Elucidation of factors shaping reactivity of 5'-deoxyadenosyl - a prominent organic radical in biology.

This study investigates the factors modulating the reactivity of 5'-deoxyadenosyl (5'dAdo˙) radical, a potent hydrogen atom abstractor that forms in the active sites of radical SAM enzymes and that otherwise undergoes a rapid self-decay in aqueous solution. Here, we compare hydrogen atom abstraction (HAA) reactions between native substrates of radical SAM enzymes and 5'dAdo˙ in aqueous solution and in two enzymatic microenvironments. With that we reveal that HAA efficiency of 5'dAdo˙ is due to (i) the in situ formation of 5'dAdo˙ in a pre-ordered complex with a substrate, which attenuates the unfavorable effect of substrate:5'dAdo˙ complex formation, and (ii) the prevention of the conformational changes associated with self-decay by a tight active-site cavity. The enzymatic cavity, however, does not have a strong effect on the HAA activity of 5'dAdo˙. Thus, we performed an analysis of in-water HAA performed by 5'dAdo˙ based on a three-component thermodynamic model incorporating the diagonal effect of the free energy of reaction, and the off-diagonal effect of asynchronicity and frustration. To this aim, we took advantage of the straightforward relationship between the off-diagonal thermodynamic effects and the electronic-structure descriptor - the redistribution of charge between the reactants during the reaction. It allows to access HAA-competent redox and acidobasic properties of 5'dAdo˙ that are otherwise unavailable due to its instability upon one-electron reduction and protonation. The results show that all reactions feature a favourable thermodynamic driving force and tunneling, the latter of which lowers systematically barriers by ∼2 kcal mol-1. In addition, most of the reactions experience a favourable off-diagonal thermodynamic contribution. In HAA reactions, 5'dAdo˙ acts as a weak oxidant as well as a base, also 5'dAdo˙-promoted HAA reactions proceed with a quite low degree of asynchronicity of proton and electron transfer. Finally, the study elucidates the crucial and dual role of asynchronicity. It directly lowers the barrier as a part of the off-diagonal thermodynamic contribution, but also indirectly increases the non-thermodynamic part of the barrier by presumably controlling the adiabatic coupling between proton and electron transfer. The latter signals that the reaction proceeds as a hydrogen atom transfer rather than a proton-coupled electron transfer.

Heterocycles as supramolecular handles for crystal engineering: a case study with 7-(diethylamino)coumarin derivatives.

In this study, we present the synthesis and detailed solid-state structural characterization of a Schiff-base-bridged derivative of 7-(diethylamino)coumarin (7-DAC), a molecular block displaying repetitive aggregation modes in the solid state despite being attached to broadly different molecular frameworks. To map the supramolecular habits of this unconventional moiety, we carry out a comparative analysis of the crystal packing in a curated dataset of 50 molecules decorated with the 7-DAC group, retrieved from the literature. We uncover that self-recognition of the 7-DAC moiety has two main components: a set of directional C-H⋯O interactions between neighboring coumarins, and antiparallel dipole-dipole interactions, taking the form of distinct π-stacking modes. The pendant 7-diethylamino group is key to the behavior of 7-DAC, favoring its solubilization through its conformational flexibility in solution, while in the crystalline matrix, it acts as a structural spacer that favors π-stacking interactions. Our findings present a comprehensive analysis of the preferential arrangements of the 7-DAC fragment in various (supra)molecular scenarios, confirming that it is (i) a mobile but mostly planar group, (ii) a group prone to antiparallel aggregation, and (iii) up to 90% likely to pack via π-stacking supported by hydrogen-bonding interactions. These findings enrich the palette of supramolecular motifs available for the bottom-up design of organic materials and their programmed construction.

Quality Control Method and Device for Producing Agarose Micropads.

In brightfield and fluorescence microscopy, capturing images that show well-focused and immobile microorganisms can be challenging. An agarose-based gel pad reduces the variability of results, especially in conditions like uneven specimen staging, variable fluid dynamics, and Brownian motion that plague conventional wet mount setups. To correct these discrepancies during image acquisition, we analyzed three micropad preparation setups. We tested the quality and consistency of pads and images resulting from each setup. Our examination reveals that improved gel pad flatness is associated with better image quality. Moreover, we observe increased consistency in gel pad construction connected to the use of a 3D-printed setup. These findings highlight the technical benefits arising from incorporating micropad-generating platforms that increase the consistency of results in imaging pipelines. Additionally, our use of a quantitative approach to examine pad flatness suggests its inclusion in quality control pipelines to reduce variation in gel pad construction and image quality over time and between investigators. Finally, our use of a 3D-printed setup coupled with a quantitative downstream routine suggests their application in microscopy experiments that involve model organisms relevant to human health and disease.

Early-life caffeine exposure induces morphological changes and altered physiology in Caenorhabditiselegans.

Caffeine, a widely consumed stimulant, is known for its effects on alertness and fatigue reduction by blockade of adenosine receptors. While it holds therapeutic potential, its diverse impacts pose risks, particularly in early development. This study explores the developmental effects of caffeine exposure using Caenorhabditis elegans (C. elegans) as a model organism. We investigated morphological and behavioral changes induced by caffeine exposure at the L1 stage and assessed their impact at the L4 stage, which roughly corresponds to human infancy and adolescence, respectively. Caffeine-exposed worms displayed increased body length, body bends, and pharyngeal pumping rates compared to control worms. These findings indicate heightened food-seeking behavior and greater food intake, leading to the observed morphological changes. While caffeine did not affect other locomotor behaviors, its stimulatory effect on growth and development highlights its significance. This study provides insights into the potential impact of early-life caffeine exposure on long-term health and development, offering a foundation for future research in vertebrates to uncover its implications on metabolism and other metrics of health.

Mechanistic Insights on Pd-Catalyzed Three-Component Reactions of Alkynols, Methyl Orthoformate, and Salicylaldehyde Derivatives. Application to the Synthesis of Steroid Chroman Ketals and Spiroketals with Antioxidant Activity.

Contrary to our previous report in which a Pd-catalyzed three-component reaction of a steroid alkynol, trimethyl orthoformate, and salicylaldehyde exclusively produced chroman ketals, the same reaction employing 2,5-dihydroxysalicylaldehyde led to a mixture of a chroman ketal and a spiroketal. Provided that both courses of the reaction imply a 4 + 2 inverse demand cycloaddition between an o-quinone methide and an enol ether, density functional theory calculations revealed that the chroman ketal/spiroketal selectivity is governed by both, the rate of the formation of the o-quinone methide and the isomerization of the initially produced exocyclic enol ether─that led to the spiroketal─to its endocyclic partner that produces the chroman ketal. Remarkably, Lewis catalysis is central to the observed reactivity, and the availability of plausible catalytic species controls the overall chemoselectivity. The methodology herein applied and scrutinized enriches the palette of reactions, leading to increased molecular complexity, as demonstrated in the obtained products, whose antioxidant activity and detailed NMR characterization are presented.

Reactivity Factors in Catalytic Methanogenesis and Their Tuning upon Coenzyme F430 Biosynthesis.

Methyl-coenzyme M reductase, responsible for the biological production of methane by catalyzing the reaction between coenzymes B (CoBS-H) and M (H3C-SCoM), hosts in its core an F430 cofactor with the low-valent NiI ion. The critical methanogenic step involves F430-assisted reductive cleavage of the H3C-S bond in coenzyme M, yielding the transient CH3 radical capable of hydrogen atom abstraction from the S-H bond in coenzyme B. Here, we computationally explored whether and why F430 is unique for methanogenesis in comparison to four identified precursors formed consecutively during its biosynthesis. Indeed, all precursors are less proficient than the native F430, and catalytic competence improves at each biosynthetic step toward F430. Against the expectation that F430 is tuned to be the strongest possible reductant to expedite the rate-determining reductive cleavage of H3C-S by NiI, we discovered the opposite. The unfavorable increase in reduction potential along the F430 biosynthetic pathway is outweighed by strengthening of the Ni-S bond formed upon reductive cleavage of the H3C-S bond. We found that F430 is the weakest electron donor, compared to its precursors, giving rise to the most covalent Ni-S bond, which stabilizes the transition state and hence reduces the rate-determining barrier. In addition, the transition state displays high pro-reactive motion of the transient CH3 fragment toward the H-S bond, superior to its biosynthetic ancestors and likely preventing the formation of a deleterious radical intermediate. Thus, we show a plausible view of how the evolutionary driving force shaped the biocatalytic proficiency of F430 toward CH4 formation.

Quantifiable polarity match effect on C-H bond cleavage reactivity and its limits in reaction design.

When oxidants favour cleaving a strong C-H bond at the expense of weaker ones, which are otherwise inherently preferred due to their favourable reaction energy, reactivity factors such as the polarity match effect are often invoked. Polarity match follows the intuition of electrophilic (nucleophilic) oxidants reacting faster with nucleophilic (electrophilic) C-H bonds. Nevertheless, this concept is purely qualitative and is best suited for a posteriori rationalization of experimental observations. Here, we propose and inspect two methods to quantify polar effects in C-H cleavage reactions, one by computation via the difference of atomic charges (Δq) of reacting atoms, and one amenable to experimental measurement through asynchronicity factors, η. By their application to three case studies, we observe that both Δq and η faithfully capture the notion of polarity match. The polarity match model, however, proves insufficient as a predictor of H-atom abstraction reactivity and we discourage its use as a standalone variable in reaction design. Besides this caveat, η and Δq (through its mapping on η) allow the implementation of polarity match into a Marcus-type model of reactivity, alleviating its shortcomings and making reaction planning feasible.

A Crystalline Dimeric Steroidal Diboronate with Electronically Impeded Rotation.

The dimeric steroid SMR-3, featuring a 1,4-phenyldiboronic ester flanked by two pregnan-triol frameworks, was synthesized to explore the intramolecular dynamics of its central component. The structural data from single-crystal X-ray diffraction studies and the Hirshfeld analyses indicate small steric effects around the aromatic ring that should favor the intended motion. However, solid-state NMR data obtained through VT 13C{1H} CPMAS and 2H spin-echo experiments, using the deuterated analogue SMR-3D4, revealed that this component is rigid even at temperatures where other reported steroidal molecular rotors experience fast rotation (85 °C). A combination of classical molecular dynamics, molecular mechanics, and correlated ab initio calculations allowed us to distinguish the steric and electronic factors that restrict the potential motion in this compound. The experimental and computational data reveal that electronic components dominate the behavior and are responsible for the high rotational barrier in the SMR-3 crystal.

H-Atom Abstraction Reactivity through the Lens of Asynchronicity and Frustration with Their Counteracting Effects on Barriers.

Hydrogen atom abstraction (HAA) is central to life, and its importance in synthetic chemistry continues to grow. Enzymes rely on HAA to trigger life-sustaining reaction cascades, and greener synthetic routes are attainable by in situ capture of the carbon-centered radicals generated by HAA. Despite the potential of HAA for the diversification of molecular complexity and the late-stage functionalization of bioactive compounds, readily applicable and reliable models translating experimentally or computationally accessible thermodynamic quantities into relative free energy barriers are missing. In this work, we discovered a complete thermodynamic basis for the description of HAA reactivity, which consists of three components. Besides, the traditional linear free energy relationship and the recently introduced factor of asynchronicity (Srnec et al., PNAS 2018, 115, E10287-E10294), we present the third thermodynamic component of H atom abstraction reactions: the factor of frustration that arises from the dissimilarity of the species competing over a hydrogen atom in their overall ability to acquire an electron and proton. Incorporating these nonclassical descriptors into a Marcus-type model, the approach herein presented allows nearly quantitative prediction of relative barriers in six sets of metal-oxo-mediated HAA reactions, outperforming existing methods even in a stringent test with >200 computational HAA reactions.

Photo Phenosizer, a rapid machine learning-based method to measure cell dimensions in fission yeast.

Cell metrics such as area, length, and width provide informative data about cell cycle dynamics. Factors that affect these dimensions include environmental conditions and genotypic differences. Fission yeast ( Schizosaccharomyces pombe ) is a rod-shaped ascomycete fungus in which cell cycle progression is linked to changes in cell length. Microscopy work to obtain these metrics places considerable burdens on time and effort. We now report on Photo Phenosizer (PP), a machine learning-based methodology that measures cell dimensions in fission yeast. It does this in an unbiased, automated manner and streamlines workflow from image acquisition to statistical analysis. Using this new approach, we constructed an efficient and flexible pipeline for experiments involving different growth media (YES and EMM) and treatments (Untreated and MMS) as well as different genotypes ( cut6-621 versus wildtype). This methodology allows for the analysis of larger sample sizes and faster image processing relative to manual segmentation. Our findings suggest that researchers using PP can quickly and efficiently determine cell size differences under various conditions that highlight genetic or environmental disruptions.

Turing patterns by supramolecular self-assembly of a single salphen building block.

In the 1950s, Alan Turing showed that concerted reactions and diffusion of activating and inhibiting chemical species can autonomously generate patterns without previous positional information, thus providing a chemical basis for morphogenesis in Nature. However, access to these patterns from only one molecular component that contained all the necessary information to execute agonistic and antagonistic signaling is so far an elusive goal, since two or more participants with different diffusivities are a must. Here, we report on a single-molecule system that generates Turing patterns arrested in the solid state, where supramolecular interactions are used instead of chemical reactions, whereas diffusional differences arise from heterogeneously populated self-assembled products. We employ a family of hydroxylated organic salphen building blocks based on a bis-Schiff-base scaffold with portions responsible for either activation or inhibition of assemblies at different hierarchies through purely supramolecular reactions, only depending upon the solvent dielectric constant and evaporation as fuel.

Self-Assembly of an Amphiphilic Bile Acid Dimer: A Combined Experimental and Theoretical Study of Its Medium-Responsive Fluorescence.

This work describes the synthesis and aggregation behavior of a dimeric bile acid derivative in which two steroid cores are bridged by a p-di(phenylethynyl)phenylene fluorophore. The studied compound contains three key characteristics: (a) restricted conformational equilibrium in solution, (b) efficient fluorescence conferred by the bridge, and (c) medium responsiveness encoded in the steroid fragments. The incorporation of the three components afforded a compound that generates nano- and micrometric spherical particles with aggregation-responsive fluorescence emission. The observed self-assembly process of the featured molecule was induced by the gradual addition of water to the tetrahydrofuran (THF) solution. This aggregation led to significant changes in fluorescence that went from two bands at λem values of 370 and 390 nm in pure THF to a new spectrum with two maxima at λem values of 395 and 418 nm at high water contents, without a decrease in emission. The observed changes can be ascribed to weakly coupled aggregation, a hypothesis supported by multiscale molecular modeling, which sheds light on the mechanism of the self-assembly of this unconventional amphiphile.

Effect of the π-bridge on the light absorption and emission in push-pull coumarins and on their supramolecular organization.

A family of eight π-extended push-pull coumarins with cross-conjugated (amide) and directly conjugated (p-phenylene, alkyne, alkene) bridges were synthesized through a convergent strategy. Using an experimentally calibrated computational protocol, their UV-Visible light absorption and emission spectra in solution were investigated. Remarkably, amide-, alkyne- and alkene-bridges undergo comparable vertical excitations. The different nature of these bridges manifests during excited-state relaxation and fluorescence. We predict that these molecules can serve as building blocks for p-type semiconductors with low reorganization energies, below 0.2 eV. Since solid-state self-assembly is crucial for this application, we examined the effect of the π-bridge over the supramolecular organization in this family of compounds to determine if stacking prevails in these π-extended coumarin derivatives. Amide and alkyne spacers allow coplanar conformations which crystallize readily; p-phenylene hinders planarity yet allows facile crystallization; alkene-bridged molecules eluded all crystallization attempts. All the crystals obtained feature dense face-to-face π-stacking with 3.5-3.7 Å interlayer distances, expected to facilitate charge transfer processes in the solid state.

Bifurcating reactions: distribution of products from energy distribution in a shared reactive mode.

Bifurcating reactions yield two different products emerging from one single transition state and are therefore archetypal examples of reactions that cannot be described within the framework of the traditional Eyring's transition state theory (TST). With the growing number and importance of these reactions in organic and biosynthetic chemistry, there is also an increasing demand for a theoretical tool that would allow for the accurate quantification of reaction outcome at low cost. Here, we introduce such an approach that fulfils these criteria, by evaluating bifurcation selectivity through the energy distribution within the reactive mode of the key transition state. The presented method yields an excellent agreement with experimentally reported product ratios and predicts the correct selectivity for 89% of nearly 50 various cases, covering pericyclic reactions, rearrangements, fragmentations and metal-catalyzed processes as well as a series of trifurcating reactions. With 71% of product ratios determined within the error of less than 20%, we also found that the methodology outperforms three other tested protocols introduced recently in the literature. Given its predictive power, the procedure makes reaction design feasible even in the presence of complex non-TST chemical steps.

A paradox of traffic and extra cars in a city as a collective behaviour.

Promoting walking or cycling and reducing cars' use is one of the city planners' main targets, contributing to a sustainable transport method. Yet, the number of vehicles worldwide is increasing as fast as the population, and motorized mobility has become the primary transport method in most cities. Here, we consider modal share as an emergent behaviour of personal decisions. All individuals minimize their commuting time and reach an equilibrium under which no person is willing to change their transportation mode. In terms of the minimum travel time, the best-case scenario is used to determine the extra commuting time and the excess cars, computed as a social inefficiency. Results show that commuting times could increase up to 25% with many more vehicles than optimum. Paradoxically, all individuals trying to minimize their time could collectively reach the maximum commuting times in the extreme case, with all individuals driving during rush hour.

Oleate-modified hyaluronan: Controlling the number and distribution of side chains by varying the reaction conditions.

In this work, low molecular weight hyaluronan was chemically modified by oleoyl moieties utilising mixed anhydrides methodology. The activation of oleic acid with benzoyl chloride in organic solvents miscible with water was followed by NMR spectroscopy. The product selectivity correlates with the solvent's Hildebrand solubility parameter. Furthermore, the effect of the solvent for the mixed anhydride formation was elucidated by density functional theory (DFT) and showed that the reactions are faster in acetonitrile or alcohols than in hexane. Furthermore, the solvent demonstrated to control the substituent distribution pattern along HA chain during esterification. An even distribution of substituents was observed in reactions performed in water mixed with ethers. The substituent distribution pattern clearly influenced the aggregation behaviour of amphiphilic HA, controlling the stability of the delivery system, while increasing the encapsulation capacity.

Palladium-Catalyzed Generation of ortho-Quinone Methides. A Three-Component Synthesis of L-Shaped Dimeric Steroidal Scaffolds.

A series of hybrid dimers having orthogonal steroidal cores bridged by a chroman ketal moiety were obtained by Pd-catalyzed three-component reactions of steroid alkynols, 2-formylestradiol 17-monoacetate, and methyl orthoformate, via ortho-quinone methide intermediates. One of the obtained L-shaped scaffolds showed an inefficient crystal packing featuring large channels within the crystal array. Monte Carlo simulations indicate that these voids preferentially allocate n-hexane, opening the way to explore further applications of similar organic crystalline materials as selective hosts for small molecules.

Understanding and Predicting Post H-Atom Abstraction Selectivity through Reactive Mode Composition Factor Analysis.

The selective functionalization of C-H bonds is one of the Grails of synthetic chemistry. In this work, we demonstrate that the selectivity toward fast hydroxylation or radical diffusion (known as the OH-rebound and dissociation mechanisms) following H-atom abstraction (HAA) from a substrate C-H bond by high-valent iron-oxo oxidants is already encoded in the HAA step when the post-HAA barriers are much lower than the preceding one. By applying the reactive mode composition factor (RMCF) analysis, which quantifies the kinetic energy distribution (KED) at the reactive mode (RM) of transition states, we show that reactions following the OH-rebound coordinate concentrate the RM kinetic energy on the motion of the reacting oxygen atom and the nascent substrate radical, whereas reactions following the dissociation channel localize most of their kinetic energy in H-atom motion. These motion signatures serve to predict the post-HAA selectivity, and since KED is affected by the free energy of reaction and asynchronicity (factor η) of HAA, we show that bimolecular HAA reactions in solution that are electron transfer-driven and highly exergonic have the lowest fraction of KED on the transferred H-atom and the highest chance to follow rebound hydroxylation. Finally, the RMCF analysis predicts that the H/D primary kinetic isotope effect can serve as a probe for these mechanisms, as confirmed in virtually all reported examples in the literature.

Reactive mode composition factor analysis of transition states: the case of coupled electron-proton transfers.

A simple method for the evaluation of the kinetic energy distribution within the reactive mode of a transition state (TS), denoted as the Reactive Mode Composition Factor (RMCF), is presented. It allows one to directly map the barrier properties onto the atomic-motion components of the reaction coordinate at the TS, which has potential to shed light onto some mechanistic features of a chemical process. To demonstrate the applicability of RMCF to reactivity, we link the kinetic energy distribution within a reactive mode with the asynchronicity (η) in C-H bond activation, as they both evolve in a series of coupled proton-electron transfer (CPET) reactions between FeIVO oxidants and 1,4-cyclohexadiene. RMCF shows how the earliness or lateness of a process manifests as a redistribution of kinetic energy in the reactive mode as a function of the free energy of reaction (ΔG0) and η. Finally, the title analysis can be applied to predict H-atom tunneling contributions and kinetic isotope effects in a set of reactions, yielding a transparent rationalization based on the kinetic energy distributions in the reactive mode.

Beyond the classical thermodynamic contributions to hydrogen atom abstraction reactivity.

Hydrogen atom abstraction (HAA) reactions are cornerstones of chemistry. Various (metallo)enzymes performing the HAA catalysis evolved in nature and inspired the rational development of multiple synthetic catalysts. Still, the factors determining their catalytic efficiency are not fully understood. Herein, we define the simple thermodynamic factor η by employing two thermodynamic cycles: one for an oxidant (catalyst), along with its reduced, protonated, and hydrogenated form; and one for the substrate, along with its oxidized, deprotonated, and dehydrogenated form. It is demonstrated that η reflects the propensity of the substrate and catalyst for (a)synchronicity in concerted H+/e- transfers. As such, it significantly contributes to the activation energies of the HAA reactions, in addition to a classical thermodynamic (Bell-Evans-Polanyi) effect. In an attempt to understand the physicochemical interpretation of η, we discovered an elegant link between η and reorganization energy λ from Marcus theory. We discovered computationally that for a homologous set of HAA reactions, λ reaches its maximum for the lowest |η|, which then corresponds to the most synchronous HAA mechanism. This immediately implies that among HAA processes with the same reaction free energy, ΔG0, the highest barrier (≡ΔG≠) is expected for the most synchronous proton-coupled electron (i.e., hydrogen) transfer. As proof of concept, redox and acidobasic properties of nonheme FeIVO complexes are correlated with activation free energies for HAA from C-H and O-H bonds. We believe that the reported findings may represent a powerful concept in designing new HAA catalysts.