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Laccases (EC 1.10.3.2) are multicopper oxidases with the capability to oxidize diverse phenolic and non-phenolic substrates. While the molecular mechanism of their activity towards phenolic substrates is well-established, their reactivity towards non-phenolic substrates, such as polycyclic aromatic hydrocarbons (PAHs), remains unclear. To elucidate the oxidation mechanism of PAHs, particularly the activation mechanism of the sp 2 aromatic C-H bond, we conducted a density functional theory investigation on the oxidation of two PAHs (anthracene and benzo[ a ]pyrene) using an extensive model of the T1 copper catalytic site of the fungal laccase from Trametes versicolor .

Nitrogen gas is a highly inert molecule and its activation under mild conditions represents a crucial goal in current research. In a recent study, the discovery of low-valence Ca(I) compounds capable of coordinating and reducing N 2 was reported [B. Rösch, T. X. Gentner, J. Langer, C. Färber, J. Eyselein, L. Zhao, C. Ding, G. Frenking and S. Harder, Science , 2021, 371 , 1125]. The study of low-valence alkaline earth complexes represents a new horizon in inorganic chemistry and demonstrates examples of spectacular reactivity. For example, complexes of the [BDI] 2 Mg 2 type are selective reducing reagents in both organic and inorganic synthesis reactions. To date, however, no activity of Mg(I) complexes in the activation of the nitrogen molecule has been reported. By computational studies, in the present work, we investigated the analogies and differences of low-valence Ca(I) and Mg(I) complexes in the coordination, activation and protonation of N 2 . We have shown that the possibility of alkaline earth metals to employ atomic orbitals of the d type is reflected in the differences in the N 2 binding energy and its coordination mode (end-on vs. side-on), as well as in the spin state of the resulting adduct (singlet vs. triplet). These divergences are finally observed in the subsequent protonation reaction, which turned out to be prohibitive in the presence of Mg.

This work originated from the need to functionalize surfactant-coated inorganic nanoparticles for biomedical applications, a process that is limited by excess unbound surfactant. These limitations are connected to the bioconjugation of targeting molecules that are often in equilibrium between the free aliquot in solution and that which binds the surface of the nanoparticles. The excess in solution can play a role in the biocompatability in vitro and in vivo of the final nanoparticles stock. For this purpose, we tested the ability of common surfactants - monothiolated polyethylene glycol and amphiphilic polymers - to colloidally stabilize nanoparticles as excess surfactant is removed and compared them to newly appearing multidentate surfactants endowed with high avidity for inorganic nanoparticles. Our results showed that monothiolated polyethylene glycol or amphiphilic polymers have an insufficient affinity to the nanoparticles and as the excess surfactant is removed the colloidal stability is lost, while multidentate high-avidity surfactants excel in the same regard, possibly allowing improvement in an array of nanoparticle applications, especially in those stated.

The extraordinary capability of [NiFe]-hydrogenases to catalyse the reversible interconversion of protons and electrons into dihydrogen (H 2 ) has stimulated numerous experimental and theoretical studies addressing the direct utilization of these enzymes in H 2 production processes. Unfortunately, the introduction of these natural H 2 -catalysts in biotechnological applications is limited by their inhibition under oxidising (aerobic and anaerobic) conditions. With the aim of contributing to overcome this limitation, we studied the oxidative inactivation mechanism of [NiFe]-hydrogenases by performing Density Functional Theory (DFT) calculations on a very large model of their active site in which all the amino acids forming the first and second coordination spheres of the NiFe cluster have been explicitly included. We identified an O 2 molecule and two H 2 O molecules as sources of the two oxygen atoms that are inserted at the active site of the inactive forms of the enzyme (Ni-A and Ni-B) under aerobic and anaerobic conditions, respectively. Furthermore, our results support the experimental evidence that the Ni-A-to-Ni-B ratio strongly depends on the number of reducing equivalents available for the process and on the oxidizing conditions under which the reaction takes place.

The angiogenin protein (Ang) is a member of the vertebrate-specific secreted ribonucleases and one of the most potent angiogenic factors known. Ang is a normal constituent of human plasma and its concentration increases under some physiological and pathological conditions to promote neovascularization. Ang was originally identified as an angiogenic tumour factor, but its biological activity has been found to extend from inducing angiogenesis to promoting cell survival in different neurodegenerative diseases. Ang exhibits weak ribonucleolytic activity, which is critical for its biological functions. The RNase catalytic sites are two histidine residues, His-13 and His-114, and the lysine Lys-40. Copper is also an essential cofactor in angiogenesis and influences angiogenin's biological properties. The main Cu(ii) anchoring site of Ang is His-114, where metal binding inhibits RNase activity of the protein. To reveal the Cu(ii) coordination environment in the C-terminal domain of the Ang protein, we report on the characterization, by means of potentiometric, voltammetric, and spectroscopic (CD, UV-Vis and EPR) methods and DFT calculations, of Cu(ii) complexes formed with a peptide fragment including the Ang sequence 112-117 (PVHLDQ). Potentiometric titrations indicated that [CuLH -2 ] is the predominant species at physiological pH. EPR, voltammetric data and DFT calculations are consistent with a CuN 3 O 2 coordination mode in which a distorted square pyramidal arrangement of the peptide was observed with the equatorial positions occupied by the nitrogen atoms of the deprotonated amides of the Asp and Leu residues, the δ-N atom of histidine and the oxygen atom of the aspartic carboxylic group. Moreover, two analogous peptides encompassing the PVHLNQ and LVHLDQ sequences were also characterized by using thermodynamic, spectroscopic and DFT studies to reveal the role they play in Cu(ii) complex formation by the carboxylate side chain of the Asp and Pro residues, a known breaking-point in metal coordination.

The [FeFe] hydrogenase is a highly sophisticated enzyme for the synthesis of hydrogen via a biological route. The rotated state of the H-cluster in the [Fe(I)Fe(I)] form was found to be an indispensable criteria for an effective catalysis. Mimicking the specific rotated geometry of the [FeFe] hydrogenase active site is highly challenging as no protein stabilization is present in model compounds. In order to simulate the sterically demanding environment of the nature's active site, the sterically crowded meso-bis(benzylthio)diphenylsilane (2) was utilized as dithiolate linker in an [2Fe2S] model complex. The reaction of the obtained hexacarbonyl complex 3 with 1,2-bis(dimethylphosphino)ethane (dmpe) results three different products depending on the amount of dmpe used in this reaction: [{Fe2(CO)5{μ-(SCHPh)2SiPh2}}2(μ-dmpe)] (4), [Fe2(CO)5(κ(2)-dmpe){μ-(SCHPh)2SiPh2}] (5) and [Fe2(CO)5(μ-dmpe){μ-(SCHPh)2SiPh2}] (6). Interestingly, the molecular structure of compound 5 shows a [FeFe] subsite comprising a semi-rotated conformation, which was fully characterized as well as the other isomers 4 and 6 by elemental analysis, IR and NMR spectroscopy, X-ray diffraction analysis (XRD) and DFT calculations. The herein reported model complex is the first example so far reported for [Fe(I)Fe(I)] hydrogenase model complex showing a semi-rotated geometry without the need of stabilization via agostic interactions (Fe···H-C).

Bromoperoxidase catalytic activity exerted by oxidated amavadin [V(HIDPA)2](-) (HIDPA = 2,2'-(hydroxyimino) dipropionate) in mono- and bis-protonated forms has been investigated by DFT. Possible reaction pathways for formation of peroxido/hydroperoxido complexes and subsequent bromide oxidation have been systematically dissected. The effect of increasing [H(+)] on catalytically active species and on halogenide oxidation has been also studied. Similarly to vanadium haloperoxidase (VHPO), the results point to a hydroperoxido amavadin adduct as the most reactive species toward bromide oxidation. However, comparison of the reactivity of amavadin and VHPO reveals also crucial differences in the catalytic mechanism of such natural V complexes.

Molecular dynamics (MD) simulations have the ability to help reveal the relationship between protein structure, dynamics and function. Here, we describe MD simulations of the representative members of family 3 of E2 enzymes that we performed and analyzed with the aim of providing a quantitative description of the functional dynamics in this biologically important set of proteins. In particular, we combined a description of the protein as a network of interacting residues with the dynamical cross-correlation method to characterize the correlated motions observed in the simulations. This approach enabled us to detect communication between distal residues in these enzymes, and thus to reliably define all the likely intramolecular pathways of communication. We observed functionally relevant differences between the closed and open conformations of the enzyme, and identified the critical residues involved in the long-range communication paths. Our results highlight how molecular simulations can be used to aid in providing atomic-level details to communication paths within proteins.

Reaction of Fe(3)(CO)(12) with pyridinyl thioester ligand PyCH(2)SCOCH(3) (L(1), Py = pyridin-2-yl) produced complex, [Fe(2)(κ-COCH(3))(μ-SCH(2)Py)(CO)(5)] (1) (PyCH(2)S = pyridin-2-ylmethanethiolate). When complex 1 reacted with PPh(3), a monosubstituted complex, [Fe(2)(κ-COCH(3))(μ-SCH(2)Py)(CO)(4)PPh(3)] (2), was derived. Reaction of the same precursor with analogous thioester ligand PyCH(2)SCOPy (L(2)) generated three novel diiron complexes, [Fe(2)(κ-Py)(μ-SCH(2)Py)(CO)(5)] (3), [Fe(2)(κ-Py)'(μ-SCH(2)Py)(CO)(5)] (4), and [Fe(2)(κ-Py)(μ-SCH(2)Py)(CO)(6)] (5). Complexes 3 and 4 are structural isomers. Complex 5 could be converted into complex 4 but the conversion from complex 5 to the isomer 3 was not observed. All the five complexes were fully characterised using FTIR, NMR, and other techniques. Their structures were determined using X-ray single crystal diffraction analysis. The oxidative formation of complexes 1, 3, 4, and 5 involved C-S and/or C-C bonds cleavages. To probe possible mechanisms for these cleavages, DFT calculations were performed. From the calculations, viable reaction pathways leading to the formation of all the isolated products were delineated. The results of the theoretic calculations also allowed rationalisation of the experimental observations.

Amavadin is an unusual octa-coordinated V(IV) complex isolated from Amanita muscaria mushrooms. The outer-sphere catalytic properties of such a complex toward several oxidation reactions are well known. Nevertheless, a remarkable example exists, in which the V(V) (d(0)) oxidized form of amavadin is able to electro-catalyze the oxidation of some thiols to the corresponding disulfides through an inner-sphere mechanism (Guedes da Silva et al. J. Am. Chem. Soc.1996, 118, 7568-7573.) The reaction mechanism implies the formation of an amavadin-substrate intermediate, whose half-life is about 0.3 s. By means of Density Functional Theory (DFT) computations and Quantum Theory of Atoms in Molecules (QTAIM) analysis of the electron density, we have first characterized the stereoelectronic features of the V(IV) (inactive) and V(V) (active) states of amavadin. Then, the formation of the V(V) complex with methyl mercaptoacetate (MMA), which has been chosen as a prototypical substrate, has been characterized both thermodynamically and kinetically. DFT results reveal that protonation of V(V) amavadin at a carboxylate oxygen not directly involved in the V coordination, favors MMA binding into the first coordination sphere of vanadium, by substitution of the amavadin carboxylate oxygen with that of the substrate and formation of an S-HO hydrogen bond interaction. The latter interaction can promote SH deprotonation and binding of the thiolate group to vanadium. The kinetic and thermodynamic feasibility of the V(V)-MMA intermediates formation is in agreement, along with electrochemical experimental data, also with the biological role exerted by amavadin. Finally, the presence of an ester functional group as an essential requisite for MMA oxidation has been rationalized., (This journal is © The Royal Society of Chemistry 2011)

Experimental and computational experiments show that the electrophile MeS(+) attacks a single Fe center in Fe(2)(propanedithiolate)(CO)(4)(PMe(3))(2) followed by isomerization of this terminal thiolato complex to the corresponding μ-SMe derivative., (This journal is © The Royal Society of Chemistry 2011)

The mechanism of terminal- to μ-hydride isomerisation in models of synthetic complexes resembling the [FeFe]-hydrogenase active site has been elucidated by DFT calculations, revealing that Ray-Dutt reaction pathways are generally favoured, and providing some clues for the rational design of novel synthetic catalysts to produce H(2).

A DFT study of protonation thermodynamics in H(2)-evolving biomimetic catalysts related to [FeFe]-hydrogenases active site is presented here. Taking as a reference system the electrocatalytic dihydrogen evolution mechanism recently proposed for the synthetic assembly [Fe(2)(CO)(4)(kappa(2)-Ph(2)PCH(2)CH(2)PPh(2))(mu-S(CH(2))(3)S)] (a, which is able to release H(2) after having undergone monoelectron reduction steps and three sequential protonation reactions), we show how the reduction of model complexes to oxidation states lower than those observed in [FeFe]-hydrogenases cofactor leads to a protonation regiochemistry that has no counterpart in the enzymatic mechanism of H(2) production. In particular, double protonation of the metal centers turned out to be disfavored in a by up to 12.5 kcal mol(-1) with respect to alternative protonation paths; as for the regiochemistry of triple protonation, the formation of eta(2)-H(2) adducts is disfavored by at least approximately 25 kcal mol(-1). Structural analysis of the theoretical models also revealed that over-reduction of synthetic complexes, though necessary for observing H(2) evolution from the currently available biomimetic electrocatalysts, can generally impair their structural integrity. Possible approaches for the modulation of protonation regiochemistry are then proposed; in particular, it turned out that a targeted use of sigma-donating ligands showing low basicity can favor double protonation of iron centers.

The stepwise formation of bridging (mu-) hydrides of diiron dithiolates is discussed with attention on the pathway for protonation and subsequent isomerizations. Our evidence is consistent with protonations occurring at a single Fe center, followed by isomerization to a series of mu-hydrides. Protonation of Fe(2)(edt)(CO)(4)(dppv) (1) gave a single mu-hydride with dppv spanning apical and basal sites, which isomerized at higher temperatures to place the dppv into a dibasal position. Protonation of Fe(2)(pdt)(CO)(4)(dppv) (2) followed an isomerization pathway similar to that for [1H](+), except that a pair of isomeric terminal hydrides were observed initially, resulting from protonation at the Fe(CO)(3) or Fe(CO)(dppv) site. The first observable product from low temperature protonation of the tris-phosphine Fe(2)(edt)(CO)(3)(PMe(3))(dppv) (3) was a single mu-hydride wherein PMe(3) is apical and the dppv ligand spans apical and basal sites. Upon warming, this isomer converted fully but in a stepwise manner to a mixture of three other isomeric hydrides. Protonation of Fe(2)(pdt)(CO)(3)(PMe(3))(dppv) (4) proceeded similarly to the edt analogue 3, however a terminal hydride was observed, albeit only briefly and at very low temperatures (-90 degrees C). Low-temperature protonation of the bis-chelates Fe(2)(xdt)(CO)(2)(dppv)(2) produced exclusively the terminal hydrides [HFe(2)(xdt)(mu-CO)(CO)(dppv)(2)](+) (xdt = edt and pdt), which subsequently isomerized to a pair of mu-hydrides. At room temperature these (dppv)(2) derivatives convert to an equilibrium of two isomers, one C(2)-symmetric and the other C(s)-symmetric. The stability of the terminal hydrides correlates with the (C(2)-isomer)/(C(s)-isomer) equilibrium ratio, which reflects the size of the dithiolate. The isomerization was found to be unaffected by the presence of excess acid, by solvent polarity, and the presence of D(2)O. This isomerization mechanism is proposed to be intramolecular, involving a 120 degrees rotation of the HFeL(3) subunit to an unobserved terminal basal hydride as the rate-determining step. The observed stability of the hydrides was supported by DFT calculations, which also highlight the instability of the basal terminal hydrides. Isomerization of the mu-hydride isomers occurs on alternating FeL(3) via 120 degree rotations without generating D(2)O-exchangeable intermediates.

The present paper shows how theoretically determined electron paramagnetic resonance (EPR) parameters can help in assigning the most favorable structure of Cu(ii) complexes in octarepeat (OR) regions (PHGGGWGQ) of the prion protein (PrP). This could contribute to a better understanding of the molecular structure of the Cu(OR) complexes, as some features of such species in solution are still unclear. The present theoretical investigation on [Cu(ii)(HGGG)] and [Cu(ii)(HGGGW)] complexes was carried out to confirm the stability of relevant isomers, and in particular, to evaluate the hyperfine coupling constants (hcc) with (63)Cu, (14)N and (17)O nuclei, as well as the g values. The hcc (and to a lesser extent the g components) are useful probes for checking whether the computed EPR parameters for specific isomers fit the experimental data, thus permitting the association of the observed spectra with a specific complex structure. The results obtained suggest that the Cu(ii) ion in the [Cu(HGGG)] isomers prefers a square pyramidal coordination with three nitrogen atoms of the peptide and one carbonyl oxygen atom in the basal plane. Also the Cu(ii) ion in the [Cu(HGGGW)] complex is penta-coordinated. The penta-coordination does not actually involve the tryptophan residue but an additional water molecule, forced to occupy the axial coordination position by a rather extended hydrogen-bond network, promoted by the tryptophan residue. The comparison between the calculated and experimental values of EPR parameters allows one to suggest the assignment of the coordination mode of the Cu(ii) ion in the considered peptide ligands. The computed values of the g components seem to be little affected by a particular coordination mode. In particular, the g( parallel) component is always underestimated by about 0.1 with respect to the experiment. The calculated values of the hcc, in contrast, are in acceptable agreement with the experimental values, in spite of the fact that the large size of the species under consideration forced us to accept a certain level of approximation in the computational procedure. Nevertheless, the present study must be considered as one of the first examples of truly ab initio calculations of EPR parameters for systems as large as the Cu(OR)-type complexes.

The new complexes Fe2(S2CnH2n)(CO)2(dppv)2 (n = 2, 3; dppv = cis-1,2-C2H2(PPh2)2) form adducts with AlBr3 and B(C6F5)3, which adopt the "rotated structure" proposed for the active site of the Fe-only hydrogenases--the propanedithiolate is significantly more Lewis basic due to nonbonded interactions between the dithiolate strap and the ligands on Fe.