Giuseppe Brancato

A hybrid explicit/implicit solvation method for first-principle molecular dynamics simulations.

In this work, we present a hybrid explicit/implicit solvation model, well suited for first-principles molecular dynamics simulations of solute-solvent systems. An effective procedure is presented that allows to reliably model a solute with a few explicit solvation shells, ensuring solvent bulk behavior at the boundary with the continuum. Such an approach is integrated with high-level ab initio methods using localized basis functions to perform first-principles or mixed quantum mechanics/molecular mechanics simulations within the extended-Lagrangian formalism. A careful validation of the model along with illustrative applications to solutions of acetone and glycine radical are presented, considering two solvents of different polarity, namely, water and chloroform. Results show that the present model describes dynamical and solvent effects with an accuracy at least comparable to that of conventional approaches based on periodic boundary conditions.

A quantum mechanical/molecular dynamics/mean field study of acrolein in aqueous solution: Analysis of H bonding and bulk effects on spectroscopic properties

A novel molecular dynamics methodology recently proposed by our group [Rega et al., Chem. Phys. Lett. 422, 367 (2006)], which is based on an integrated hybrid potential rooted in high level quantum mechanical methods using localized basis functions and nonperiodic boundary conditions, has been applied to study acrolein in aqueous solution. The solute structural rearrangement and its hydrogen-bonding pattern due to the interactions with water have been analyzed in some detail. Moreover, the solvent effects on the UV n-->pi* vertical transition and on the NMR 13C and 17O shielding constants of acrolein have been investigated theoretically by performing a posteriori quantum mechanical calculations on a statistically significant number of snapshots extracted from both gas-phase and aqueous solution simulations. Results show that such effective computational strategy can be successfully used to improve our understanding, at atomic level, of important spectroscopic observables.

A mean field approach for molecular simulations of fluid systems

In this paper we introduce a mean field method for simulating complex molecular systems like liquids and solutions. Using well-established theoretical principles and models, we obtained a relatively simple approach which seems to provide a reliable description of the bulk molecular behavior of liquid water. Moreover, we have applied this approach to study simple solutes in solution, like sodium and chloride ions and acetone. Comparison with standard simulations, performed with periodic boundary conditions, shows that such a mean field method can reproduce the same structural and thermodynamical properties at low computational costs and represents a valid alternative for simulating solute-solvent systems, like solutions of large biomolecules.

Dual fluorescence through Kasha's rule breaking: an unconventional photomechanism for intracellular probe design.

Dual fluorescence is an anomalous photophysical phenomenon observed in very few chromophores in which a two-color radiative process occurs that involves two distinct excited electronic states. To date its observation was linked either to electronic rearrangement of an excited fluorophore leading to two conformers with distinct emissive properties, or to a photochemical modification leading to different fluorescent species. In both cases, emission originates from the lowest excited state of the resulting molecular configurations, in line with the so-called Kashas rule. We report here a combined theoretical and spectroscopic study showing, for the first time, an anti-Kasha dual-emission mechanism, in which simultaneous two-color emission takes place from the first and second excited state of a coumarin derivative. We argue that the observed environmental sensitivity of this peculiar optical response makes the present compound ideally suited for biosensing applications in living cells.

Reliable molecular simulations of solute-solvent systems with a minimum number of solvent shells

In this work, the mean field (MF) method, a continuum-based model designed for treating complex molecular systems, such as liquids and solutions, recently presented by Brancato et al. [J. Chem. Phys. 122, 154109 (2005)], has been further developed and improved especially in the treatment of the electrostatics. The revised model has been used to investigate the size effects on several physical properties of various solute-solvent systems by increasing the number of explicitly included solvent molecules from few tens up to thousands. Results on simple ions, such as sodium and chloride ions, and on a small peptide, such as alanine dipeptide analog (AcAlaNHMe), have shown that solvation structures and dynamics, as well as solvent-induced changes in the solute conformation, can be correctly reproduced by the MF model, providing that only two or three solvent layers are treated explicitly.

Reversible vapochromic response of polymer films doped with a highly emissive molecular rotor

We report on a new vapochromic system suitable for sensing volatile organic compounds (VOCs) based on polymer films doped with 4-(diphenylamino)phthalonitrile (DPAP), a fluorescent molecular rotor sensitive to both solvent polarity and viscosity. Poly(methyl methacrylate) (PMMA) and polycarbonate (PC) films containing small amounts of DPAP (≤0.1 wt%) were prepared and exposed to saturated atmospheres of different VOCs. DPAP/PMMA films show a good and reversible vapochromism when exposed to VOCs with high polarity index and favourable interaction with polymer matrices such as THF, CHCl3, and acetonitrile. Analogously, DPAP/PC films exposed to polar and highly polymer-interacting solvents, that is, toluene, THF, and CHCl3, show a gradual decrease and red-shift of the emission. In contrast to DPAP/PMMA films, an unexpected increase and further red-shift of fluorescence are observed at longer exposure times as a consequence of an irreversible, solvent-induced crystallization process of PC. The vapochromism of DPAP-doped films is rationalized on the basis of alterations of the rotor intramolecular motion and polarity effects stemming from the environment, which, in concert, influence the deactivation pathways of the DPAP intramolecular charge transfer state. Overall, the present results support the use of DPAP-enriched plastic films as a new chromogenic material suitable for the detection of VOCs.

A fluorescent molecular rotor showing vapochromism, aggregation-induced emission, and environmental sensing in living cells

Among the plethora of recently proposed molecular sensors, those belonging to the class of fluorescent molecular rotors (FMRs) have attracted much attention owing to their peculiar photophysical properties that enable an unprecedented sensitivity towards environmental microviscosity. The usual FMR synthetic design prescribes chromophores characterized by an intramolecular rotation between two well-defined excited states, a locally excited state and a twisted internal charge transfer (TICT) state, where the sensing capabilities arise from a dual competition of the corresponding radiative/non-radiative decay processes. However, we have recently demonstrated a different modus operandi of a new subclass of solvatochromic FMRs, which exploit a solvent-independent, barrier-free intramolecular rotation of the excited dye. The rotational dynamics is modulated by local viscosity and, in turn, manifested through a variable spectral signal. In order to translate the same rotational mechanism in a versatile sensor of polarity and viscosity, we designed and thoroughly characterized a novel FMR, namely 4-(triphenylamino)-phthalonitrile (TPAP). Remarkably, in addition to a high sensitivity versus solvent polarity and viscosity, TPAP is also able to form stable fluorescent nanoparticles characterized by aggregation-induced emission, via a simple sonochemical treatment. Such peculiar features are tested in different applications aiming at illustrating its capability to report on solvatochromic and vapochromic effects, as well as to provide detailed intracellular information through bioimaging studies.

Vibrational analysis of x-ray absorption fine structure thermal factors by ab initio molecular dynamics: the Zn(II) ion in aqueous solution as a case study.

In this work, we consider a new combination of vibrational analysis and normal-like mode decomposition of Debye-Waller factors of solvated ions entirely based on molecular dynamics data. Such a novel time-dependent analysis procedure provides a direct link between x-ray absorption fine structure parameters and normal mode contributions for an ion-solvent system. The potentialities of such a methodology rely on two fundamental aspects which distinguish it from already available tools. First, a general vibrational analysis that does not require any Gaussian or harmonic model for describing atomic fluctuations in liquids. Second, a very accurate sampling of the short range motions around the structural probe via the recently developed atom centered density matrix propagation/general liquid optimized boundary method. This novel molecular dynamics methodology is based on an integrated ab initio/classical potential using localized basis functions and nonperiodic boundary conditions. As a case study we have chosen the Zn(II) ion in aqueous solution. The consistency of our results and the observed good agreement with experiments show how the key support to advanced structural techniques from molecular dynamics can be further expanded and investigated.

Pathways and Barriers for Ion Translocation through the 5-HT3A Receptor Channel.

Pentameric ligand gated ion channels (pLGICs) are ionotropic receptors that mediate fast intercellular communications at synaptic level and include either cation selective (e.g., nAChR and 5-HT3) or anion selective (e.g., GlyR, GABAA and GluCl) membrane channels. Among others, 5-HT3 is one of the most studied members, since its first cloning back in 1991, and a large number of studies have successfully pinpointed protein residues critical for its activation and channel gating. In addition, 5-HT3 is also the target of a few pharmacological treatments due to the demonstrated benefits of its modulation in clinical trials. Nonetheless, a detailed molecular analysis of important protein features, such as the origin of its ion selectivity and the rather low conductance as compared to other channel homologues, has been unfeasible until the recent crystallization of the mouse 5-HT3A receptor. Here, we present extended molecular dynamics simulations and free energy calculations of the whole 5-HT3A protein with the aim of better understanding its ion transport properties, such as the pathways for ion permeation into the receptor body and the complex nature of the selectivity filter. Our investigation unravels previously unpredicted structural features of the 5-HT3A receptor, such as the existence of alternative intersubunit pathways for ion translocation at the interface between the extracellular and the transmembrane domains, in addition to the one along the channel main axis. Moreover, our study offers a molecular interpretation of the role played by an arginine triplet located in the intracellular domain on determining the characteristic low conductance of the 5-HT3A receptor, as evidenced in previous experiments. In view of these results, possible implications on other members of the superfamily are suggested.

Vapochromic behavior of polycarbonate films doped with a luminescent molecular rotor

We report on vapochromic films suitable for detecting volatile organic compounds (VOCs), based on polycarbonate (PC) doped with 4-(triphenylamino)phthalonitrile (TPAP), a fluorescent molecular rotor sensitive to solvent polarity and viscosity. PC films of variable thickness (from 20 up to 80 µm) and containing small amounts of TPAP (0.05 wt.%) were prepared and exposed to a saturated atmosphere of different VOCs. TPAP/PC films showed a gradual decrease and red-shift of the emission during the exposure to solvents with high polarity index and favourable interaction with the polymer matrix such as THF, CHCl3, and acetonitrile. In the case of the most interacting solvents (THF and CHCl3), TPAP/PC films also showed a fluorescence increase at longer exposure times, as a consequence of an irreversible, solvent-induced crystallization process of the polymeric matrix. The vapochromism of TPAP/PC films is rationalized on the basis of alterations of the rotor intramolecular motion upon solvent uptake by PC and polarity effects of the microenvironment. Interestingly, the fluorescence response of the TPAP/PC films shows a non-trivial, tuneable dependence on film thickness during the second solvent-exposure stage. The latter effect is attributed to a variable extent of the crystallization process occurring in the PC films. This observation promptly suggests, in turn, an effective procedure to modulate the spectroscopic response in such functionalized polymeric materials through the precise control of the film thickness.