Computer-Driven Development of Ylide Functionalized Phosphines for Palladium-Catalyzed Hiyama Couplings

Palladium-catalyzed couplings of silicon enolates with aryl electrophiles are of great synthetic utility, but often limited to expensive bromide substrates. A comparative experimental study confirmed that none of the established ligand systems allows to couple inexpensive aryl chlorides with α-trimethylsilyl alkylnitriles. In contrast, ylide functionalized phosphines (YPhos) led to encouraging results. A statistical model was developed that correlates the reaction yields with ligand features. It was employed to predict catalyst structures with superior performance. With this cheminformatics approach, YPhos ligands were tailored specifically to the demands of Hiyama couplings. The newly synthesized ligands displayed record-setting activities, enabling the elusive coupling of aryl chlorides with α-trimethylsilyl alkyl nitriles. The preparative utility of the catalyst system was demonstrated by the synthesis of pharmaceutically meaningful α-aryl alkylnitriles, α-arylcarbonyls and biaryls.

A negative-solvatochromic fluorescent probe for visualizing intracellular distributions of fatty acid metabolites

Metabolic distribution of fatty acid to organelles is an essential biological process for energy homeostasis as well as for the maintenance of membrane integrity, and the metabolic pathways are strictly regulated in response to environmental stimuli. Herein, we report a fluorescent fatty acid probe, which bears an azapyrene dye that changes its absorption and emission features depending on the microenvironment polarity of the organelle into which it is transported. Owing to the environmental sensitivity of this dye, the distribution of the metabolically incorporated probe in non-polar lipid droplets, medium-polarity membranes, and the polar aqueous regions, can be visualized in different colors. Based on density scatter plots of the fluorophore, we demonstrate that the degradation of triacylglycerols in lipid droplets occurs predominantly via lipolysis rather than lipophagy in nutrition-starved hepatocytes. This tool can thus be expected to significantly advance our understanding of the lipid metabolism in living organisms.

Metabolic distribution of fatty acids to organelles is an essential biological process for energy homeostasis. Here the authors report a fluorescent probe that allows multicolour visualisation of the intracellular distribution of exogenous fatty acids, metabolically incorporated as lipid components.

A Comprehensive Discovery Platform for Organophosphorus Ligands for Catalysis

The design of molecular catalysts typically involves reconciling multiple conflicting property requirements, largely relying on human intuition and local structural searches. However, the vast number of potential catalysts requires pruning of the candidate space by efficient property prediction with quantitative structure-property relationships. Data-driven workflows embedded in a library of potential catalysts can be used to build predictive models for catalyst performance and serve as a blueprint for novel catalyst designs. Herein we introduce kraken, a discovery platform covering monodentate organophosphorus(III) ligands providing comprehensive physicochemical descriptors based on representative conformer ensembles. Using quantum-mechanical methods, we calculated descriptors for 1558 ligands, including commercially available examples, and trained machine learning models to predict properties of over 300000 new ligands. We demonstrate the application of kraken to systematically explore the property space of organophosphorus ligands and how existing data sets in catalysis can be used to accelerate ligand selection during reaction optimization.

The Evolution of Data-Driven Modeling in Organic Chemistry

Organic chemistry is replete with complex relationships: for example, how a reactant's structure relates to the resulting product formed; how reaction conditions relate to yield; how a catalyst's structure relates to enantioselectivity. Questions like these are at the foundation of understanding reactivity and developing novel and improved reactions. An approach to probing these questions that is both longstanding and contemporary is data-driven modeling. Here, we provide a synopsis of the history of data-driven modeling in organic chemistry and the terms used to describe these endeavors. We include a timeline of the steps that led to its current state. The case studies included highlight how, as a community, we have advanced physical organic chemistry tools with the aid of computers and data to augment the intuition of expert chemists and to facilitate the prediction of structure-activity and structure-property relationships.

A Striking Mode of Activation of Carbon Disulfide with a Cooperative Bis(silylene)

The reactivity of the 1,4-substituted bis(silylenyl)terphenylene 1, 1,4-[ortho-(LSi)C₆ H₄ ]₂ C₆ H₄ , (L=RC(NtBu)₂ , R=Ph, Mes) towards CS₂ is reported. It results in a dearomatization of the phenylene ring, affording the 1,3-substituted cyclohexadiene derivative 2. According to DFT calculations, a transient silene containing a Si=C bond capable of π(C=C) addition at the aromatic phenylene ring is a key intermediate. In contrast, addition of CS₂ to the biphenyl-substituted mono-silylene ortho-(LSi)C₆ H₄ -C₆ H₅ 3 leaves the aromatic π-system intact and forms, in a [1+2] cycloaddition reaction, the corresponding thiasilirane 4 with a three-membered SiSC ring. Further experimental studies led to the isolation of the novel mesoionic five-membered Si₂ S₂ C heterocycle 6, which reacts with CS₂ under C-C bond formation. All isolated new compounds were fully characterized and their molecular structures determined by single-crystal X-ray diffraction analyses.

Univariate classification of phosphine ligation state and reactivity in cross-coupling catalysis

[Figure: see text].

Data-science driven autonomous process optimization

Autonomous process optimization involves the human intervention-free exploration of a range process parameters to improve responses such as product yield and selectivity. Utilizing off-the-shelf components, we develop a closed-loop system for carrying out parallel autonomous process optimization experiments in batch. Upon implementation of our system in the optimization of a stereoselective Suzuki-Miyaura coupling, we find that the definition of a set of meaningful, broad, and unbiased process parameters is the most critical aspect of successful optimization. Importantly, we discern that phosphine ligand, a categorical parameter, is vital to determination of the reaction outcome. To date, categorical parameter selection has relied on chemical intuition, potentially introducing bias into the experimental design. In seeking a systematic method for selecting a diverse set of phosphine ligands, we develop a strategy that leverages computed molecular feature clustering. The resulting optimization uncovers conditions to selectively access the desired product isomer in high yield.

Twofold C-H Activation Enables Synthesis of a Diazacoronene-Type Fluorophore with Near Infrared Emission Through Isosteric Replacement

The synthesis and photophysical properties of a soluble amide-embedded coronene is reported. The key step in this synthesis is the twofold C-H activation of diazaperylene by a rhodium(III)Cp* catalyst. This unprecedented structural motif shows intense fluorescence in the near infrared region with a small Stokes shift and a distinct vibronic structure, which exhibits a slight extent of negative solvatochromism. Comparison of this compound with some relevant compounds revealed the importance of the amide incorporation in the peripheral concave region including an angular position to retain high aromaticity reflecting that of parent coronene. Treatment of this compound with Lewis acid B(C₆ F₅ )₃ formed a bis-adduct, which exhibited enhanced aromaticity as a consequence of the increased double bond character of the amide C-N bonds.

Enantioselective Allenoate-Claisen Rearrangement Using Chiral Phosphate Catalysts

Herein we report the first highly enantioselective allenoate-Claisen rearrangement using doubly axially chiral phosphate sodium salts as catalysts. This synthetic method provides access to β-amino acid derivatives with vicinal stereocenters in up to 95% ee. We also investigated the mechanism of enantioinduction by transition state (TS) computations with DFT as well as statistical modeling of the relationship between selectivity and the molecular features of both the catalyst and substrate. The mutual interactions of charge-separated regions in both the zwitterionic intermediate generated by reaction of an amine to the allenoate and the Na⁺-salt of the chiral phosphate leads to an orientation of the TS in the catalytic pocket that maximizes favorable noncovalent interactions. Crucial arene-arene interactions at the periphery of the catalyst lead to a differentiation of the TS diastereomers. These interactions were interrogated using DFT calculations and validated through statistical modeling of parameters describing noncovalent interactions.

Enantiodivergent Pd-catalyzed C-C bond formation enabled through ligand parameterization

Despite the enormous potential for the use of stereospecific cross-coupling reactions to rationally manipulate the three-dimensional structure of organic molecules, the factors that control the transfer of stereochemistry in these reactions remain poorly understood. Here we report a mechanistic and synthetic investigation into the use of enantioenriched alkylboron nucleophiles in stereospecific Pd-catalyzed Suzuki cross-coupling reactions. By developing a suite of molecular descriptors of phosphine ligands, we could apply predictive statistical models to select or design distinct ligands that respectively promoted stereoinvertive and stereoretentive cross-coupling reactions. Stereodefined branched structures were thereby accessed through the predictable manipulation of absolute stereochemistry, and a general model for the mechanism of alkylboron transmetallation was proposed.

Mild, visible light-mediated decarboxylation of aryl carboxylic acids to access aryl radicals

Herein we present the first example of aryl radical formation via the visible light-mediated decarboxylation of aryl carboxylic acids using photoredox catalysis.

Herein we present the first example of aryl radical formation via the visible light-mediated decarboxylation of aryl carboxylic acids using photoredox catalysis. This method constitutes a mild protocol for the decarboxylation of cheap and abundant aryl carboxylic acids and tolerates both electron-rich substrates and those lacking ortho-substitution. The in situ formation of an acyl hypobromite is proposed to prevent unproductive hydrogen atom abstraction and trapping of the intermediate aroyloxy radical, enabling mild decarboxylation.

Synthesis of Stable Diarylpalladium(II) Complexes: Detailed Study of the Aryl-Aryl Bond-Forming Reductive Elimination

The synthesis of diarylpalladium(II) complexes by twofold aryl C-H bond activation was developed. These intermediates of oxidative cyclization reactions are stabilized by chelation with acetyl groups while still maintaining sufficient reactivity to study their reductive elimination. Four distinct triggers were found for the reductive elimination of these complexes to dibenzofurans and carbazoles. Thermal elimination occurs at very high temperatures, whereas ligand-promoted and oxidatively induced reductive eliminations proceed readily at room temperature. Under these conditions, no isomerization occurs. In contrast, weak Brønsted acids, such as acetic acid, lead to a sequence of proto-demetalation, isomerization to a κ(3) -diarylpalladium(II) complex, and reductive elimination to non-symmetrical cyclization products.

Mild metal-catalyzed C–H activation: examples and concepts

C–H Activation reactions that proceed under mild conditions are more attractive for applications in complex molecule synthesis. Mild C–H transformations reported since 2011 are reviewed and the different concepts and strategies that have enabled their mildness are discussed.

Highly selective synthesis of 6-substituted benzothiophenes by Sc(OTf)3-catalyzed intermolecular cyclization and sulfur migration

A series of 6-substituted benzo[b]thiophenes was synthesized using a Sc(OTf)₃-catalyzed intermolecular cyclization between para-substituted N-(arylthio)succinimides and alkynes taking advantage of a unique and selective 1,2-sulfur migration occuring via an electrophilic ipso cyclization to a key spirocyclic thiete intermediate.

Co(III)-catalyzed C-H activation/formal SN-type reactions: selective and efficient cyanation, halogenation, and allylation

The first cobalt-catalyzed cyanation, halogenation, and allylation via C-H activation have been realized. These formal SN-type reactions generate valuable (hetero)aryl/alkenyl nitriles, iodides, and bromides as well as allylated indoles using a bench-stable Co(III) catalyst. High regio- and mono-selectivity were achieved for these reactions. Additionally, allylation proceeded efficiently with a turnover number of 2200 at room temperature, which is unprecedented for this Co(III) catalyst. Alkenyl substrates and amides have been successfully utilized in Cp*Co(III)-catalyzed C-H activation for the first time.

The C-H activation/1,3-diyne strategy: highly selective direct synthesis of diverse bisheterocycles by Rh(III) catalysis

The reactivity and selectivity of 1,3-diynes in transition-metal-catalyzed CH activation is exploited to quickly assemble diverse polysubstituted bisheterocycles, which are highly important but difficult to access. By using the CH activation/1,3-diyne strategy, we overcame the challenges of selectivity (chemo-, regio-, and mono-/diannulation) and constructed seven kinds of adjacent bisheterocycles through the formation of four strategic bonds with high efficiency and high selectivity.

Snapshot of the palladium(II)-catalyzed oxidative biaryl bond formation by X-ray analysis of the intermediate diaryl palladium(II) complex

Pd(II) caught in the act: The diaryl Pd(II) intermediate of a Pd(II)-catalyzed oxidative biaryl bond formation proceeding via a double C-H bond activation has been isolated and fully characterized, including an X-ray crystal structure analysis. Stabilization due to chelation by adjacent pivaloyloxy and acetyl groups has allowed the isolation of this long-sought crucial intermediate. On gentle warming, the complex is transformed into a carbazole product, and the catalytically active Pd(II) species is regenerated by oxidation with Cu(II).

(Sub)-Picosecond Spectral Evolution of Fluorescence in Photoactive Proteins Studied with a Synchroscan Streak Camera System

The spectral evolution of three photoactive proteins has been investigated by measuring the fluorescence with good temporal and wavelength resolution and a high signal-to-noise ratio. Upon excitation at 400 nm wild-type (wt) PYP both at neutral pH and in the low-pH blueshifted pBdark state exhibited a strong quenching of the fluorescence, the major part of which could be described by lifetimes of about 1.7 and 7.7 ps. The remaining fluorescence decay occurred multiexponentially with lifetimes between 30 and 125 ps. Additionally, in wtPYP at neutral pH, a dynamic Stokes shift was found to occur with a time constant of about 0.25 ps. In a PYP preparation that was reconstituted with the chromophore 7-hydroxy-coumarin-3- carboxylic acid rather than the native coumaric acid, and which is therefore not capable of performing the cis-trans-isomerization that initiates the photocycle in wtPYP, the fluorescence was found to decay multiexponentially with lifetimes of 51 ps, 0.33 and 3.77 ns. Additionally, dynamic Stokes shifts were observed with time constants of about 0.1 and 3.5 ps. Upon comparison of the dynamics of this preparation with that of wtPYP the multiexponential decay with lifetimes of 1.7 and 7.7 ps found in wtPYP was attributed to photochemistry of the p-coumaric-acid chromophore. The emission from bacteriorhodopsin mutant D85S upon excitation at 635 nm decays biexponentially with estimated lifetimes of 5.2 and 19.1 ps. No dynamic Stokes shift was observed here. Four lifetimes were needed to describe the decay of the emission from the A* state in the green fluorescent protein. From a target analysis it was concluded that the longer lifetimes are accompanied by a decreasing probability of forming I*, which approaches zero with the longest A* lifetime of 1.5 ns. These observations may be explained by heterogeneity of A and by relaxation of A*. In all three systems studied, multiexponential decay of emission was present, suggesting that heterogeneity is a common feature of these chromophore protein complexes.

Triplet states as non-radiative traps in multichromophoric entities: single molecule spectroscopy of an artificial and natural antenna system

Energy transfer in antenna systems, ordered arrays of chromophores, is one of the key steps in the photosynthetic process. The photophysical processes taking place in such multichromophoric systems, even at the single molecule level, are complicated and not yet fully understood. Instead of directly studying individual antenna systems, we have chosen to focus first on systems for which the amount of chromophores and the interactions among the chromophores can be varied in a systematic way. Dendrimers with a controlled number of chromophores at the rim fulfill those requirements perfectly. A detailed photophysical study of a second-generation dendrimer, containing eight peryleneimide chromophores at the rim, was performed 'J. Am. Chem. Soc., 122 (2000) 9278'. One of the most intriguing findings was the presence of collective on/off jumps in the fluorescence intensity traces of the dendrimers. This phenomenon can be explained by assuming a simultaneous presence of both a radiative trap (energetically lowest chromophoric site) and a non-radiative trap (triplet state of one chromophore) within one individual dendrimer. It was shown that an analogue scheme could explain the collective on/off jumps in the fluorescence intensity traces of the photosynthetic pigment B-phycoerythrin (B-PE) (Porphyridium cruentum). The different values of the triplet lifetime that could be recovered for a fluorescence intensity trace of B-PE were correlated with different intensity levels in the trace, suggesting different chromophores acting as a trap as function of time.

An Experimental Comparison of the Maximum Likelihood Estimation and Nonlinear Least-Squares Fluorescence Lifetime Analysis of Single Molecules

Two procedures based on the weighted least-squares (LS) and the maximum likelihood estimation (MLE) method to confidently analyze single-molecule (SM) fluorescence decays with a total number (N) of 2,500-60,000 counts have been elucidated and experimentally compared by analyzing measured bulk and SM decays. The key observation of this comparison is that the LS systematically underestimates the fluorescence lifetimes by approximately 5%, for the range of 1,000-20,000 events, whereas the MLE method gives stable results over the whole intensity range, even at counts N less than 1,000, where the LS analysis delivers unreasonable values. This difference can be attributed to the different statistics approaches and results from improper weighting of the LS method. As expected from theory, the results of both methods become equivalent above a certain threshold of N detected photons per decay, which is here experimentally determined to be approximately 20,000. In contrast to the bulk lifetime distributions, the SM fluorescence lifetime distributions exhibit standard deviations that are sizably larger than the statistically expected values. This comparison proves the strong influence of the inhomogenuous microenvironment on the photophysical behavior of single molecules embedded in a 10-30-nm thin polymer layer.

Microscopy and optical manipulation of dendrimer-built vesicles

A fifth-generation poly(propylene imine) dendrimer decorated with palmitoyl- and azobenzene-containing alkyl groups forms giant vesicles in aqueous solutions with diameters from 50 nm up to 20 mm and a multilaminar onion-like structure. Dense and ordered arrangement of the azobenzene chromophores in the bilayer structure leads to fluorescence with lmax= 600 nm. The fluorescence intensity can be increased by irradiation with blue light, and at low pH a distinctive blue shift of the spectrum is observed. With the aid of a single-beam optical tweezers it is possible to trap vesicles and direct them in a billiard-like fashion against each other using forces in the range of several pN. In collision experiments, the vesicles behave like hard spheres, and merging is not observed.

Isolation, reconstitution and functional characterisation of the Rhodobacter sphaeroides photoactive yellow protein

We report the isolation, functional reconstitution and photophysical characterisation of Rhodobacter sphaeroides photoactive yellow protein (PYP), of which the gene was recently cloned. Reconstitution of the his-tagged purified apo-protein with 4-hydroxy-cinnamic acid yields the characteristic blue absorbance at 446 nm, but surprisingly also an absorbance peak at 360 nm. This additional peak is not caused by binding of a second chromophore, as confirmed with mass spectroscopy. Moreover, reconstitution with the 'locked' analogue 7-hydroxy-coumarin-3-carboxylic acid yields only a single absorbance peak at 441 nm. The 446 nm and 360 nm species are part of a temperature- and pH-dependent equilibrium. Photoactivation of the protein leads to formation of a blue-shifted intermediate as in other PYPs, with a 100-fold increased groundstate recovery rate (k(pB-->pG)=500 s(-1)) compared to E-PYP.