2-Chloro-4-(4-methoxy­benzyl­oxy)­pyrimidine

The structure of the title compound, C₁₂H₁₁ClN₂O₂, prepared in a synthetic study on spicamycin derivatives, has been determined. In the crystal structure, the mol­ecules lie on mirror planes and form a herring-bone structure.

Key indicators

• Single-crystal X-ray study
• T = 299 K
• Mean [sigma](C-C) = 0.009 Å
• R factor = 0.141
• wR factor = 0.417
• Data-to-parameter ratio = 14.3

checkCIF results

No syntax errors found

ADDSYM reports no extra symmetry


 Alert Level B:



RFACR_01  Alert B The value of the weighted R factor is > 0.35
          Weighted R factor given   0.417

Author response: Please see the _publ_section_exptl_refinement section.

 Alert Level C:



RFACG_01  Alert C The value of the R factor is > 0.10
          R factor given   0.141


 0 Alert Level A = Potentially serious problem

 1 Alert Level B = Potential problem

 1 Alert Level C = Please check

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Computing details

Data collection: WinAFC Diffractometer Control Software (Rigaku, 1999); cell refinement: WinAFC Diffractometer Control Software (Rigaku, 1999); data reduction: TEXSAN (Molecular Structure Corporation, 2001); program(s) used to solve structure: SIR92 (Altomare et al., 1994); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: ORTEPII (Johnson, 1976); software used to prepare material for publication: TEXSAN.

(I)

Crystal data

C12H11ClN2O2	Dx = 1.401 Mg m^−3
Mr = 250.68	Mo Kα radiation, λ = 0.7107 Å
Orthorhombic, Pnma	Cell parameters from 25 reflections
a = 12.311 (2) Å	θ = 12.0–12.5°
b = 6.788 (2) Å	µ = 0.31 mm^−1
c = 14.222 (2) Å	T = 299 K
V = 1188.5 (4) Å^3	Prism, colourless
Z = 4	0.50 × 0.50 × 0.50 mm
F(000) = 520.0

Data collection

Rigaku AFC-7R diffractometer	Rint = 0.024
ω–2θ scans	θmax = 27.5°
Absorption correction: integration (Coppens et al., 1965)	h = −6→15
Tmin = 0.861, Tmax = 0.875	k = −3→8
1660 measured reflections	l = 0→18
1477 independent reflections	3 standard reflections every 150 reflections
1017 reflections with I > 2σ(I)	intensity decay: 3.9%

Refinement

Refinement on F^2	H-atom parameters constrained
R[F^2 > 2σ(F^2)] = 0.141	w = 1/[σ^2(Fo^2) + (0.2P)^2] where P = (Fo^2 + 2Fc^2)/3
wR(F^2) = 0.417	(Δ/σ)max < 0.001
S = 1.79	Δρmax = 0.43 e Å^−3
1477 reflections	Δρmin = −1.06 e Å^−3
103 parameters

Special details

Refinement. X-ray intensity data were measured for +h, +k, +l (θ < 27.5°). Additionally, the intensity data of +h, -k, +l; -h, -k, +l; and -h, +k, +l were measured (θ < 11°). However, the crystal specimen moved a little before completing the data collection, and the reorientation procedure for the setting parameters failed unfortunately by a shutter error. The observed intensities of almost all the +h, -k, +l reflections were apparently smaller than the equivalent reflections. Therefore, the +h, -k, +l reflections were omitted from the analysis. All the independent reflections were used in the refinement. The weighted R-factor (wR) and goodness of fit (S) are based on F². R-factor (gt) are based on F. The threshold expression of F² 2.0 σ(F²) is used only for calculating R-factor (gt).

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

	x	y	z	Uiso*/Ueq
Cl1	0.4717 (2)	0.2500	0.9021 (1)	0.127 (1)
O2	0.5141 (3)	0.2500	0.5594 (3)	0.075 (1)
O3	0.2294 (5)	0.2500	0.1856 (4)	0.115 (2)
N4	0.4988 (4)	0.2500	0.7204 (3)	0.071 (1)
N5	0.6569 (4)	0.2500	0.8166 (4)	0.081 (1)
C6	0.5531 (4)	0.2500	0.8012 (4)	0.076 (2)
C7	0.7173 (5)	0.2500	0.7386 (4)	0.080 (2)
C8	0.6717 (5)	0.2500	0.6499 (4)	0.076 (1)
C9	0.5605 (4)	0.2500	0.6453 (3)	0.064 (1)
C10	0.3984 (5)	0.2500	0.5571 (4)	0.077 (2)
C11	0.3607 (4)	0.2500	0.4552 (4)	0.066 (1)
C12	0.4306 (5)	0.2500	0.3788 (4)	0.072 (1)
C13	0.3895 (5)	0.2500	0.2868 (4)	0.074 (1)
C14	0.2801 (6)	0.2500	0.2722 (4)	0.080 (2)
C15	0.2087 (6)	0.2500	0.3488 (5)	0.087 (2)
C16	0.2504 (5)	0.2500	0.4400 (4)	0.080 (2)
C17	0.2978 (10)	0.2500	0.1051 (5)	0.121 (3)
H7	0.7942	0.2500	0.7444	0.0959*
H8	0.7153	0.2500	0.5948	0.0912*
H10A	0.3717	0.1357	0.5880	0.0917*
H12	0.5069	0.2500	0.3888	0.0858*
H13	0.4378	0.2500	0.2348	0.0882*
H15	0.1324	0.2500	0.3388	0.1042*
H16	0.2021	0.2500	0.4920	0.0965*
H17A	0.3424	0.1357	0.1058	0.1453*
H17B	0.2545	0.2500	0.0498	0.1453*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
Cl1	0.074 (1)	0.259 (3)	0.049 (1)	0.0000	0.0030 (6)	0.0000
O2	0.066 (2)	0.106 (3)	0.054 (2)	0.0000	−0.004 (2)	0.0000
O3	0.112 (4)	0.174 (6)	0.059 (3)	0.0000	−0.027 (3)	0.0000
N4	0.066 (2)	0.096 (3)	0.052 (2)	0.0000	0.000 (2)	0.0000
N5	0.069 (2)	0.117 (4)	0.056 (3)	0.0000	−0.007 (2)	0.0000
C6	0.061 (3)	0.114 (4)	0.052 (3)	0.0000	−0.001 (2)	0.0000
C7	0.060 (3)	0.120 (5)	0.059 (3)	0.0000	−0.004 (2)	0.0000
C8	0.064 (3)	0.103 (4)	0.061 (3)	0.0000	0.003 (2)	0.0000
C9	0.070 (3)	0.077 (3)	0.045 (2)	0.0000	−0.006 (2)	0.0000
C10	0.062 (3)	0.109 (4)	0.059 (3)	0.0000	−0.007 (2)	0.0000
C11	0.070 (3)	0.075 (3)	0.052 (3)	0.0000	−0.002 (2)	0.0000
C12	0.078 (3)	0.081 (3)	0.055 (3)	0.0000	−0.005 (2)	0.0000
C13	0.083 (4)	0.082 (3)	0.056 (3)	0.0000	0.005 (2)	0.0000
C14	0.085 (4)	0.101 (4)	0.055 (3)	0.0000	−0.013 (3)	0.0000
C15	0.071 (3)	0.120 (5)	0.069 (4)	0.0000	−0.011 (3)	0.0000
C16	0.071 (3)	0.114 (5)	0.056 (3)	0.0000	−0.006 (3)	0.0000
C17	0.158 (9)	0.158 (7)	0.047 (4)	0.0000	−0.022 (4)	0.0000

Geometric parameters (Å, º)

Cl1—C6	1.751 (6)	C10—H10A^i	0.950
O2—C9	1.349 (6)	C11—C12	1.386 (8)
O2—C10	1.426 (7)	C11—C16	1.375 (8)
O3—C14	1.381 (8)	C12—C13	1.403 (8)
O3—C17	1.42 (1)	C12—H12	0.950
N4—C6	1.330 (7)	C13—C14	1.362 (9)
N4—C9	1.310 (6)	C13—H13	0.950
N5—C6	1.296 (8)	C14—C15	1.400 (9)
N5—C7	1.336 (8)	C15—C16	1.394 (9)
C7—C8	1.381 (8)	C15—H15	0.949
C7—H7	0.950	C16—H16	0.950
C8—C9	1.370 (8)	C17—H17A	0.950
C8—H8	0.950	C17—H17A^i	0.950
C10—C11	1.522 (8)	C17—H17B	0.950
C10—H10A	0.950
C9—O2—C10	116.4 (4)	C10—C11—C16	116.8 (5)
C14—O3—C17	116.8 (7)	C12—C11—C16	119.3 (5)
C6—N4—C9	114.4 (5)	C11—C12—C13	120.5 (6)
C6—N5—C7	114.1 (5)	C11—C12—H12	119.8
Cl1—C6—N4	114.9 (4)	C13—C12—H12	119.8
Cl1—C6—N5	115.2 (4)	C12—C13—C14	119.9 (5)
N4—C6—N5	129.9 (5)	C12—C13—H13	120.0
N5—C7—C8	122.2 (5)	C14—C13—H13	120.1
N5—C7—H7	118.9	O3—C14—C13	125.6 (6)
C8—C7—H7	118.9	O3—C14—C15	114.2 (6)
C7—C8—C9	116.7 (5)	C13—C14—C15	120.2 (6)
C7—C8—H8	121.6	C14—C15—C16	119.5 (6)
C9—C8—H8	121.7	C14—C15—H15	120.3
O2—C9—N4	119.5 (5)	C16—C15—H15	120.3
O2—C9—C8	117.8 (5)	C11—C16—C15	120.7 (6)
N4—C9—C8	122.7 (5)	C11—C16—H16	119.7
O2—C10—C11	109.1 (5)	C15—C16—H16	119.6
O2—C10—H10A	109.5	O3—C17—H17A	109.5
O2—C10—H10A^i	109.5	O3—C17—H17A^i	109.5
C11—C10—H10A	109.6	O3—C17—H17B	109.5
C11—C10—H10A^i	109.6	H17A—C17—H17A^i	109.4
H10A—C10—H10A^i	109.4	H17A—C17—H17B	109.5
C10—C11—C12	123.9 (5)	H17A^i—C17—H17B	109.5

Symmetry code: (i) x, −y+1/2, z.