Elucidation of the tyrosinase/O2/monophenol ternary intermediate that dictates the monooxygenation mechanism in melanin biosynthesis.

Melanins are highly conjugated biopolymer pigments that provide photoprotection in a wide array of organisms, from bacteria to humans. The rate-limiting step in melanin biosynthesis, which is the ortho-hydroxylation of the amino acid L-tyrosine to L-DOPA, is catalyzed by the ubiquitous enzyme tyrosinase (Ty). Ty contains a coupled binuclear copper active site that binds O2 to form a µ:η2:η2-peroxide dicopper(II) intermediate (oxy-Ty), capable of performing the regioselective monooxygenation of para-substituted monophenols to catechols. The mechanism of this critical monooxygenation reaction remains poorly understood despite extensive efforts. In this study, we have employed a combination of spectroscopic, kinetic, and computational methods to trap and characterize the elusive catalytic ternary intermediate (Ty/O2/monophenol) under single-turnover conditions and obtain molecular-level mechanistic insights into its monooxygenation reactivity. Our experimental results, coupled with quantum-mechanics/molecular-mechanics calculations, reveal that the monophenol substrate docks in the active-site pocket of oxy-Ty fully protonated, without coordination to a copper or cleavage of the µ:η2:η2-peroxide O-O bond. Formation of this ternary intermediate involves the displacement of active-site water molecules by the substrate and replacement of their H bonds to the µ:η2:η2-peroxide by a single H bond from the substrate hydroxyl group. This H-bonding interaction in the ternary intermediate enables the unprecedented monooxygenation mechanism, where the µ-η2:η2-peroxide O-O bond is cleaved to accept the phenolic proton, followed by substrate phenolate coordination to a copper site concomitant with its aromatic ortho-hydroxylation by the nonprotonated µ-oxo. This study provides insights into O2 activation and reactivity by coupled binuclear copper active sites with fundamental implications in biocatalysis.

Hydration numbers of biologically relevant divalent metal cations from ab initio molecular dynamics and continuum solvation methods.

Hydration and, in particular, the coordination number of a metal ion is of paramount importance as it defines many of its (bio)physicochemical properties. It is not only essential for understanding its behavior in aqueous solutions but also determines the metal ion reference state and its binding energy to (bio)molecules. In this paper, for divalent metal cations Ca2+, Cd2+, Cu2+, Fe2+, Hg2+, Mg2+, Ni2+, Pb2+, and Zn2+, we compare two approaches for predicting hydration numbers: (1) a mixed explicit/continuum DFT-D3//COSMO-RS solvation model and (2) density functional theory based ab initio molecular dynamics. The former approach is employed to calculate the Gibbs free energy change for the sequential hydration reactions, starting from [M(H2O)2]2+ aqua complexes to [M(H2O)9]2+, allowing explicit water molecules to bind in the first or second coordination sphere and determining the most stable [M(H2O)n]2+ structure. In the latter approach, the hydration number is obtained by integrating the ion-water radial distribution function. With a couple of exceptions, the metal ion hydration numbers predicted by the two approaches are in mutual agreement, as well as in agreement with the experimental data.

Experimental Evidence and Mechanistic Description of the Phenolic H-Transfer to the Cu2O2 Active Site of oxy-Tyrosinase.

Tyrosinase is a ubiquitous coupled binuclear copper enzyme that activates O2 toward the regioselective monooxygenation of monophenols to catechols via a mechanism that remains only partially defined. Here, we present new mechanistic insights into the initial steps of this monooxygenation reaction by employing a pre-steady-state, stopped-flow kinetics approach that allows for the direct measurement of the monooxygenation rates for a series of para-substituted monophenols by oxy-tyrosinase. The obtained biphasic Hammett plot and the associated solvent kinetic isotope effect values provide direct evidence for an initial H-transfer from the protonated phenolic substrate to the Cu2O2 core of oxy-tyrosinase. The correlation of these experimental results to quantum mechanics/molecular mechanics calculations provides a detailed mechanistic description of this H-transfer step. These new mechanistic insights revise and expand our fundamental understanding of Cu2O2 active sites in biology.

Acidity constants and protonation sites of cyclic dinucleotides determined by capillary electrophoresis, quantum chemical calculations, and NMR spectroscopy.

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 ∼2 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.

Can Copper(I) and Silver(I) be Hydrogen Bond Acceptors?

Gold(I) centers can form moderately strong (Au⋅⋅⋅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 Au⋅⋅⋅H bond originally observed in 3AuCl+ can be strengthened by replacing Cl with Br or I. Experimental gas-phase IR spectra in the ∼3000 cm-1 region showed only a small effect of the halogen on the Au⋅⋅⋅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 Ag⋅⋅⋅H interaction is only marginal in this complex, and a Cl⋅⋅⋅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 Ag⋅⋅⋅H and Cu⋅⋅⋅H hydrogen bonds, with a strength similar to the Au⋅⋅⋅H bond in 3AuCl+ . We, therefore, propose possible complexes where the presence of (Ag/Cu)⋅⋅⋅H bonds could be experimentally verified to broaden our understanding of these unusual interactions.

Quantum Bio-Inorganic Chemistry (QBIC) Society Special Collection.

This Editorial by Guest Editors L. Rulísek, M. Gruden, M. Orio and QBIC Society President R. J. Deeth summarizes the Chemistry Europe Special Collection on quantum bioinorganic chemistry, published in collaboration with the Quantum Bioinorganic Chemistry (QBIC) Society. The Collection, which recognizes of the strides made in this area of research, spans several of our portfolio journals Chemistry-A European Journal, the European Journal of Inorganic Chemistry, ChemPlusChem, ChemBioChem, ChemPhysChem, and ChemistryOpen, includes outstanding work in the field by authors across the world and we hope you enjoy reading them!

Cationic Gold(II) Complexes: Experimental and Theoretical Study.

Gold(II) complexes are rare, and their application to the catalysis of chemical transformations is underexplored. The reason is their easy oxidation or reduction to more stable gold(III) or gold(I) complexes, respectively. We explored the thermodynamics of the formation of [AuII (L)(X)]+ complexes (L=ligand, X=halogen) from the corresponding gold(III) precursors and investigated their stability and spectral properties in the IR and visible range in the gas phase. The results show that the best ancillary ligands L for stabilizing gaseous [AuII (L)(X)]+ complexes are bidentate and tridentate ligands with nitrogen donor atoms. The electronic structure and spectral properties of the investigated gold(II) complexes were correlated with quantum chemical calculations. The results show that the molecular and electronic structure of the gold(II) complexes as well as their spectroscopic properties are very similar to those of analogous stable copper(II) complexes.

Comprehensive Theoretical View of the [Cu2 O2 ] Side-on-Peroxo-/Bis-µ-Oxo Equilibria.

Coupled binuclear copper (CBC) sites are employed by many metalloenzymes to catalyze a broad set of biochemical transformations. Typically, the CBC catalytic sites are activated by the O2 molecule to form various [Cu2 O2 ] reactive species. This has also inspired synthesis and development of various biomimetic inorganic complexes featuring the CBC core. From theoretical perspective, the [Cu2 O2 ] reactivity often hinges on the side-on-peroxo-dicopper(II) (P) vs. bis-µ-oxo-dicopper(III) (O) isomerism - an equilibrium that has become almost iconic in theoretical bioinorganic chemistry. Herein, we present a comprehensive calibration and evaluation of the performance of various composite computational protocols available in contemporary computational chemistry, involving coupled-cluster and multireference (relativistic) wave function methods, popular density functionals and solvation models. Starting with the well-studied reference [Cu2 O2 (NH3 )6 ]2+ system, we compared the performance of electronic structure methods and discussed the relativistic effects. This allowed us to select several 'calibrated' DFT functionals that can be conveniently employed to study ten experimentally well-characterized [Cu2 O2 ] inorganic systems. We mostly predicted the lowest-energy structures (P vs. O) of the studied systems correctly. In addition, we present calibration of the used electronic structure methods for prediction of the spectroscopic features of the [Cu2 O2 ] core, mostly provided by the resonance Raman (rR) spectroscopy.

Ir-Catalyzed Cycloaddition of Tribenzocyclyne with Biphenylenes.

We demonstrate that Ir-catalyzed C-C bond activation in biphenylenes followed by a reaction with tribenzocyclyne is a suitable method for synthesizing strained and unknown monoadducts with the tetradehydrotetrabenzo[a,c,e,i]cyclododecene scaffold ([12]annulenes). Modification of reaction conditions also furnished [12]annulene products with cis and/or trans double bonds formed by hydrogen transfer. The [9]annulene side product was formed upon the reaction of the benzyl radical with tribenzocyclyne during the Bergman cyclization. All isolated compounds were fully characterized by HRMS, NMR, and X-ray diffraction analysis.

Protein-Ligand Interactions in the STING Binding Site Probed by Rationally Designed Single-Point Mutations: Experiment and Theory.

STING protein (stimulator of interferon genes) plays an important role in the innate immune system. A number of potent compounds regulating its activity have been reported, mostly derivatives of cyclic dinucleotides (CDNs), natural STING agonists. Here, we aim to provide complementary information to large-scale "ligand-profiling" studies by probing the importance of STING-CDN protein-ligand interactions on the protein side. We examined in detail six typical CDNs each in complex with 13 rationally devised mutations in STING: S162A, S162T, Y167F, G230A, R232K, R232H, A233L, A233I, R238K, T263A, T263S, R293Q, and G230A/R293Q. The mutations switch on and off various types of protein-ligand interactions: π-π stacking, hydrogen bonding, ionic pairing, and nonpolar contacts. We correlated experimental data obtained by differential scanning fluorimetry, X-ray crystallography, and isothermal titration calorimetry with theoretical calculations. This enabled us to provide a mechanistic interpretation of the differences in the binding of representative CDNs to STING. We observed that the G230A mutation increased the thermal stability of the protein-ligand complex, indicating an increased level of ligand binding, whereas R238K and Y167F led to a complete loss of stabilization (ligand binding). The effects of the other mutations depended on the type of ligand (CDN) and varied, to some extent. A very good correlation (R2 = 0.6) between the experimental binding affinities and interaction energies computed by quantum chemical methods enabled us to explain the effect of the studied mutations in detail and evaluate specific interactions quantitatively. Our work may inspire development of high-affinity ligands against the common STING haplotypes by targeting the key (sometimes non-intuitive) protein-ligand interactions.

Enzymatic Synthesis of 3'-5', 3'-5' Cyclic Dinucleotides, Their Binding Properties to the Stimulator of Interferon Genes Adaptor Protein, and Structure/Activity Correlations.

The 3'-5', 3'-5' cyclic dinucleotides (3'3'CDNs) are bacterial second messengers that can also bind to the stimulator of interferon genes (STING) adaptor protein in vertebrates and activate the host innate immunity. Here, we profiled the substrate specificity of four bacterial dinucleotide synthases from Vibrio cholerae (DncV), Bacillus thuringiensis (btDisA), Escherichia coli (dgcZ), and Thermotoga maritima (tDGC) using a library of 33 nucleoside-5'-triphosphate analogues and then employed these enzymes to synthesize 24 3'3'CDNs. The STING affinity of CDNs was evaluated in cell-based and biochemical assays, and their ability to induce cytokines was determined by employing human peripheral blood mononuclear cells. Interestingly, the prepared heterodimeric 3'3'CDNs bound to the STING much better than their homodimeric counterparts and showed similar or better potency than bacterial 3'3'CDNs. We also rationalized the experimental findings by in-depth STING-CDN structure-activity correlations by dissecting computed interaction free energies into a set of well-defined and intuitive terms. To this aim, we employed state-of-the-art methods of computational chemistry, such as quantum mechanics/molecular mechanics (QM/MM) calculations, and complemented the computed results with the {STING:3'3'c-di-ara-AMP} X-ray crystallographic structure. QM/MM identified three outliers (mostly homodimers) for which we have no clear explanation of their impaired binding with respect to their heterodimeric counterparts, whereas the R2 = 0.7 correlation between the computed ΔG'int_rel and experimental ΔTm's for the remaining ligands has been very encouraging.

Thiolation and Carboxylation of Glutathione Synergistically Enhance Its Lead-Detoxification Capabilities.

The natural tripeptide glutathione (GSH) is a ubiquitous compound harboring various biological tasks, among them interacting with essential and toxic metal ions. Yet, although weakly binding the poisonous metal lead (Pb), GSH poorly detoxifies it. ß-Mercaptoaspartic acid is a new-to-nature novel amino acid that was found to enhance the Pb-detoxification capability of a synthetic cyclic tetrapeptide. Aiming to explore the advantages of noncanonical amino acids (ncAAs) of this nature, we studied the detoxification capabilities of GSH and three analogue peptides, each of which contains at least one ncAA that harbors both free carboxylate and thiolate groups. A thorough investigation that includes in vitro detoxification and mechanistic evaluations, metal-binding affinity, metal selectivity, and computational studies shows that these ncAAs are highly beneficial in additively enhancing Pb binding and reveals the importance of both high affinity and metal selectivity in synergistically reducing Pb toxicity in cells. Hence, such ncAAs join the chemical toolbox against Pb poisoning and pollution, enabling peptides to strongly and selectively bind the toxic metal ion.

Conformational energies and equilibria of cyclic dinucleotides in vacuo and in solution: computational chemistry vs. NMR experiments.

Performance of computational methods in modelling cyclic dinucleotides - an important and challenging class of compounds - has been evaluated by two different benchmarks: (1) gas-phase conformational energies and (2) qualitative agreement with NMR observations of the orientation of the χ-dihedral angle in solvent. In gas-phase benchmarks, where CCSD(T) and DLPNO-CCSD(T) methods have been used as the reference, most of the (dispersion corrected) density functional approximations are accurate enough to justify prioritizing computational cost and compatibility with other modelling options as the criterion of choice. NMR experiments of 3'3'-c-di-AMP, 3'3'-c-GAMP, and 3'3'-c-di-GMP show the overall prevalence of the anti-conformation of purine bases, but some population of syn-conformations is observed for guanines. Implicit solvation models combined with quantum-chemical methods struggle to reproduce this behaviour, probably due to a lack of dynamics and explicitly modelled solvent, leading to structures that are too compact. Molecular dynamics simulations overrepresent the syn-conformation of guanine due to the overestimation of an intramolecular hydrogen bond. Our combination of experimental and computational benchmarks provides "error bars" for modelling cyclic dinucleotides in solvent, where such information is generally difficult to obtain, and should help gauge the interpretability of studies dealing with binding of cyclic dinucleotides to important pharmaceutical targets. At the same time, the presented analysis calls for improvement in both implicit solvation models and force-field parameters.

Beyond the classical thermodynamic contributions to hydrogen atom abstraction reactivity.

Hydrogen atom abstraction (HAA) reactions are cornerstones of chemistry. Various (metallo)enzymes performing the HAA catalysis evolved in nature and inspired the rational development of multiple synthetic catalysts. Still, the factors determining their catalytic efficiency are not fully understood. Herein, we define the simple thermodynamic factor η by employing two thermodynamic cycles: one for an oxidant (catalyst), along with its reduced, protonated, and hydrogenated form; and one for the substrate, along with its oxidized, deprotonated, and dehydrogenated form. It is demonstrated that η reflects the propensity of the substrate and catalyst for (a)synchronicity in concerted H+/e- transfers. As such, it significantly contributes to the activation energies of the HAA reactions, in addition to a classical thermodynamic (Bell-Evans-Polanyi) effect. In an attempt to understand the physicochemical interpretation of η, we discovered an elegant link between η and reorganization energy λ from Marcus theory. We discovered computationally that for a homologous set of HAA reactions, λ reaches its maximum for the lowest |η|, which then corresponds to the most synchronous HAA mechanism. This immediately implies that among HAA processes with the same reaction free energy, ΔG0, the highest barrier (≡ΔG≠) is expected for the most synchronous proton-coupled electron (i.e., hydrogen) transfer. As proof of concept, redox and acidobasic properties of nonheme FeIVO complexes are correlated with activation free energies for HAA from C-H and O-H bonds. We believe that the reported findings may represent a powerful concept in designing new HAA catalysts.

Potent Cyclic Tetrapeptide for Lead Detoxification.

Lead (Pb) is a ubiquitous poisonous metal, affecting the health of vast populations worldwide. Medications to treat Pb poisoning suffer from various limitations and are often toxic owing to insufficient metal selectivity. Here, we report a cyclic tetrapeptide that selectively binds Pb and eradicates its toxic effect on the cellular level, with superior potency than state-of-the-art drugs. The Pb-peptide complex is remarkably strong and was characterized experimentally and computationally. Accompanied by the lack of toxicity and enhanced stability of this peptide, these qualities indicate its merit as a potential remedy for Pb poisoning.

Ligand Strain and Its Conformational Complexity Is a Major Factor in the Binding of Cyclic Dinucleotides to STING Protein.

STING (stimulator of interferon genes) is a key regulator of innate immunity that has recently been recognized as a promising drug target. STING is activated by cyclic dinucleotides (CDNs) which eventually leads to expression of type I interferons and other cytokines. Factors underlying the affinity of various CDN analogues are poorly understood. Herein, we correlate structural biology, isothermal calorimetry (ITC) and computational modeling to elucidate factors contributing to binding of six CDNs-three pairs of natural (ribo) and fluorinated (2'-fluororibo) 3',3'-CDNs. X-ray structural analyses of six {STING:CDN} complexes did not offer any explanation for the different affinities of the studied ligands. ITC showed entropy/enthalpy compensation up to 25 kcal mol-1 for this set of similar ligands. The higher affinities of fluorinated analogues are explained with help of computational methods by smaller loss of entropy upon binding and by smaller strain (free) energy.

Proton-Electron Transfer to the Active Site Is Essential for the Reaction Mechanism of Soluble Δ9-Desaturase.

A full understanding of the catalytic action of non-heme iron (NHFe) and non-heme diiron (NHFe2) enzymes is still beyond the grasp of contemporary computational and experimental techniques. Many of these enzymes exhibit fascinating chemo-, regio-, and stereoselectivity, in spite of employing highly reactive intermediates which are necessary for activations of most stable chemical bonds. Herein, we study in detail one intriguing representative of the NHFe2 family of enzymes: soluble Δ9 desaturase (Δ9D), which desaturates rather than performing the thermodynamically favorable hydroxylation of substrate. Its catalytic mechanism has been explored in great detail by using QM(DFT)/MM and multireference wave function methods. Starting from the spectroscopically observed 1,2-µ-peroxo diferric P intermediate, the proton-electron uptake by P is the favored mechanism for catalytic activation, since it allows a significant reduction of the barrier of the initial (and rate-determining) H-atom abstraction from the stearoyl substrate as compared to the "proton-only activated" pathway. Also, we ruled out that a Q-like intermediate (high-valent diamond-core bis-µ-oxo-[FeIV]2 unit) is involved in the reaction mechanism. Our mechanistic picture is consistent with the experimental data available for Δ9D and satisfies fairly stringent conditions required by Nature: the chemo-, stereo-, and regioselectivity of the desaturation of stearic acid. Finally, the mechanisms evaluated are placed into a broader context of NHFe2 chemistry, provided by an amino acid sequence analysis through the families of the NHFe2 enzymes. Our study thus represents an important contribution toward understanding the catalytic action of the NHFe2 enzymes and may inspire further work in NHFe(2) biomimetic chemistry.

Closed Shell Iron(IV) Oxo Complex with an Fe-O Triple Bond: Computational Design, Synthesis, and Reactivity.

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 450 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 960.5 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.

Preparation of (Pentafluorosulfanyl)benzenes by Direct Fluorination of Diaryldisulfides: Synthetic Approach and Mechanistic Aspects.

Direct fluorination of ortho-, meta- and para-substituted aromatic thiols and disulfides using elemental fluorine afforded substituted (pentafluorosulfanyl)benzenes. This work thus represents the first study of the scope and limitation of direct fluorination for the synthesis of new SF5 -containing building blocks. Fluorinations in batch and flow modes were compared. A comprehensive computational study was carried out employing density functional and wave function methods to elucidate the reaction mechanism of the transformation of ArSF3 into ArSF5 . Eliminating various nonradical pathways, it has been shown that the reaction proceeds by a radical mechanism, initiated by the attack of the F. on the ArSF3 moiety, propagated via an almost barrierless F2 +ArSF4 . →ArSF5 +F. step and terminated by the ArSF4 . +F. →ArSF5 . Most of the calculated data are in very good agreement with experimental observations concerning the ortho-substituent effect on the reaction rates and yields.

A New Insight into the Stereoelectronic Control of the Pd0 -Catalyzed Allylic Substitution: Application for the Synthesis of Multisubstituted Pyran-2-ones via an Unusual 1,3-Transposition.

Pyran-2-ones 3 undergo a novel Pd0 -catalyzed 1,3-rearrangement to afford isomers 6. The reaction proceeds via an η2 -Pd complex, the pyramidalization of which (confirmed by quantum chemistry calculations) offers a favorable antiperiplanar alignment of the Pd-C and allylic C-O bonds (C), thus allowing the formation of an η3 -Pd intermediate. Subsequent rotation and rate-limiting recombination with the carboxylate arm then gives isomeric pyran-2-ones 6. The calculated free energies reproduce the observed kinetics semi-quantitatively.