title: Joyce and Ulysses: integrated and user-friendly tools for the parameterization of intramolecular force fields from quantum mechanical data.
abstract: 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.
authors: Scuola Normale Superiore, piazza dei Cavalieri 7, I-56126 Pisa, Italy.
authors: Vincenzo
authors: V
authors: Barone
authors: Ivo
authors: I
authors: Cacelli
authors: Nicola
authors: N
authors: De Mitri
authors: Daniele
authors: D
authors: Licari
authors: Susanna
authors: S
authors: Monti
authors: Giacomo
authors: G
authors: Prampolini
mesh_terms: D001713:Biphenyl Compounds / Q000737:chemistry; D020407:Internet; D056004:Molecular Dynamics Simulation; D010545:Peroxides / Q000737:chemistry; D011743:Pyrimidines / Q000737:chemistry; D011789:Quantum Theory; D012984:Software; D014584:User-Computer Interface
chemical_list: D001713:Biphenyl Compounds; D010545:Peroxides; D011743:Pyrimidines; C010574:biphenyl; C030986:pyrimidine