Methyl N-{2-[(4,6-dimethoxy­pyrimidin-2-yl)(hydr­oxy)meth­yl]phen­yl}carbamate

In the title compound, C₁₅H₁₆N₃O₅, the hydr­oxy group is disordered over two positions, with site-occupation factors of 0.211 (4) and 0.789 (4). The pyrimidine and benzene rings are oriented at a dihedral angle of 72.31 (3)°. Intra­molecular C—H...O and N—H...N hydrogen bonds result in the formation of five-, six- and seven-membered rings. In the crystal structure, inter­molecular C—H...O and O—H...O hydrogen bonds link the mol­ecules. Further stability is provided by offset π–π stacking inter­actions; adjacent pyrimidine rings have a centroid-to-centroid distance of 3.81 (1) Å.

Key indicators

• Single-crystal X-ray study
• T = 292 K
• Mean [sigma](C-C) = 0.004 Å
• Disorder in main residue
• R factor = 0.064
• wR factor = 0.149
• Data-to-parameter ratio = 14.3

checkCIF/PLATON results

No syntax errors found



Alert level C
PLAT154_ALERT_1_C The su's on the Cell Angles are Equal  (x 10000)        400 Deg.
PLAT230_ALERT_2_C Hirshfeld Test Diff for    O1     -   C7      ..       5.39 su
PLAT301_ALERT_3_C Main Residue  Disorder .........................       4.00 Perc.
PLAT432_ALERT_2_C Short Inter X...Y Contact  C2     ..  O3'     ..       2.99 Ang.

Alert level G
PLAT860_ALERT_3_G Note: Number of Least-Squares Restraints .......          4

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

   1 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
   2 ALERT type 2 Indicator that the structure model may be wrong or deficient
   2 ALERT type 3 Indicator that the structure quality may be low
   0 ALERT type 4 Improvement, methodology, query or suggestion
   0 ALERT type 5 Informative message, check

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S1. Comment

Pyrimidine derivatives have broad biological properties: in particular pyrimidinylbenzoate is a highly effective herbicide with acetohydroxy acid synthese (AHAS) as target (Duggleby & Pang, 2000). We report herein the crystal structure of one such pyrimidine derivative, the title compound, (I).

In the molecule of (I), (Fig. 1) the bond lengths and angles are generally within normal ranges (Allen et al., 1987). When the crystal structure was solved, the atoms O3 and H3A were found to be disordered.

Rings A (C1—C6) and B (N2/N3/C10–C13) are, of course, planar and the dihedral angle between them is A/B = 72.31 (3)°. The intramolecular C—H···O hydrogen bonds (Table 1) result in the formation of five- and six-membered rings, while intramolecular N—H···N hydrogen bond (Table 1) results in the formation of a seven-membered ring.

In the crystal structure, intermolecular C—H···O and O—H···O hydrogen bonds (Table 1, Fig. 2) link the molecules, in which they may be effective in the stabilization of the structure. Further stability is provided by offset π–π stacking interactions (Janiak, 2000). The adjacent B rings have a centroid-centroid distance of 3.81 (1) Å [symmetry code: 1 - x, - y, - z].

Related literature

For general background, see: Duggleby & Pang (2000). For related literature, see: Li & Wang (2007). For bond-length data, see: Allen et al. (1987). For definitions of π–π stacking interactions, see: Janiak (2000).

S2. Experimental

The title compound was synthesized according to the literature method (Li & Wang, 2007). Crystals appropriate for X-ray analysis were obtained by slow evaporation of the dichloromethane solution at 283 K.

S3. Refinement

When the crystal structure was solved, the atoms O3 and H3A were found to be disordered. During refinement with isotropic thermal parameters, the occupancies of disordered H atoms were refined as H3A = 0.789 (4) and H3B = 0.211 (4). The remaining site occupancy factors were also refined as O3 = 0.789 (4) and O3' = 0.211 (4), during anisotropic refinement. H atoms (for NH and OH groups) were located in difference syntheses and refined [N—H = 0.88 (2) Å, O—H = 0.814 (10) and 0.819 (10) Å and U_iso(H) = 1.2U_eq(N,O)]. The remaining H atoms were positioned geometrically, with C—H = 0.93 and 0.96 Å, for aromatic and methyl H atoms and constrained to ride on their parent atoms, with U_iso(H) = xU_eq(C), where x = 1.2 for aromatic H and x = 1.5 for methyl H atoms.

Computing details

Data collection: SMART (Bruker, 2001); cell refinement: SAINT (Bruker, 2001); data reduction: SAINT (Bruker, 2001); program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: PLATON (Spek, 2003); software used to prepare material for publication: SHELXTL (Bruker, 2001).

Figures

	Fig. 1. The molecular structure of the title molecule, with the atom-numbering scheme. Displacement ellipsoids are drawn at the 50% probability level.
	Fig. 2. A packing diagram of (I). Hydrogen bonds are shown as dashed lines.

Methyl N-{2-[(4,6-dimethoxypyrimidin-2-yl)(hydroxy)methyl]phenyl}carbamate

Crystal data

C15H16N3O5	Z = 2
Mr = 318.31	F(000) = 334
Triclinic, P1	Dx = 1.385 Mg m^−3
Hall symbol: -P 1	Mo Kα radiation, λ = 0.71073 Å
a = 7.894 (2) Å	Cell parameters from 1926 reflections
b = 9.302 (2) Å	θ = 2.4–25.0°
c = 11.697 (3) Å	µ = 0.11 mm^−1
α = 111.518 (4)°	T = 292 K
β = 98.887 (4)°	Block, colourless
γ = 100.230 (4)°	0.20 × 0.10 × 0.10 mm
V = 763.4 (3) Å^3

Data collection

Bruker SMART 4K CCD area-detector diffractometer	2064 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tube	Rint = 0.099
Graphite monochromator	θmax = 27.0°, θmin = 1.9°
ϕ and ω scans	h = −10→10
8360 measured reflections	k = −11→11
3292 independent reflections	l = −14→14

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)] = 0.064	Hydrogen site location: inferred from neighbouring sites
wR(F^2) = 0.149	H atoms treated by a mixture of independent and constrained refinement
S = 1.01	w = 1/[σ^2(Fo^2) + (0.0617P)^2] where P = (Fo^2 + 2Fc^2)/3
3292 reflections	(Δ/σ)max = 0.003
230 parameters	Δρmax = 0.22 e Å^−3
4 restraints	Δρmin = −0.27 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.

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 (Ų)

	x	y	z	Uiso*/Ueq	Occ. (<1)
O1	1.3432 (2)	0.29230 (18)	0.54228 (15)	0.0468 (4)
O2	1.1760 (2)	0.42049 (18)	0.46153 (15)	0.0530 (5)
O3	0.6181 (3)	−0.1852 (3)	0.26033 (19)	0.0491 (7)	0.789 (4)
H3A	0.632 (4)	−0.196 (4)	0.3268 (17)	0.059*	0.789 (4)
O3'	0.7255 (12)	0.0317 (10)	0.3606 (7)	0.060 (3)	0.211 (4)
H3B	0.789 (11)	0.060 (12)	0.4314 (19)	0.072*	0.211 (4)
O4	0.6414 (3)	−0.2561 (2)	−0.17285 (15)	0.0648 (6)
O5	0.8081 (3)	0.2944 (2)	0.09025 (15)	0.0647 (6)
N1	1.1052 (3)	0.1588 (2)	0.37305 (18)	0.0423 (5)
H1	1.017 (3)	0.177 (3)	0.329 (2)	0.051*
N2	0.7001 (2)	−0.1685 (2)	0.04352 (17)	0.0434 (5)
N3	0.7866 (3)	0.1109 (2)	0.17055 (16)	0.0432 (5)
C1	1.1024 (3)	−0.0018 (3)	0.35143 (19)	0.0372 (5)
C2	1.2571 (3)	−0.0466 (3)	0.3780 (2)	0.0469 (6)
H2	1.3658	0.0289	0.4089	0.056*
C3	1.2498 (4)	−0.2038 (3)	0.3586 (2)	0.0529 (7)
H3	1.3536	−0.2329	0.3783	0.064*
C4	1.0900 (4)	−0.3174 (3)	0.3104 (2)	0.0506 (6)
H4	1.0853	−0.4227	0.2983	0.061*
C5	0.9383 (3)	−0.2735 (3)	0.2805 (2)	0.0432 (6)
H5	0.8312	−0.3513	0.2449	0.052*
C6	0.9393 (3)	−0.1169 (3)	0.30152 (19)	0.0361 (5)
C7	1.2198 (3)	0.2899 (3)	0.4654 (2)	0.0385 (5)
C8	1.2710 (4)	0.5698 (3)	0.5647 (2)	0.0595 (7)
H8A	1.2637	0.5621	0.6436	0.089*
H8B	1.2198	0.6535	0.5583	0.089*
H8C	1.3931	0.5933	0.5613	0.089*
C9	0.7669 (3)	−0.0706 (3)	0.2735 (2)	0.0415 (6)
C10	0.7478 (3)	−0.0409 (3)	0.1541 (2)	0.0373 (5)
C11	0.6872 (3)	−0.1352 (3)	−0.0576 (2)	0.0456 (6)
C12	0.7191 (3)	0.0175 (3)	−0.0535 (2)	0.0483 (6)
H12	0.7068	0.0371	−0.1264	0.058*
C13	0.7701 (3)	0.1383 (3)	0.0652 (2)	0.0452 (6)
C14	0.6185 (5)	−0.4148 (3)	−0.1773 (3)	0.0813 (10)
H14A	0.7297	−0.4267	−0.1404	0.122*
H14B	0.5775	−0.4911	−0.2637	0.122*
H14C	0.5329	−0.4327	−0.1307	0.122*
C15	0.7919 (5)	0.3374 (3)	−0.0168 (3)	0.0796 (10)
H15A	0.8728	0.2971	−0.0661	0.119*
H15B	0.8192	0.4516	0.0126	0.119*
H15C	0.6727	0.2920	−0.0682	0.119*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
O1	0.0433 (10)	0.0482 (10)	0.0397 (9)	0.0037 (7)	−0.0066 (7)	0.0180 (8)
O2	0.0629 (12)	0.0366 (9)	0.0471 (10)	0.0079 (8)	−0.0085 (8)	0.0141 (8)
O3	0.0354 (12)	0.0678 (16)	0.0463 (14)	−0.0004 (10)	0.0016 (10)	0.0351 (12)
O3'	0.089 (7)	0.051 (5)	0.036 (5)	0.029 (5)	−0.004 (4)	0.015 (4)
O4	0.0996 (15)	0.0478 (11)	0.0307 (9)	0.0177 (10)	−0.0025 (9)	0.0056 (8)
O5	0.1001 (15)	0.0386 (10)	0.0433 (10)	−0.0004 (9)	−0.0001 (10)	0.0181 (8)
N1	0.0411 (12)	0.0386 (11)	0.0397 (11)	0.0060 (9)	−0.0060 (9)	0.0155 (9)
N2	0.0503 (13)	0.0415 (11)	0.0326 (11)	0.0097 (9)	0.0018 (9)	0.0129 (9)
N3	0.0515 (13)	0.0412 (11)	0.0310 (10)	0.0049 (9)	0.0019 (9)	0.0143 (9)
C1	0.0432 (14)	0.0392 (13)	0.0293 (12)	0.0118 (10)	0.0070 (10)	0.0141 (10)
C2	0.0413 (15)	0.0486 (15)	0.0461 (15)	0.0127 (11)	0.0053 (11)	0.0155 (12)
C3	0.0512 (17)	0.0581 (17)	0.0549 (16)	0.0255 (14)	0.0103 (13)	0.0245 (14)
C4	0.0620 (18)	0.0427 (14)	0.0515 (15)	0.0210 (13)	0.0127 (13)	0.0210 (12)
C5	0.0474 (15)	0.0411 (14)	0.0399 (13)	0.0080 (11)	0.0107 (11)	0.0165 (11)
C6	0.0406 (13)	0.0434 (13)	0.0238 (11)	0.0091 (10)	0.0063 (9)	0.0144 (10)
C7	0.0403 (14)	0.0407 (13)	0.0359 (13)	0.0053 (11)	0.0091 (11)	0.0195 (11)
C8	0.0704 (19)	0.0387 (14)	0.0553 (17)	0.0056 (13)	−0.0012 (14)	0.0139 (13)
C9	0.0387 (14)	0.0519 (15)	0.0379 (13)	0.0093 (11)	0.0074 (11)	0.0246 (12)
C10	0.0310 (12)	0.0455 (14)	0.0330 (12)	0.0073 (10)	0.0017 (9)	0.0167 (11)
C11	0.0525 (16)	0.0475 (15)	0.0311 (13)	0.0109 (12)	0.0017 (11)	0.0138 (11)
C12	0.0598 (17)	0.0520 (16)	0.0321 (13)	0.0107 (12)	0.0044 (11)	0.0202 (12)
C13	0.0533 (15)	0.0413 (14)	0.0349 (14)	0.0021 (11)	0.0000 (11)	0.0174 (11)
C14	0.125 (3)	0.0447 (17)	0.0528 (18)	0.0280 (17)	−0.0066 (18)	0.0044 (14)
C15	0.118 (3)	0.0553 (18)	0.0591 (19)	−0.0033 (17)	−0.0007 (17)	0.0368 (16)

Geometric parameters (Å, º)

C1—C2	1.386 (3)	C9—C10	1.511 (3)
C1—C6	1.402 (3)	C10—N3	1.324 (3)
C1—N1	1.416 (3)	C10—N2	1.337 (3)
C2—C3	1.384 (3)	C11—N2	1.322 (3)
C2—H2	0.9300	C11—O4	1.344 (3)
C3—C4	1.376 (3)	C11—C12	1.379 (3)
C3—H3	0.9300	C12—C13	1.368 (3)
C4—C5	1.368 (3)	C12—H12	0.9300
C4—H4	0.9300	C13—O5	1.338 (3)
C5—C6	1.384 (3)	C13—N3	1.339 (3)
C5—H5	0.9300	C14—O4	1.435 (3)
C6—C9	1.523 (3)	C14—H14A	0.9600
C7—O1	1.211 (2)	C14—H14B	0.9600
C7—O2	1.335 (3)	C14—H14C	0.9600
C7—N1	1.346 (3)	C15—O5	1.443 (3)
C8—O2	1.438 (3)	C15—H15A	0.9600
C8—H8A	0.9600	C15—H15B	0.9600
C8—H8B	0.9600	C15—H15C	0.9600
C8—H8C	0.9600	N1—H1	0.88 (2)
C9—O3'	1.246 (6)	O3—H3A	0.814 (10)
C9—O3	1.385 (3)	O3'—H3B	0.819 (10)
C2—C1—C6	119.8 (2)	N3—C10—C9	115.8 (2)
C2—C1—N1	121.3 (2)	N2—C10—C9	117.5 (2)
C6—C1—N1	118.9 (2)	N2—C11—O4	118.9 (2)
C3—C2—C1	120.0 (2)	N2—C11—C12	124.3 (2)
C3—C2—H2	120.0	O4—C11—C12	116.8 (2)
C1—C2—H2	120.0	C13—C12—C11	115.5 (2)
C4—C3—C2	120.5 (2)	C13—C12—H12	122.3
C4—C3—H3	119.7	C11—C12—H12	122.3
C2—C3—H3	119.7	O5—C13—N3	112.35 (19)
C5—C4—C3	119.2 (2)	O5—C13—C12	125.1 (2)
C5—C4—H4	120.4	N3—C13—C12	122.6 (2)
C3—C4—H4	120.4	O4—C14—H14A	109.5
C4—C5—C6	122.0 (2)	O4—C14—H14B	109.5
C4—C5—H5	119.0	H14A—C14—H14B	109.5
C6—C5—H5	119.0	O4—C14—H14C	109.5
C5—C6—C1	118.3 (2)	H14A—C14—H14C	109.5
C5—C6—C9	120.7 (2)	H14B—C14—H14C	109.5
C1—C6—C9	120.9 (2)	O5—C15—H15A	109.5
O1—C7—O2	124.1 (2)	O5—C15—H15B	109.5
O1—C7—N1	126.3 (2)	H15A—C15—H15B	109.5
O2—C7—N1	109.6 (2)	O5—C15—H15C	109.5
O2—C8—H8A	109.5	H15A—C15—H15C	109.5
O2—C8—H8B	109.5	H15B—C15—H15C	109.5
H8A—C8—H8B	109.5	C7—N1—C1	126.21 (19)
O2—C8—H8C	109.5	C7—N1—H1	115.0 (15)
H8A—C8—H8C	109.5	C1—N1—H1	118.3 (16)
H8B—C8—H8C	109.5	C11—N2—C10	114.8 (2)
O3'—C9—O3	90.7 (5)	C10—N3—C13	116.22 (19)
O3'—C9—C10	112.9 (4)	C7—O2—C8	116.31 (18)
O3—C9—C10	108.42 (19)	C9—O3—H3A	105 (2)
O3'—C9—C6	119.2 (4)	C9—O3'—H3B	115.2 (15)
O3—C9—C6	113.1 (2)	C11—O4—C14	116.9 (2)
C10—C9—C6	110.68 (18)	C13—O5—C15	116.94 (19)
N3—C10—N2	126.6 (2)
C6—C1—C2—C3	−1.8 (3)	N2—C11—C12—C13	1.2 (4)
N1—C1—C2—C3	178.5 (2)	O4—C11—C12—C13	−178.3 (2)
C1—C2—C3—C4	1.4 (4)	C11—C12—C13—O5	179.7 (2)
C2—C3—C4—C5	0.7 (4)	C11—C12—C13—N3	−0.6 (4)
C3—C4—C5—C6	−2.4 (4)	O1—C7—N1—C1	2.8 (4)
C4—C5—C6—C1	2.0 (3)	O2—C7—N1—C1	−176.3 (2)
C4—C5—C6—C9	−176.8 (2)	C2—C1—N1—C7	−32.3 (3)
C2—C1—C6—C5	0.1 (3)	C6—C1—N1—C7	148.0 (2)
N1—C1—C6—C5	179.84 (19)	O4—C11—N2—C10	179.4 (2)
C2—C1—C6—C9	178.94 (19)	C12—C11—N2—C10	−0.1 (4)
N1—C1—C6—C9	−1.4 (3)	N3—C10—N2—C11	−1.9 (3)
C5—C6—C9—O3'	121.1 (5)	C9—C10—N2—C11	−179.4 (2)
C1—C6—C9—O3'	−57.7 (6)	N2—C10—N3—C13	2.5 (3)
C5—C6—C9—O3	16.4 (3)	C9—C10—N3—C13	180.0 (2)
C1—C6—C9—O3	−162.4 (2)	O5—C13—N3—C10	178.7 (2)
C5—C6—C9—C10	−105.4 (2)	C12—C13—N3—C10	−1.1 (4)
C1—C6—C9—C10	75.8 (3)	O1—C7—O2—C8	−7.3 (3)
O3'—C9—C10—N3	35.3 (6)	N1—C7—O2—C8	171.83 (19)
O3—C9—C10—N3	134.2 (2)	N2—C11—O4—C14	−3.2 (4)
C6—C9—C10—N3	−101.3 (2)	C12—C11—O4—C14	176.4 (2)
O3'—C9—C10—N2	−146.9 (5)	N3—C13—O5—C15	−179.1 (2)
O3—C9—C10—N2	−48.0 (3)	C12—C13—O5—C15	0.7 (4)
C6—C9—C10—N2	76.5 (2)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
C5—H5···O3	0.93	2.46	2.796 (3)	101
C2—H2···O1	0.93	2.43	2.913 (3)	112
N1—H1···N3	0.88 (2)	2.20 (2)	3.020 (3)	154 (2)
C14—H14B···O1^i	0.96	2.58	3.471 (3)	154
O3—H3A···O1^ii	0.81 (1)	2.04 (1)	2.827 (3)	163 (3)

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