On the Number of π-Electrons Involved in Stepwise Cycloaddition Reactions.

The development of higher-order cycloadditions has mainly been restricted by the requisite usage of highly conjugated and reactive π-systems. Recent years have witnessed organocatalysis as a potent mediator for several of the challenges associated herein, rendering higher-order cycloadditions a legitimate option for achieving the selective construction of specific molecular scaffolds. These developments reinvigorate the efforts to try to understand the underlying principles for cycloadditions involving a higher number of π-electrons than the "classical" cycloadditions; how do we properly address the impact which the addition of further π-electrons have on the reactivity of a system? Herein, computational investigations of two model higher-order cycloaddition systems have been performed to try to provide insights on changes in energetic barriers induced by the presence of benzofusions in a position which is unobstructive to the reactivity. With experimental substantiation as support, these studies might open up for a discussion on whether the π-electrons of benzofused systems simply act as spectator electrons, or play a tangible role on the observed reactivity to an extent where a distinct nomenclature is meritable.

Organocatalytic Enantioselective Construction of Conformationally Stable C(sp2)-C(sp3) Atropisomers.

Nonbiaryl atropisomers are molecules defined by a stereogenic axis featuring at least one nonarene moiety. Among these, scaffolds bearing a conformationally stable C(sp2)-C(sp3) stereogenic axis have been observed in natural compounds; however, their enantioselective synthesis remains almost completely unexplored. Herein we disclose a new class of chiral C(sp2)-C(sp3) atropisomers obtained with high levels of stereoselectivity (up to 99% ee) by means of an organocatalytic asymmetric methodology. Multiple molecular motifs could be embedded in this class of C(sp2)-C(sp3) atropisomers, showing a broad and general protocol. Experimental data provide strong evidence of the conformational stability of the C(sp2)-C(sp3) stereogenic axis (up to t1/225 °C >1000 y) in the obtained compounds and show kinetic control over this rare stereogenic element. This, coupled with density functional theory calculations, suggests that the observed stereoselectivity arises from a Curtin-Hammett scenario establishing an equilibrium of intermediates. Furthermore, the experimental investigation led to evidence of the operating principle of central-to-axial chirality conversions.

Isotope Effects Reveal the Catalytic Mechanism of the Archetypical Suzuki-Miyaura Reaction.

Experimental and theoretical 13C kinetic isotope effects (KIEs) are utilized to obtain atomistic insight into the catalytic mechanism of the Pd(PPh3)4-catalyzed Suzuki-Miyaura reaction of aryl halides and aryl boronic acids. Under catalytic conditions, we establish that oxidative addition of aryl bromides occurs to a 12-electron monoligated palladium complex (Pd-(PPh3)). This is based on the congruence of the experimental KIE for the carbon attached to bromine (KIEC-Br = 1.020) and predicted KIEC-Br for the transition state for oxidative addition to the Pd(PPh3) complex (1.021). For aryl iodides, the near-unity KIEC-I of ~1.003 suggests that the first irreversible step in the catalytic cycle precedes oxidative addition and is likely the binding of the iodoarene to Pd(PPh3). Our results suggest that the commonly proposed oxidative addition to the 14-electron Pd(PPh3)2 complex can occur only in the presence of excess added ligand or under stoichiometric conditions; in both cases, experimental KIEC-Br of 1.031 is measured, which is identical to the predicted KIEC-Br for the transition state for oxidative addition to the Pd(PPh3)2 complex (1.031). The transmetalation step, under catalytic conditions, is shown to proceed via a tetracoordinate boronate (8B4) intermediate with a Pd-O-B linkage based on the agreement between an experimental KIE for the carbon atom involved in transmetalation (KIEC-Boron = 1.035) and a predicted KIEC-Boron for the 8B4 transmetalation transition state (1.034).

Study of Ground State Interactions of Enantiopure Chiral Quaternary Ammonium Salts and Amides, Nitroalkanes, Nitroalkenes, Esters, Heterocycles, Ketones and Fluoroamides.

Chiral phase-transfer catalysis provides high level of enantiocontrol, however no experimental data showed the interaction of catalysts and substrates. 1 H NMR titration was carried out on Cinchona and Maruoka ammonium bromides vs. nitro, carbonyl, heterocycles, and N-F containing compounds. It was found that neutral organic species and quaternary ammonium salts interacted via an ensemble of catalyst + N-C-H and (sp2 )C-H, specific for each substrate studied. The correspondent BArF salts interacted with carbonyls via a diverse set of + N-C-H and (sp2 )C-H compared to bromides. This data suggests that BArF ammonium salts may display a different enantioselectivity profile. Although not providing quantitative data for the affinity constants, the data reported proofs that chiral ammonium salts coordinate with substrates, prior to transition state, through specific C-H positions in their structures, providing a new rational to rationalize the origin of enantioselectivity in their catalyses.

Organocatalytic Asymmetric Multicomponent Cascade Reaction for the Synthesis of Contiguously Substituted Tetrahydronaphthols.

Isobenzopyrylium ions are unique, highly reactive, aromatic intermediates which are largely unexplored in asymmetric catalysis despite their high potential synthetic utility. In this study, an organocatalytic asymmetric multicomponent cascade via dienamine catalysis, involving a cycloaddition, a nucleophilic addition, and a ring-opening reaction, is disclosed. The reaction furnishes chiral tetrahydronaphthols containing four contiguous stereocenters in good to high yield, high diastereoselectivity (up to >20:1), and excellent enantioselectivity (93-98% ee). The obtained products are important synthetic intermediates, and it is demonstrated that they can be used for the generation of frameworks such as octahydrobenzo[h]isoquinoline and [2.2.2]octane scaffolds. Furthermore, mechanistic experiments involving oxygen-18-labeling studies and density functional theory calculations provide a vivid picture of the reaction mechanism. Finally, the bioactivity of 16 representative tetrahydronaphthol compounds has been evaluated in U-2OS cancer cells with some compounds showing a unique profile and a clear morphological change.

Insights on the Pseudo-Enantiomeric Properties of Bifunctional Cinchona Alkaloid Squaramide-Derived Organocatalyst.

The use of pseudo enantiomers is a well-known method of achieving products of complementary stereochemistry. Only rarely can different enantiomers of a product be accessed without modulation of the catalyst. Recently, a system was reported wherein two different enantiomers of spirocycles were obtained by a cascade reaction of unsaturated pyrrolin-4-ones with mercaptoacetaldehyde catalyzed by a single optimized cinchona alkaloid squaramide-derived organocatalyst. It was originally proposed that the E/Z geometry of the unsaturated pyrrolin-4-one dictated the stereochemistry of the spirocycle product, but this was not investigated further. In the present work, we have investigated the nature of a pseudo-enantiomeric organocatalyst conformation applying density functional theory calculations for investigating the transition states for the reaction. Furthermore, the influence of the double-bond geometry of the pyrrolin-4-one has been studied beyond what is possible to test experimentally. The results provide a greater understanding for this class of reactions that may be applicable in future methodology development.

Transition state analysis of an enantioselective Michael addition by a bifunctional thiourea organocatalyst.

The mechanism of the enantioselective Michael addition of diethyl malonate to trans-ß-nitrostyrene catalyzed by a tertiary amine thiourea organocatalyst is explored using experimental 13C kinetic isotope effects and density functional theory calculations. Large primary 13C KIEs on the bond-forming carbon atoms of both reactants suggest that carbon-carbon bond formation is the rate-determining step in the catalytic cycle. This work resolves conflicting mechanistic pictures that have emerged from prior experimental and computational studies.

Diagnostic accuracy of a rapid telemedicine encounter in the Emergency Department.

OBJECTIVES: Emergency Department crowding is an increasing problem, leading to treatment delays and higher risk of mortality. Our institution recently implemented a telemedicine physician intake ("tele-intake") process as a mitigating front-end strategy. Previous studies have focused on ED throughput metrics such as door to disposition; our work aimed to specifically assess the tele-intake model for clinical accuracy. METHODS: We retrospectively reviewed ED visits at a high acuity, tertiary care academic hospital before and after tele-intake implementation. We defined the primary outcome as the degree of additional laboratory, imaging, and medication orders placed by the subsequent ED provider. Our secondary outcomes were the cancellation rate of intake orders and the percentage of encounters where no additional second provider orders were necessary. RESULTS: For in-person and tele-intake physician encounters between September 2015 and February 2017, most labs and diagnostic radiology studies, and approximately half of CT, ultrasound, and pharmacy orders were initiated by the intake physician. We found no significant difference for our primary outcome (p = 0.2449). For both tele-intake and in-person encounters, <1% of orders were cancelled by the second provider. Additionally, 30.8% of in-person and 31.5% of telemedicine patient encounters required no additional orders to make a disposition decision. DISCUSSION: This novel analysis of an innovative patient care model suggests that the benefits of tele-intake as a replacement for in-person physician directed intake are not at the cost of over or under utilization of diagnostic testing or interventions.

Isotope Effects Reveal an Alternative Mechanism for "Iminium-Ion" Catalysis.

A novel mechanism for the epoxidation of enals with hydrogen peroxide catalyzed by diarylprolinol silyl ether supported by experimental 13C kinetic isotope effects (KIEs) and density functional theory calculations is presented. Normal 13C KIEs, measured on both the carbonyl- and ß-carbon atoms of the enal, suggest participation of both carbon atoms in the rate-determining step. Calculations show that the widely accepted iminium-ion mechanism does not account for this experimental observation. A syn-SN2' substitution mechanism, which avoids formation of a discrete iminium-ion intermediate, emerges as the most likely mechanism based on agreement between experimental and predicted KIEs.

Pyro-Borates, Spiro-Borates, and Boroxinates of BINOL-Assembly, Structures, and Reactivity.

VANOL and VAPOL ligands are known to react with three equivalents of B(OPh)3 to form a catalytic species that contains a boroxinate core with three boron atoms, and these have proven to be effective catalysts for a number of reactions. However, it was not known whether the closely related BINOL ligand will likewise form a boroxinate species. It had simply been observed that mixtures of BINOL and B(OPh)3 were very poor catalysts compared to the same mixtures with VANOL or VAPOL. Borate esters of BINOL have been investigated as chiral catalysts, and these include meso-borates, spiro-borates, and diborabicyclo-borate esters. Borate esters are often in equilibrium, and their structures can be determined by stoichiometry and/or thermodynamics, especially in the presence of a base. The present study examines the structures of borate esters of BINOL that are produced with different stoichiometric combinations of BINOL with B(OPh)3 in the presence and absence of a base. Depending on conditions, pyro-borates, spiro-borates, and boroxinate species can be generated and their effectiveness in a catalytic asymmetric aziridination was evaluated. The finding is that BINOL borate species are not necessarily inferior catalysts to those of VANOL and VAPOL but that, under the conditions, BINOL forms two different catalytic species (a boroxinate and a spiro-borate) that give opposite asymmetric inductions. However, many BINOL derivatives with substitutents in the 3- and 3'-positions gave only the boroxinate species and the 3,3'-Ph2BINOL ligand gave a boroxinate catalyst that gives excellent inductions in the aziridination reaction. BINOL derivatives with larger groups in the 3,3'-position will not form either spiro-borates or boroxinate species and thus are not effective catalysts at all.

Bifunctional Ammonium Salt Catalyzed Asymmetric α-Hydroxylation of ß-Ketoesters by Simultaneous Resolution of Oxaziridines.

Chiral bifunctional urea-containing ammonium salts were found to be very efficient catalysts for asymmetric α-hydroxylation reactions of ß-ketoesters with oxaziridines under base-free conditions. The reaction is accompanied by a simultaneous kinetic resolution of the oxaziridine and a plausible and so far unprecedented bifunctional transition-state model has been obtained by means of DFT calculations.

Isotope Effects Reveal the Mechanism of Enamine Formation in l-Proline-Catalyzed α-Amination of Aldehydes.

The mechanism of l-proline-catalyzed α-amination of 3-phenylpropionaldehyde was studied using a combination of experimental kinetic isotope effects (KIEs) and theoretical calculations. Observation of a significant carbonyl (13)C KIE and a large primary α-deuterium KIE support rate-determining enamine formation. Theoretical predictions of KIEs exclude the widely accepted mechanism of enamine formation via intramolecular deprotonation of an iminium carboxylate intermediate. An E2 elimination mechanism catalyzed by a bifunctional base that directly forms an N-protonated enamine species from an oxazolidinone intermediate accounts for the experimental KIEs. These findings provide the first experimental picture of the transition-state geometry of enamine formation and clarify the role of oxazolidinones as nonparasitic intermediates in proline catalysis.

RAG: an update to the RNA-As-Graphs resource.

BACKGROUND: In 2004, we presented a web resource for stimulating the search for novel RNAs, RNA-As-Graphs (RAG), which classified, catalogued, and predicted RNA secondary structure motifs using clustering and build-up approaches. With the increased availability of secondary structures in recent years, we update the RAG resource and provide various improvements for analyzing RNA structures. DESCRIPTION: Our RAG update includes a new supervised clustering algorithm that can suggest RNA motifs that may be "RNA-like". We use this utility to describe RNA motifs as three classes: existing, RNA-like, and non-RNA-like. This produces 126 tree and 16,658 dual graphs as candidate RNA-like topologies using the supervised clustering algorithm with existing RNAs serving as the training data. A comparison of this clustering approach to an earlier method shows considerable improvements. Additional RAG features include greatly expanded search capabilities, an interface to better utilize the benefits of relational database, and improvements to several of the utilities such as directed/labeled graphs and a subgraph search program. CONCLUSIONS: The RAG updates presented here augment the database's intended function - stimulating the search for novel RNA functionality - by classifying available motifs, suggesting new motifs for design, and allowing for more specific searches for specific topologies. The updated RAG web resource offers users a graph-based tool for exploring available RNA motifs and suggesting new RNAs for design.

Computational generation and screening of RNA motifs in large nucleotide sequence pools.

Although identification of active motifs in large random sequence pools is central to RNA in vitro selection, no systematic computational equivalent of this process has yet been developed. We develop a computational approach that combines target pool generation, motif scanning and motif screening using secondary structure analysis for applications to 10(12)-10(14)-sequence pools; large pool sizes are made possible using program redesign and supercomputing resources. We use the new protocol to search for aptamer and ribozyme motifs in pools up to experimental pool size (10(14) sequences). We show that motif scanning, structure matching and flanking sequence analysis, respectively, reduce the initial sequence pool by 6-8, 1-2 and 1 orders of magnitude, consistent with the rare occurrence of active motifs in random pools. The final yields match the theoretical yields from probability theory for simple motifs and overestimate experimental yields, which constitute lower bounds, for aptamers because screening analyses beyond secondary structure information are not considered systematically. We also show that designed pools using our nucleotide transition probability matrices can produce higher yields for RNA ligase motifs than random pools. Our methods for generating, analyzing and designing large pools can help improve RNA design via simulation of aspects of in vitro selection.

Analysis of riboswitch structure and function by an energy landscape framework.

The thiamine pyrophosphate (TPP) riboswitch employs modular domains for binding TPP to form a platform for gene expression regulation. Specifically, TPP binding triggers a conformational switch in the RNA from a transcriptionally active "on" state to an inactive "off" state that concomitantly causes the formation of a terminator hairpin and halting of transcription. Here, clustering analysis of energy landscapes at different nucleotide lengths suggests a novel computational tool for analysis of the mechanics of transcription elongation in the presence or absence of the ligand. Namely, we suggest that the riboswitch's kinetics are tightly governed by a length-dependent switch, whereby the energy landscape has two clusters available during transcription elongation and where TPP's binding shifts the preference to one form. Significantly, the biologically active and inactive structures determined experimentally matched well the structures predominant in each computational set. These clustering/structural analyses combined with modular computational design suggest design principles that exploit the above features to analyze as well as create new functions and structures of RNA systems.