Roberto Improta | Consiglio Nazionale delle Ricerche (CNR) (original) (raw)

Papers by Roberto Improta

Chemical Physics, 2007

The authors present a new method for the computation of vibrationally resolved optical spectra of... more The authors present a new method for the computation of vibrationally resolved optical spectra of large molecules, including the Duschinsky [Acta Physicochim. URSS 7, 551 (1937)] rotation of the normal modes. The method automatically selects the relevant vibronic contributions to the spectrum, independent of their frequency, and it is able to provide fully converged spectra with a quite modest computational time, both in vacuo and in condensed phase. Starting from the rigorous time-dependent expression they discuss indeed in which limits the spectrum of a molecule embedded in a solvent, described as a polarizable continuum, can be computed in a time-independent formalism, defining both nonequilibrium and equilibrium limits. In these cases the polarizable continuum model provides a suitable description of the solvent field. By computing the absorption spectra of anthracene in gas phase and of coumarin C153 in gas phase and cyclohexane, and the phosphorescence spectrum of the unsubstituted coumarin in ethanol they show that the method is fast and efficient.

Chemical Physics, 2008

The authors extend their recent method for the computation of vibrationally resolved optical spec... more The authors extend their recent method for the computation of vibrationally resolved optical spectra of large molecules, including both the Duschinsky rotation and the effect of finite temperature in the framework of the Franck-Condon (FC) approximation, to deal with the more general case of the Herzberg-Teller (HT) model, where also the linear dependence of the transition dipole moment on the

Quantitative Structure-Activity Relationships, 2002

The impact of density functional theory in the computation of reliable spectroscopic parameters i... more The impact of density functional theory in the computation of reliable spectroscopic parameters is reviewed with special reference to IR, Raman, UV, visible, NMR and EPR techniques. In general terms, the results delivered by the most recent density functionals (especially hybrid ones) are remarkably accurate. Proper treatment of solvent effects by continuum models and of vibrational averaging effects by suitable Hamiltonians governing the nuclear motions, significantly increases the reliability of the results and the fields of application of theoretical computations. Some case examples have been reported to better illustrate the potentialities of this approach also for non specialists.

Journal of the American Chemical Society, Jan 10, 2015

UV radiation creates excited states in DNA that lead to mutagenic photoproducts. Photoexcitation ... more UV radiation creates excited states in DNA that lead to mutagenic photoproducts. Photoexcitation of single-stranded DNA can transfer an electron between stacked bases, but the fate of excited states in the double helix has been intensely debated. Here, photoinduced interstrand proton transfer (PT) triggered by intrastrand electron transfer (ET) is detected for the first time by time-resolved vibrational spectroscopy and quantum mechanical calculations. Long-lived excited states are shown to be oppositely charged base pair radical ions. In two of the duplexes, the base pair radical anions are present as tautomers formed by interstrand PT. Charge recombination occurs on the picosecond time scale preventing the accumulation of damaging radicals or mutagenic tautomers.

Acta crystallographica. Section D, Biological crystallography, 2015

By combining quantum-mechanical analysis of small model peptides and statistical surveys of high-... more By combining quantum-mechanical analysis of small model peptides and statistical surveys of high-resolution protein structures, a systematic conformational dependence of bond lengths in polypeptide backbones has been unveiled which involves both the peptide bond (C-O and C-N) and those bonds centred on the C(α) atom. All of these bond lengths indeed display a systematic variability in the ψ angle according to both calculations and surveys of protein structures. The overall agreement between the computed and the statistical data suggests that these trends are essentially driven by local effects. The dependence of C(α) distances on ψ is governed by interactions between the σ system of the C(α) moiety and the C-O π system of the peptide bond. Maximum and minimum values for each bond distance are found for conformations with the specific bond perpendicular and parallel to the adjacent CONH peptide plane, respectively. On the other hand, the variability of the C-O and C-N distances is re...

Journal of computational chemistry, 2004

The role of intraresidue interactions in determining the conformational behavior of polypeptides ... more The role of intraresidue interactions in determining the conformational behavior of polypeptides is analyzed by means of density functional and post-Hartree-Fock computations on the alanine dipeptide analog and other model compounds. Our computations show that the accuracy of current density functionals is sufficient for H-bond, electrostatic, inductive, and short-range repulsive interactions, whereas medium-range attractions between electron-rich atoms and/or bonds are underestimated. This leads, in turn, to an underestimation of the stability of helical structures w.r.t. extended or folded conformers involving H-bonds. Those results could pave the route for devising local ad hoc corrections able to significantly improve structural and dynamic predictions for polypeptides issuing from DFT computations.

The journal of physical chemistry. A, Jan 18, 2015

The fluorescence properties of the 8-hydroxy-2'-deoxyguanosine (8-oxo-dG) in aqueous solution... more The fluorescence properties of the 8-hydroxy-2'-deoxyguanosine (8-oxo-dG) in aqueous solution at pH 6.5 are studied by steady-state spectroscopy and femtosecond fluorescence up-conversion and compared with those of 2'-deoxyguanine (dG) and 2'-deoxyguanine monophosphate (dGMP). The steady-state fluorescence spectrum of 8-oxo-dG is composed of a broad band that peaks at 356 nm and extends over the entire visible spectral region, and its fluorescence quantum yield is twice that of dG/dGMP. After excitation at 267 nm, the initial fluorescence anisotropy at all wavelengths is lower than 0.1, giving evidence of an ultrafast internal conversion (<100 fs) between the two lowest excited ππ* states (Lb and La). The fluorescence decays of 8-oxo-dG are biexponential with an average lifetime of 0.7 ± 0.1 ps, which is about two times longer than that of dGMP. In contrast with dGMP, only a moderate dynamical shift (∼1400 vs 10 000 cm(-1)) of the fluorescence spectra of 8-oxo-dG is o...

The journal of physical chemistry. B, Jan 20, 2005

The physicochemical effects modulating the conformational behavior and the rate of intramolecular... more The physicochemical effects modulating the conformational behavior and the rate of intramolecular dissociative electron transfer in phthalimide-Aibn-peroxide peptides (n = 0-3) have been studied by an integrated density functional/continuum solvent model. We found that three different orientations of the phthalimide ring are possible, labeled Phihel, PhiC7, and PhipII. In the condensed phase, they are very close in energy when the system is neutral and short. When the peptide chain length increases and the system is negatively charged, Phihel becomes instead the most stable conformer. Our calculations confirm that the 3(10)-helix is the most stable secondary structure for the peptide bridge. However, upon charge injection in the phthalimide end of the phthalimide-Aib3-peroxide, the peptide bridge can adopt an alpha-helix conformation as well. The study of the dependence of the frontier orbitals on the length and on the conformation of the peptide bridge (in agreement with experiment...

The Journal of Physical Chemistry A, 2015

We study the absorption and emission electronic spectra in an aqueous solution of N-methyl-6-oxyq... more We study the absorption and emission electronic spectra in an aqueous solution of N-methyl-6-oxyquinolinium betaine (MQ), an interesting dye characterized by a large change of polarity and H-bond ability between the ground (S0) and the excited (S1) states. To that end we compare alternative approaches based either on explicit solvent models and density functional theory (DFT)/molecular-mechanics (MM) calculations or on DFT calculations on clusters models embedded in a polarizable continuum (PCM). In the first approach (ClMD), the spectrum is computed according to the classical Franck-Condon principle, from the dispersion of the time-dependent (TD)-DFT vertical transitions at selected snapshots of molecular dynamics (MD) on the initial state. In the cluster model (Qst) the spectrum is simulated by computing the quantum vibronic structure, estimating the inhomogeneous broadening from state-specific TD-DFT/PCM solvent reorganization energies. While both approaches provide absorption and emission spectral shapes in nice agreement with experiment, the Stokes shift is perfectly reproduced by Qst calculations if S0 and S1 clusters are selected on the grounds of the MD trajectory. Furthermore, Qst spectra better fit the experimental line shape, mostly in absorption. Comparison of the predictions of the two approaches is very instructive: the positions of Qst and ClMD spectra are shifted due to the different solvent models and the ClMD spectra are narrower than the Qst ones, because MD underestimates the width of the vibrational density of states of the high-frequency modes coupled to the electronic transition. On the other hand, both Qst and ClMD approaches highlight that the solvent has multiple and potentially opposite effects on the spectral width, so that the broadening due to solute-solvent vibrations and electrostatic interaction with bulk solvent is (partially) counterbalanced by a narrowing of the contribution due to the solute vibrational modes. Qst analysis evidences a pure quantum broadening effect of the spectra in water due to vibronic progressions along the solute/solvent H-bonds.

The effect substitutions at nitrogen atom 1 of thymine and nitrogen atom 9 of adenine have on low... more The effect substitutions at nitrogen atom 1 of thymine and nitrogen atom 9 of adenine have on lowest energy excited electronic states has been studied by means of time-dependent PBE0 calculations in aqueous solution.

Journal of Molecular Structure: THEOCHEM, 1998

The X-ray structure of molsidomine (3-morpholine-sydnoneimine) reveals a widening of the CNC angl... more The X-ray structure of molsidomine (3-morpholine-sydnoneimine) reveals a widening of the CNC angle of morpholine substituted at the N 3 atom of the sydnone moiety. This might be due to lone-pair delocalization, since sydnone is a mesoionic aromatic heterocycle, and its N 3 nitrogen atom is expected to undergo an important p-electron loss. With a view to clarifying this problem, the results of an extensive analysis of the literature and theoretical computations carried out with standard empirical and ab initio methods have been discussed with the help of the IML-EH method, a version of the EHT method which includes hybridization, a localization and mutual charge adjustment. Although the computational results can be interpreted as favouring the prediction that N 3 of sydnones is p-electron deficient, no significant delocalization of the lone pair of the amine substituent is predicted. The CNC angle widening appears to be due to hybridization-polarization effects. In the course of the paper, numerical information relevant to further research on the sydnones and on the N-N bond is presented and discussed. ᭧