Stalling chromophore synthesis of the fluorescent protein Venus reveals the molecular basis of the final oxidation step.

Fluorescent proteins (FPs) have revolutionised the life sciences, but the mechanism of chromophore maturation is still not fully understood. Here we show that incorporation of a photo-responsive non-canonical amino acid within the chromophore stalls maturation of Venus, a yellow FP, at an intermediate stage; a crystal structure indicates the presence of O2 located above a dehydrated enolate form of the imidazolone ring, close to the strictly conserved Gly67 that occupies a twisted conformation. His148 adopts an "open" conformation so forming a channel that allows O2 access to the immature chromophore. Absorbance spectroscopy supported by QM/MM simulations suggests that the first oxidation step involves formation of a hydroperoxyl intermediate in conjunction with dehydrogenation of the methylene bridge. A fully conjugated mature chromophore is formed through release of H2O2, both in vitro and in vivo. The possibility of interrupting and photochemically restarting chromophore maturation and the mechanistic insights open up new approaches for engineering optically controlled fluorescent proteins.

Beyond generative models: superfast traversal, optimization, novelty, exploration and discovery (STONED) algorithm for molecules using SELFIES.

Inverse design allows the generation of molecules with desirable physical quantities using property optimization. Deep generative models have recently been applied to tackle inverse design, as they possess the ability to optimize molecular properties directly through structure modification using gradients. While the ability to carry out direct property optimizations is promising, the use of generative deep learning models to solve practical problems requires large amounts of data and is very time-consuming. In this work, we propose STONED - a simple and efficient algorithm to perform interpolation and exploration in the chemical space, comparable to deep generative models. STONED bypasses the need for large amounts of data and training times by using string modifications in the SELFIES molecular representation. First, we achieve non-trivial performance on typical benchmarks for generative models without any training. Additionally, we demonstrate applications in high-throughput virtual screening for the design of drugs, photovoltaics, and the construction of chemical paths, allowing for both property and structure-based interpolation in the chemical space. Overall, we anticipate our results to be a stepping stone for developing more sophisticated inverse design models and benchmarking tools, ultimately helping generative models achieve wider adoption.

Oxidative Rearrangement of MIDA (N-Methyliminodiacetic Acid) Boronates: Mechanistic Insights and Synthetic Applications.

Herein we report that coordinative hemilability allows the MIDA (N-methyliminodiacetic acid) nitrogen to behave as a nucleophile and intramolecularly intercept palladium π-allyl intermediates. A mechanistic investigation indicates that this rearrangement proceeds through an SN2-like displacement at tetrasubstituted boron to furnish novel DABN boronates. Oxidative addition into the N-C bond of the DABN scaffold furnishes borylated π-allyl intermediates that can then be trapped with a variety of nucleophiles, including in a three-component coupling.

Isonitriles as Stereoelectronic Chameleons: The Donor-Acceptor Dichotomy in Radical Additions.

Radical addition to isonitriles (isocyanides) starts and continues all the way to the transition state (TS) mostly as a simple addition to a polarized π-bond. Only after the TS has been passed, the spin density moves to the α-carbon to form the imidoyl radical, the hallmark intermediate of the 1,1-addition-mediated cascades. Addition of alkyl, aryl, heteroatom-substituted, and heteroatom-centered radicals reveals a number of electronic, supramolecular, and conformational effects potentially useful for the practical control of isonitrile-mediated radical cascade transformations. Addition of alkyl radicals reveals two stereoelectronic preferences. First, the radical attack aligns the incipient C···C bond with the aromatic π-system. Second, one of the C-H/C-C bonds at the radical carbon eclipses the isonitrile N-C bond. Combination of these stereoelectronic preferences with entropic penalty explains why the least exergonic reaction (addition of the t-Bu radical) is also the fastest. Heteroatomic radicals reveal further unusual trends. In particular, the Sn radical addition to the PhNC is much faster than addition of the other group IV radicals, despite forming the weakest bond. This combination of kinetic and thermodynamic properties is ideal for applications in control of radical reactivity via dynamic covalent chemistry and may be responsible for the historically broad utility of Sn radicals ("the tyranny of tin"). In addition to polarity and low steric hindrance, radical attack at the relatively strong π-bond of isonitriles is assisted by "chameleonic" supramolecular interactions of the radical center with both the isonitrile π*-system and lone pair. These interactions are yet another manifestation of supramolecular control of radical chemistry.

Five Roads That Converge at the Cyclic Peroxy-Criegee Intermediates: BF3-Catalyzed Synthesis of ß-Hydroperoxy-ß-peroxylactones.

We have discovered synthetic access to ß-hydroperoxy-ß-peroxylactones via BF3-catalyzed cyclizations of a variety of acyclic precursors, ß-ketoesters and their silyl enol ethers, alkyl enol ethers, enol acetates, and cyclic acetals, with H2O2. Strikingly, independent of the choice of starting material, these reactions converge at the same ß-hydroperoxy-ß-peroxylactone products, i.e., the peroxy analogues of the previously elusive cyclic Criegee intermediate of the Baeyer-Villiger reaction. Computed thermodynamic parameters for the formation of the ß-hydroperoxy-ß-peroxylactones from silyl enol ethers, enol acetates, and cyclic acetals confirm that the ß-peroxylactones indeed correspond to a deep energy minimum that connects a variety of the interconverting oxygen-rich species at this combined potential energy surface. The target ß-hydroperoxy-ß-peroxylactones were synthesized from ß-ketoesters, and their silyl enol ethers, alkyl enol ethers, enol acetates, and cyclic acetals were obtained in 30-96% yields. These reactions proceed under mild conditions and open synthetic access to a broad selection of ß-hydroperoxy-ß-peroxylactones that are formed selectively even in those cases when alternative oxidation pathways can be expected. These ß-peroxylactones are stable and can be useful for further synthetic transformations.

Ozone-Free Synthesis of Ozonides: Assembling Bicyclic Structures from 1,5-Diketones and Hydrogen Peroxide.

Reactions of 1,5-diketones with H2O2 open an ozone-free approach to ozonides. Bridged ozonides are formed readily at room temperature in the presence of strong Brønsted or Lewis acids such as H2SO4, p-TsOH, HBF4, or BF3·Et2O. The expected bridged tetraoxanes, the products of double H2O2 addition, were not detected. This procedure is readily scalable to produce gram quantities of the ozonides. Bridged ozonides are stable and can be useful as building blocks for bioconjugation and further synthetic transformations. Although less stabilized by anomeric interactions than bis-peroxides, ozonides have an intrinsic advantage of having only one weak O-O bond. The role of the synergetic framework of anomeric effects in bis-peroxides is to overcome this intrinsic disadvantage. As the computational data have shown, this is only possible when all anomeric effects in bis-peroxides are activated to their fullest degree. Consequently, the cyclization selectivity is determined by the length of the bridge between the two carbonyl groups of the diketone. The generally large thermodynamic preference for the formation of cyclic bis-peroxides disappears when 1,5-diketones are used as the bis-cyclization precursors. Stereoelectronic analysis suggests that the reason for the bis-peroxide absence is the selective deactivation of anomeric effects in a [3.2.2]tetraoxanonane skeleton by a structural distortion imposed on the tetraoxacyclohexane subunit by the three-carbon bridge.

Substituent effects on stereoselectivity of dihalocarbene reactions with cyclohexadiene and on the reactivity of bis-dihalocyclopropanes in electrophilic nitrations en route to pyrimidine N-oxides.

Tricyclic bis-adducts of cyclohexa-1,4-diene with bromofluorocarbene and non-symmetric adducts with both bromofluoro- and dichlorocarbenes were synthesised selectively. The treatment of the bis-adducts with nitrating reagents in acetonitrile affords the products of heterocyclization of a sole dihalogenocyclopropane into 4-fluoropyrimidine N-oxide. The difference in the reactivity of bis-cyclopropanes with different sets of halogen substituents leads to selective heterocyclization of bromofluorocyclopropanes without affecting the dichlorocyclopropane moiety.

Erratum: Organocatalyzed synthesis of fluorinated poly(aryl thioethers).

A correction to this article has been published and is linked from the HTML version of this article.

Coupling N-H Deprotonation, C-H Activation, and Oxidation: Metal-Free C(sp3)-H Aminations with Unprotected Anilines.

An intramolecular oxidative C(sp3)-H amination from unprotected anilines and C(sp3)-H bonds readily occurs under mild conditions using t-BuOK, molecular oxygen and N,N-dimethylformamide (DMF). Success of this process, which requires mildly acidic N-H bonds and an activated C(sp3)-H bond (BDE < 85 kcal/mol), stems from synergy between basic, radical, and oxidizing species working together to promote a coordinated sequence of deprotonation: H atom transfer and oxidation that forges a new C-N bond. This process is applicable for the synthesis of a wide variety of N-heterocycles, ranging from small molecules to extended aromatics without the need for transition metals or strong oxidants. Computational results reveal the mechanistic details and energy landscape for the sequence of individual steps that comprise this reaction cascade. The importance of base in this process stems from the much greater acidity of transition state and product for the 2c,3e C-N bond formation relative to the reactant. In this scenario, selective deprotonation provides the driving force for the process.

Organocatalyzed synthesis of fluorinated poly(aryl thioethers).

The preparation of high-performance fluorinated poly(aryl thioethers) has received little attention compared to the corresponding poly(aryl ethers), despite the excellent physical properties displayed by many polysulfides. Herein, we report a highly efficient route to fluorinated poly(aryl thioethers) via an organocatalyzed nucleophilic aromatic substitution of silyl-protected dithiols. This approach requires low catalyst loadings, proceeds rapidly at room temperature, and is effective for many different perfluorinated or highly activated aryl monomers. Computational investigations of the reaction mechanism reveal an unexpected, concerted SNAr mechanism, with the organocatalyst playing a critical, dual-activation role in facilitating the process. Not only does this remarkable reactivity enable rapid access to fluorinated poly(aryl thioethers), but also opens new avenues for the processing, fabrication, and functionalization of fluorinated materials with easy removal of the volatile catalyst and TMSF byproducts.Fluorinated poly(aryl thioethers), unlike their poly(aryl ethers) counterparts, have received little attention despite excellent physical properties displayed by many polysulfides. Here the authors show a highly efficient route to fluorinated poly(aryl thioethers) via an organocatalyzed nucleophilic aromatic substitution of silyl-protected dithiols.

Changing the path of least resistance, or access to endo-dig products via a sequence of three exo-trig transition states: electronic effects in homoallyic ring expansion cascades of alkenyl isonitriles.

Chemoselective addition of radicals to isonitriles can be harnessed for initiating reaction cascades designed to overcome the stereoelectronic restrictions on homoallylic ring expansion in alkyne reactions and to develop a new general route for the preparation of N-heteroaromatics. This method utilizes alkenes as synthetic equivalents of alkynes by coupling homoallylic ring expansion to yield the formal "6-endo" products with aromatization via stereoelectronically assisted C-C bond scission. Detailed computational analysis of the individual steps of the homoallylic expansion sequence maps effects of substituents and structural constraints on this multi-step potential energy surface.

Coupling Radical Homoallylic Expansions with C-C Fragmentations for the Synthesis of Heteroaromatics: Quinolines from Reactions of o-Alkenylarylisonitriles with Aryl, Alkyl, and Perfluoroalkyl Radicals.

Selective addition of radicals to isonitriles can be harnessed for initiating reaction cascades designed to overcome the stereoelectronic restrictions on homoallylic ring expansion in alkyne reactions and to develop a new general route for the preparation of N-heteroaromatics. This method utilizes alkenes as synthetic equivalents of alkynes by coupling homoallylic ring expansion to yield the formal "6-endo" products with aromatization via stereoelectronically assisted C-C bond scission. Computational analysis of the homoallyic expansion potential energy surface reveals that the indirect 5-exo/3-exo/retro-3-exo path is faster than the direct 6-endo-trig closure, revealing the general exo-preference for the cyclization processes.

Domino Fragmentations in Traceless Directing Groups of Radical Cascades: Evidence for the Formation of Alkoxy Radicals via C-O Scission.

Direct evidence for the formation of alkoxy radicals is reported in radical cascades using traceless directing groups. Despite the possibility of hydrogen abstraction in the fragmenting step, followed by loss of R-OH, ß-scission is preferred for the formation of alkoxy radicals. For the first time, the C-O radical was intermolecularly trapped using a silyl enol ether. Various C-X fragmenting groups were explored as possible traceless directing groups for the preparation of extended polyaromatics. Computational evidence shows that a combination of aromatization, steric and stereoelectronic effects assists the fragmentation to alkoxy radicals. Additionally, a new through-space interaction was discovered between O and Sn in the fragmentation as a specific transition state stabilizing effect.

Discovery of a Long-Range Perlin Effect in a Conformationally Constrained Oxocane.

Herein, we present the crystal structure, NMR J analysis, and conformational and natural bond order analyses of tricyclic oxocane (1), resulting in the discovery of a long-range Perlin effect at C4 and C5. The normal Perlin effect (NPE) of Δ(1)JC-H = 18.38 Hz at C5 is the largest to date for a nonanomeric methylene due to an unprecedented through-space n → σ* stabilizing interaction. The NPE at C4 where Δ(1)JC-H = 6.91 Hz is nearly double those found in cyclohexanone.

Fused Catechol Ethers from Gold(I)-Catalyzed Intramolecular Reaction of Propargyl Ethers with Acetals.

Selective gold(I)-catalyzed rearrangement of aromatic methoxypropynyl acetals leads to fused catechol ethers (1,2-dialkoxynapthalenes) in excellent yields. Furthermore, this process extends to the analogous heterocyclic and aliphatic substrates. Alkyne activation triggers nucleophilic addition of the acetal oxygen that leads to an equilibrating mixture of oxonium ions of similar stability. This mixture is "kinetically self-sorted" via a highly exothermic cyclization. Selective formation of 1,2-dialkoxy naphthalenes originates from chemoselective aromatization of the cyclic intermediate via 1,4-elimination of methanol.

Synthesis of Functionalized Phenanthrenes via Regioselective Oxidative Radical Cyclization.

The majority of Sn-mediated cyclizations are reductive and, thus, cannot give a fully conjugated product. This is a limitation in the application of Sn-mediated radical cascades for the preparation of fully conjugated molecules. In this work, we report an oxidatively terminated Bu3Sn-mediated cyclization of an alkyne where AIBN, the commonly used initiator, takes on a new function as an oxidative agent. Sn-mediated radical transformation of biphenyl aryl acetylenes into functionalized phenanthrenyl stannanes can be initiated via two potentially equilibrating vinyl radicals, one of which can be trapped by the fast 6-endoclosure at the biphenyl moiety in good to excellent yields. The efficient preparation of Sn-substituted phenanthrenes opens access to convenient building blocks for the construction of larger polyaromatics.

tert-Butyl Carbocation in Condensed Phases: Stabilization via Hyperconjugation, Polarization, and Hydrogen Bonding.

Despite the seeming similarity of the infrared (IR) spectra between tert-butyl cations (t-Bu(+)) in gaseous and condensed phases, there are important but so far unrecognized differences. The IR spectroscopic investigation of the hydrogen (H)-bonding of t-Bu(+) with the immediate environment together with the X-ray crystallographic data shows that one CH3 group of t-Bu(+) differs from the other two. In the Ar-tagged t-Bu(+) in vacuum, this group is predominantly polarized, showing three C-H stretch vibrations at 2913, 2965, and 3036 cm(-1) whereas the other two methyls are predominantly involved in strong hyperconjugation, yielding an intense triple IR band with a maximum at 2839 cm(-1). In a condensed phase, the bulk solvent effect promoted participation of the polarized CH3 group in additional hyperconjugation, decreasing its νCH3 frequencies by approximately 120 cm(-1), whereas frequencies of the other CH3 groups decreased by only ca. 4-10 cm(-1). This observation indicates that the influence of the condensed phase on t-Bu(+) stabilization is substantial. Thus, enhancement of H-bonding between t-Bu(+) and Anion(-) strengthens hyperconjugation and promotes further cation stabilization.

Stereoelectronic source of the anomalous stability of bis-peroxides.

The unusual stability of bis- and tris-peroxides contradicts the conventional wisdom - some of them can melt without decomposition at temperatures exceeding 100 °C. In this work, we disclose a stabilizing stereoelectronic effect that two peroxide groups can exert on each other. This stabilization originates from strong anomeric nO → σ*CO interactions that are absent in mono-peroxides but reintroduced in molecules where two peroxide moieties are separated by a CH2 group. Furthermore, such effects can be induced by other σ-acceptors and amplified by structural constraints imposed by cyclic and bicyclic frameworks.