Controllable DNA strand displacement by independent metal–ligand complexation

Introduction of artificial metal–ligand base pairs can enrich the structural diversity and functional controllability of nucleic acids. In this work, we revealed a novel approach by placing a ligand-type nucleoside as an independent toehold to control DNA strand-displacement reactions based on metal–ligand complexation. This metal-mediated artificial base pair could initiate strand invasion similar to the natural toehold DNA, but exhibited flexible controllability to manipulate the dynamics of strand displacement that was only governed by its intrinsic coordination properties. External factors that influence the intrinsic properties of metal–ligand complexation, including metal species, metal concentrations and pH conditions, could be utilized to regulate the strand dynamics. Reversible control of DNA strand-displacement reactions was also achieved through combination of the metal-mediated artificial base pair with the conventional toehold-mediated strand exchange by cyclical treatments of the metal ion and the chelating reagent. Unlike previous studies of embedded metal-mediated base pairs within natural base pairs, this metal–ligand complexation is not integrated into the nucleic acid structure, but functions as an independent toehold to regulate strand displacement, which would open a new door for the development of versatile dynamic DNA nanotechnologies.

This metal-mediated artificial base pair can function as an independent toehold based on metal–ligand coordination and exhibit flexible and reversible controllability to manipulate the dynamics of strand displacement.     

Metal–ligand cooperativity in the soluble hydrogenase-1 from Pyrococcus furiosus

Metal–ligand cooperativity is an essential feature of bioinorganic catalysis. The design principles of such cooperativity in metalloenzymes are underexplored, but are critical to understand for developing efficient catalysts designed with earth abundant metals for small molecule activation. The simple substrate requirements of reversible proton reduction by the [NiFe]-hydrogenases make them a model bioinorganic system. A highly conserved arginine residue (R355) directly above the exogenous ligand binding position of the [NiFe]-catalytic core is known to be essential for optimal function because mutation to a lysine results in lower catalytic rates. To expand on our studies of soluble hydrogenase-1 from Pyrococcus furiosus (Pf SH1), we investigated the role of R355 by site-directed-mutagenesis to a lysine (R355K) using infrared and electron paramagnetic resonance spectroscopic probes sensitive to active site redox and protonation events. It was found the mutation resulted in an altered ligand binding environment at the [NiFe] centre. A key observation was destabilization of the Ni_a³⁺–C state, which contains a bridging hydride. Instead, the tautomeric Ni_a⁺–L states were observed. Overall, the results provided insight into complex metal–ligand cooperativity between the active site and protein scaffold that modulates the bridging hydride stability and the proton inventory, which should prove valuable to design principles for efficient bioinspired catalysts.

Metal–ligand cooperativity is an essential feature of bioinorganic catalysis.     

Switchable electrical conductivity in a three-dimensional metal–organic framework via reversible ligand n-doping

Redox-active metal–organic frameworks (MOFs) are promising materials for a number of next-generation technologies, and recent work has shown that redox manipulation can dramatically enhance electrical conductivity in MOFs. However, ligand-based strategies for controlling conductivity remain under-developed, particularly those that make use of reversible redox processes. Here we report the first use of ligand n-doping to engender electrical conductivity in a porous 3D MOF, leading to tunable conductivity values that span over six orders of magnitude. Moreover, this work represents the first example of redox switching leading to reversible conductivity changes in a 3D MOF.

Redox-active ligands are used to reversibly tune electrical conductivity in a porous 3D metal–organic framework (MOF).     

Experimental evidence for a general model of modulated MOF nanoparticle growth

Nanoparticles of metal–organic frameworks (nanoMOFs) boast superior properties compared to their bulk analogs, yet little is known about how common synthetic parameters dictate particle sizes. Here, we provide experimental evidence for the “seesaw” model of nanoMOF growth. Solution acidity, ligand excess, and reactant concentrations are decoupled and shown to form the key independent determinants of nanoMOF sizes, thereby validating the proposal that nanoMOFs arise from coupled equilibria involving ligand deprotonation and metal–ligand complexation. By achieving the first demonstration of a seesaw relationship between nanoMOF sizes and ligand excess, these results provide further proof of the model, as they required deliberate manipulation of relationships outlined by the model. Exploring the relative impacts of these parameters reveals that ligand excess has the greatest ability to decrease sizes, although low acidity and high concentrations can exhibit similar effects. As a complement to existing models of polymer formation and crystal growth, the seesaw model therefore offers a powerful tool for reliable control over nanoMOF sizes.

Nanoparticles of metal–organic frameworks (nanoMOFs) boast superior properties compared to their bulk analogs, yet little is known about how common synthetic parameters dictate particle sizes.     

Pressure-induced phosphorescence enhancement and piezochromism of a carbazole-based cyclic trinuclear Cu(i) complex

Interest in piezochromic luminescence has increased in recent decades, even though it is mostly limited to pure organic compounds and fluorescence. In this work, a Cu₃Pz₃ (Cu3, Pz: pyrazolate) cyclic trinuclear complex (CTC) with two different crystalline polymorphs, namely 1a and 1b, was synthesized. The CTC consists of two functional moieties: carbazole (Cz) chromophore and Cu3 units. In crystals of 1a, discrete Cz–Cu3–Cu3–Cz stacking was found, showing abnormal pressure-induced phosphorescence enhancement (PIPE), which was 12 times stronger at 2.23 GPa compared to under ambient conditions. This novel observation is ascribed to cooperation between heavy-atom effects (i.e., from Cu atoms) and metal–ligand charge-transfer promotion. The infinite π–π stacking of Cz motifs was observed in 1b and it exhibited good piezochromism as the pressure increased. This work demonstrates a new concept in the design of piezochromic materials to achieve PIPE via combining organic chromophores and metal–organic phosphorescence emitters.

One molecule, two response mechanisms: a pair of newly-designed cyclic trinuclear Cu(i) complex crystalline polymorphs are engineered, which show excellent luminescent piezochromism and pressure-induced phosphorescence enhancement, respectively.     

Single-step synthesis and interface tuning of core–shell metal–organic framework nanoparticles

Control over the spatial distribution of components in metal–organic frameworks has potential to unlock improved performance and new behaviour in separations, sensing and catalysis. We report an unprecedented single-step synthesis of multi-component metal–organic framework (MOF) nanoparticles based on the canonical ZIF-8 (Zn) system and its Cd analogue, which form with a core–shell structure whose internal interface can be systematically tuned. We use scanning transmission electron microscopy, X-ray energy dispersive spectroscopy and a new composition gradient model to fit high-resolution X-ray diffraction data to show how core–shell composition and interface characteristics are intricately controlled by synthesis temperature and reaction composition. Particle formation is investigated by in situ X-ray diffraction, which reveals that the spatial distribution of components evolves with time and is determined by the interplay of phase stability, crystallisation kinetics and diffusion. This work opens up new possibilities for the control and characterisation of functionality, component distribution and interfaces in MOF-based materials.

Core–shell metal–organic framework nanoparticles have been synthesised in which the internal interface and distribution of components is found to be highly tunable using simple variations in reaction conditions.     

Catalysis using transition metal complexes featuring main group metal and metalloid compounds as supporting ligands

Recent development in catalytic application of transition metal complexes having an M–E bond (E = main group metal or metalloid element), which is stabilized by a multidentate ligand, is summarized. Main group metal and metalloid supporting ligands furnish unusual electronic and steric environments and molecular functions to transition metals, which are not easily available with standard organic supporting ligands such as phosphines and amines. These characteristics often realize remarkable catalytic activity, unique product selectivity, and new molecular transformations. This perspective demonstrates the promising utility of main group metal and metalloid compounds as a new class of supporting ligands for transition metal catalysts in synthetic chemistry.

Recent development in catalytic application of transition metal complexes having an M–E bond (E = main group metal or metalloid element), which is stabilized by a multidentate ligand, is summarized.     

A 2,2′-diphosphinotolane as a versatile precursor for the synthesis of P-ylidic mesoionic carbenes via reversible C–P bond formation

A metal-templated synthetic route to cyclic (aryl)(ylidic) mesoionic carbenes (CArY-MICs) featuring an endocyclic P-ylide is presented. This approach, which requires metal templates with two cis-positioned open coordination sites, is based on the controlled cyclisation of a P,P′-diisopropyl-substituted 2,2′-diphosphinotolane (1) and leads to chelate complexes coordinated by a phosphine donor and the CArY-MIC carbon atom. The C–P bond formation involved in the former partial cyclisation of 1 proceeds under mild conditions and was shown to be applicable all over the d-block. In the presence of a third fac-positioned open coordination site, the P–C bond formation was found to be reversible, as shown for a series of molybdenum complexes. DFT modelling studies are in line with an interpretation of the target compounds as CArY-MICs.

A metal-templated synthesis of cyclic (aryl)(ylidic)mesoionic carbene complexes (CArY-MICs) is presented. In the case of molybdenum carbonyls, the crucial P–C bond formation, which occurs during CArY-MIC formation, was found to be reversible.     

Photo-induced copper-catalyzed alkynylation and amination of remote unactivated C(sp3)-H bonds

A method for remote radical C–H alkynylation and amination of diverse aliphatic alcohols has been developed. The reaction features a copper nucleophile complex formed in situ as a photocatalyst, which reduces the silicon-tethered aliphatic iodide to an alkyl radical to initiate 1,n-hydrogen atom transfer. Unactivated secondary and tertiary C–H bonds at β, γ, and δ positions can be functionalized in a predictable manner.

Remote C−H alkynylation and amination of aliphatic alcohols.     

Metal–ligand–Lewis acid multi-cooperative catalysis: a step forward in the Conia-ene reaction

An original multi-cooperative catalytic approach was developed by combining metal–ligand cooperation and Lewis acid activation. The [(SCS)Pd]₂ complex featuring a non-innocent indenediide-based ligand was found to be a very efficient and versatile catalyst for the Conia-ene reaction, when associated with Mg(OTf)₂. The reaction operates at low catalytic loadings under mild conditions with HFIP as a co-solvent. It works with a variety of substrates, including those bearing internal alkynes. It displays complete 5-exo vs. 6-endo regio-selectivity. In addition, except for the highly congested ^tBu-substituent, the reaction occurs with high Z vs. E stereo-selectivity, making it synthetically useful and complementary to known catalysts.

An original multi-cooperative catalytic approach was developed by combining metal–ligand cooperation and Lewis acid activation.     

Catalytic three-component C–C bond forming dearomatization of bromoarenes with malonates and diazo compounds

A Pd-catalyzed dearomative three-component C–C bond formation of bromoarenes with diazo compounds and malonates was developed. Various bromoarenes ranging from benzenoids to azines and heteroles were transformed to the corresponding substituted alicyclic molecules. The key to this reaction is the generation of a benzyl–palladium intermediate, which reacts with malonates to form a Pd–O-enolate species. Strikingly, the present method enabled rapid access to multi-substituted alicycles through subsequent elaboration of dearomatized products.

A catalytic three-component C–C bond forming dearomatization of bromoarenes was developed, enabling rapid access to multi-substituted alicycles.     

Effects of ruthenium hydride species on primary amine synthesis by direct amination of alcohols over a heterogeneous Ru catalyst

Heterogeneously catalysed synthesis of primary amines by direct amination of alcohols with ammonia has long been an elusive goal. In contrast to reported Ru-based catalytic systems, we report that Ru–MgO/TiO₂ acts as an effective heterogeneous catalyst for the direct amination of a variety of alcohols to primary amines at low temperatures of ca. 100 °C without the introduction of H₂ gas. The present system could be applied to a variety of alcohols and provides an efficient synthetic route for 2,5-bis(aminomethyl)furan (BAMF), an attention-getting biomonomer. The high catalytic performance can be rationalized by the reactivity tuning of Ru–H species using MgO. Spectroscopic measurements suggest that MgO enhances the reactivity of hydride species by electron donation from MgO to Ru.

Ru–MgO/TiO₂ exhibited high catalytic performance for direct amination of alcohols based on the acceleration effects of MgO.     

Self-healing and shape memory functions exhibited by supramolecular liquid-crystalline networks formed by combination of hydrogen bonding interactions and coordination bonding

We here report a new approach to develop self-healing shape memory supramolecular liquid-crystalline (LC) networks through self-assembly of molecular building blocks via combination of hydrogen bonding and coordination bonding. We have designed and synthesized supramolecular LC polymers and networks based on the complexation of a forklike mesogenic ligand with Ag⁺ ions and carboxylic acids. Unidirectionally aligned fibers and free-standing films forming layered LC nanostructures have been obtained for the supramolecular LC networks. We have found that hybrid supramolecular LC networks formed through metal–ligand interactions and hydrogen bonding exhibit both self-healing properties and shape memory functions, while hydrogen-bonded LC networks only show self-healing properties. The combination of hydrogen bonds and metal–ligand interactions allows the tuning of intermolecular interactions and self-assembled structures, leading to the formation of the dynamic supramolecular LC materials. The new material design presented here has potential for the development of smart LC materials and functional LC membranes with tunable responsiveness.

New supramolecular hybrid liquid-crystalline networks exhibiting self-healing and shape memory properties are developed by self-assembly of small components through hydrogen bonding interactions and coordination bonding.     

Reversible cooperative dihydrogen binding and transfer with a bis-phosphenium complex of chromium

The reversible reaction of H₂ with a bis-phosphenium complex of chromium provides a rare example of 3d transition metal/phosphenium cooperativity. Photolysis induces the activation of H₂ and yields a spectroscopically detectable phosphenium-stabilized (σ–H₂)-complex, readily showing exchange with gaseous H₂ and D₂. Further reaction of this complex affords a phosphine-functionalized metal hydride, representing a unique example of reversible H₂ cleavage across a 3d M P bond. The same species is also accessible via stepwise H⁺/H⁻ transfer to the bis-phosphenium complex, and releases H₂ upon heating or irradiation. Dihydrogen transfer from the H₂-complex to styrene is exploited to demonstrate the first example of promoting hydrogenation with a phosphenium complex.

Photolysis of a phosphenium complex enables reversible activation of H₂ to yield a dihydrogen complex which stimulates H₂ cleavage or catalytic hydrogenation.     

Effects of ligands on the migratory insertion of alkenes into rhodium–oxygen bonds

Migratory insertions of olefins into metal–oxygen bonds are elementary steps of important catalytic processes, but well characterised complexes that undergo this reaction are rare, and little information on the effects of ancillary ligands on such reactions has been gained. We report a series of alkoxo alkene complexes of rhodium(i) that contain a range of bidentate ligands and that undergo insertion of the alkene. Our results show that complexes containing less electron-donating ancillary ligands react faster than their counterparts containing more electron-donating ancillary ligands, and that complexes possessing ligands with larger bite angles react faster than those with smaller bite angles. External added ligands had several effects on the reactions, including an inhibition of olefin isomerisation in the product and acceleration of the displacement of the product from complexes of ancillary ligands with small bite angles. Complementary computational studies help elucidate the details of these insertion processes.

A series of diphosphine-ligated rhodium(i) alkoxo alkene complexes is reported and the migratory insertion of the alkene moiety into the rhodium–oxygen bond in these complexes was studied, revealing the effects of the ligand on the insertion process.     

Lattice oxygen self-spillover on reducible oxide supported metal cluster: the water–gas shift reaction on Cu/CeO2 catalyst

In this work we have tackled one of the most challenging problems in nanocatalysis namely understanding the role of reducible oxide supports in metal catalyzed reactions. As a prototypical example, the very well-studied water gas shift reaction catalyzed by CeO₂ supported Cu nanoclusters is chosen to probe how the reducible oxide support modifies the catalyst structures, catalytically active sites and even the reaction mechanisms. By employing density functional theory calculations in conjunction with a genetic algorithm and ab initio molecular dynamics simulations, we have identified an unprecedented spillover of the surface lattice oxygen from the ceria support to the Cu cluster, which is rarely considered previously but may widely exist in oxide supported metal catalysts under realistic conditions. The oxygen spillover causes a highly energetic preference of the monolayered configuration of the supported Cu nanocluster, compared to multilayered configurations. Due to the strong metal–oxide interaction, after the O spillover the monolayered cluster is highly oxidized by transferring electrons to the Ce 4f orbitals. The water–gas-shift reaction is further found to more favorably take place on the supported copper monolayer than the copper-ceria periphery, where the on-site oxygen and the adjacent oxidized Cu sites account for the catalytically active sites, synergistically facilitating the water dissociation and the carboxyl formation. The present work provides mechanistic insights into the strong metal–support interaction and its role in catalytic reactions, which may pave a way towards the rational design of metal–oxide catalysts with promising stability, dispersion and catalytic activity.

The lattice oxygen on the reducible CeO₂ support could self-spillover to surface of Cu cluster, generating the on-site oxygen to promote the catalytic water–gas shift reaction.     

Reversible metathesis of ammonia in an acyclic germylene–Ni0 complex

Carbenes, a class of low-valent group 14 ligand, have shifted the paradigm in our understanding of the effects of supporting ligands in transition-metal reactivity and catalysis. We now seek to move towards utilizing the heavier group 14 elements in effective ligand systems, which can potentially surpass carbon in their ability to operate via ‘non-innocent’ bond activation processes. Herein we describe our initial results towards the development of scalable acyclic chelating germylene ligands (viz.1a/b), and their utilization in the stabilization of Ni⁰ complexes (viz.4a/b), which can readily and reversibly undergo metathesis with ammonia with no net change of oxidation state at the Ge^II and Ni⁰ centres, through ammonia bonding at the germylene ligand as opposed to the Ni⁰ centre. The DFT-derived metathesis mechanism, which surprisingly demonstrates the need for three molecules of ammonia to achieve N–H bond activation, supports reversible ammonia binding at Ge^II, as well as the observed reversibility in the overall reaction.

Chelating single-centre ambiphile ligands based upon low-coordinate, acyclic germylenes have been developed, remaining highly Lewis acidic even when bound to Ni⁰, remarkably allowing for the reversible metathesis of the N–H bonds in ammonia at Ge^II.     

Backbonding contributions to small molecule chemisorption in a metal–organic framework with open copper(i) centers

Metal–organic frameworks are promising materials for applications such as gas capture, separation, and storage, due to their ability to selectively adsorb small molecules. The metal–organic framework Cu^I-MFU-4l, which contains coordinatively unsaturated copper(i) centers, can engage in backbonding interactions with various small molecule guests, motivating the design of frameworks that engage in backbonding and other electronic interactions for highly efficient and selective adsorption. Here, we examine several gases expected to bind to the open copper(i) sites in Cu^I-MFU-4l via different electronic interactions, including σ-donation, π-backbonding, and formal electron transfer. We show that in situ Cu L-edge near edge X-ray absorption fine structure (NEXAFS) spectroscopy can elucidate π-backbonding by directly probing excitations to unoccupied backbonding orbitals with Cu d-character, even for gases that participate in other dominant interactions, such as ligand-to-metal σ-donation. First-principles calculations based on density functional theory and time-dependent density functional theory additionally reveal the backbonding molecular orbitals associated with these spectroscopic transitions. The energies of the transitions correlate with the energy levels of the isolated small molecule adsorbates, and the transition intensities are proportional to the binding energies of the guest molecules within Cu^I-MFU-4l. By elucidating the molecular and electronic structure origins of backbonding interactions between electron rich metal centers in metal–organic frameworks and small molecule guests, it is possible to develop guidelines for further molecular-level design of solid-state adsorbents for energy-efficient separations of relevance to industry.

In situ near edge X-ray absorption fine structure spectroscopy directly probes unoccupied states associated with backbonding interactions between the open metal site in a metal–organic framework and various small molecule guests.     

Radical condensation between benzylic alcohols and acetamides to form 3-arylpropanamides

A new radical condensation reaction is developed where benzylic alcohols and acetamides are coupled to generate 3-arylpropanamides with water as the only byproduct. The transformation is performed with potassium tert-butoxide as the only additive and gives rise to a variety of 3-arylpropanamides in good yields. The mechanism has been investigated experimentally with labelled substrates, trapping experiments and spectroscopic measurements. The findings indicate a radical pathway where potassium tert-butoxide is believed to serve a dual role as both base and radical initiator. The radical anion of the benzylic alcohol is proposed as the key intermediate, which undergoes coupling with the enolate of the amide to form the new C–C bond. Subsequent elimination to the corresponding cinnamamide and olefin reduction then affords the 3-arylpropanamides.

Benzylic alcohols and acetamides are coupled into 3-arylpropanamides by a new radical condensation through the radical anion of the alcohol.     

Ligand design by targeting a binding site water

Solvent reorganization is a major driving force of protein–ligand association, but the contribution of binding site waters to ligand affinity is poorly understood. We investigated how altered interactions with a water network can influence ligand binding to a receptor. A series of ligands of the A_2A adenosine receptor, which either interacted with or displaced an ordered binding site water, were studied experimentally and by molecular dynamics simulations. An analog of the endogenous ligand that was unable to hydrogen bond to the ordered water lost affinity and this activity cliff was captured by molecular dynamics simulations. Two compounds designed to displace the ordered water from the binding site were then synthesized and evaluated experimentally, leading to the discovery of an A_2A agonist with nanomolar activity. Calculation of the thermodynamic profiles resulting from introducing substituents that interacted with or displaced the ordered water showed that the gain of binding affinity was enthalpy driven. Detailed analysis of the energetics and binding site hydration networks revealed that the enthalpy change was governed by contributions that are commonly neglected in structure-based drug optimization. In particular, simulations suggested that displacement of water from a binding site to the bulk solvent can lead to large energy contributions. Our findings provide insights into the molecular driving forces of protein–ligand binding and strategies for rational drug design.

Solvent reorganization is a major driving force of protein–ligand association, but the contribution of binding site waters to ligand affinity is poorly understood.