Vincenzo Barone
Scuola Normale Superiore, Classe di Scienze, Faculty Member
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We describe an integrated computational strategy aimed at providing reliable thermochemical and kinetic information on the formation processes of astrochemical complex organic molecules. The approach involves state-of-the-art... more
We describe an integrated computational strategy aimed at providing reliable thermochemical and kinetic information on the formation processes of astrochemical complex organic molecules. The approach involves state-of-the-art quantum-mechanical computations, second-order vibrational perturbation theory, and kinetic models based on capture and transition state theory together with the master equation approach. Notably, tunneling, quantum reflection, and leading anharmonic contributions are accounted for in our model. Formamide has been selected as a case study in view of its interest as a precursor in the abiotic amino acid synthesis. After validation of the level of theory chosen for describing the potential energy surface, we have investigated several pathways of the OH + CH2NH and NH2 + H2CO reaction channels. Our results show that both reaction channels are essentially barrierless (in the sense that all relevant transition states lie below or only marginally above the reactants) ...
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We present the implementation of the SOlid State (SoS)NMR module for the simulation of several 1D and 2D NMR spectra of all the elements in the periodic table in the virtual multifrequency spectrometer (VMS). This module is fully... more
We present the implementation of the SOlid State (SoS)NMR module for the simulation of several 1D and 2D NMR spectra of all the elements in the periodic table in the virtual multifrequency spectrometer (VMS). This module is fully integrated with the graphical user interface of VMS (VMS-Draw) [Licari et al., J. Comput. Chem. 36, 2015, 321-334], a freeware tool which allows a user-friendly handling of structures and analyses of advanced spectroscopical properties of chemical compounds - from model systems to real-world applications. Besides the numerous modules already available in VMS for the study of electronic, optical, vibrational, vibronic and EPR properties, here the simulation of NMR spectra is presented with a particular emphasis on those techniques usually employed to investigate solid state systems. The SOSNMR module benefits from its ability to work under both periodic and non-periodic conditions, such that small molecules/molecular clusters can be treated, as well as exten...
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In this work, semi-experimental (SE) and theoretical equilibrium geometries of 10 sulfur-containing organic molecules, as well as 4 oxygenated ones, are determined by means of a computational protocol based on density functional theory.... more
In this work, semi-experimental (SE) and theoretical equilibrium geometries of 10 sulfur-containing organic molecules, as well as 4 oxygenated ones, are determined by means of a computational protocol based on density functional theory. The results collected in the present paper further enhance our online database of accurate SE equilibrium molecular geometries, adding 13 new molecules containing up to 8 atoms, for 12 of which, to the best of our knowledge, the first SE equilibrium structure is reported. We focus in particular on sulfur-containing compounds, aiming both to provide new accurate data on some rather important chemical moieties, only marginally represented in the literature of the field, and to examine the structural features of carbon–sulfur bonds in the light of the previously presented linear regression approach. The structural changes issuing from substitution of oxygen by sulfur are discussed to get deeper insights on how modifications in electronic structure and n...
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The aim of this paper is twofold. First, we want to report the extension of our virtual multifrequency spectrometer (VMS) to anharmonic intensities for Raman Optical Activity (ROA) with the full inclusion of first- and second-order... more
The aim of this paper is twofold. First, we want to report the extension of our virtual multifrequency spectrometer (VMS) to anharmonic intensities for Raman Optical Activity (ROA) with the full inclusion of first- and second-order resonances for both frequencies and intensities in the framework of the generalized second-order vibrational perturbation theory (GVPT2) for all kinds of vibrational spectroscopies. Then, from a more general point of view, we want to present and validate the performance of VMS for the parallel analysis of different vibrational spectra for medium-sized molecules (IR, Raman, VCD, ROA) including both mechanical and electric/magnetic anharmonicity. For the well-known methyloxirane benchmark, careful selection of density functional, basis set, and resonance tresholds permitted to reach qualitative and quantitative vis-à-vis comparison between experimental and computed band positions and shapes. Next, the whole series of halogenated azetidinones is analyzed, sh...
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This article presents the setup and implementation of a graphical user interface (VMS-Draw) for a virtual multifrequency spectrometer. Special attention is paid to ease of use, generality and robustness for a panel of spectroscopic... more
This article presents the setup and implementation of a graphical user interface (VMS-Draw) for a virtual multifrequency spectrometer. Special attention is paid to ease of use, generality and robustness for a panel of spectroscopic techniques and quantum mechanical approaches. Depending on the kind of data to be analyzed, VMS-Draw produces different types of graphical representations, including two-dimensional or three-dimesional (3D) plots, bar charts, or heat maps. Among other integrated features, one may quote the convolution of stick spectra to obtain realistic line-shapes. It is also possible to analyze and visualize, together with the structure, the molecular orbitals and/or the vibrational motions of molecular systems thanks to 3D interactive tools. On these grounds, VMS-Draw could represent a useful additional tool for spectroscopic studies integrating measurements and computer simulations.
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Toward a comprehensive and robust computational protocol for simulation of fully anharmonic vibrational (IR) spectra of nucleic acid base complexes and their adsorption on solid supports (organic/inorganic).
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The Joyce program is augmented with several new features, including the user friendly Ulysses GUI, the possibility of complete excited state parameterization and a more flexible treatment of the force field electrostatic terms. A first... more
The Joyce program is augmented with several new features, including the user friendly Ulysses GUI, the possibility of complete excited state parameterization and a more flexible treatment of the force field electrostatic terms. A first validation is achieved by successfully comparing results obtained with Joyce2.0 to literature ones, obtained for the same set of benchmark molecules. The parameterization protocol is also applied to two other larger molecules, namely nicotine and a coumarin based dye. In the former case, the parameterized force field is employed in molecular dynamics simulations of solvated nicotine, and the solute conformational distribution at room temperature is discussed. Force fields parameterized with Joyce2.0, for both the dye's ground and first excited electronic states, are validated through the calculation of absorption and emission vertical energies with molecular mechanics optimized structures. Finally, the newly implemented procedure to handle polarizable force fields is discussed and applied to the pyrimidine molecule as a test case.
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The role of local geometric and stereo-electronic effects in tuning the preference for different cross-linked adducts between thymine and purinic bases has been analyzed by a computational approach rooted in density functional theory. Our... more
The role of local geometric and stereo-electronic effects in tuning the preference for different cross-linked adducts between thymine and purinic bases has been analyzed by a computational approach rooted in density functional theory. Our study points out that G--T and T--G tandem lesions are produced according to the same mechanism as A--T and T--A intrastrand adducts, and in both cases purine--T adducts are preferred rather than the opposite sequences. Moreover, use of conceptual DFT tools allows the rationalization of the preferential occurrence of G--T and T--G tandem lesions in place of their A--T and T--A counterparts.
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The role of local geometric and stereo-electronic effects in tuning the radiation-induced formation of intrastrand crosslinks between adenine and thymine has been analyzed by a computational approach rooted in density functional theory.... more
The role of local geometric and stereo-electronic effects in tuning the radiation-induced formation of intrastrand crosslinks between adenine and thymine has been analyzed by a computational approach rooted in density functional theory. Our study points out that together with steric accessibility, stereo-electronic effects play a major role in determining the reaction mechanism and the observed predominance of the thymine-adenine lesion over the opposite sequence isomer.
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ABSTRACT Spectroscopic observables can be used for monitoring relaxation processes of molecules. In particular, electron spin resonance of stable multi-radicals is sensitive to the details of the rotational and internal dynamics in rigid... more
ABSTRACT Spectroscopic observables can be used for monitoring relaxation processes of molecules. In particular, electron spin resonance of stable multi-radicals is sensitive to the details of the rotational and internal dynamics in rigid and flexible molecules. Integration with advanced theoretical/computational methods proves to be particularly effective to acquire direct information on long-range relaxation processes, based on molecular dynamics, multi-scale approaches and coarse-graining treatments. Together, experimental data and computational interpretation provide a way to understand the effect of chemical changes on specific systems. In this paper we review computational tools aimed at the characterisation of dynamical properties of molecules gathered from electron spin resonance measurements. Stochastic models are employed, based on a number of structural parameters that are calculated at atomistic and/or mesoscopic level depending on their nature. Open source software tools built as user-friendly ‘virtual spectroscopes’ targeted for use by experimentalists are provided as a kind of extension of the laboratory equipment. An overview of their range of applicability is provided.
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A general quantum‐mechanical protocol for the study of nonrigid free radicals has been applied to the series CH, CHF, CHF, and CF. Electronic structures have been computed by highly correlated ab initio methods and vibrational modulation... more
A general quantum‐mechanical protocol for the study of nonrigid free radicals has been applied to the series CH, CHF, CHF, and CF. Electronic structures have been computed by highly correlated ab initio methods and vibrational modulation effects have been studied by a nonrigid ...
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ABSTRACT Abstract The graphical description of molecular systems has always been a fundamental topic of chemistry. The introduction of interactive computer graphics led to the development of a new research field known as computer... more
ABSTRACT Abstract The graphical description of molecular systems has always been a fundamental topic of chemistry. The introduction of interactive computer graphics led to the development of a new research field known as computer molecular graphics. The aim of this article is to provide a survey on the vast field of molecular graphics, describing the techniques and the algorithms used to create computer-generated representations of molecular systems. The emerging role of immersive virtual reality and natural user interfaces is also examined. Finally, some applications are presented as examples about the role of graphical user interfaces in modern chemical research.
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Research Interests: Biochemistry, Computer Science, Computer Graphics, Biophysics, Quantum Theory, and 13 moreMedicine, Analysis, Software, Isotopologue, Implementation, Computer User Interface Design, Determination, Equilibrium, Coordinate, THEORETICAL AND COMPUTATIONAL CHEMISTRY, Molecular Conformation, MSR, and Molecule
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... and Kanamori to develop the qualitative rules 7 that aided experimentalists for many years and were recovered by the orbital model of the exchange ... et al., 8 a series of papers appeared dealing with the calculation of the... more
... and Kanamori to develop the qualitative rules 7 that aided experimentalists for many years and were recovered by the orbital model of the exchange ... et al., 8 a series of papers appeared dealing with the calculation of the singlet−triplet splitting in binuclear copper(II) complexes. ...
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Interpretation of structural properties and dynamic behavior of molecular systems is of fundamental importance to understand their stability, chemical reactivity, and catalytic action. While information can be gained, in principle, by a... more
Interpretation of structural properties and dynamic behavior of molecular systems is of fundamental importance to understand their stability, chemical reactivity, and catalytic action. While information can be gained, in principle, by a variety of spectroscopic techniques, the interpretation of the rich indirect information that can be inferred from the analysis of experimental spectra is seldom straightforward because of the subtle
Research Interests: Quantum Chemistry, Soft Matter, Electron Spin Resonance, Nuclear Magnetic Resonance, Self Assembly, and 15 moreNanoparticles, DNA, Microemulsion, Colloids, Environmental Effect, Microemulsions, Infrared, Excited states, Time Dependent, Gel, Structural Properties, THEORETICAL AND COMPUTATIONAL CHEMISTRY, Spectral Properties, Spectroscopic Techniques, and Level
... glycine radical in its zwitterionic form Vincenzo Barone a Carlo Adamo b Andre Grand c Robert Subra da Dipartiraento di Chimica, Universit Federico 11, via Mezzocannone 4, 80134 Napoli, Italy b Dipartiraento di Chiraica, Universit... more
... glycine radical in its zwitterionic form Vincenzo Barone a Carlo Adamo b Andre Grand c Robert Subra da Dipartiraento di Chimica, Universit Federico 11, via Mezzocannone 4, 80134 Napoli, Italy b Dipartiraento di Chiraica, Universit della Basilicata, via Nazario Sauro 85, 85100 ...