Functional Molecular Architectures Research Articles

Structural and Energetic Features of Base-Base Stacking Contacts in RNA.

Nucleobase π-π stacking is one of the crucial organizing interactions within three-dimensional (3D) RNA architectures. Characterizing the structural variability of these contacts in RNA crystal structures will help delineate their subtleties and their role in determining function. This analysis of different stacking geometries found in RNA X-ray crystal structures is the largest such survey to date; coupled with quantum-mechanical calculations on typical representatives of each possible stacking arrangement, we determined the distribution of stacking interaction energies. A total of 1,735,481 stacking contacts, spanning 359 of the 384 theoretically possible distinct stacking geometries, were identified. Our analysis reveals preferential occurrences of specific consecutive stacking arrangements in certain regions of RNA architectures. Quantum chemical calculations suggest that 88 of the 359 contacts possess intrinsically stable stacking geometries, whereas the remaining stacks require the RNA backbone or surrounding macromolecular environment to force their formation and maintain their stability. Our systematic analysis of π-π stacks in RNA highlights trends in the occurrence and localization of these noncovalent interactions and may help better understand the structural intricacies of functional RNA-based molecular architectures.

A breath of sunshine: oxygenic photosynthesis by functional molecular architectures.

The conversion of light into chemical energy is the game-changer enabling technology for the energetic transition to renewable and clean solar fuels. The photochemistry of interest includes the overall reductive/oxidative splitting of water into hydrogen and oxygen and alternatives based on the reductive conversion of carbon dioxide or nitrogen, as primary sources of energy-rich products. Devices capable of performing such transformations are based on the integration of three sequential core functions: light absorption, photo-induced charge separation, and the photo-activated breaking/making of molecular bonds via specific catalytic routes. The key to success does not rely simply on the individual components' performance, but on their optimized integration in terms of type, number, geometry, spacing, and linkers dictating the photosynthetic architecture. Natural photosynthesis has evolved along this concept, by integrating each functional component in one specialized "body" (from the Greek word "soma") to enable the conversion of light quanta with high efficiency. Therefore, the natural "quantasome" represents the key paradigm to inspire man-made constructs for artificial photosynthesis. The case study presented in this perspective article deals with the design of artificial photosynthetic systems for water oxidation and oxygen production, engineered as molecular architectures then rendered on electrodic surfaces. Water oxidation to oxygen is indeed the pervasive oxidative reaction used by photosynthetic organisms, as the source of reducing equivalents (electrons and protons) to be delivered for the processing of high-energy products. Considering the vast and abundant supply of water (including seawater) as a renewable source on our planet, this is also a very appealing option for photosynthetic energy devices. We will showcase the progress in the last 15 years (2009-2023) in the strategies for integrating functional building blocks as molecular photosensitizers, multi-redox water oxidation catalysts and semiconductor materials, highlighting how additional components such as redox mediators, hydrophilic/hydrophobic pendants, and protective layers can impact on the overall photosynthetic performance. Emerging directions consider the modular tuning of the multi-component device, in order to target a diversity of photocatalytic oxidations, expanding the scope of the primary electron and proton sources while enhancing the added-value of the oxidation product beyond oxygen: the selective photooxidation of organics combines the green chemistry vision with renewable energy schemes and is expected to explode in coming years.

ZnI2-Mediated β-Galactosylation of C2-Ether-Type Donor.

Conventional glycosylation with galactosyl donors having C-2 benzyl (Bn) ether-type functionality often leads to anomeric mixtures, due to the anomeric and steric effects that stabilize the 1,2-cis-α- and 1,2-trans-β-glycosides, respectively. Herein we report a versatile ZnI2-directed β-galactosylation approach employing a 4,6-O-tethered and 2-O-Bn galactosyl donor for the stereoselective and efficient synthesis of β-O-galactosides. With a broad substrate scope, the reaction tolerates a wide range of functional groups and complex molecular architectures, providing stereocontrolled β-galactosides in moderate to excellent yields. The practicality of this transformation is demonstrated through the synthesis of a tetrasaccharide arabinogalactan fragment with high stereoselectivity.

Excited-State Palladium-Catalyzed α-Selective C1-Ketonylation.

C-Glycosides are important carbohydrate mimetics found in natural products, bioactive compounds, and marketed drugs. However, stereoselective preparation of this class of glycomimetics remains a significant challenge in organic synthesis. Herein, we report an excited-state palladium-catalyzed α-selective C-ketonylation strategy using readily available 1-bromosugars to access a range of C-glycosides. The reaction features excellent α-selectivity and mild conditions that tolerate a wide range of functional groups and complex molecular architectures. The resulting α-ketonylsugars can serve as versatile precursors for their β-isomers and other C-glycosides. Preliminary experimental and computational studies of the mechanism suggest a radical pathway involving the formation of palladoradical and glycosyl radical that undergoes polarity-mismatched coupling with silyl enol ether, affording the desired α-ketonylsugars. Insight into the reactivity and mechanism will inspire new reaction development and provide straightforward access to both α- and β-C-glycosides, greatly expanding the chemical and patent spaces of glycomimetics.

Use of Porphyrin Containing Porous Materials in Heterogeneous Catalyst

Due to their potential applications in catalysis, separation, gas storage, drug delivery, and biosensing, porous materials (PMs) such as porous organic polymers (POPs), polymers with intrinsic microporosity (PIMs), porous coordination polymers (PCPs), and metal–organic frameworks (MOFs), have received much attention. Various building blocks have been prepared and demonstrated various functional materials. Among the various organic building blocks, porphyrin has become one of the most important building blocks for the construction of such materials witnessed by a wide range of molecular architectures using porphyrin derivatives with various applications. Mn(III)- and Fe(III)-containing metalloporphyrins are often used to fabricate various functional molecular architectures and to mimic the extraordinary behavior of enzymes in both homogeneous and heterogeneous catalytic systems. In the case of homogeneous catalysis, Mn(III)- and Fe(III)-containing metalloporphyrins have frequent trouble with fast catalytic degradation because of µ-oxo dimer formation or ligand oxidation. To avoid the catalyst degradation, the immobilization and/or site-isolation of homogeneous catalysts using supporters such as polymers, membranes, and MOFs, are widely used strategy. In addition, they are often used to modify the surface of porous silica materials such as SBA-15, MCM-41 and MCM-48, because these porous silica materials exhibit narrow pore size distributions, high thermal stability and easy accessibility.In this presentation, we like to show the use of metalloporphyrins in various porous materials and their use as heterogeneous catalysts.References D. Y. Shin, J. H. Yoon, S. H. Kim, H. Baik, S. J. Lee,* "Immobilization of Porphyrinic Mn(III) Catalyst on a New Class of Silica Support Comprising Three-Dimensionally Interconnected Network with Two Different Sizes of Pores", Catal. Sci. Technol. 2018, 8, 6306-6310.J. Yi, H. Y. Jeong, D. Y. Shin, C. Kim, S. J. Lee,* "Mn(III)-Porphyrin Containing Heterogeneous Catalyst based on Microporous Polymeric Constituents as a New Class of Catalyst Support", ChemCatChem 2018, 10, 3974-3977.J. Yoon, H. M. Choi, S. J. Lee,* "Cu(II)Cl2 containing bispyridine-based porous organic polymer support prepared via alkyne–azide cycloaddition as a heterogeneous catalyst for oxidation of various olefins", New J. Chem. 2020, 44, 9149-9152.H. M. Choi, Y. J. Kim, E. T. Choi, S. J. Lee,* "Selective Photocatalytic Oxidative Detoxification of a Chemical Warfare Agent Simulant by Porphyrin-Containing Polymers of Intrinsic Microporocity." ACS Appl. Polym. Mater.2021, submitted .

Rigid Bay-Conjugated Perylene Bisimide Rotors: Solvent-Induced Excited-State Symmetry Breaking and Resonance-Enhanced Two-Photon Absorption

Intramolecular charge transfer and excited-state symmetry breaking have a significant effect on the nonlinear optical properties of multipolar chromophores. Rigid and nonplanar perylene bisimide derivatives (PBIs) functionalized at bay positions were comparatively and comprehensively investigated. In apolar solvents, two quadrupolar molecular rotors showed an obvious decrease of the A0-0/A0-1 ratios, suggesting strong exciton coupling with the adjacent PBI units initiated by the π-π stacking. The vanishment of the preferable dimer emission in polar solvents supported the plausible phenomena of excited-state symmetry breaking, thanks to the facile rotation around the rigid linkers. Comparative femtosecond transition absorption studies confirmed their notable differences in relaxation dynamics and the generation of radical anions (PBI•-) and cations (PBI•+). The maxima two-photon absorption (2PA) wavelengths obtained for the molecular rotors were slightly red-shifted to 670 nm with intrinsic resonance-enhanced characteristics, reflecting the synergistic effect of functional positions and molecular architectures. Meanwhile, the obvious increase of significant 2PA cross-section values in polar solvents illustrated the stabilization of the symmetry-broken dipolar states. Further femtosecond Z-scan also manifested the contribution of excited-state dynamics on the nonlinear optical properties of multipolar chromophores.

Excited-State Palladium-Catalyzed Radical Migratory Mizoroki-Heck Reaction Enables C2-Alkenylation of Carbohydrates.

Excited-state palladium catalysis has emerged as a promising strategy for developing novel and valuable reactions. Herein, we report the first excited-state Pd-catalyzed 1,2-radical migratory Mizoroki-Heck reaction that enables C2-alkenylation of carbohydrates using readily available 1-bromosugars and alkenes. The reaction tolerates a wide variety of functional groups and complex molecular architectures, including derivatives of natural products and marketed drugs. Preliminary mechanistic studies and DFT calculations suggest the involvement of visible-light-induced photoexcitation of Pd species, 1,2-spin-centered-shift (SCS) process, and Heck-type cross-coupling reaction. The reaction expands the reactivity profile of excited-state Pd catalysis and provides a streamlined protocol for the preparation of a wide variety of C2-alkenylated carbohydrate mimetics to aid the discovery and development of new therapeutics, agrochemicals, and materials.

Nucleic Acid Architectonics for pH-Responsive DNA Systems and Devices.

Nucleic acid-based architectures have opened up numerous opportunities for basic and applied research in the field of DNA nanotechnology. The scheme of molecular architectonics of nucleic acids exploits conventional and unconventional base pairing interactions to integrate molecular partners in constructing functional molecular architectures and devices. The pH-responsive functional nucleic acid systems and devices have gained interest in diagnostics and therapeutics because of their biocompatibility and structural programmability. In this Mini-Review, we discuss recent advancements in the area of nucleic acid architectonics with a special emphasis on pH-driven molecular systems including molecular and nanoarchitectures, templated architectures and nanoclusters, nanomachines, hydrogels, targeted bioimaging, and drug delivery architectures. Finally, the Mini-Review is concluded by highlighting the challenges and opportunities for future developments.

Nickel-Catalyzed Radical Migratory Coupling Enables C-2 Arylation of Carbohydrates.

Nickel catalysis offers exciting opportunities to address unmet challenges in organic synthesis. Herein we report the first nickel-catalyzed radical migratory cross-coupling reaction for the direct preparation of 2-aryl-2-deoxyglycosides from readily available 1-bromosugars and arylboronic acids. The reaction features a broad substrate scope and tolerates a wide range of functional groups and complex molecular architectures. Preliminary experimental and computational studies suggest a concerted 1,2-acyloxy rearrangement via a cyclic five-membered-ring transition state followed by nickel-catalyzed carbon-carbon bond formation. The novel reactivity provides an efficient route to valuable C-2-arylated carbohydrate mimics and building blocks, allows for new strategic bond disconnections, and expands the reactivity profile of nickel catalysis.

Excited-State Palladium-Catalyzed 1,2-Spin-Center Shift Enables Selective C-2 Reduction, Deuteration, and Iodination of Carbohydrates.

Excited-state catalysis, a process that involves one or more excited catalytic species, has emerged as a powerful tool in organic synthesis because it allows access to the excited-state reaction landscape for the discovery of novel chemical reactivity. Herein, we report the first excited-state palladium-catalyzed 1,2-spin-center shift reaction that enables site-selective functionalization of carbohydrates. The strategy features mild reaction conditions with high levels of regio- and stereoselectivity that tolerate a wide range of functional groups and complex molecular architectures. Mechanistic studies suggest a radical mechanism involving the formation of hybrid palladium species that undergoes a 1,2-spin-center shift followed by the reduction, deuteration, and iodination to afford functionalized 2-deoxy sugars. The new reactivity will provide a general approach for the rapid generation of natural and unnatural carbohydrates.

Emergence of low-symmetry foldamers from single monomers.

Self-assembly is a powerful method to obtain large discrete functional molecular architectures. When using a single building block, self-assembly generally yields symmetrical objects in which all the subunits relate similarly to their neighbours. Here we report the discovery of a family of self-constructing cyclic macromolecules with stable folded conformations of low symmetry, which include some with a prime number (13, 17 and 23) of units, despite being formed from a single component. The formation of these objects amounts to the production of polymers with a perfectly uniform length. Design rules for the spontaneous emergence of such macromolecules include endowing monomers with a strong potential for non-covalent interactions that remain frustrated in competing entropically favoured yet conformationally restrained smaller cycles. The process can also be templated by a guest molecule that itself has an asymmetrical structure, which paves the way to molecular imprinting techniques at the level of single polymer chains.

Self-Metalation of Porphyrins by Cobalt Oxide: Photoemission Spectroscopic Investigation

Understanding the electronic structure between porphyrins and ultrathin metal-oxide film interfaces is vital for the rational design of functional molecular architectures. Here, we have studied the...

Site Isolation of Catalytically Active Mn(III)-Porphyrin into Porous Materials

Porous materials (PMs) including porous coordination polymers (PCPs), metal–organic frameworks (MOFs), porous organic polymers (POPs), and polymers with intrinsic microporosity (PIMs), have received much attention and they often show novel and/or enhanced performances in wide range of applications such as catalysis, separation, gas storage, drug delivery, biosensing, and imaging. Although they can be successfully obtained by controlling the growth conditions, their fabrication is still a major challenge because of lack of information regarding the crucial factors for the precise control of particles during the synthesis. Furthermore, the translation of building blocks into well-defined structures, whose properties and functions are regulated in the building block level, still remains very challenging. In this regard, metalloporphyrins would be good building blocks for the construction of such functional materials witnessed by a wide range of molecular architectures, such as molecular boxes, self-assembled arrays, CPs and MOFs with various applications. Particularly, Mn(III)- and Fe(III)-containing metalloporphyrins are often used to fabricate various functional molecular architectures and to mimic the extraordinary behavior of enzymes in both homogeneous and heterogeneous catalytic systems.In the case of homogeneous catalysis, these materials have frequent trouble with fast catalytic degradation because of µ-oxo dimer formation or ligand oxidation. To avoid the catalyst degradation, the heterogenization of homogeneous catalysts, such as immobilization and/or site-isolation of homogeneous catalysts using supporters are widely used alternative strategies. In this regard, I like to present the preparations and heterogeneous catalytic uses of Mn(III)–porphyrin in various porous materials (PMs).

Partial depolymerization of hydroxypropylmethyl cellulose for production of low molar mass polymer chains

Low molar mass (LMM) biopolymers are highly required to design functional nanomaterials, which mainly find application in biomedical fields. However, the synthesis of LMM polymer is a challenging task. In this work, we report a partial enzymatic depolymerization process which allows to produce a series of LMM hydroxypropylmethyl cellulose (HPMC) polymer, with a weight average molar mass (Mw) under and over 10,000 g mol−1 and low dispersity (Ɖ < 1.5). Variation of the starting HPMC grade, reaction time, and enzyme concentration were the key parameters to control the Mw and yield of the target molecules. This approach provides a versatile way of producing LMM HPMCs with varying degrees of substitution, and having a single reactive aldehyde function at one chain extremity. LMM HPMC can find for instance application as building blocks for the development of new functional molecular architectures.

Self-Sorting of Heteroanions in the Assembly of Cross-Shaped Polyoxometalate Clusters.

Heteroanion (HA) moieties have a key role in templating of heteropolyoxometalate (HPA) architectures, but clusters templated by two different templates are rarely reported. Herein, we show how a cross-shaped HPA-based architecture can self-sort the HA templates by pairing two different guests into a divacant {XYW15O54} building block, with four of these building block units being linked together to complete the cross-shaped architecture. We exploited this observation to incorporate HA templates into well-defined positions within the clusters, leading to the isolation of a collection of mixed-HA templated cross-shaped polyanions [(XYW15O54)4(WO2)4]32-/36- (X = H-P, Y = Se, Te, As). The template positions have been unambiguously determined by single crystal X-ray diffraction, NMR spectroscopy, and high-resolution electrospray ionization mass spectrometry; these studies demonstrated that the mixed template containing HPA clusters are the preferred products which crystallize from the solution. Theoretical studies using DFT calculations suggest that the selective self-sorting originates from the coordination of the template in solution. The cross-shaped polyoxometalate clusters are redox-active, and the ability of molecules to accept electrons is slightly modulated by the HA incorporated as shown by differential pulse voltammetry experiments. These results indicate that the cross-shaped HPAs can be used to select templates from solution, and themselves have interesting geometries, which will be useful in developing functional molecular architectures based upon HPAs with well-defined structures and electronic properties.

Architectonics: Design of Molecular Architecture for Functional Applications.

The term architectonics has its roots in the architectural and philosophical (as early as 1600s) literature that refers to "the theory of structure" and "the structure of theory", respectively. The concept of architectonics has been adapted to advance the field of molecular self-assembly and termed as molecular architectonics. In essence, the methodology of organizing molecular units in the required and controlled configurations to develop advanced functional systems for materials and biological applications comprises the field of molecular architectonics. This concept of designing noncovalent systems enables to focus on different functional aspects of designer molecules for biological and nonbiological applications and also strengthens our efforts toward the mastery over the art of controlled molecular self-assemblies. Programming complex molecular interactions and assemblies for specific functions has been one of the most challenging tasks in the modern era. Meticulously ordered molecular assemblies can impart remarkable developments in several areas spanning energy, health, and environment. For example, the well-defined nano-, micro-, and macroarchitectures of functional molecules with specific molecular ordering possess potential applications in flexible electronics, photovoltaics, photonic crystals, microreactors, sensors, drug delivery, biomedicine, and superhydrophobic coatings, among others. The functional molecular architectures having unparalleled properties are widely evident in various designs of Nature. By drawing inspirations from Nature, intended molecular architectures can be designed and developed to harvest various functions, as there is an inexhaustible resource and scope. In this Account, we present exquisite designer molecules developed by our group and others with an objective to master the art of molecular recognition and self-assembly for functional applications. We demonstrate the tailor-ability of molecular self-assemblies by employing biomolecules like amino acids and nucleobases as auxiliaries. Naphthalenediimide (NDI), perylenediimide (PDI), and few other molecular systems serve as functional modules. The effects of stereochemistry and minute structural modifications in the molecular designs on the supramolecular interactions, and construction of self-assembled zero-dimensional (OD), one-dimensional (1D), and two-dimensional (2D) nano- and microarchitectures like particles, spheres, cups, bowls, fibers, belts, helical belts, supercoiled helices, sheets, fractals, and honeycomb-like arrays are discussed in extensive detail. Additionally, we present molecular systems that showcase the elegant designs of coassembly, templated assembly, hierarchical assembly, transient self-assembly, chiral denaturation, retentive helical memory, self-replication, supramolecular regulation, supramolecular speciation, supernon linearity, dynamic pathway complexity, supramolecular heterojunction, living supramolecular polymerization, and molecular machines. Finally, we describe the molecular engineering principles learnt over the years that have led to several applications, namely, organic electronics, self-cleaning, high-mechanical strength, and tissue engineering.

Probing functional self-assembled molecular architectures with solution/solid scanning tunnelling microscopy.

Over the past two decades, solution/solid STM has made clear contributions to our fundamental understanding of the thermodynamic and kinetic processes that occur in molecular self-assembly at surfaces. As the field matures, we provide an overview of how solution/solid STM is emerging as a tool to elucidate and guide the use of self-assembled molecular systems in practical applications, focusing on small molecule device engineering, molecular recognition and sensing and electronic modification of 2D materials.

Functional molecular architectures based on tetrathiafulvalene building blocks

GRAPHICAL ABSTRACT

Tailor-made Covalent Organic-Inorganic Polyoxometalate Hybrids: Versatile Platforms for the Elaboration of Functional Molecular Architectures.

Post-functionalization of organically modified polyoxometalates (POMs) is a powerful synthetic tool to devise functional building blocks for the rational elaboration of POM-based molecular materials. In this personal account we focus on iodoaryl-terminated POM platforms, describe reliable routes to the synthesis of covalent organic-inorganic POM-based hybrids and their integration into advanced molecular architectures or multi-scale assemblies as well as their immobilization onto surfaces. Valorisation of the remarkable redox properties of POMs in the fields of artificial synthesis and molecular electronic is especially considered.

(Invited) Controlled Growth of Porphyrin Based Nano/Micro Coordination Polymers and Their Use in Olefin Oxidation

Porous coordination polymers (PCPs), also called metal–organic frameworks (MOFs) for three-dimensional (3D) PCPs, have received much attention due to their potential applications. Currently, nano- and microsized PCPs (nPCPs or mPCPs) have often been reported with their promising applications. They could possess numerous advantages over both the PCPs and inorganic nanomaterials, and their novel and/or enhanced performances are frequently reported with potential applications in catalysis, separation, gas storage, drug delivery, biosensing, and imaging. Although a variety of nPCPs or mPCPs can be successfully obtained by controlling the growth conditions, their fabrication is still a major challenge because of lack of information regarding the crucial factors for the precise control of particles during the synthesis. Furthermore, the translation of building blocks into well-defined structures, whose properties and functions are regulated in the building block level, still remains very challenging. In this regard, metalloporphyrins would be good building blocks for the construction of such functional materials witnessed by a wide range of molecular architectures, such as molecular boxes, self-assembled arrays, and CPs, and MOFs with various applications in catalysis, gas storage, and separation. Particularly, Mn(III)- and Fe(III)-containing metalloporphyrins are often used to fabricate various functional molecular architectures and to mimic the extraordinary behavior of enzymes in both homogeneous and heterogeneous catalysis. In the case of homogeneous catalysis, these materials have frequent trouble with fast catalytic degradation because of µ-oxo dimer formation or ligand oxidation. To avoid the catalyst degradation, the heterogenization of homogeneous catalysts, such as immobilization and site-isolation of homogeneous catalysts on polymers, membranes, and MOF supports, is widely used alternative strategy. Here I like to present the preparation and heterogeneous catalytic uses of Mn(III)–porphyrin that contain size-controlled amorphous and crystalline nano- and microsized CPs. Particularly, I like to focus on the conversion of kinetically controlled amorphous assemblies into thermodynamically controlled crystalline structures based on the self-assembly of Mn(III)–porphyrin biscarboxylic acid and Co(OAc)2.