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Several mammalian genes have originated from the domestication of retrotransposons, selfish mobile elements related to retroviruses. Some of the proteins encoded by these genes have maintained virus-like features; including self-processing, capsid structure formation, and the generation of different isoforms through −1 programmed ribosomal frameshifting. Using quantitative approaches in molecular evolution and biophysical analyses, we studied 28 retrotransposon-derived genes, with a focus on the evolution of virus-like features. By analyzing the rate of synonymous substitutions, we show that the −1 programmed ribosomal frameshifting mechanism in three of these genes (PEG10, PNMA3, and PNMA5) is conserved across mammals and originates alternative proteins. These genes were targets of positive selection in primates, and one of the positively selected sites affects a B-cell epitope on the spike domain of the PNMA5 capsid, a finding reminiscent of observations in infectious viruses. More generally, we found that retrotransposon-derived proteins vary in their intrinsically disordered region content and this is directly associated with their evolutionary rates. Most positively selected sites in these proteins are located in intrinsically disordered regions and some of them impact protein posttranslational modifications, such as autocleavage and phosphorylation. Detailed analyses of the biophysical properties of intrinsically disordered regions showed that positive selection preferentially targeted regions with lower conformational entropy. Furthermore, positive selection introduces variation in binary sequence patterns across orthologues, as well as in chain compaction. Our results shed light on the evolutionary trajectories of a unique class of mammalian genes and suggest a novel approach to study how intrinsically disordered region biophysical characteristics are affected by evolution.

Ion pairing in water solutions alters both the water hydrogen-bond network and ion solvation, modifying the dynamics and properties of electrolyte water solutions. Here, we report an anomalous intrinsic fluorescence of KCl aqueous solution at room temperature and show that its intensity increases with the salt concentration. From the ab initio density functional theory (DFT) and time-dependent DFT modeling, we propose that the fluorescence emission could originate from the stiffening of the hydrogen bond network in the hydration shell of solvated ion-pairs that suppresses the fast nonradiative decay and allows the slower radiative channel to become a possible decay pathway. Because computations suggest that the fluorophores are the local ion-water structures present in the prenucleation phase, this band could be the signature of the incoming salt precipitation.

Determining the redox potentials of protein cofactors and how they are influenced by their molecular neighborhoods is essential for basic research and many biotechnological applications, from biosensors and biocatalysis to bioremediation and bioelectronics. The laborious determination of redox potential with current experimental technologies pushes forward the need for computational approaches that can reliably predict it. Although current computational approaches based on quantum and molecular mechanics are accurate, their large computational costs hinder their usage. In this work, we explored the possibility of using more efficient QSPR models based on machine learning (ML) for the prediction of protein redox potential, as an alternative to classical approaches. As a proof of concept, we focused on flavoproteins, one of the most important families of enzymes directly involved in redox processes. To train and test different ML models, we retrieved a dataset of flavoproteins with a known midpoint redox potential (Em) and 3D structure. The features of interest, accounting for both short- and long-range effects of the protein matrix on the flavin cofactor, have been automatically extracted from each protein PDB file. Our best ML model (XGB) has a performance error below 1 kcal/mol (∼36 mV), comparing favorably to more sophisticated computational approaches. We also provided indications on the features that mostly affect the Emvalue, and when possible, we rationalized them on the basis of previous studies.

The unique properties of liquid water mainly arise from its hydrogen bond network. The geometry and dynamics of this network play a key role in shaping the characteristics of soft matter, from simple solutions to biosystems. Here we report an anomalous intrinsic fluorescence of HCl and NaOH aqueous solutions at room temperature that shows important differences in the excitation and emission bands between the two solutes. From ab initio time-dependent density functional theory modeling we propose that fluorescence emission could originate from hydrated ion species contained in transient cavities of the bulk solvent. These cavities, which are characterized by a stiff surface, could provide an environment that, upon trapping the excited state, suppresses the fast nonradiative decay and allows the slower radiative channel to become a possible decay pathway.

The unique properties of liquid water mainly arise from its hydrogen bond network. The geometry and dynamics of this network play a key role in shaping the characteristics of soft matter, from simple solutions to biosystems. Here we report an anomalous intrinsic fluorescence of HCl and NaOH aqueous solutions at room temperature that shows important differences in the excitation and emission bands between the two solutes. From ab initio time-dependent density functional theory modeling we propose that fluorescence emission could originate from hydrated ion species contained in transient cavities of the bulk solvent. These cavities, which are characterized by a stiff surface, could provide an environment that, upon trapping the excited state, suppresses the fast nonradiative decay and allows the slower radiative channel to become a possible decay pathway.

The potentials of redox systems involving nitrogen, oxygen, and metal ions of the first-row transition series have been computed according to the general approach of the grand canonical ensemble, which leads to the equilibrium value of the reduction potential via a (complete) sampling of configuration space at a given temperature. The approach is a single configuration approach in the sense that identical molecular structures are sampled for both the oxidized and reduced species considered in water solution. In this study, the solute and a cluster of 11-12 water molecules are treated explicitly at the same level of theory and embedded in a continuum solvent. The molecular energies are computed in the framework of the density functional theory. Our approach is basically different from the approach based on the ThermoDynamic Cycle involving gas-phase calculations of the electron affinity of the oxidized species, corrected by the differential hydration energy (obtained from continuum solvent models only) between oxidized and reduced forms. The calculated redox potentials are in agreement with the available experimental data much closer than other results so far presented in the literature. Our results are very satisfactory also in the case of the 3+/2+ redox states of the first-row transition metals, i.e., systems with a high positive charge for which enhanced effects of the solvent are expected.

Filovirus infection is mediated by engagement of the surface-exposed glycoprotein (GP) by its cellular receptor, NPC1 (Niemann-Pick C1). Two loops in the C domain of NPC1 (NPC1-C) bind filovirus GP. Herein, we show that filovirus GP and NPC1-C evolve under mutual selective pressure. Analysis of a large mammalian phylogeny indicated that strong functional/structural constraints limit the NPC1 sequence space available for adaptive change and most sites at the contact interface with GP are under negative selection. These constraints notwithstanding, we detected positive selection at NPC1-C in all mammalian orders, from Primates to Xenarthra. Different codons evolved adaptively in distinct mammals, and most selected sites are located within the two NPC1-C loops that engage GP, or at their anchor points. In Homininae, NPC1-C was a preferential selection target, and the T419I variant possibly represents a human-specific adaptation to filovirus infection. On the other side of the arms-race, GP evolved adaptively during filovirus speciation. One of the selected sites (S142Q) establishes several atom-to-atom contacts with NPC1-C. Additional selected sites are located within epitopes recognized by neutralizing antibodies, including the 14G7 epitope, where sites selected during the recent EBOV epidemic also map. Finally, pairs of co-evolving sites in Marburgviruses and Ebolaviruses were found to involve antigenic determinants. These findings suggest that the host humoral immune response was a major selective pressure during filovirus speciation. The S142Q variant may contribute to determine Ebolavirus host range in the wild. If this were the case, EBOV/BDBV (S142) and SUDV (Q142) may not share the same reservoir(s).

Lytic polysaccharide monooxygenases (LPMOs) are Cu-containing enzymes that facilitate the degradation of recalcitrant polysaccharides by the oxidative cleavage of glycosidic bonds. They are gaining rapidly increasing attention as key players in biomass conversion, especially for the production of second-generation biofuels. Elucidation of the detailed mechanism of the LPMO reaction is a major step toward the assessment and optimization of LPMO efficacy in industrial biotechnology, paving the way to utilization of sustainable fuel sources. Here, we used density functional theory calculations to study the reaction pathways suggested to date, exploiting a very large active-site model for a fungal AA9 LPMO and using a celloheptaose unit as a substrate mimic. We identify a copper oxyl intermediate as being responsible for H-atom abstraction from the substrate, followed by a rapid, water-assisted hydroxyl rebound, leading to substrate hydroxylation.

The protein product of the myxovirus resistance 2 (MX2) gene restricts HIV-1 and simian retroviruses. We demonstrate that MX2 evolved adaptively in mammals with distinct sites representing selection targets in distinct branches; selection mainly involved residues in loop 4, previously shown to carry antiviral determinants. Modeling data indicated that positively selected sites form a continuous surface on loop 4, which folds into two antiparallel a-helices protruding from the stalk domain. A population genetics-phylogenetics approach indicated that the coding region of MX2 mainly evolved under negative selection in the human lineage. Nonetheless, population genetic analyses demonstrated that natural selection operated on MX2 during the recent history of human populations: distinct selective events drove the frequency increase of two haplotypes in the populations of Asian and European ancestry. The Asian haplotype carries a susceptibility allele for melanoma; the European haplotype is tagged by rs2074560, an intronic variant. Analyses performed on three independent European cohorts of HIV-1-exposed seronegative individuals with different geographic origin and distinct exposure route showed that the ancestral (G) allele of rs2074560 protects from HIV-1 infection with a recessive effect (combined P=1.55×10-4). The same allele is associated with lower in vitro HIV-1 replication and increases MX2 expression levels in response to IFN-a. Data herein exploit evolutionary information to identify a novel host determinant of HIV-1 infection susceptibility.

Aim of this contribution is to review some recent quantum mechanical approaches used to compute the redox potentials of transition metal complexes, with the emphasis on copper and iron species, which are particularly relevant in inorganic biochemistry and in synthetic chemistry of bio-mimetic compounds. The paper presents also new DFT results obtained on Cu and Fe aquo ions in the framework of the Thermodynamic Integration and Grand Canonical Ensemble approaches. Such results show that without explicit inclusion of water molecules in the external solvation shells (even using a continuum solvation model) also very advanced methodologies fail to predict the redox potential in an acceptable manner. This is a confirmation of some previous studies which however never addressed this specific problem along the aforementioned approaches. Better results are obtained, on the contrary, on a series of Cu(II) complexes with Gly, Ala, en, Im, and water ligands with coordination type N2O2 or N4. In this case, the complexes are surrounded by nine water molecules which may partially alleviate the inadequacy of the continuum solvent models, especially in the case of highly positively charged species.

The antigenic repertoire presented by MHC molecules is generated by the antigen processing and presentation (APP) pathway. We analyzed the evolutionary history of 45 genes involved in APP at the inter- and intra-species level. Results showed that 11 genes evolved adaptively in mammals. Several positively selected sites involve positions of fundamental importance to the protein function (e.g. the TAP1 peptide-binding domains, the sugar binding interface of langerin, and the CD1D trafficking signal region). In CYBB, all selected sites cluster in two loops protruding into the endosomal lumen; analysis of missense mutations responsible for chronic granulomatous disease (CGD) showed the action of different selective forces on the very same gene region, as most CGD substitutions involve aminoacid positions that are conserved in all mammals. As for ERAP2, different computational methods indicated that positive selection has driven the recurrent appearance of protein-destabilizing variants during mammalian evolution. Application of a population-genetics phylogenetics approach showed that purifying selection represented a major force acting on some APP components (e.g. immunoproteasome subunits and chaperones) and allowed identification of positive selection events in the human lineage.We also investigated the evolutionary history of APP genes in human populations by developing a new approach that uses several different tests to identify the selection target, and that integrates low-coverage whole-genome sequencing data with Sanger sequencing. This analysis revealed that 9 APP genes underwent local adaptation in human populations. Most positive selection targets are located within noncoding regions with regulatory function in myeloid cells or act as expression quantitative trait loci. Conversely, balancing selection targeted nonsynonymous variants in TAP1 and CD207 (langerin). Finally, we suggest that selected variants in PSMB10 and CD207 contribute to human phenotypes. Thus

A comparative analysis of a series of DFT models of [NiFe]-hydrogenases, ranging from minimal NiFe clusters to very large systems including both the first and second coordination sphere of the bimetallic cofactor, was carried out with the aim of unraveling which stereoelectronic properties of the active site of [NiFe]-hydrogenases are crucial for efficient H2 binding and cleavage. H2 binding to the Ni-SIa redox state is energetically favored (by 4.0 kcal mol-1) only when H2 binds to Ni, the NiFe metal cluster is in a low spin state, and the Ni cysteine ligands have a peculiar seesaw coordination geometry, which in the enzyme is stabilized by the protein environment. The influence of the Ni coordination geometry on the H2 binding affinity was then quantitatively evaluated and rationalized analyzing frontier molecular orbitals and populations. Several plausible reaction pathways leading to H2 cleavage were also studied. It turned out that a two-step pathway, where H2 cleavage takes place on the Ni-SIa redox state of the enzyme, is characterized by very low reaction barriers and favorable reaction energies. More importantly, the seesaw coordination geometry of Ni was found to be a key feature for facile H2 cleavage. The discovery of the crucial influence of the Ni coordination geometry on H2 binding and activation in the active site of [NiFe]-hydrogenases could be exploited in the design of novel biomimetic synthetic catalysts. © 2014 American Chemical Society.

This paper reports on the protonation of phosphine-substituted diiron diphosphido carbonyls, analogues of diiron dithiolato centers at the active sites of hydrogenase enzymes. Reaction of the diphosphines (CH2)(n)(PPhH)(2) (n = 2 (edpH(2)) and n = 3 (pdpH(2))) with Fe-3(CO)(12) gave excellent yields of Fe-2(edp)(CO)(6) (1) and Fe-2(pdp)(CO)(6) (2). Substitution of Fe-2(edp)(CO)(6) with PMe3 afforded Fe-2(edp)(CO)(2)(PMe3)(4) (3; nu(CO) 1855 and 1836 cm(-1)). Crystallographic analysis showed that 3 adopts an idealized C-2 symmetry, with pairs of phosphine ligands occupying apical-basal sites on each Fe center. Relative to that in the dithiolato complex, the Fe-Fe bond (2.7786(8) angstrom) is elongated by 0.15 angstrom. Treatment of 3 with H(OEt2)(2)BAr4F (Ar-F = C6H3-3,5-(CF3)(2)) gave exclusively the C-2-symmetric mu-hydride complex [HFe2(edp)(CO)(2)(PMe3)(4)](+). This result contrasts with the behavior of the analogous ethanedithiolate Fe-2(edt)(CO)(2)(PMe3)(4) (edt = 1,2-C2H4S2), protonation of which gives both the bridging and terminal hydride complexes. This difference points to the participation of the sulfur centers in the formation of terminal hydrides. The absence of terminal hydride intermediates was also revealed in the protonation of the diphosphine diphosphido complexes Fe-2(pdp)(CO)(4)(dppv) (4; dppv = cis-1,2-C2H2(PPh2)(2)) and Fe-2(edp)(CO)(4)(dppbz) (5; dppbz = 1,2-C6H4(PPh2)(2)). Protonation of these cliphosphine complexes afforded mu-hydrido cations with apical-basal diphosphine ligands, which convert to the isomer where the diphosphine is dibasal. In contrast, protonation of the dithiolato complex Fe-2(pdt)(CO)(4)(dppv) gave terminal hydrides, which isomerize to mu-hydrides. In a competition experiment, 4 was shown to protonate faster than Fe-2(pdt)(CO)(4)(dppv)

The transport of small ligands to active sites of proteins is the basis of vital processes in biology such as enzymatic catalysis and cell signaling, but also of more destructive ones including enzyme inhibition and oxidative damage. Here, we show how a diffusion-reaction model solved by means of molecular dynamics and density functional theory calculations provides novel insight into the transport of small ligands in proteins. In particular, we unravel the existence of an elusive, dynamically formed gas channel, which CO2 takes to diffuse from the solvent to the active site (C-cluster) of the bifunctional multisubunit enzyme complex carbon monoxide dehydrogenase/acetyl-CoA synthase (CODH/ACS). Two cavities forming this channel are temporarily created by protein fluctuations and are not apparent in the X-ray structures. The ligand transport is controlled by two residues at the end of this tunnel, His113 and His 116, and occurs on the same time scale on which chemical binding to the active site takes place (0.1-1 ms), resulting in an overall binding rate on the second time scale. We find that upon reduction of CO2 to CO, the newly formed Fe-hydroxy ligand greatly strengthens the hydrogen-bond network, preventing CO from exiting the protein through the same way that CO2 takes to enter the protein. This is the basis for directional transport of CO from the production site (C-cluster of CODH subunit) to the utilization site (A-cluster of ACS subunit). In view of these results, a general picture emerges of how large proteins guide small ligands toward their active sites

The ubiquitin (Ub) system controls almost every aspect of eukaryotic cell biology. Protein ubiquitination depends on the sequential action of three classes of enzymes (E1, E2 and E3). E2 Ub-conjugating enzymes have a central role in the ubiquitination pathway, interacting with both E1 and E3, and influencing the ultimate fate of the substrates. Several E2s are characterized by an extended acidic insertion in loop 7 (L7), which if mutated is known to impair the proper E2-related functions. In the present contribution, we show that acidic loop is a conserved ancestral motif in E2s, relying on the presence of alternate hydrophobic and acidic residues. Moreover, the dynamic properties of a subset of family 3 E2s, as well as their binary and ternary complexes with Ub and the cognate E3, have been investigated. Here we provide a model of L7 role in the different steps of the ubiquitination cascade of family 3 E2s. The L7 hydrophobic residues turned out to be the main determinant for the stabilization of the E2 inactive conformations by a tight network of interactions in the catalytic cleft. Moreover, phosphorylation is known from previous studies to promote E2 competent conformations for Ub charging, inducing electrostatic repulsion and acting on the L7 acidic residues. Here we show that these active conformations are stabilized by a network of hydrophobic interactions between L7 and L4, the latter being a conserved interface for E3-recruitment in several E2s. In the successive steps, L7 conserved acidic residues also provide an interaction interface for both Ub and the Rbx1 RING subdomain of the cognate E3. Our data therefore suggest a crucial role for L7 of family 3 E2s in all the E2-mediated steps of the ubiquitination cascade. Its different functions are exploited thank to its conserved hydrophobic and acidic residues in a finely orchestrate mechanism.

The reactivity of [Fe-2(CO)(4)(kappa(2)-LL)(mu-pdt)](+) complexes (pdt = S(CH2)(3)S, propanedithiolate) with different substrates L' (L' = CO, MeCN, P(OMe)(3)) was investigated electrochemically in order to assess the influence of the chelating ligand kappa(2)-LL (LL = I-Me-CH2-I-Me (1(+)), dppe (2(+)); I-Me = 1-methylimidazol-2-ylidene). This latter ligand is effectively shown to affect the reactivity of the cations in different ways: when L' = CO, the adduct [Fe-2(CO)(4)(mu-CO)(kappa(2)-dppe)(mu-pdt)](+) (2-CO+) was clearly observed by cyclic voltammetry, whereas [Fe-2(CO)(4)(mu-CO)(kappa(2)-I-Me-CH2-I-Me)(mu-pdt)](+) (1-CO+) was not detected, although DFT calculations show that the energies of the products and the activation barriers to their formation are similar. When L' = MeCN, the adducts X-MeCN+ with X = 1, 2 are both observed, but the formation is easier when LL = dppe. Finally, the reaction of [Fe-2(CO)(4)(kappa(2)-I-Me-CH2-I-Me)(mu-pdt)](+) (1(+)) with P(OMe)(3) produces the disubstituted dication [Fe-2(CO)(2){P(OMe)3}(2)(kappa(2)-I-Me-CH2-I-Me)(mu-CO)(mu-pdt)](2+) (4(2+)) via a disproportionation reaction, while previous studies demonstrated that monocationic derivatives were obtained when LL = dppe. Complex 4[PF6](2) was fully characterized, and its X-ray crystal structure confirms the presence of a carbonyl ligand in a bridging position, which did not exist in the related P(OMe)(3)-substituted kappa(2)-dppe cations.

The DFTB and DFT methods are applied to the study of different forms of the [Cu(HGGG)(Py)] complex in water, with the aim of identifying the most stable isomer. The DFTB calculations were possible thanks to a careful parametrization of the atom–atom repulsive energy terms for Cu–H, Cu–C, Cu–N, and Cu–O. The speciation process is carried out by computing different DFTB-steered molecular dynamics (SMD) trajectories, each of which ends in a well-defined different form. The last frame of each trajectory is subjected to geometry optimization at both DFTB and DFT levels, leading to a different isomer. From the corresponding energy values, a rank of relative stability of the isomers can be established. The computational protocol developed here is of general applicability to other metal–peptide systems and represents a new powerful tool for the study of speciation of metal-containing systems in water solution, particularly useful when the full characterization of the compound cannot be carried out on the basis of experimental results only

The one-electron oxidation of the diiron complex [Fe-2(CO)(4)(kappa(2)-dppe)(mu-pdt)] (1) (dppe = Ph2PCH2CH2PPh2; pdt = S(CH2)(3)S) has been investigated in the absence and in the presence of P(OMe)(3), by both electrochemical and theoretical methods, to shed light on the mechanism and the location of the oxidatively induced structure change. While cyclic voltammetric experiments did not allow to discriminate between a two-step (EC) and a concerted, quasi-reversible (QR) process, density functional theory (DFT) calculations favor the first option. When P(OMe)(3) is present, the one-electron oxidation produces singly and doubly substituted cations, [Fe-2(CO)(4-n){P(OMe)(3)}(n)(kappa(2)-dppe)(mu-pdt)](+) (n = 1: 2(+); n = 2: 3(+)) following mechanisms that were investigated in detail by DFT. Although the most stable isomer 1(+) and 2(+) (and 3(+)) show a rotated Fe(dppe) center, binding of P(OMe)(3) occurs at the neighboring iron center of both 1(+) and 2(+). The neutral compound 3 was obtained by controlled-potential reduction of the corresponding cation, while 2 was quantitatively produced by reaction of 3 with CO. The CO dependent conversion of 3 into 2 as well as the 2(+) <-> 3(+) interconversion were examined by DFT.

Carbon monoxide is often described as a competitive inhibitor of FeFe hydrogenases, and it is used for probing H2 binding to synthetic or in silico models of the active site H-cluster. Yet it does not always behave as a simple inhibitor. Using an original approach which combines accurate electrochemical measurements and theoretical calculations, we elucidate the mechanism by which, under certain conditions, CO binding can cause permanent damage to the H-cluster. Like in the case of oxygen inhibition, the reaction with CO engages the entire H-cluster, rather than only the Fe2 subsite.

The active site of the [FeFe] hydrogenases contains two Fe ions bound to one Cys ligand, three CO molecules, two CN- ions, and a dithiolate ligand. The nature of the last of these has been much discussed, and it has been suggested that it contains C, N, or O as the bridgehead atom. Most experimental studies indicate a N atom, whereas a recent density functional theory (DFT) study of a crystal structure indicated an O atom. Here, we performed quantum refinement on the same crystal structure with five different models of the dithiolate ligand X(CH2S-)2, with X = CH 2, NH2+, NH (two conformations), or O; we found that structures with a N bridgehead atom actually provide the best fit to the raw crystallographic data. Quantum refinement is standard crystallographic refinement in which the molecular mechanics force field normally used to supplement the experimental raw data to give a more chemical structure is replaced by more accurate DFT calculations for the active site. Thereby, we obtain structures that are an ideal compromise between DFT and crystallography.

[FeFe]-hydrogenases are highly efficient H-2-evolving metalloenzymes that include cyanides and carbonyls in the active site. The latter is an Fe6S6 cluster (the so-called H-cluster) that can be subdivided into a binuclear portion carrying the CO and CN- groups and a tetranuclear subcluster. The fundamental role of cyanide ligands in increasing the basicity of the H-cluster has been highlighted previously. Here a more subtle but crucial role played by the two CN- ligands in the active site of [FeFe]-hydrogenases is disclosed. In fact, QM/MM calculations on all-atom models of the enzyme from Desulfovibrio desulfuricans show that the cyanide groups fine-tune the electronic and redox properties of the active site, affecting both the protonation regiochemistry and electron transfer between the two subclusters of the H-cluster. Despite the crucial role of cyanides in the protein active site, the currently available bioinspired electrocatalysts generally lack CN- groups in order to avoid competition between the latter and the catalytic metal centers for proton binding. In this respect, we show that a targeted inclusion of phosphine ligands in hexanuclear biomimetic clusters may restore the electronic and redox features of the wild-type H-cluster.

This study probes the impact of electronic asymmetry of diiron(I) dithiolato carbonyls. Treatment of Fe-2(S2Cn,H-2n)(CO)(6-x)(PMe3)(x). compounds (n = 2, 3; x = 1, 2, 3) with NOBF4 gave the derivatives [Fe-2(S2CnH2n)(CO)(5-x)(PMe3)(x)(NO)]BF4, which are electronically unsymmetrical because of the presence of a single NO+ ligand. Whereas the monophosphine derivative is largely undistorted, the bis(PMe3) derivatives are distorted such that the CO ligand on the Fe(CO)(PMe3)(NO)(+) subunit is semibridging. Two isomers of [Fe-2(S2C3H6)(CO)(3)(PMe3)(2)(NO)]BF4 were characterized spectroscopically and crystallographically. Each isomer features electron-rich Fe(CO)(2)PMe3 and electrophilic Fe(CO)(PMe3)(NO)(+) subunits. These species are in equilibrium with an unobserved isomer that reversibly binds CO (Delta H = -35 kJ/mol, Delta S = -139 J mol(-1) K-1) to give the symmetrical adduct [Fe-2(S2C3H6)(mu-NO)(CO)(4)(PMe3)(2)]BF4. In contrast to Fe2(S2C3H6)(CO)4(PMe3)2, the bis(PMe3) nitrosyl complexes readily undergo CO substitution to give the (PMe3)(3) derivatives. The nitrosyl complexes reduce at potentials that are similar to 1 V milder than their carbonyl counterparts. Results of density functional theory calculations, specifically natural bond orbital analysis, reinforce the electronic resemblance of the nitrosyl complexes to the corresponding mixed-valence diiron complexes. Unlike other diiron dithiolato carbonyls, these species undergo reversible reductions at mild potentials. The results show that the novel structural and chemical features associated with mixed-valence diiron dithiolates (the so-called H-ox models) can be replicated in the absence of mixed-valency by the introduction of electronic asymmetry.

Density functional theory has been used to investigate the reaction between H-2 and [Ni(NHPnPr(3))('S3')] or [Pd(NHPnPr(3))('S3')], where 'S3' = bis(2-sulfanylphenyl)sulfide(2-), which are among the few synthetic complexes featuring a metal coordination environment similar to that observed in the [NiFe] hydrogenase active site and capable of catalyzing H-2 heterolytic cleavage. Results allowed us to unravel the reaction mechanism, which is consistent with an oxidative addition-hydrogen migration pathway for [Ni(NHPnPr(3))('S3')], whereas metathesis is also possible with [Pd(NHPnPr(3))('S3')]. Unexpectedly, H-2 binding and activation implies structural reorganization of the metal coordination environment. It turns out that the structural rearrangement in [Ni(NHPnPr(3))('S3')] and [Pd(NHPnPr(3))('S3')] can take place due to the peculiar structural features of the Ni and Pd ligands, explaining the remarkable catalytic properties. However, the structural reorganization is the most unfavorable step along the H-2 cleavage pathway (Delta G > 100 kJ mol(-1)), an observation that is relevant for the design and synthesis of novel biomimetic catalysts.

Density functional theory has been used to investigate structural and electronic properties of complexes related to the resting form of the active site of vanadium haloperoxidase as a function of environment and protonation state. Results obtained by studying models of varying size and complexity highlight the influence of environment and protonation state on the structure and stability of the metal cofactor. The study shows that, in the trigonal bipyramidal active site, where one axial position is occupied by a key histidine, the trans position cannot contain a terminal oxo group. Further, a highly negatively charged vanadate unit is not stable. Protonation of at least one equatorial oxo ligand appears necessary to stabilize the metal cofactor. The study also indicates that, while at rest within the protein, the vanadate unit is most likely an anion with an axial hydroxide and an equatorial plane containing two oxos and a hydroxide. For the neutral, protonated state of the vanadate unit, there were two minima found. The first structure is characterized by an axial water with two oxo and one hydroxo group in the equatorial plane. The second structure contains an axial hydroxo group and an equatorial plane composed of one oxo and two hydroxo oxygen atoms. These two species are not significantly different in energy, indicating that either form may be important during the catalytic cycle. These data support the initial crystallographic assignment of an axially bound hydroxide, but an axial water is also a possibility. This study also shows that the protonation state of the vanadate ion is most likely greater than previously proposed.