Umberto Raucci

Intrinsic and dynamical reaction pathways of an excited state proton transfer.

The detailed knowledge of excited state proton transfer mechanisms in complex environments is of paramount importance in chemistry. However, the definition of an effective reaction coordinate and the understanding of the driving force of the reaction can be difficult from both the experimental and the theoretical points of view. Here we analyzed by theoretical approaches the mechanism and the driving forces of the excited state proton transfer reaction occurring between the 7-hydroxy-4-(trifluoromethyl)coumarin photoacid and the 1-methylimidazole base molecules in toluene solution. In particular, we compared the intrinsic and the dynamical reaction pathways, obtained by integrating the reaction coordinate, and by performing ab initio simulations of molecular dynamics, respectively. Time-dependent density functional theory and polarizable solvation continuum models were adopted to define the excited state potential energy surface. Results were analyzed by means of the D(CT) electronic density based index. Our findings suggest that the reaction coordinate is mainly composed of several intra- and intermolecular modes of the reactants. An analysis of both the intrinsic coordinate and the dynamical results shows that the charge transfer induced by electronic excitation of the coumarin molecule is the main proton transfer driving force. With regards to the methodological validation, the combination of ab initio molecular dynamics with time-dependent density functional theory appears to be feasible and reliable to study excited state proton transfer reactions in the condensed phase.

Integration of binding peptide selection and multifunctional particles as tool-box for capture of soluble proteins in serum

In this paper, we report on a general approach for the detection of a specific tumoural biomarker directly in serum. Such detection is made possible using a protein-binding peptide selected through an improved phage display technique and then conjugated to engineered microparticles (MPs). Protein biomarkers represent an unlimited source of information for non-invasive diagnostic and prognostic tests; MP-based assays are becoming largely used in manipulation of soluble biomarkers, but their direct use in serum is hampered by the complex biomolecular environment. Our technique overcomes the current limitations as it produces a selective MP—engineered with an antifouling layer—that ‘captures’ the relevant protein staying impervious to the background. Our system succeeds in fishing-out the human tumour necrosis factor alpha directly in serum with a high selectivity degree. Our method could have great impact in soluble protein manipulation and detection for a wide variety of diagnostic applications.

On the different strength of photoacids

AbstractIn spite of the detailed information provided by advanced time-resolved spectroscopy, the understanding of the excited-state proton transfer (ESPT) reactivity remains difficult to obtain at molecular level. In this work we studied three photoacids showing different strength: the 8-hydroxy-1,3,6-pyrenetrisulfonate weak photoacid, the N-methyl-6-hydroxyquinolinium strong photoacid and the phenol-carboxyether dipicolinium cyanine (QCy9) superphotoacid, focusing on the intermolecular ESPT toward a solvent molecule or a base molecule in aqueous solution. To this aim, the ground and the first singlet excited-state potential energy surfaces of the three systems were characterized by means of the time-dependent density functional theory and a hybrid implicit/explicit model of the solvent. Main structural and photophysical features of the photoacids were assessed and satisfactorily compared with the experimental data. Energy profiles along the PT coordinate were analyzed in both the electronic states. We reproduced many important features of the photoacidity experimentally observed. The results suggest that the relative strength is mainly due to the different extent of charge transfer caused by the electronic transition in proximity of the acid group. Remarkably, we found that even in the case of the strongest photoacid (QCy9), showing a ESPT rate as rapid as to escape the solvent dynamics control, the PT is modulated and supported by the first solvation shell of the proton-accepting molecule. However, a complete understanding of this fascinating field needs the full account for the electronic and the molecular dynamics in play at different timescales.

Comparing the performance of TD-DFT and SAC-CI methods in the description of excited states potential energy surfaces: An excited state proton transfer reaction as case study

The performances, in the description of excited state potential energy surfaces, of several density functional approximations representative of the currently most applied exchange correlation functionals’ families have been tested with respect to post Hartree‐Fock references (here Symmetry Adapted Cluster‐Configuration Interaction results). An experimentally well‐characterized intermolecular proton transfer reaction has been considered as test case. The computed potential energy profiles were analyzed both in the gas phase and in toluene solution, here represented as a polarizable continuum model. The presence of intermolecular (dark) and intramolecular (bright) charge transfer excited states, whose polarity strongly differs along the reaction pathway, makes clear that only subtle compensation between spurious electronic effects—related to the incorrect asymptotic behavior of the functional—and solvent stabilization of polar states leads to the overall correct description of this excited state reaction when using global hybrids with low percentage of Hartree Fock exchange.

Turn-on fluorescence detection of protein by molecularly imprinted hydrogels based on supramolecular assembly of peptide multi-functional blocks

Synthetic receptors for biomacromolecules lack the supramolecular self-assembly behavior typical of biological systems. Here we propose a new method for the preparation of protein imprinted polymers based on the specific interaction of a peptide multi-functional block with a protein target. This peptide block contains a protein-binding peptide domain, a polymerizable moiety at the C-terminus and an environment-sensitive fluorescent molecule at the N-terminus. The method relies on a preliminary step consisting of peptide/protein supramolecular assembly, followed by copolymerization with the most common acrylate monomers (acrylamide, acrylic acid and bis-acrylamide) to produce a protein imprinted hydrogel polymer. Such a peptide block can function as an active assistant recognition element to improve affinity, and guarantees its effective polymerization at the protein/cavity interface, allowing for proper placement of a dye. As a proof of concept, we chose Bovine Serum Albumin (BSA) as the protein target and built the peptide block around a BSA binding dodecapeptide, with an allyl group as the polymerizable moiety and a dansyl molecule as the responsive dye. Compared to conventional approaches these hydrogels showed higher affinity (more than 45%) and imprinted sensitivity (about twenty fold) to the target, with a great BSA selectivity with respect to ovalbumin (α = 1.25) and lysozyme (α = 6.02). Upon protein binding, computational and experimental observations showed a blue shift of the emission peak (down to 440 nm) and an increase of fluorescence emission (twofold) and average lifetime (Δτ = 4.3 ns). Such an approach generates recognition cavities with controlled chemical information and represents an a priori method for self-responsive materials. Provided a specific peptide and minimal optimization conditions are used, such a method could be easily implemented for any protein target.

Unveiling the structure of a novel artificial heme-enzyme with peroxidase-like activity: A theoretical investigation

Fe(III)‐Mimochrome VI (MC6) is a recently reported artificial heme‐peptide conjugate system with a high peroxidase‐like activity. By design, its structure features a five‐coordinated Fe(III)‐deuteroporphyrin active site, embedded in a compact α‐helix–heme–α‐helix “sandwich” motif. Up to now, no detailed MC6 structural characterization is available. In this work we propose a theoretical investigation based on molecular dynamics (MD) simulations and hybrid quantum mechanics/molecular mechanics (QM/MM) optimizations, aimed to shed light on several Fe(III)‐MC6 structural features and to validate the de novo designed fold. Key structural elements were analyzed to achieve indirect insight relevant to understand Fe(III)‐MC6 catalytic performances in solution. Extensive MD simulations showed a partial stability of the “sandwich” fold in water solution. The smaller peptide chain bonded to the heme revealed a high conformational freedom, which promoted the exposition of the heme distal side to the solvent. Regarding the accessibility of water molecules, even in Fe(III)‐MC6 “closed” structure the heme cavity appeared hydrated, suggesting an easy accessibility by exogenous ligands. Fe(III)‐MC6 structure in both high and low spin states was then further characterized through hybrid QM/MM optimizations. In particular, an accurate description of the active site structure was obtained, allowing a direct comparison of Fe(III)‐MC6 coordination environment with that observed in the Horseradish Peroxidase crystal structures. Our results suggest a structural similarity between Fe(III)‐MC6 and the natural enzyme. This study supports the interpretation of data from experimental Fe(III)‐MC6 structural and functional characterization and the rational design of new artificial mimics with improved catalytic performances.