Divergent Elementoboration: 1,3-Haloboration versus 1,1-Carboboration of Propargyl Esters.

This work showcases the 1,3-haloboration reaction of alkynes in which boron and chlorine add to propargyl systems in a proposed sequential oxazoliumborate formation with subsequent ring-opening and chloride migration. In addition, the functionalization of these propargyl esters with dimethyl groups in the propargylic position leads to stark differences in reactivity whereby a formal 1,1-carboboration prevails to give the 2,2-dichloro-3,4-dihydrodioxaborinine products as an intramolecular chelate. Density functional theory calculations are used to rationalize the distinct carboboration and haloboration pathways. Significantly, this method represents a metal-free route to highly functionalized compounds in a single step to give structurally complex products.

Tris(2,4,6-trifluorophenyl)borane: An Efficient Hydroboration Catalyst.

The metal-free catalyst tris(2,4,6-trifluorophenyl)borane has demonstrated its extensive applications in the 1,2-hydroboration of numerous unsaturated reagents, namely alkynes, aldehydes and imines, consisting of a wide array of electron-withdrawing and donating functionalities. A range of over 50 borylated products are reported, with many reactions proceeding with low catalyst loading under ambient conditions. These pinacol boronate esters, in the case of aldehydes and imines, can be readily hydrolyzed to leave the respective alcohol and amine, whereas alkynyl substrates result in vinyl boranes. This is of great synthetic use to the organic chemist.

Tris(pentafluorophenyl)borane and Beyond: Modern Advances in Borylation Chemistry.

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(C6F5)3 (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(C6F5)3 is derived from the electronic effects of its three C6F5 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(C6F5)3 in borylation reactions while also focusing on current advances in novel borane and borocation usage that eclipses that of the stalwart B(C6F5)3.

Synthesis and reactivity of N,N'-1,4-diazabutadiene derived borocations.

A series of borocations have been synthesised from the addition of haloboranes to synthetically accessible N,N'-1,4-diazabutadiene precursors, which are derived from commercially available anilines. The synthesis and structural studies of the borocations are described.

The Propargyl Rearrangement to Functionalised Allyl-Boron and Borocation Compounds.

A diverse range of Lewis acidic alkyl, vinyl and aryl boranes and borenium compounds that are capable of new carbon-carbon bond formation through selective migratory group transfer have been synthesised. Utilising a series of heteroleptic boranes [PhB(C6 F5 )2 (1), PhCH2 CH2 B(C6 F5 )2 (2), and E-B(C6 F5 )2 (C6 F5 )C=C(I)R (R=Ph 3 a, nBu 3 b)] and borenium cations [phenylquinolatoborenium cation ([QOBPh][AlCl4 ], 4)], it has been shown that these boron-based compounds are capable of producing novel allyl- boron and boronium compounds through complex rearrangement reactions with various propargyl esters and carbamates. These reactions yield highly functionalised, synthetically useful boron substituted organic compounds with substantial molecular complexity in a one-pot reaction.

Contrasting Frustrated Lewis Pair Reactivity with Selenium- and Boron-Based Lewis Acids.

The activation of π-bonds in diynyl esters has been investigated by using soft and hard Lewis acids. In the case of the soft selenium Lewis acid PhSeCl, sequential activation of the alkyne bonds leads initially to an isocoumarin (1 equiv PhSeCl) and then to a tetracyclic conjugated structure with the isocoumarin subunit fused to a benzoselenopyran (3 equiv PhSeCl). Conversely, the reaction with the hard Lewis acidic borane B(C6 F5 )3 initiates a cascade reaction to yield a complex π-conjugated system containing phthalide and indene subunits.

The carboboration of Me3Si-substituted alkynes and allenes with boranes and borocations.

The 1,1-carboboration of 1-Me3Si-1-alkynes is the dominant reaction observed using [PhBCl(2-DMAP)][AlCl4], 1, and PhBCl2 electrophiles, with highly substituted vinyl pinacol boronate esters isolated post esterification. Other aryl and heteroaryl congeners of both 1 and PhBCl2 have a limited scope in the 1,1-carboboration of 1-Me3Si-1-alkynes, with desilylboration more prevalent. PhBCl2 converts Me3Si-substituted allenes to allylboranes via a formal 1,3-carboboration with Me3Si-migration. [Cl2B(2-DMAP)][AlCl4] reacts with a number of 1-Me3Si-1-alkynes by desilylboration, whilst with Me3Si-ethyne a 1,1-boroamination reaction proceeds, which with excess boron electrophile is followed by an intermolecular desilylboration to form a tricationic-borate. The use of excess 1-Me3Si-1-propyne relative to 1 (and a thienyl congener of 1) formed 2-boradienes in low yields from the reaction with two equivalents of alkyne. Vinyl borocations ligated by 2,6-lutidine of the general formula, [(vinyl)BCl(2,6-lutidine)][AlCl4] formed 1-boradienes with 1-Me3Si-1-alkynes.

Formation of C(sp(2))-boronate esters by borylative cyclization of alkynes using BCl3.

BCl3 is an inexpensive electrophile which induces the borylative cyclization of a wide range of substituted alkynes to regioselectively form polycycles containing synthetically versatile C(sp(2) )boronate esters. It proceeds rapidly, with good yields and is compatible with a range of functional groups and substitution patterns. Intermolecular 1,2-carboboration of alkynes is also achieved using BCl3 to generate trisubstituted vinyl boronate esters.

Haloboration of internal alkynes with boronium and borenium cations as a route to tetrasubstituted alkenes.

Hail boration! 2-Dimethylaminopyridine-ligated dihaloborocations [X2B(2-DMAP)](+) with a strained four-membered boracycle were used for the haloboration of terminal and dialkyl internal alkynes (see scheme). Esterification then provided vinyl boronate esters as useful precursors to tetrasubstituted alkenes. Following mechanistic studies, the scope of the haloboration was expanded simply by variation of the amine. Pin = 2,3-dimethyl-2,3-butanedioxy.

Mechanistic studies into amine-mediated electrophilic arene borylation and its application in MIDA boronate synthesis.

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.

Model annotation for synthetic biology: automating model to nucleotide sequence conversion.

MOTIVATION: The need for the automated computational design of genetic circuits is becoming increasingly apparent with the advent of ever more complex and ambitious synthetic biology projects. Currently, most circuits are designed through the assembly of models of individual parts such as promoters, ribosome binding sites and coding sequences. These low level models are combined to produce a dynamic model of a larger device that exhibits a desired behaviour. The larger model then acts as a blueprint for physical implementation at the DNA level. However, the conversion of models of complex genetic circuits into DNA sequences is a non-trivial undertaking due to the complexity of mapping the model parts to their physical manifestation. Automating this process is further hampered by the lack of computationally tractable information in most models. RESULTS: We describe a method for automatically generating DNA sequences from dynamic models implemented in CellML and Systems Biology Markup Language (SBML). We also identify the metadata needed to annotate models to facilitate automated conversion, and propose and demonstrate a method for the markup of these models using RDF. Our algorithm has been implemented in a software tool called MoSeC. AVAILABILITY: The software is available from the authors' web site http://research.ncl.ac.uk/synthetic_biology/downloads.html.

The CellML Model Repository.

SUMMARY: The CellML Model Repository provides free access to over 330 biological models. The vast majority of these models are derived from published, peer-reviewed papers. Model curation is an important and ongoing process to ensure the CellML model is able to accurately reproduce the published results. As the CellML community grows, and more people add their models to the repository, model annotation will become increasingly important to facilitate data searches and information retrieval. AVAILABILITY: The CellML Model Repository is publicly accessible at http://www.cellml.org/models.