1,4-Dihydro-6-methyl-5-(N-methyl­carbamo­yl)-4-(4-nitro­phen­yl)pyrimidine-2(3H)-thione monohydrate

The title compound, C₁₃H₁₄N₄O₃S·H₂O, is an isomer of 1,4-dihydro-6-methyl-5-(N-methyl­carbamo­yl)-4-(2-nitro­phen­yl)­pyrimidine-2(3H)-thione. The nitro group is coplanar with the benzene ring to which it is attached. Inter­molecular hydrogen bonds stabilize the crystal structure.

Key indicators

• Single-crystal X-ray study
• T = 273 K
• Mean [sigma](C-C) = 0.003 Å
• R factor = 0.043
• wR factor = 0.129
• Data-to-parameter ratio = 13.1

checkCIF/PLATON results

No syntax errors found



Alert level A
PLAT093_ALERT_1_A No su's on H-atoms, but refinement reported as .      mixed

Alert level C
PLAT220_ALERT_2_C Large Non-Solvent    O     Ueq(max)/Ueq(min) ...       2.59 Ratio
PLAT230_ALERT_2_C Hirshfeld Test Diff for    N5     -   C6      ..       5.85 su
PLAT242_ALERT_2_C Check Low       Ueq as Compared to Neighbors for        N10
PLAT790_ALERT_4_C Centre of Gravity not Within Unit Cell: Resd.  #          2
              H2 O

   1 ALERT level A = In general: serious problem
   0 ALERT level B = Potentially serious problem
   4 ALERT level C = Check and explain
   0 ALERT level G = General alerts; check

   1 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
   3 ALERT type 2 Indicator that the structure model may be wrong or deficient
   0 ALERT type 3 Indicator that the structure quality may be low
   1 ALERT type 4 Improvement, methodology, query or suggestion

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Computing details

Data collection: SMART (Bruker, 2001); cell refinement: SAINT (Bruker, 2001); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: SHELXTL/PC (Sheldrick, 1990); software used to prepare material for publication: SHELXL97.

1,4-Dihydro-6-methyl-5-(N-methylcarbamoyl)-4-(4-nitrophenyl)pyrimidine- 2(3H)-thione monohydrate

Crystal data

C13H14N4O3S·H2O	Z = 2
Mr = 324.36	F(000) = 340
Triclinic, P1	Dx = 1.422 Mg m^−3
Hall symbol: -P 1	Mo Kα radiation, λ = 0.71073 Å
a = 4.8373 (5) Å	Cell parameters from 5088 reflections
b = 9.8906 (11) Å	θ = 2.3–28.0°
c = 16.0930 (17) Å	µ = 0.24 mm^−1
α = 81.414 (2)°	T = 273 K
β = 84.968 (2)°	Block, colorless
γ = 86.248 (2)°	0.23 × 0.12 × 0.09 mm
V = 757.32 (14) Å^3

Data collection

CCD Area Detector diffractometer	2437 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tube	Rint = 0.019
Graphite monochromator	θmax = 25.0°, θmin = 2.1°
ω scans	h = −5→5
7319 measured reflections	k = −11→11
2669 independent reflections	l = −19→19

Refinement

Refinement on F^2	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F^2 > 2σ(F^2)] = 0.043	Hydrogen site location: inferred from neighbouring sites
wR(F^2) = 0.129	H atoms treated by a mixture of independent and constrained refinement
S = 1.03	w = 1/[σ^2(Fo^2) + (0.0786P)^2 + 0.2758P] where P = (Fo^2 + 2Fc^2)/3
2669 reflections	(Δ/σ)max = 0.001
203 parameters	Δρmax = 0.27 e Å^−3
0 restraints	Δρmin = −0.20 e Å^−3

Special details

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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Ų)

	x	y	z	Uiso*/Ueq
S1	0.22159 (12)	0.32036 (5)	1.03144 (3)	0.0535 (2)
O1	0.7157 (7)	−0.0868 (3)	0.57059 (16)	0.1371 (12)
O2	0.9306 (4)	−0.13280 (19)	0.68207 (15)	0.0870 (6)
O32	−0.1496 (3)	0.52334 (16)	0.64859 (9)	0.0531 (4)
N1	0.3530 (3)	0.47444 (16)	0.88578 (9)	0.0408 (4)
H1	0.4849	0.5018	0.9106	0.049*
N5	0.0320 (3)	0.31622 (16)	0.88289 (10)	0.0437 (4)
H5	−0.0947	0.2659	0.9098	0.052*
N10	0.7519 (5)	−0.0709 (2)	0.64167 (15)	0.0692 (6)
N33	0.2908 (3)	0.58341 (16)	0.61511 (9)	0.0417 (4)
H33	0.4565	0.5788	0.6312	0.050*
C2	0.3069 (3)	0.53838 (18)	0.80380 (11)	0.0360 (4)
C3	0.1618 (3)	0.47495 (17)	0.75560 (11)	0.0357 (4)
C4	0.0511 (4)	0.33593 (18)	0.79000 (11)	0.0388 (4)
H4	−0.1369	0.3343	0.7720	0.047*
C6	0.2019 (4)	0.37278 (18)	0.92738 (11)	0.0409 (4)
C7	0.2299 (4)	0.22314 (18)	0.75365 (11)	0.0392 (4)
C8	0.2060 (4)	0.2045 (2)	0.67065 (12)	0.0491 (5)
H8	0.0750	0.2578	0.6395	0.059*
C9	0.3745 (5)	0.1080 (2)	0.63396 (13)	0.0551 (5)
H9	0.3581	0.0957	0.5785	0.066*
C10	0.5666 (4)	0.0304 (2)	0.68112 (13)	0.0508 (5)
C11	0.5931 (4)	0.0437 (2)	0.76353 (14)	0.0538 (5)
H11	0.7228	−0.0111	0.7945	0.065*
C12	0.4225 (4)	0.1407 (2)	0.79972 (12)	0.0471 (5)
H12	0.4373	0.1506	0.8557	0.057*
C21	0.4218 (4)	0.67709 (19)	0.78349 (12)	0.0472 (5)
H21A	0.3630	0.7210	0.7302	0.071*
H21B	0.6211	0.6681	0.7806	0.071*
H21C	0.3553	0.7312	0.8266	0.071*
C31	0.0888 (3)	0.53147 (18)	0.66881 (11)	0.0367 (4)
C34	0.2435 (5)	0.6479 (2)	0.53012 (12)	0.0554 (5)
H34A	0.1820	0.5814	0.4990	0.083*
H34B	0.4133	0.6837	0.5028	0.083*
H34C	0.1039	0.7211	0.5323	0.083*
O1W	−0.2550 (5)	0.0799 (2)	0.98922 (15)	0.0898 (6)
H1W	−0.2063	0.0098	0.9728	0.23 (3)*
H2W	−0.3607	0.0561	1.0291	0.58 (10)*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
S1	0.0707 (4)	0.0556 (3)	0.0343 (3)	−0.0093 (3)	−0.0041 (2)	−0.0043 (2)
O1	0.186 (3)	0.141 (2)	0.0876 (17)	0.077 (2)	−0.0173 (17)	−0.0592 (16)
O2	0.0750 (12)	0.0633 (11)	0.1208 (17)	0.0150 (9)	−0.0012 (11)	−0.0188 (11)
O32	0.0327 (7)	0.0765 (10)	0.0507 (8)	−0.0022 (6)	−0.0106 (6)	−0.0069 (7)
N1	0.0436 (8)	0.0469 (8)	0.0337 (8)	−0.0087 (6)	−0.0072 (6)	−0.0064 (6)
N5	0.0430 (8)	0.0502 (9)	0.0388 (8)	−0.0157 (7)	0.0009 (6)	−0.0062 (7)
N10	0.0747 (14)	0.0511 (11)	0.0803 (15)	−0.0015 (10)	0.0110 (11)	−0.0153 (10)
N33	0.0349 (8)	0.0549 (9)	0.0347 (8)	−0.0019 (6)	−0.0052 (6)	−0.0038 (7)
C2	0.0343 (8)	0.0400 (9)	0.0339 (9)	−0.0011 (7)	−0.0021 (7)	−0.0061 (7)
C3	0.0318 (8)	0.0401 (9)	0.0354 (9)	−0.0018 (7)	−0.0010 (7)	−0.0067 (7)
C4	0.0361 (9)	0.0469 (10)	0.0348 (9)	−0.0099 (7)	−0.0033 (7)	−0.0067 (7)
C6	0.0422 (9)	0.0432 (10)	0.0369 (9)	0.0003 (7)	0.0014 (7)	−0.0085 (7)
C7	0.0416 (9)	0.0384 (9)	0.0384 (9)	−0.0121 (7)	−0.0023 (7)	−0.0041 (7)
C8	0.0611 (12)	0.0468 (11)	0.0400 (10)	−0.0019 (9)	−0.0082 (9)	−0.0063 (8)
C9	0.0750 (14)	0.0494 (11)	0.0418 (10)	−0.0078 (10)	0.0013 (10)	−0.0108 (9)
C10	0.0538 (11)	0.0393 (10)	0.0590 (13)	−0.0079 (8)	0.0060 (9)	−0.0096 (9)
C11	0.0539 (12)	0.0444 (11)	0.0633 (13)	−0.0023 (9)	−0.0121 (10)	−0.0043 (9)
C12	0.0542 (11)	0.0455 (10)	0.0435 (10)	−0.0069 (8)	−0.0100 (8)	−0.0067 (8)
C21	0.0581 (11)	0.0428 (10)	0.0425 (10)	−0.0116 (8)	−0.0071 (8)	−0.0068 (8)
C31	0.0319 (8)	0.0407 (9)	0.0387 (9)	0.0021 (7)	−0.0052 (7)	−0.0097 (7)
C34	0.0614 (13)	0.0656 (13)	0.0371 (10)	−0.0033 (10)	−0.0049 (9)	0.0002 (9)
O1W	0.0962 (14)	0.0797 (14)	0.0885 (14)	−0.0181 (11)	−0.0064 (11)	0.0090 (11)

Geometric parameters (Å, º)

S1—C6	1.6867 (18)	C4—H4	0.9800
O1—N10	1.207 (3)	C7—C12	1.387 (3)
O2—N10	1.206 (3)	C7—C8	1.391 (3)
O32—C31	1.236 (2)	C8—C9	1.381 (3)
N1—C6	1.343 (2)	C8—H8	0.9300
N1—C2	1.405 (2)	C9—C10	1.373 (3)
N1—H1	0.8600	C9—H9	0.9300
N5—C6	1.336 (2)	C10—C11	1.370 (3)
N5—C4	1.474 (2)	C11—C12	1.385 (3)
N5—H5	0.8600	C11—H11	0.9300
N10—C10	1.477 (3)	C12—H12	0.9300
N33—C31	1.323 (2)	C21—H21A	0.9600
N33—C34	1.451 (2)	C21—H21B	0.9600
N33—H33	0.8600	C21—H21C	0.9600
C2—C3	1.336 (2)	C34—H34A	0.9600
C2—C21	1.494 (2)	C34—H34B	0.9600
C3—C31	1.488 (2)	C34—H34C	0.9600
C3—C4	1.517 (2)	O1W—H1W	0.79
C4—C7	1.522 (3)	O1W—H2W	0.80
C6—N1—C2	123.39 (15)	C9—C8—H8	119.6
C6—N1—H1	118.3	C7—C8—H8	119.6
C2—N1—H1	118.3	C10—C9—C8	118.64 (19)
C6—N5—C4	123.18 (15)	C10—C9—H9	120.7
C6—N5—H5	118.4	C8—C9—H9	120.7
C4—N5—H5	118.4	C11—C10—C9	122.33 (19)
O2—N10—O1	123.7 (2)	C11—C10—N10	118.7 (2)
O2—N10—C10	118.4 (2)	C9—C10—N10	118.9 (2)
O1—N10—C10	117.9 (2)	C10—C11—C12	118.5 (2)
C31—N33—C34	122.52 (16)	C10—C11—H11	120.7
C31—N33—H33	118.7	C12—C11—H11	120.7
C34—N33—H33	118.7	C11—C12—C7	120.93 (19)
C3—C2—N1	118.99 (16)	C11—C12—H12	119.5
C3—C2—C21	128.00 (17)	C7—C12—H12	119.5
N1—C2—C21	112.94 (15)	C2—C21—H21A	109.5
C2—C3—C31	125.15 (16)	C2—C21—H21B	109.5
C2—C3—C4	119.69 (16)	H21A—C21—H21B	109.5
C31—C3—C4	115.14 (14)	C2—C21—H21C	109.5
N5—C4—C3	109.94 (14)	H21A—C21—H21C	109.5
N5—C4—C7	112.41 (15)	H21B—C21—H21C	109.5
C3—C4—C7	110.42 (14)	O32—C31—N33	122.79 (16)
N5—C4—H4	108.0	O32—C31—C3	119.91 (16)
C3—C4—H4	108.0	N33—C31—C3	117.22 (14)
C7—C4—H4	108.0	N33—C34—H34A	109.5
N5—C6—N1	117.01 (16)	N33—C34—H34B	109.5
N5—C6—S1	121.41 (14)	H34A—C34—H34B	109.5
N1—C6—S1	121.58 (14)	N33—C34—H34C	109.5
C12—C7—C8	118.73 (18)	H34A—C34—H34C	109.5
C12—C7—C4	122.19 (16)	H34B—C34—H34C	109.5
C8—C7—C4	119.05 (16)	H1W—O1W—H2W	103
C9—C8—C7	120.85 (19)
C6—N1—C2—C3	−18.6 (3)	C12—C7—C8—C9	−1.4 (3)
C6—N1—C2—C21	158.66 (17)	C4—C7—C8—C9	176.72 (17)
N1—C2—C3—C31	178.01 (14)	C7—C8—C9—C10	0.0 (3)
C21—C2—C3—C31	1.2 (3)	C8—C9—C10—C11	1.3 (3)
N1—C2—C3—C4	−0.1 (2)	C8—C9—C10—N10	−178.58 (18)
C21—C2—C3—C4	−176.98 (17)	O2—N10—C10—C11	−4.1 (3)
C6—N5—C4—C3	−30.1 (2)	O1—N10—C10—C11	175.9 (3)
C6—N5—C4—C7	93.4 (2)	O2—N10—C10—C9	175.7 (2)
C2—C3—C4—N5	21.6 (2)	O1—N10—C10—C9	−4.2 (4)
C31—C3—C4—N5	−156.71 (14)	C9—C10—C11—C12	−1.1 (3)
C2—C3—C4—C7	−102.98 (18)	N10—C10—C11—C12	178.75 (18)
C31—C3—C4—C7	78.69 (18)	C10—C11—C12—C7	−0.3 (3)
C4—N5—C6—N1	14.9 (3)	C8—C7—C12—C11	1.5 (3)
C4—N5—C6—S1	−166.02 (14)	C4—C7—C12—C11	−176.48 (17)
C2—N1—C6—N5	11.3 (3)	C34—N33—C31—O32	6.4 (3)
C2—N1—C6—S1	−167.79 (13)	C34—N33—C31—C3	−176.77 (16)
N5—C4—C7—C12	−20.1 (2)	C2—C3—C31—O32	−134.96 (19)
C3—C4—C7—C12	103.07 (19)	C4—C3—C31—O32	43.3 (2)
N5—C4—C7—C8	161.89 (16)	C2—C3—C31—N33	48.1 (2)
C3—C4—C7—C8	−74.9 (2)	C4—C3—C31—N33	−133.69 (17)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1···S1^i	0.86	2.65	3.4586 (16)	157
N5—H5···O1W	0.86	2.22	3.022 (3)	155
N33—H33···O32^ii	0.86	1.98	2.8144 (19)	163
O1W—H1W···O1W^iii	0.79	2.44	2.860 (5)	114
O1W—H2W···O1W^iv	0.80	2.43	2.901 (4)	119

Symmetry codes: (i) −x+1, −y+1, −z+2; (ii) x+1, y, z; (iii) −x, −y, −z+2; (iv) −x−1, −y, −z+2.