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...
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...
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-Ã -vis comparison between experimental and computed band positions and shapes. Next, the whole series of halogenated azetidinones is analyzed, sh...
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.
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).
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.
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.
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.
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...
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...
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-Ã -vis comparison between experimental and computed band positions and shapes. Next, the whole series of halogenated azetidinones is analyzed, sh...
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.
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).
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.
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.
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.
Uploads