Functional Mimics Research Articles

Rings of Power: Controlling SOD Mimic Activity by the Addition of Pyridine Rings within the Pyridinophane Scaffold.

Superoxide dismutase enzymes are a major defense against superoxide, which is a potent reactive oxygen species. Misregulation of reactive oxygen species and subsequent neuronal damage are etiological hallmarks of neurodegenerative disease. Macrocyclic small molecules have offered inroads toward functional SOD1 mimics. Herein, we report a series of five tetra-aza macrocyclic RPy2N2 ligands, varied by 4-position substitution of the pyridine ring with both electron-donating (R = OMe) and withdrawing groups (R = Cl, I, and CF3) to offer the first comparison to well-studied RPyN3 congeners and other mimics in the literature. New ligands have been characterized by NMR, mass spectrometry, elemental analysis, and potentiometric titrations (pKa). Cyclic voltammetry and X-ray diffraction analysis of the copper(II) complexes (CuII(RPy2N2)2+) demonstrate how pyridine substitution impacts the metal center. This data, and evaluation of the log βCu(II) and log βCu(I) within the series, indicates significant improvement to the binding affinity for Cu(I) without sacrifice of Cu(II) binding. The CuII(RPy2N2)2+ series yield the highest kcat for any Cu(II)-based small molecule functional SOD1 mimic (kcat = 45.36 M-1 s-1). Furthermore, the CuII(OMePy2N2)2+ and CuII(CF3Py2N2)2+ complexes were studied in FRDA cells to determine cell toxicity as a first step toward the application of these mimics as therapeutics for neurological disease.

A Structural and Functional Mimic of P680+

AbstractOne or multiple chlorophyll a molecules are employed in the reaction center of photosystem II′s main electron donor (defined as P680). We have a poor understanding of how the reaction center facilitates water oxidation in photosystem II and the roles that mono‐ and/or multimeric chlorophyll groups play when P680 oxidizes a neighboring tyrosine in order to drive water oxidation at the oxygen evolving complex. We have prepared a dimeric MgII‐porphyrin complex [Mg2(BTPP)] (1, H4‐BTPP=1,2‐bis‐(10,15,20‐triphenylporphyrin‐5‐yl)‐benzene) as a structural and functional mimic of the dimeric core of P680. 1 was oxidized by one‐electron to the corresponding π‐cation radical complex 2. The radical cation was characterized by UV/Vis‐NIR, FT‐IR, and EPR spectroscopic techniques. 2 was shown to be reactive towards phenols to give the corresponding phenoxyl radicals, mimicking the reactivity of the P680 cation radical which oxidizes tyrosine to tyrosyl radical. Critically, the dimeric π‐cation radical showed markedly higher rates of proton coupled electron transfer oxidation (PCET) of phenols when compared to its monomeric counterpart [Mg(TPP)] (TPP=5,10,15,20‐tetraphenylporphyrin). Our findings demonstrate that MgII‐porphyrin complexes are reliable mimics of photosynthetic PCET processes and suggest that photosynthetic reaction centers with multiple π‐conjugated complexes likely lower the barrier to PCET oxidation by π‐cation radical species.

Cleavage of a Peroxide Bond via a Dual Attack by Functional Mimics of Glutathione Peroxidase.

Nonmetal-containing peroxidase enzymes, including glutathione peroxidase (GPx), and peroxiredoxins, control cellular redox levels by catalyzing the reduction of H2O2. The remarkably higher reactivity of GPx enzyme as compared to the fully dissociated synthetic selenolate/thiolate molecule is probably due to the dual-attack on the peroxide bond (HO1-O2H) by the enzyme; The first one is a nucleophilic attack of the selenolate/thiolate moiety to O1 atom and the second attack at the O2 atom of the peroxide bond by the acidic "parked proton" from Trp or His residue present at the enzyme's active site, leading to the facile cleavage of O-O bond. Herein, we report two synthetic compounds (1 and 2), having a selenolate (Se-) and a proton donor (imidazolium or -COOH group) moieties, which showed excellent GPx-like activity via dual-attack on the peroxide bond. The combined effect of selenolate moiety that donates electrons to the antibonding (σ*) orbital of O1-O2 bond and the imidazolium or carboxylic acid moiety at the side chain that forms a strong H-bonding with the O2 atom facilitates O-O bond cleavage of H2O2 more efficiently. 1 and 2 exhibit remarkable ability in protecting Cu(I)-complex [TpmCu(CH3CN)]+ (9) against H2O2 by acting as a sacrificial antioxidant, thereby preventing metal-mediated ROS production.

A Structural and Functional Mimic of P680.

One or multiple chlorophyll molecules are employed in the reaction center of photosystem II's main electron donor (defined as P680). We have a poor understanding of how the reaction center facilitates water oxidation and the roles that mono- and/or multimeric chlorophyll groups play when P680 oxidizes a neighboring tyrosine in order to drive water oxidation at the oxygen evolving complex. We have prepared a dimeric MgII-porphyrin complex [Mg2(BTPP)] (1, H4-BTPP = 1,2-bis-(10,15,20-triphenylporphyrin-5-yl)-benzene) as a structural and functional mimic of the dimeric core of P680. 1 was oxidized by one-electron to the corresponding π-cation radical complex 2. The radical cation was characterized by UV-Vis-NIR, FT-IR, and EPR spectroscopic techniques. 2 was shown to be reactive towards phenols to give the corresponding phenoxyl radicals, mimicking the reactivity of the P680 cation radical which oxidizes tyrosine to tyrosyl radical. Critically, the dimeric π-cation radical showed markedly higher rates of proton coupled electron transfer oxidation (PCET) of phenols when compared to its monomeric counterpart [Mg(TPP)] (TPP = 5,10,15,20-tetraphenylporphyrin). Our findings demonstrate that MgII-porphyrin complexes are reliable mimics of photosynthetic PCET processes and suggest that photosynthetic reaction centers with multiple π-conjugated complexes likely lower the barrier to PCET oxidation by π-cation radical species.

Clinical characteristics and management of functional neurological disorders (FND) mimicking stroke in emergency settings: a functional stroke mimic cases.

FNDs mimicking a stroke represent a growing challenge in the emergency department (ED). A comprehensive diagnostic approach involving clinical evaluation and neuroimaging is essential to differentiate stroke from mimics. The safety profile of thrombolysis justifies its use where FNDs cannot be ruled out. This approach highlights the need for more precise diagnostic tools and protocols to improve patient care and reduce unnecessary treatments. Distinguishing FNDs from actual cerebrovascular events is critical yet difficult, particularly under time constraints. Given the urgency and potential severity of strokes, intravenous thrombolysis is frequently administered even when FNDs cannot be definitively excluded. This retrospective study analyzed data of participants admitted to the Trieste University Hospital Stroke Unit between January 2018 and December 2022, focusing on those presenting with sudden-onset focal neurological deficits mimicking a stroke, with some presenting within the reperfusion treatment window (<4.5 h from symptoms onset). We obtained detailed clinical evaluations and neuroimaging, and administered thrombolytic therapy in selected cases. We included 84 participants presenting with stroke mimics (average age of 45 yo) predominantly female (65.5%). Most common presentations: hemiparesis or hemisensory loss (75%), speech disorder (10.7%), vertigo/gait disorders (4.8%). History of psychiatric disorders was found in 32.1% of cases, and 48.8% had prior neurological disease or stroke risk factors. Advanced neuroimaging was performed in 43 cases yielding normal or non-specific results. Thrombolysis was safely administered in 31%. Patients mostly recovered within the first 24 h from admission (44.7%). We compared this FND's sample with 291 patients with mild ischemic stroke (NIHSS ≤7).

New BDNF and NT-3 Cyclic Mimetics Concur with Copper to Activate Trophic Signaling Pathways as Potential Molecular Entities to Protect Old Brains from Neurodegeneration.

A low level of Neurotrophins (NTs), their Tyrosine Kinase Receptors (Trks), Vascular Endothelial Growth Factors (VEGFs) and their receptors, mainly VEGFR1 and VEGFR2, characterizes AD brains. The use of NTs and VEGFs as drugs presents different issues due to their low permeability of the blood-brain barrier, the poor pharmacokinetic profile, and the relevant side effects. To overcome these issues, different functional and structural NT mimics have been employed. Being aware that the N-terminus domain as the key domain of NTs for the binding selectivity and activation of Trks and the need to avoid or delay proteolysis, we herein report on the mimicking ability of two cyclic peptide encompassing the N-terminus of Brain Derived Growth Factor (BDNF), (c-[HSDPARRGELSV-]), cBDNF(1-12) and of Neurotrophin3 (NT3), (c-[YAEHKSHRGEYSV-]), cNT3(1-13). The two cyclic peptide features were characterized by a combined thermodynamic and spectroscopic approach (potentiometry, NMR, UV-vis and CD) that was extended to their copper(II) ion complexes. SH-SY5Y cell assays show that the Cu2+ present at the sub-micromolar level in the complete culture media affects the treatments with the two peptides. cBDNF(1-12) and cNT3(1-13) act as ionophores, induce neuronal differentiation and promote Trks and CREB phosphorylation in a copper dependent manner. Consistently, both peptide and Cu2+ stimulate BDNF and VEGF expression as well as VEGF release; cBDNF(1-12) and cNT3(1-13) induce the expression of Trks and VEGFRs.

A smartphone-based tunable tyrosinase functional mimic modulated portable amperometric sensor for the rapid and real-time monitoring of catechol

A smartphone-based electrochemical sensor for rapid detection of catechol (CC) was designed. The system contained a smartphone, a hand-held detector, and tyrosinase enzyme mimicking material modified screen-printed carbon electrode (SPCE). Metal nanoparticles confined in porous carbon have been widely used as enzyme mimics owing to their enhanced electrochemical activity. However, the fabrication of enzyme-mimicking catalysts in a scalable and tunable manner is challenging. A two-step synthesis strategy was followed: carbonization of the silica template to form cubic-structured mesoporous carbon (CMC) and high-temperature calcination for copper confinement into CMC (Cu–CMC). The non-covalent interactions enable the Cu precursors to coordinate with the carbon atoms in the face-centered cubic lattice of CMC. The uncalcined material is the as-synthesized (As–Cu–CMC), while the 900 °C calcined are stage 1 (Cu–CMCS1) and stage 2 (Cu–CMCS2) materials with different Cu loadings. The Cu–CMCS2 possess a large pore volume (0.224 cm3g−1) and high surface area (104.2 m2/g). The Cu–CMCS2 modulated sensors enable rapid and real-time detection of CC. Under optimized conditions, the linear range of 1.0–1000 µM (0.0 V vs. integrated Ag/AgCl reference electrode) with the sensitivity and lower detection limit of 10.21 µA µM−1 cm−2 and 0.099 μM (S/N=3) was achieved. The excellent sensor performance is attributed to the increased number of Cu vacancies that mimic the native tyrosinase enzyme. The sensor connected to a portable potentiostat enable high-throughput real-time testing of the CC without sophisticated equipment. Furthermore, the sensor detected CC in green tea and water samples, and the results were validated using UV–visible spectrophotometry and high-performance liquid chromatography.Abbreviations: CMC, cubic-structured mesoporous carbon; Cu–CMCS2, copper loaded stage 2 material; CC, catechol; CMS, cubic mesoporous silica; SPCE, screen-printed carbon electrode; HF, hydrofluoric acid; P123, Pluronic 123; TEOS, Tetraethyl orthosilicate; AA, ascorbic acid; Glu, glucose; HQ, hydroquinone; 4-NP, 4-nitrophenol; CA, caffeic acid; RS, resorcinol; Cu–CMCS1, copper loaded stage 1 material; UV–Vis, UV–visible spectrophotometry; FE-SEM, field-–emission scanning electron microscopy; EDS, energy–dispersive X–-ray spectroscopy; Si, silica; TEM, transmission electron microscopy; NPs, nanoparticles; SAED, selected area electron diffraction; FT-IR, Fourier-Transform Infrared Spectroscopy; BET, Brunauer–Emmett–Teller; BJH, Barrett–Joyner–Halenda; TGA, Thermogravimetric analysis; CV, cyclic voltammetry; ipa, anodic peak current; ECSA, electrochemically active surface area; EIS, electrochemical impedance spectroscopy; Rct, charge-transfer resistance; CA, chronoamperometry; LOD, limit of detection.

Observation of oxygenated intermediates in functional mimics of aminophenol dioxygenase

Aminophenol dioxygenases (APDO) are mononuclear nonheme iron enzymes that utilize dioxygen (O2) to catalyze the conversion of o-aminophenols to 2-picolinic acid derivatives in metabolic pathways. This study describes the synthesis and O2 reactivity of two synthetic models of substrate-bound APDO: [FeII(TpMe2)(tBu2APH)] (1) and [FeII(TpMe2)(tBuAPH)] (2), where TpMe2 = hydrotris(3,5-dimethylpyrazole-1-yl)borate, tBu2APH = 4,6-di-tert-butyl-2-aminophenolate, and tBuAPH2 = 4-tert-butyl-2-aminophenolate. Both Fe(II) complexes behave as functional APDO mimics, as exposure to O2 results in oxidative CC bond cleavage of the o-aminophenolate ligand. The ring-cleaved products undergo spontaneous cyclization to give substituted 2-picolinic acids, as verified by 1H NMR spectroscopy, mass spectrometry, and X-ray crystallography. Reaction of the APDO models with O2 at low temperature reveals multiple intermediates, which were probed with UV–vis absorption, electron paramagnetic resonance (EPR), Mössbauer (MB), and resonance Raman (rRaman) spectroscopies. The most stable intermediate at −70 °C in THF exhibits multiple isotopically-sensitive features in rRaman samples prepared with 16O2 and 18O2, confirming incorporation of O2-derived atom(s) into its molecular structure. Insights into the geometric structures, electronic properties, and spectroscopic features of the observed intermediates were obtained from density functional theory (DFT) calculations. Although functional APDO models have been previously reported, this is the first time that an oxygenated ligand-based radical has been detected and spectroscopically characterized in the ring-cleaving mechanism of a relevant synthetic system.

Genetic Encoding of Phosphorylated Amino Acids into Proteins.

Reversible phosphorylation is a fundamental mechanism for controlling protein function. Despite the critical roles phosphorylated proteins play in physiology and disease, our ability to study individual phospho-proteoforms has been hindered by a lack of versatile methods to efficiently generate homogeneous proteins with site-specific phosphoamino acids or with functional mimics that are resistant to phosphatases. Genetic code expansion (GCE) is emerging as a transformative approach to tackle this challenge, allowing direct incorporation of phosphoamino acids into proteins during translation in response to amber stop codons. This genetic programming of phospho-protein synthesis eliminates the reliance on kinase-based or chemical semisynthesis approaches, making it broadly applicable to diverse phospho-proteoforms. In this comprehensive review, we provide a brief introduction to GCE and trace the development of existing GCE technologies for installing phosphoserine, phosphothreonine, phosphotyrosine, and their mimics, discussing both their advantages as well as their limitations. While some of the technologies are still early in their development, others are already robust enough to greatly expand the range of biologically relevant questions that can be addressed. We highlight new discoveries enabled by these GCE approaches, provide practical considerations for the application of technologies by non-GCE experts, and also identify avenues ripe for further development.

Preparation and characterization of MnIIMnIII complexes with relevance to class Ib ribonucleotide reductases

The Mn2 complex [MnII2(TPDP)(O2CPh)2](BPh4) (1, TPDP = 1,3-bis(bis(pyridin-2-ylmethyl)amino)propan-2-ol, Ph =phenyl) was prepared and subsequently characterized via single-crystal X-ray diffraction, X-ray absorption, electronic absorption, and infrared spectroscopies, and mass spectrometry. 1 was prepared in order to explore its properties as a structural and functional mimic of class Ib ribonucleotide reductases (RNRs). 1 reacted with superoxide anion (O2•–) to generate a peroxido-MnIIMnIII complex, 2. The electronic absorption and electron paramagnetic resonance (EPR) spectra of 2 were similar to previously published peroxido-MnIIMnIII species. Furthermore, X-ray near edge absorption structure (XANES) studies indicated the conversion of a MnII2 core in 1 to a MnIIMnIII state in 2. Treatment of 2 with para-toluenesulfonic acid (p-TsOH) resulted in the conversion to a new MnIIMnIII species, 3, rather than causing O—O bond scission, as previously encountered. 3 was characterized using electronic absorption, EPR, and X-ray absorption spectroscopies. Unlike other reported peroxido-MnIIMnIII species, 3 was capable of oxidative O—H activation, mirroring the generation of tyrosyl radical in class Ib RNRs, however without accessing the MnIIIMnIV state.

Enantioselective Transformations by "1 + x" Synergistic Catalysis with Chiral Primary Amines.

ConspectusSynergistic catalysis is a powerful tool that involves two or more distinctive catalytic systems to activate reaction partners simultaneously, thereby expanding the reactivity space of individual catalysis. As an established catalytic strategy, organocatalysis has found numerous applications in enantioselective transformations under rather mild conditions. Recently, the introduction of other catalytic systems has significantly expanded the reaction space of typical organocatalysis. In this regard, aminocatalysis is a prototypical example of synergistic catalysis. The combination of aminocatalyst and transition metal could be traced back to the early days of organocatalysis and has now been well explored as an enabling catalytic strategy. Particularly, the acid-base properties of aminocatalysis can be significantly expanded to include usually electrophiles generated in situ via metal-catalyzed cycles. Later on, aminocatalyst has also been exploited in synergistically combining with photochemical and electrochemical processes to facilitate redox transformations. However, synergistically combining one type of aminocatalyst with many different catalytic systems remains a great challenge. One of the most daunting challenges is the compatibility of aminocatalysts in coexistence with other catalytic species. As nucleophilic species, aminocatalysts may also bind with metal, which leads to mutual inhibition or even quenching of the individual catalytic activity. In addition, oxidative stability of aminocatalyst is also a non-neglectable issue, which causes difficulties in exploring oxidative enamine transformations.In 2007, we developed a vicinal diamine type of chiral primary aminocatalysts. This class of primary aminocatalysts was developed and evolved as functional and mechanistic mimics to the natural aldolase and has been widely applied in a number of enamine/iminium ion-based transformations. By following a "1 + x" synergistic strategy, the chiral primary amine catalysts were found to work synergistically or cooperatively with a number of transition metal catalysts, such as Pd, Rh, Ag, Co, and Cu, or other organocatalysts, such as B(C6F5)3, ketone, selenium, and iodide. Photocatalysis and electrochemical processes can also be incorporated to work together with the chiral primary amine catalysts. The 1 + x catalytic strategy enabled us to execute unexploited transformations by fine-tuning the acid-base and redox properties of the enamine intermediates and to achieve effective reaction and stereocontrol beyond the reach individually. During these efforts, an unprecedented excited-state chemistry of enamine was uncovered to make possible an effective deracemization process. In this Account, we describe our recent efforts since 2015 in exploring synergistic chiral primary amine catalysis, and the content is categorized according to the type of synergistic partner such that in each section the developed synergistic catalysis, reaction scopes, and mechanistic features are presented and discussed.

A CoII-Hydroxide Complex That Converts Directly to a CoII-Acetamide during Catalytic Nitrile Hydration.

In exploring structural and functional mimics of nitrile hydratases, we report the synthesis of the pseudo-trigonal bipyramidal CoII complexes (K)[CoII(DMF)(LPh)] (1(DMF)), (NMe4)2[CoII(OAc)(LPh)] (1(OAc)), and (NMe4)2[CoII(OH)(LPh)] (1(OH)) (LPh = 2,2',2''-nitrilo-tris-(N-phenylacetamide; DMF = N,N-dimethylformamide; -OAc = acetate)). The complexes were characterized using NMR, FT-IR, ESI-MS, electronic absorption spectroscopy, and X-ray crystallography, showing the LPh ligand to bind in a tetradentate tripodal fashion alongside the respective ancillary donor. One of the complexes, 1(OH), is an unusual structural and functional mimic of the Co active site in Co nitrile hydratases. 1(OH) reacted with acetonitrile to yield the CoII-acetamide complex (NMe4)2[CoII(NHC(O)CH3)(LPh)], 2, which was also thoroughly characterized. In the presence of excess hydroxide, 1(OH) was found to catalyze quantitative conversion of the added hydroxide into acetamide. Despite the differences in Co oxidation state in nitrile hydratases and 1(OH) (CoIII versus CoII, respectively), 1(OH) was nonetheless an effective nitrile hydration catalyst, selectively producing acetamide over multiple turnovers.

High-Copy Transposons from a Pathogen Give Rise to a Conserved sRNA Family with a Novel Host Immunity Target.

Small RNAs (sRNAs) are involved in gene silencing in multiple ways, including through cross-kingdom transfers from parasites to their hosts. Little is known about the evolutionary mechanisms enabling eukaryotic microbes to evolve functional mimics of host small regulatory RNAs. Here, we describe the identification and functional characterization of SINE_sRNA1, an sRNA family derived from highly abundant short interspersed nuclear element (SINE) retrotransposons in the genome of the wheat powdery mildew pathogen. SINE_sRNA1 is encoded by a sequence motif that is conserved in multiple SINE families and corresponds to a functional plant microRNA (miRNA) mimic targeting Tae_AP1, a wheat gene encoding an aspartic protease only found in monocots. Tae_AP1 has a novel function enhancing both pattern-triggered immunity (PTI) and effector-triggered immunity (ETI), thereby contributing to the cross activation of plant defenses. We conclude that SINE_sRNA1 and Tae_AP1 are functional innovations, suggesting the contribution of transposons to the evolutionary arms race between a parasite and its host. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Identification and characterization of novel drought-responsive lncRNAs in stone apple (Aegle marmelos L.) through whole-transcriptome analysis

Stone apple (Aegle marmelos L.) is a subtropical fruit tree of the Rutaceae family, highly valued in traditional medicine across the Indian subcontinent. We conceived this study with the objective of developing a comprehensive transcriptome dataset, identifying SSRs for marker-assisted breeding, and delineating regulators of gene expression, with a specific emphasis on non-coding RNA (ncRNA), particularly related to drought stress. To achieve this, RNA-seq was conducted using RNA pooled from various tissues, including roots, leaves, inflorescence, and developing seeds from stone apple, and the clean reads were assembled into 40,886 unigenes. Subsequently, the unigenes were categorized into gene ontology categories encompassing biological processes, molecular functions, and cellular components. Within the unigenes, we identified a total of 9174 perfect simple sequence repeats (SSRs), 2167 transcription factors (TFs) distributed among 69 families, and 415 transcription regulators (TRs) across 27 families. Additionally, 19 microRNAs (miRNAs) from 12 families, 16,811 potential long noncoding RNAs (lncRNAs), and six functional endogenous target mimics (eTMs) were detected. Analysis of lncRNA-miRNA-mRNA interactions unveiled multiple regulatory nodes, elucidating lncRNA/miRNA-driven gene expression control in stone apple. The increased co-expression of selected drought-related lncRNAs and their cognate target mRNAs supported the aforementioned findings under drought conditions. Overall, this study significantly advances our understanding of stone apple genomics and lays a foundation for future omics-based studies, thereby facilitating the deployment of climate-resilient strategies in the species.

Computational Analysis of the Superoxide Dismutase Mimicry Exhibited by a Zinc(II) Complex with a Redox-Active Organic Ligand.

Previously, we found that a Zn(II) complex with the redox-active ligand N-(2,5-dihydroxybenzyl)-N,N',N'-tris(2-pyridinylmethyl)-1,2-ethanediamine (H2qp1) was able to act as a functional mimic of superoxide dismutase, despite its lack of a redox-active transition metal. As the complex catalyzes the dismutation of superoxide to form O2 and H2O2, the quinol in the ligand is believed to cycle between three oxidation states: quinol, quinoxyl radical, and para-quinone. Although the metal is not the redox partner, it nonetheless is essential to the reactivity since the free ligand by itself is inactive as a catalyst. In the present work, we primarily use calculations to probe the mechanism. The calculations support the inner-sphere decomposition of superoxide, suggest that the quinol/quinoxyl radical couple accounts for most of the catalysis, and elucidate the many roles that proton transfer between the zinc complexes and buffer has in the reactivity. Acid/base reactions involving the nonmetal-coordinating hydroxyl group on the quinol are predicted to be key to lowering the energy of the intermediates. We prepared a Zn(II) complex with N-(2-hydroxybenzyl)-N,N',N'-tris(2-pyridinylmethyl)-1,2-ethanediamine (Hpp1) that lacks this functional group and found that it could not catalyze the dismutation of superoxide; this confirms the importance of the second, distal hydroxyl group of the quinol.

Scalar Relativistic All-Electron and Pseudopotential Ab Initio Study of a Minimal Nitrogenase [Fe(SH)4H]- Model Employing Coupled-Cluster and Auxiliary-Field Quantum Monte Carlo Many-Body Methods.

Nitrogenase is the only enzyme that can cleave the triple bond in N2, making nitrogen available to organisms. The detailed mechanism of this enzyme is currently not known, and computational studies are complicated by the fact that different density functional theory (DFT) methods give very different energetic results for calculations involving nitrogenase models. Recently, we designed a [Fe(SH)4H]- model with the fifth proton binding either to Fe or S to mimic different possible protonation states of the nitrogenase active site. We showed that the energy difference between these two isomers (ΔE) is hard to estimate with quantum-mechanical methods. Based on nonrelativistic single-reference coupled-cluster (CC) calculations, we estimated that the ΔE is 101 kJ/mol. In this study, we demonstrate that scalar relativistic effects play an important role and significantly affect ΔE. Our best revised single-reference CC estimates for ΔE are 85-91 kJ/mol, including energy corrections to account for contributions beyond triples, core-valence correlation, and basis-set incompleteness error. Among coupled-cluster approaches with approximate triples, the canonical CCSD(T) exhibits the largest error for this problem. Complementary to CC, we also used phaseless auxiliary-field quantum Monte Carlo calculations (ph-AFQMC). We show that with a Hartree-Fock (HF) trial wave function, ph-AFQMC reproduces the CC results within 5 ± 1 kJ/mol. With multi-Slater-determinant (MSD) trials, the results are 82-84 ± 2 kJ/mol, indicating that multireference effects may be rather modest. Among the DFT methods tested, τ-HCTH, r2SCAN with 10-13% HF exchange with and without dispersion, and O3LYP/O3LYP-D4, and B3LYP*/B3LYP*-D4 generally perform the best. The r2SCAN12 (with 12% HF exchange) functional mimics both the best reference MSD ph-AFQMC and CC ΔE results within 2 kJ/mol.

A functional hydrogenase mimic that catalyzes robust H2 evolution spontaneously in aqueous environment

A functional hydrogenase mimic that catalyzes robust H2 evolution spontaneously in aqueous environment

Amphoteric reactivity of a putative Cu(II)-mCPBA intermediate.

In copper-based enzymes, Cu-hydroperoxo/alkylperoxo species are proposed as key intermediates for their biological activity. A vast amount of literature is available on the functional and structural mimics of enzymatic systems with heme and non-heme ligand frameworks to stabilize high valent metal intermediates, mostly at low temperatures. Herein, we report a reaction between [CuI(NCCH3)4]+ and meta-chloroperoxybenzoic acid (mCPBA) in CH3CN that produces a putative CuII(mCPBA) species (1). 1 was characterized by UV/Vis, resonance Raman, and EPR spectroscopies. 1 can catalyze both electrophilic and nucleophilic reactions, demonstrating its amphoteric behavior. Additionally, 1 can also conduct electron transfer reactions with a weak reducing agent such as diacetyl ferrocene, making it one of the reactive copper-based intermediates. One of the most important aspects of the current work is the easy synthesis of a CuII(mCPBA) adduct with no complicated ligands for stabilization. Over time, 1 decays to form a CuII paddle wheel complex (2) and is found to be unreactive towards substrate oxidation.

A pdc-pinched copper complex for sustainable hydrogen production through ligand supported-metal centric proton-coupled electron transfer

A water-stable [Cu(pdc)(H2O)2] complex, promising functional mimics of hydrogenase active sites and promoting sustainable hydrogen production in acidic water has been designed and synthesised using an ONO-type pincer ligand, 2,6-pyridine...

Electronic isomerism in a heterometallic nickel-iron-sulfur cluster models substrate binding and cyanide inhibition of carbon monoxide dehydrogenase.

The nickel-iron carbon monoxide dehydrogenase (CODH) enzyme uses a heterometallic nickel-iron-sulfur ([NiFe4S4]) cluster to catalyze the reversible interconversion of carbon dioxide (CO2) and carbon monoxide (CO). These reactions are essential for maintaining the global carbon cycle and offer a route towards sustainable greenhouse gas conversion but have not been successfully replicated in synthetic models, in part due to a poor understanding of the natural system. Though the general protein architecture of CODH is known, the electronic structure of the active site is not well-understood, and the mechanism of catalysis remains unresolved. To better understand the CODH enzyme, we have developed a protein-based model containing a heterometallic [NiFe3S4] cluster in the Pyrococcus furiosus (Pf) ferredoxin (Fd). This model binds small molecules such as carbon monoxide and cyanide, analogous to CODH. Multiple redox- and ligand-bound states of [NiFe3S4] Fd (NiFd) have been investigated using a suite of spectroscopic techniques, including resonance Raman, Ni and Fe K-edge X-ray absorption spectroscopy, and electron paramagnetic resonance, to resolve charge and spin delocalization across the cluster, site-specific electron density, and ligand activation. The facile movement of charge through the cluster highlights the fluidity of electron density within iron-sulfur clusters and suggests an electronic basis by which CN- inhibits the native system while the CO-bound state continues to elude isolation in CODH. The detailed characterization of isolable states that are accessible in our CODH model system provides valuable insight into unresolved enzymatic intermediates and offers design principles towards developing functional mimics of CODH.