2-Amino-4-chloro-6-(4-carbamoyl­piperidin-1-yl)­pyrimidine hemihydrate

The structure of the title compound, C₁₀H₁₅ClN₅O·0.5H₂O, comprises non-planar mol­ecules that associate via N—H...N and N—H...O interactions to form a three-dimensional hydrogen-bonded array. The water mol­ecule resides on a twofold axis and is also involved in the hydrogen-bonding network.

Key indicators

• Single-crystal X-ray study
• T = 150 K
• Mean [sigma](C-C) = 0.002 Å
• R factor = 0.041
• wR factor = 0.116
• Data-to-parameter ratio = 14.6

checkCIF results

No syntax errors found

ADDSYM reports no extra symmetry

General Notes



FORMU_01  There is a discrepancy between the atom counts in the
          _chemical_formula_sum and _chemical_formula_moiety. This is
          usually due to the moiety formula being in the wrong format.
          Atom count from _chemical_formula_sum:   C10 H15 Cl1 N5 O1.5
          Atom count from _chemical_formula_moiety:C10 H16 Cl1 N5 O1.5

---

S1. Comment

NO COMMENT

S2. Experimental

The title compound, (I), was prepared by Spa Contract Synthesis. Crystals of (I) were grown from a dimethylformamide/water (1:25) solution.

S3. Refinement

All H atoms were included in the refinement at calculated positions as riding models with C—H set to 0.95 (Ar—H) and 0.99 Å (CH₂), except for the H atoms involved in the hydrogen-bonding associations, which were located on difference syntheses and for which both positional and displacement parameters were refined.

Computing details

Data collection: DENZO (Otwinowski & Minor, 1997) and COLLECT (Hooft, 1998); cell refinement: DENZO and COLLECT; data reduction: DENZO and COLLECT; program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); software used to prepare material for publication: SHELXL97.

Figures

Fig. 1. The molecular configuration and atom-numbering scheme for (I), showing 30% probability displacement ellipsoids.

2-Amino-4-chloro-6-(4-carbamoylpyperidinyl)pyrimidine hemihydrate

Crystal data

C10H15ClN5O·0.5H2O	Dx = 1.505 Mg m^−3
Mr = 264.72	Melting point: 479-481 K K
Monoclinic, C2/c	Mo Kα radiation, λ = 0.71073 Å
a = 15.559 (3) Å	Cell parameters from 5223 reflections
b = 9.3139 (19) Å	θ = 2.9–27.5°
c = 16.493 (3) Å	µ = 0.33 mm^−1
β = 102.08 (3)°	T = 150 K
V = 2337.2 (8) Å^3	Block, colourless
Z = 8	0.26 × 0.14 × 0.14 mm
F(000) = 1112

Data collection

Enraf Nonius KappaCCD area-detector diffractometer	2672 independent reflections
Radiation source: Enraf Nonius FR591 rotating anode	2113 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.047
Detector resolution: 9.091 pixels mm^-1	θmax = 27.5°, θmin = 3.0°
ϕ and ω scans	h = −20→19
Absorption correction: multi-scan (SORTAV; Blessing, 1995)	k = −12→12
Tmin = 0.920, Tmax = 0.956	l = −21→21
10159 measured reflections

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)] = 0.041	Hydrogen site location: inferred from neighbouring sites
wR(F^2) = 0.116	H atoms treated by a mixture of independent and constrained refinement
S = 1.02	w = 1/[σ^2(Fo^2) + (0.0659P)^2 + 0.5619P] where P = (Fo^2 + 2Fc^2)/3
2672 reflections	(Δ/σ)max < 0.001
183 parameters	Δρmax = 0.24 e Å^−3
0 restraints	Δρmin = −0.41 e Å^−3

Special details

Experimental. PLEASE NOTE cell_measurement_ fields are not relevant to area detector data, the entire data set is used to refine the cell, which is indexed from all observed reflections in a 10 degree phi range.

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

	x	y	z	Uiso*/Ueq
N1	0.00203 (8)	0.37886 (15)	0.59398 (7)	0.0250 (3)
C2	−0.04182 (10)	0.27801 (18)	0.54389 (9)	0.0249 (4)
N21	−0.12341 (9)	0.24368 (18)	0.55424 (9)	0.0296 (3)
H21	−0.1456 (13)	0.301 (3)	0.5787 (13)	0.046 (6)*
H22	−0.1510 (13)	0.186 (2)	0.5205 (12)	0.035 (5)*
N3	−0.01179 (8)	0.20299 (15)	0.48564 (8)	0.0261 (3)
C4	0.06786 (10)	0.24364 (18)	0.47735 (9)	0.0257 (4)
Cl4	0.10767 (3)	0.14798 (5)	0.40232 (3)	0.03639 (17)
C5	0.11831 (10)	0.34908 (17)	0.51986 (9)	0.0262 (4)
H5	0.1743	0.3740	0.5096	0.033*
C6	0.08140 (10)	0.41912 (17)	0.58057 (9)	0.0238 (3)
N61	0.12211 (8)	0.52898 (15)	0.62697 (8)	0.0268 (3)
C62	0.21122 (10)	0.57591 (18)	0.62698 (9)	0.0277 (4)
H621	0.2128	0.6820	0.6243	0.035*
H622	0.2297	0.5374	0.5774	0.035*
C63	0.27461 (10)	0.52464 (18)	0.70472 (9)	0.0252 (3)
H631	0.3334	0.5665	0.7061	0.032*
H632	0.2801	0.4189	0.7027	0.032*
C64	0.24399 (10)	0.56704 (18)	0.78406 (9)	0.0239 (3)
H641	0.2505 (11)	0.671 (2)	0.7900 (11)	0.030 (5)*
C65	0.14788 (10)	0.52713 (19)	0.77775 (9)	0.0273 (4)
H651	0.1274	0.5666	0.8261	0.034*
H652	0.1422	0.4213	0.7789	0.034*
C66	0.09035 (10)	0.5856 (2)	0.69799 (9)	0.0295 (4)
H661	0.0285	0.5563	0.6944	0.037*
H662	0.0929	0.6918	0.6980	0.037*
C67	0.30207 (10)	0.50032 (17)	0.86049 (9)	0.0256 (4)
O67	0.26969 (7)	0.44034 (13)	0.91439 (7)	0.0330 (3)
N67	0.38837 (9)	0.50667 (17)	0.86607 (9)	0.0309 (4)
H671	0.4097 (11)	0.548 (2)	0.8278 (11)	0.034 (5)*
H672	0.4210 (12)	0.462 (2)	0.9058 (11)	0.036 (5)*
O1W	0.0000	0.8089 (3)	0.2500	0.0459 (5)
H1W	0.0084 (16)	0.752 (3)	0.2890 (15)	0.077 (9)*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
N1	0.0209 (7)	0.0322 (8)	0.0218 (6)	0.0004 (6)	0.0046 (5)	0.0001 (6)
C2	0.0222 (8)	0.0292 (9)	0.0228 (7)	0.0020 (7)	0.0039 (6)	0.0048 (6)
N21	0.0231 (8)	0.0367 (9)	0.0305 (8)	−0.0039 (7)	0.0092 (6)	−0.0070 (7)
N3	0.0240 (7)	0.0296 (8)	0.0252 (7)	0.0008 (6)	0.0062 (5)	−0.0015 (6)
C4	0.0253 (8)	0.0286 (9)	0.0243 (7)	0.0047 (7)	0.0075 (6)	0.0022 (6)
Cl4	0.0337 (3)	0.0403 (3)	0.0387 (3)	0.00087 (18)	0.01579 (19)	−0.01113 (18)
C5	0.0230 (8)	0.0307 (9)	0.0263 (8)	0.0008 (7)	0.0081 (6)	0.0025 (6)
C6	0.0221 (8)	0.0273 (9)	0.0209 (7)	0.0021 (6)	0.0021 (6)	0.0035 (6)
N61	0.0222 (7)	0.0322 (8)	0.0264 (6)	−0.0020 (6)	0.0063 (5)	−0.0028 (6)
C62	0.0259 (8)	0.0297 (9)	0.0281 (8)	−0.0042 (7)	0.0073 (6)	0.0010 (7)
C63	0.0214 (8)	0.0272 (9)	0.0276 (8)	−0.0022 (7)	0.0064 (6)	−0.0002 (7)
C64	0.0225 (8)	0.0214 (9)	0.0275 (8)	0.0004 (6)	0.0046 (6)	−0.0012 (6)
C65	0.0237 (8)	0.0331 (9)	0.0264 (8)	0.0016 (7)	0.0081 (6)	−0.0042 (7)
C66	0.0233 (8)	0.0359 (10)	0.0286 (8)	0.0024 (7)	0.0040 (6)	−0.0068 (7)
C67	0.0255 (8)	0.0242 (9)	0.0274 (8)	0.0012 (6)	0.0060 (6)	−0.0031 (6)
O67	0.0288 (6)	0.0401 (7)	0.0314 (6)	0.0026 (5)	0.0092 (5)	0.0083 (5)
N67	0.0231 (8)	0.0391 (9)	0.0295 (7)	0.0012 (6)	0.0031 (6)	0.0073 (6)
O1W	0.0504 (13)	0.0568 (14)	0.0289 (10)	0.000	0.0046 (8)	0.000

Geometric parameters (Å, º)

N1—C2	1.340 (2)	C63—C64	1.535 (2)
N1—C6	1.3523 (19)	C63—H631	0.99
C2—N3	1.348 (2)	C63—H632	0.99
C2—N21	1.354 (2)	C64—C67	1.521 (2)
N21—H21	0.79 (2)	C64—C65	1.523 (2)
N21—H22	0.83 (2)	C64—H641	0.979 (19)
N3—C4	1.3299 (19)	C65—C66	1.528 (2)
C4—C5	1.357 (2)	C65—H651	0.99
C4—Cl4	1.7407 (16)	C65—H652	0.99
C5—C6	1.414 (2)	C66—H661	0.99
C5—H5	0.95	C66—H662	0.99
C6—N61	1.353 (2)	C67—O67	1.2425 (18)
N61—C62	1.4536 (19)	C67—N67	1.328 (2)
N61—C66	1.4617 (19)	N67—H671	0.862 (18)
C62—C63	1.522 (2)	N67—H672	0.85 (2)
C62—H621	0.99	O1W—H1W	0.82 (2)
C62—H622	0.99
C2—N1—C6	117.27 (13)	C64—C63—H631	109.2
N1—C2—N3	126.53 (14)	C62—C63—H632	109.2
N1—C2—N21	117.24 (14)	C64—C63—H632	109.2
N3—C2—N21	116.19 (15)	H631—C63—H632	107.9
C2—N21—H21	115.2 (16)	C67—C64—C65	111.18 (13)
C2—N21—H22	116.0 (13)	C67—C64—C63	111.39 (13)
H21—N21—H22	124 (2)	C65—C64—C63	110.76 (13)
C4—N3—C2	113.28 (13)	C67—C64—H641	107.0 (11)
N3—C4—C5	127.12 (15)	C65—C64—H641	109.1 (10)
N3—C4—Cl4	113.91 (12)	C63—C64—H641	107.2 (10)
C5—C4—Cl4	118.97 (12)	C64—C65—C66	111.20 (13)
C4—C5—C6	115.03 (14)	C64—C65—H651	109.4
C4—C5—H5	122.5	C66—C65—H651	109.4
C6—C5—H5	122.5	C64—C65—H652	109.4
N1—C6—N61	116.91 (13)	C66—C65—H652	109.4
N1—C6—C5	120.54 (14)	H651—C65—H652	108.0
N61—C6—C5	122.55 (14)	N61—C66—C65	109.03 (13)
C6—N61—C62	124.13 (13)	N61—C66—H661	109.9
C6—N61—C66	121.95 (13)	C65—C66—H661	109.9
C62—N61—C66	111.96 (13)	N61—C66—H662	109.9
N61—C62—C63	110.83 (12)	C65—C66—H662	109.9
N61—C62—H621	109.5	H661—C66—H662	108.3
C63—C62—H621	109.5	O67—C67—N67	121.74 (14)
N61—C62—H622	109.5	O67—C67—C64	121.13 (14)
C63—C62—H622	109.5	N67—C67—C64	117.12 (14)
H621—C62—H622	108.1	C67—N67—H671	120.5 (12)
C62—C63—C64	112.06 (13)	C67—N67—H672	117.7 (12)
C62—C63—H631	109.2	H671—N67—H672	121.6 (17)
C6—N1—C2—N3	6.2 (2)	C5—C6—N61—C66	−170.24 (14)
C6—N1—C2—N21	−176.29 (14)	C6—N61—C62—C63	−103.75 (17)
N1—C2—N3—C4	−3.7 (2)	C66—N61—C62—C63	60.50 (18)
N21—C2—N3—C4	178.74 (14)	N61—C62—C63—C64	−52.92 (18)
C2—N3—C4—C5	−0.5 (2)	C62—C63—C64—C67	173.35 (13)
C2—N3—C4—Cl4	−179.95 (11)	C62—C63—C64—C65	49.05 (18)
N3—C4—C5—C6	1.7 (2)	C67—C64—C65—C66	−176.14 (13)
Cl4—C4—C5—C6	−178.88 (11)	C63—C64—C65—C66	−51.73 (18)
C2—N1—C6—N61	174.85 (14)	C6—N61—C66—C65	101.90 (17)
C2—N1—C6—C5	−4.5 (2)	C62—N61—C66—C65	−62.74 (18)
C4—C5—C6—N1	0.9 (2)	C64—C65—C66—N61	58.02 (18)
C4—C5—C6—N61	−178.32 (14)	C65—C64—C67—O67	−9.6 (2)
N1—C6—N61—C62	173.21 (13)	C63—C64—C67—O67	−133.68 (15)
C5—C6—N61—C62	−7.5 (2)	C65—C64—C67—N67	169.11 (13)
N1—C6—N61—C66	10.5 (2)	C63—C64—C67—N67	45.05 (19)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N21—H21···O67^i	0.79 (2)	2.35 (2)	3.049 (2)	148 (2)
N21—H22···O67^ii	0.83 (2)	2.25 (2)	3.069 (2)	170.6 (19)
N67—H671···O1W^iii	0.862 (18)	2.481 (19)	3.320 (2)	164.6 (16)
N67—H672···N3^iv	0.85 (2)	2.15 (2)	2.972 (2)	163.7 (18)
O1W—H1W···N1^v	0.82 (2)	2.32 (2)	3.1171 (19)	164 (2)

Symmetry codes: (i) −x, y, −z+3/2; (ii) x−1/2, −y+1/2, z−1/2; (iii) −x+1/2, −y+3/2, −z+1; (iv) x+1/2, −y+1/2, z+1/2; (v) −x, −y+1, −z+1.