Crystal structure of (2-benzyloxypyrimidin-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 molecules are linked via pairs of O—H⋯O interactions, 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 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).

The molecular structure of 1 shows that the 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.

S2. Crystallization
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).

S3. Refinement
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). Labelling of atoms and estimation of their atomic thermal motion as Anisotropic Displacement Parameters (ADPs, 50% probability level) for 1.

Figure 2
The molecular chains in 1. Hydrogen bonds are shown as red, dashed lines. Aromatic and aliphatic hydrogen atoms are omitted for clarity.
(2-Benzyloxypyrimidin-5-yl)boronic acid Refinement. Refinement of F 2 against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F 2 , conventional R-factors R are based on F, with F set to zero for negative F 2 . The threshold expression of F 2 > σ(F 2 ) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F 2 are statistically about twice as large as those based on F, and R-factors based on all data will be even larger.