organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

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ISSN: 2056-9890

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

(Received 15 June 2010; accepted 12 July 2010; online 17 July 2010)

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 ([\overline{2}]01), respectively.

Related literature

For reviews on the synthesis and biological activity of fused 1,3,5-triazines see: Dolzhenko et al. (2006[Dolzhenko, A. V., Dolzhenko, A. V. & Chui, W. K. (2006). Heterocycles, 68, 1723-1759.], 2008a[Dolzhenko, A. V., Dolzhenko, A. V. & Chui, W. K. (2008a). Heterocycles, 75, 1575-1622.]). 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[Agasimundin, Y. S., Oakes, F. T. & Leonard, N. J. (1985). J. Org. Chem. 50, 2474-2480.]); Dolzhenko et al. (2008b[Dolzhenko, A. V., Dolzhenko, A. V. & Chui, W. K. (2008b). J. Heterocycl. Chem. 45, 173-176.], 2009a[Dolzhenko, A. V., Foo, M. C., Tan, B. J., Dolzhenko, A. V., Chiu, G. N. C. & Chui, W. K. (2009a). Heterocycles, 78, 1761-1775.],b[Dolzhenko, A. V., Sachdeva, N., Tan, G. K., Koh, L. L. & Chui, W. K. (2009b). Acta Cryst. E65, o684.]). For the graph-set analysis of hydrogen bonding, see: Bernstein et al. (1995[Bernstein, J., Davis, R. E., Shimoni, L. & Chang, N. L. (1995). Angew. Chem. Int. Ed. Engl. 34, 1555-1573.]).

[Scheme 1]

Experimental

Crystal data
  • C8H9N5O

  • Mr = 191.20

  • Orthorhombic, P n a 21

  • a = 11.1369 (19) Å

  • b = 18.913 (3) Å

  • c = 4.0311 (7) Å

  • V = 849.1 (3) Å3

  • Z = 4

  • Mo Kα radiation

  • μ = 0.11 mm−1

  • T = 100 K

  • 0.60 × 0.08 × 0.06 mm

Data collection
  • Bruker SMART APEX CCD diffractometer

  • Absorption correction: multi-scan (SADABS; Sheldrick, 2001[Sheldrick, G. M. (2001). SADABS. University of Göttingen, Germany.]) Tmin = 0.938, Tmax = 0.994

  • 5774 measured reflections

  • 1119 independent reflections

  • 1019 reflections with I > 2σ(I)

  • Rint = 0.050

Refinement
  • R[F2 > 2σ(F2)] = 0.053

  • wR(F2) = 0.117

  • S = 1.15

  • 1119 reflections

  • 137 parameters

  • 1 restraint

  • H atoms treated by a mixture of independent and constrained refinement

  • Δρmax = 0.33 e Å−3

  • Δρmin = −0.25 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA 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+{\script{1\over 2}}, -y+{\script{3\over 2}}, z-1].

Data collection: SMART (Bruker, 2001[Bruker (2001). SMART and SAINT. Bruker AXS GmbH, Karlsruhe, Germany.]); cell refinement: SAINT (Bruker, 2001[Bruker (2001). SMART and SAINT. Bruker AXS GmbH, Karlsruhe, Germany.]); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); molecular graphics: SHELXTL (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); software used to prepare material for publication: SHELXTL.

Supporting information


Comment top

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 C6O1 further extends this delocalization by resonance assisted N—H···OC 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.

Related literature top

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 top

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.

Refinement top

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 anomalous scattering effects 706 Friedel pairs have been merged.

Structure description top

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 C6O1 further extends this delocalization by resonance assisted N—H···OC 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).

Computing details top

Data collection: SMART (Bruker, 2001); cell refinement: 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).

Figures top
[Figure 1] Fig. 1. The molecular structure of the title compound showing the atomic numbering scheme. Displacement ellipsoids are drawn at the 50% probability level.
[Figure 2] Fig. 2. Crystal packing of the title compound, viewed down the c axis.
4-Amino-2,8-dimethyl-6H-pyrimido[1,2-a][1,3,5]triazin-6-one top
Crystal data top
C8H9N5ODx = 1.496 Mg m3
Mr = 191.20Melting point: 545 K
Orthorhombic, Pna21Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2c -2nCell parameters from 614 reflections
a = 11.1369 (19) Åθ = 2.8–26.8°
b = 18.913 (3) ŵ = 0.11 mm1
c = 4.0311 (7) ÅT = 100 K
V = 849.1 (3) Å3Needle, colourless
Z = 40.60 × 0.08 × 0.06 mm
F(000) = 400
Data collection top
Bruker SMART APEX CCD
diffractometer
1119 independent reflections
Radiation source: fine-focus sealed tube1019 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.050
φ and ω scansθmax = 27.5°, θmin = 2.2°
Absorption correction: multi-scan
(SADABS; Sheldrick, 2001)
h = 1314
Tmin = 0.938, Tmax = 0.994k = 2422
5774 measured reflectionsl = 54
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.053Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.117H 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 parametersΔρmax = 0.33 e Å3
1 restraintΔρmin = 0.25 e Å3
Crystal data top
C8H9N5OV = 849.1 (3) Å3
Mr = 191.20Z = 4
Orthorhombic, Pna21Mo Kα radiation
a = 11.1369 (19) ŵ = 0.11 mm1
b = 18.913 (3) ÅT = 100 K
c = 4.0311 (7) Å0.60 × 0.08 × 0.06 mm
Data collection top
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 = 0.994Rint = 0.050
5774 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0531 restraint
wR(F2) = 0.117H atoms treated by a mixture of independent and constrained refinement
S = 1.15Δρmax = 0.33 e Å3
1119 reflectionsΔρmin = 0.25 e Å3
137 parameters
Special details top

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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
O10.61240 (19)0.88225 (11)0.2411 (7)0.0229 (6)
N10.3706 (2)0.71578 (13)0.3214 (8)0.0145 (6)
N20.5341 (2)0.67258 (13)0.0011 (7)0.0137 (6)
N30.4963 (2)0.79702 (13)0.0265 (7)0.0119 (5)
N40.3255 (2)0.83294 (13)0.3415 (7)0.0138 (6)
N50.6531 (2)0.74865 (15)0.2904 (7)0.0154 (6)
H510.673 (3)0.793 (2)0.326 (11)0.018 (9)*
H520.689 (3)0.7098 (19)0.349 (11)0.019 (9)*
C10.4393 (3)0.66472 (15)0.2008 (8)0.0134 (6)
C20.5625 (2)0.73778 (15)0.0888 (8)0.0128 (6)
C30.3965 (2)0.78262 (15)0.2314 (8)0.0121 (6)
C40.3465 (2)0.90073 (15)0.2475 (9)0.0139 (6)
C50.4418 (3)0.91978 (16)0.0552 (8)0.0147 (6)
H50.45310.96830.00190.018*
C60.5246 (3)0.86906 (15)0.0674 (8)0.0155 (7)
C70.4091 (3)0.59100 (15)0.3046 (10)0.0191 (7)
H7A0.45590.57840.50170.029*
H7B0.42820.55820.12390.029*
H7C0.32320.58800.35620.029*
C80.2543 (3)0.95324 (15)0.3617 (9)0.0182 (7)
H8A0.17960.94600.23810.027*
H8B0.28401.00130.32240.027*
H8C0.23920.94670.59920.027*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O10.0225 (11)0.0152 (11)0.0310 (14)0.0048 (8)0.0116 (12)0.0017 (11)
N10.0125 (11)0.0128 (12)0.0183 (14)0.0008 (9)0.0027 (11)0.0007 (11)
N20.0132 (11)0.0131 (13)0.0149 (13)0.0011 (9)0.0009 (11)0.0029 (11)
N30.0101 (10)0.0113 (12)0.0144 (13)0.0013 (8)0.0024 (10)0.0011 (10)
N40.0116 (10)0.0137 (12)0.0162 (13)0.0004 (9)0.0017 (11)0.0011 (11)
N50.0139 (12)0.0123 (13)0.0200 (15)0.0017 (10)0.0064 (12)0.0007 (12)
C10.0124 (12)0.0152 (14)0.0126 (15)0.0014 (11)0.0034 (12)0.0002 (13)
C20.0101 (12)0.0167 (15)0.0114 (14)0.0023 (11)0.0002 (12)0.0034 (13)
C30.0108 (12)0.0161 (14)0.0096 (14)0.0022 (10)0.0013 (12)0.0003 (13)
C40.0142 (13)0.0136 (14)0.0139 (15)0.0001 (10)0.0048 (12)0.0030 (14)
C50.0190 (14)0.0085 (14)0.0165 (16)0.0027 (11)0.0031 (13)0.0007 (12)
C60.0156 (13)0.0122 (15)0.0187 (17)0.0050 (11)0.0018 (13)0.0009 (13)
C70.0215 (14)0.0126 (14)0.0232 (18)0.0004 (11)0.0046 (15)0.0005 (13)
C80.0182 (13)0.0154 (15)0.0209 (16)0.0021 (11)0.0018 (13)0.0010 (14)
Geometric parameters (Å, º) top
O1—C61.228 (4)N5—H520.87 (4)
N1—C11.324 (4)C1—C71.494 (4)
N1—C31.346 (4)C4—C51.363 (4)
N2—C21.321 (4)C4—C81.501 (4)
N2—C11.342 (4)C5—C61.420 (4)
N3—C31.411 (4)C5—H50.9500
N3—C21.420 (4)C7—H7A0.9800
N3—C61.449 (4)C7—H7B0.9800
N4—C31.314 (4)C7—H7C0.9800
N4—C41.357 (4)C8—H8A0.9800
N5—C21.311 (4)C8—H8B0.9800
N5—H510.89 (4)C8—H8C0.9800
C1—N1—C3117.5 (3)C5—C4—C8122.2 (3)
C2—N2—C1117.0 (2)C4—C5—C6121.7 (3)
C3—N3—C2116.6 (2)C4—C5—H5119.2
C3—N3—C6120.4 (2)C6—C5—H5119.2
C2—N3—C6122.9 (2)O1—C6—C5125.3 (3)
C3—N4—C4119.1 (3)O1—C6—N3120.9 (3)
C2—N5—H51116 (2)C5—C6—N3113.8 (3)
C2—N5—H52113 (2)C1—C7—H7A109.5
H51—N5—H52130 (3)C1—C7—H7B109.5
N1—C1—N2126.6 (3)H7A—C7—H7B109.5
N1—C1—C7116.6 (3)C1—C7—H7C109.5
N2—C1—C7116.8 (3)H7A—C7—H7C109.5
N5—C2—N2119.7 (3)H7B—C7—H7C109.5
N5—C2—N3118.6 (3)C4—C8—H8A109.5
N2—C2—N3121.6 (3)C4—C8—H8B109.5
N4—C3—N1117.4 (3)H8A—C8—H8B109.5
N4—C3—N3122.1 (3)C4—C8—H8C109.5
N1—C3—N3120.5 (3)H8A—C8—H8C109.5
N4—C4—C5122.9 (3)H8B—C8—H8C109.5
N4—C4—C8114.9 (3)
C3—N1—C1—N20.9 (5)C2—N3—C3—N4177.1 (3)
C3—N1—C1—C7179.8 (3)C6—N3—C3—N40.7 (4)
C2—N2—C1—N10.2 (5)C2—N3—C3—N12.8 (4)
C2—N2—C1—C7178.8 (3)C6—N3—C3—N1179.4 (3)
C1—N2—C2—N5178.8 (3)C3—N4—C4—C53.2 (5)
C1—N2—C2—N30.4 (4)C3—N4—C4—C8174.9 (3)
C3—N3—C2—N5177.4 (3)N4—C4—C5—C61.6 (5)
C6—N3—C2—N50.3 (4)C8—C4—C5—C6176.3 (3)
C3—N3—C2—N21.8 (4)C4—C5—C6—O1179.9 (3)
C6—N3—C2—N2179.5 (3)C4—C5—C6—N31.0 (4)
C4—N4—C3—N1177.9 (3)C3—N3—C6—O1178.8 (3)
C4—N4—C3—N32.0 (4)C2—N3—C6—O13.6 (4)
C1—N1—C3—N4177.5 (3)C3—N3—C6—C52.1 (4)
C1—N1—C3—N32.4 (4)C2—N3—C6—C5175.5 (3)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N5—H51···O10.89 (4)1.84 (4)2.575 (3)139 (3)
N5—H51···N1i0.89 (4)2.63 (4)2.961 (4)103 (3)
N5—H52···N4i0.87 (4)2.12 (4)2.876 (4)144 (3)
Symmetry code: (i) x+1/2, y+3/2, z1.

Experimental details

Crystal data
Chemical formulaC8H9N5O
Mr191.20
Crystal system, space groupOrthorhombic, Pna21
Temperature (K)100
a, b, c (Å)11.1369 (19), 18.913 (3), 4.0311 (7)
V3)849.1 (3)
Z4
Radiation typeMo Kα
µ (mm1)0.11
Crystal size (mm)0.60 × 0.08 × 0.06
Data collection
DiffractometerBruker SMART APEX CCD
Absorption correctionMulti-scan
(SADABS; Sheldrick, 2001)
Tmin, Tmax0.938, 0.994
No. of measured, independent and
observed [I > 2σ(I)] reflections
5774, 1119, 1019
Rint0.050
(sin θ/λ)max1)0.649
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.053, 0.117, 1.15
No. of reflections1119
No. of parameters137
No. of restraints1
H-atom treatmentH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å3)0.33, 0.25

Computer programs: SMART (Bruker, 2001), SAINT (Bruker, 2001), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), SHELXTL (Sheldrick, 2008).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N5—H51···O10.89 (4)1.84 (4)2.575 (3)139 (3)
N5—H51···N1i0.89 (4)2.63 (4)2.961 (4)103 (3)
N5—H52···N4i0.87 (4)2.12 (4)2.876 (4)144 (3)
Symmetry code: (i) x+1/2, y+3/2, z1.
 

Footnotes

1Part 15 in the series `Fused heterocyclic systems with s-triazine ring'. For Part 14, see Dolzhenko et al. (2009a).

Thomson Reuters ResearcherID: B-1130-2008.

Acknowledgements

This work was supported by the National Medical Research Council, Singapore (grant No. NMRC/NIG/0020/2008).

References

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