Crystal structure of (2-benzyl­oxy­pyrimidin-5-yl)boronic acid

Durka, K.; Kliś, T.; Serwatowski, J.

doi:10.1107/S1600536814024519

organic compounds

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Volume 70| Part 12| December 2014| Pages o1259-o1260

doi:10.1107/S1600536814024519

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Crystal structure of (2-benzyloxypyrimidin-5-yl)boronic acid

Krzysztof Durka,^a ^* Tomasz Kliś ^a and Janusz Serwatowski ^a

^aPhysical Chemistry Department, Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland
^*Correspondence e-mail: kdurka@ch.pw.edu.pl

Edited by M. Zeller, Youngstown State University, USA (Received 24 October 2014; accepted 7 November 2014; online 15 November 2014)

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 molecules are linked via pairs of O—H⋯O interactions, forming centrosymmetric dimers with an R₂²(8) motif, which have recently been shown to be energetically very favorable (Durka et al., 2012 , 2014 ). The hydroxy groups in an anti conformation are engaged in lateral hydrogen-bonding interactions with N atoms from neighbouring molecules, leading to the formation of chains along [001]. O⋯B [3.136 (2) Å] and C(π)⋯B [3.393 (2) Å] stacking interactions in turn link parallel chains of centrosymmetric dimers into layers parallel to (010).

Keywords: crystal structure; arylboronic acid; hydrogen-bonding interactions.

CCDC reference: 937427

1. 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 ).

2. Experimental

2.1. Crystal data

C₁₁H₁₁BN₂O₃
M_r = 230.03
Monoclinic, P 2₁ /n
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

2.2. 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

2.3. Refinement

R[F² > 2σ(F²)] = 0.053
wR(F²) = 0.135
S = 1.03
4167 reflections
160 parameters
H atoms treated by a mixture of independent and constrained refinement
Δρ_max = 0.57 e Å⁻³
Δρ_min = −0.30 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

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)
Symmetry codes: (i) -x, -y, -z; (ii) -x, -y, -z-1; (iii) x, y, z-1.

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 ).

Supporting information

CCDC reference: 937427

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

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

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

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

checkCIF report

Comment top

Heterocyclic boronic acids have been intensively studied in the recent years. They have found numerous application as Suzuki-Miyaura cross-coupling partners. However, pyrimidylboronic acids have been largely neglected, although some derivatives were synthesized (Clapham et al., 2007; Liao et al., 1964; Peters et al., 1990; Saygili et al., 2004). In this manuscript we focus our attention on a pyrimidine boronic acid derivative containing a benzyloxy group at the 2^nd position.

The molecular structure of 1 shows that the B(OH)₂ group adopts the usual syn-anti conformation. The entire molecule including both aromatic rings and boronic group remains essentially planar (Figure 1). On the first level of material organization, centrosymmetric O—H···O hydrogen-bonded dimers are formed. They are linked via lateral hydrogen-bonding interactions with nitrogen atoms from neighbouring molecules. It results in the formation of molecular chains propagated along the [001] direction (Figure 2). Molecules from adjacent chains interact by weak O···B and C(π)···B stacking interactions, which link parallel oriented chains into 2D layers. These contacts are additionally supported by weak C—H···N interactions between the methylene group and one of the N atoms of the pyrimidyl ring, and also by C—H···O interactions formed between the C(pyrimidyl)—H group and an oxygen atom from the B(OH)₂ group. The supramolecular architecture extends further due to weak C—H···C(π) contacts leading to a three-dimensional network.

Crystallization top

The title compound was received from Aldrich. Crystals suitable for single-crystal X-ray diffraction analysis were grown by cooling a solution of the boronic acid (0.2 g) in acetone (4 ml).

Refinement top

Crystal data, data collection and structure refinement details are summarized in Table 1. All CH (methylene, phenyl) hydrogen atoms were placed in calculated positions with C—H distances of 0.95Å (phenyl) and 0.99Å (methylene). They were included in the refinement in riding-motion approximation with U_iso(phenyl H)=1.2U_eq(C), and U_iso(methyl H) = 1.5U_eq(C). The positions of OH hydrogen atoms were refined with U_iso(hydroxy H) = 1.5U_eq(C).

Related literature top

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).

Computing details top

Data collection: CrysAlis PRO (Agilent, 2013); cell refinement: CrysAlis PRO (Agilent, 2013); data reduction: CrysAlis PRO (Agilent, 2013); 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).

Figures top

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

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

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

(2-Benzyloxypyrimidin-5-yl)boronic acid top

Crystal data top

C₁₁H₁₁BN₂O₃	F(000) = 480
M_r = 230.03	D_x = 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

Data collection top

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

Refinement top

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(F_o²) + (0.0561P)² + 0.4141P] where P = (F_o² + 2F_c²)/3
S = 1.03	(Δ/σ)_max < 0.001
4167 reflections	Δρ_max = 0.57 e Å⁻³
160 parameters	Δρ_min = −0.30 e Å⁻³

Crystal data top

C₁₁H₁₁BN₂O₃	V = 1029.0 (4) Å³
M_r = 230.03	Z = 4
Monoclinic, P2₁/n	Mo Kα radiation
a = 5.498 (1) Å	µ = 0.11 mm⁻¹
b = 30.4320 (17) Å	T = 100 K
c = 6.7086 (19) Å	0.20 × 0.15 × 0.15 mm
β = 113.54 (4)°

Data collection top

Kuma KM-4 CCD diffractometer	4167 independent reflections
Absorption correction: multi-scan (CrysAlis PRO; Agilent, 2013)	2975 reflections with I > 2σ(I)
T_min = 0.993, T_max = 1.000	R_int = 0.044
18472 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.053	0 restraints
wR(F²) = 0.135	H atoms treated by a mixture of independent and constrained refinement
S = 1.03	Δρ_max = 0.57 e Å⁻³
4167 reflections	Δρ_min = −0.30 e Å⁻³
160 parameters

Special details top

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 (Å²) top

	x	y	z	U_iso*/U_eq
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*

Atomic displacement parameters (Å²) top

	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)

Geometric parameters (Å, º) top

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)

Hydrogen-bond geometry (Å, º) top

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)

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

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
C2—H2···O2ⁱ	0.95	2.60	3.5104 (15)	161.4
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)

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

Acknowledgements

The X-ray measurements were undertaken in the Crystallographic Unit of the Physical Chemistry Laboratory at the Chemistry Department of the University of Warsaw. This work was supported by the Aldrich Chemical Co. through donation of chemicals and equipment, and by the Warsaw University of Technology.

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Volume 70| Part 12| December 2014| Pages o1259-o1260

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