Geometry of trigonal boron coordination sphere in boronic acids derivatives – a bond-valence vector model approach

Abstract

The systematic analysis of the geometry of three-coordinate boron in boronic acid derivatives with a common [CBO2] skeleton is presented. The study is based on the bond-valence vector (BVV) model [Zachara (2007). Inorg. Chem. 46, 9760-9767], a simple tool for the identification and quantitative estimation of both steric and electronic factors causing deformations of the coordination sphere. The empirical bond-valence (BV) parameters in the exponential equation [Brown & Altermatt (1985). Acta Cryst. B41, 244-247] rij and b, for B-O and B-C bonds were determined using data deposited in the Cambridge Structural Database. The values obtained amount to rBO = 1.364 Å, bBO = 0.37 Å, rBC = 1.569 Å, bBC = 0.28 Å, and they were further used in the calculation of BVV lengths. The values of the resultant BVV were less than 0.10 v.u. for 95% of the set comprising 897 [CBO2] fragments. Analysis of the distribution of BVV components allowed for the description of subtle in- and out-of plane deviations from the `ideal' (sp(2)) geometry of boron coordination sphere. The distortions specific for distinct groups of compounds such as boronic acids, cyclic and acyclic esters, benzoxaboroles and hemiesters were revealed. In cyclic esters the direction of strains was found to be controlled by the ring size effect. It was shown that the syn or anti location of substituents on O atoms is decisive for the deformations direction for both acids and acyclic esters. The greatest strains were observed in the case of benzoxaboroles which showed the highest deviation from the zero value of the resultant BVV. The out-of-plane distortions, described by the vz component of the resultant BVV, were ascertained to be useful in the identification of weak secondary interactions on the fourth coordination site of the boron centre.

Synthesis and Influence of 3-Amino Benzoxaboroles Structure on Their Activity against Candida albicans

“…However, in the case of 14 the insertion of the formyl substituent in the ortho position relative to the boronic moiety causes the significant O1-B1-O2 angle narrowing (from 123.1(1) in 11 to 118.4(2)° in 14) with simultaneous O1-B1-C1 angle broadening (from 128.3(1) in 11 to 133.5(2)° in 14), whereas the five-membered ring inner O2-B1-C1 angle is retained. This is following the findings by Czerwińska et al [29] associating the strains in the boron coordination sphere with the position of the hydrogen atom in syn (11) or anti position (14). In the latter such a conformation may be imposed by the presence of a relatively strong intramolecular O1-H…O3 hydrogen bond (H…O and O…O distances equal 2.15(2) and 2.867(2) Å , respectively; O-H…O angle equals 147(2)°), leading to a formation of a six-membered H-bonded ring, essentially flat and coplanar with the benzoxaborole unit (deviation from a plane defined by all atoms except the phenylpiperazine substituent is only 0.019(2) Å ).…”

Hydrogen-Bonded Chains and Networks of Triptycene-Based Triboronic Acid and Tripyridinone

“…The monoclinic unit cell contains eight molecules of triptycene triboronic acid 1 and 56 molecules of water. It is known that boronic acids can form cyclic hydrogen-bonded dimers, − ,− similar to that found in the carboxylic acid dimer, and in most cases the two hydroxyl groups prefer the syn-anti conformations according to the H atom locations (Scheme , type I) . However, the three boronic groups of 1 play different roles in the formation of hydrogen bonds: two boronic groups form a cyclic hydrogen-bonded dimer with both hydroxyls on one boronic acid as the donor and the other one as the acceptor interacting in the way of syn-syn and anti-anti orientation (type II); the third one with a conformation of syn-syn interacts with one of the two hydroxyls groups to form a hydrogen bond with the oxygen atom of the aforementioned hydrogen bond donor site.…”

“…The values of the same dimeric unit O–B–O angles are also different, with ∠(O11–B–O12) = 121°, ∠(O21–B–O22) = 121°, and ∠(O31–B–O32) = 114°. The boronic group with a syn-syn arrangement gives a bigger O–B–O angle than the boronic group in the anti-anti conformation, which is probably caused by the repulsion of H--H contacts . The value of the O–B–O angle in type I bonding is in the range of 116–120°, just between the angles in type II bonding .…”

“…It is known that boronic acids can form cyclic hydrogen-bonded dimers, 44−46,76−78 similar to that found in the carboxylic acid dimer, 79 and in most cases the two hydroxyl groups prefer the syn-anti conformations according to the H atom locations (Scheme 2, type I). 80 However, the three boronic groups of 1 play different roles in the formation of hydrogen bonds: two boronic groups form a cyclic hydrogenbonded dimer with both hydroxyls on one boronic acid as the donor and the other one as the acceptor interacting in the way of syn-syn and anti-anti orientation (type II); the third one with a conformation of syn-syn interacts with one of the two hydroxyls groups to form a hydrogen bond with the oxygen atom of the aforementioned hydrogen bond donor site. The presence of the third hydrogen bond influences the two hydrogen bonds of the cyclic dimer, which is weakening one bond and thus becoming different in lengths O−B−O angle in type I bonding is in the range of 116−120°, just between the angles in type II bonding.…”

Effect of substituents in novel bioactive tavaborole derivatives on the intermolecular interaction hierarchy

“…3 It is noteworthy that in many different derivatives of phenylboronic acids, the benzoxaboroles exhibit the highest reactivity, 4 which might be related to their unbalanced coordination sphere, as shown in studies of a large group of such derivatives based on the bond-valencevector (BVV) model. 5 On the other hand, the lower activity of the unsubstituted benzoxaborole (Bx in Scheme 1) compared to tavaborole points out the significance of the presence of the fluorine atom. 6,7 Generally, it is considered that the effect of substitution by the fluorine atom on the action of drugs is complex and includes effects on acidity and lipophilicity, among others.…”