Crystal structure of aqua-2-(3-aminophenyl)-1,3,2-dioxaborole dihydrate, C12H12BNO3 · 2H2O

Abstract

Source of materialFor the preparation of the compound, as olution of 3-aminophenylboronic acid monohydrate (0.250 g, 1.61 mmol) and catechol (0.177 g, 1.61 mmol) in 20 mL of asolvent mixture of methanol and benzene (1:4) was refluxed for 1hinthe presence of aD ean-Stark trap. Ap recipitate formed upon cooling was recrystallized from as olvent mixture of methanol, dichloromethane and water to give crystals suitable for X-ray diffraction analysis (m.p. 448 K). Experimental detailsHatoms were positioned geometrically and constrained using the riding-model approximationw ith d(C-H aryl )=0 .93 Å and U iso (H aryl )=1 .2 U eq (C). Hydrogen atoms bonded to O( H3, H31A, H31B, H31C, H32A, H32B and H32C) and N(H1A, H1B and H1C) were located in difference Fourier maps. One of the two hydrogen atoms in each water molecule is disordered over two positions with an occupancy factor of 0.50 (H31B and H31C for O31; H32B and H32C for O32). The disorder arises from the presence of crystallographic inversion centers in the O31···O31 and O32···O32 H-bonds. As aconsequence disorder is observed also in the O31···O32 hydrogen bonds. This is the only remaining site for disorder, since the remaining coordination sites in each water molecule are already involved in hydrogen-bonds with an occupancy of 1.0 (for O31: O3-H···O31 and O31-H···p;for O32: N1-H···O32 and O32-H···O1). The coordinates of the O-Hand N-Hh ydrogen atoms were refined with restraints: DiscussionDuring the past few years al arge series of substituted phenylboronic acid derivatives have been prepared, mainly for applications in organic synthesis [1,2] and for molecular recognition of biochemically active molecules [3]. More recently, such boronic acid derivatives have attracted attention also as building blocks for the self-assembly of macrocyclic and polymeric assemblies. For this purpose, the boronic acid is generally converted to an ester (boronate) via condensation with an aliphatic or aromatic diol, which is then assembled to amacromolecular structure via reaction of the additional functional group attached to the B-phenyl ring [4][5][6]. In this context, 3-aminophenylboronic acid has been employed for the generation of macrocycles and cages [7][8][9][10][11]. In contrast to the analogous ester derived from pinacol [12], in this case the water adduct has been obtained, which has converted to the corresponding zwitterion and crystallized as dihydrate. A search of the Cambridge Structural Database (CSD, version 5.31) [13], revealed that there is no entry so far for an aqua complex of a boronic acid ester. Until now, solid-state structures of aqua-boron complexes have been reported only for triphenylborane derivatives, in particular for tris(pentafluorophenyl)borane [14,15]. The asymmetric unit of the aqua-catecholboronate contains one aqua-boronate and two uncoordinated water molecules (figure, top). Upon coordination to the boron atom the coordinated water molecule is deprotonated to form the corresponding zwitterion.

Analysis of the relative stability of trigonal and tetrahedral boronate cyclic esters in terms of boronic acid and diol acidities and the strain release effect

“…Available structural data show that for 1,2‐diols, the O–B–O angles in trigonal esters are around 113°, [ 13–16 ] sufficiently small to create a considerable strain and for 1,3‐diols these angles are about 123°, [ 13–15 ] quite close to the normal sp 2 angle. The results for tetrahedral hydroxyboronates are limited by catechol esters [ 17–19 ] with O–B–O angles about 102°, whereas in the trigonal catechol ester of PBA, the O–B–O angle is 109.8°. [ 20 ] Thus, the reduced O–B–O angle in the trigonal ester is not conserved in the tetrahedral ester but is further decreasing much below the tetrahedral angle.…”

A Tetrahedral Boronic Acid Diester Formed by an Unnatural Amino Acid in the Ligand Pocket of an Engineered Lipocalin

“…D) Fluorescence titration of the Borocalin (36Bpa‐NFW: •, K D =4.8±0.04μ m ) with 4‐nitrocatechol in comparison with the Asn134→Ala mutant (36Bpa‐AFW: ○, K D =29.3±0.7μ m ). E) Structural comparison between the unbound Bpa in the apo‐Borocalin (left), the Bpa/4‐nitrocatechol diester in the Borocalin ligand pocket (middle), and aqua‐2‐(3‐aminophenyl)benzo‐1,3,2‐dioxaborole (right) . Cα atoms are indicated as spheres; hydrogen positions were modeled for the first two molecules.…”

“…Even though the sugar/diol‐binding activity of boric acid and its derivatives has been known for almost a century, structural information on corresponding complexes has remained scarce and was mainly based on conductivity and/or spectroscopic as well as NMR measurements . So far, only a few X‐ray structures have been elucidated for cyclic diesters between boronic acids and diol compounds: 1) a small‐molecule complex between m ‐aminophenylboronate and catechol [aqua‐2‐(3‐aminophenyl)benzo‐1,3,2‐dioxaborole] and 2) complexes between enzymes and boronic acid inhibitors conjugated to glycerol . In the first case, the boron atom forms part of a five‐membered ring annealed to a benzene ring.…”

“…Data for a protein crystal, flash‐frozen after addition of glycerol (30 %, v / v ) to the mother liquor, were collected at BESSY beamline 14.1 at the Helmholtz‐Zentrum Berlin, Germany, and processed as described . After molecular replacement (see text), the covalent protein ⋅ ligand complex was refined by using B−C (1.610 Å), B−OC (1.520 Å), and B−OH (1.450 Å) bond length parameters from a published small‐molecule crystal structure . The simulated annealing omit density map was calculated with PHENIX …”

β-Boronic Acid-Substituted Bodipy Dyes for Fluorescence Anisotropy Analysis of Carbohydrate Binding

“…As boronic acids rapidly and reversibly form cyclic esters with cis -1,2- or cis -1,3-diols in aqueous media, they became preferred reagents in carbohydrate research. − The thermodynamic cycle of ester formation between a neutral boronic acid and a diol takes the geometry change of the boron atom into account. ,− A trigonal, planar, and neutral boron atom with sp 2 -hybridization is converted in an equilibrium reaction into an anionic and tetrahedral boron atom with sp 3 -hybridization. In addition, boronate ester formation is entropically favored because of the release of two water molecules.…”