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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

We present a DFT study of the structural and spectroscopic properties of the complex formed by Cu2? with the peptide fragment Ac-PHREN-NH2, which encompasses the putative cell binding domain of angiogenin, as well as with its Ac-PHRQN-NH2 variant. Analysis of structures, energies and spectroscopic parameters has allowed to conclude that the metal coordination environment at pH 8 is formed by a nitrogen atom of His, two deprotonated amide groups, and an oxygen atom from the COO- side chain of Glu, in nice agreement with recent experimental results (La Mendola et al. in Dalton Trans, 39:10678, 2010). Moreover, DFT results allowed to reveal that the Glu side chain of the Ac-PHREN-NH2 peptide is coordinated in equatorial position, in a tetrahedrically distorted square planar arrangement, fully disclosing the effects of Cu2? binding on the structural properties of this key angiogenin portion. In the Ac-PHRQN-NH2 variant, the carboxylate group is replaced by a H2O molecule in a coordination arrangement similar to that of the wild-type system.

Recent advances aimed at modeling the chemistry of the active site of [FeFe]-hydrogenases (the H-cluster, composed by a catalytic Fe 2S 2 subcluster and an Fe 4S 4 portion) have led to the synthesis of binuclear coordination compounds containing a noninnocent organophosphine ligand [2,3-bis(diphenylphosphino)maleic anhydride, bma] that is able to undergo monoelectron reduction, analogously to the tetranuclear Fe 4S 4 subcluster portion of the H-cluster. However, such a synthetic model was shown to feature negligible electronic communication between the noninnocent ligand and the remaining portion of the cluster, at variance with the enzyme active site. Here, we report a theoretical investigation that shows why the electron transfer observed in the enzyme upon protonation of the catalytic Fe 2S 2 subsite cannot take place in the bma-containing cluster. In addition, we show that targeted modifications of the bma ligand are sufficient to restore the electronic communication within the model, such that electron density can be more easily withdrawn from the noninnocent ligand, as a result of protonation of the iron centers. Similar results were also obtained with a ligand derived from cobaltocene. The relevance of our findings is discussed from the perspective of biomimetic reproduction of proton reduction to yield molecular hydrogen. © 2011 American Chemical Society.

A density functional theory study is presented regarding the energetics and the Mulliken population analyses of a quantum mechanical/molecular mechanical (QM/MM) system including multiple iron-sulfur clusters in the QM region. The [FeFe]-hydrogenase from Desulfovibrio desulfuricans was studied, and both the active site (an Fe6S6 assembly generally referred to as the H-cluster) and an ancillary Fe4S4 site were treated at the BP86-RI/TZVP level. The antiferromagnetic coupling that characterizes both sites was modeled using the broken-symmetry (BS) approach. For such a QM system, 36 different BS couplings can be defined, depending on the localization of spin excess on the various spin centers. All the BS states were obtained by means of an effective and simple method for spin localization, that is here described and compared with more sophisticated approaches already available in literature. The variation of the QM/MM energy among the various geometry-optimized protein models was found to be less than 25 kJ mol-1. This energy variation almost doubles if no geometry optimization is performed. A detailed analysis of the additive nature of these variations in QM/MM energy is reported. The Mulliken charges show very small variations among the 36 BS states, whereas the Mulliken spin populations were found to be somewhat more variable. The relevance of such variations is discussed in light of the available Mössbauer and Electron Paramagnetic Resonance (EPR) spectroscopic data for the enzyme. Finally, the influence of the basis set on the spin populations, charges, and structural parameters of the models was investigated, by means of QM/MM computations on the same system at the BP86-RI/SVP level. © 2010 Wiley Periodicals, Inc.

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.

Experimental and computational experiments show that the electrophile MeS+ attacks a single Fe center in Fe-2(propanedithiolate)(CO)(4)(PMe3)(2) followed by isomerization of this terminal thiolato complex to the corresponding mu-SMe derivative

IDPs in their unbound state can transiently acquire secondary and tertiary structure. Describing such intrinsic structure is important to understand the transition between free and bound state, leading to supramolecular complexes with physiological interactors. IDP structure is highly dynamic and, therefore, difficult to study by conventional techniques. This work focuses on conformational analysis of the KID fragment of the Sic1 protein, an IDP with a key regulatory role in the cell-cycle of Saccharomyces cerevisiae. FT-IR spectroscopy, ESI-MS, and IM measurements are used to capture dynamic and short-lived conformational states, probing both secondary and tertiary protein structure. The results indicate that the isolated Sic1 KID retains dynamic helical structure and populates collapsed states of different compactness. A metastable, highly compact species is detected. Comparison between the fragment and the full-length protein suggests that chain length is crucial to the stabilization of compact states of this IDP. The two proteins are compared by a length-independent compaction index.

A QM/MM investigation of the active-ready (Hox) form of [FeFe]-hydrogenase from D. desulfuricans, in which the electronic properties of all Fe-S clusters (H, F and F') have been simultaneously described using DFT, was carried out with the aim of disclosing a possible interplay between the H-cluster and the accessory iron-sulfur clusters in the initial steps of the catalytic process leading to H2 formation. It turned out that one-electron addition to the active-ready form leads to reduction of the F'-cluster and not of the H-cluster. Protonation of the H-cluster in H ox is unlikely, and in any case it would not trigger electron transfer from the accessory Fe4S4 clusters to the active site. Instead, one-electron reduction and protonation of the active-ready form trigger electron transfer within the protein, a key event in the catalytic cycle. In particular, protonation of the H-cluster after one-electron reduction of the enzyme lowers the energy of the lowest unoccupied molecular orbitals localized on the H-cluster to such an extent that a long-range electron transfer from the F'-cluster towards the H-cluster itself is allowed. © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

In the present contribution, we report a theoretical investigation of the magnetic properties of the dihydrogen-evolving enzyme [FeFe]-hydrogenase, based on both DFT models of the active site (the H-cluster, a Fe6S 6 assembly including a binuclear portion directly involved in substrates binding), and QM/MM models of the whole enzyme. Antiferromagnetic coupling within the H-cluster has been treated using the broken-symmetry approach, along with the use of different density functionals. Results of g value calculations turned out to vary as a function of the level of theory and of the extension of the model. The choice of the broken-symmetry coupling scheme also had a significant influence on the calculated g values, for both the active-ready (Hox) and the CO-inhibited (Hox-CO) enzyme forms. However, hyperfine coupling-constant calculations were found to provide more consistent results. This allowed us to show that the experimentally detected delocalization of an unpaired electron at the binuclear subcluster in Desulfovibrio desulfuricans Hox is compatible with a weak interaction between the catalytic centre and a low-weight exogenous ligand like a water molecule. © 2011 Wiley-VCH Verlag GmbH & Co. KGaA.

Key stereoelectronic properties of Desulfovibrio desulfuricans [FeFe]-hydrogenase (DdH) were investigated by quantum mechanical description of its complete inorganic core, which includes a Fe6S6 active site (the H-cluster), as well as two ancillary Fe4S4 assemblies (the F and F' clusters). The partially oxidized, active-ready form of DdH is able to efficiently bind dihydrogen, thus starting H2 oxidation catalysis. The calculations allow us to unambiguously assign a mixed Fe(II)Fe(I) state to the catalytic core of the activeready enzyme and show that H2 uptake exerts subtle, yet crucial influences on the redox properties of DdH. In fact, H2 binding can promote electron transfer from the H-cluster to the solvent-exposed F'-cluster, thanks to a 50% decrease of the energy gap between the HOMO (that is localized on the H-cluster) and the LUMO (which is centered on the F'-cluster). Our results also indicate that the binding of the redox partners of DdH in proximity of its F'-cluster can trigger one-electron oxidation of the H2-bound enzyme, a process that is expected to have an important role in H2 activation. Our findings are analyzed not only from a mechanistic perspective, but also in consideration of the physiological role of DdH. In fact, this enzyme is known to be able to catalyze both the oxidation and the evolution of H2, depending on the cellular metabolic requirements. Hints for the design of targeted mutations that could lead to the enhancement of the oxidizing properties of DdH are proposed and discussed. © 2011 American Chemical Society.

The presence of Fe-bound cyanide ligands in the active site of the proton-reducing enzymes [FeFe]-hydrogenases has led to the hypothesis that such Brønsted-Lowry bases could be protonated during the catalytic cycle, thus implying that hydrogen isocyanide (HNC) might have a relevant role in such crucial microbial metabolic paths. We present a hybrid quantum mechanical/molecular mechanical (QM/MM) study of the energetics of CN - protonation in the enzyme, and of the effects that cyanide protonation can have on [FeFe]-hydrogenase active sites. A detailed analysis of the electronic properties of the models and of the energy profile associated with H2 evolution clearly shows that such protonation is dysfunctional for the catalytic process. However, the inclusion of the protein matrix surrounding the active site in our QM/MM models allowed us to demonstrate that the amino acid environment was finely selected through evolution, specifically to lower the Brønsted-Lowry basicity of the cyanide ligands. In fact, the conserved hydrogen-bonding network formed by these ligands and the neighboring amino acid residues is able to impede CN- protonation, as shown by the fact that the isocyanide forms of [FeFe]-hydrogenases do not correspond to stationary points on the enzyme QM/MM potential-energy surface. © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A small virtual library of iminosugar derivatives was evaluated by docking experiments carried out by sampling a protein region corresponding to the phosphoinositide binding site of the PH domain of Akt. Four compounds were selected and efficiently synthesised from a common precursor. All compounds were subjected to preliminary biological evaluation on purified enzyme, and - among them - compound 9 exhibited the best inhibitory activity. A small virtual library of iminosugar-based Akt inhibitors have been designed and evaluated by using docking calculations. Selected compounds have been conveniently synthesised, and preliminary biological evaluation identified compound 9 as a possible lead compound for further development of iminosugar-based Akt inhibitors.

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 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 p

Reaction of 2-(1-(pyridin-2-yl)ethyl)propane-1,3-dithiol with tri-iron dodecacarbonyl afforded a diiron pentacarbonyl complex, [Fe(2)L(CO)(5)] (A and H(2)L = 2-methyl-2-(1,2,5,6-tetrahydropyridin-2-yl)propane-1,3-dithiol). In the reaction, the pyridinyl ring of the original ligand was partially hydrogenated during the reaction. This complex was fully characterised by using crystallographic, infrared, and NMR spectroscopic techniques. Formation reaction of its bridging hydride and subsequent conversion into its protonated diiron hexacarbonyl complex, [Fe(2)L(CO)(6)] (ACOH(+) in which the N atom of L is decoordinated and protonated), were experimentally and theoretically investigated. Results for this complex alongside with theoretic investigations into other diiron pentacarbonyl analogues revealed positive correlation of basicity of the internal bases of these investigated complexes to bridging hydrides formation. But subsequent conversion of these bridging hydrides into protonated diiron hexacarbonyl complexes was not solely dictated by the basicity. Protophilicity of the internal base and lability of its coordination with the diiron centre play also an important role as revealed by experimental and theoretic investigations. (C) 2009 Elsevier B.V. All rights reserved.

Reacting a bidentate ligand H2L, 2-(2-methoxybenzyl)-2-methylpropane-1,3-dithiol, with Fe-3(CO)(12) formed a diiron hexacarbonyl complex (1Me) from which a diiron hexacarbonyl complex (1H) pendant with a phenolic group was derived via in-situ demethylation. Further deprotonation of complex 1H gave a diiron pentacarbonyl species (1) in which a rare bond between the soft metal Fe-I and the relatively hard base phenolate formed, Fe-I-OR (R = phenolic moiety). This bonding may be a suitable mimic of the bonding feature, ((FeFeI)-Fe-I)R-OH/OH2 found in the FeFel-hydrogenase. (C) 2010 Elsevier B.V. All rights reserved.

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)-Ph2PCH2CH2PPh2)(mu-S(CH2)(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 similar to 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 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.

The mechanism of terminal- to mu-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.

Natriuretic peptides (NP) are a family of structurally related but genetically distinct hormones/paracrine factors that regulate blood volume, blood pressure, ventricular hypertrophy, pulmonary hypertension, fat metabolism, and long bone growth. In this work we present computational structural analysis of the three human NP in solution, the synthesis and preliminary biological assays of a short fragment of CNP, I(14)GSM(17), together with one small mimetic, GGSM. Synthetic peptides IGSM, GGSM, and full length CNP were preliminary tested for their ability to influence cell growth of three human osteosarcoma cell lines. Synthetic peptides were shown to successfully mimic the biological activity of the full length natural peptide: their effects, although different upon the cell types used, are in accordance with the current literature, designating a possible role for CNP, and its derivatives, in skeletogenesis.

Natriuretic peptides (NPs) are a family of structurally related hormone/paracrine factors (ANP, BNP and CNP), which mediate a broad array of physiological effects by interacting with specific guanylyl cyclase receptors (NPR) and have promising therapeutic and clinical applications. NPs are specific for different NPRs and share a common ring structure in which a disulfide bond between two conserved cysteine residues is formed. Residues within the cyclic loop are largely responsible for receptor selectivity. Structural features of free NPs in solution have not been investigated in details even if their characterization would be very useful in order to identify important aspects related to NPs function and receptor selectivity. In light of the above scenario, we carried out a 0.1 mu s molecular dynamics investigation of NPs with the aim of providing a high-resolution atomistic view of specific of their conformational ensemble in solution. Our results clearly indicate that NP receptor-bound conformations are not stable solution structure and that induced-fit mechanisms are involved in the formation of NP-NPR complexes. Moreover, in agreement with the current view on strictly relationship between protein dynamics and protein function and activity, it turns out that differences in activity and NPR specificity of CNP and ANP/BNP might be correlated to different amino acid composition of the cyclic loop, propensity to form beta-sheet structures, flexibility patterns, dynamics properties and free conformations explored during the simulations. (C) 2010 Elsevier Inc. All rights reserved.

This paper reports the synthesis of a panel of small molecules with arylamides and arylsulfonamides groups and their biological activity in inhibiting nucleotide exchange on human Ras. The design of these molecules was guided by experimental and molecular modelling data previously collected on similar compounds. Aim of this work is the validation of the hypothesis that a phenyl hydroxylamine group linked to a second aromatic moiety generates a pharmacophore capable to interact with Ras and to inhibit its activation. In vitro experiments on purified human Ras clearly show that the presence of an aromatic hydroxylamine and a sulfonamide group in the same molecule is a necessary condition for Ras binding and nucleotide exchange inhibition. The inhibitor potency is lower in molecules in which either the hydroxylamine has been replaced by other functional groups or the sulfonamide has been replaced by an amide. In the case both these moieties, the hydroxylamine and sulfonamide are absent, inactive compounds are obtained.

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.

[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.

Mutation of RAS genes is a critical event in the pathogenesis of different human tumors and in some developmental disorders. Here we present an arabinose-derived bicyclic compound displaying selective cytotoxicity in human colorectal cancer cells expressing K-RasG13D, that shows high intrinsic nucleotide exchange rate. We characterize binding of bicyclic compounds by docking and NMR experiments and their inhibitory activity on GEF-mediated nucleotide exchange on wild-type and mutant Ras proteins. We demonstrate that the in vitro inhibition of Ras nucleotide exchange depends on the molar ratio between Ras and its GEF activator, suggesting that the observed in vivo selective effect may depend on biochemical parameters and actual intracellular concentration of the Ras protein and its regulators

By combining in the same molecule Ras-interacting aromatic moieties and a sugar, we prepared a water-soluble Ras ligand that binds Ras and inhibits guanine nucleotide exchange. With this compound it was possible to determine experimentally by a 15N-edited HSQC NMR experiment the ligand-Ras binding interface

Fe2(S2C3H6)(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-Cµ 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-Cµ 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 11A′′ excited-state PES, an Fe(CO)3 semirotated structure is the lowest-energy stationary point, while the exploration of the 11A′ and 21A′′ singlet excited PESs evidences the stabilization of the rotated over the all-ter

The DFT investigation of protonation regiochemistry for a series of [Fe(l)](2)(edt)(PR)(x)(CO)((6-x))] complexes differing for steric and electronic properties of ligands has allowed the disclosure of several key relations between the structure of the complexes and reactivity toward acids, from both a thermodynamics and kinetics perspective. The phosphine/CO ratio strongly affects both the thermodynamics and kinetics of protonation. In particular, with the exception of dppv complexes, in which steric factors become more important, the presence of phosphines, which are better electron donors than CO ligands, leads to lower reaction barriers. The presence of bulky phosphine ligands, which severely hinder the accessibility to the Fe-Fe bond, is a crucial factor responsible for kinetic preference of terminal- versus mu-protonation in symmetric complexes. The investigation of asymmetric models allowed us to rationalize why protonation takes place preferentially on the less electron-rich iron atom, i. e., the iron atom coordinated by the largest number of CO ligands. Importantly, the presence of at least one electron-donor ligand on the protonating Fe atom is fundamental to allow facile terminal protonation, suggesting that one of the reasons for the presence of CN(-) ligands in the enzyme might be related to the facile formation of catalytically relevant terminally protonated species. Finally, it was found that poorly reacting mu-H Fe(II)Fe(II) species are always thermodynamically more stable than corresponding terminal-hydride forms, indicating that one of the main challenges for the development of efficient synthetic catalysts inspired to the [FeFe] hydrogenase active site will be the design of complexes that undergo terminal protonation but cannot interconvert to the corresponding mu-H forms.

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.

Lipopolysaccharide is an essential component of the outer membrane of Gram-negative bacteria and consists of three elements: lipid A, the core oligosaccharide and the O-antigen. The inner core region is highly conserved and contains at least one residue of 3-deoxy-d-manno-octulosonate (Kdo). The first committed step of Kdo biosynthesis is the aldol-keto isomerisation of d-ribulose 5-phosphate to d-arabinose 5-phosphate catalyzed by arabinose 5-phosphate isomerase encoded in Escherichia coli by the kdsD gene. KdsD contains an N-terminal sugar isomerase (SIS) domain commonly found in phosphosugar isomerases but its three-dimensional structure is unknown. The structure of the KdsD SIS domain has been predicted by homology modeling using the hypothetical 3etn protein as a template. Moreover by sequence alignments, comparison with other sugar isomerases structurally related to KdsD, and site-directed mutagenesis we implicated four residues in KdsD activity or substrate recognition. A possible role of these residues in the catalysis is discussed. © 2009 Elsevier Inc. All rights reserved.

Nature's recipe: A theoretical study analyzes how the environment of the [FeFe] hydrogenase's catalytic cofactor affects its chemical properties, particularly the relative stability of complexes with bridging and terminal hydride ligands (see picture; Fe teal, S yellow, C green, N blue, O red, H gray). The results help to elucidate key rules for the design of bioinspired synthetic catalysts for H2 production. © 2009 Wiley-VCH Verlag GmbH & Co. KGaA.

We have studied the accessibility of the structural calcium ion in the Burkholderia glumae lipase and the consequences of its removal on the protein conformation by different biophysical techniques (circular dichroism, fluorimetry, and mass spectrometry) and by molecular-dynamics simulations. We show that, in the native protein, calcium is not accessible unless specific flexible loops are displaced, for example, by a temperature increase. Such movements concern the whole calcium-binding pocket and particularly the environment of the coordinating aspartate residue 241. As a consequence of metal depletion the protein unfolds irreversibly and undergoes aggregation. The removal of the metal ion causes major structural transitions and leads to an increase in beta-structure, in particular in protein regions that are largely unstructured in the native protein and encompass the calcium coordination residues

The one-electron oxidations of a series of diiron(I) dithiolato carbonyls were examined to evaluate the factors that affect the oxidation state assignments, structures, and reactivity of these low-molecular weight models for the Hox state of the [FeFe]-hydrogenases. The propanedithiolates Fe2(S2C3H6)(CO)3(L)(dppv) (L = CO, PMe3, Pi-Pr3) oxidize at potentials ∼180 mV milder than the related ethanedithiolates (Angew. Chem., Int. Ed. 2007, 46, 6152). The steric clash between the central methylene of the propanedithiolate and the phosphine favors the rotated structure, which forms upon oxidation. Electron Paramagnetic Resonance (EPR) spectra for the mixed-valence cations indicate that the unpaired electron is localized on the Fe(CO)(dppv) center in both [Fe2(S2C3H6)(CO) 4(dppv)]BF4 and [Fe2(S2C 3H6)(CO)3(PMe3)(dppv)]BF 4, as seen previously for the ethanedithiolate [Fe2(S 2C2H4)(CO)3(PMe3)(dppv)] BF4. For [Fe2(S2CnH 2n)(CO)3(Pi-Pr3)(dppv)]BF4; however, the spin is localized on the Fe(CO)2(Pi-Pr3) center, although the Fe(CO)(dppv) site is rotated in the crystalline state. IR and EPR spectra, as well as redox potentials and density-functional theory (DFT) calculations, suggest that the Fe(CO)2(Pi-Pr3) site is rotated in solution, driven by steric factors. Analysis of the DFT-computed partial atomic charges for the mixed-valence species shows that the Fe atom featuring a vacant apical coordination position is an electrophilic Fe(I) center. One-electron oxidation of [Fe2(S2C 2H4)(CN)(CO)3(dppv)]- re

Super model: Diiron dithiolates exist in nature in [FeFe]-hydrogenase, for the purpose of making or oxidizing molecular hydrogen. Evidence for how H2 interacts with diiron complexes has been realized using model diiron dithiolato carbonyl complexes. The pathway for this interaction has been elucidated computationally as well as synthetically, by using silanes in place of H2.

Reaction of a trithiol ligand, 2-(mercaptomethyl)-2-methylpropane-1,3-dithiol (H3L), with tri-iron dodecacarbonyl in toluene produces two hexa-iron clusters (1 and 2). The two clusters are characterised crystallographically and spectroscopically. NMR spectroscopy reveals that the cluster 2 exists in two conformations in equilibrium 2anti ⇔ 2syn and the equilibrium constant Keq = 0.55 under CO atmosphere. In the cluster 2, the central {Fe2S2(CO)6} sub-unit is flanked by two identical {Fe2S2(CO)6} satellite sub-units through thiolate linkages whereas one of the thiolate linkages can further form Fe-S bond with the proximal Fe atom in one of the two satellite sub-units to produce the cluster 1 by expelling one CO. This conversion can be entirely reversed by continuously purging CO through the solution of the cluster 1. As suggested by DFT calculations, the conversion features a key step, the rotation of the Feprox(CO)3 to expose a vacant site for exogenic ligand binding (the S atom from the central sub-unit in this case) with concomitant switch for one of the three CO ligands in the unit of Feprox(CO)3 from terminal to bridging orientation. The conversion from the clusters 1-2 involving one CO uptake is much faster than its reverse process since the latter is an endergonic process characterised by large reaction barriers, as revealed by the DFT calculations. © 2008 Elsevier B.V. All rights reserved.

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.

Condensation of Fe2(SH)2(CO)6, acetaldehyde, and (NH4)2CO3 affords the methyl-substituted azadithiolate Fe2[(SCHMe)2NH](CO) 6 (1). The complex exists mainly ∼95%) as the meso diastereomer, but the d,l diastereoisomers could be detected. DFT calculations predict that the meso isomer would be 2.5 kcal/mol more stable than the d,l isomer due to conventional nonbonding interactions between the methyl groups and the ring hydrogen atoms. Crystallographic analysis of meso-1 confirms that the two methyl groups are equatorial, constraining the diferraazadithiolate bicycle to a conformation that desymmetrizes the diiron center. The lowered symmetry is confirmed by the observation of two 13C NMR signals in the FeCO region under conditions of fast turnstile rotation at the Fe(CO)3 groups. The pKa value of the amine in 1 is 7.89 (all pKa's determined in MeCN solution), which is similar to a redetermined value for Fe2[(SCH2)2NH](CO)6 (2, pK a = 7.98) and only slightly less basic than the tertiary amine Fe2[(SCH2)2NMe](CO)6 (pKa = 8.14). Substitution of 1 with PMe3 proceeded via the intermediacy of two isomers of Fe2[(SCHMe)2NH](CO)5(PMe 3), affording Fe2[(SCHMe)2NH](CO) 4(PMe3)2 (3). 31P NMR spectra confirm that the two PMe3 ligands in 3 are nonequivalent, consistent with the desymmetrizing effect of the dithiolate. The pKa value of the amine in 3 was found to be 11.3. Using triphenylphosphine, we prepared Fe2[SCHMe)2NH](CO)5(PPh3) as a single regioisomer. © 2008 American Chemical Society.

In the present contribution, a density functional theory (DFT) investigation is described regarding a recently synthesized Fe6S6 complex - see C. Tard, X. Liu, S.K. Ibrahim, M. Bruschi,next term L. De Gioia, S.C. Davies, X. Yang, L.-S. Wang, G. Sawers, C.J. Pickett, Nature 433 (2005) 610 - that is structurally and functionally related to the [FeFe]-hydrogenases active site (the so-called H-cluster, which includes a binuclear subsite directly involved in catalysis and an Fe4S4 cubane). The analysis of relative stabilities and atomic charges of different isomers evidenced that the structural and redox properties of the synthetic assembly are significantly different from those of the enzyme active site. A comparison between the hexanuclear cluster and simpler synthetic diiron models is also described; the results of such a comparison indicated that the cubane moiety can favour the stabilization of the cluster in a structure closely resembling the H-cluster geometry when the synthetic Fe6S6 complex is in its dianionic state. However, the opposite effect is observed when the synthetic cluster is in its monoanionic form.

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 63Cu, 14N and 17O 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 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

The molecular and electronic structure of the Fe6S6 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 Fe6S6 and Fe2S2 DFT models shows that the presence of the Fe4S4 moiety does not affect appreciably the geometry of the [2Fe](H) cluster. In particular, the Fe4S4 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 Fe4S4 and the Fe2S2 moieties forming the H-cluster.

Computational approaches based on Molecular Dynamics simulations, Quantum Mechanical methods and 3D Quantitative Structure-Activity Relationships were employed by computational chemistry groups at the University of Milano-Bicocca to study biological processes at the molecular level. The paper reports the methodologies adopted and the results obtained on Aryl hydrocarbon Receptor and homologous PAS proteins mechanisms, the properties of prion protein peptides, the reaction pathway of hydrogenase and peroxidase enzymes and the defibrillogenic activity of tetracyclines. © Springer-Verlag 2007.