organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

Journal logoCRYSTALLOGRAPHIC
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ISSN: 2056-9890
Volume 70| Part 12| December 2014| Pages o1259-o1260

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

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[Durka, K., Jarzembska, K. N., Kamiński, R., Luliński, S., Serwatowski, J. & Woźniak, K. (2012). Cryst. Growth Des. 12, 3720-3734.], 2014[Durka, K., Luliński, S., Jarzembska, K. N., Smętek, J., Serwatowski, J. & Woźniak, K. (2014). Acta Cryst. B70, 157-171.]). 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).

1. Related literature

For general background to the structures of boronic acids, see, for example: Hall (2011[Hall, D. G. (2011). Boronic Acids, pp. 3-8. Weinheim: Wiley-VCH.]); Luliński et al. (2007[Luliński, S., Madura, I., Serwatowski, J., Szatyłowicz, H. & Zachara, J. (2007). New J. Chem. 31, 144-15.]); Maly et al. (2006[Maly, K. E., Maris, T. & Wuest, J. D. (2006). CrystEngComm, 8, 33-35.]); Shimpi et al. (2007[Shimpi, M. R., SeethaLekshmi, N. & Pedireddi, V. R. (2007). Cryst. Growth Des. 7, 1958-1963.]). For the characterization of related pyrymidylboronic acids, see: Clapham et al. (2007[Clapham, K. M., Smith, A. E., Batsanov, A. S., McIntyre, L., Pountney, A., Bryce, M. R. & Tarbit, B. (2007). Eur. J. Org. Chem. pp. 5712-5716.]); Liao et al. (1964[Liao, T. K., Podrebarac, E. G. & Cheng, C. C. (1964). J. Am. Chem. Soc. 86, 1869-1870.]); Peters et al. (1990[Peters, D., Hörnfeldt, A. B. & Gronowitz, S. (1990). J. Heterocycl. Chem. 27, 2165-2173.]); Saygili et al. (2004[Saygili, N., Batsanov, A. S. & Bryce, M. R. (2004). Org. Biomol. Chem. 2, 852-857.]).

[Scheme 1]

2. Experimental

2.1. Crystal data

  • C11H11BN2O3

  • Mr = 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[Agilent (2013). CrysAlis PRO. Agilent Technologies, Santa Clara, USA.]) Tmin = 0.993, Tmax = 1.000

  • 18472 measured reflections

  • 4167 independent reflections

  • 2975 reflections with I > 2σ(I)

  • Rint = 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

  • Δρmax = 0.57 e Å−3

  • Δρmin = −0.30 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA 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[Agilent (2013). CrysAlis PRO. Agilent Technologies, Santa Clara, USA.]); cell refinement: CrysAlis PRO; data reduction: CrysAlis PRO; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXL2013 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); molecular graphics: DIAMOND (Brandenburg, 2005[Brandenburg, K. (2005). DIAMOND. Crystal Impact GbR, Bonn, Germany.]); software used to prepare material for publication: publCIF (Westrip, 2010[Westrip, S. P. (2010). J. Appl. Cryst. 43, 920-925.]).

Supporting information


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 2nd 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 Uiso(phenyl H)=1.2Ueq(C), and Uiso(methyl H) = 1.5Ueq(C). The positions of OH hydrogen atoms were refined with Uiso(hy­droxy H) = 1.5Ueq(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
C11H11BN2O3F(000) = 480
Mr = 230.03Dx = 1.485 Mg m3
Monoclinic, P21/nMo Kα radiation, λ = 0.71073 Å
a = 5.498 (1) ÅCell parameters from 4979 reflections
b = 30.4320 (17) Åθ = 2.0–34.4°
c = 6.7086 (19) ŵ = 0.11 mm1
β = 113.54 (4)°T = 100 K
V = 1029.0 (4) Å3Unspecified, colourless
Z = 40.20 × 0.15 × 0.15 mm
Data collection top
Kuma KM-4 CCD
diffractometer
4167 independent reflections
Radiation source: fine-focus sealed tube2975 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.044
ω scanθmax = 34.5°, θmin = 2.7°
Absorption correction: multi-scan
(CrysAlis PRO; Agilent, 2013)
h = 88
Tmin = 0.993, Tmax = 1.000k = 4847
18472 measured reflectionsl = 1010
Refinement top
Refinement on F20 restraints
Least-squares matrix: fullHydrogen site location: mixed
R[F2 > 2σ(F2)] = 0.053H 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 reflectionsΔρmax = 0.57 e Å3
160 parametersΔρmin = 0.30 e Å3
Crystal data top
C11H11BN2O3V = 1029.0 (4) Å3
Mr = 230.03Z = 4
Monoclinic, P21/nMo Kα radiation
a = 5.498 (1) ŵ = 0.11 mm1
b = 30.4320 (17) ÅT = 100 K
c = 6.7086 (19) Å0.20 × 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)
Tmin = 0.993, Tmax = 1.000Rint = 0.044
18472 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0530 restraints
wR(F2) = 0.135H atoms treated by a mixture of independent and constrained refinement
S = 1.03Δρmax = 0.57 e Å3
4167 reflectionsΔρmin = 0.30 e Å3
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
xyzUiso*/Ueq
C10.7668 (2)0.09979 (4)0.33931 (19)0.0119 (2)
C20.4044 (2)0.05846 (4)0.16000 (19)0.0129 (2)
H20.25410.04260.15700.016*
C30.4464 (2)0.06065 (4)0.03164 (19)0.0120 (2)
C40.6720 (2)0.08390 (4)0.01318 (19)0.0135 (2)
H40.71430.08560.13710.016*
C51.1273 (2)0.14700 (4)0.5176 (2)0.0144 (2)
H5A1.05150.16940.40230.017*
H5B1.25160.12860.48030.017*
C61.2746 (2)0.16928 (4)0.73226 (19)0.0119 (2)
C71.1923 (2)0.16861 (4)0.9030 (2)0.0152 (2)
H71.04050.15210.89080.018*
C81.3326 (3)0.19224 (4)1.0918 (2)0.0178 (2)
H81.27570.19161.20810.021*
C91.5544 (3)0.21671 (4)1.1128 (2)0.0170 (2)
H91.64660.23331.24100.020*
C101.6401 (3)0.21665 (4)0.9434 (2)0.0161 (2)
H101.79330.23290.95670.019*
C111.5022 (2)0.19294 (4)0.7556 (2)0.0143 (2)
H111.56300.19280.64150.017*
B10.2490 (3)0.03690 (4)0.2435 (2)0.0129 (2)
N10.5624 (2)0.07726 (3)0.34800 (16)0.0133 (2)
N20.8334 (2)0.10406 (4)0.16971 (17)0.0137 (2)
O10.28595 (18)0.03484 (3)0.43207 (14)0.01608 (19)
O20.03654 (19)0.01745 (3)0.22897 (15)0.0177 (2)
O30.91719 (17)0.11992 (3)0.52723 (14)0.01468 (18)
H1A0.416 (3)0.0477 (6)0.445 (3)0.022*
H2A0.068 (3)0.0034 (6)0.340 (3)0.022*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
C10.0114 (5)0.0120 (5)0.0124 (5)0.0016 (4)0.0048 (4)0.0011 (4)
C20.0135 (5)0.0138 (5)0.0122 (5)0.0028 (4)0.0059 (4)0.0002 (4)
C30.0129 (5)0.0125 (5)0.0112 (5)0.0013 (4)0.0054 (4)0.0001 (4)
C40.0150 (5)0.0157 (5)0.0119 (5)0.0016 (4)0.0074 (4)0.0008 (4)
C50.0134 (5)0.0163 (5)0.0144 (5)0.0052 (4)0.0066 (4)0.0024 (4)
C60.0112 (5)0.0111 (5)0.0128 (5)0.0006 (4)0.0039 (4)0.0003 (4)
C70.0145 (5)0.0163 (5)0.0159 (5)0.0030 (4)0.0073 (5)0.0007 (4)
C80.0201 (6)0.0202 (6)0.0149 (5)0.0038 (5)0.0088 (5)0.0018 (5)
C90.0167 (6)0.0169 (6)0.0152 (5)0.0021 (4)0.0040 (5)0.0029 (4)
C100.0121 (5)0.0165 (6)0.0183 (6)0.0027 (4)0.0046 (5)0.0012 (4)
C110.0136 (5)0.0149 (5)0.0153 (5)0.0008 (4)0.0067 (4)0.0002 (4)
B10.0134 (6)0.0125 (6)0.0133 (6)0.0003 (4)0.0060 (5)0.0019 (5)
N10.0130 (5)0.0154 (5)0.0119 (4)0.0033 (4)0.0054 (4)0.0013 (4)
N20.0141 (5)0.0157 (5)0.0125 (4)0.0035 (4)0.0064 (4)0.0016 (4)
O10.0171 (4)0.0204 (4)0.0126 (4)0.0069 (3)0.0079 (3)0.0029 (3)
O20.0179 (4)0.0240 (5)0.0124 (4)0.0093 (4)0.0071 (3)0.0041 (4)
O30.0148 (4)0.0175 (4)0.0121 (4)0.0069 (3)0.0057 (3)0.0036 (3)
Geometric parameters (Å, º) top
C1—N21.3336 (15)C6—C111.3972 (16)
C1—N11.3375 (15)C7—C81.3912 (18)
C1—O31.3474 (15)C7—H70.9500
C2—N11.3407 (16)C8—C91.3870 (18)
C2—C31.3957 (17)C8—H80.9500
C2—H20.9500C9—C101.3933 (19)
C3—C41.3898 (16)C9—H90.9500
C3—B11.5775 (19)C10—C111.3856 (18)
C4—N21.3415 (16)C10—H100.9500
C4—H40.9500C11—H110.9500
C5—O31.4412 (14)B1—O21.3475 (16)
C5—C61.5028 (18)B1—O11.3602 (16)
C5—H5A0.9900O1—H1A0.849 (18)
C5—H5B0.9900O2—H2A0.852 (19)
C6—C71.3898 (17)
N2—C1—N1127.51 (11)C6—C7—H7120.1
N2—C1—O3118.63 (10)C8—C7—H7120.1
N1—C1—O3113.86 (10)C9—C8—C7121.03 (12)
N1—C2—C3124.24 (11)C9—C8—H8119.5
N1—C2—H2117.9C7—C8—H8119.5
C3—C2—H2117.9C8—C9—C10119.09 (12)
C4—C3—C2114.36 (11)C8—C9—H9120.5
C4—C3—B1125.58 (11)C10—C9—H9120.5
C2—C3—B1120.05 (10)C11—C10—C9120.12 (12)
N2—C4—C3123.72 (11)C11—C10—H10119.9
N2—C4—H4118.1C9—C10—H10119.9
C3—C4—H4118.1C10—C11—C6120.71 (12)
O3—C5—C6110.46 (10)C10—C11—H11119.6
O3—C5—H5A109.6C6—C11—H11119.6
C6—C5—H5A109.6O2—B1—O1120.19 (12)
O3—C5—H5B109.6O2—B1—C3116.12 (11)
C6—C5—H5B109.6O1—B1—C3123.67 (11)
H5A—C5—H5B108.1C1—N1—C2114.70 (10)
C7—C6—C11119.14 (11)C1—N2—C4115.40 (10)
C7—C6—C5123.72 (11)B1—O1—H1A121.3 (12)
C11—C6—C5117.11 (11)B1—O2—H2A117.4 (12)
C6—C7—C8119.86 (11)C1—O3—C5114.90 (9)
N1—C2—C3—C40.78 (18)C4—C3—B1—O2177.72 (12)
N1—C2—C3—B1179.43 (11)C2—C3—B1—O23.78 (17)
C2—C3—C4—N22.18 (18)C4—C3—B1—O13.3 (2)
B1—C3—C4—N2179.25 (12)C2—C3—B1—O1175.21 (12)
O3—C5—C6—C78.77 (17)N2—C1—N1—C22.59 (19)
O3—C5—C6—C11173.27 (10)O3—C1—N1—C2177.44 (10)
C11—C6—C7—C81.58 (19)C3—C2—N1—C11.38 (18)
C5—C6—C7—C8176.34 (12)N1—C1—N2—C41.33 (19)
C6—C7—C8—C90.2 (2)O3—C1—N2—C4178.69 (11)
C7—C8—C9—C101.5 (2)C3—C4—N2—C11.25 (18)
C8—C9—C10—C110.98 (19)N2—C1—O3—C54.30 (16)
C9—C10—C11—C60.78 (19)N1—C1—O3—C5175.72 (10)
C7—C6—C11—C102.06 (18)C6—C5—O3—C1177.64 (10)
C5—C6—C11—C10176.00 (11)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C2—H2···O2i0.952.603.5104 (15)161
O2—H2A···O1ii0.852 (19)1.915 (19)2.7615 (16)172.7 (17)
O1—H1A···N1iii0.849 (18)2.067 (18)2.8188 (15)147.2 (16)
Symmetry codes: (i) x, y, z; (ii) x, y, z1; (iii) x, y, z1.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C2—H2···O2i0.952.603.5104 (15)161.4
O2—H2A···O1ii0.852 (19)1.915 (19)2.7615 (16)172.7 (17)
O1—H1A···N1iii0.849 (18)2.067 (18)2.8188 (15)147.2 (16)
Symmetry codes: (i) x, y, z; (ii) x, y, z1; (iii) x, y, z1.
 

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.

References

First citationAgilent (2013). CrysAlis PRO. Agilent Technologies, Santa Clara, USA.  Google Scholar
First citationBrandenburg, K. (2005). DIAMOND. Crystal Impact GbR, Bonn, Germany.  Google Scholar
First citationClapham, K. M., Smith, A. E., Batsanov, A. S., McIntyre, L., Pountney, A., Bryce, M. R. & Tarbit, B. (2007). Eur. J. Org. Chem. pp. 5712–5716.  Web of Science CSD CrossRef Google Scholar
First citationDurka, K., Jarzembska, K. N., Kamiński, R., Luliński, S., Serwatowski, J. & Woźniak, K. (2012). Cryst. Growth Des. 12, 3720–3734.  Web of Science CSD CrossRef CAS Google Scholar
First citationDurka, K., Luliński, S., Jarzembska, K. N., Smętek, J., Serwatowski, J. & Woźniak, K. (2014). Acta Cryst. B70, 157–171.  Web of Science CSD CrossRef IUCr Journals Google Scholar
First citationHall, D. G. (2011). Boronic Acids, pp. 3–8. Weinheim: Wiley-VCH.  Google Scholar
First citationLiao, T. K., Podrebarac, E. G. & Cheng, C. C. (1964). J. Am. Chem. Soc. 86, 1869–1870.  CrossRef CAS Web of Science Google Scholar
First citationLuliński, S., Madura, I., Serwatowski, J., Szatyłowicz, H. & Zachara, J. (2007). New J. Chem. 31, 144–15.  Google Scholar
First citationMaly, K. E., Maris, T. & Wuest, J. D. (2006). CrystEngComm, 8, 33–35.  CAS Google Scholar
First citationPeters, D., Hörnfeldt, A. B. & Gronowitz, S. (1990). J. Heterocycl. Chem. 27, 2165–2173.  CrossRef CAS Google Scholar
First citationSaygili, N., Batsanov, A. S. & Bryce, M. R. (2004). Org. Biomol. Chem. 2, 852–857.  Web of Science CSD CrossRef PubMed CAS Google Scholar
First citationSheldrick, G. M. (2008). Acta Cryst. A64, 112–122.  Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationShimpi, M. R., SeethaLekshmi, N. & Pedireddi, V. R. (2007). Cryst. Growth Des. 7, 1958–1963.  Web of Science CSD CrossRef CAS Google Scholar
First citationWestrip, S. P. (2010). J. Appl. Cryst. 43, 920–925.  Web of Science CrossRef CAS IUCr Journals Google Scholar

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ISSN: 2056-9890
Volume 70| Part 12| December 2014| Pages o1259-o1260
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