hydrogen bond pattern (Bernstein et al., 1995). The chains are organized in two types of sheets parallel to (201) and (201) planes, respectively.