Methyl 2-[2-(benzyl-oxycarbon-ylamino)-propan-2-yl]-5-hy-droxy-1-methyl-6-oxo-1,6-dihydro-pyrimidine-4-carboxyl-ate.

The title pyrimidine derivative, C(18)H(21)N(3)O(6), was obtained by the reaction of methyl 2-[2-(benzyl-oxycarbon-yl)amino-propan-2-yl]-5-hy-droxy-6-oxo-1,6-dihydro-pyrimidine-4-carboxyl-ate with dimethyl sulfate in dimethyl sulfoxide. The mol-ecule has a V-shaped structure, the phenyl and the pyrimidine rings making a dihedral angle of 43.1 (1)°. The methyl group substituting the pyrimidine ring deviates slightly from the ring mean-plane [C-N-C-C torsion angle = 5.49 (15)°], and the methyl ester substituent has a conformation suitable for the formation of an intra-molecular O-H⋯O hydrogen bond with the hydroxyl functionality. In the crystal, molecules are linked into chains along the b axis by N-H⋯O hydrogen bonds.

Related literature

For the anti­retroviral drug raltegravir [systematic name: N-(2-(4-(4-fluoro­benzyl­carbamo­yl)-5-hy­droxy-1-methyl-6-oxo-1,6-dihydro­pyrimidin-2-yl)propan-2-yl)], see: Steigbigel et al. (2008 ▶). For the synthesis of raltegravir, see: Belyk et al. (2006 ▶); For related structures, see: Fun et al. (2011 ▶); Shang, Ha, Yu & Zhao (2011 ▶); Shang, Qi, Tao & Zhang (2011 ▶).

Experimental

Crystal data

C18H21N3O6

M = 375.38

Monoclinic,

a = 10.540 (2) Å

b = 12.927 (3) Å

c = 13.751 (3) Å

β = 109.74 (3)°

V = 1763.5 (6) Å3

Z = 4

Mo Kα radiation

μ = 0.11 mm−1

T = 113 K

0.20 × 0.16 × 0.12 mm

Data collection

Rigaku Saturn diffractometer

Absorption correction: multi-scan (CrystalClear; Rigaku/MSC, 2005 ▶) T min = 0.979, T max = 0.987

12669 measured reflections

4184 independent reflections

2889 reflections with I > 2σ(I)

R int = 0.032

Refinement

R[F 2 > 2σ(F 2)] = 0.035

wR(F 2) = 0.093

S = 1.00

4184 reflections

255 parameters

H atoms treated by a mixture of independent and constrained refinement

Δρmax = 0.28 e Å−3

Δρmin = −0.20 e Å−3

Data collection: CrystalClear (Rigaku/MSC, 2005 ▶); cell refinement: CrystalClear; data reduction: CrystalClear; 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: CrystalStructure (Rigaku/MSC, 2005 ▶).

Click here for additional data file.

Crystal structure: contains datablock(s) global, I. DOI: 10.1107/S160053681204233X/bh2453sup1.cif

Click here for additional data file.

Structure factors: contains datablock(s) I. DOI: 10.1107/S160053681204233X/bh2453Isup2.hkl

Click here for additional data file.

Supplementary material file. DOI: 10.1107/S160053681204233X/bh2453Isup3.cml

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

C18H21N3O6	F(000) = 792
Mr = 375.38	Dx = 1.414 Mg m−3
Monoclinic, P21/n	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2yn	Cell parameters from 5478 reflections
a = 10.540 (2) Å	θ = 2.1–27.9°
b = 12.927 (3) Å	µ = 0.11 mm−1
c = 13.751 (3) Å	T = 113 K
β = 109.74 (3)°	Plate, colourless
V = 1763.5 (6) Å3	0.20 × 0.16 × 0.12 mm
Z = 4

Rigaku Saturn diffractometer	4184 independent reflections
Radiation source: rotating anode	2889 reflections with I > 2σ(I)
Confocal monochromator	Rint = 0.032
Detector resolution: 7.31 pixels mm-1	θmax = 27.9°, θmin = 2.1°
ω and φ scans	h = −13→13
Absorption correction: multi-scan (CrystalClear; Rigaku/MSC, 2005)	k = −16→16
Tmin = 0.979, Tmax = 0.987	l = −18→10
12669 measured reflections

Refinement on F2	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.035	Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.093	H atoms treated by a mixture of independent and constrained refinement
S = 1.00	w = 1/[σ2(Fo2) + (0.0545P)2] where P = (Fo2 + 2Fc2)/3
4184 reflections	(Δ/σ)max = 0.001
255 parameters	Δρmax = 0.28 e Å−3
0 restraints	Δρmin = −0.20 e Å−3
0 constraints

	x	y	z	Uiso*/Ueq
N1	0.06467 (9)	0.00568 (6)	0.24005 (7)	0.0175 (2)
N2	0.12798 (9)	0.17823 (6)	0.22657 (8)	0.0184 (2)
N3	0.23993 (10)	0.16037 (7)	0.45582 (8)	0.0200 (2)
O1	0.01828 (8)	0.27591 (6)	0.08460 (7)	0.0245 (2)
O2	−0.13087 (8)	0.11324 (6)	−0.01134 (6)	0.02320 (19)
H2	−0.1711 (14)	0.0529 (10)	−0.0243 (12)	0.035*
O3	−0.18898 (8)	−0.07843 (6)	0.00815 (7)	0.0248 (2)
O4	−0.07643 (7)	−0.16439 (5)	0.15296 (6)	0.02110 (19)
O5	0.01416 (8)	0.16353 (6)	0.42853 (7)	0.0296 (2)
O6	0.16194 (8)	0.26344 (6)	0.55086 (7)	0.0251 (2)
C1	0.13702 (11)	0.08557 (8)	0.28038 (9)	0.0170 (2)
C2	0.03246 (11)	0.19213 (8)	0.12974 (9)	0.0184 (2)
C3	−0.04554 (11)	0.10083 (8)	0.08528 (9)	0.0180 (2)
C4	−0.02494 (10)	0.01226 (8)	0.14162 (9)	0.0168 (2)
C5	0.21999 (12)	0.26756 (8)	0.26136 (10)	0.0272 (3)
H5A	0.2792	0.2719	0.2198	0.041*
H5B	0.2747	0.2586	0.3343	0.041*
H5C	0.1671	0.3313	0.2531	0.041*
C6	−0.10441 (11)	−0.08065 (8)	0.09481 (9)	0.0188 (2)
C7	−0.15552 (12)	−0.25469 (9)	0.10665 (10)	0.0263 (3)
H7A	−0.2505	−0.2422	0.0978	0.039*
H7B	−0.1230	−0.3147	0.1517	0.039*
H7C	−0.1465	−0.2681	0.0391	0.039*
C8	0.23999 (11)	0.07215 (8)	0.38845 (9)	0.0191 (2)
C9	0.38107 (12)	0.06442 (9)	0.37925 (11)	0.0272 (3)
H9A	0.3937	0.1212	0.3362	0.041*
H9B	0.3899	−0.0018	0.3475	0.041*
H9C	0.4495	0.0689	0.4482	0.041*
C10	0.21098 (13)	−0.02658 (8)	0.43885 (10)	0.0257 (3)
H10A	0.2773	−0.0336	0.5084	0.038*
H10B	0.2169	−0.0866	0.3971	0.038*
H10C	0.1202	−0.0227	0.4432	0.038*
C11	0.12831 (11)	0.19193 (8)	0.47419 (9)	0.0212 (3)
C12	0.05270 (13)	0.30190 (10)	0.58204 (12)	0.0345 (3)
H12A	0.0272	0.2496	0.6247	0.041*
H12B	−0.0271	0.3166	0.5204	0.041*
C13	0.09959 (12)	0.39926 (9)	0.64339 (10)	0.0244 (3)
C14	0.01477 (13)	0.48439 (10)	0.62565 (11)	0.0355 (3)
H14	−0.0716	0.4813	0.5736	0.043*
C15	0.05509 (15)	0.57377 (10)	0.68321 (12)	0.0389 (4)
H15	−0.0034	0.6319	0.6701	0.047*
C16	0.17894 (14)	0.57887 (9)	0.75897 (11)	0.0332 (3)
H16	0.2059	0.6402	0.7987	0.040*
C17	0.26443 (12)	0.49493 (9)	0.77748 (10)	0.0269 (3)
H17	0.3503	0.4983	0.8301	0.032*
C18	0.22509 (11)	0.40592 (9)	0.71942 (10)	0.0225 (3)
H18	0.2849	0.3486	0.7318	0.027*
H3	0.3174 (15)	0.1854 (10)	0.4951 (12)	0.034 (4)*

	U11	U22	U33	U12	U13	U23
N1	0.0181 (4)	0.0182 (5)	0.0144 (5)	0.0006 (4)	0.0032 (4)	−0.0008 (4)
N2	0.0202 (5)	0.0163 (4)	0.0165 (5)	−0.0014 (4)	0.0036 (4)	0.0010 (4)
N3	0.0203 (5)	0.0181 (5)	0.0179 (6)	−0.0007 (4)	0.0015 (4)	−0.0041 (4)
O1	0.0277 (4)	0.0203 (4)	0.0230 (5)	0.0020 (3)	0.0052 (4)	0.0066 (4)
O2	0.0259 (4)	0.0229 (4)	0.0154 (5)	0.0030 (4)	0.0000 (4)	0.0016 (4)
O3	0.0215 (4)	0.0273 (4)	0.0199 (5)	−0.0012 (3)	−0.0006 (4)	−0.0012 (4)
O4	0.0229 (4)	0.0179 (4)	0.0205 (5)	−0.0035 (3)	0.0048 (4)	−0.0013 (3)
O5	0.0224 (4)	0.0287 (5)	0.0340 (6)	−0.0044 (3)	0.0046 (4)	−0.0112 (4)
O6	0.0226 (4)	0.0261 (4)	0.0266 (5)	−0.0024 (3)	0.0082 (4)	−0.0108 (4)
C1	0.0183 (5)	0.0157 (5)	0.0162 (6)	0.0022 (4)	0.0048 (5)	0.0004 (5)
C2	0.0191 (5)	0.0194 (5)	0.0165 (6)	0.0033 (4)	0.0058 (5)	0.0018 (5)
C3	0.0170 (5)	0.0217 (6)	0.0142 (6)	0.0044 (4)	0.0039 (5)	0.0003 (5)
C4	0.0159 (5)	0.0182 (5)	0.0154 (6)	0.0019 (4)	0.0040 (5)	−0.0004 (5)
C5	0.0293 (6)	0.0217 (6)	0.0260 (7)	−0.0075 (5)	0.0033 (6)	0.0011 (5)
C6	0.0174 (5)	0.0214 (6)	0.0175 (6)	0.0020 (4)	0.0056 (5)	−0.0007 (5)
C7	0.0293 (6)	0.0217 (6)	0.0270 (8)	−0.0084 (5)	0.0083 (6)	−0.0034 (5)
C8	0.0218 (5)	0.0157 (5)	0.0161 (6)	0.0017 (4)	0.0016 (5)	−0.0016 (5)
C9	0.0219 (6)	0.0276 (6)	0.0264 (7)	0.0045 (5)	0.0008 (6)	−0.0051 (6)
C10	0.0346 (6)	0.0174 (6)	0.0182 (7)	0.0016 (5)	0.0000 (6)	0.0008 (5)
C11	0.0248 (6)	0.0156 (5)	0.0209 (7)	−0.0010 (4)	0.0047 (5)	−0.0004 (5)
C12	0.0265 (6)	0.0389 (7)	0.0416 (9)	−0.0076 (6)	0.0162 (7)	−0.0178 (7)
C13	0.0228 (5)	0.0272 (6)	0.0248 (7)	−0.0021 (5)	0.0102 (5)	−0.0060 (5)
C14	0.0261 (6)	0.0450 (8)	0.0305 (8)	0.0079 (6)	0.0031 (6)	−0.0096 (7)
C15	0.0456 (8)	0.0335 (7)	0.0368 (9)	0.0159 (6)	0.0129 (7)	−0.0038 (6)
C16	0.0455 (8)	0.0265 (6)	0.0318 (8)	−0.0058 (6)	0.0185 (7)	−0.0094 (6)
C17	0.0254 (6)	0.0351 (7)	0.0214 (7)	−0.0069 (5)	0.0095 (6)	−0.0034 (5)
C18	0.0231 (6)	0.0236 (6)	0.0229 (7)	0.0012 (5)	0.0106 (5)	0.0020 (5)

N1—C1	1.2923 (13)	C7—H7B	0.9800
N1—C4	1.3667 (15)	C7—H7C	0.9800
N2—C2	1.3833 (15)	C8—C10	1.5317 (15)
N2—C1	1.3943 (13)	C8—C9	1.5376 (15)
N2—C5	1.4797 (14)	C9—H9A	0.9800
N3—C11	1.3473 (14)	C9—H9B	0.9800
N3—C8	1.4694 (14)	C9—H9C	0.9800
N3—H3	0.875 (15)	C10—H10A	0.9800
O1—C2	1.2320 (13)	C10—H10B	0.9800
O2—C3	1.3390 (14)	C10—H10C	0.9800
O2—H2	0.876 (13)	C12—C13	1.5028 (17)
O3—C6	1.2239 (15)	C12—H12A	0.9900
O4—C6	1.3187 (13)	C12—H12B	0.9900
O4—C7	1.4507 (13)	C13—C18	1.3843 (18)
O5—C11	1.2109 (14)	C13—C14	1.3865 (17)
O6—C11	1.3562 (14)	C14—C15	1.3838 (19)
O6—C12	1.4457 (14)	C14—H14	0.9500
C1—C8	1.5255 (17)	C15—C16	1.369 (2)
C2—C3	1.4503 (16)	C15—H15	0.9500
C3—C4	1.3581 (15)	C16—C17	1.3781 (17)
C4—C6	1.4813 (15)	C16—H16	0.9500
C5—H5A	0.9800	C17—C18	1.3819 (16)
C5—H5B	0.9800	C17—H17	0.9500
C5—H5C	0.9800	C18—H18	0.9500
C7—H7A	0.9800
C1—N1—C4	119.05 (10)	C1—C8—C9	108.47 (10)
C2—N2—C1	121.31 (9)	C10—C8—C9	109.24 (9)
C2—N2—C5	113.23 (9)	C8—C9—H9A	109.5
C1—N2—C5	125.38 (10)	C8—C9—H9B	109.5
C11—N3—C8	122.65 (10)	H9A—C9—H9B	109.5
C11—N3—H3	117.7 (9)	C8—C9—H9C	109.5
C8—N3—H3	118.5 (9)	H9A—C9—H9C	109.5
C3—O2—H2	102.2 (10)	H9B—C9—H9C	109.5
C6—O4—C7	114.62 (10)	C8—C10—H10A	109.5
C11—O6—C12	116.08 (9)	C8—C10—H10B	109.5
N1—C1—N2	122.28 (11)	H10A—C10—H10B	109.5
N1—C1—C8	116.74 (9)	C8—C10—H10C	109.5
N2—C1—C8	120.89 (9)	H10A—C10—H10C	109.5
O1—C2—N2	121.61 (10)	H10B—C10—H10C	109.5
O1—C2—C3	123.23 (11)	O5—C11—N3	126.06 (11)
N2—C2—C3	115.13 (10)	O5—C11—O6	124.26 (10)
O2—C3—C4	126.26 (10)	N3—C11—O6	109.67 (10)
O2—C3—C2	114.58 (10)	O6—C12—C13	108.10 (9)
C4—C3—C2	119.14 (11)	O6—C12—H12A	110.1
C3—C4—N1	122.78 (10)	C13—C12—H12A	110.1
C3—C4—C6	118.53 (11)	O6—C12—H12B	110.1
N1—C4—C6	118.69 (10)	C13—C12—H12B	110.1
N2—C5—H5A	109.5	H12A—C12—H12B	108.4
N2—C5—H5B	109.5	C18—C13—C14	118.59 (11)
H5A—C5—H5B	109.5	C18—C13—C12	121.68 (11)
N2—C5—H5C	109.5	C14—C13—C12	119.71 (12)
H5A—C5—H5C	109.5	C15—C14—C13	120.45 (13)
H5B—C5—H5C	109.5	C15—C14—H14	119.8
O3—C6—O4	123.35 (10)	C13—C14—H14	119.8
O3—C6—C4	121.54 (10)	C16—C15—C14	120.33 (12)
O4—C6—C4	115.10 (10)	C16—C15—H15	119.8
O4—C7—H7A	109.5	C14—C15—H15	119.8
O4—C7—H7B	109.5	C15—C16—C17	119.91 (12)
H7A—C7—H7B	109.5	C15—C16—H16	120.0
O4—C7—H7C	109.5	C17—C16—H16	120.0
H7A—C7—H7C	109.5	C16—C17—C18	119.93 (13)
H7B—C7—H7C	109.5	C16—C17—H17	120.0
N3—C8—C1	111.98 (9)	C18—C17—H17	120.0
N3—C8—C10	108.59 (9)	C17—C18—C13	120.79 (11)
C1—C8—C10	110.51 (9)	C17—C18—H18	119.6
N3—C8—C9	107.98 (9)	C13—C18—H18	119.6
C4—N1—C1—N2	−0.69 (14)	N1—C4—C6—O4	−2.56 (13)
C4—N1—C1—C8	−177.17 (9)	C11—N3—C8—C1	56.33 (14)
C2—N2—C1—N1	5.48 (15)	C11—N3—C8—C10	−65.98 (14)
C5—N2—C1—N1	−170.84 (10)	C11—N3—C8—C9	175.69 (11)
C2—N2—C1—C8	−178.18 (9)	N1—C1—C8—N3	−136.08 (10)
C5—N2—C1—C8	5.49 (15)	N2—C1—C8—N3	47.39 (13)
C1—N2—C2—O1	175.31 (9)	N1—C1—C8—C10	−14.88 (13)
C5—N2—C2—O1	−7.95 (14)	N2—C1—C8—C10	168.59 (9)
C1—N2—C2—C3	−6.35 (14)	N1—C1—C8—C9	104.85 (10)
C5—N2—C2—C3	170.39 (9)	N2—C1—C8—C9	−71.68 (12)
O1—C2—C3—O2	2.85 (15)	C8—N3—C11—O5	−11.11 (19)
N2—C2—C3—O2	−175.46 (8)	C8—N3—C11—O6	170.45 (10)
O1—C2—C3—C4	−178.65 (10)	C12—O6—C11—O5	3.79 (17)
N2—C2—C3—C4	3.04 (14)	C12—O6—C11—N3	−177.74 (10)
O2—C3—C4—N1	179.76 (9)	C11—O6—C12—C13	−164.02 (10)
C2—C3—C4—N1	1.45 (15)	O6—C12—C13—C18	−45.05 (16)
O2—C3—C4—C6	−1.11 (16)	O6—C12—C13—C14	136.37 (12)
C2—C3—C4—C6	−179.41 (9)	C18—C13—C14—C15	−0.22 (19)
C1—N1—C4—C3	−2.74 (15)	C12—C13—C14—C15	178.41 (12)
C1—N1—C4—C6	178.12 (9)	C13—C14—C15—C16	−0.5 (2)
C7—O4—C6—O3	−0.77 (14)	C14—C15—C16—C17	0.6 (2)
C7—O4—C6—C4	179.58 (8)	C15—C16—C17—C18	0.13 (19)
C3—C4—C6—O3	−1.39 (15)	C16—C17—C18—C13	−0.87 (18)
N1—C4—C6—O3	177.78 (9)	C14—C13—C18—C17	0.91 (17)
C3—C4—C6—O4	178.27 (9)	C12—C13—C18—C17	−177.69 (10)

D—H···A	D—H	H···A	D···A	D—H···A
O2—H2···O3	0.876 (13)	1.782 (14)	2.5879 (12)	151.9 (14)
N3—H3···O1i	0.875 (15)	2.118 (15)	2.9854 (16)	170.9 (12)

Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
O2—H2⋯O3	0.876 (13)	1.782 (14)	2.5879 (12)	151.9 (14)
N3—H3⋯O1i	0.875 (15)	2.118 (15)	2.9854 (16)	170.9 (12)

Symmetry code: (i) .