Papers by Giuseppe Zampella
Applied Surface Science, 2006
a b s t r a c t Inhibitory effect of three Schiff bases 2-{[(2-sulfanylphenyl)imino]methyl}]pheno... more a b s t r a c t Inhibitory effect of three Schiff bases 2-{[(2-sulfanylphenyl)imino]methyl}]phenol (A), 2-{[(2)-1-(4methylphenyl)methylidene]amino}-1-benznethiol (B), and 2-[(2-sulfanylphen-yl)ethanimidoyl)
![Research paper thumbnail of Reductive Behavior of [Fe 2 (CO) 4 (κ 2 -dmpe){μ-(SCH 2 ) 2 NBn}]: Effect of Symmetrization on the Rotated Conformation in Fe I -Fe I Models of [2Fe] H Subsite of [Fe-Fe]H 2 ases](https://a.academia-assets.com/images/blank-paper.jpg)
European Journal of Inorganic Chemistry, 2014
ABSTRACT The reduction of the compound [Fe2(CO)4(κ2-dmpe){μ-(SCH2)2NBn}] [dmpe = 1,2-bis(dimethyl... more ABSTRACT The reduction of the compound [Fe2(CO)4(κ2-dmpe){μ-(SCH2)2NBn}] [dmpe = 1,2-bis(dimethylphosphino)ethane], which is considered as an FeI-FeI model of the [2Fe]H subsite of [Fe-Fe]H2ases with a rotated conformation in the solid state, was investigated by cyclic voltammetry. Under reductive conditions, [Fe2(CO)4(κ2-dmpe){μ-(SCH2)2NBn}] undergoes electron-transfer-catalyzed isomerization to afford an isomer featuring a bridging diphosphine [Fe2(CO)4(μ-dmpe){μ-(SCH2)2NBn}]. Comparison of the crystallographic structures of the two isomers affords unique and direct experimental evidence that dissymmetrical coordination of the chelate ligand is required to promote the rotated conformation at one iron atom in this compound. DFT calculations were performed to rationalize this isomerization process and the slightly distorted structure of [Fe2(CO)4(μ-dmpe){μ-(SCH2)2NBn}]. The symmetrization of the coordination sphere results in the disruption of the agostic interaction that stabilized the rotated isomer.
Theoretical Chemistry Accounts
We present a DFT study of the structural and spectroscopic properties of the complex formed by Cu... more 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 coordinat...
International Journal of Hydrogen Energy
[FeFe]-hydrogenases are the most efficient biological catalysts available for the H2 evolution re... more [FeFe]-hydrogenases are the most efficient biological catalysts available for the H2 evolution reaction. Their active site – the H-cluster – features a diiron subsite which has the peculiar characteristic of bearing cyanide groups hydrogen-bonded to the apoprotein as well as carbonyl ligands. Notably, one of the CO ligands is disposed in bridging position between the metal centers. This allows one of the Fe ions to retain a square pyramidal coordination – which determines the assumption of the so-called “rotated structure” – with a vacant coordination site in trans to the μ-CO group, ready to bind protons when the active site is in the FeIFeI state. Many FeIFeI biomimetic models have been synthesized and characterized so far, but most of them fail to reproduce the orientation of the diatomic ligands that is observed in the enzyme active site. In the present contribution we carried out a density functional theory investigation, with the aim of evaluating whether the establishment of ...
Chemistry (Weinheim an der Bergstrasse, Germany), Jan 23, 2015
To learn from Nature how to create an efficient hydrogen-producing catalyst, much attention has b... more To learn from Nature how to create an efficient hydrogen-producing catalyst, much attention has been paid to the investigation of structural and functional biomimics of the active site of [FeFe]-hydrogenase. To understand their catalytic activities, the μ-S atoms of the dithiolate bridge have been considered as possible basic sites during the catalytic processes. For this reason, a series of [FeFe]-H2 ase mimics have been synthesized and characterized. Different [FeFe]-hydrogenase model complexes containing bulky Si-heteroaromatic systems or fluorene directly attached to the dithiolate moiety as well as their mono-PPh3 -substituted derivatives have been prepared and investigated in detail by spectroscopic, electrochemical, X-ray diffraction, and computational methods. The assembly of the herein reported series of complexes shows that the μ-S atoms can be a favored basic site in the catalytic process. Small changes in the (hetero)-aromatic system of the dithiolate moiety are responsi...
Inorganic Chemistry, 2015
The reduction of the Fe(II)Fe(II) complex [Fe2(CO)2{P(OMe)3}2(κ(2)-IMe-CH2-IMe)(μ-CO)(μ-pdt)](2+)... more The reduction of the Fe(II)Fe(II) complex [Fe2(CO)2{P(OMe)3}2(κ(2)-IMe-CH2-IMe)(μ-CO)(μ-pdt)](2+) (2P(2+); pdt = S(CH2)3S), which is a synthetic model of the H cluster of the [FeFe] hydrogenases in its inactive state, has been investigated electrochemically and theoretically (by density functional theory, DFT) in order to determine the mechanisms, intermediates, and products of the related processes. The electrochemical reduction of 2P(2+) occurs according to an ECE-type reaction where the intervening chemical step is the loss of one P(OMe)3 ligand. This outcome, which is based on cyclic voltammetric experiments, is strongly supported by DFT calculations that provide additional information on the intermediates and the energetics of the reactions involved. The electrochemical reoxidation of the neutral product of the reduction follows an EEC process where the chemical step is the binding of P(OMe)3 to a dicationic intermediate. DFT calculations reveal that this intermediate has an unusual geometry wherein one of the two C-H bonds of a side methylene from the pdt group forms an agostic interaction with one Fe center. This interaction is crucial to stabilize the 32e(-) diferrous center and concomitantly to preserve Fe(II) from binding of weakly coordinating species. Nonetheless, it could be displaced by a relatively stronger electron donor such as H2, which could be relevant for the design of new oxidation catalysts.
The di-iron complex Fe2(S2C3H6)(CO)6 (a), one of the simplest functional models of the Fe-hydroge... more The di-iron complex Fe2(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 H2 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-muH-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 mu7-CO species. H2 release from a-muH-SH, and its less stable isomer a-H2 is kinetically unfavorable, while the corresponding monoanionic compounds (a-muH-SH- and a-H2-) 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.
Chemical communications (Cambridge, England), Jan 28, 2007
The new complexes Fe2(S2CnH2n)(CO)2(dppv)2 (n = 2, 3; dppv = cis-1,2-C2H2(PPh2)2) form adducts wi... more The new complexes Fe2(S2CnH2n)(CO)2(dppv)2 (n = 2, 3; dppv = cis-1,2-C2H2(PPh2)2) form adducts with AlBr3 and B(C6F5)3, which adopt the "rotated structure" proposed for the active site of the Fe-only hydrogenases--the propanedithiolate is significantly more Lewis basic due to nonbonded interactions between the dithiolate strap and the ligands on Fe.
Inorganic Chemistry Communications, 2003
Recently, it has been demonstrated that the prion protein binds Cu(II) ions by the N-terminal dom... more Recently, it has been demonstrated that the prion protein binds Cu(II) ions by the N-terminal domain [Chem. Eur. J. 6 (2000) 4195; Biochemistry 38 (1999) 11560], which is composed of four or more repeats of the eight-residue sequence PHGGGWGQ (octarepeat). X-ray diffraction experiments [Biochemistry 41 (2002) 3991] have shown that the peptide HGGGW embraces the fundamental Cu2+ binding unit and
Tryptophan 2,3-dioxygenase (TDO) and indoleamine 2,3-dioxygenase (IDO) constitute an important, y... more Tryptophan 2,3-dioxygenase (TDO) and indoleamine 2,3-dioxygenase (IDO) constitute an important, yet relatively poorly understood, family of heme-containing enzymes. Here, we report extensive structural and biochemical studies of the Xanthomonas campestris TDO and a related protein SO4414 from Shewanella oneidensis, including the structure at 1.6-Å resolution of the catalytically active, ferrous form of TDO in a binary complex with the substrate L-Trp. The carboxylate and ammonium moieties of tryptophan are recognized by electrostatic and hydrogen-bonding interactions with the enzyme and a propionate group of the heme, thus defining the L-stereospecificity. A second, possibly allosteric, L-Trp-binding site is present at the tetramer interface. The sixth coordination site of the heme-iron is vacant, providing a dioxygenbinding site that would also involve interactions with the ammonium moiety of L-Trp and the amide nitrogen of a glycine residue.
The Journal of Physical Chemistry B, 2012
The DFTB and DFT methods are applied to the study of different forms of the [Cu(HGGG)(Py)] comple... more 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.
Dalton Trans., 2014
The [FeFe] hydrogenase is a highly sophisticated enzyme for the synthesis of hydrogen via a biolo... more The [FeFe] hydrogenase is a highly sophisticated enzyme for the synthesis of hydrogen via a biological route. The rotated state of the H-cluster in the [Fe(I)Fe(I)] form was found to be an indispensable criteria for an effective catalysis. Mimicking the specific rotated geometry of the [FeFe] hydrogenase active site is highly challenging as no protein stabilization is present in model compounds. In order to simulate the sterically demanding environment of the nature's active site, the sterically crowded meso-bis(benzylthio)diphenylsilane (2) was utilized as dithiolate linker in an [2Fe2S] model complex. The reaction of the obtained hexacarbonyl complex 3 with 1,2-bis(dimethylphosphino)ethane (dmpe) results three different products depending on the amount of dmpe used in this reaction: [{Fe2(CO)5{μ-(SCHPh)2SiPh2}}2(μ-dmpe)] (4), [Fe2(CO)5(κ(2)-dmpe){μ-(SCHPh)2SiPh2}] (5) and [Fe2(CO)5(μ-dmpe){μ-(SCHPh)2SiPh2}] (6). Interestingly, the molecular structure of compound 5 shows a [FeFe] subsite comprising a semi-rotated conformation, which was fully characterized as well as the other isomers 4 and 6 by elemental analysis, IR and NMR spectroscopy, X-ray diffraction analysis (XRD) and DFT calculations. The herein reported model complex is the first example so far reported for [Fe(I)Fe(I)] hydrogenase model complex showing a semi-rotated geometry without the need of stabilization via agostic interactions (Fe···H-C).
Topics in Current Chemistry, 2006
Luca Bertini1 · Maurizio Bruschi2 · Luca de Gioia1 (u) · Piercarlo Fantucci1 · Claudio Greco1 · G... more Luca Bertini1 · Maurizio Bruschi2 · Luca de Gioia1 (u) · Piercarlo Fantucci1 · Claudio Greco1 · Giuseppe Zampella1 1Department of Biotechnology and Biosciences, Universita' degli Studi di Milano-Bicocca, Piazza della Scienza, 2, 20126 Milan, Italy [email protected] ...
Methods in Molecular Biology, 2014
It is well known that transition metal ions are often bound to proteins, conveying very specific ... more It is well known that transition metal ions are often bound to proteins, conveying very specific functional properties. In fact, metalloproteins play crucial biological roles in the transport and activation of small molecules such as H2, O2, and N2, as well as in several other biochemical processes. However, even if the presence of transition metals in the active site of proteins allows a very rich biochemistry, the experimental disclosure of structure-activity relationships in metalloproteins is generally difficult exactly because of the presence of transition metals, which are intrinsically characterized by a very versatile and often elusive chemistry. For this reason, computational methods are becoming very popular tools in the characterization of metalloproteins. In particular, since computing power is becoming less and less expensive, due to the continuous technological development of CPUs, the computational tools suited to investigate metalloproteins are becoming more accessible and therefore more commonly used also in molecular biology and biochemistry laboratories. Here, we present the main procedures and computational methods based on quantum mechanics, which are commonly used to study the structural, electronic, and reactivity properties of metalloproteins and related bioinspired compounds, with a specific focus on the practical and technical aspects that must be generally tackled to properly study such biomolecular systems.
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Papers by Giuseppe Zampella