2-[(E)-(6-Amino-1,3-dimethyl-2,4-dioxo-1,2,3,4-tetra-hydro-pyrimidin-5-yl)imino-meth-yl]pyridinium chloride monohydrate.

The title compound, C(12)H(14)N(5)O(2) (+)·Cl(-)·H(2)O, is the monohydrate of the hydro-chloride of an oxopurine-derived Schiff base in which protonation took place at the pyridine N atom. The organic cation is essentially planar (r.m.s. of all fitted non-H atoms = 0.0373 Å). In the crystal, N-H⋯O and N-H⋯Cl hydrogen bonds as well as C-H⋯O and C-H⋯Cl contacts connect the different entities into a three-dimensional network. The shortest centroid-centroid distance between two pyrimidine rings is 3.6364 (9) Å.

Related literature

For the development of radiopharmaceuticals, see: Gerber et al. (2011 ▶). For the crystal structure of the neutral organic parent ligand, see: Booysen et al. (2011a ▶). For the crystal structures of polymorphs of 6-amino-1,3-dimethyl-5-[(E-2-(methyl­sulfan­yl)benzyl­idene­amino]pyrimidine-2,4(1H,3H)-dione, see: Booy­sen et al. (2011b ▶,c ▶). For graph-set analysis of hydrogen bonds, see: Etter et al. (1990 ▶); Bernstein et al. (1995 ▶). For puckering analysis, see: Cremer & Pople (1975 ▶).

Experimental

Crystal data

C12H14N5O2 +·Cl−·H2O

M = 313.75

Orthorhombic,

a = 13.3797 (4) Å

b = 15.7975 (5) Å

c = 12.9998 (4) Å

V = 2747.71 (15) Å3

Z = 8

Mo Kα radiation

μ = 0.30 mm−1

T = 200 K

0.49 × 0.09 × 0.08 mm

Data collection

Bruker APEXII CCD diffractometer

Absorption correction: multi-scan (SADABS; Bruker, 2008 ▶) T min = 0.879, T max = 1.000

24436 measured reflections

3415 independent reflections

2327 reflections with I > 2σ(I)

R int = 0.053

Refinement

R[F 2 > 2σ(F 2)] = 0.042

wR(F 2) = 0.111

S = 1.03

3415 reflections

212 parameters

H atoms treated by a mixture of independent and constrained refinement

Δρmax = 0.34 e Å−3

Δρmin = −0.22 e Å−3

Data collection: APEX2 (Bruker, 2010 ▶); cell refinement: SAINT (Bruker, 2010 ▶); data reduction: SAINT; program(s) used to solve structure: SIR97 (Altomare et al., 1999 ▶); 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/S1600536811033307/dn2714sup1.cif

Supplementary material file. DOI: 10.1107/S1600536811033307/dn2714Isup2.cdx

Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536811033307/dn2714Isup3.hkl

Supplementary material file. DOI: 10.1107/S1600536811033307/dn2714Isup4.cml

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

C12H14N5O2+·Cl−·H2O	F(000) = 1312
Mr = 313.75	Dx = 1.517 Mg m−3
Orthorhombic, Pbcn	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2n 2ab	Cell parameters from 5575 reflections
a = 13.3797 (4) Å	θ = 2.5–28.1°
b = 15.7975 (5) Å	µ = 0.30 mm−1
c = 12.9998 (4) Å	T = 200 K
V = 2747.71 (15) Å3	Needle, brown
Z = 8	0.49 × 0.09 × 0.08 mm

Bruker APEXII CCD diffractometer	3415 independent reflections
Radiation source: fine-focus sealed tube	2327 reflections with I > 2σ(I)
graphite	Rint = 0.053
φ and ω scans	θmax = 28.3°, θmin = 2.0°
Absorption correction: multi-scan (SADABS; Bruker, 2008)	h = −17→17
Tmin = 0.879, Tmax = 1.000	k = −21→20
24436 measured reflections	l = −17→12

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)] = 0.042	Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.111	H atoms treated by a mixture of independent and constrained refinement
S = 1.03	w = 1/[σ2(Fo2) + (0.0549P)2 + 0.7712P] where P = (Fo2 + 2Fc2)/3
3415 reflections	(Δ/σ)max < 0.001
212 parameters	Δρmax = 0.34 e Å−3
0 restraints	Δρmin = −0.22 e Å−3

	x	y	z	Uiso*/Ueq
O1	0.75612 (9)	−0.02776 (9)	0.13036 (10)	0.0310 (3)
O2	0.43377 (9)	−0.11801 (8)	0.12425 (10)	0.0282 (3)
N1	0.63382 (10)	0.07221 (9)	0.12603 (11)	0.0222 (3)
N2	0.59510 (11)	−0.07228 (9)	0.13227 (11)	0.0224 (3)
N3	0.36366 (10)	0.05754 (9)	0.12000 (11)	0.0201 (3)
N4	0.51074 (12)	0.17487 (10)	0.11875 (13)	0.0260 (3)
H741	0.5501 (17)	0.2148 (14)	0.1230 (14)	0.026 (5)*
H742	0.4432 (19)	0.1906 (15)	0.1194 (16)	0.040 (6)*
N5	0.18069 (11)	0.13375 (9)	0.11007 (12)	0.0246 (3)
H751	0.2352 (17)	0.1666 (15)	0.1123 (15)	0.034 (6)*
C1	0.46118 (12)	0.02987 (11)	0.12260 (12)	0.0194 (3)
C2	0.53451 (12)	0.09375 (11)	0.12252 (13)	0.0202 (3)
C3	0.66668 (13)	−0.01110 (11)	0.12946 (13)	0.0224 (4)
C4	0.49100 (13)	−0.05750 (11)	0.12589 (13)	0.0205 (3)
C5	0.71013 (14)	0.13949 (12)	0.12604 (18)	0.0344 (5)
H5A	0.7050	0.1723	0.0623	0.052*
H5B	0.7767	0.1140	0.1307	0.052*
H5C	0.6994	0.1769	0.1851	0.052*
C6	0.62944 (15)	−0.16046 (12)	0.13966 (17)	0.0329 (5)
H6A	0.6593	−0.1777	0.0741	0.049*
H6B	0.5725	−0.1973	0.1554	0.049*
H6C	0.6794	−0.1652	0.1945	0.049*
C7	0.28582 (12)	0.00923 (11)	0.12190 (13)	0.0230 (4)
H7	0.2925	−0.0506	0.1257	0.028*
C8	0.18734 (13)	0.04871 (11)	0.11802 (13)	0.0221 (4)
C9	0.09840 (14)	0.00262 (12)	0.12149 (15)	0.0281 (4)
H9	0.1001	−0.0572	0.1288	0.034*
C10	0.00810 (15)	0.04423 (13)	0.11423 (16)	0.0332 (5)
H10	−0.0525	0.0130	0.1171	0.040*
C11	0.00552 (15)	0.13148 (13)	0.10267 (17)	0.0368 (5)
H11	−0.0564	0.1603	0.0951	0.044*
C12	0.09408 (14)	0.17558 (12)	0.10235 (16)	0.0315 (5)
H12	0.0938	0.2355	0.0967	0.038*
Cl1	0.31571 (3)	0.28729 (3)	0.11637 (4)	0.03282 (15)
O90	0.39829 (14)	0.33807 (11)	0.34015 (17)	0.0472 (4)
H901	0.350 (2)	0.373 (2)	0.359 (2)	0.063 (8)*
H902	0.393 (2)	0.326 (2)	0.279 (3)	0.082 (12)*

	U11	U22	U33	U12	U13	U23
O1	0.0182 (6)	0.0340 (7)	0.0406 (8)	0.0043 (5)	0.0002 (6)	0.0034 (7)
O2	0.0245 (7)	0.0204 (6)	0.0397 (8)	−0.0011 (5)	0.0006 (6)	−0.0014 (6)
N1	0.0162 (7)	0.0237 (7)	0.0267 (8)	−0.0009 (6)	0.0007 (6)	0.0023 (7)
N2	0.0199 (7)	0.0202 (7)	0.0271 (8)	0.0037 (6)	0.0004 (6)	0.0006 (6)
N3	0.0189 (7)	0.0230 (7)	0.0184 (7)	0.0015 (6)	0.0006 (6)	−0.0013 (6)
N4	0.0205 (8)	0.0209 (7)	0.0366 (9)	−0.0011 (6)	0.0005 (7)	0.0001 (7)
N5	0.0193 (7)	0.0204 (7)	0.0342 (9)	−0.0008 (6)	−0.0009 (7)	−0.0007 (7)
C1	0.0183 (8)	0.0210 (8)	0.0187 (8)	0.0012 (6)	−0.0001 (7)	0.0005 (7)
C2	0.0185 (8)	0.0250 (8)	0.0170 (8)	0.0026 (7)	0.0005 (7)	0.0010 (7)
C3	0.0219 (8)	0.0280 (9)	0.0174 (9)	0.0035 (7)	0.0005 (7)	0.0019 (8)
C4	0.0207 (8)	0.0224 (8)	0.0183 (8)	0.0021 (7)	0.0002 (7)	−0.0001 (7)
C5	0.0192 (9)	0.0264 (10)	0.0575 (14)	−0.0036 (7)	0.0026 (9)	0.0057 (10)
C6	0.0263 (9)	0.0220 (9)	0.0505 (13)	0.0058 (7)	−0.0019 (9)	−0.0013 (9)
C7	0.0218 (8)	0.0227 (8)	0.0244 (9)	0.0020 (7)	−0.0001 (8)	−0.0010 (7)
C8	0.0213 (8)	0.0220 (8)	0.0229 (9)	0.0010 (7)	−0.0018 (7)	−0.0020 (7)
C9	0.0252 (9)	0.0220 (8)	0.0370 (11)	−0.0016 (7)	−0.0011 (9)	−0.0005 (8)
C10	0.0210 (9)	0.0332 (10)	0.0455 (12)	−0.0050 (8)	0.0005 (9)	−0.0027 (10)
C11	0.0202 (9)	0.0298 (10)	0.0603 (15)	0.0047 (8)	−0.0007 (9)	−0.0005 (10)
C12	0.0260 (9)	0.0218 (9)	0.0467 (13)	0.0033 (8)	0.0011 (9)	−0.0006 (8)
Cl1	0.0254 (2)	0.0196 (2)	0.0535 (3)	0.00017 (17)	−0.0032 (2)	−0.0015 (2)
O90	0.0466 (10)	0.0376 (9)	0.0575 (12)	0.0172 (8)	−0.0031 (9)	−0.0016 (8)

O1—C3	1.225 (2)	C5—H5A	0.9800
O2—C4	1.225 (2)	C5—H5B	0.9800
N1—C2	1.372 (2)	C5—H5C	0.9800
N1—C3	1.388 (2)	C6—H6A	0.9800
N1—C5	1.474 (2)	C6—H6B	0.9800
N2—C3	1.361 (2)	C6—H6C	0.9800
N2—C4	1.415 (2)	C7—C8	1.459 (2)
N2—C6	1.470 (2)	C7—H7	0.9500
N3—C7	1.291 (2)	C8—C9	1.396 (2)
N3—C1	1.377 (2)	C9—C10	1.379 (3)
N4—C2	1.321 (2)	C9—H9	0.9500
N4—H741	0.82 (2)	C10—C11	1.387 (3)
N4—H742	0.94 (2)	C10—H10	0.9500
N5—C12	1.338 (2)	C11—C12	1.374 (3)
N5—C8	1.350 (2)	C11—H11	0.9500
N5—H751	0.90 (2)	C12—H12	0.9500
C1—C2	1.407 (2)	O90—H901	0.89 (3)
C1—C4	1.437 (2)	O90—H902	0.82 (3)
C2—N1—C3	122.87 (15)	N1—C5—H5C	109.5
C2—N1—C5	119.47 (15)	H5A—C5—H5C	109.5
C3—N1—C5	117.66 (14)	H5B—C5—H5C	109.5
C3—N2—C4	125.03 (14)	N2—C6—H6A	109.5
C3—N2—C6	117.05 (14)	N2—C6—H6B	109.5
C4—N2—C6	117.90 (14)	H6A—C6—H6B	109.5
C7—N3—C1	125.19 (15)	N2—C6—H6C	109.5
C2—N4—H741	125.9 (15)	H6A—C6—H6C	109.5
C2—N4—H742	119.3 (14)	H6B—C6—H6C	109.5
H741—N4—H742	114 (2)	N3—C7—C8	118.36 (16)
C12—N5—C8	123.66 (16)	N3—C7—H7	120.8
C12—N5—H751	114.9 (14)	C8—C7—H7	120.8
C8—N5—H751	121.4 (14)	N5—C8—C9	117.73 (16)
N3—C1—C2	115.66 (15)	N5—C8—C7	119.18 (16)
N3—C1—C4	124.67 (15)	C9—C8—C7	123.09 (16)
C2—C1—C4	119.67 (15)	C10—C9—C8	119.75 (17)
N4—C2—N1	118.34 (16)	C10—C9—H9	120.1
N4—C2—C1	121.85 (15)	C8—C9—H9	120.1
N1—C2—C1	119.81 (15)	C9—C10—C11	120.20 (18)
O1—C3—N2	122.31 (16)	C9—C10—H10	119.9
O1—C3—N1	120.87 (16)	C11—C10—H10	119.9
N2—C3—N1	116.82 (15)	C12—C11—C10	118.85 (18)
O2—C4—N2	119.19 (15)	C12—C11—H11	120.6
O2—C4—C1	125.12 (16)	C10—C11—H11	120.6
N2—C4—C1	115.68 (15)	N5—C12—C11	119.75 (18)
N1—C5—H5A	109.5	N5—C12—H12	120.1
N1—C5—H5B	109.5	C11—C12—H12	120.1
H5A—C5—H5B	109.5	H901—O90—H902	111 (3)
C7—N3—C1—C2	−178.39 (16)	C6—N2—C4—O2	−1.7 (3)
C7—N3—C1—C4	1.2 (3)	C3—N2—C4—C1	−4.0 (3)
C3—N1—C2—N4	−179.57 (16)	C6—N2—C4—C1	177.82 (16)
C5—N1—C2—N4	0.3 (3)	N3—C1—C4—O2	1.9 (3)
C3—N1—C2—C1	0.2 (3)	C2—C1—C4—O2	−178.50 (17)
C5—N1—C2—C1	−179.93 (17)	N3—C1—C4—N2	−177.63 (15)
N3—C1—C2—N4	−0.9 (2)	C2—C1—C4—N2	2.0 (2)
C4—C1—C2—N4	179.47 (17)	C1—N3—C7—C8	−179.65 (15)
N3—C1—C2—N1	179.36 (15)	C12—N5—C8—C9	−2.0 (3)
C4—C1—C2—N1	−0.3 (2)	C12—N5—C8—C7	177.56 (18)
C4—N2—C3—O1	−176.43 (17)	N3—C7—C8—N5	1.6 (3)
C6—N2—C3—O1	1.8 (3)	N3—C7—C8—C9	−178.81 (17)
C4—N2—C3—N1	3.9 (3)	N5—C8—C9—C10	1.6 (3)
C6—N2—C3—N1	−177.86 (16)	C7—C8—C9—C10	−177.98 (18)
C2—N1—C3—O1	178.46 (16)	C8—C9—C10—C11	0.5 (3)
C5—N1—C3—O1	−1.4 (3)	C9—C10—C11—C12	−2.3 (3)
C2—N1—C3—N2	−1.9 (3)	C8—N5—C12—C11	0.3 (3)
C5—N1—C3—N2	178.23 (16)	C10—C11—C12—N5	1.9 (3)
C3—N2—C4—O2	176.49 (17)

D—H···A	D—H	H···A	D···A	D—H···A
N4—H741···O90i	0.82 (2)	2.12 (2)	2.901 (2)	158 (2)
N4—H742···Cl1	0.94 (2)	2.29 (2)	3.1565 (16)	153 (2)
N5—H751···Cl1	0.90 (2)	2.19 (2)	3.0255 (16)	155 (2)
O90—H901···O1ii	0.89 (3)	2.01 (3)	2.874 (2)	164 (3)
O90—H902···Cl1	0.82 (3)	2.43 (3)	3.213 (2)	159 (3)
C5—H5A···Cl1iii	0.98	2.83	3.642 (2)	141.
C9—H9···Cl1iv	0.95	2.71	3.5912 (19)	155.
C10—H10···O1v	0.95	2.65	3.564 (2)	163.
C12—H12···O2vi	0.95	2.37	3.294 (2)	164.

Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N4—H741⋯O90i	0.82 (2)	2.12 (2)	2.901 (2)	158 (2)
N4—H742⋯Cl1	0.94 (2)	2.29 (2)	3.1565 (16)	153 (2)
N5—H751⋯Cl1	0.90 (2)	2.19 (2)	3.0255 (16)	155 (2)
O90—H901⋯O1ii	0.89 (3)	2.01 (3)	2.874 (2)	164 (3)
O90—H902⋯Cl1	0.82 (3)	2.43 (3)	3.213 (2)	159 (3)
C5—H5A⋯Cl1iii	0.98	2.83	3.642 (2)	141
C9—H9⋯Cl1iv	0.95	2.71	3.5912 (19)	155
C10—H10⋯O1v	0.95	2.65	3.564 (2)	163
C12—H12⋯O2vi	0.95	2.37	3.294 (2)	164

Symmetry codes: (i) ; (ii) ; (iii) ; (iv) ; (v) ; (vi) .