Cleaving DNA with DNA: Cooperative Tuning of Structure and Reactivity Driven by Copper Ions

A copper-dependent self-cleaving DNA (DNAzyme or deoyxyribozyme) previously isolated by in vitro selection has been analyzed by a combination of Molecular Dynamics (MD) simulations and advanced Electron Paramagnetic Resonance (Electron Spin Resonance) EPR/ESR spectroscopy, providing insights on the structural and mechanistic features of the cleavage reaction. The modeled 46-nucleotide deoxyribozyme in MD simulations forms duplex and triplex sub-structures that flank a highly conserved catalytic core. The DNA self-cleaving construct can also form a bimolecular complex that has a distinct substrate and enzyme domains. The highly dynamic structure combined with an oxidative site-specific cleavage of the substrate are two key-aspects to elucidate. By combining EPR/ESR spectroscopy with selectively isotopically labeled nucleotides it has been possible to overcome the major drawback related to the "metal-soup" scenario, also known as "super-stoichiometric" ratios of cofactors versus substrate, conventionally required for the DNA cleavage reaction within those nucleic acids-based enzymes. The focus on the endogenous paramagnetic center (Cu2+) here described paves the way for analysis on mixtures where several different cofactors are involved. Furthermore, the insertion of cleavage reaction within more complex architectures is now a realistic perspective towards the applicability of EPR/ESR spectroscopic studies.

Syntheses and Electrochemical and EPR Studies of Porphyrins Functionalized with Bulky Aromatic Amine Donors

A series of nickel(II) porphyrins bearing one or two bulky nitrogen donors at the meso positions were prepared by using Ullmann methodology or more classical Buchwald-Hartwig amination reactions to create the new C-N bonds. For several new compounds, single crystals were obtained, and the X-ray structures were solved. The electrochemical data of these compounds are reported. For a few representative examples, spectroelectrochemical measurements were used to clarify the electron exchange process. In addition, a detailed electron paramagnetic resonance (EPR) study was performed to estimate the extent of delocalization of the generated radical cations. In particular, electron nuclear double resonance spectroscopy (ENDOR) was used to determine the coupling constants. DFT calculations were conducted to corroborate the EPR spectroscopic data.

Multi-Electron Visible Light Photoaccumulation on a Dipyridylamine Copper(II)-Polyoxometalate Conjugate Applied to Photocatalytic Generation of CF3 Radicals

This article describes the synthesis and characterization of an organic-inorganic hybrid polyoxometalate functionalized by a short link with a tripodal N-based ligand and its copper complex. Upon visible light irradiation, the latter is able to store up to three reducing equivalents. The locus of the reduction is discussed based on physicochemical measurements and DFT calculations. In the presence of Togni's reagent, this complex allows for the photocatalytic generation of CF₃ radicals, opening the road to valuable synthetic applications.

How Metal Nuclearity Impacts Electrocatalytic H2 Production in Thiocarbohydrazone-Based Complexes

Thiocarbohydrazone-based catalysts feature ligands that are potentially electrochemically active. From the synthesis point of view, these ligands can be easily tailored, opening multiple strategies for optimization, such as using different substituent groups or metal substitution. In this work, we show the possibility of a new strategy, involving the nuclearity of the system, meaning the number of metal centers. We report the synthesis and characterization of a trinuclear nickel-thiocarbohydrazone complex displaying an improved turnover rate compared with its mononuclear counterpart. We use DFT calculations to show that the mechanism involved is metal-centered, unlike the metal-assisted ligand-centered mechanism found in the mononuclear complex. Finally, we show that two possible mechanisms can be assigned to this catalyst, both involving an initial double reduction of the system.

Structural Features Governing the Metabolic Stability of Tetraethyl-Substituted Nitroxides in Rat Liver Microsomes

Nitroxides are potent tools for studying biological systems by electron paramagnetic resonance (EPR). Whatever the application, a certain stability is necessary for successful detection. Since conventional tetramethyl-substituted cyclic nitroxides have insufficient in vivo stability, efforts have recently been made to synthesize more stable, tetraethyl-substituted nitroxides. In our previous study on piperidine nitroxides, the introduction of steric hindrance around the nitroxide moiety successfully increased the resistance to reduction into hydroxylamine. However, it also rendered the carbon backbone susceptible to modifications by xenobiotic metabolism due to increased lipophilicity. Here, we focus on a new series of three nitroxide candidates with tetraethyl substitution, namely with pyrrolidine, pyrroline, and isoindoline cores, to identify which structural features afford increased stability for future probe design and application in in vivo EPR imaging. In the presence of rat liver microsomes, pyrrolidine and pyrroline tetraethyl nitroxides exhibited a higher stability than isoindoline nitroxide, which was studied in detail by HPLC-HRMS. Multiple metabolites suggest that the aerobic transformation of tetraethyl isoindoline nitroxide is initiated by hydrogen abstraction by P450-Fe^V = O from one of the ethyl groups, followed by rearrangement and further modifications by cytochrome P450, as supported by DFT calculations. Under anaerobic conditions, only reduction by rat liver microsomes was observed with involvement of P450-Fe^II.

Computational Insights of Selective Intramolecular O-atom Transfer Mediated by Bioinspired Copper Complexes

The stereoselective copper-mediated hydroxylation of intramolecular C-H bonds from tridentate ligands is reinvestigated using DFT calculations. The computational study aims at deciphering the mechanism of C-H hydroxylation obtained after reaction of Cu(I) precursors with dioxygen, using ligands bearing either activated (L¹ ) or non-activated (L² ) C-H bonds. Configurational analysis allows rationalization of the experimentally observed regio- and stereoselectivity. The computed mechanism involves the formation of a side-on peroxide species (P) in equilibrium with the key intermediate bis-(μ-oxo) isomer (O) responsible for the C-H activation step. The P/O equilibrium yields the same activation barrier for the two complexes. However, the main difference between the two model complexes is observed during the C-H activation step, where the complex bearing the non-activated C-H bonds yields a higher energy barrier, accounting for the experimental lack of reactivity of this complex under those conditions.

Decoding the Ambiguous Electron Paramagnetic Resonance Signals in the Lytic Polysaccharide Monooxygenase from Photorhabdus luminescens

Understanding the structure and function of lytic polysaccharide monooxygenases (LPMOs), copper enzymes that degrade recalcitrant polysaccharides, requires the reliable atomistic interpretation of electron paramagnetic resonance (EPR) data on the Cu(II) active site. Among various LPMO families, the chitin-active PlAA10 shows an intriguing phenomenology with distinct EPR signals, a major rhombic and a minor axial signal. Here, we combine experimental and computational investigations to uncover the structural identity of these signals. X-band EPR spectra recorded at different pH values demonstrate pH-dependent population inversion: the major rhombic signal at pH 6.5 becomes minor at pH 8.5, where the axial signal dominates. This suggests that a protonation change is involved in the interconversion. Precise structural interpretations are pursued with quantum chemical calculations. Given that accurate calculations of Cu g-tensors remain challenging for quantum chemistry, we first address this problem via a thorough calibration study. This enables us to define a density functional that achieves accurate and reliable prediction of g-tensors, giving confidence in our evaluation of PlAA10 LPMO models. Large models were considered that include all parts of the protein matrix surrounding the Cu site, along with the characteristic second-sphere features of PlAA10. The results uniquely identify the rhombic signal with a five-coordinate Cu ion bearing two water molecules in addition to three N-donor ligands. The axial signal is attributed to a four-coordinate Cu ion where only one of the waters remains bound, as hydroxy. Alternatives that involve decoordination of the histidine brace amino group are unlikely based on energetics and spectroscopy. These results provide a reliable spectroscopy-consistent view on the plasticity of the resting state in PlAA10 LPMO as a foundation for further elucidating structure-property relationships and the formation of catalytically competent species. Our strategy is generally applicable to the study of EPR parameters of mononuclear copper-containing metalloenzymes.

From Ligand- to Metal-centered Reactivity: Metal Substitution Effect in Thiosemicarbazone-based Complexes for H2 Production

The quest to develop and optimize catalysts for H 2 production requires a thorough understanding in the possible catalytic mechanisms involved. Transition metals are very often the centers of reactivity in the catalysis, although this can change in the presence of a redox-active ligand. Investigating the differences in catalysis when considering ligand- and metal-centered reactivity is important to find the most optimal mechanisms for hydrogen evolution reaction. Here, we investigated this change of reactivity in two versions of a thiosemicarbazone-based complex, using Co and Ni metal centers. While the Ni version has a ligand-centered reactivity, Co switches it toward a metal-centered one. Comparison between the mechanisms show differences in rate-limiting steps, and shows the importance of identifying those steps in order to optimize the system for hydrogen production.

Magnetic exchange coupling in Cu dimers studied with modern multireference methods and broken-symmetry coupled cluster theory

Spin-state energetics of exchange-coupled copper complexes pose a persistent challenge for applied quantum chemistry. Here, we provide a comprehensive comparison of all available theoretical approaches to the problem of exchange coupling in two antiferromagnetically coupled bis-μ-hydroxo Cu(II) dimers. The evaluated methods include multireference methods based on the density matrix renormalization group (DMRG), multireference methods that incorporate dynamic electron correlation either perturbatively, such as the N-electron valence state perturbation theory, or variationally, such as the difference-dedicated configuration interaction. In addition, we contrast the multireference results with those obtained using broken-symmetry approaches that utilize either density functional theory or, as demonstrated here for the first time in such systems, a local implementation of coupled cluster theory. The results show that the spin-state energetics of these copper dimers are dominated by dynamic electron correlation and represent an impossible challenge for multireference methods that rely on brute-force expansion of the active space to recover correlation energy. Therefore, DMRG-based methods even at the limit of their applicability cannot describe quantitatively the antiferromagnetic exchange coupling in these dimers, in contrast to dinuclear complexes of earlier transition metal ions. The convergence of the broken-symmetry coupled cluster approach is studied and shown to be a limiting factor for the practical application of the method. The advantages and disadvantages of all approaches are discussed, and recommendations are made for future developments.

Self-assembled nickel cubanes as oxygen evolution catalysts

Ni₄O₄ cubanes [(μ₃-L¹O)NiCl(MeOH)]₄ (1) and [(μ₃-L²O)NiCl(H₂O)]₄ (2) (L¹OH = 1-H-2-benzimidazolylmethanol, L²OH = 1-methyl-2-benzimidazolylmethanol) self-assemble from commercially available 1-H- and 1-methyl-2-benzimidazolylmethanol and NiCl₂·6H₂O in high yields under mild conditions. Both complexes were characterised spectroscopically and by X-ray crystallography. The cubanes oxidise water electrocatalytically to dioxygen at neutral pH in aqueous potassium phosphate buffer solutions.

Quantum dynamics of Mn2+ in dimethylammonium magnesium formate

Dimethylammonium magnesium formate, [(CH₃)₂NH₂][Mg(HCOO)₃] or DMAMgF, is a model used to study high temperature hybrid perovskite-like dielectrics. This compound displays an order-disorder phase transition at about 260 K. Using multifrequency electron spin resonance in continuous wave and pulsed modes, we herein present the quantum dynamics of the Mn²⁺ ion probe in DMAMgF. In the high temperature paraelectric phase, we observe a large distribution of the zero field splitting that is attributed to the high local disorder and further supported by density functional theory computations. In the low temperature ferroelastic phase, a single structure phase is detected and shown to contain two magnetic structures. The complex electron paramagnetic resonance signals were identified by means of the Rabi oscillation method combined with the crystal field kernel density estimation.

Unraveling the catalytic mechanisms of H2 production with thiosemicarbazone nickel complexes

Thiosemicarbazone-based complexes have been explored as a new class of redox-active catalysts H2 production due to their flexibility for extensive optimization. To rationalize the process, we need to understand how these complexes function. In this work, we used DFT calculations to investigate the various mechanisms that could take place for three previously characterized Ni complexes. We found that two possible mechanisms are compatible with previously published experimental data, involving protonation of two adjacent N atoms close to the metal center. The first step likely involves a proton-coupled electron transfer process from a proton source to one of the distal N atoms in the ligand. From here, a second proton can be transferred either to the coordinating N atom situated in between the first protonated atom and the Ni atom, or to the second distal N atom. The former case then has the protons in close distance for H2 production. However, the latter will require a third protonation event to occur, which would fall in one of the N atoms adjacent to the Ni center, resulting in a similar mechanism. Finally, we show that the H-H bond formation is the rate-limiting step, and suggest additional strategies that can be taken into account to further optimize these complexes.

A hybrid bioinspired catechol-alloxazine triangular nickel complex stabilizing protons and electrons

A new class of redox-active ligands merging catechol and alloxazine structures is reported. A trimetallic triangular complex is formed upon complexation to nickel.

Successes, challenges, and opportunities for quantum chemistry in understanding metalloenzymes for solar fuels research

Overview of the rich and diverse contributions of quantum chemistry to understanding the structure and function of the biological archetypes for solar fuel research, photosystem II and hydrogenases.

Comparison of Density Functional and Correlated Wave Function Methods for the Prediction of Cu(II) Hyperfine Coupling Constants

The reliable prediction of Cu(II) hyperfine coupling constants remains a challenge for quantum chemistry. Until recently only density functional theory (DFT) could target this property for systems of realistic size. However, wave function based methods become increasingly applicable. In the present work, we define a large set of Cu(II) complexes with experimentally known hyperfine coupling constants and use it to investigate the performance of modern quantum chemical methods for the prediction of this challenging spectroscopic parameter. DFT methods are evaluated against orbital‐optimized second‐order Møller‐Plesset (OO‐MP2) theory and coupled cluster calculations including singles and doubles excitations, driven by the domain‐based local pair natural orbital approach (DLPNO‐CCSD). Special attention is paid to the definition of a basis set that converges adequately toward the basis set limit for the given property for all methods considered in this study, and a specifically optimized basis set is proposed for this purpose. The results suggest that wave function based methods can supplant but do not outcompete DFT for the calculation of Cu(II) hyperfine coupling constants. Mainstream hybrid functionals such as B3PW91 remain on average the best choice.

Unexpected rapid aerobic transformation of 2,2,6,6-tetraethyl-4-oxo(piperidin-1-yloxyl) radical by cytochrome P450 in the presence of NADPH: Evidence against a simple reduction of the nitroxide moiety to the hydroxylamine

Aminoxyl radicals (nitroxides) are a class of compounds with important biomedical applications, serving as antioxidants, spin labels for proteins, spin probes of oximetry, pH, or redox status in electron paramagnetic resonance (EPR), or as contrast agents in magnetic resonance imaging (MRI). However, the fast reduction of the radical moiety in common tetramethyl-substituted cyclic nitroxides within cells, yielding diamagnetic hydroxylamines, limits their use in spectroscopic and imaging studies. In vivo half-lives of commonly used tetramethyl-substituted nitroxides span no more than a few minutes. Therefore, synthetic efforts have focused on enhancing the nitroxide stability towards reduction by varying the electronic and steric environment of the radical. Tetraethyl-substitution at alpha position to the aminoxyl function proved efficient in vitro against reduction by ascorbate or cytosolic extracts. Moreover, 2,2,6,6-tetraethyl-4-oxo(piperidin-1-yloxyl) radical (TEEPONE) was used successfully for tridimensional EPR and MRI in vivo imaging of mouse head, with a reported half-life of over 80 min. We decided to investigate the stability of tetraethyl-substituted piperidine nitroxides in the presence of hepatic microsomal fractions, since no detailed study of their "metabolic stability" at the molecular level had been reported despite examples of the use of these nitroxides in vivo. In this context, the rapid aerobic transformation of TEEPONE observed in the presence of rat liver microsomal fractions and NADPH was unexpected. Combining EPR, HPLC-HRMS, and DFT studies on a series of piperidine nitroxides - TEEPONE, 4-oxo-2,2,6,6-tetramethyl(piperidin-1-yloxyl) (TEMPONE), and 2,2,6,6-tetraethyl-4-hydroxy(piperidin-1-yloxyl) (TEEPOL), we propose that the rapid loss in paramagnetic character of TEEPONE is not due to reduction to hydroxylamine but is a consequence of carbon backbone modification initiated by hydrogen radical abstraction in alpha position to the carbonyl by the P450-Fe^(V)=O species. Besides, hydrogen radical abstraction by P450 on ethyl substituents, leading to dehydrogenation or hydroxylation products, leaves the aminoxyl function intact but could alter the linewidth of the EPR signal and thus interfere with methods relying on measurement of this parameter (EPR oximetry).

Tuning Inner-Sphere Electron Transfer in a Series of Copper/Nitrosoarene Adducts

A series of copper/nitrosoarene complexes was created that mimics several steps in biomimetic O₂ activation by copper(I). The reaction of the copper(I) complex of N,N,N',N'-tetramethypropylenediamine with a series of para-substituted nitrosobenzene derivatives leads to adducts in which the nitrosoarene (ArNO) is reduced by zero, one, or two electrons, akin to the isovalent species dioxygen, superoxide, and peroxide, respectively. The geometric and electronic structures of these adducts were characterized by means of X-ray diffraction, vibrational analysis, ultraviolet-visible spectroscopy, NMR, electrochemistry, and density functional theory (DFT) calculations. The bonding mode of the NO moiety depends on the oxidation state of the ArNO moiety: κN for ArNO, mononuclear η²-NO and dinuclear μ-η²:η¹ for ArNO^•-, and dinuclear μ-η²:η² for ArNO^2-. ¹⁵N isotopic labeling confirms the reduction state by measuring the NO stretching frequency (1392 cm^-1 for κN-ArNO, 1226 cm^-1 for η²-ArNO^•-, 1133 cm^-1 for dinuclear μ-η²:η¹-ArNO^•-, and 875 cm^-1 for dinuclear μ-η²:η² for ArNO^2-). The ¹⁵N NMR signal disappears for the ArNO^•- species, establishing a unique diagnostic for the radical state. Electrochemical studies indicate reduction waves that are consistent with one-electron reduction of the adducts and are compared with studies performed on Cu-O₂ analogues. DFT calculations were undertaken to confirm our experimental findings, notably to establish the nature of the charge-transfer transitions responsible for the intense green color of the complexes. In fine, this family of complexes is unique in that it walks through three redox states of the ArNO moiety while keeping the metal and its supporting ligand the same. This work provides snapshots of the reactivity of the toxic nitrosoarene molecules with the biologically relevant Cu(I) ion.

Optimizing Group Transfer Catalysis by Copper Complex with Redox-Active Ligand in an Entatic State

Metalloenzymes use earth-abundant non-noble metals to perform high-fidelity transformations in the biological world. To ensure chemical efficiency, metalloenzymes have acquired evolutionary reactivity-enhancing tools. Among these, the entatic state model states that a strongly distorted geometry induced by ligands around a metal center gives rise to an energized structure called entatic state, strongly improving the reactivity. However, the original definition refers both to the transfer of electrons or chemical groups, whereas the chemical application of this concept in synthetic systems has mostly focused on electron transfer, therefore eluding chemical transformations. Here we report that a highly strained redox-active ligand enables a copper complex to perform catalytic nitrogen- and carbon-group transfer in as fast as 2 min, thus exhibiting a strong increase in reactivity compared with its unstrained analogue. This report combines two reactivity-enhancing features from metalloenzymes, entasis and redox cofactors, applied to group-transfer catalysis.

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We design a catalyst interfacing two reactivity-enhancing tools from metalloenzymes

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This work merges redox-active cofactors and entatic state reactivity

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The modifications in the coordination sphere lead to enhanced catalytic behavior

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These results open perspectives in bioinspired catalysis and group-transfer reactions

Hydrogen evolution reaction mediated by an all-sulfur trinuclear nickel complex

A trinuclear nickel complex with S-based ligands is reported as a bio-inspired model of the [NiFe] hydrogenases' active site. DFT calculations indicate that thiolate and thioether functions are involved as proton relays in the H₂ evolution mechanism.

Ligand-based electronic effects on the electrocatalytic hydrogen production by thiosemicarbazone nickel complexes

This work reports on the synthesis and characterization of a series of mononuclear thiosemicarbazone nickel complexes that display significant catalytic activity for hydrogen production in DMF using trifluoroacetic acid as the proton source.

Molecular Electrocatalysts for the Hydrogen Evolution Reaction: Input from Quantum Chemistry

In the pursuit of carbon-free fuels, hydrogen can be considered as an apt energy carrier. The design of molecular electrocatalysts for hydrogen production is important for the development of renewable energy sources that are abundant, inexpensive, and environmentally benign. Over the last 20 years, a large number of electrocatalysts have been developed, and considerable efforts have been directed toward the design of earth-abundant, first-row transition-metal complexes capable of promoting electrocatalytic hydrogen evolution reaction (HER). In this context, numerical approaches have emerged as powerful tools to study the catalytic performances of these complexes. This review covers some of the most significant theoretical mechanistic studies of biomimetic and bioinspired homogeneous HER catalysts. The approaches employed to study the free energy landscapes are discussed and methods used to obtain accurate estimates of relevant observables required to study the HER are presented. Furthermore, the structural and electronic parameters that govern the reactivity, and are necessary to achieve efficient hydrogen production, are discussed in view of future research directions.

Efficient Light-Driven Hydrogen Evolution Using a Thiosemicarbazone-Nickel (II) Complex

In the following work, we carried out a systematic study investigating the behavior of a thiosemicarbazone-nickel (II) complex (NiTSC-OMe) as a molecular catalyst for photo-induced hydrogen production. A comprehensive comparison regarding the combination of three different chromophores with this catalyst has been performed, using [Ir(ppy)₂(bpy)]PF₆, [Ru(bpy)₃]Cl₂ and [ZnTMePy]PCl₄ as photosensitizers. Thorough evaluation of the parameters affecting the hydrogen evolution experiments (i.e., concentration, pH, solvent nature, and ratio), has been performed in order to probe the most efficient photocatalytic system, which was comprised by NiTSC-OMe and [Ir(ppy)₂(bpy)]PF₆ as catalyst and chromophore, respectively. The electrochemical together with the photophysical investigation clarified the properties of this photocatalytic system and allowed us to propose a possible reaction mechanism for hydrogen production.

Superlattice Induced by Charge Order in the Organic Spin Chain (TMTTF)2X (X = SbF6, AsF6, and PF6) Revealed by High-Field Electron Paramagnetic Resonance

We have investigated the charge ordering phase of the quasi-one-dimensional quantum antiferromagnet (TMTTF)₂X (X = SbF₆, AsF₆, and PF₆) using high-fields/frequency electron paramagnetic resonance. In addition to the uniform displacement of the counteranions involved in the charge-order phase, we report the existence of a superlattice between the spin chains in the direction c, caused by the space modulation of the charge order. When the field is high enough, the magnetic decoupling of the spin chains allows us to estimate the interaction between the chains, J _c < 1 mK, three orders of magnitude lower than expected from the mean field theory.

Copper-Catalyzed Aziridination with Redox-Active Ligands: Molecular Spin Catalysis

Small-molecule catalysts as mimics of biological systems illustrate the chemists' attempts at emulating the tantalizing abilities displayed by nature's metalloenzymes. Among these innate behaviors, spin multistate reactivity is used by biological systems as it offers thermodynamic leverage towards challenging chemical reactivity but this concept is difficult to translate into the realm of synthetic organometallic catalysis. Here, we report a rare example of molecular spin catalysis involving multistate reactivity in a small-molecule biomimetic copper catalyst applied to aziridination. This behavior is supported by spin state flexibility enabled by the redox-active ligand.

Circumventing Intrinsic Metal Reactivity: Radical Generation with Redox-Active Ligands

Nickel complexes have gained sustained attention as efficient catalysts in cross-coupling reactions and co-catalysts in dual systems due to their ability to react with radical species. Central to this reactivity is nickel's propensity to shuttle through several accessible redox states from Ni⁰ to Ni^IV . Here, we report the catalytic generation of trifluoromethyl radicals from a nickel complex bearing redox-active iminosemiquinone ligands. This unprecedented reactivity is enabled through ligand-based oxidation performing electron transfer to an electrophilic CF₃⁺ source while the nickel oxidation state is preserved. Additionally, extension of this reactivity to a copper complex bearing a single redox equivalent is reported, thus providing a unified reactivity scheme. These results open new pathways in radical chemistry with redox-active ligands.