The average amino acid identity (AAI) is an index of pairwise genomic relatedness, and multiple studies have proposed its application in prokaryotic taxonomy and related disciplines. AAI demonstrates ...better resolution in elucidating taxonomic structure beyond the species rank when compared with average nucleotide identity (ANI), which is a standard criterion in species delineation. However, an efficient and easy-to-use computational tool for AAI calculation in large-scale taxonomic studies is not yet available. Here, we introduce a bioinformatic pipeline, named EzAAI, which allows for rapid and accurate AAI calculation in prokaryote sequences. The EzAAI tool is based on the MMSeqs2 program and computes AAI values almost identical to those generated by the standard BLAST algorithm with significant improvements in the speed of these evaluations. Our pipeline also provides a function for hierarchical clustering to create dendrograms, which is an essential part of any taxonomic study. EzAAI is available for download as a standalone JAVA program at
http://leb.snu.ac.kr/ezaai
.
Conspectus Since the seminal work of Tang and Vanslyke in 1987 on small-molecule emitters and that of Friend and co-workers in 1990 on conjugated-polymer emitters, organic light-emitting diodes ...(OLEDs) have attracted much attention from academia as well as industry, as the OLED market is estimated to reach the $30 billion mark by the end of 2018. In these first-generation organic emitters, on the basis of simple spin statistics, electrical excitation resulted in the formation of ∼25% singlet excitons and ∼75% triplet excitons. Radiative decay of the singlet excitons to the singlet ground state leads to a prompt fluorescence emission, while the triplet excitons only lead to weak phosphorescence due to the very small spin–orbit couplings present in purely organic molecules. The consequence is a ca. 75% energy loss, which triggered wide-ranging efforts to try and harvest as many of the triplet excitons as possible. In 1998, Thompson, Forrest, and their co-workers reported second-generation OLED emitters based on coordination complexes with heavy transition metals (e.g., iridium or platinum). Here, the triplet excitons stimulate efficient and fast phosphorescence due to the strong spin–orbit couplings enabled by the heavy-metal atoms. Internal quantum efficiencies (IQE) up to 100% have been reported, which means that for every electron injected into the device, a photon is emitted. While these second-generation emitters are those mainly exploited in current OLED applications, there is strong impetus from both cost and environmental standpoints to find new ways of exploiting purely organic emitters, which in addition can offer greater flexibility to fine-tune the electronic and optical properties by exploiting the synthetic organic chemistry toolbox. In 2012, Adachi and co-workers introduced a promising strategy, based on thermally activated delayed fluorescence (TADF), to harvest the triplet excitons in purely organic molecular materials. These materials now represent the third generation of OLED emitters. Impressive photophysical properties and device performances have been reported, with internal quantum efficiencies also reaching nearly 100%. Our objectives in this Account are threefold: (i) to lay out a comprehensive description, at the molecular level, of the fundamental photophysical processes behind TADF emitters; (ii) to discuss some of the challenges facing the design of TADF emitters, such as the need to balance the efficiency of thermal activation of triplet excitons into the singlet manifold with the efficiency of radiative transition to the ground state; and (iii) to highlight briefly some of the recent molecular-design strategies that pave the way to new classes of TADF materials.
Construction of carbon–carbon bonds is one of the most important tools in chemical synthesis. In the previously established cross-coupling reactions, prefunctionalized starting materials were usually ...employed in the form of aryl or alkyl (pseudo)halides or their metalated derivatives. However, the direct use of arenes and alkanes via a 2-fold oxidative C–H bond activation strategy to access chemoselective C(sp2)–C(sp3) cross-couplings is highly challenging due to the low reactivity of carbon–hydrogen (C–H) bonds and the difficulty in suppressing side reactions such as homocouplings. Herein, we present the new development of a copper-catalyzed cross-dehydrogenative coupling of polyfluoroarenes with alkanes under mild conditions. Relatively weak sp3 C–H bonds at the benzylic or allylic positions, and nonactivated hydrocarbons could be alkylated by the newly developed catalyst system. A moderate-to-high site selectivity was observed among various C–H bonds present in hydrocarbon reactants, including gaseous feedstocks and complex molecules. Mechanistic information was obtained by performing combined experimental and computational studies to reveal that the copper catalyst plays a dual role in activating both alkane sp3 C–H bonds and sp2 polyfluoroarene C–H bonds. It was also suggested that the noncovalent π–π interaction and weak hydrogen bonds formed in situ between the optimal ligand and arene substrates are key to facilitating the current coupling reactions.
β2-Amino carbonyls, an α-substituted β-amino scaffold, hold a prominent place in the development of new pharmaceuticals and peptidomimetics. Herein, we report a highly efficient Rh-catalyzed ...ring-opening amidation of substituted cyclopropanols, which turned out to serve as a linchpin for the selective synthesis of β2-amino ketones to outcompete the formation of β3-isomers. Instead of the generally accepted rationale to consider steric factors for the β2-selectivity, orbital interaction was elucidated to play a more critical role in the amidative ring-opening of cyclopropanols to generate the key Rh–C intermediate. Subsequent inner-sphere acylnitrene transfer was achieved in excellent efficiency (TON > 5000) by using readily accessible dioxazolones as the amino source to afford β2-amino ketones with broad applicability.
The rates for up-conversion intersystem crossing (UISC) from the T1 state to the S1 state are calculated for a series of organic emitters with an emphasis on thermally activated delayed fluorescence ...(TADF) materials. Both the spin–orbit coupling and the energy difference between the S1 and T1 states (ΔE ST) are evaluated, at the density functional theory (DFT) and time-dependent DFT levels. The calculated UISC rates and ΔE ST values are found to be in good agreement with available experimental data. Our results underline that small ΔE ST values and sizable spin–orbit coupling matrix elements have to be simultaneously realized in order to facilitate UISC and ultimately TADF. Importantly, the spatial separation of the highest occupied and lowest unoccupied molecular orbitals of the emitter, a widely accepted strategy for the design of TADF molecules, does not necessarily lead to a sufficient reduction in ΔE ST; in fact, either a significant charge-transfer (CT) contribution to the T1 state or a minimal energy difference between the local-excitation and charge-transfer triplet states is required to achieve a small ΔE ST. Also, having S1 and T1 states of a different nature is found to strongly enhance spin–orbit coupling, which is consistent with the El-Sayed rule for ISC rates. Overall, our results indicate that having either similar energies for the local-excitation and charge-transfer triplet states or the right balance between a substantial CT contribution to T1 and somewhat different natures of the S1 and T1 states, paves the way toward UISC enhancement and thus TADF efficiency improvement.
A single molecular rhodium catalyst system (PC2-Cp#RhIII) bearing two functional domains for both photosensitization and C–H carbometalation was designed to enable an intramolecular redox process. ...The hypothesized charge-transfer species (PC2•–-Cp#RhIV) was characterized by spectroscopic and electrochemical analyses. This photoinduced internal oxidation allows a facile access to the triplet state of the key post-transmetalation intermediate that readily undergoes C–C bond-forming reductive elimination with a lower activation barrier than in its singlet state, thus enabling catalytic C–H arylation and methylation processes.
The formal hydroamination/hydroamidation utilizing metal hydride is an appealing synthetic tool for the construction of valuable nitrogen-containing compounds from unsaturated hydrocarbons. While ...significant advances have been made for the functionalizations of alkenes in this realm, the direct hydroamidation of alkynes remains rather limited due to the high feasibility of the key metal-alkenyl intermediate to choose other reaction pathways. Herein, we report a NiH-catalyzed strategy for the hydroamidation of alkynes with dioxazolones, which allows convenient access to synthetically useful secondary enamides in (E)-anti-Markovnikov or Markovnikov selectivity. The reaction is viable for both terminal and internal alkynes and is also tolerant with a range of subtle functional groups. With H2O found as an essential component for high catalyst turnovers, the involvement of inner-sphere nitrenoid transfer is proposed that outcompetes an undesired semireduction process, thus representing the first example to show the competence of Ni catalysis for metal-nitrenoid formation from dioxazolones.
Intramolecular alkyne hydroamidation represents a straightforward approach for the access to synthetically valuable cyclic enamides. Despite some advances made in this realm, the ability to attain a ...precise regiocontrol still remains challenging, especially for endo cyclization that leads to six-membered and larger azacyclic rings. Herein, we report a NiH-catalyzed intramolecular hydroamidation of alkynyl dioxazolones that allows for an excellent endo selectivity, thus affording a range of six- to eight-membered endocyclic enamides with a broad scope. Mechanistic investigations revealed that Ni(I) catalysis is operative in the current system, proceeding via regioselective syn-hydronickelation, alkenylnickel E/Z isomerization, and Ni-centered inner-sphere nitrenoid transfer. In particular, the key alkenylnickel isomerization step, which previously lacked mechanistic understandings, was found to take place through the η2-vinyl transition state. The synthetic value of this protocol was demonstrated by diastereoselective modifications of the obtained endocyclic enamides to highly functionalized δ-lactam scaffolds.
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