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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.

International audience; FeFe hydrogenases catalyse H2 oxidation and production using a "H-cluster", where two Fe ions are bound by an aza-dithiolate (adt) ligand. Various hypotheses have been proposed (by us and others) to explain that the enzyme reversibly inactivates under oxidizing, anaerobic conditions: intramolecular binding of the N atom of adt, formation of the so-called Hox/inact state or non-productive binding of H2 to isomers of the H-cluster. Here we show that none of the above explains the new finding that the anaerobic, oxidative, H2-dependent reversible inactivation is strictly dependent on the presence of Cl- or Br-. We provide experimental evidence that chloride uncompetitively inhibits the enzyme: it reversibly binds to catalytic intermediates of H2 oxidation (but not to the resting "Hox" state), after which oxidation locks the active site into a stable, saturated, inactive form, the structure of which is proposed here based on DFT calculations. The halides interact with the amine group of the H-cluster but do not directly bind to iron. It should be possible to stabilize the inhibited state in amounts compatible with spectroscopic investigations to explore further this unexpected reactivity of the H-cluster of hydrogenase.

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 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 photochemistry originated by the Fe2(CO)6S 2 low-lying excited states is investigated using density functional theory (DFT), time-dependent density functional theory (TDDFT), and the quantum theory of atoms in molecules (QTAIM) methods.The 11A1 excitation is the most intense among the low-lying excited states computed at the TDDFT level, which is assigned to the 449 nm metal-to-ligand charge transfer (MLCT) band observed experimentally. We then investigated the nine excited states in a range of ±35 nm centered on the 11A1 excitation energy, which reproduces the range of wavelengths covered by a recent 450 ± 35 nm low-energy laser photolysis experiment. The results presented in this paper suggest that the 450 nm photochemistry recently investigated proceeds mainly through the 11B2 lowest energy singlet excited state. The comparison between tetrahedrane ground state and 11B2 vertical excited state QTAIM atomic net charges evidenced the Fe→S MLCT character but also a significant CO→S ligand-to-ligand charge transfer (LLCT). Geometry relaxation of the nine excited state structures shows a S-S bond distance elongation that reaches the highest value for the 11B2 state. Moreover, during geometry optimization of the 11B2 state, the HOMO/LUMO crossing occurs, favoring the formation of the Fe-Fe butterfly isomer upon decay to the ground state, in agreement with experimental findings. Delocalization indexes allow us to describe the shift of the bonding electron density along the 1 1B2 photochemical reaction path that connects the tetrahedrane ground state to the Fe-Fe butterfly intermediate. Along this path, the S-S bond is progressively weakened until its breaking in the Fe-Fe butterfly isomer, while the Fe-Fe bond is only partially weakened. The S atom is progressively reduced with a total increasing of its negative charge by 0.211 electron, leading to the Fe-Fe butterfly intermediate suitable for oxidative addition. In light of the results obtained, a mechanism of the photochemical ethylene oxidative addition to Fe2(CO)6S2 is proposed. © 2011 American Chemical Society.

In this work a density functional theory study of the CO addition reaction to FeIFeI and FeIFeII models of the active site of [FeFe] hydrogenases is presented. A series of model complexes, ranging from simple diiron model complexes of the binuclear [2Fe]H subcluster to the full H-cluster, have been investigated. For each system, the thermodynamic parameters for the CO adduct formation, a reaction that mimics the enzyme CO inhibition, were computed. Parallel to the investigation of the CO addition reaction, the structural features of the various FeIFeI and FeIFeII species have been evaluated, with particular attention to the issue of the ligand arrangement as a function of the redox state. CO affinity depends on the redox state of the model and the chemical nature of its ligands. FeIFeII species are more favorable to form the CO adducts than the reduced FeIFeI species. According to the computed free energies and enthalpies for the CO adduct formation from Fe2(pdt)(CO)5L models, the CO affinity follows the ligand sequence L = SCH3- > CN- > PPh3 > CO (FeIFeI) and L = CO > CN- > PPh3 > SCH3- (FeIFeII). As the models become more similar to the H-cluster, the CO affinity increases, although the FeIFeI CO -inhibited H-cluster is not stable. The bonding properties of the models considered have been investigated by means of the quantum theory of atoms in molecules approach. Upon CO addiction, the new Fe-C bond is formed to the detriment of the Fe-Fe bonds and, to a lesser extent, the Fe-S bonds. Regarding the FeIFeII systems investigated, the spin density is initially localized on the rotated Fe atom, and the formation of the CO adducts results in a delocalization of the spin density. Consequently, the FeIFeII CO-inhibited forms are better described as (Fe+1.5)2.

The cold-active, chloride-dependent a-amylase from Pseudoalteromonas haloplanktis (AHA) is one of the best characterized psychrophilic enzymes, and shares high sequence and structural similarity with its mesophilic porcine counterpart (PPA). An atomic detail comparative analysis was carried out by performing more than 60 ns of multiple-replica explicit-solvent molecular dynamics simulations on the two enzymes in order to characterize the differences in ensemble properties and dynamics in solution between the two homologues. We find in both enzymes high flexibility clusters in the surroundings of the substrate-binding groove, primarily involving the long loops that protrude from the main domain's barrel structure. These loops are longer in PPA and extend further away from the core of the barrel, where the active site is located: essential fluctuations in PPA mainly affect the highly solvent-accessible portions of these loops, whereas AHA is characterized by greater flexibility in the immediate surroundings of the active site. Furthermore, detailed analysis of active- site dynamics has revealed that elements previously identified through X-ray crystallography as involved in substrate binding in both enzymes undergo concerted motions that may be linked to catalysis. © 2009 American Chemical Society.

Fe(2)(S(2)C(3)H(6))(CO)(6) (a) is a simple model of the [FeFe] hydrogenase catalytic site. The topology of the potential energy surface (PES) of this complex, of its cationic and anionic species (a(+) and a(-)), and of its lowest triplet state was studied using density functional theory (DFT) with BP86 and B3LYP functionals, while selected low- and high-lying singlet excited states were studied with the time-dependent density functional theory (TDDFT). The global minima of a and a(-) PESs are characterized by an all-terminal CO ligand arrangement, while the two rotated forms are transition states (TS). On the contrary, for the a(+) and lowest triplet state PES, the three forms considered are local minima, and the syn rotated form is the global minimum. The relative stability of the rotated forms and the all-terminal CO form on the a, a(+), and a(-) PESs is discussed in light of the Quantum Theory of Atoms in Molecules (QTAIM) analysis of the electron density. By comparing the Fe-Fe bond features of the three forms for each PES, we found that the global minimum structure is characterized by the shortest Fe-Fe bond distance and highest electron density at the Fe-Fe critical point. This approach gave evidence that in the a rotated forms, the weak Fe-C(mu) interaction between the Fe atom of the unrotated Fe(CO)(3) and the C atom of the semibridged CO is formed to the detriment of the Fe-Fe bond interaction. These results suggest that the stabilization of the rotated forms on the cationic PES might be due to the formation of the weak Fe-C(mu) interaction minimizing the weakening of the Fe-Fe bond. The low-lying and lowest triplet excited-state PES investigated are characterized by the stabilization of the rotated forms over the all-terminal CO ligand arrangement. On the first singlet 1(1)A'' excited-state PES, an Fe(CO)(3) semirotated structure is the lowest-energy stationary point, while the exploration of the 1(1)A' and 2(1)A'' singlet excited PESs evidences the stabilization of the rotated over the all-terminal CO forms. Singlet excited-state optimized geometry results are compared with excited-state nuclear distortions recently obtained from resonance Raman excitation profiles. Finally, the results of the exploration of the 6(1)A' and 9(1)A' high-lying excited PESs are discussed in light of the recent ultraviolet photolysis experiments on a.

The molecular and electronic structure of the Fe 6S 6 H-cluster of [FeFe] hydrogenase in relevant redox and protonation states have been investigated by DFT. The calculations have been carried out according to the broken symmetry approach and considering different environmental conditions. The large negative charge of the H-cluster leads, in a vacuum, to structures different from those observed experimentally in the protein. A better agreement with experimental data is observed for solvated complexes, suggesting that the protein environment could buffer the large negative charge of the H-cluster. The comparison of Fe 6S 6 and Fe 2S 2 DFT models shows that the presence of the Fe 4S 4 moiety does not affect appreciably the geometry of the [2Fe] H cluster. In particular, the Fe 4S 4 cluster alone cannot be invoked to explain the stabilization of the mu-CO forms observed in the enzyme (relative to all-terminal CO species). As for protonation of the hydrogen cluster, it turned out that mu-H species are always more stable than terminal hydride isomers, leading to the conclusion that specific interactions of the H-cluster with the environment, not considered in our calculations, would be necessary to reverse the stability order of mu-H and terminal hydrides. Otherwise, protonation of the metal center and H 2 evolution in the enzyme are predicted to be kinetically controlled processes. Finally, subtle modifications in the H-cluster environment can change the relative stability of key frontier orbitals, triggering electron transfer between the Fe 4S 4 and the Fe 2S 2 moieties forming the H-cluster.

The singlet and triplet state potential energy surfaces (PES) of Fe-2(CO)(8) are explored by means of density functional theory (DFT) techniques. The two PES have different global mimima: the dibriged C-2v isomer for the singlet and the unbridged D-2d isomer for the triplet. The sign of the energy gap between singlet and triplet global minima depends on the type of adopted DFT functional: hybrid functionals predict the triplet is more stable than the singlet, but the opposite applies to generalized gradient approximated (GGA) functionals. The analysis of the computed CO stretching frequencies demonstrates that the experimental data for the unbridged form is compatible also with the unbridged triplet D-2d isomer. Starting from these two facts, the electronic structure of unbridged D-2d Fe-2(CO)(8) is discussed herein. Single-point energy computations at the coupled-cluster single and double (CCSD) level favor the D-2d triplet state.

Reaction of R-styreneoxide with glycine-tert-butylester yielded amino alcohols of the general formula (NRRR3)-R-1-R-2, where R-1 = CH2COO t Bu and R-2 = R-3 = 2-phenyl-2-hydroxyethyl (H(2)LA); R-2 = 2-phenyl-2-hydroxyethyl and R-3 = 1-phenyl-2-hydroxyethyl (H2LB); R-2 = H and R-3 = 2-phenyl-2-hydroxyethyl (HLC); and R-2 = H and R-3 = 1-phenyl-2-hydroxyethyl (HLD). The corresponding reaction with sarcosine-tert-butylester and subsequent hydrolysis provided the zwitterion (CH3){CH2CHPh(OH)}(CH2CO2-), HLE* (asterisk refers to unprotected carboxylate). Reaction of these ligands with VO(OiPr)(3) in CH2Cl2 gave the oxovanadium(V) complexes [VOL(OiPr)(2)] and [VOL2-(OiPr)] (for L-C and L-D) or, when reacted in the presence of MeOH, [VOL'(OMe)], where L' represents the methyl ester of L-A, L-B, and L-E. The crystal and molecular structures of R-HLC, S-HLD, R,S-HLE*center dot H2O, and Lambda[VO(R,S-L-B')OMe] have been determined. The complex [VOLB'(OMe)] contains vanadium in a distorted trigonal-bipyramidal array (tau = 0.72), the oxo group in the equatorial plane, and methoxide and N in the apical positions, and thus, it structurally models the active center of vanadate-dependent haloperoxidases. The structure and the bonding parameters, including a particularly long d(V-N) of 2.562 angstrom, are backed up by DFT calculations. The isolated oxovanadium(V) complexes and the in situ systems L VO(OiPr)(3) catalyze the oxidation, by cumylhydroperoxide HO2R', of prochiral sulfides (MeSPh, MeSp-Tol, PhSBn) to chiral sulfoxides plus some sulfone. The best results with respect to enantioselectivity (enantiomeric excess (ee) = 38%) were obtained with the system VO(OiPr)(3)/L-A, and the best selectivity with respect to sulfoxide (100%) was obtained with [VOLA(OiPr)]. The reaction with the hexacoordinated [VO(OMe)(HOMe)L-D*] was very slow. Oxidation of PhSBn is faster than that of MeSPh and MeSpTol. Turn-over numbers are up to 60 mol of sulfoxide mol(-1) of catalyst h(-1) (-20 degrees C). The unspectacular ee apparently is a consequence of flexibility of the active catalyst in solution, as shown by the V-51 NMR of the catalysts [VOL(OR)] and the oxo-peroxo intermediates [VOL(O2R')]. As shown by DFT calculations, the peroxo ligand coordinates in the tilted end-on fashion in the axial or equatorial position (energy difference = 17.6 kJ/mol).

The di-iron complex Fe-2(S2C3H6)(CO)(6) (a), one of the simplest functional models of the Fe-hydrogenases active site, is able to electrocatalyze proton reduction. In the present study, the H-2 evolving path catalyzed by a has been characterized using density functional theory. It is showed that, in the early stages of the catalytic cycle, a neutral mu-H adduct is formed; monoelectron reduction and subsequent protonation can give rise to a diprotonated neutral species (a-mu H-SH), which is characterized by a mu-H group, a protonated sulfur atom, and a CO group bridging the two iron centers, in agreement with experimental IR data indicating the formation of a long-lived mu-CO species. H-2 release from a-mu H-SH, and its less stable isomer a-H-2 is kinetically unfavorable, while the corresponding monoanionic compounds (a-mu H-SH- and a-H-2(-)) are more reactive in terms of dihydrogen evolution, in agreement with experimental data. The key species involved in electrocatalysis have structural features different from the hypothetical intermediates recently proposed to be involved in the enzymatic process, an observation that is possibly correlated with the reduced catalytic efficiency of the biomimetic di-iron assembly.

Density functional theory (DFT) has been used to investigate the catalytic properties of the isolated vanadium cofactor found in vanadium haloperoxidases, with a particular emphasis on the steps going from the resting form of the cofactor to the peroxo complex. Computation of transition states, intermediate species, and UV-vis spectra, as well as comparison of reaction energies, demonstrated the important role of protonation in cofactor activation. This illustrates that the resting form of the vanadium cofactor reacts with hydrogen peroxide according to a mechanism that implies formation of an aqua complex, release of the apical water molecule according to a dissociative pathway, and binding of hydrogen peroxide to vanadium. This process leads to a side-on peroxo species corresponding to the peroxo form observed in the enzyme. In addition, it appears that an acid-base catalysts strongly accelerates the conversion to the side-on peroxo form. The comparison of computed and experimental UV-vis spectra corroborated the proposed reaction pathway and allowed us to explain the effects of the vanadium ligands on the electronic properties of the cofactor. © 2006 American Chemical Society.

The isomerization reaction cyanamide --> carbodiimide in vacuo and in the presence of up to six water molecules has been investigated by means of DFT and MP2 calculations, using a flexible basis set. The reliability of such methods has been checked against results of coupled cluster calculations on isolated molecules. The effect of water molecules has also been investigated in the case of the hydrolysis reaction of cyanamide and carbodiimide, leading to isourea. The number of water molecules considered is large enough to give results converged in activation and hydration energies. In addition to the water molecules explicitly described, the effect of water bulk solvent is taken into account according to the polarizable continuum model. The results show that the direct hydrolysis of H2NCN is hindered by an activation energy much higher than that for HNCNH, which in turn can be obtained from cyanamide with a relatively easy process.

Hydrogenases catalyze the reversible oxidation of dihydrogen to protons and electrons. The structures of two Fe-only hydrogenases have been recently reported [Peters, J. W.; Lanzilotta, W. N.; Lemon, B. J.; Seefeldt, L. C. Science 1998, 282, 1853-1858. Nicolet, Y.; Piras, C.; Legrand, P.; Hatchikian, E. C.; Fontecilla-Camps, J. C. Structure 1999, 7, 13-23], showing that the likely site of dihydrogen activation is the so-called [2Fe](H) cluster, where each Fe ion is coordinated by CO and CN(-) ligands and the two metals are bridged by a chelating S-X(3)-S ligand. Moreover, the presence of a water molecule coordinated to the distal Fe2 center suggested that the Fe2 atom could be a suitable site for binding and activation of H(2). In this contribution, we report a density functional theory investigation of the structural and electronic properties of complexes derived from the [(CO)(CH(3)S)(CN)Fe(II)(mu-PDT)Fe(II)(CO)(2)(CN)](-1) species, which is related to the [2Fe](H) cluster observed in Fe-only hydrogenases. Our results show that the structure of the [2Fe](H) cluster observed in the enzyme does not correspond to a stable form of the isolated cluster, in the absence of the protein. As a consequence, the reactivity of [(CO)(CH(3)S)(CN)Fe(II)(mu-PDT)Fe(II)(CO)(2)(CN)](-1) derivatives in solution may be expected to be quite different from that of the active site of Fe-only hydrogenases. In fact, the most favorable path for H(2) activation involves the two metal atoms and one of the bridging S atoms and is associated with a very low activation energy (5.3 kcal mol(-1)). The relevance of these observations for the catalytic properties of Fe-only hydrogenases is discussed in light of available experimental and theoretical data.

[FeFe]-hydrogenases harbor a {2Fe3S} assembly bearing two CO and two CN- groups, a mu-CO ligand, and a vacant coordination site trans to the mu-CO group. Recent theoretical results obtained studying the isolated {2Fe3S} subsite indicated that one of the CN- ligands can easily move from the crystallographic position to the coordination site trans to the mu-CO group; such an isomerization would have a major impact on substrates and inhibitors binding regiochemistry and, consequently, on the catalytic mechanism. To shed light on this crucial issue, we have carried out hybrid QM/MM and free energy perturbation calculations on the whole enzyme, which demonstrate that the protein environment plays a crucial role and maintains the CN- group fixed in the position observed in the crystal structure; these results strongly support the hypothesis that the vacant coordination site trans to the mu-CO group has a crucial functional relevance both in the context of CO-mediated inhibition of the enzyme and in dihydrogen oxidation/evolution catalysis.