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Monti S.,CNR Institute of Chemistry of organometallic Compounds | Walsh T.R.,University of Warwick
Journal of Physical Chemistry C | Year: 2010

The potential of mean constraint force approach, in partnership with atomistic molecular dynamics simulations, is used to calculate the change in free energy upon adsorption of amino acid side chain analogues at the aqueous rutile titania (110) interface. Our results indicate that both positively charged and negatively charged moieties have favorable free energy of binding to the titania surface. Stable contact, mediated via the first two solvent layers at the interface, is also indicated for the charged adsorbates. Hydrophobic adsorbates showed no appreciable binding to the titania surface. In contrast, the binding for our serine analogue (methanol) features a slight possibility to bind via hydrogen bonding to the titania surface. Our calculated results indicate very good agreement with available experimental data. In partnership with other information regarding peptide conformation and intrapeptide interactions, our findings should be helpful in building design principles for peptide sequences with predictable and controllable binding to titania. © 2010 American Chemical Society.


Barone V.,Normal School of Pisa | Biczysko M.,Normal School of Pisa | Bloino J.,Normal School of Pisa | Bloino J.,CNR Institute of Chemistry of organometallic Compounds
Physical Chemistry Chemical Physics | Year: 2014

Computation of full infrared (IR) and Raman spectra (including absolute intensities and transition energies) for medium- and large-sized molecular systems beyond the harmonic approximation is one of the most interesting challenges of contemporary computational chemistry. Contrary to common beliefs, low-order perturbation theory is able to deliver results of high accuracy (actually often better than those issuing from current direct dynamics approaches) provided that anharmonic resonances are properly managed. This perspective sketches the recent developments in our research group toward the development of a robust and user-friendly virtual spectrometer rooted in second-order vibrational perturbation theory (VPT2) and usable also by non-specialists essentially as a black-box procedure. Several examples are explicitly worked out in order to illustrate the features of our computational tool together with the most important ongoing developments. This journal is © 2014 the Owner Societies.


Liguori F.,CNR Institute of Chemistry of organometallic Compounds | Barbaro P.,CNR Institute of Chemistry of organometallic Compounds
Journal of Catalysis | Year: 2014

Palladium nanoparticles were immobilized onto an unconventional polymeric borate macroporous monolith and the resulting mesoreactor (i.d. 3 mm, length 25 mm) used in liquid-phase catalytic semi-hydrogenation reaction of substituted alkynes under continuous flow. The catalytic system showed excellent efficiency, both in terms of activity and selectivity, and long-term stability under mild reaction conditions (methanol, room temperature, 1.5 bar H2 max), with no need of additives. Particularly, the leaf alcohol cis-3-hexen-1-ol was for the first time obtained with selectivity comparable to that of the industrial batch process. The performance of the catalyst is discussed and compared with those of the analogous batch and industrial processes. © 2013 Elsevier Inc. All rights reserved.


Caporali M.,CNR Institute of Chemistry of organometallic Compounds | Gonsalvi L.,CNR Institute of Chemistry of organometallic Compounds | Rossin A.,CNR Institute of Chemistry of organometallic Compounds | Peruzzini M.,CNR Institute of Chemistry of organometallic Compounds
Chemical Reviews | Year: 2010

A comprehensive review of research conducted between 1970 and the end of 2008 in the field of white phosphorus (P4) activation by late-transition metal complexes is presented. The first stable tetrahedro-tetraphosphorus complex ever reported was the rhenium derivative obtained by the straightforward reaction of P4 with the Re(I) species. Complexes containing the intact P4 molecule coordinated as a tetrahedro-η1-P4 ligand, were characterized by spectroscopic and X-ray crystallographic measurements. The molecular structure of the tetraphosphaferrocene derivative shows perfectly planar arrangement of the two five-membered rings and the P-C and P-P bonds in the tetraphospholyl ring are at intermediate values between single and double bonds. The pentaphosphaferrocene and its homologues are found to have additional reactivity and behave as adaptable synthetic platforms for bringing about a flourishing chemistry.


Avila Ferrer F.J.,CNR Institute of Chemistry of organometallic Compounds | Santoro F.,CNR Institute of Chemistry of organometallic Compounds
Physical Chemistry Chemical Physics | Year: 2012

The calculation of the vibrational structure associated to electronic spectra in large molecules requires a Taylor expansion of the initial and final state potential energy surface (PES) around some reference nuclear structure. Vertical (V) and adiabatic (A) approaches expand the final state PES around the initial-state (V) or final-state (A) equilibrium structure. Simplest models only take into account displacements of initial- and final-state minima, intermediate ones also allow for difference in frequencies and more accurate models introduce the Dushinsky effect through the computation of the Hessians of both the initial and final state. In this contribution we summarize and compare the mathematical expressions of the complete hierarchy of V and A harmonic models and we implement them in a numerical code, presenting a detailed comparison of their performance on a number of prototypical systems. We also address non-Condon effects through linear expansions of the transition dipole as a function of nuclear coordinates (Herzberg-Teller effect) and compare the results of expansions around initial and final state equilibrium geometries. By a throughout analysis of our results we highlight a number of general trends in the relative performance of the models that can provide hints for their proper choice. Moreover we show that A and V models including final state PES Hessian outperform the simpler ones and that discrepancies in their predictions are diagnostic for failure of harmonic approximation and/or of Born-Oppenheimer approximation (existence of remarkable geometry-dependent mixing of electronic states). © 2012 the Owner Societies.


Barone V.,Normal School of Pisa | Biczysko M.,CNR Institute of Chemistry of organometallic Compounds | Puzzarini C.,University of Bologna
Accounts of Chemical Research | Year: 2015

ConspectusFor many years, scientists suspected that the interstellar medium was too hostile for organic species and that only a few simple molecules could be formed under such extreme conditions. However, the detection of approximately 180 molecules in interstellar or circumstellar environments in recent decades has changed this view dramatically. A rich chemistry has emerged, and relatively complex molecules such as C60 and C70 are formed. Recently, researchers have also detected complex organic and potentially prebiotic molecules, such as amino acids, in meteorites and in other space environments. Those discoveries have further stimulated the debate on the origin of the building blocks of life in the universe. Many efforts continue to focus on the physical, chemical, and astrophysical processes by which prebiotic molecules can be formed in the interstellar dust and dispersed to Earth or to other planets.Spectroscopic techniques, which are widely used to infer information about molecular structure and dynamics, play a crucial role in the investigation of planetary atmosphere and the interstellar medium. Increasingly these astrochemical investigations are assisted by quantum-mechanical calculations of structures as well as spectroscopic and thermodynamic properties, such as transition frequencies and reaction enthalpies, to guide and support observations, line assignments, and data analysis in these new and chemically complicated situations. However, it has proved challenging to extend accurate quantum-chemical computational approaches to larger systems because of the unfavorable scaling with the number of degrees of freedom (both electronic and nuclear).In this Account, we show that it is now possible to compute physicochemical properties of building blocks of biomolecules with an accuracy rivaling that of the most sophisticated experimental techniques, and we summarize specific contributions from our groups. As a test case, we present the underlying computational machinery through the investigation of oxirane. We describe how we determine the molecular structure and then how we characterize the rotational and IR spectra, the most important issues for a correct theoretical description and a proper comparison with experiment. Next, we analyze the spectroscopic properties of representative building blocks of DNA bases (uracil and pyrimidine) and of proteins (glycine and glycine dipeptide analogue).Solvation, surface chemistry (dust fraction, adsorption, desorption), and inter- and intramolecular interactions, such as self-organization and self-interaction, are important molecular processes for understanding astrochemistry. Using the specific cases of uracil dimers and glycine adsorbed on silicon grains, we also illustrate approaches in which we treat different regions, interactions, or effects at different levels of sophistication. © 2015 American Chemical Society.


Melchionna M.,CNR Institute of Chemistry of organometallic Compounds | Fornasiero P.,CNR Institute of Chemistry of organometallic Compounds
Materials Today | Year: 2014

Ceria (CeO2) is enjoying increasing popularity in catalytic applications, and in some cases has established itself as an irreplaceable component. The reasons for such success stem from the intrinsic structural and redox properties of ceria. Reducing the ceria particles to the nanoscale has a profound impact on the catalytic behavior. The proliferation of improved synthetic methods that allow control over the final morphology and size of the nano-structures is opening new possibilities in terms of catalytic potential, particularly for energy-related applications. © 2014 Elsevier Ltd. All rights reserved.


Villani G.,CNR Institute of Chemistry of organometallic Compounds
Chemical Physics | Year: 2012

The hydrated A-T base pair has been studied in order to understand the structural modifications and their electronic rearrangements induced by the movement of the hydrogen atoms in the H-bonds. The comparison of these results with that of the nonhydrated system can explain the role of the H-bonds of the water molecules in this system. Two naïve schemes have been considered, one where the hydrogen bonds of the water molecules are only indirectly involved in the hydrogen atoms transfer between the bases and another where the water molecules are directly involved in this transfer. The results support the idea that the real mechanisms are more complexes than these schemes. Some new stable structures of the A-T(H 2O) 2 and the A-T(H 2O) 4 systems have been found and the mechanisms of their generations have been analysed. © 2011 Elsevier B.V. All rights reserved.


Villani G.,CNR Institute of Chemistry of organometallic Compounds
Journal of Physical Chemistry B | Year: 2014

Four different complexes of two base pairs, an adenine-thymine and a guanine-cytosine one, have been studied in order to understand the modifications induced by the staking interaction between the two base pairs on the hydrogen atoms transfers between the bases in either base pair. The inclusion of these two kinds of interactions allows us to clarify if some properties, as the mechanism of hydrogen transfer, is exclusively a local effect of a base pair or can be modified by a more long-range interaction between the base pairs. The results on these four complexes are compared with those of the monomeric systems, the A-T and G-C base pair, and with those of the A-T and G-C dimers. The specificity of each complex and of each hydrogen bond has been analyzed. © 2014 American Chemical Society.


Moreno-Marrodan C.,CNR Institute of Chemistry of organometallic Compounds | Barbaro P.,CNR Institute of Chemistry of organometallic Compounds
Green Chemistry | Year: 2014

A bifunctional heterogeneous catalyst based on sulfonated cation exchange resin and embedded Ru nanoparticles shows complete conversion and selectivity at low temperatures and H2 pressure in the direct, one-pot conversion of levulinic acid to GVL under continuous flow conditions, with excellent durability and no need for additives. This journal is © the Partner Organisations 2014.

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