6-[(Dimethyl-amino)methyl-ene-amino]-1,3-dimethyl-pyrimidine-2,4(1H,3H)-dione dihydrate.

Uracil, the pyrimidine nucleobase, which combined with adenine forms one of the major motifs present in the biopolymer RNA, is also involved in the self-assembly of RNA. In the title compound, C(9)H(14)N(4)O(2)·2H(2)O, the asymmetric unit contains one dimethyl-amino-uracil group and two water mol-ecules. The plane of the N=C-NMe(2) side chain is inclined at 27.6 (5)° to the plane of the uracil ring. Both water mol-ecules form O-H⋯O hydrogen bonds with the carbonyl O atoms of the uracil group. Additional water-water hydrogen-bond inter-actions are also observed in the crystal structure. The O-H⋯O hydrogen bonds lead to the formation of a two-dimensional hydrogen-bonded network cage consisting of two dimethyl-amino-uracil groups and six water mol-ecules.

Related literature

For related literature, see: Pontikis & Monneret (1994 ▶); Sasaki et al. (1998 ▶); Sivakova & Rowan (2005 ▶); Thakur et al. (2001 ▶).

Experimental

Crystal data

C9H14N4O2·2H2O

M = 246.27

Triclinic,

a = 7.1310 (5) Å

b = 9.8571 (7) Å

c = 9.9160 (7) Å

α = 92.921 (1)°

β = 101.916 (1)°

γ = 109.912 (1)°

V = 635.62 (8) Å3

Z = 2

Mo Kα radiation

μ = 0.10 mm−1

T = 294 (2) K

0.23 × 0.17 × 0.12 mm

Data collection

Bruker SMART APEX CCD area-detector diffractometer

Absorption correction: none

6112 measured reflections

2231 independent reflections

2017 reflections with I > 2˘I)

R int = 0.019

Refinement

R[F 2 > 2σ(F 2)] = 0.051

wR(F 2) = 0.155

S = 1.07

2231 reflections

175 parameters

4 restraints

H atoms treated by a mixture of independent and constrained refinement

Δρmax = 0.34 e Å−3

Δρmin = −0.21 e Å−3

Data collection: SMART (Bruker, 2001 ▶); cell refinement: 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/PC (Sheldrick, 2008 ▶) and PLATON (Spek, 2003 ▶); software used to prepare material for publication: SHELXL97.

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536808024021/er2056sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536808024021/er2056Isup2.hkl

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

C9H14N4O2·2H2O	Z = 2
Mr = 246.27	F000 = 264
Triclinic, P1	Dx = 1.287 Mg m−3
Hall symbol: -P 1	Mo Kα radiation λ = 0.71073 Å
a = 7.1310 (5) Å	Cell parameters from 3875 reflections
b = 9.8571 (7) Å	θ = 2.4–27.9º
c = 9.9160 (7) Å	µ = 0.10 mm−1
α = 92.921 (1)º	T = 294 (2) K
β = 101.916 (1)º	Block, colorless
γ = 109.912 (1)º	0.23 × 0.17 × 0.12 mm
V = 635.62 (8) Å3

Bruker SMART APEX CCD area-detector diffractometer	2017 reflections with I > 2˘I)
Radiation source: fine-focus sealed tube	Rint = 0.019
Monochromator: graphite	θmax = 25.0º
T = 294(2) K	θmin = 2.1º
ω scans	h = −8→8
Absorption correction: none	k = −11→11
6112 measured reflections	l = −11→11
2231 independent reflections

Refinement on F2	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.051	H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.155	w = 1/[σ2(Fo2) + (0.0891P)2 + 0.1375P] where P = (Fo2 + 2Fc2)/3
S = 1.07	(Δ/σ)max = 0.001
2231 reflections	Δρmax = 0.34 e Å−3
175 parameters	Δρmin = −0.21 e Å−3
4 restraints	Extinction correction: SHELXL97 (Sheldrick, 2008), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
Primary atom site location: structure-invariant direct methods	Extinction coefficient: 0.063 (11)

Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell e.s.d.'s are taken into account individually in the estimation of e.s.d.'s in distances, angles and torsion angles; correlations between e.s.d.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell e.s.d.'s is used for estimating e.s.d.'s 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
C2	0.2362 (3)	0.44519 (18)	0.63139 (17)	0.0495 (4)
C4	0.0848 (3)	0.29150 (17)	0.40673 (18)	0.0509 (4)
C5	0.1553 (3)	0.41767 (17)	0.34303 (17)	0.0513 (4)
H5	0.1232	0.4100	0.2465	0.062*
C6	0.2691 (2)	0.55089 (16)	0.41829 (17)	0.0459 (4)
C8	0.3784 (2)	0.67157 (17)	0.24338 (18)	0.0508 (4)
H8	0.3574	0.5808	0.1980	0.061*
C11	0.4645 (4)	0.9307 (2)	0.2396 (3)	0.0780 (6)
H11A	0.3631	0.9631	0.1863	0.117*
H11B	0.5992	0.9970	0.2397	0.117*
H11C	0.4489	0.9274	0.3334	0.117*
C12	0.4759 (4)	0.7733 (3)	0.0408 (2)	0.0826 (7)
H12A	0.4610	0.6745	0.0139	0.124*
H12B	0.6128	0.8368	0.0423	0.124*
H12C	0.3791	0.7997	−0.0247	0.124*
C13	0.4247 (3)	0.70386 (19)	0.64897 (19)	0.0633 (5)
H13A	0.3316	0.7448	0.6760	0.095*
H13B	0.5070	0.7687	0.5970	0.095*
H13C	0.5123	0.6902	0.7305	0.095*
C14	0.0539 (3)	0.1852 (2)	0.6239 (2)	0.0682 (5)
H14A	0.1497	0.1355	0.6337	0.102*
H14B	−0.0781	0.1206	0.5708	0.102*
H14C	0.0426	0.2164	0.7142	0.102*
N1	0.3072 (2)	0.56267 (14)	0.56224 (14)	0.0491 (4)
N3	0.1267 (2)	0.31263 (14)	0.55177 (15)	0.0515 (4)
N7	0.3477 (2)	0.67916 (14)	0.36771 (15)	0.0520 (4)
N9	0.4379 (2)	0.78672 (15)	0.17847 (16)	0.0601 (4)
O1	−0.0098 (2)	0.16688 (13)	0.34493 (14)	0.0693 (4)
O2	0.2732 (2)	0.45919 (15)	0.75861 (13)	0.0659 (4)
O1W	0.0831 (3)	0.39489 (19)	0.97812 (18)	0.0879 (5)
H1W	0.142 (4)	0.408 (3)	0.910 (2)	0.107 (9)*
H2W	0.063 (13)	0.462 (7)	1.025 (6)	0.29 (4)*
O2W	−0.0201 (5)	0.1195 (2)	0.0614 (2)	0.1259 (9)
H3W	0.002 (6)	0.117 (4)	0.1489 (12)	0.137 (13)*
H4W	0.035 (9)	0.202 (3)	0.035 (6)	0.27 (3)*

	U11	U22	U33	U12	U13	U23
C2	0.0571 (9)	0.0503 (9)	0.0474 (9)	0.0243 (7)	0.0172 (7)	0.0084 (7)
C4	0.0550 (9)	0.0433 (9)	0.0534 (10)	0.0150 (7)	0.0150 (7)	0.0052 (7)
C5	0.0591 (10)	0.0438 (9)	0.0457 (9)	0.0122 (7)	0.0123 (7)	0.0056 (7)
C6	0.0500 (8)	0.0412 (8)	0.0497 (9)	0.0182 (7)	0.0154 (7)	0.0067 (6)
C8	0.0543 (9)	0.0401 (8)	0.0540 (9)	0.0115 (7)	0.0134 (7)	0.0075 (7)
C11	0.0987 (16)	0.0435 (10)	0.0887 (15)	0.0145 (10)	0.0328 (12)	0.0165 (9)
C12	0.1047 (17)	0.0728 (13)	0.0695 (13)	0.0182 (12)	0.0398 (12)	0.0212 (10)
C13	0.0772 (12)	0.0492 (10)	0.0566 (11)	0.0160 (9)	0.0158 (9)	−0.0056 (8)
C14	0.0869 (13)	0.0527 (10)	0.0671 (12)	0.0213 (9)	0.0260 (10)	0.0223 (9)
N1	0.0591 (8)	0.0421 (7)	0.0469 (8)	0.0178 (6)	0.0158 (6)	0.0026 (6)
N3	0.0620 (8)	0.0434 (7)	0.0532 (8)	0.0191 (6)	0.0203 (6)	0.0126 (6)
N7	0.0604 (8)	0.0392 (7)	0.0539 (8)	0.0132 (6)	0.0163 (6)	0.0073 (6)
N9	0.0686 (9)	0.0455 (8)	0.0609 (9)	0.0098 (7)	0.0210 (7)	0.0130 (6)
O1	0.0873 (9)	0.0408 (7)	0.0646 (8)	0.0042 (6)	0.0191 (7)	0.0023 (5)
O2	0.0870 (9)	0.0680 (8)	0.0465 (7)	0.0292 (7)	0.0213 (6)	0.0099 (6)
O1W	0.1212 (14)	0.0829 (11)	0.0666 (10)	0.0319 (10)	0.0444 (9)	0.0144 (8)
O2W	0.226 (3)	0.0825 (13)	0.0787 (13)	0.0549 (15)	0.0575 (15)	0.0108 (10)

C2—O2	1.225 (2)	C12—N9	1.454 (3)
C2—N3	1.373 (2)	C12—H12A	0.9600
C2—N1	1.376 (2)	C12—H12B	0.9600
C4—O1	1.236 (2)	C12—H12C	0.9600
C4—N3	1.397 (2)	C13—N1	1.471 (2)
C4—C5	1.408 (2)	C13—H13A	0.9600
C5—C6	1.365 (2)	C13—H13B	0.9600
C5—H5	0.9300	C13—H13C	0.9600
C6—N7	1.365 (2)	C14—N3	1.469 (2)
C6—N1	1.388 (2)	C14—H14A	0.9600
C8—N7	1.299 (2)	C14—H14B	0.9600
C8—N9	1.320 (2)	C14—H14C	0.9600
C8—H8	0.9300	O1W—H1W	0.86 (1)
C11—N9	1.449 (3)	O1W—H2W	0.86 (7)
C11—H11A	0.9600	O2W—H3W	0.85 (1)
C11—H11B	0.9600	O2W—H4W	0.86 (3)
C11—H11C	0.9600
O2—C2—N3	122.04 (16)	H12B—C12—H12C	109.5
O2—C2—N1	120.84 (16)	N1—C13—H13A	109.5
N3—C2—N1	117.11 (14)	N1—C13—H13B	109.5
O1—C4—N3	118.78 (15)	H13A—C13—H13B	109.5
O1—C4—C5	125.42 (16)	N1—C13—H13C	109.5
N3—C4—C5	115.80 (14)	H13A—C13—H13C	109.5
C6—C5—C4	122.19 (16)	H13B—C13—H13C	109.5
C6—C5—H5	118.9	N3—C14—H14A	109.5
C4—C5—H5	118.9	N3—C14—H14B	109.5
N7—C6—C5	127.10 (15)	H14A—C14—H14B	109.5
N7—C6—N1	114.39 (14)	N3—C14—H14C	109.5
C5—C6—N1	118.48 (15)	H14A—C14—H14C	109.5
N7—C8—N9	123.01 (16)	H14B—C14—H14C	109.5
N7—C8—H8	118.5	C2—N1—C6	122.46 (14)
N9—C8—H8	118.5	C2—N1—C13	116.47 (14)
N9—C11—H11A	109.5	C6—N1—C13	121.06 (14)
N9—C11—H11B	109.5	C2—N3—C4	123.83 (14)
H11A—C11—H11B	109.5	C2—N3—C14	117.92 (15)
N9—C11—H11C	109.5	C4—N3—C14	118.23 (15)
H11A—C11—H11C	109.5	C8—N7—C6	117.17 (14)
H11B—C11—H11C	109.5	C8—N9—C11	121.75 (16)
N9—C12—H12A	109.5	C8—N9—C12	121.00 (16)
N9—C12—H12B	109.5	C11—N9—C12	117.25 (15)
H12A—C12—H12B	109.5	H1W—O1W—H2W	125 (6)
N9—C12—H12C	109.5	H3W—O2W—H4W	116 (5)
H12A—C12—H12C	109.5
O1—C4—C5—C6	−176.21 (17)	N1—C2—N3—C4	0.1 (2)
N3—C4—C5—C6	4.2 (3)	O2—C2—N3—C14	−0.2 (3)
C4—C5—C6—N7	178.88 (15)	N1—C2—N3—C14	178.55 (15)
C4—C5—C6—N1	−3.3 (3)	O1—C4—N3—C2	177.81 (15)
O2—C2—N1—C6	179.72 (15)	C5—C4—N3—C2	−2.6 (2)
N3—C2—N1—C6	1.0 (2)	O1—C4—N3—C14	−0.6 (3)
O2—C2—N1—C13	−1.1 (2)	C5—C4—N3—C14	179.01 (15)
N3—C2—N1—C13	−179.84 (14)	N9—C8—N7—C6	174.40 (15)
N7—C6—N1—C2	178.70 (13)	C5—C6—N7—C8	−24.2 (3)
C5—C6—N1—C2	0.6 (2)	N1—C6—N7—C8	157.94 (14)
N7—C6—N1—C13	−0.5 (2)	N7—C8—N9—C11	−2.9 (3)
C5—C6—N1—C13	−178.56 (14)	N7—C8—N9—C12	178.23 (18)
O2—C2—N3—C4	−178.64 (15)

D—H···A	D—H	H···A	D···A	D—H···A
O1W—H1W···O2	0.86 (1)	1.93 (1)	2.784 (2)	173 (3)
O1W—H2W···O1Wi	0.86 (7)	2.01 (4)	2.771 (4)	147 (6)
O2W—H3W···O1	0.85 (1)	2.01 (2)	2.808 (2)	157 (3)
O2W—H4W···O1Wii	0.86 (3)	1.95 (2)	2.777 (3)	163 (6)

Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
O1W—H1W⋯O2	0.86 (1)	1.93 (1)	2.784 (2)	173 (3)
O1W—H2W⋯O1Wi	0.86 (7)	2.01 (4)	2.771 (4)	147 (6)
O2W—H3W⋯O1	0.85 (1)	2.01 (2)	2.808 (2)	157 (3)
O2W—H4W⋯O1Wii	0.86 (3)	1.95 (2)	2.777 (3)	163 (6)

Symmetry codes: (i) ; (ii) .