(E)-6-Amino-1,3-dimethyl-5-[(pyridin-2-yl-methyl-idene)amino]-pyrimidine-2,4(1H,3H)-dione.

In the title compound, C(12)H(13)N(5)O(2), a Schiff-base-derived chelate ligand, the non-aromatic heterocycle and its substituents essentially occupy one common plane (r.m.s. of fitted non-H atoms = 0.0503 Å). The N=C bond is E-configured. Intra-cyclic angles in the pyridine moiety cover the range 117.6 (2)-124.1 (2)°. Intra- and inter-molecular N-H⋯N and N-H⋯O hydrogen bonds are observed in the crystal structure, as are intra- and inter-molecular C-H⋯O contacts which, in total, connect the mol-ecules into a three-dimensional network. The shortest ring-centroid-to-ring-centroid distance of 3.5831 (14) Å is between the two different types of six-membered rings.

Related literature

For the crystal structures of two polymorphs of 6-amino-1,3-dimethyl-5-[(E-2-(methyl­sulfan­yl)benzyl­idene­amino]­pyrim­idine-2,4(1H,3H)-dione, see: Booysen et al. (2011a ▶,b ▶). For graph-set analysis of hydrogen bonds, see: Etter et al. (1990 ▶); Bernstein et al. (1995 ▶). For puckering analysis, see: Cremer & Pople (1975 ▶). For general information about the chelate effect in coordination chemistry, see: Gade (1998 ▶).

Experimental

Crystal data

C12H13N5O2

M = 259.27

Orthorhombic,

a = 26.5036 (8) Å

b = 28.9987 (14) Å

c = 6.2193 (1) Å

V = 4780.0 (3) Å3

Z = 16

Mo Kα radiation

μ = 0.10 mm−1

T = 200 K

0.27 × 0.14 × 0.06 mm

Data collection

Bruker APEXII CCD diffractometer

11316 measured reflections

1620 independent reflections

1171 reflections with I > 2σ(I)

R int = 0.049

Refinement

R[F 2 > 2σ(F 2)] = 0.039

wR(F 2) = 0.079

S = 0.94

1620 reflections

182 parameters

1 restraint

H atoms treated by a mixture of independent and constrained refinement

Δρmax = 0.17 e Å−3

Δρmin = −0.19 e Å−3

Data collection: APEX2 (Bruker, 2010 ▶); cell refinement: SAINT (Bruker, 2010 ▶); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ▶); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 ▶); molecular graphics: ORTEP-3 (Farrugia, 1997 ▶) and Mercury (Macrae et al., 2008 ▶); software used to prepare material for publication: SHELXL97 and PLATON (Spek, 2009 ▶).

Crystal structure: contains datablock(s) I, global. DOI: 10.1107/S1600536811031618/lh5299sup1.cif

Supplementary material file. DOI: 10.1107/S1600536811031618/lh5299Isup2.cdx

Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536811031618/lh5299Isup3.hkl

Supplementary material file. DOI: 10.1107/S1600536811031618/lh5299Isup4.cml

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

C12H13N5O2	F(000) = 2176
Mr = 259.27	Dx = 1.441 Mg m−3
Orthorhombic, Fdd2	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: F 2 -2d	Cell parameters from 2610 reflections
a = 26.5036 (8) Å	θ = 2.8–25.2°
b = 28.9987 (14) Å	µ = 0.10 mm−1
c = 6.2193 (1) Å	T = 200 K
V = 4780.0 (3) Å3	Platelet, red
Z = 16	0.27 × 0.14 × 0.06 mm

Bruker APEXII CCD diffractometer	1171 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tube	Rint = 0.049
graphite	θmax = 28.3°, θmin = 2.1°
φ and ω scans	h = −35→32
11316 measured reflections	k = −38→38
1620 independent reflections	l = −8→8

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)] = 0.039	Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.079	H atoms treated by a mixture of independent and constrained refinement
S = 0.94	w = 1/[σ2(Fo2) + (0.0422P)2] where P = (Fo2 + 2Fc2)/3
1620 reflections	(Δ/σ)max < 0.001
182 parameters	Δρmax = 0.17 e Å−3
1 restraint	Δρmin = −0.19 e Å−3

Refinement. Due to the absence of a strong anomalous scatterer, the Flack parameter is meaningless. Thus, Friedel opposites (1312 pairs) have been merged and the item was removed from the CIF.

	x	y	z	Uiso*/Ueq
O1	0.15951 (6)	0.02666 (6)	0.6362 (3)	0.0368 (5)
O2	0.24640 (6)	0.08960 (6)	0.0779 (2)	0.0332 (4)
N1	0.11534 (7)	0.06900 (7)	0.3925 (3)	0.0284 (5)
N2	0.20212 (7)	0.05684 (7)	0.3521 (3)	0.0267 (5)
N3	0.15107 (7)	0.12779 (6)	−0.0955 (3)	0.0246 (4)
N4	0.06933 (8)	0.10885 (8)	0.1366 (4)	0.0347 (5)
H71	0.0405 (11)	0.0991 (9)	0.207 (5)	0.056 (9)*
H72	0.0709 (8)	0.1246 (8)	0.023 (4)	0.021 (7)*
N5	0.21612 (7)	0.17411 (7)	−0.5455 (3)	0.0290 (5)
C1	0.15777 (9)	0.10106 (8)	0.0864 (4)	0.0247 (5)
C2	0.11379 (9)	0.09303 (8)	0.2032 (4)	0.0250 (5)
C3	0.15934 (9)	0.04947 (8)	0.4708 (4)	0.0269 (6)
C4	0.20500 (8)	0.08359 (8)	0.1627 (4)	0.0245 (5)
C5	0.07022 (10)	0.06475 (12)	0.5270 (5)	0.0497 (8)
H5A	0.0523	0.0943	0.5301	0.075*
H5B	0.0801	0.0562	0.6735	0.075*
H5C	0.0480	0.0409	0.4675	0.075*
C6	0.24849 (9)	0.03686 (9)	0.4392 (4)	0.0360 (6)
H6A	0.2572	0.0524	0.5741	0.054*
H6B	0.2760	0.0409	0.3354	0.054*
H6C	0.2433	0.0039	0.4665	0.054*
C7	0.18654 (9)	0.13865 (8)	−0.2257 (4)	0.0274 (6)
H7	0.2197	0.1272	−0.2021	0.033*
C8	0.17658 (9)	0.16845 (8)	−0.4101 (3)	0.0242 (5)
C9	0.13029 (9)	0.18992 (9)	−0.4462 (4)	0.0321 (6)
H9	0.1032	0.1861	−0.3479	0.039*
C10	0.12463 (10)	0.21673 (8)	−0.6268 (4)	0.0366 (6)
H10	0.0935	0.2319	−0.6536	0.044*
C11	0.16425 (10)	0.22156 (9)	−0.7690 (4)	0.0393 (7)
H11	0.1607	0.2392	−0.8968	0.047*
C12	0.20894 (10)	0.20008 (9)	−0.7199 (4)	0.0362 (7)
H12	0.2365	0.2039	−0.8161	0.043*

	U11	U22	U33	U12	U13	U23
O1	0.0386 (10)	0.0401 (10)	0.0316 (10)	0.0016 (8)	0.0004 (8)	0.0116 (10)
O2	0.0224 (9)	0.0446 (11)	0.0328 (9)	0.0016 (8)	0.0037 (7)	0.0052 (9)
N1	0.0219 (11)	0.0349 (12)	0.0284 (10)	0.0010 (8)	0.0044 (9)	0.0071 (10)
N2	0.0239 (10)	0.0303 (11)	0.0261 (10)	0.0031 (8)	−0.0012 (8)	0.0042 (9)
N3	0.0214 (10)	0.0288 (11)	0.0237 (10)	−0.0008 (8)	0.0020 (9)	−0.0003 (10)
N4	0.0223 (12)	0.0480 (14)	0.0340 (12)	−0.0001 (10)	0.0035 (10)	0.0164 (12)
N5	0.0261 (11)	0.0345 (12)	0.0263 (10)	−0.0002 (9)	0.0031 (8)	0.0030 (10)
C1	0.0237 (12)	0.0276 (13)	0.0229 (11)	−0.0003 (9)	0.0002 (10)	−0.0009 (11)
C2	0.0239 (13)	0.0261 (12)	0.0251 (12)	0.0020 (9)	−0.0016 (10)	0.0002 (11)
C3	0.0253 (14)	0.0273 (13)	0.0281 (13)	−0.0017 (10)	0.0004 (10)	0.0013 (12)
C4	0.0239 (13)	0.0249 (12)	0.0248 (12)	0.0003 (9)	−0.0003 (10)	−0.0029 (11)
C5	0.0290 (15)	0.078 (2)	0.0423 (16)	0.0069 (15)	0.0112 (13)	0.0267 (16)
C6	0.0270 (13)	0.0416 (15)	0.0393 (15)	0.0055 (11)	−0.0034 (11)	0.0085 (13)
C7	0.0237 (13)	0.0321 (14)	0.0264 (12)	0.0014 (10)	0.0002 (11)	0.0000 (11)
C8	0.0224 (11)	0.0272 (13)	0.0230 (11)	−0.0021 (10)	0.0004 (10)	−0.0026 (10)
C9	0.0264 (14)	0.0350 (14)	0.0349 (14)	0.0036 (11)	0.0006 (11)	−0.0011 (12)
C10	0.0311 (14)	0.0306 (14)	0.0480 (17)	0.0049 (11)	−0.0141 (13)	−0.0018 (14)
C11	0.0456 (18)	0.0349 (14)	0.0373 (15)	−0.0021 (12)	−0.0090 (13)	0.0100 (13)
C12	0.0395 (16)	0.0392 (16)	0.0298 (14)	−0.0032 (13)	0.0050 (12)	0.0073 (12)

O1—C3	1.223 (3)	C5—H5A	0.9800
O2—C4	1.230 (3)	C5—H5B	0.9800
N1—C2	1.368 (3)	C5—H5C	0.9800
N1—C3	1.385 (3)	C6—H6A	0.9800
N1—C5	1.465 (3)	C6—H6B	0.9800
N2—C3	1.370 (3)	C6—H6C	0.9800
N2—C4	1.413 (3)	C7—C8	1.460 (3)
N2—C6	1.463 (3)	C7—H7	0.9500
N3—C7	1.280 (3)	C8—C9	1.394 (3)
N3—C1	1.383 (3)	C9—C10	1.374 (4)
N4—C2	1.330 (3)	C9—H9	0.9500
N4—H71	0.93 (3)	C10—C11	1.380 (4)
N4—H72	0.84 (2)	C10—H10	0.9500
N5—C12	1.334 (3)	C11—C12	1.373 (4)
N5—C8	1.354 (3)	C11—H11	0.9500
C1—C2	1.393 (3)	C12—H12	0.9500
C1—C4	1.431 (3)
C2—N1—C3	122.4 (2)	H5A—C5—H5C	109.5
C2—N1—C5	120.6 (2)	H5B—C5—H5C	109.5
C3—N1—C5	116.9 (2)	N2—C6—H6A	109.5
C3—N2—C4	125.46 (19)	N2—C6—H6B	109.5
C3—N2—C6	115.73 (19)	H6A—C6—H6B	109.5
C4—N2—C6	118.74 (19)	N2—C6—H6C	109.5
C7—N3—C1	124.1 (2)	H6A—C6—H6C	109.5
C2—N4—H71	118.6 (18)	H6B—C6—H6C	109.5
C2—N4—H72	113.8 (16)	N3—C7—C8	120.6 (2)
H71—N4—H72	127 (2)	N3—C7—H7	119.7
C12—N5—C8	117.6 (2)	C8—C7—H7	119.7
N3—C1—C2	114.4 (2)	N5—C8—C9	121.8 (2)
N3—C1—C4	125.6 (2)	N5—C8—C7	114.8 (2)
C2—C1—C4	120.0 (2)	C9—C8—C7	123.4 (2)
N4—C2—N1	118.0 (2)	C10—C9—C8	118.7 (2)
N4—C2—C1	121.4 (2)	C10—C9—H9	120.6
N1—C2—C1	120.6 (2)	C8—C9—H9	120.6
O1—C3—N2	122.3 (2)	C9—C10—C11	119.9 (2)
O1—C3—N1	121.4 (2)	C9—C10—H10	120.1
N2—C3—N1	116.3 (2)	C11—C10—H10	120.1
O2—C4—N2	118.9 (2)	C12—C11—C10	117.9 (3)
O2—C4—C1	126.0 (2)	C12—C11—H11	121.0
N2—C4—C1	115.1 (2)	C10—C11—H11	121.0
N1—C5—H5A	109.5	N5—C12—C11	124.1 (2)
N1—C5—H5B	109.5	N5—C12—H12	118.0
H5A—C5—H5B	109.5	C11—C12—H12	118.0
N1—C5—H5C	109.5
C7—N3—C1—C2	−179.2 (2)	C6—N2—C4—O2	−0.6 (3)
C7—N3—C1—C4	3.4 (4)	C3—N2—C4—C1	−4.6 (3)
C3—N1—C2—N4	177.2 (2)	C6—N2—C4—C1	178.8 (2)
C5—N1—C2—N4	−5.7 (3)	N3—C1—C4—O2	−0.3 (4)
C3—N1—C2—C1	−3.6 (3)	C2—C1—C4—O2	−177.6 (2)
C5—N1—C2—C1	173.4 (2)	N3—C1—C4—N2	−179.7 (2)
N3—C1—C2—N4	2.3 (3)	C2—C1—C4—N2	3.0 (3)
C4—C1—C2—N4	179.9 (2)	C1—N3—C7—C8	−177.8 (2)
N3—C1—C2—N1	−176.8 (2)	C12—N5—C8—C9	−2.0 (3)
C4—C1—C2—N1	0.8 (3)	C12—N5—C8—C7	178.4 (2)
C4—N2—C3—O1	−178.5 (2)	N3—C7—C8—N5	−174.6 (2)
C6—N2—C3—O1	−1.8 (3)	N3—C7—C8—C9	5.8 (3)
C4—N2—C3—N1	2.1 (3)	N5—C8—C9—C10	1.4 (4)
C6—N2—C3—N1	178.7 (2)	C7—C8—C9—C10	−179.0 (2)
C2—N1—C3—O1	−177.2 (2)	C8—C9—C10—C11	0.6 (4)
C5—N1—C3—O1	5.6 (4)	C9—C10—C11—C12	−1.9 (4)
C2—N1—C3—N2	2.2 (3)	C8—N5—C12—C11	0.6 (4)
C5—N1—C3—N2	−174.9 (2)	C10—C11—C12—N5	1.4 (4)
C3—N2—C4—O2	176.0 (2)

D—H···A	D—H	H···A	D···A	D—H···A
N4—H71···N5i	0.93 (3)	2.08 (3)	2.928 (3)	151 (3)
N4—H72···N3	0.84 (2)	2.25 (2)	2.661 (3)	110.2 (18)
N4—H72···O2ii	0.84 (2)	2.54 (2)	3.108 (3)	125.8 (19)
C7—H7···O2	0.95	2.17	2.847 (3)	127.
C11—H11···O1iii	0.95	2.54	3.313 (3)	138.

Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N4—H71⋯N5i	0.93 (3)	2.08 (3)	2.928 (3)	151 (3)
N4—H72⋯N3	0.84 (2)	2.25 (2)	2.661 (3)	110.2 (18)
N4—H72⋯O2ii	0.84 (2)	2.54 (2)	3.108 (3)	125.8 (19)
C7—H7⋯O2	0.95	2.17	2.847 (3)	127
C11—H11⋯O1iii	0.95	2.54	3.313 (3)	138

Symmetry codes: (i) ; (ii) ; (iii) .