Structural and functional models of nitrile hydratase

A novel one-dimensional thiocyanate-bridged cobalt(III) complex: synthesis, crystal structure characterization and Hirshfeld surface analysis

A new one-dimensional thiocyanate-bridged cobalt(III) Schiff base complex, namely, catena-poly[[[4-bromo-2-((Z)-{[2-(thiophen-2-yl)ethyl]imino}methyl)phenolato-κ2N,O]cobalt(III)]-μ-thiocyanato-κ2N:S], [Co(SCN)(C13H11BrNOS)2]n or [Co(μ1,3-SCN)L2]n (1), where HL is 4-bromo-2-((Z)-{[2-(thiophene-2-yl)ethyl]imino}methyl)phenol, a bidentate Schiff base prepared from the condensation reaction of 5-bromosalicylaldehyde and 2-(thiophen-2-yl)ethylamine, has been synthesized by stirring Co(ClO4)2·6H2O, the Schiff base HL and ammonium thiocyanate (in a 1:2:1 molar ratio) in ethanol medium. The complex was characterized by FT-IR, electronic spectra and single-crystal X-ray diffraction (SC-XRD) studies. The SC-XRD data suggest that the compound crystallizes in the orthorhombic space group Pca21. The CoIII ion in 1 adopts a distorted octahedral geometry, the metal sites being six-coordinated by one thiocyanate N atom and one thiocyanate S atom in apical positions, and by two imine N atoms and two phenolate O atoms from two anionic L- ligands which form the basal plane. The thiocyanate ligand acts as a μ-1,3 bridge, joining neighbouring CoIII atoms and forming a uniform zigzag one-dimensional polymeric chain. The crystallographic data were also used in the Hirshfeld surface (HS) analysis, which aimed to investigate the nature and quantitative significance of any noncovalent intermolecular interactions inside the crystal lattice. The crystal void parameters have also been computed and show the molecules to be tightly packed.

Broad-spectrum hydrocarbon-degrading microbes in the global ocean metagenomes

Understanding the diversity and functions of hydrocarbon-degrading microorganisms in marine environments is crucial for both advancing knowledge of biogeochemical processes and improving bioremediation methods. In this study, we leveraged nearly 20,000 metagenome-assembled genomes (MAGs), recovered from a wide array of marine samples across the global oceans, to map the diversity of aerobic hydrocarbon-degrading microorganisms. A broad bacterial diversity was uncovered, with a notable preference for degrading aliphatic hydrocarbons over aromatic ones, primarily within Proteobacteria and Actinobacteriota. Three types of broad-spectrum hydrocarbon-degrading bacteria were identified for their ability to degrade various hydrocarbons and possession of multiple copies of hydrocarbon biodegradation genes. These bacteria demonstrate extensive metabolic versatility, aiding their survival and adaptability in diverse environmental conditions. Evidence of gene duplication and horizontal gene transfer in these microbes suggested a potential enhancement in the diversity of hydrocarbon-degrading bacteria. Positive correlations were observed between the abundances of hydrocarbon-degrading genes and environmental parameters such as temperature (-5 to 35 °C) and salinity (20 to 42 PSU). Overall, our findings offer valuable insights into marine hydrocarbon-degrading microorganisms and suggest considerations for selecting microbial strains for oil pollution remediation.

Sustainable Phenylalanine-Derived SAILs for Solubilization of Polycyclic Aromatic Hydrocarbons

The solubilization capacity of a series of sustainable phenylalanine-derived surface-active ionic liquids (SAILs) was evaluated towards polycyclic aromatic hydrocarbons-naphthalene, anthracene and pyrene. The key physico-chemical parameters of the studied systems (critical micelle concentration, spectral properties, solubilization parameters) were determined, analyzed and compared with conventional cationic surfactant, CTABr. For all studied PAH solubilization capacity increases with extension of alkyl chain length of PyPheOC_n SAILs reaching the values comparable to CTABr for SAILs with n = 10-12. A remarkable advantage of the phenylalanine-derived SAILs PyPheOC_n and PyPheNHC_n is a possibility to cleave enzymatically ester and/or amide bonds under mild conditions, to separate polycyclic aromatic hydrocarbons in situ. A series of immobilized enzymes was tested to determine the most suitable candidates for tunable decomposition of SAILs. The decomposition pathway could be adjusted depending on the choice of the enzyme system, reaction conditions, and selection of SAILs type. The evaluated systems can provide selective cleavage of the ester and amide bond and help to choose the optimal decomposition method of SAILs for enzymatic recycling of SAILs transformation products or as a pretreatment towards biological mineralization. The concept of a possible practical application of studied systems for PAHs solubilization/separation was also discussed focusing on sustainability and a green chemistry approach.

Identification of an Intermediate Species along the Nitrile Hydratase Reaction Pathway by EPR Spectroscopy

A new method to trap catalytic intermediate species was employed with Fe-type nitrile hydratase from Rhodococcus equi TG328-2 (ReNHase). ReNHase was incubated with substrates in a 23% (w/w) NaCl/H₂O eutectic system that remained liquid at -20 °C, thereby permitting the observation of transient species that were present at electron paramagnetic resonance (EPR)-detectable levels in samples frozen while in the steady state. Fe^III-EPR signals from the resting enzyme were unaffected by the presence of 23% NaCl, and the catalytic activity was ∼55% that in the absence of NaCl at the optimum pH of 7.5. The reaction of ReNHase in the eutectic system at -20 °C with the substrates acetonitrile or benzonitrile induced significant changes in the EPR spectra. A previously unobserved signal with highly rhombic g-values (g₁ = 2.31) was observed during the steady state but did not persist beyond the exhaustion of the substrate, indicating that it arises from a catalytically competent intermediate. Distinct signals due to product complexes provide a detailed mechanism for product release, the rate-limiting step of the reaction. Assignment of the observed EPR signals was facilitated by density functional theory calculations, which provided candidate structures and g-values for various proposed ReNHase intermediates. Collectively, these results provide new insights into the catalytic mechanism of NHase and offer a new approach for isolating and characterizing EPR-active intermediates in metalloenzymes.

Phosphine-Catalyzed (4 + 2) Cycloaddition of Conjugated Dienes with Enones and Its Asymmetric Variant

Herein we reported a novel phosphine-catalyzed (4 + 2) cyclization reaction of electron-deficient conjugated dienes with enones to generate functionalized dihydropyran skeletons. A mechanistic investigation reveals that the reaction produces a new phosphonium zwitterion, which undergoes consecutive reactions. In addition, an asymmetric variant was developed by efficient and economical chiral phosphine catalysis.

Ru(ii)- and Ru(iv)-dmso complexes catalyze efficient and selective aqueous-phase nitrile hydration reactions under mild conditions

Synthesis and characterization of new water-soluble Ru(ii)- and Ru(iv)-dmso complexes are reported which show good efficiency and selectivity for aqueous-phase nitrile hydration at 60 °C in air. Best performance is achieved using complex [RuCl2(dmso)3(NH3)]·PF6·Cl (3).

The Effects of the Metal Ion Substitution into the Active Site of Metalloenzymes: A Theoretical Insight on Some Selected Cases

A large number of enzymes need a metal ion to express their catalytic activity. Among the different roles that metal ions can play in the catalytic event, the most common are their ability to orient the substrate correctly for the reaction, to exchange electrons in redox reactions, to stabilize negative charges. In many reactions catalyzed by metal ions, they behave like the proton, essentially as Lewis acids but are often more effective than the proton because they can be present at high concentrations at neutral pH. In an attempt to adapt to drastic environmental conditions, enzymes can take advantage of the presence of many metal species in addition to those defined as native and still be active. In fact, today we know enzymes that contain essential bulk, trace, and ultra-trace elements. In this work, we report theoretical results obtained for three different enzymes each of which contains different metal ions, trying to highlight any differences in their working mechanism as a function of the replacement of the metal center at the active site.

Enzyme immobilized in BioMOFs: Facile synthesis and improved catalytic performance

Biological metal-organic frameworks (BioMOFs), an emerging sub-class of MOFs, are prepared from metals and biological ligands (bioligands). Benefit from the low toxicity and good biocompatibility of bioligands, BioMOFs can be used in biomedicine and biocatalysis. In this work, a novel approach was developed for fabricating BioMOFs materials (Co-Cys BioMOFs) from cobalt salt and cystine, meanwhile nitrile hydratase (NHase) was in-situ encapsulated during the synthesis process. The obtained NHase-BioMOFs biocomposits named NHase@Co-Cys was characterized by SEM, TEM, XPS, etc. The preparation parameters and stabilities of NHase@Co-Cys were investigated. The maximum encapsulation yield and specific activity of NHase@Co-Cys were 92.71% and 139.04 U/g_{immobilized NHase}, respectively. The thermal stability of NHase@Co-Cys was improved by approximately 5-fold at 55 °C. The activity of NHase after immobilization was retained nearly 60% after incubating at pH 4.0 and 10.0 for 7 h. The NHase@Co-Cys showed similar catalytic capacity compared with free NHase in producing nicotinamide. After 7 h of reaction catalyzed by free NHase (14.51 U) and NHase@Co-Cys (12.76 U), the yield of nicotinamide was 90.94% and 86.36%, respectively. The activity of NHase@Co-Cys remained 83.85% of the original activity after recycling for 10 times. These results suggested that the NHase@Co-Cys is an effective approach to enhance the enzymatic properties and demonstrated a broad application prospect in industrial production.

A non-innocent pincer H3LONS ligand and its corresponding octahedral low-spin Fe(iii) complex formation via ligand-centric homolytic S-S bond scission

In the presence of FeCl3 and Et3N, a ligand H4Ldtda(AP) underwent S-S bond cleavage and generated a pincer non-innocent H3LONS ligand, which formed a homoleptic, six-coordinate, low-spin Fe(iii) complex (1). The complex comprised two 2-iminobenzosemiquinone (1-) π-radicals and one thiyl π-radical.

Molecular basis of Cd+2 stress response in Candida tropicalis

This study examines the bioremediation potential and cadmium-induced cellular response on a molecular level in Candida tropicalis 3Aer. Spectroscopic analysis clearly illustrated the involvement of yeast cell wall components in biosorption. Cadmium bioaccumulation was confirmed by TEM, SEM, and EDX examination. TEM images revealed extracellular as well as cytoplasmic and vacuolar cadmium nanoparticle formation, further validated by presence of ycf1 gene and increased biosynthesis of GSH under cadmium stress. Fourteen proteins exhibited differential expression and during cellular redox homeostasis are found to involve in nitrogen metabolism, nucleotide biosynthesis, and carbohydrate catabolism. Interestingly, C. tropicalis 3Aer is equipped with nitrile hydratase enzyme, rarely been reported in yeast. It has the potential to remove nitriles from the environment. The Cd⁺² toxicity not only caused growth stasis but also upregulated the cysteine biosynthesis, protein folding and cytoplasmic detoxification response elements. The present study suggests that C. tropicalis 3Aer is a potential candidate for bioremediating environmental pollution by Cd⁺².

Low-spin [MII(L)2] and [MIII(L)2]+ (M = Fe and Co) complexes of tridentate azo-containing pyridine/pyrazine amide ligands: structures, properties and redox potential correlations

Using deprotonated forms of tridentate azo-containing pyridine-2-/pyrazine-2-carboxamide 2-[N-(2-phenylazo)carbamoyl]-pyridine/pyrazine, seven bis-ligand complexes of Fe^II/Co^II and Fe^III/Co^III have been synthesized. Molecular structures of six of them reveal that these six-coordinate complexes utilize all available donor sites of the ligands and assume M^II/IIIN₂(pyridine/pyrazine)N'₂(amide)N''₂(azo) coordination. Complexes of Fe^II and Co^III are diamagnetic and those of Fe^III and Co^II are paramagnetic (S = 1/2; room-temperature magnetic data and EPR spectra). Cyclic voltammetry experiments in CH₂Cl₂ reveal facile metal-centred Fe^III/Fe^II and Co^III/Co^II redox responses, and all complexes display quasireversible-to-irreversible ligand(azo)-centred redox processes. The E_1/2 values of M^III/M^II redox processes for Fe, Co and Ni (reported earlier) complexes of the pyridine amide ligand linearly correlate with those for six-coordinate [M^III(bpy)₃]³⁺/[M^II(bpy)₃]²⁺, [M^III(terpy)₂]³⁺/[M^II(terpy)₂]²⁺, [M^III(L)]⁺/[M^II(L)]⁰ or [M^III(L')₂]⁺/[M^II(L')₂]⁰ (bpy = 2,2'-bipyridine, terpy = 2,2':6',2''-terpyridine, hexadentate L(2-) = 1,4-bis[o-(pyridine-2-carboxamidophenyl)]-1,4-dithiobutane and tridentate L'(-) = {2-[2-(arylimino)phenylazo]-pyridine}) couples. Density functional theory (DFT) at the B3LYP level and time-dependent (TD)-DFT calculations rationalize the electronic structure of the present complexes and throw light on the origin of observed electronic transitions.

Hemilability-Driven Water Activation: A NiII Catalyst for Base-Free Hydration of Nitriles to Amides

The Ni^II complex 1 containing pyridyl- and hydroxy-functionalized N-heterocyclic carbenes (NHCs) is synthesized and its catalytic utility for the selective nitrile hydration to the corresponding amide under base-free conditions is evaluated. The title compound exploits a hemilabile pyridyl unit to interact with a catalytically relevant water molecule through hydrogen-bonding and promotes a nucleophilic water attack to the nitrile. A wide variety of nitriles is hydrated to the corresponding amides including the pharmaceutical drugs rufinamide, Rifater, and piracetam. Synthetically challenging α-hydroxyamides are accessed from cyanohydrins under neutral conditions. Related catalysts that lack the pyridyl unit (i.e., compounds 2 and 4) are not active whereas those containing both the pyridyl and the hydroxy or only the pyridyl pendant (i.e., compounds 1 and 3) show substantial activity. The linkage isomer 1' where the hydroxy group is bound to the metal instead of the pyridyl group was isolated under different crystallization conditions insinuating a ligand hemilabile behavior. Additional pK_a measurements reveal an accessible pyridyl unit under the catalytic conditions. Kinetic studies support a ligand-promoted nucleophilic water addition to a metal-bound nitrile group. This work reports a Ni-based catalyst that exhibits functional hemilability for hydration chemistry.

Cooperative influence of pseudohalides and ligand backbone of Schiff-bases on nuclearity and stereochemistry of cobalt(iii) complexes: experimental and theoretical investigation

The ligand backbone effect of homologous Schiff-bases in combination with influences of SCN⁻ and N₃⁻ is instrumental in controlling nuclearity and stereochemistry of catecholase active cobalt(iii) complexes.

High stability and biological activity of the copper(II) complexes of alloferon 1 analogues containing tryptophan

Copper(II) complex formation processes between the alloferon 1 (Allo1) (HGVSGHGQHGVHG) analogues where the tryptophan residue is introducing in the place His residue H1W, H6W, H9W and H12W have been studied by potentiometric, UV-visible, CD and EPR spectroscopic, and MS methods. For all analogues of alloferon 1 complex speciation have been obtained for a 1:1 metal-to-ligand molar ratio and 2:1 of H1W because of precipitation at higher (2:1, 3:1 and 4:1) ratios. At physiological pH7.4 and a 1:1 metal-to-ligand molar ratio the tryptophan analogues of alloferon 1 form the CuH_-1L and/or CuH_-2L complexes with the 4N binding mode. The introduction of tryptophan in place of histidine residues changes the distribution diagram of the complexes formed with the change of pH and their stability constants compared to the respective substituted alanine analogues of alloferon 1. The CuH_-1L, CuH_-2L and CuH_-3L complexes of the tryptophan analogues are more stable from 1 to 5 log units in comparison to those of the alanine analogues. This stabilization of the complexes may result from cation(Cu(II))-π and indole/imidazole ring interactions. The induction of apoptosis in vivo, in Tenebrio molitor cells by the ligands and their copper(II) complexes at pH7.4 was studied. The biological results show that copper(II) ions in vivo did not cause any apparent apoptotic features. The most active were the H12W peptide and Cu(II)-H12W complex formed at pH7.4.

The wonderful world of pyridine-2,6-dicarboxamide based scaffolds

This perspective focusses on a variety of scaffolds based on a pyridine-2,6-dicarboxamide fragment and their noteworthy roles in coordination chemistry, biomimetic studies, catalysis, and sensing.

Synthesis and structural characterisation of amides from picolinic acid and pyridine-2,6-dicarboxylic acid

Coupling picolinic acid (pyridine-2-carboxylic acid) and pyridine-2,6-dicarboxylic acid with N-alkylanilines affords a range of mono- and bis-amides in good to moderate yields. These amides are of interest for potential applications in catalysis, coordination chemistry and molecular devices. The reaction of picolinic acid with thionyl chloride to generate the acid chloride in situ leads not only to the N-alkyl-N-phenylpicolinamides as expected but also the corresponding 4-chloro-N-alkyl-N-phenylpicolinamides in the one pot. The two products are readily separated by column chromatography. Chlorinated products are not observed from the corresponding reactions of pyridine-2,6-dicarboxylic acid. X-Ray crystal structures for six of these compounds are described. These structures reveal a general preference for cis amide geometry in which the aromatic groups (N-phenyl and pyridyl) are cis to each other and the pyridine nitrogen anti to the carbonyl oxygen. Variable temperature ¹H NMR experiments provide a window on amide bond isomerisation in solution.

Synthesis, characterization, single crystal X-ray determination, fluorescence and electrochemical studies of new dinuclear nickel(II) and oxovanadium(IV) complexes containing double Schiff base ligands

A series of new bimetallic complexes of nickel(II) and vanadium(IV) have been synthesized by the reaction of the new double bidentate Schiff base ligands with nickel acetate and vanadyl acetylacetonate in 1:1 M ratio. In nickel and also vanadyl complexes the ligands were coordinated to the metals via the imine N and enolic O atoms. The complexes have been found to possess 1:1 metals to ligands stoichiometry and the molar conductance data revealed that the metal complexes were non-electrolytes. The nickel and vanadyl complexes exhibited distorted square planar and square pyramidal coordination geometries, respectively. The emission spectra of the ligands and their complexes were studied in methanol. Electrochemical properties of the ligands and their metal complexes were also investigated in DMSO solvent at 150 mV s(-1) scan rate. The ligands and metal complexes showed both quasi-reversible and irreversible processes at this scan rate. The Schiff bases and their complexes have been characterized by FT-IR, 1H NMR, UV/Vis spectroscopies, elemental analysis and conductometry. The crystal structure of the nickel complex has been determined by single crystal X-ray diffraction.

Transition-metal-free hydration of nitriles using potassium tert-butoxide under anhydrous conditions

Potassium tert-butoxide acts as a nucleophilic oxygen source during the hydration of nitriles to give the corresponding amides under anhydrous conditions. The reaction proceeds smoothly for a broad range of substrates under mild conditions, providing an efficient and economically affordable synthetic route to the amides in excellent yields. This protocol does not need any transition-metal catalyst or any special experimental setup and is easily scalable to bulk scale synthesis. A single-electron-transfer radical mechanism as well as an ionic mechanism have been proposed for the hydration process.