JOYCE release v2.10 (March 2015)

The energy and its first and second geometrical derivatives obtained by Quantum Mechanical (QM) calculations for a number of conformations of a single molecule in its ground- or excited states are used to parameterize intra-molecular force fields, suitable for classical computer simulations.

A classical force-field (FF) is built up by essentially three ingredients, namely:

  1. A set of selected generalized (or redundant) internal coordinates (RIC), as bond lengths, angles, dihedrals or non-bonded distances, which completely define the molecular geometry;
  2. A set of model potential functions associated with each RIC;
  3. A set of parameters (force constants and RIC’s equilibrium values) which complete the definition of the model functions, settling molecular chemical specificity onto the FF functional.

As the first two points are regarded, Joyce, a FORTRAN77 program, reads a trial FF file in which both all the selected RIC and the associated model functions, which define the intra-molecular potential, are specified. This file can be automatically generated by the Joyce program, created by the user or built by standard MD software.

Currently supported formats for the input FF files are presently MOSCITO and GROMACS topology files.

The equilibrium values of the selected internal coordinates are read by the Joyce program from a formatted checkpoint file (.fchk) produced by the GAUSSIAN09 package. Finally, the force constants are computed by the Joyce [1-2] procedure from the first and second derivatives again read from the .fchk file.

The JOYCE program was written by Ivo Cacelli, Giacomo Prampolini and Nicola De Mitri.

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation (version3).

For further information please contact Giacomo Prampolini

Clicking Submit button you accept to cite the references specified in this page in any article whose results are obtained, also partially, by using Joyce

List of the references that should be cited in any article whose results are obtained, also partially, by using JOYCE:

    Method's development:

      [1] I. Cacelli and G. Prampolini, "Parametrization and Validation of of Intramolecular Force Fields Derived from DFT Calculations" J. Chem. Theory Comput., 3, 1803 (2007)

      [2] V. Barone, I. Cacelli, N. De Mitri, D. Licari, S. Monti and G. Prampolini "JOYCE and ULYSSES: integrated and user-friendly tools for the parameterization of intra-molecular force fields from quantum mechanical data" Phys. Chem. Chem. Phys., 15, 3736 (2013)

    Selected applications performed by the authors:

    Tritc – (organic dye, solvated and embedded in silica nanoparticles)

      V. Barone, J. Bloino, S. Monti, A. Pedone and G. Prampolini "Theoretical Multilevel Approach for studying the Photophysical Properties of Organic Dyes in solution"
      Phys. Chem. Chem. Phys., 12, 10550 (2010)

      V. Barone, J. Bloino, S. Monti, A. Pedone and G. Prampolini "Fluorescence Spectra of Organic Dyes in Solution: A Time DependentMultilevel Approach"
      Phys. Chem. Chem. Phys., 13, 2160 (2011)

      A. Pedone, G. Prampolini, S. Monti, and V. Barone "Realistic modeling of fluorescent dye-doped silica nanoparticles: A step toward the understanding of their enhanced photophysical properties"
      Chem. Mater., 23, 5016 (2011)

    Pyrimidine – (solvatochromic shift in solution)

      M. Biczysko, J. Bloino, G. Brancato, I. Cacelli, C. Cappelli, A. Ferretti, A. Lami, S. Monti, A. Pedone, G. Prampolini, C. Puzzarini, F. Santoro, F. Trani and G. Villani "Integrated computational approaches for spectroscopic studies of molecular systems in the gas phase and in solution: Pyrimidine as a test case"
      Theor. Chem. Acc., 131, 1 (2012)

      I. Cacelli, A. Ferretti, and G. Prampolini "Perturbative Multi-Reference Configuration Interaction (CI-MRPT2) Calculations in a Focused Dynamical Approach: a Computational Study of Solvatochromism in Pyrimidine"
      J. Phys. Chem. A, (2015) DOI: 10.1021/jp509877q

    Nfo-TEMPO - (organic dye, solvated and grafted onto polymer matrices)

      N. De Mitri, S. Monti, G. Prampolini and V. Barone "Absorption and Emission Spectra of a Flexible Dye in Solution: a Computational Time-Dependent Approach"
      J. Chem. Theory and Comput., 9, 4507 (2013)

      G. Prampolini, S. Monti, N. De Mitri and V. Barone "Evidences of long lived cages in functionalized polymers: Effects on chromophore dynamic and spectroscopic properties"
      Chem. Phys. Lett., 601, 134 (2014)

      N. De Mitri, G. Prampolini, S. Monti and V. Barone "Structural, dynamic and photophysical properties of a fluorescent dye incorporated in an amorphous hydrophobic polymer bundle"
      Phys.Chem.Chem.Phys., 16, 16573 (2014)

    Fe-cyanides ions - (2D-IR spectrocopy for ions in solution)

      G. Prampolini, P. Yu, S. Pizzanelli, I. Cacelli, F. Yang, J. Zhao, and J. Wang "Structure and Dynamics of Ferrocyanide and Ferricyanide Anions in Water and Heavy Water: An Insight by MD Simulations and 2D IR Spectroscopy"
      J. Phys. Chem. B, 118 14899 (2014)