The use of computational modeling to describe and analyze biological systems is at the heart of systems biology. This Perspective discusses the development and use of ontologies that are designed to add semantic information to computational models and simulations.
Direct electrophilic borylation using Y(2)BCl (Y(2) = Cl(2) or o-catecholato) with equimolar AlCl(3) and a tertiary amine has been applied to a wide range of arenes and heteroarenes. In situ functionalization of the ArBCl(2) products is possible with TMS(2)MIDA, to afford bench-stable and easily isolable MIDA-boronates in moderate to good yields. According to a combined experimental and computational study, the borylation of activated arenes at 20 °C proceeds through an S(E)Ar mechanism with borenium cations, [Y(2)B(amine)](+), the key electrophiles. For catecholato-borocations, two amine dependent reaction pathways were identified: (i) With [CatB(NEt(3))](+), an additional base is necessary to accomplish rapid borylation by deprotonation of the borylated arenium cation (σ complex), which otherwise would rather decompose to the starting materials than liberate the free amine to effect deprotonation. Apart from amines, the additional base may also be the arene itself when it is sufficiently basic (e.g., N-Me-indole). (ii) When the amine component of the borocation is less nucleophilic (e.g., 2,6-lutidine), no additional base is required due to more facile amine dissociation from the boron center in the borylated arenium cation intermediate. Borenium cations do not borylate poorly activated arenes (e.g., toluene) even at high temperatures; instead, the key electrophile in this case involves the product from interaction of AlCl(3) with Y(2)BCl. When an extremely bulky amine is used, borylation again does not proceed via a borenium cation; instead, a number of mechanisms are feasible including via a boron electrophile generated by coordination of AlCl(3) to Y(2)BCl, or by initial (heteroarene)AlCl(3) adduct formation followed by deprotonation and transmetalation.
PMR2 is available under an open source license at http://www.cellml.org/tools/pmr/; a fully functional instance of this software can be accessed at http://models.physiomeproject.org/.
As main-group chemistry, in particular boron chemistry, has expanded and developed over the past 20 years, one reagent has risen to prominence as well. Tris(pentafluorophenyl)borane, B(CF) (commonly known as BCF), has demonstrated extensive applications in a wide variety of reactions, including borylation, hydrogenation, hydrosilylation, frustrated Lewis pair (FLP) chemistry, Lewis acid catalysis, and more. The high Lewis acidity of B(CF) is derived from the electronic effects of its three CF rings, rendering it a versatile reagent for a great number of reactions. In addition, the steric bulk of these rings also allows it to function as the Lewis acid in a FLP, granting this reagent yet another synthetically useful application. However, as main-group chemistry continues to evolve as a field, new reagents are required that go beyond BCF, increasing not only the range of reactions available but also the breadth of compounds attainable. Great strides have already been made in order to accomplish this task, and this review will highlight modern advances in boron chemistry relating to borylation reactions. Herein, we will show the recent uses of B(CF) in borylation reactions while also focusing on current advances in novel borane and borocation usage that eclipses that of the stalwart B(CF).
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