Vincenzo Barone | Scuola Normale Superiore (original) (raw)

Papers by Vincenzo Barone

The Astronomical Journal, 2017

To gain information on the abiotic synthesis of the building blocks of life from simple molecules... more To gain information on the abiotic synthesis of the building blocks of life from simple molecules, and their subsequent chemical evolution to biological systems, the starting point is the identification of target species in Titan-like planets; i.e., planets that resemble the primitive Earth, as well as in Earth-like planets in the habitable zone of their star, namely planets where life can be already originated. In this scenario, molecular spectroscopy plays a crucial role because spectroscopic signatures are at the basis of an unequivocal proof for the presence of these target molecules. Thanks to advances in many different techniques and NASA's successful Kepler exoplanet transit mission, thousands of diverse planets outside of our solar system have been discovered. The James Webb Space Telescope (JWST), scheduled to be launched in 2018, will be very helpful in the identification of biosignature gases in Earth-like planets' atmospheres and prebiotic molecule signatures in Titan-like atmospheres, by observing their absorption during transits. Although the search for key-target molecules in exoplanet atmospheres can be carried out by the JWST Transit Spectroscopy in the infrared (IR) region (0.6-29 μm wavelength range), opportunities for their detection in protostellar cores, protoplanetary disks, and on Titan are also offered by interferometric high spectral and spatial resolution observations using the Atacama Large Millimeter/submillimeter Array. In the present work, target molecules have been selected, and their spectroscopic characterization presented in view of supporting their infrared and complementary millimeter/submillimeter-wave spectral observations. In detail, the selected target molecules include: (1) the three-membered oxygen-containing heterocycles, oxirane and protonated oxirane; (2) the cyclopropenyl cation and its methyl derivative; (3) two examples of ortho-and peri-fused tri-cyclic aromatic rings, i.e., the phenalenyl cation (C H 13 9 +) and anion (C H 13 9-); and (4) uracil, a specific RNA base.

Journal of chemical theory and computation, Jan 8, 2016

We describe an integrated computational strategy aimed at providing reliable thermochemical and k... 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) ...

Journal of chemical theory and computation, Jan 12, 2017

We present the implementation of the SOlid State (SoS)NMR module for the simulation of several 1D... 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...

Canadian Journal of Chemistry, 2016

In this work, semi-experimental (SE) and theoretical equilibrium geometries of 10 sulfur-containi... 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...

DOAJ (DOAJ: Directory of Open Access Journals), 2012

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

The aim of this paper is twofold. First, we want to report the extension of our virtual multifreq... 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...

Journal of Chemical Theory and Computation, 2015

The Journal of Physical Chemistry, 1991

ABSTRACT

The Journal of Physical Chemistry, 1993

The structure and EPR parameters of dihydronitrosyl radical HzNO have been investigated by highly... more The structure and EPR parameters of dihydronitrosyl radical HzNO have been investigated by highly correlated ab-initio methods. The relative stabilities of planar and pyramidal structures have been analyzed in detail, taking also into account the effect of small-amplitude vibrations perpendicular to the inversion motion. Vibrational averaging of hyperfine coupling constants has been computed by a quantum-mechanical treatment based on the vibrational adiabatic zero curvature approximation. The general picture emerging from this study, substantiated by several checks, consists in a quasi-planar molecule with a nearly free inversion motion for out-of-plane angles as large as 30'. Due to compensation of different terms, vibrational averaging gives results very close to those obtained from a static treatment at an out-of-plane angle of about 20'. An equally important outcome of this work is the introduction of a general and reliable ab-initio strategy for the study of magnetic properties in nonrigid radicals.

The Journal of Physical Chemistry A, 2015

This work aims at extending the semi-experimental (SE) approach for deriving accurate equilibrium... more This work aims at extending the semi-experimental (SE) approach for deriving accurate equilibrium structures to large molecular systems of organic and biological interest. SE equilibrium structures are derived by a least-squares fit of the structural parameters to the experimental ground-state rotational constants of several isotopic species corrected by vibrational contributions computed by quantum mechanical (QM) methods. A systematic benchmark study on 21 small molecules (CCse set) is carried * To whom correspondence should be addressed † Scuola Normale Superiore ‡ Dipartimento di Chimica "Giacomo Ciamician" ¶ ICCOM-CNR out to evaluate the performance of hybrid density functionals (in particular B3LYP) in the derivation of vibrational corrections to rotational constants. The resulting SE equilibrium structures show a very good agreement with the corresponding geometries obtained employing post-Hartree-Fock vibrational corrections. The use of B3LYP in conjunction with the double-ζ SNSD basis set strongly reduces the computational costs, thus allowing for the evaluation of accurate SE equilibrium structures for medium-sized molecular systems. On these grounds, an additional set of 26 SE equilibrium structures including the most common organic moieties has been set up by collecting the most accurate geometries available in the literature together with new determinations from the present work. The overall set of 47 SE equilibrium structures determined using B3LYP/SNSD vibrational corrections (B3se set) provides a high quality benchmark for validating the structural predictions of other experimental and/or computational approaches. Finally, we present a new strategy (referred to as template approach) to deal with the cases for which it is not possible to fit all geometrical parameters due to the lack of experimental data.

The Journal of chemical physics, 2014

Oxirane derivatives are the most used benchmarks for chiroptical spectroscopies in view of their ... more Oxirane derivatives are the most used benchmarks for chiroptical spectroscopies in view of their small size and relative rigidity. The molecular structure, vibrational harmonic and anharmonic frequencies, and infrared intensities of the ground electronic states are analyzed in this paper. Equilibrium structure and harmonic force fields have been evaluated by means of high-level quantum-chemical calculations at the coupled-cluster level including single and double excitations together with a perturbative treatment of triples (CCSD(T)). Extrapolation to the complete basisset limit as well as core-correlation effects have also been taken into account. Anharmonic contributions have been computed at the CCSD(T)/cc-pVTZ level for trans-2,3-dideuterooxirane. These data can serve as references to evaluate the accuracy of less expensive computational approaches rooted in the density functional theory (DFT). The latter have been used within hybrid CC/DFT approaches, which have been applied to simulate fully anharmonic infrared (IR) spectra. Finally, the best theoretical estimates of the equilibrium structures and vibrational wavenumbers are compared to the most accurate experimental data and show in all cases very good agreement, i.e., within 0.001 Å, 0.1 degrees and 10 cm −1 and 0.5 km mol −1 , for bond lengths, angles, wavenumbers and IR intensities, respectively.

Journal of Computational Chemistry, 2014

This article presents the setup and implementation of a graphical user interface (VMS-Draw) for a... 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.

The Journal of Physical Chemistry A, 2014

A comprehensive study of the molecular structure and IR spectrum of cis and trans acrolein has be... more A comprehensive study of the molecular structure and IR spectrum of cis and trans acrolein has been performed by an integrated computational approach coupling methods rooted in the coupled-cluster ansatz and the density functional theory. From the one side, DFT anharmonic force fields allow us to determine very reliable semiexperimental structures for both isomers, which are in remarkable agreement with the geometries issuing from CCSD(T) computations accounting for the extrapolation to the complete basis set and core correlation. The same kind of coupled-cluster computations provide dipole moment, relative energies, and interconversion barrier in remarkable agreement with experiments. Finally, harmonic CCSD(T) results coupled to DFT evaluation of mechanical and electrical anharmonicity allow us, in the framework of second-order perturbative vibrational theory, to confirm most of the experimental assignments of IR spectra, and to suggest some additional interpretations for congested regions including fundamental bands together with overtones and combination bands.

Phys. Chem. Chem. Phys., 2014

Toward a comprehensive and robust computational protocol for simulation of fully anharmonic vibra... more 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).

Phys. Chem. Chem. Phys., 2014

Computation of full infrared (IR) and Raman spectra (including absolute intensities and transitio... more 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 a robust and user-friendly virtual spectrometer rooted into the 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.

Physical Chemistry Chemical Physics, 2014

An integrated computational approach allowed an unbiased analysis of optical and structural prope... more An integrated computational approach allowed an unbiased analysis of optical and structural properties of alizarin-based pigments, which can be directly compared with experimental results. Madder lake pigments have been modeled by Mg(II)-and Al(III)-coordinated alizarin taking into account solvation and metal-linkage effects, responsible for colour modifications. Moreover, different environmental conditions have been analyzed for free alizarin, showing in all cases semiquantitative agreement with experimental spectroscopic data (UV-VIS). Our results point out the ability of in silico approaches to unravel the subtle interplay of stereo-electronic, dynamic, and environmental effects in tuning the physico-chemical properties of pigments relevant for cultural heritage.

Physical Chemistry Chemical Physics, 2013

The structures, relative stabilities, and infrared spectra of the six low-energy conformers of gl... more The structures, relative stabilities, and infrared spectra of the six low-energy conformers of glycine have been characterized by a state-of-the-art quantum-mechanical approach allowing the bond distances, conformational enthalpies and vibrational frequencies to be determined well within chemical accuracy. Transition state structures governing interconversion among the different energy minima have also been characterized. In detail, the gas-phase thermodynamic properties (at 15 K and 410 K) of the glycine conformers considered have been obtained with a 1 kJ•mol −1 accuracy, and it has been shown that the employment of DFT geometries usually reduces such accuracy by at most 0.1 kJ•mol −1. As concerns molecular structures, the use of two different composite schemes allowed us to further confirm the suitability of a rather cost-effective approach and provide geometrical parameters with an overall accuracy better than 0.002 Å for distances and 1 degree for angles. Thanks to a hybrid CC/DFT approach, the infrared spectra of all conformers considered and of several deuterated isotopologues have been reproduced (when experimental data were available) or predicted with an accuracy of 10 cm −1. Finally, the joint thermodynamic and spectroscopic investigation allowed us to shed some light on the possible observation of elusive conformers. On the whole, the high accuracy of the computational results allows us to draw a fully consistent interpretation of the available experimental data and to obtain a more complete characterization of the potential energy surface of glycine. † Electronic Supplementary Information (ESI) available: (i) Equilibrium structures computed at the MP2 level using different basis

Physical Chemistry Chemical Physics, 2013

The Joyce program is augmented with several new features, including the user friendly Ulysses GUI... 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.

Organic & Biomolecular Chemistry, 2008

The role of local geometric and stereo-electronic effects in tuning the preference for different ... 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.

Organic & Biomolecular Chemistry, 2006

The role of local geometric and stereo-electronic effects in tuning the radiation-induced formati... 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.

The Astronomical Journal, 2017

To gain information on the abiotic synthesis of the building blocks of life from simple molecules... more To gain information on the abiotic synthesis of the building blocks of life from simple molecules, and their subsequent chemical evolution to biological systems, the starting point is the identification of target species in Titan-like planets; i.e., planets that resemble the primitive Earth, as well as in Earth-like planets in the habitable zone of their star, namely planets where life can be already originated. In this scenario, molecular spectroscopy plays a crucial role because spectroscopic signatures are at the basis of an unequivocal proof for the presence of these target molecules. Thanks to advances in many different techniques and NASA's successful Kepler exoplanet transit mission, thousands of diverse planets outside of our solar system have been discovered. The James Webb Space Telescope (JWST), scheduled to be launched in 2018, will be very helpful in the identification of biosignature gases in Earth-like planets' atmospheres and prebiotic molecule signatures in Titan-like atmospheres, by observing their absorption during transits. Although the search for key-target molecules in exoplanet atmospheres can be carried out by the JWST Transit Spectroscopy in the infrared (IR) region (0.6-29 μm wavelength range), opportunities for their detection in protostellar cores, protoplanetary disks, and on Titan are also offered by interferometric high spectral and spatial resolution observations using the Atacama Large Millimeter/submillimeter Array. In the present work, target molecules have been selected, and their spectroscopic characterization presented in view of supporting their infrared and complementary millimeter/submillimeter-wave spectral observations. In detail, the selected target molecules include: (1) the three-membered oxygen-containing heterocycles, oxirane and protonated oxirane; (2) the cyclopropenyl cation and its methyl derivative; (3) two examples of ortho-and peri-fused tri-cyclic aromatic rings, i.e., the phenalenyl cation (C H 13 9 +) and anion (C H 13 9-); and (4) uracil, a specific RNA base.

Journal of chemical theory and computation, Jan 8, 2016

We describe an integrated computational strategy aimed at providing reliable thermochemical and k... 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) ...

Journal of chemical theory and computation, Jan 12, 2017

We present the implementation of the SOlid State (SoS)NMR module for the simulation of several 1D... 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...

Canadian Journal of Chemistry, 2016

In this work, semi-experimental (SE) and theoretical equilibrium geometries of 10 sulfur-containi... 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...

DOAJ (DOAJ: Directory of Open Access Journals), 2012

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

The aim of this paper is twofold. First, we want to report the extension of our virtual multifreq... 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...

Journal of Chemical Theory and Computation, 2015

The Journal of Physical Chemistry, 1991

ABSTRACT

The Journal of Physical Chemistry, 1993

The structure and EPR parameters of dihydronitrosyl radical HzNO have been investigated by highly... more The structure and EPR parameters of dihydronitrosyl radical HzNO have been investigated by highly correlated ab-initio methods. The relative stabilities of planar and pyramidal structures have been analyzed in detail, taking also into account the effect of small-amplitude vibrations perpendicular to the inversion motion. Vibrational averaging of hyperfine coupling constants has been computed by a quantum-mechanical treatment based on the vibrational adiabatic zero curvature approximation. The general picture emerging from this study, substantiated by several checks, consists in a quasi-planar molecule with a nearly free inversion motion for out-of-plane angles as large as 30'. Due to compensation of different terms, vibrational averaging gives results very close to those obtained from a static treatment at an out-of-plane angle of about 20'. An equally important outcome of this work is the introduction of a general and reliable ab-initio strategy for the study of magnetic properties in nonrigid radicals.

The Journal of Physical Chemistry A, 2015

This work aims at extending the semi-experimental (SE) approach for deriving accurate equilibrium... more This work aims at extending the semi-experimental (SE) approach for deriving accurate equilibrium structures to large molecular systems of organic and biological interest. SE equilibrium structures are derived by a least-squares fit of the structural parameters to the experimental ground-state rotational constants of several isotopic species corrected by vibrational contributions computed by quantum mechanical (QM) methods. A systematic benchmark study on 21 small molecules (CCse set) is carried * To whom correspondence should be addressed † Scuola Normale Superiore ‡ Dipartimento di Chimica "Giacomo Ciamician" ¶ ICCOM-CNR out to evaluate the performance of hybrid density functionals (in particular B3LYP) in the derivation of vibrational corrections to rotational constants. The resulting SE equilibrium structures show a very good agreement with the corresponding geometries obtained employing post-Hartree-Fock vibrational corrections. The use of B3LYP in conjunction with the double-ζ SNSD basis set strongly reduces the computational costs, thus allowing for the evaluation of accurate SE equilibrium structures for medium-sized molecular systems. On these grounds, an additional set of 26 SE equilibrium structures including the most common organic moieties has been set up by collecting the most accurate geometries available in the literature together with new determinations from the present work. The overall set of 47 SE equilibrium structures determined using B3LYP/SNSD vibrational corrections (B3se set) provides a high quality benchmark for validating the structural predictions of other experimental and/or computational approaches. Finally, we present a new strategy (referred to as template approach) to deal with the cases for which it is not possible to fit all geometrical parameters due to the lack of experimental data.

The Journal of chemical physics, 2014

Oxirane derivatives are the most used benchmarks for chiroptical spectroscopies in view of their ... more Oxirane derivatives are the most used benchmarks for chiroptical spectroscopies in view of their small size and relative rigidity. The molecular structure, vibrational harmonic and anharmonic frequencies, and infrared intensities of the ground electronic states are analyzed in this paper. Equilibrium structure and harmonic force fields have been evaluated by means of high-level quantum-chemical calculations at the coupled-cluster level including single and double excitations together with a perturbative treatment of triples (CCSD(T)). Extrapolation to the complete basisset limit as well as core-correlation effects have also been taken into account. Anharmonic contributions have been computed at the CCSD(T)/cc-pVTZ level for trans-2,3-dideuterooxirane. These data can serve as references to evaluate the accuracy of less expensive computational approaches rooted in the density functional theory (DFT). The latter have been used within hybrid CC/DFT approaches, which have been applied to simulate fully anharmonic infrared (IR) spectra. Finally, the best theoretical estimates of the equilibrium structures and vibrational wavenumbers are compared to the most accurate experimental data and show in all cases very good agreement, i.e., within 0.001 Å, 0.1 degrees and 10 cm −1 and 0.5 km mol −1 , for bond lengths, angles, wavenumbers and IR intensities, respectively.

Journal of Computational Chemistry, 2014

This article presents the setup and implementation of a graphical user interface (VMS-Draw) for a... 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.

The Journal of Physical Chemistry A, 2014

A comprehensive study of the molecular structure and IR spectrum of cis and trans acrolein has be... more A comprehensive study of the molecular structure and IR spectrum of cis and trans acrolein has been performed by an integrated computational approach coupling methods rooted in the coupled-cluster ansatz and the density functional theory. From the one side, DFT anharmonic force fields allow us to determine very reliable semiexperimental structures for both isomers, which are in remarkable agreement with the geometries issuing from CCSD(T) computations accounting for the extrapolation to the complete basis set and core correlation. The same kind of coupled-cluster computations provide dipole moment, relative energies, and interconversion barrier in remarkable agreement with experiments. Finally, harmonic CCSD(T) results coupled to DFT evaluation of mechanical and electrical anharmonicity allow us, in the framework of second-order perturbative vibrational theory, to confirm most of the experimental assignments of IR spectra, and to suggest some additional interpretations for congested regions including fundamental bands together with overtones and combination bands.

Phys. Chem. Chem. Phys., 2014

Toward a comprehensive and robust computational protocol for simulation of fully anharmonic vibra... more 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).

Phys. Chem. Chem. Phys., 2014

Computation of full infrared (IR) and Raman spectra (including absolute intensities and transitio... more 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 a robust and user-friendly virtual spectrometer rooted into the 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.

Physical Chemistry Chemical Physics, 2014

An integrated computational approach allowed an unbiased analysis of optical and structural prope... more An integrated computational approach allowed an unbiased analysis of optical and structural properties of alizarin-based pigments, which can be directly compared with experimental results. Madder lake pigments have been modeled by Mg(II)-and Al(III)-coordinated alizarin taking into account solvation and metal-linkage effects, responsible for colour modifications. Moreover, different environmental conditions have been analyzed for free alizarin, showing in all cases semiquantitative agreement with experimental spectroscopic data (UV-VIS). Our results point out the ability of in silico approaches to unravel the subtle interplay of stereo-electronic, dynamic, and environmental effects in tuning the physico-chemical properties of pigments relevant for cultural heritage.

Physical Chemistry Chemical Physics, 2013

The structures, relative stabilities, and infrared spectra of the six low-energy conformers of gl... more The structures, relative stabilities, and infrared spectra of the six low-energy conformers of glycine have been characterized by a state-of-the-art quantum-mechanical approach allowing the bond distances, conformational enthalpies and vibrational frequencies to be determined well within chemical accuracy. Transition state structures governing interconversion among the different energy minima have also been characterized. In detail, the gas-phase thermodynamic properties (at 15 K and 410 K) of the glycine conformers considered have been obtained with a 1 kJ•mol −1 accuracy, and it has been shown that the employment of DFT geometries usually reduces such accuracy by at most 0.1 kJ•mol −1. As concerns molecular structures, the use of two different composite schemes allowed us to further confirm the suitability of a rather cost-effective approach and provide geometrical parameters with an overall accuracy better than 0.002 Å for distances and 1 degree for angles. Thanks to a hybrid CC/DFT approach, the infrared spectra of all conformers considered and of several deuterated isotopologues have been reproduced (when experimental data were available) or predicted with an accuracy of 10 cm −1. Finally, the joint thermodynamic and spectroscopic investigation allowed us to shed some light on the possible observation of elusive conformers. On the whole, the high accuracy of the computational results allows us to draw a fully consistent interpretation of the available experimental data and to obtain a more complete characterization of the potential energy surface of glycine. † Electronic Supplementary Information (ESI) available: (i) Equilibrium structures computed at the MP2 level using different basis

Physical Chemistry Chemical Physics, 2013

The Joyce program is augmented with several new features, including the user friendly Ulysses GUI... 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.

Organic & Biomolecular Chemistry, 2008

The role of local geometric and stereo-electronic effects in tuning the preference for different ... 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.

Organic & Biomolecular Chemistry, 2006

The role of local geometric and stereo-electronic effects in tuning the radiation-induced formati... 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.