Crystal structure of (2-benzyl-oxy-pyrimidin-5-yl)boronic acid.

The boronic acid group in the title compound, C11H11BN2O3, adopts a syn-anti conformation and is almost coplanar with the aromatic rings , making a dihedralangle of 3.8 (2)°. In the crystal, adjacent mol-ecules are linked via pairs of O-H⋯O inter-actions, forming centrosymmetric dimers with an R 2 (2)(8) motif, which have recently been shown to be energetically very favorable (Durka et al., 2012 ▶, 2014 ▶). The hy-droxy groups in an anti conformation are engaged in lateral hydrogen-bonding inter-actions with N atoms from neighbouring mol-ecules, leading to the formation of chains along [001]. O⋯B [3.136 (2) Å] and C(π)⋯B [3.393 (2) Å] stacking inter-actions in turn link parallel chains of centrosymmetric dimers into layers parallel to (010).

Related literature

For general background to the structures of boronic acids, see, for example: Hall (2011 ▶); Luliński et al. (2007 ▶); Maly et al. (2006 ▶); Shimpi et al. (2007 ▶). For the characterization of related pyrymidylboronic acids, see: Clapham et al. (2007 ▶); Liao et al. (1964 ▶); Peters et al. (1990 ▶); Saygili et al. (2004 ▶).

Experimental

Crystal data

C11H11BN2O3

M = 230.03

Monoclinic,

a = 5.498 (1) Å

b = 30.4320 (17) Å

c = 6.7086 (19) Å

β = 113.54 (4)°

V = 1029.0 (4) Å3

Z = 4

Mo Kα radiation

μ = 0.11 mm−1

T = 100 K

0.20 × 0.15 × 0.15 mm

Data collection

Kuma KM-4 CCD diffractometer

Absorption correction: multi-scan (CrysAlis PRO; Agilent, 2013 ▶) T min = 0.993, T max = 1.000

18472 measured reflections

4167 independent reflections

2975 reflections with I > 2σ(I)

R int = 0.044

Refinement

R[F 2 > 2σ(F 2)] = 0.053

wR(F 2) = 0.135

S = 1.03

4167 reflections

160 parameters

H atoms treated by a mixture of independent and constrained refinement

Δρmax = 0.57 e Å−3

Δρmin = −0.30 e Å−3

Data collection: CrysAlis PRO (Agilent, 2013 ▶); cell refinement: CrysAlis PRO; data reduction: CrysAlis PRO; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ▶); program(s) used to refine structure: SHELXL2013 (Sheldrick, 2008 ▶); molecular graphics: DIAMOND (Brandenburg, 2005 ▶); software used to prepare material for publication: publCIF (Westrip, 2010 ▶).

Crystal structure: contains datablock(s) I. DOI: 10.1107/S1600536814024519/zl2604sup1.cif

Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536814024519/zl2604Isup2.hkl

Click here for additional data file.

Supporting information file. DOI: 10.1107/S1600536814024519/zl2604Isup3.mol

Click here for additional data file.

Supporting information file. DOI: 10.1107/S1600536814024519/zl2604Isup4.cml

Click here for additional data file.

1 . DOI: 10.1107/S1600536814024519/zl2604fig1.tif

Labelling of atoms and estimation of their atomic thermal motion as Anisotropic Displacement Parameters (ADPs, 50% probability level) for 1.

Click here for additional data file.

1 . DOI: 10.1107/S1600536814024519/zl2604fig2.tif

The mol­ecular chains in 1. Hydrogen bonds are shown as red, dashed lines. Aromatic and aliphatic hydrogen atoms are omitted for clarity.

Click here for additional data file.

. DOI: 10.1107/S1600536814024519/zl2604fig3.tif

Structural graph displaying the inter­molecular O⋯B, C(π)⋯B (blue), C—H⋯N (orange) and O—H⋯O, O—H⋯N (red) inter­actions.

CCDC reference: 937427

Additional supporting information: crystallographic information; 3D view; checkCIF report

C11H11BN2O3	F(000) = 480
Mr = 230.03	Dx = 1.485 Mg m−3
Monoclinic, P21/n	Mo Kα radiation, λ = 0.71073 Å
a = 5.498 (1) Å	Cell parameters from 4979 reflections
b = 30.4320 (17) Å	θ = 2.0–34.4°
c = 6.7086 (19) Å	µ = 0.11 mm−1
β = 113.54 (4)°	T = 100 K
V = 1029.0 (4) Å3	Unspecified, colourless
Z = 4	0.20 × 0.15 × 0.15 mm

Kuma KM-4 CCD diffractometer	4167 independent reflections
Radiation source: fine-focus sealed tube	2975 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.044
ω scan	θmax = 34.5°, θmin = 2.7°
Absorption correction: multi-scan (CrysAlis PRO; Agilent, 2013)	h = −8→8
Tmin = 0.993, Tmax = 1.000	k = −48→47
18472 measured reflections	l = −10→10

Refinement on F2	0 restraints
Least-squares matrix: full	Hydrogen site location: mixed
R[F2 > 2σ(F2)] = 0.053	H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.135	w = 1/[σ2(Fo2) + (0.0561P)2 + 0.4141P] where P = (Fo2 + 2Fc2)/3
S = 1.03	(Δ/σ)max < 0.001
4167 reflections	Δρmax = 0.57 e Å−3
160 parameters	Δρmin = −0.30 e Å−3

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.

	x	y	z	Uiso*/Ueq
C1	0.7668 (2)	0.09979 (4)	0.33931 (19)	0.0119 (2)
C2	0.4044 (2)	0.05846 (4)	0.16000 (19)	0.0129 (2)
H2	0.2541	0.0426	0.1570	0.016*
C3	0.4464 (2)	0.06065 (4)	−0.03164 (19)	0.0120 (2)
C4	0.6720 (2)	0.08390 (4)	−0.01318 (19)	0.0135 (2)
H4	0.7143	0.0856	−0.1371	0.016*
C5	1.1273 (2)	0.14700 (4)	0.5176 (2)	0.0144 (2)
H5A	1.0515	0.1694	0.4023	0.017*
H5B	1.2516	0.1286	0.4803	0.017*
C6	1.2746 (2)	0.16928 (4)	0.73226 (19)	0.0119 (2)
C7	1.1923 (2)	0.16861 (4)	0.9030 (2)	0.0152 (2)
H7	1.0405	0.1521	0.8908	0.018*
C8	1.3326 (3)	0.19224 (4)	1.0918 (2)	0.0178 (2)
H8	1.2757	0.1916	1.2081	0.021*
C9	1.5544 (3)	0.21671 (4)	1.1128 (2)	0.0170 (2)
H9	1.6466	0.2333	1.2410	0.020*
C10	1.6401 (3)	0.21665 (4)	0.9434 (2)	0.0161 (2)
H10	1.7933	0.2329	0.9567	0.019*
C11	1.5022 (2)	0.19294 (4)	0.7556 (2)	0.0143 (2)
H11	1.5630	0.1928	0.6415	0.017*
B1	0.2490 (3)	0.03690 (4)	−0.2435 (2)	0.0129 (2)
N1	0.5624 (2)	0.07726 (3)	0.34800 (16)	0.0133 (2)
N2	0.8334 (2)	0.10406 (4)	0.16971 (17)	0.0137 (2)
O1	0.28595 (18)	0.03484 (3)	−0.43207 (14)	0.01608 (19)
O2	0.03654 (19)	0.01745 (3)	−0.22897 (15)	0.0177 (2)
O3	0.91719 (17)	0.11992 (3)	0.52723 (14)	0.01468 (18)
H1A	0.416 (3)	0.0477 (6)	−0.445 (3)	0.022*
H2A	−0.068 (3)	0.0034 (6)	−0.340 (3)	0.022*

	U11	U22	U33	U12	U13	U23
C1	0.0114 (5)	0.0120 (5)	0.0124 (5)	−0.0016 (4)	0.0048 (4)	−0.0011 (4)
C2	0.0135 (5)	0.0138 (5)	0.0122 (5)	−0.0028 (4)	0.0059 (4)	−0.0002 (4)
C3	0.0129 (5)	0.0125 (5)	0.0112 (5)	−0.0013 (4)	0.0054 (4)	−0.0001 (4)
C4	0.0150 (5)	0.0157 (5)	0.0119 (5)	−0.0016 (4)	0.0074 (4)	−0.0008 (4)
C5	0.0134 (5)	0.0163 (5)	0.0144 (5)	−0.0052 (4)	0.0066 (4)	−0.0024 (4)
C6	0.0112 (5)	0.0111 (5)	0.0128 (5)	−0.0006 (4)	0.0039 (4)	−0.0003 (4)
C7	0.0145 (5)	0.0163 (5)	0.0159 (5)	−0.0030 (4)	0.0073 (5)	−0.0007 (4)
C8	0.0201 (6)	0.0202 (6)	0.0149 (5)	−0.0038 (5)	0.0088 (5)	−0.0018 (5)
C9	0.0167 (6)	0.0169 (6)	0.0152 (5)	−0.0021 (4)	0.0040 (5)	−0.0029 (4)
C10	0.0121 (5)	0.0165 (6)	0.0183 (6)	−0.0027 (4)	0.0046 (5)	−0.0012 (4)
C11	0.0136 (5)	0.0149 (5)	0.0153 (5)	−0.0008 (4)	0.0067 (4)	0.0002 (4)
B1	0.0134 (6)	0.0125 (6)	0.0133 (6)	0.0003 (4)	0.0060 (5)	0.0019 (5)
N1	0.0130 (5)	0.0154 (5)	0.0119 (4)	−0.0033 (4)	0.0054 (4)	−0.0013 (4)
N2	0.0141 (5)	0.0157 (5)	0.0125 (4)	−0.0035 (4)	0.0064 (4)	−0.0016 (4)
O1	0.0171 (4)	0.0204 (4)	0.0126 (4)	−0.0069 (3)	0.0079 (3)	−0.0029 (3)
O2	0.0179 (4)	0.0240 (5)	0.0124 (4)	−0.0093 (4)	0.0071 (3)	−0.0041 (4)
O3	0.0148 (4)	0.0175 (4)	0.0121 (4)	−0.0069 (3)	0.0057 (3)	−0.0036 (3)

C1—N2	1.3336 (15)	C6—C11	1.3972 (16)
C1—N1	1.3375 (15)	C7—C8	1.3912 (18)
C1—O3	1.3474 (15)	C7—H7	0.9500
C2—N1	1.3407 (16)	C8—C9	1.3870 (18)
C2—C3	1.3957 (17)	C8—H8	0.9500
C2—H2	0.9500	C9—C10	1.3933 (19)
C3—C4	1.3898 (16)	C9—H9	0.9500
C3—B1	1.5775 (19)	C10—C11	1.3856 (18)
C4—N2	1.3415 (16)	C10—H10	0.9500
C4—H4	0.9500	C11—H11	0.9500
C5—O3	1.4412 (14)	B1—O2	1.3475 (16)
C5—C6	1.5028 (18)	B1—O1	1.3602 (16)
C5—H5A	0.9900	O1—H1A	0.849 (18)
C5—H5B	0.9900	O2—H2A	0.852 (19)
C6—C7	1.3898 (17)
N2—C1—N1	127.51 (11)	C6—C7—H7	120.1
N2—C1—O3	118.63 (10)	C8—C7—H7	120.1
N1—C1—O3	113.86 (10)	C9—C8—C7	121.03 (12)
N1—C2—C3	124.24 (11)	C9—C8—H8	119.5
N1—C2—H2	117.9	C7—C8—H8	119.5
C3—C2—H2	117.9	C8—C9—C10	119.09 (12)
C4—C3—C2	114.36 (11)	C8—C9—H9	120.5
C4—C3—B1	125.58 (11)	C10—C9—H9	120.5
C2—C3—B1	120.05 (10)	C11—C10—C9	120.12 (12)
N2—C4—C3	123.72 (11)	C11—C10—H10	119.9
N2—C4—H4	118.1	C9—C10—H10	119.9
C3—C4—H4	118.1	C10—C11—C6	120.71 (12)
O3—C5—C6	110.46 (10)	C10—C11—H11	119.6
O3—C5—H5A	109.6	C6—C11—H11	119.6
C6—C5—H5A	109.6	O2—B1—O1	120.19 (12)
O3—C5—H5B	109.6	O2—B1—C3	116.12 (11)
C6—C5—H5B	109.6	O1—B1—C3	123.67 (11)
H5A—C5—H5B	108.1	C1—N1—C2	114.70 (10)
C7—C6—C11	119.14 (11)	C1—N2—C4	115.40 (10)
C7—C6—C5	123.72 (11)	B1—O1—H1A	121.3 (12)
C11—C6—C5	117.11 (11)	B1—O2—H2A	117.4 (12)
C6—C7—C8	119.86 (11)	C1—O3—C5	114.90 (9)
N1—C2—C3—C4	0.78 (18)	C4—C3—B1—O2	−177.72 (12)
N1—C2—C3—B1	179.43 (11)	C2—C3—B1—O2	3.78 (17)
C2—C3—C4—N2	−2.18 (18)	C4—C3—B1—O1	3.3 (2)
B1—C3—C4—N2	179.25 (12)	C2—C3—B1—O1	−175.21 (12)
O3—C5—C6—C7	−8.77 (17)	N2—C1—N1—C2	−2.59 (19)
O3—C5—C6—C11	173.27 (10)	O3—C1—N1—C2	177.44 (10)
C11—C6—C7—C8	1.58 (19)	C3—C2—N1—C1	1.38 (18)
C5—C6—C7—C8	−176.34 (12)	N1—C1—N2—C4	1.33 (19)
C6—C7—C8—C9	0.2 (2)	O3—C1—N2—C4	−178.69 (11)
C7—C8—C9—C10	−1.5 (2)	C3—C4—N2—C1	1.25 (18)
C8—C9—C10—C11	0.98 (19)	N2—C1—O3—C5	4.30 (16)
C9—C10—C11—C6	0.78 (19)	N1—C1—O3—C5	−175.72 (10)
C7—C6—C11—C10	−2.06 (18)	C6—C5—O3—C1	177.64 (10)
C5—C6—C11—C10	176.00 (11)

D—H···A	D—H	H···A	D···A	D—H···A
C2—H2···O2i	0.95	2.60	3.5104 (15)	161
O2—H2A···O1ii	0.852 (19)	1.915 (19)	2.7615 (16)	172.7 (17)
O1—H1A···N1iii	0.849 (18)	2.067 (18)	2.8188 (15)	147.2 (16)

Table 1

Hydrogen-bond geometry (, )

DHA	DH	HA	D A	DHA
C2H2O2i	0.95	2.60	3.5104(15)	161
O2H2AO1ii	0.852(19)	1.915(19)	2.7615(16)	172.7(17)
O1H1AN1iii	0.849(18)	2.067(18)	2.8188(15)	147.2(16)

Symmetry codes: (i) ; (ii) ; (iii) .