Crystal structure of 6-chloro-5-iso-propyl-pyrimidine-2,4(1H,3H)-dione.

In the mol-ecule of the title compound, C7H9ClN2O2, the conformation is determined by intra-molecular C-H⋯O and C-H⋯Cl hydrogen bonds, which generate S(6) and S(5) ring motifs. The isopropyl group is almost perpendicular to the pyrimidine ring with torsion angles of -70.8 (3) and 56.0 (3)°. In the crystal, two inversion-related mol-ecules are linked via a pair of N-H⋯O hydrogen bonds into R 2 (2)(8) dimers; these dimers are connected into chains extending along the bc plane via an additional N-H⋯O hydrogen bond and weaker C-H⋯O hydrogen bonds. The crystal structure is further stabilized by a weak π-π inter-action [3.6465 (10) Å] between adjacent pyrimidine-dione rings arranged in a head-to-tail fashion, producing a three-dimensional network.

Related literature

For the biological activity of pyrimidine-2,4(1H,3H)-diones, see: Miyasaka et al. (1989 ▶); Tanaka et al. (1995 ▶); Hopkins et al. (1996 ▶); El-Brollosy et al. (2009 ▶); Klein et al. (2001 ▶); Nencka et al. (2006 ▶); El-Emam et al. (2004 ▶). For the use of 5-alkyl-6-chloro­pyrimidine-2,4(1H,3H)-diones in synthesis, see: El-Emam et al. (2004 ▶). For related pyrimidine-2,4-dione structures, see: El-Brollosy et al. (2011 ▶); Al-Omary et al. (2014 ▶); Haress et al. (2014 ▶). For the synthesis of the title compound, see: Al-Turkistani et al. (2011 ▶); Koroniak et al. (1993 ▶). For hydrogen-bond motifs, see: Bernstein et al. (1995 ▶).

Experimental

Crystal data

C7H9ClN2O2

M = 188.61

Monoclinic,

a = 11.2244 (4) Å

b = 6.8288 (3) Å

c = 11.6641 (5) Å

β = 104.577 (2)°

V = 865.26 (6) Å3

Z = 4

Cu Kα radiation

μ = 3.62 mm−1

T = 296 K

0.45 × 0.28 × 0.26 mm

Data collection

Bruker APEXII CCD diffractometer

Absorption correction: multi-scan (SADABS; Bruker, 2009 ▶) T min = 0.292, T max = 0.458

5647 measured reflections

1553 independent reflections

1444 reflections with I > 2σ(I)

R int = 0.027

Refinement

R[F 2 > 2σ(F 2)] = 0.040

wR(F 2) = 0.114

S = 1.06

1553 reflections

122 parameters

H atoms treated by a mixture of independent and constrained refinement

Δρmax = 0.27 e Å−3

Δρmin = −0.32 e Å−3

Data collection: APEX2 (Bruker, 2009 ▶); cell refinement: SAINT (Bruker, 2009 ▶); data reduction: SAINT; 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 and PLATON (Spek, 2009 ▶).

Crystal structure: contains datablock(s) global, I. DOI: 10.1107/S1600536814021382/sj5429sup1.cif

Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536814021382/sj5429Isup2.hkl

Click here for additional data file.

Supporting information file. DOI: 10.1107/S1600536814021382/sj5429Isup3.cml

Click here for additional data file.

. DOI: 10.1107/S1600536814021382/sj5429fig1.tif

The mol­ecular structure of the title compound with atom labels and 30% probability displacement ellipsoids.

Click here for additional data file.

. DOI: 10.1107/S1600536814021382/sj5429fig2.tif

Crystal packing of the title compound, showing the hydrogen bonding inter­actions as dashed lines. H-atoms not involved in the hydrogen bonding are omited for clarity.

CCDC reference: 1026350

Additional supporting information: crystallographic information; 3D view; checkCIF report

C7H9ClN2O2	F(000) = 392
Mr = 188.61	Dx = 1.448 Mg m−3
Monoclinic, P21/c	Cu Kα radiation, λ = 1.54178 Å
Hall symbol: -P 2ybc	Cell parameters from 3341 reflections
a = 11.2244 (4) Å	θ = 3.9–69.4°
b = 6.8288 (3) Å	µ = 3.62 mm−1
c = 11.6641 (5) Å	T = 296 K
β = 104.577 (2)°	Block, colourless
V = 865.26 (6) Å3	0.45 × 0.28 × 0.26 mm
Z = 4

Bruker APEXII CCD diffractometer	1553 independent reflections
Radiation source: fine-focus sealed tube	1444 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.027
φ and ω scans	θmax = 69.7°, θmin = 4.1°
Absorption correction: multi-scan (SADABS; Bruker, 2009)	h = −12→13
Tmin = 0.292, Tmax = 0.458	k = −8→7
5647 measured reflections	l = −13→10

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)] = 0.040	H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.114	w = 1/[σ2(Fo2) + (0.0664P)2 + 0.3263P] where P = (Fo2 + 2Fc2)/3
S = 1.06	(Δ/σ)max < 0.001
1553 reflections	Δρmax = 0.27 e Å−3
122 parameters	Δρmin = −0.32 e Å−3
0 restraints	Extinction correction: SHELXL, Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
Primary atom site location: structure-invariant direct methods	Extinction coefficient: 0.0181 (15)

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
Cl1	0.20279 (5)	0.71985 (9)	0.34179 (6)	0.0644 (3)
O1	0.55744 (12)	0.3674 (2)	0.28760 (12)	0.0465 (4)
O2	0.35879 (13)	0.0719 (2)	0.53323 (13)	0.0522 (4)
N1	0.39383 (14)	0.5227 (2)	0.32786 (14)	0.0386 (4)
N2	0.45727 (14)	0.2261 (2)	0.41291 (14)	0.0394 (4)
C1	0.29636 (16)	0.5181 (3)	0.37878 (16)	0.0371 (4)
C2	0.47498 (15)	0.3710 (3)	0.33892 (15)	0.0354 (4)
C3	0.36295 (16)	0.2134 (3)	0.46972 (15)	0.0371 (4)
C4	0.27390 (15)	0.3729 (3)	0.44806 (15)	0.0368 (4)
C5	0.16037 (17)	0.3635 (3)	0.49593 (17)	0.0437 (5)
C6	0.1871 (2)	0.3338 (5)	0.6280 (2)	0.0697 (7)
H6A	0.2438	0.4322	0.6675	0.105*
H6B	0.2226	0.2065	0.6480	0.105*
H6C	0.1119	0.3437	0.6527	0.105*
C7	0.0719 (2)	0.2127 (5)	0.4302 (3)	0.0815 (9)
H7A	0.0568	0.2355	0.3465	0.122*
H7B	−0.0041	0.2217	0.4533	0.122*
H7C	0.1065	0.0845	0.4486	0.122*
H1N1	0.403 (2)	0.617 (4)	0.2856 (19)	0.043 (6)*
H1N2	0.506 (2)	0.132 (4)	0.422 (2)	0.059 (7)*
H5	0.125 (2)	0.489 (4)	0.481 (2)	0.058 (7)*

	U11	U22	U33	U12	U13	U23
Cl1	0.0662 (4)	0.0486 (4)	0.0892 (5)	0.0249 (2)	0.0395 (3)	0.0243 (3)
O1	0.0481 (7)	0.0421 (8)	0.0587 (9)	0.0001 (6)	0.0307 (6)	−0.0012 (6)
O2	0.0522 (8)	0.0506 (9)	0.0614 (9)	0.0157 (6)	0.0286 (6)	0.0227 (7)
N1	0.0458 (8)	0.0321 (8)	0.0424 (9)	0.0018 (6)	0.0197 (7)	0.0042 (6)
N2	0.0394 (8)	0.0381 (8)	0.0451 (9)	0.0095 (7)	0.0187 (7)	0.0061 (6)
C1	0.0392 (9)	0.0358 (9)	0.0379 (10)	0.0053 (7)	0.0124 (7)	−0.0011 (7)
C2	0.0373 (8)	0.0343 (9)	0.0365 (9)	−0.0012 (7)	0.0129 (7)	−0.0044 (7)
C3	0.0376 (9)	0.0394 (10)	0.0361 (10)	0.0033 (7)	0.0125 (7)	0.0025 (7)
C4	0.0380 (9)	0.0393 (10)	0.0346 (9)	0.0044 (7)	0.0120 (7)	0.0005 (7)
C5	0.0420 (9)	0.0460 (11)	0.0485 (11)	0.0095 (8)	0.0215 (8)	0.0060 (8)
C6	0.0585 (13)	0.108 (2)	0.0512 (14)	0.0016 (14)	0.0296 (11)	−0.0019 (13)
C7	0.0472 (13)	0.120 (3)	0.0849 (19)	−0.0208 (14)	0.0314 (13)	−0.0335 (17)

Cl1—C1	1.7200 (18)	C4—C5	1.516 (2)
O1—C2	1.222 (2)	C5—C7	1.500 (3)
O2—C3	1.226 (2)	C5—C6	1.507 (3)
N1—C2	1.364 (2)	C5—H5	0.95 (3)
N1—C1	1.370 (2)	C6—H6A	0.9600
N1—H1N1	0.83 (2)	C6—H6B	0.9600
N2—C2	1.360 (2)	C6—H6C	0.9600
N2—C3	1.386 (2)	C7—H7A	0.9600
N2—H1N2	0.84 (3)	C7—H7B	0.9600
C1—C4	1.342 (3)	C7—H7C	0.9600
C3—C4	1.457 (2)
C2—N1—C1	121.92 (16)	C7—C5—C6	111.5 (2)
C2—N1—H1N1	117.6 (15)	C7—C5—C4	110.49 (17)
C1—N1—H1N1	120.4 (15)	C6—C5—C4	114.38 (17)
C2—N2—C3	126.87 (16)	C7—C5—H5	109.6 (16)
C2—N2—H1N2	116.1 (17)	C6—C5—H5	106.3 (15)
C3—N2—H1N2	116.9 (17)	C4—C5—H5	104.3 (15)
C4—C1—N1	124.69 (16)	C5—C6—H6A	109.5
C4—C1—Cl1	123.17 (14)	C5—C6—H6B	109.5
N1—C1—Cl1	112.13 (13)	H6A—C6—H6B	109.5
O1—C2—N2	123.07 (17)	C5—C6—H6C	109.5
O1—C2—N1	122.60 (17)	H6A—C6—H6C	109.5
N2—C2—N1	114.32 (15)	H6B—C6—H6C	109.5
O2—C3—N2	119.22 (16)	C5—C7—H7A	109.5
O2—C3—C4	124.43 (16)	C5—C7—H7B	109.5
N2—C3—C4	116.35 (16)	H7A—C7—H7B	109.5
C1—C4—C3	115.60 (16)	C5—C7—H7C	109.5
C1—C4—C5	123.76 (16)	H7A—C7—H7C	109.5
C3—C4—C5	120.54 (16)	H7B—C7—H7C	109.5
C2—N1—C1—C4	3.4 (3)	N1—C1—C4—C5	−175.22 (17)
C2—N1—C1—Cl1	−175.53 (14)	Cl1—C1—C4—C5	3.6 (3)
C3—N2—C2—O1	−176.48 (18)	O2—C3—C4—C1	177.94 (19)
C3—N2—C2—N1	4.4 (3)	N2—C3—C4—C1	−2.5 (2)
C1—N1—C2—O1	175.02 (17)	O2—C3—C4—C5	−5.7 (3)
C1—N1—C2—N2	−5.8 (2)	N2—C3—C4—C5	173.89 (16)
C2—N2—C3—O2	179.34 (18)	C1—C4—C5—C7	105.3 (2)
C2—N2—C3—C4	−0.3 (3)	C3—C4—C5—C7	−70.8 (3)
N1—C1—C4—C3	1.0 (3)	C1—C4—C5—C6	−128.0 (2)
Cl1—C1—C4—C3	179.85 (13)	C3—C4—C5—C6	56.0 (3)

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1N1···O1i	0.83 (3)	2.01 (3)	2.833 (2)	169 (2)
N2—H1N2···O2ii	0.83 (3)	2.03 (3)	2.854 (2)	171 (2)
C5—H5···Cl1	0.94 (3)	2.57 (2)	3.132 (2)	118.7 (17)
C6—H6A···O1iii	0.96	2.56	3.455 (3)	156
C6—H6B···O2	0.96	2.45	3.034 (3)	119

Table 1

Hydrogen-bond geometry (, )

DHA	DH	HA	D A	DHA
N1H1N1O1i	0.83(3)	2.01(3)	2.833(2)	169(2)
N2H1N2O2ii	0.83(3)	2.03(3)	2.854(2)	171(2)
C5H5Cl1	0.94(3)	2.57(2)	3.132(2)	118.7(17)
C6H6AO1iii	0.96	2.56	3.455(3)	156
C6H6BO2	0.96	2.45	3.034(3)	119

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