Adalgisa Sinicropi | University of Siena / Università di Siena (original) (raw)

Papers by Adalgisa Sinicropi

The Journal of Physical Chemistry B, 2015

Peroxide-activated Auricularia auricula-judae dye-decolorizing peroxidase (DyP) forms a mixed Trp... more Peroxide-activated Auricularia auricula-judae dye-decolorizing peroxidase (DyP) forms a mixed Trp377 and Tyr337 radical, the former being responsible for oxidation of the typical DyP substrates (Linde et al. Biochem. J., 2015, 466, 253-262). However, a pure tryptophanyl radical EPR signal is detected at pH = 7 (where the enzyme is inactive) in contrast with the mixed signal observed at pH for optimum activity, pH = 3. On the other hand, the presence of a second tyrosine radical (at Tyr147) is deduced by a multifrequency EPR study of a variety of simple and double directed variants (including substitution of the above and other tryptophan and tyrosine residues) at different freezing times after their activation by H2O2 (at pH = 3). This points out that subsidiary long-range electron transfer pathways enter into operation when the main pathway/s is/are removed by directed mutagenesis, with catalytic efficiencies progressively decreasing. Finally, self-reduction of the Trp377 neutral radical is observed when reaction time (before freezing) is increased in the absence of reducing substrates (from 10 to 60 seconds). Interesting, the tryptophanyl radical is stable in the Y147S/Y337S variant, indicating that these two tyrosine residues are involved in the self-reduction reaction.

In this communication we show how the development of a hybrid quantum mechanics/molecular mechani... more In this communication we show how the development of a hybrid quantum mechanics/molecular mechanics computational strategy based on multiconfigurational perturbation theory and complete-active-space-self-consistent-field geometry optimization has recently allowed for the correct evaluation of the excited-state properties of chemically different chromophores embedded in different protein environments and in solution. In particular, we show how this strategy can be applied to the

Faraday Discussions, 2004

In this paper we employ a CASSCF/AMBER quantum-mechanics/molecular-mechanics tool to map the inte... more In this paper we employ a CASSCF/AMBER quantum-mechanics/molecular-mechanics tool to map the intersection space (IS) of a protein. In particular, we provide evidence that the S1 excited-state potential-energy surface of the visual photoreceptor rhodopsin is spanned by an IS segment located right at the bottom of the surface. Analysis of the molecular structures of the protein chromophore (a protonated Schiff base of retinal) along IS reveals a type of geometrical deformation not observed in vacuo. Such a structure suggests that conical intersections mediating different photochemical reactions reside along the same intersection space. This conjecture is investigated by mapping the intersection space of the rhodopsin chromophore model 2-Z-hepta-2,4,6-trieniminium cation and of the conjugated hydrocarbon 3-Z-deca-1,3,5,6,7-pentaene.

Cellular and Molecular Life Sciences, 2015

Laccases are multicopper oxidases which oxidize a wide variety of aromatic compounds with the con... more Laccases are multicopper oxidases which oxidize a wide variety of aromatic compounds with the concomitant reduction of oxygen to water as by-product. Due to their high stability and biochemical versatility, laccases are key enzymes to be used as eco-friendly biocatalyst in biotechnological applications. The presence of copper paramagnetic species in the catalytic site paired with the substrate radical species produced in the catalytic cycle makes laccases particularly attractive to be studied by spectroscopic approaches. In this review, the potentiality of a combined multifrequency electron paramagnetic spectroscopy /computational approach to gain information on the nature of the catalytic site and radical species is presented. The knowledge at molecular level of the enzyme oxidative process can be of great help to model new enzymes with increased efficiency and robustness.

Physical Chemistry Chemical Physics, 2008

Suitable low molecular-weight compounds, called mediators, can be used in combination with the ph... more Suitable low molecular-weight compounds, called mediators, can be used in combination with the phenol-oxidase enzyme laccase to indirectly oxidize large organic substrates, such as environmental pollutants, which are not laccase natural substrates. The oxidation of two different synthetic redox mediators, violuric acid (VIO) and 2,2&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;#39;-azino-bis-(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) has been studied under catalysis of two laccases from white-rot fungi (Trametes versicolor and Pleurotus ostreatus). VIO was selected as a prototype of the -NOH type of mediators and compared to ABTS, a well-known two-step redox system. To characterize the radical intermediates formed from both mediators after the enzymatic oxidation, a multifrequency EPR approach has been adopted. The radical species have been investigated employing 9.4 GHz (X-band), 34 GHz (Q-band) and 244 GHz (high field) EPR and pulse electron nuclear double resonance (ENDOR) techniques. Theoretical calculations based on density functional theory (DFT/PCM) have been performed to support and further interpret the experimental EPR and ENDOR data. This integrated approach allowed us to obtain a complete characterization of both radicals and to elucidate the type of the radical state (neutral or cationic).

Proceedings of the National Academy of Sciences, 2008

This article contains supporting information online at www.pnas.org/cgi/content/full/ 0802376105/... more This article contains supporting information online at www.pnas.org/cgi/content/full/ 0802376105/DCSupplemental.

ABSTRACT Quantum mechanics/molecular mechanics molecular dynamics simulations have been used to p... more ABSTRACT Quantum mechanics/molecular mechanics molecular dynamics simulations have been used to predict the hydrogen-bonding networks in the active site of three double variants of Pleurotus eryngii versatile peroxidase containing a redox-active tyrosine in place of a tryptophan residue in position 164. The adopted computational strategy has proved to be adequate to correctly reproduce the hydrogen-bonding environment of tyrosyl radical (Tyr√) in the single W164Y variant of the enzyme that has been directly identified by electron paramagnetic resonance spectroscopy. In this study, we have investigated the effect of the mutation of a specific amino acid in the local environment of tyrosine 164. We show that the substitution of arginine 257 with a glutamic acid, a leucine or an alanine residue is able to induce the stabilisation of different hydrogen-bonding networks involving Tyr√ that can potentially affect its physico-chemical properties.

Cytochrome c peroxidase (CcP) is a heme-containing enzyme that catalyzes the oxidation of the fer... more Cytochrome c peroxidase (CcP) is a heme-containing enzyme that catalyzes the oxidation of the ferrocytochrome c to ferricytochrome c with concomitant reduction of H2O2 to H2O. Its catalytic cycle involves the formation of a double oxidized species (compound I) consisting of an oxoferryl center (Fe(IV)═O) and an amino acid radical (R(•)). Here we use a quantum-mechanics/molecular-mechanics (QM/MM) computational protocol based on density functional theory (DFT) and multiconfigurational perturbation theory (CASPT2) methods to reproduce specific features of compound I EPR and UV-vis spectra. The results show that the employed QM/MM models can correctly predict the magnetic, electronic and vibrational properties of the observed amino acid radicals of compound I. Furthermore, we have been able to confirm that the principal radical species of compound I is a tryptophan cationic radical located on residue 191 (Trp191(•+)) and that three tyrosine residues (Tyr203, Tyr236, and Tyr251), located along two possible ET pathways involving Trp191(•+), are possible candidates to host the secondary radical species.

The ability of Time-Dependent Density Functional Theory (TD-DFT) to provide excited state geometr... more The ability of Time-Dependent Density Functional Theory (TD-DFT) to provide excited state geometries and reproduce emission energies of organic D-π-A dyes designed for DSSC applications is evaluated. The performance of six functionals (CAM-B3LYP, MPW1K, ωB97X-D, LC-BLYP, LC-ωPBE, and M06-HF) in combination with three basis sets (cc-pVDZ, 6-31+G(d,p), and 6-311+G(2d,p)) has been analyzed. Solvent effects have been taken into account by means of a Polarizable Continuum Model in both LR and SS formalisms. Our LR-PCM/TD-DFT results show that accurate emission energies are obtained only when solvent effects are included in the computation of excited state geometries and when a range separated hybrid functional is used. Vertical emission energies are reproduced with a mean absolute error of at most 0.2 eV. The accuracy is further improved using the SS-PCM formalism.

Energy lies at the heart of any nation's technological, economical and social development. In rec... more Energy lies at the heart of any nation's technological, economical and social development. In recent years, energy demand has grown constantly and is bound to further increase. In this context, the interest of the scientific community is progressively moving towards renewable energy sources, with a particular focus on developing the technologies necessary for their exploitation, and towards sustainable growth. The search for alternative energy sources, able to combine efficiency, ease of use and reduced environmental impact is therefore, together with energy saving, an important challenge for our civilization. Among the various renewable energy sources available on our planet, solar energy is particularly attractive. One of the technologies available to produce electricity from solar energy is photovoltaics. With the aim of achieving a larger distribution of photovoltaics, research turned itself to the development of new technologies based on alternative materials, such as organic compounds. Some of these technologies exploit the capacity of organic dyes to liberate electrons as in natural photosynthesis. To this category belong the solar cells known as dye sensitized solar cells (DSSC), also known as Grätzel-type cells (Nature 1991). Such cells have attracted much interest, especially in the last decade, because of their potentially low cost of production. Thanks to the employment of readily available materials, produced by well-established processes, they actually present drastically lower economic and environmental costs compared with traditional silicon-based cells even though they are not efficient enough yet to be industrially competitive. An emerging challenge is to find the right set of materials to obtain DSSC of improved performances. Progress in this field requires major investments in terms of research and development aimed at the optimization of all parameters. In this study we present the preliminary results of life cycle assessment for the production of a DSSC. These results have been obtained through a multidisciplinary project for the design and synthesis of new organic sensitizers for DSSC. The life cycle assessment has been developed based on actual production data along all the project stages in order to evaluate the environmental impacts and the energy consumption associated with the production process. This analysis will be pivotal in understanding the environmental dynamics, the benefits and drawbacks associated with the production of DSSC in comparison with other photovoltaic technologies.

In the context of a constant energy demand growth, the interest of the scientific community is pr... more In the context of a constant energy demand growth, the interest of the scientific community is progressively moving towards renewable energy sources. Among these, photovoltaics has a prominent role. With the aim of overcoming the limits of silicon production, research turned itself to the development of new photovoltaic technologies based on alternative materials, such as organic compounds.

We report the results of a multidisciplinary research effort where the methods of computational p... more We report the results of a multidisciplinary research effort where the methods of computational photochemistry and retrosynthetic analysis/synthesis have contributed to the preparation of a novel N-alkylated indanylidene-pyrroline Schiff base featuring an exocyclic double bond and a permanent zwitterionic head. We show that, due to its large dipole moment and efficient photoisomerization, such a system may constitute the prototype of a novel generation of electrostatic switches achieving a reversible light-induced dipole moment change on the order of 30 D. The modeling of a peptide fragment incorporating the zwitterionic head into a conformationally rigid side chain shows that the switch can effectively modulate the fluorescence of a tryptophan probe. (3) Harvey, J. H.; Trauner, D. Chembiochem 2008, 9, 191-193. (4) Numano, R.; Szobota, S.; Lau, A. Y.; Gorostiza, P.; Volgraf, M.; Roux, B.; Trauner, D.; Isacoff, E. Y. Proc. Natl. Acad. Sci. U.S.A. 2009, 106, 6814-6819. (5) Schierling, B.; Noël, A.-J.; Wende, W.; Hien, L. T.; Volkov, E.; Kubareva, E.; Oretskaya, T.; Kokkinidis, M.; Römpp, A.; Spengler, B.; Pingoud, A.

Physical Chemistry Chemical Physics, 2011

Quantum mechanics/molecular mechanics (QM/MM) methods, employing density functional theory (DFT),... more Quantum mechanics/molecular mechanics (QM/MM) methods, employing density functional theory (DFT), have been used to compute the electron paramagnetic resonance (EPR) parameters of tryptophan and tyrosyl radical intermediates involved in the catalytic cycle of Pleurotus eryngii versatile peroxidase (VP) and its W164Y variant, respectively. These radicals have been previously experimentally detected and characterized both in the two-electron and one-electron activated forms of the enzymes. In this work, the well-studied W164 radical in VP has been chosen for calibration purposes because its spectroscopic properties have been extensively studied by multifrequency EPR and ENDOR spectroscopies. Using a B3LYP/CHARMM procedure, appropriately accounting for electrostatic, such as hydrogen bonding, and steric environmental interactions, a good agreement between the calculated and measured EPR parameters for both radicals has been achieved; g-tensors, hyperfine coupling constants (hfcc) and Mulliken spin densities have been correlated to changes in geometries, hydrogen bond networks and electrostatic environment, with the aim of understanding the influence of the protein surroundings on EPR properties. In addition, the present calculations demonstrate, for VP, the formation of a neutral tryptophan radical, hydrogen bonded to the nearby E243, via a stepwise electron and proton transfer with earlier involvement of a short-lived tryptophan cationic species. Instead, for W164Y, the QM/MM dynamics simulation shows that the tyrosine oxidation proceeds via a concerted electron and proton transfer and is accompanied by a significant reorganization of residues and water molecules surrounding the tyrosyl radical.

ABSTRACT Thanks to the research and development for achieving a larger distribution, many photovo... more ABSTRACT Thanks to the research and development for achieving a larger distribution, many photovoltaic technologies are available in the market presently. Those accepted as "conventional" are well along in the process of commercialization while those classified as "new generation" photovoltaics are at an early stage of industrialization as of yet. To the latter category belong the non-conventional technology of dye sensitized solar cells. Since their first assembling at the beginning of the 1990s, these devices have attracted much interest and have been extensively investigated, because of their ease for assembling of readily available materials and the employment of well-established processes. So far, many configurations have been developed, tested and reported in literature. Each of them is based on the improvement and/or replacement of one or more components of a single solar cell: the substrate, the semiconductor, the dye, the electrolyte and the counter electrode. The efficiency of dye sensitized solar cells at lab scale is now comparable with amorphous silicon photovoltaics technology, but with much more potential than silicon for performance improvements and for becoming a cost-effective means for electricity production. In spite of these favourable aspects, dye sensitized solar cell prototypes for large scale production are not yet sufficiently efficient to be industrially competitive. In this study, we present an environmental sustainability overview of the principal dye sensitized solar cell configurations proposed to select the proper set of materials suitable for improving their performances. This is done on the basis of data published in literature, pre-industrialization tests by several companies and lab data obtained through the Fotosensorg Project. The analysis will be integrated with considerations on the potential for a larger distribution and competition of dye sensitized solar cells with presently available solar electric technologies on the photovoltaic market.

Photochemical & Photobiological Sciences, 2009

We report the outcomes of our recent computational and experimental work for the development of a... more We report the outcomes of our recent computational and experimental work for the development of a novel biomimetic molecular switch. Furthermore, we present the new results on the design and computational characterization of a &amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;quot;functional&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;quot; cyclic peptidomimetic formed by the switch conjugated to a biologically active peptide: the RGD sequence involved in the control of cell adhesion. Structural properties of the construct are investigated in aqueous solution using molecular dynamics (MD) simulations. Analysis of MD trajectories reveals that, for each diastereoisomer of the switch (E or Z), different conformations are stabilized. Electrostatic and spectroscopic properties of such conformers are evaluated by means of ab initio multiconfiguration quantum chemical method implemented in a quantum-mechanical/molecular-mechanic (CASPT2//CASSCF/6-31G*/AMBER) scheme.

Three new thiazolo[5,4-d]thiazole-based organic dyes have been designed and synthesized for emplo... more Three new thiazolo[5,4-d]thiazole-based organic dyes have been designed and synthesized for employment as DSSC sensitizers. Alternation of the electron poor thiazolothiazole unit with two propylenedioxythiophene (ProDOT) groups ensured very intense light absorption in the visible region (ε up to 9.41 × 10(4) M(-1) cm(-1) in THF solution). The dyes were particularly suitable for application in transparent and opaque thin-layer DSSCs (TiO2 thickness: 5.5-6.5 μm, efficiencies up to 7.71%), thus being good candidates for production of solar cells under simple fabrication conditions.

In recent years there has been an increasing awareness of the key role of radicals in both normal... more In recent years there has been an increasing awareness of the key role of radicals in both normal cellular metabolism and biological processes, and their role as key intermediates in many deleterious processes in disease and ageing. Since free radicals are extremely reactive and highly unstable compounds, a rapid growth in applications of spin-trapping methods was developed. These methods involve