6-[(Dimethyl­amino)methyl­ene­amino]-1,3-dimethyl­pyrimidine-2,4(1H,3H)-dione dihydrate

Das, S.; Saikia, B.K.; Sridhar, B.; Thakur, A.J.

doi:10.1107/S1600536808024021

organic compounds

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ISSN: 2056-9890

Volume 64| Part 9| September 2008| Page o1662

doi:10.1107/S1600536808024021

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6-[(Dimethylamino)methyleneamino]-1,3-dimethylpyrimidine-2,4(1H,3H)-dione dihydrate

Subrata Das,^a Binoy K. Saikia,^a B. Sridhar ^b and Ashim J. Thakur ^a ^*

^aDepartment of Chemical Sciences, Tezpur University, Tezpur 784 028, India, and ^bLaboratory of X-ray Crystallography, Indian Institute of Chemical Technology, Hyderabad 500 607, India
^*Correspondence e-mail: ashim@tezu.ernet.in

(Received 8 May 2008; accepted 29 July 2008; online 6 August 2008)

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, C₉H₁₄N₄O₂·2H₂O, the asymmetric unit contains one dimethylaminouracil group and two water molecules. The plane of the N=C—NMe₂ side chain is inclined at 27.6 (5)° to the plane of the uracil ring. Both water molecules form O—H⋯O hydrogen bonds with the carbonyl O atoms of the uracil group. Additional water–water hydrogen-bond interactions 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 dimethylaminouracil groups and six water molecules.

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_r = 246.27
Triclinic, $[P \overline 1]$
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[F² > 2σ(F²)] = 0.051
wR(F²) = 0.155
S = 1.07
2231 reflections
175 parameters
4 restraints
H atoms treated by a mixture of independent and constrained refinement
Δρ_max = 0.34 e Å⁻³
Δρ_min = −0.21 e Å⁻³

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) -x, -y+1, -z+2; (ii) x, y, z-1.

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.

Supporting information

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

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

checkCIF report

Comment top

Uracil, the pyrimidine nucleobase, combined with Adenine comprises one of the major motifs present in the biopolymer RNA, is also involved in the self-assembly of RNA(Sivakova & Rowan, 2005) The versatility of uracil and its derivatives, particularly the annulated one, is well recognized by synthetic (Sasaki et al., 1998) as well as biological chemists (Pontikis & Monneret, 1994) owing to their wide range of biological activities. The chemistry of uracil moiety and its derivatives have expanded enormously in the past decades only because of its mechanistic, synthetic and biological importance which made them of substantial experimental and theoretical interest.

Synthesis and characterization of the title compound (I) was reported recently from our laboratory (Thakur et al., 2001), through the reaction of 6–amino–1,3–dimethylbarbituric acid with (DMF–DMA) under thermal condition or Microwave irradiation in the solid state. Our ongoing present research program is aimed at synthesizing fused pyrimidine derivatives of biological significances. Also we have been investigating the rotational barrier of the two methyl groups in the exocyclic N9-Me₂ part in (I), which will help us in understanding the mechanism of the Diels Alder reaction of (I).

The asymmetric unit of (I), comprises one dimethylamino uracil moiety and two water molecules (Fig. 1). The six-membered uracil ring is planar and the plane of its attached side chain is inclined 27.6 (5)° to the plane of the uracil ring. The torsion (C6-N7-C8-C9) = 174.4 (2)°.

The crystal structure is stabilized by O—H···O hydrogen bonds (Table 1). Both the water (O1W and O2W) molecules form O—H···O hydrogen bonds with the carbonyl (O1 and O2) atoms of the uracil moiety. In addition, water···water interactions are also observed in the crystal structure. The water molecules interconnect each other and in turn links the uracil moiety, thereby forming a two-dimensional hydrogen-bonded network cage consists of two dimethylamino uracil moieties and six water molecules (Fig.2).

Related literature top

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

Experimental top

In order to obtain suitable single crystals for this study, the title compound was dissolved in ethanol (98%) and the solution was allowed to evaporate very slowly.

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/PC (Sheldrick, 2008) and PLATON (Spek, 2003); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008).

Figures top

	Fig. 1. A view of the (I), with the atom-numbering scheme. Displacement ellipsoids are drawn at the 30% probability level and H atoms are shown as small spheres of arbitrary radii. Dashed lines indicates hydrogen bonds.
	Fig. 2. A packing diagram for (I), viewed down the b axis. H atoms not involved in hydrogen bonding have been omitted for clarity. [Symmetry code:(i) -x, -y + 1, -z + 2; (ii) x, y, z - 1].

6-[(Dimethylamino)methyleneamino]-1,3-dimethylpyrimidine-2,4(1H,3H)-dione dihydrate top

Crystal data top

C₉H₁₄N₄O₂·2H₂O	Z = 2
M_r = 246.27	F(000) = 264
Triclinic, P1	D_x = 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 = 2.4–27.9°
c = 9.9160 (7) Å	µ = 0.10 mm⁻¹
α = 92.921 (1)°	T = 294 K
β = 101.916 (1)°	Block, colorless
γ = 109.912 (1)°	0.23 × 0.17 × 0.12 mm
V = 635.62 (8) Å³

Data collection top

Bruker SMART APEX CCD area-detector diffractometer	2017 reflections with I > 2˘I)
Radiation source: fine-focus sealed tube	R_int = 0.019
Graphite monochromator	θ_max = 25.0°, θ_min = 2.1°
ω scans	h = −8→8
6112 measured reflections	k = −11→11
2231 independent reflections	l = −11→11

Refinement top

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(F_o²) + (0.0891P)² + 0.1375P] where P = (F_o² + 2F_c²)/3
S = 1.07	(Δ/σ)_max = 0.001
2231 reflections	Δρ_max = 0.34 e Å⁻³
175 parameters	Δρ_min = −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)

Crystal data top

C₉H₁₄N₄O₂·2H₂O	γ = 109.912 (1)°
M_r = 246.27	V = 635.62 (8) Å³
Triclinic, P1	Z = 2
a = 7.1310 (5) Å	Mo Kα radiation
b = 9.8571 (7) Å	µ = 0.10 mm⁻¹
c = 9.9160 (7) Å	T = 294 K
α = 92.921 (1)°	0.23 × 0.17 × 0.12 mm
β = 101.916 (1)°

Data collection top

Bruker SMART APEX CCD area-detector diffractometer	2017 reflections with I > 2˘I)
6112 measured reflections	R_int = 0.019
2231 independent reflections

Refinement top

R[F² > 2σ(F²)] = 0.051	4 restraints
wR(F²) = 0.155	H atoms treated by a mixture of independent and constrained refinement
S = 1.07	Δρ_max = 0.34 e Å⁻³
2231 reflections	Δρ_min = −0.21 e Å⁻³
175 parameters

Special details top

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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å²) top

	x	y	z	U_iso*/U_eq
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)*

Atomic displacement parameters (Å²) top

	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)

Geometric parameters (Å, º) top

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)

Hydrogen-bond geometry (Å, º) top

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) −x, −y+1, −z+2; (ii) x, y, z−1.

Experimental details

Crystal data
Chemical formula	C₉H₁₄N₄O₂·2H₂O
M_r	246.27
Crystal system, space group	Triclinic, P1
Temperature (K)	294
a, b, c (Å)	7.1310 (5), 9.8571 (7), 9.9160 (7)
α, β, γ (°)	92.921 (1), 101.916 (1), 109.912 (1)
V (Å³)	635.62 (8)
Z	2
Radiation type	Mo Kα
µ (mm⁻¹)	0.10
Crystal size (mm)	0.23 × 0.17 × 0.12

Data collection
Diffractometer	Bruker SMART APEX CCD area-detector diffractometer
Absorption correction	–
No. of measured, independent and observed [I > 2˘I)] reflections	6112, 2231, 2017
R_int	0.019
(sin θ/λ)_max (Å⁻¹)	0.595

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.051, 0.155, 1.07
No. of reflections	2231
No. of parameters	175
No. of restraints	4
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
Δρ_max, Δρ_min (e Å⁻³)	0.34, −0.21

Computer programs: SMART (Bruker, 2001), SAINT (Bruker, 2001), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), SHELXTL/PC (Sheldrick, 2008) and PLATON (Spek, 2003).

Hydrogen-bond geometry (Å, º) top

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) −x, −y+1, −z+2; (ii) x, y, z−1.

Acknowledgements

AJT thanks the Department of Science and Technology (DST), Government of India, New Delhi, for financial support and SD thanks Tezpur University for an Institutional Fellowship.

References

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Volume 64| Part 9| September 2008| Page o1662

doi:10.1107/S1600536808024021

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

6-[(Di­methyl­amino)methyl­ene­amino]-1,3-di­methyl­pyrimidine-2,4(1H,3H)-dione dihydrate

Related literature

Experimental

Crystal data

Data collection

Refinement

Supporting information

Acknowledgements

References

organic compounds

6-[(Dimethylamino)methyleneamino]-1,3-dimethylpyrimidine-2,4(1H,3H)-dione dihydrate