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Cyclic dinucleotides (CDNs) are important second messengers in bacteria and eukaryotes. Detailed characterization of their physicochemical properties is a prerequisite for understanding their biological functions. Herein, we examine acid-base and electromigration properties of selected CDNs employing capillary electrophoresis (CE), density functional theory (DFT), and nuclear magnetic resonance (NMR) spectroscopy to provide benchmark pKa values, as well as to unambiguously determine the protonation sites. Acidity constants (pKa ) of the NH+ moieties of adenine and guanine bases and actual and limiting ionic mobilities of CDNs were determined by nonlinear regression analysis of the pH dependence of their effective electrophoretic mobilities measured by CE in aqueous background electrolytes in a wide pH range (0.98-11.48), at constant temperature (25°C), and constant ionic strength (25 mM). The thermodynamic pKa values were found to be in the range 3.31-4.56 for adenine and 2.28-3.61 for guanine bases, whereas the pKa of enol group of guanine base was in the range 10.21-10.40. Except for systematic shifts of â¼2 pKa , the pKa values calculated by the DFT-D3//COSMO-RS composite protocol that included large-scale conformational sampling and "cross-morphing" were in a relatively good agreement with the pKa s determined by CE and predict N1 atom of adenine and N7 atom of guanine as the protonation sites. The protonation of the N1 atom of adenine and N7 atom of guanine in acidic background electrolytes (BGEs) and the dissociation of the enol group of guanine in alkaline BGEs was confirmed also by NMR spectroscopy.
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A collaborative, open-science team undertook discovery of novel small molecule inhibitors of the SARS-CoV-2 nsp16-nsp10 2'-O-methyltransferase using a high throughput screening approach with the potential to reveal new inhibition strategies. This screen yielded compound 5a, a ligand possessing an electron-deficient double bond, as an inhibitor of SARS-CoV-2 nsp16 activity. Surprisingly, X-ray crystal structures revealed that 5a covalently binds within a previously unrecognized cryptic pocket near the S-adenosylmethionine binding cleft in a manner that prevents occupation by S-adenosylmethionine. Using a multidisciplinary approach, we examined the mechanism of binding of compound 5a to the nsp16 cryptic pocket and developed 5a derivatives that inhibited nsp16 activity and murine hepatitis virus replication in rat lung epithelial cells but proved cytotoxic to cell lines canonically used to examine SARS-CoV-2 infection. Our study reveals the druggability of this newly discovered SARS-CoV-2 nsp16 cryptic pocket, provides novel tool compounds to explore the site, and suggests a new approach for discovery of nsp16 inhibition-based pan-coronavirus therapeutics through structure-guided drug design.
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COVID-19 , SARS-CoV-2 , Ratones , Ratas , Animales , SARS-CoV-2/metabolismo , S-Adenosilmetionina/química , S-Adenosilmetionina/metabolismo , MetiltransferasasRESUMEN
Histone deacetylase (HDAC) inhibitors used in the clinic typically contain a hydroxamate zinc-binding group (ZBG). However, more recent work has shown that the use of alternative ZBGs, and, in particular, the heterocyclic oxadiazoles, can confer higher isoenzyme selectivity and more favorable ADMET profiles. Herein, we report on the synthesis and biochemical, crystallographic, and computational characterization of a series of oxadiazole-based inhibitors selectively targeting the HDAC6 isoform. Surprisingly, but in line with a very recent finding reported in the literature, a crystal structure of the HDAC6/inhibitor complex revealed that hydrolysis of the oxadiazole ring transforms the parent oxadiazole into an acylhydrazide through a sequence of two hydrolytic steps. An identical cleavage pattern was also observed both in vitro using the purified HDAC6 enzyme as well as in cellular systems. By employing advanced quantum and molecular mechanics (QM/MM) and QM calculations, we elucidated the mechanistic details of the two hydrolytic steps to obtain a comprehensive mechanistic view of the double hydrolysis of the oxadiazole ring. This was achieved by fully characterizing the reaction coordinate, including identification of the structures of all intermediates and transition states, together with calculations of their respective activation (free) energies. In addition, we ruled out several (intuitively) competing pathways. The computed data (ΔG ≈ 21 kcal·mol-1 for the rate-determining step of the overall dual hydrolysis) are in very good agreement with the experimentally determined rate constants, which a posteriori supports the proposed reaction mechanism. We also clearly (and quantitatively) explain the role of the -CF3 or -CHF2 substituent on the oxadiazole ring, which is a prerequisite for hydrolysis to occur. Overall, our data provide compelling evidence that the oxadiazole warheads can be efficiently transformed within the active sites of target metallohydrolases to afford reaction products possessing distinct selectivity and inhibition profiles.
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Inhibidores de Histona Desacetilasas , Oxadiazoles , Histona Desacetilasa 6/química , Hidrólisis , Inhibidores de Histona Desacetilasas/farmacología , Ácidos Hidroxámicos/químicaRESUMEN
Gold(I) centers can form moderately strong (Auâ â â H) hydrogen bonds with tertiary ammonium groups, as has been demonstrated in the 3AuCl+ (3+ =1-(tert-butyl)-3-phenyl-4-(2-((dimethylammonio)methyl)phenyl)-1,2,4-triazol-5-ylidene) complex. However, similar hydrogen bonding interactions with isoelectronic silver(I) or copper(I) centers are unknown. Herein, we first explored whether the Auâ â â H bond originally observed in 3AuCl+ can be strengthened by replacing Cl with Br or I. Experimental gas-phase IR spectra in the â¼3000â cm-1 region showed only a small effect of the halogen on the Auâ â â H bond. Next, we measured the spectra of 3AgCl+ , which exhibited significant differences compared to its 3AuX+ counterparts. The difference has been explained by DFT calculations which indicated that the Agâ â â H interaction is only marginal in this complex, and a Clâ â â H hydrogen bond is formed instead. Calculations predicted the same for the 3CuCl+ complex. However, we noticed that for Ag and Cu complexes with less flexible ligands, such as dimethyl(2-(dimethylammonio)phenyl)phosphine (L7 H+ ), the computations predict the presence of the respective Agâ â â H and Cuâ â â H hydrogen bonds, with a strength similar to the Auâ â â H bond in 3AuCl+ . We, therefore, propose possible complexes where the presence of (Ag/Cu)â â â H bonds could be experimentally verified to broaden our understanding of these unusual interactions.
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We extensively mapped energy landscapes and conformations of 22 (including three His protonation states) proteinogenic α-amino acids in trans configuration and the corresponding 484 (222) dipeptides. To mimic the environment in a protein chain, the N- and C-termini of the studied systems were capped with acetyl and N-methylamide groups, respectively. We systematically varied the main chain dihedral angles (Ï, ψ) by 40° steps and all side chain angles by 90° or 120° steps. We optimized the molecular geometries with the GFN2-xTB semiempirical (SQM) method and performed single point density functional theory calculations at the BP86-D3/DGauss-DZVP//COSMO-RS level in water, 1-octanol, N,N-dimethylformamide, and n-hexane. For each restrained (nonequilibrium) structure, we also calculated energy gradients (in water) and natural atomic charges. The exhaustive and unprecedented QM-based sampling enabled us to construct Ramachandran plots of quantum mechanical (QM(BP86-D3)//COSMO-RS) energies calculated on SQM structures, for all 506 (484 dipeptides and 22 amino acids) studied systems. We showed how the character of an amino acid side chain influences the conformational space of single amino acids and dipeptides. With clustering techniques, we were able to identify unique minima of amino acids and dipeptides (i.e., minima on the GFN2-xTB potential energy surfaces) and analyze the distribution of their BP86-D3//COSMO-RS conformational energies in all four solvents. We also derived an empirical formula for the number of unique minima based on the overall number of rotatable bonds within each peptide. The final peptide conformer data set (PeptideCs) comprises over 400 million structures, all of them annotated with QM(BP86-D3)//COSMO-RS energies. Thanks to its completeness and unbiased nature, the PeptideCs can serve, inter alia, as a data set for the validation of new methods for predicting the energy landscapes of protein structures. This data set may also prove to be useful in the development and reparameterization of biomolecular force fields. The data set is deposited at Figshare (10.25452/figshare.plus.19607172) and can be accessed using a simple web interface at http://peptidecs.uochb.cas.cz.
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Dipéptidos , Péptidos , Aminoácidos , Dipéptidos/química , Péptidos/química , Teoría Cuántica , Termodinámica , Agua/químicaRESUMEN
Combating biofilm infections remains a challenge due to the shield and acidic conditions. Herein, an acid-responsive nanoporphyrin (PN3-NP) based on the self-assembly of a water-soluble porphyrin derivative (PN3) is constructed. Additional kinetic control sites formed by the conjugation of the spermine molecules to a porphyrin macrocycle make PN3 self-assemble into stable nanoparticles (PN3-NP) in the physiological environment. Noteworthily, near-infrared (NIR) fluorescence monitoring and synergistic photodynamic therapy (PDT) and photothermal therapy (PTT) effects of PN3-NP can be triggered by the acidity in biofilms, accompanied by intelligent transformation into dot-like nanospheres. Thus, damage to normal tissue is effectively avoided and accurate diagnosis and treatment of biofilms is achieved successfully. The good results of fluorescence imaging-guided photo-ablation of antibiotic-resistant strains methicillin-resistant Staphylococcus aureus (MRSA) biofilms verify that PN3-NP is a promising alternative to antibiotics. Meanwhile, this strategy also opens new horizons to engineer smart nano-photosensitizer for accurate diagnosis and treatment of biofilms.
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Staphylococcus aureus Resistente a Meticilina , Fotoquimioterapia , Porfirinas , Antibacterianos/farmacología , Biopelículas , Fotoquimioterapia/métodos , Fármacos Fotosensibilizantes/farmacología , Fototerapia/métodos , Porfirinas/farmacologíaRESUMEN
The factors that control the diverse reactivity of the µ-η2:η2-peroxo dicopper(II) oxy-intermediates in the coupled binuclear copper proteins remain elusive. Here, spectroscopic and computational methods reveal H-bonding interactions between active-site waters and the µ-η2:η2-peroxide of oxy-tyrosinase, and define their effects on the Cu(II)2O2 electronic structure and O2 activation.
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Cobre , Peróxidos , Dominio Catalítico , Cobre/química , Monofenol Monooxigenasa/metabolismo , Oxígeno/química , Peróxidos/química , Análisis EspectralRESUMEN
CuI /TEMPO (TEMPO=2,2,6,6-tetramethylpiperidinyloxyl) catalyst systems are versatile catalysts for aerobic alcohol oxidation reactions to selectively yield aldehydes. However, several aspects of the mechanism are yet unresolved, mainly because of the lack of identification of any reactive intermediates. Herein, we report the synthesis and characterization of a dinuclear [L12 Cu2 ]2+ complex 1, which in presence of TEMPO can couple the catalytic 4 H+ /4 e- reduction of O2 to water to the oxidation of benzylic and aliphatic alcohols. The mechanisms of the O2 -reduction and alcohol oxidation reactions have been clarified by the spectroscopic detection of the reactive intermediates in the gas and condensed phases, as well as by kinetic studies on each step in the catalytic cycles. Bis(µ-oxo)dicopper(III) (2) and bis(µ-hydroxo)dicopper(II) species 3 are shown as viable reactants in oxidation catalysis. The present study provides deep mechanistic insight into the aerobic oxidation of alcohols that should serve as a valuable foundation for ongoing efforts dedicated towards the understanding of transition-metal catalysts involving redox-active organic cocatalysts.
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Plasmon assistance promotes a range of chemical transformations by decreasing their activation energies. In a common case, thermal and plasmon assistance work synergistically: higher temperature results in higher plasmon-enhanced catalysis efficiency. Herein, we report an unexpected tenfold increase in the reaction efficiency of surface plasmon-assisted Huisgen dipolar azide-alkyne cycloaddition (AAC) when the reaction mixture is cooled from room temperature to -35 °C. We attribute the observed increase in the reaction efficiency to complete plasmon-induced annihilation of the reaction barrier, prolongation of plasmon lifetime, and decreased relaxation of plasmon-excited-states under cooling. Furthermore, control quenching experiments supported by theoretical calculations indicate that plasmon-mediated substrate excitation to an electronic triplet state may play the key role in plasmon-assisted chemical transformation. Last but not least, we demonstrated the possible applicability of plasmon assistance to biological systems by AAC coupling of biotin to gold nanoparticles performed at -35 °C.
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Iron(IV)-oxo intermediates in nature contain two unpaired electrons in the Fe-O antibonding orbitals, which are thought to contribute to their high reactivity. To challenge this hypothesis, we designed and synthesized closed-shell singlet iron(IV) oxo complex [(quinisox)Fe(O)]+ (1+ ; quinisox-H=(N-(2-(2-isoxazoline-3-yl)phenyl)quinoline-8-carboxamide). We identified the quinisox ligand by DFT computational screening out of over 450â candidates. After the ligand synthesis, we detected 1+ in the gas phase and confirmed its spin state by visible and infrared photodissociation spectroscopy (IRPD). The Fe-O stretching frequency in 1+ is 960.5â cm-1 , consistent with an Fe-O triple bond, which was also confirmed by multireference calculations. The unprecedented bond strength is accompanied by high gas-phase reactivity of 1+ in oxygen atom transfer (OAT) and in proton-coupled electron transfer reactions. This challenges the current view of the spin-state driven reactivity of the Fe-O complexes.
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We report and analyze chemoselectivity in the gas phase reactions of cycloalkenes (cyclohexene, cycloheptene, cis-cyclooctene, 1,4-cyclohexadiene) with a non-heme iron(IV)-oxo complex [(PyTACN)Fe(O)(Cl)]+, which models the active species in iron-dependent halogenases. Unlike in the halogenases, we did not observe any chlorination of the substrate. However, we observed two other reaction pathways: allylic hydrogen atom transfer (HAT) and alkene epoxidation. The HAT is clearly preferred in the case of 1,4-cyclohexadiene, both pathways have comparable reaction rates in reaction with cyclohexene, and epoxidation is strongly favored in reactions with cycloheptene and cis-cyclooctene. This preference for epoxidation differs from the reactivity of iron(IV)-oxo complexes in the condensed phase, where HAT usually prevails. To understand the observed selectivity, we analyze effects of the substrate, spin state, and solvation. Our DFT and CASPT2 calculations suggest that all the reactions occur on the quintet potential energy surface. The DFT-calculated energies of the transition states for the epoxidation and hydroxylation pathways explain the observed chemoselectivity. The SMD implicit solvation model predicts the relative increase of the epoxidation barriers with solvent polarity, which explains the clear preference of HAT in the condensed phase.
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Terminal oxo complexes of late transition metals are frequently proposed reactive intermediates. However, they are scarcely known beyond Groupâ 8. Using mass spectrometry, we prepared and characterized two such complexes: [(N4Py)CoIII (O)]+ (1) and [(N4Py)CoIV (O)]2+ (2). Infrared photodissociation spectroscopy revealed that the Co-O bond in 1 is rather strong, in accordance with its lack of chemical reactivity. On the contrary, 2 has a very weak Co-O bond characterized by a stretching frequency of ≤659â cm-1 . Accordingly, 2 can abstract hydrogen atoms from non-activated secondary alkanes. Previously, this reactivity has only been observed in the gas phase for small, coordinatively unsaturated metal complexes. Multireference ab-initio calculations suggest that 2, formally a cobalt(IV)-oxo complex, is best described as cobalt(III)-oxyl. Our results provide important data on changes to metal-oxo bonding behind the oxo wall and show that cobalt-oxo complexes are promising targets for developing highly active C-H oxidation catalysts.
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FeV(O)(OH) species have long been proposed to play a key role in a wide range of biomimetic and enzymatic oxidations, including as intermediates in arene dihydroxylation catalyzed by Rieske oxygenases. However, the inability to accumulate these intermediates in solution has thus far prevented their spectroscopic and chemical characterization. Thus, we use gas-phase ion spectroscopy and reactivity analysis to characterize the highly reactive [FeV(O)(OH)(5tips3tpa)]2+ (32+) complex. The results show that 32+ hydroxylates C-H bonds via a rebound mechanism involving two different ligands at the Fe center and dihydroxylates olefins and arenes. Hence, this study provides a direct evidence of FeV(O)(OH) species in non-heme iron catalysis. Furthermore, the reactivity of 32+ accounts for the unique behavior of Rieske oxygenases. The use of gas-phase ion characterization allows us to address issues related to highly reactive intermediates that other methods are unable to solve in the context of catalysis and enzymology.
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Compuestos de Hierro/química , Hierro/química , Oxidación-Reducción , Oxigenasas/metabolismo , CatálisisRESUMEN
Despite substantial evidence of short Auâ â â H-X contacts derived from a number of X-ray structures of AuI compounds, the nature of AuI â â â H bonding in these systems has not been clearly understood. Herein, we present the first spectroscopic evidence for an intramolecular AuI â â â H+ -N hydrogen bond in a [Cl-Au-L]+ complex, where L is a protonated N-heterocyclic carbene. The complex was isolated in the gas phase and characterized with helium-tagging infrared photodissociation (IRPD) spectra, in which H+ -N-mode-derived bands evidence the intramolecular AuI â â â H+ -N bond. Quantum chemical calculations reproduce the experimental IRPD spectra and allow to characterize the intramolecular Auâ â â H+ -N bonding with a short rAuâ â â H distance of 2.17â Å and an interaction energy of approximately -10â kcal mol-1 . Various theoretical descriptors of chemical bonding calculated for the Auâ â â H+ -N interaction provide strong evidence for a hydrogen bond of moderate strength.
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The CuO+ core is a central motif of reactive intermediates in copper-catalysed oxidations occurring in nature. The high reactivity of CuO+ stems from a weak bonding between the atoms, which cannot be described by a simple classical model. To obtain the correct picture, we have investigated the acetonitrile-ligated CuO+ ion using neon-tagging photodissociation spectroscopy at 5â K. The spectra feature complex vibronic absorption progressions in NIR and visible regions. Employing Franck-Condon analyses, we derived low-lying triplet potential energy surfaces that were further correlated with multireference calculations. This provided insight into the ground and low-lying excited electronic states of the CuO+ unit and elucidated how these states are perturbed by the change in ligation. Thus, we show that the bare CuO+ ion has prevailingly a copper(I)-biradical oxygen character. Increasing the number of ligands coordinated to copper changes the CuO+ character towards the copper(II)-oxyl radical structure.
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Terminal non-heme iron(IV)-oxo compounds are among the most powerful and best studied oxidants of strong C-H bonds. In contrast to the increasing number of such complexes (>80 thus far), corresponding one-electron-reduced derivatives are much rarer and presumably less stable, and only two iron(III)-oxo complexes have been characterized to date, both of which are stabilized by hydrogen-bonding interactions. Herein we have employed gas-phase techniques to generate and identify a series of terminal iron(III)-oxo complexes, all without built-in hydrogen bonding. Some of these complexes exhibit â¼70 cm-1 decrease in ν(Fe-O) frequencies expected for a half-order decrease in bond order upon one-electron reduction to an S = 5/2 center, while others have ν(Fe-O) frequencies essentially unchanged from those of their parent iron(IV)-oxo complexes. The latter result suggests that the added electron does not occupy a d orbital with FeâO antibonding character, requiring an S = 3/2 spin assignment for the nascent FeIII-O- species. In the latter cases, water is found to hydrogen bond to the FeIII-O- unit, resulting in a change from quartet to sextet spin state. Reactivity studies also demonstrate the extraordinary basicity of these iron(III)-oxo complexes. Our observations show that metal-oxo species at the boundary of the "Oxo Wall" are accessible, and the data provide a lead to detect iron(III)-oxo intermediates in biological and biomimetic reactions.
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The formation and detailed spectroscopic characterization of the first biuret-containing monoanionic superoxido-NiII intermediate [LNiO2 ]- as the Li salt [2; L=MeN[C(=O)NAr)2 ; Ar=2,6-iPr2 C6 H3 )] is reported. It results from oxidation of the corresponding [Li(thf)3 ]2 [LNiII Br2 ] complex M with excess H2 O2 in the presence of Et3 N. The [LNiO2 ]- core of 2 shows an unprecedented nucleophilic reactivity in the oxidative deformylation of aldehydes, in stark contrast to the electrophilic character of the previously reported neutral Nacnac-containing superoxido-NiII complex 1, [L'NiO2 ] (L'=CH(CMeNAr)2 ). According to density-functional theory (DFT) calculations, the remarkably different behaviour of 1 versus 2 can be attributed to their different charges and a two-state reactivity, in which a doublet ground state and a nearby spin-polarized doublet excited-state both contribute in 1 but not in 2. The unexpected nucleophilicity of the superoxido-NiII core of 2 suggests that such a reactivity may also play a role in catalytic cycles of Ni-containing oxygenases and oxidases.
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Complejos de Coordinación/química , Litio/química , Níquel/química , Superóxidos/química , Modelos Moleculares , Oxidación-Reducción , Oxidorreductasas/química , Oxígeno/química , Oxigenasas/química , Teoría Cuántica , Sales (Química)/químicaRESUMEN
Attractive metallophilic (aurophilic, argentophilic, cuprophilic, etc.) interactions play an important role in arrangement and stabilization of oligonuclear metal ion complexes. We report a combined experimental and theoretical assessment of aurophilic interactions in closed-shell gold(I) dimers. The experimental binding energies were obtained for charged [(LH)AuCl]+...[(L')AuCl] dimers (L is either a phosphine or an N-heterocyclic carbene ligand) in the gas phase. These energies served for benchmarking of correlated quantum chemical calculations (CCSD(T)-calibrated SCS-MP2/CBS method) that were then applied to neutral [(L)AuCl]...[(L')AuCl] dimers. The overall attractive interactions between monomeric units are in the order of 100-165 kJ mol-1 in the charged dimers and of 70-105 kJ mol-1 in the corresponding neutral dimers. In the neutral dimers, pure aurophilic interactions account for 25-30 kJ mol-1, the dipole-dipole interactions for 30-45 kJ mol-1, and the L···L' "inter-ligand" dispersion interactions for 5-25 kJ mol-1. Energy of the aurophilic interactions is thus comparable or even larger than that of strong hydrogen bonds.
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We report for the first time infrared spectra of three non-heme pseudo-octahedral iron(V) nitride complexes with assigned Fe-N stretching vibrations. The intensities of the Fe-N bands in two of the complexes are extremely weak. Their detection was enabled by the high resolution and sensitivity of the experiments performed at 3â K for isolated complexes in the gas phase. Multireference CASPT2 calculations revealed that the Fe-N bond in the ground doublet state is influenced by two low-lying excited doublet states. In particular, configuration interaction between the ground and the second excited state leads to avoided crossing of their potential energy surfaces along the Fe-N coordinate, which thus affects the ground-state Fe-N stretching frequency and intensity. Therefore, DFT calculated Fe-N stretching frequency strongly depends on the amount of Hartree-Fock exchange potential. As a result, by tuning the amount of Hartree-Fock exchange potential in the B3LYP functional, it was possible to obtain theoretical spectra perfectly consistent with the experimental data. The theory shows that the intensity of the Fe-N stretching vibration can almost vanish due to strong coupling with other stretching modes of the ligands.
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The generation of iron(V) nitride complexes, which are targets of biomimetic chemistry, is reported. Temperature-dependent ion spectroscopy shows that this reaction is governed by the spin-state population of their iron(III) azide precursors and can be tuned by temperature. The complex [(MePy2 TACN)Fe(N3 )]2+ (MePy2 TACN=N-methyl-N,N-bis(2-picolyl)-1,4,7-triazacyclononane) exists as a mixture of sextet and doublet spin states at 300â K, whereas only the doublet state is populated at 3â K. Photofragmentation of the sextet state complex leads to the reduction of the iron center. The doublet state complex photodissociates to the desired iron(V) nitride complex. To generalize these findings, we show results for complexes with cyclam-based ligands.