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.

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.

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.

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.

Experimental-Theoretical Approach to the Adsorption Mechanisms for Anionic, Cationic, and Zwitterionic Surfactants at the Calcite-Water Interface.

The adsorption of surfactants (DTAB, SDS, and CAPB) at the calcite-water interface was studied through surface zeta potential measurements and multiscale molecular dynamics. The ground-state polarization of surfactants proved to be a key factor for the observed behavior; correlation was found between adsorption and the hard or soft charge distribution of the amphiphile. SDS exhibits a steep aggregation profile, reaching saturation and showing classic ionic-surfactant behavior. In contrast, DTAB and CAPB featured diversified adsorption profiles, suggesting interplay between supramolecular aggregation and desorption from the solid surface and alleviating charge buildup at the carbonate surface when bulk concentration approaches CMC. This manifests as an adsorption profile with a fast initial step, followed by a metastable plateau and finalizing with a sharp decrease and stabilization of surface charge. Suggesting this competition of equilibria, elicited at the CaCO3 surface, this study provides atomistic insight into the adsorption mechanism for ionic surfactants on calcite, which is in accordance with experimental evidence and which is a relevant criterion for developing enhanced oil recovery processes.

Design, synthesis, in vitro evaluation and preliminary SAR studies of N-(2-(heteroaryloxy)propyl)phenothiazines against Rhipicephalus microplus cattle tick.

A family of 15 N-substituted phenothiazines was designed, synthesized and their acaricidal activity against Rhipicephalus microplus was determined in vitro. The synthetic methodology is simple and can be employed in multigram scale. The rationale for the structure-based design of these compounds is the potential for azines and phenothiazine to engage in π-π interactions; these fragments, joined together by a short, flexible alkoxide linker, structurally resemble phenothiazine-based cholinesterase inhibitors, while their weak basicity implies a neutral active form, rather than a cationic one, thus facilitating penetration of the cuticle of ticks. One compound displayed excellent acaricidal activity (LD50=0.58 µg/mL). Preliminary SAR analysis suggests that the activity is influenced by the presence of a weakly basic nitrogen atom, as well as the substitution pattern within the heterocycles.