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.

Absorption and Emission Spectra of a Flexible Dye in Solution: A Computational Time-Dependent Approach

“…A good agreement is achieved, resulting in a root mean square deviation of 38 and 37 cm −1 , for GS and EES, respectively. It may be worth noticing that the achieved accuracy is in line with the results obtained in previous parameterizations, 50 hence a rather reliable representation of the NfO-TEMPO vibrational behavior is expected during MD simulations.…”

“…The intramolecular FF employed for the description of NfO-TEMPO-Me, E intra , takes the standard form: (1) where the first three terms are represented by harmonic expressions (2) In equation (2) , , and , , are the force constants and equilibrium values for stretching, bending and stiff torsional internal coordinates, 50 respectively. The potential energies governing rotations around dihedrals δ 1 -δ 4 are described by sums of cosines, namely (3) where is the force constant, δ μ the dihedral, and the multiplicity and a phase factor for the j th cosine.…”

“…Although a lot of work has been done to describe GS structures and reliable FFs are available in the literature, much less effort has been devoted to the development of "ad hoc" FFs for the EES conformations. 35,[47][48][49][50] Recently, the JOYCE 51 parameterization protocol, devised to obtain accurate and specific FFs from QM computed data, has been extended to the automated treatment of both GS and EES. 50 In the present work, the above mentioned "dynamic" approach is applied to compute the electronic spectra of a flexible dye, namely the 4-naphthoyloxy-1-methoxy-2,2,6,6-tetramethylpiperidine (NfO-TEMPO-Me) molecule (see Figure 2), in toluene solution, where solvent molecules are modeled explicitly.…”

“…35,[47][48][49][50] Recently, the JOYCE 51 parameterization protocol, devised to obtain accurate and specific FFs from QM computed data, has been extended to the automated treatment of both GS and EES. 50 In the present work, the above mentioned "dynamic" approach is applied to compute the electronic spectra of a flexible dye, namely the 4-naphthoyloxy-1-methoxy-2,2,6,6-tetramethylpiperidine (NfO-TEMPO-Me) molecule (see Figure 2), in toluene solution, where solvent molecules are modeled explicitly. This compound is interesting because of its potential application in the design of "smart" polymers with mechanochromic attributes as proven by the experimental characterization obtained through spectroscopic techniques and reported in a recent paper.…”

Developing accurate molecular mechanics force fields for conjugated molecular systems

“…28 JOYCE -a program to derive all-atom and united-atom FFs for small molecules has been developed by the Barone group. 29,30 Inputs to this program are QM equilibrium geometry, energy, gradient and the hessian matrix. FFs parameters are obtained by minimizing a cost function, which measures the errors between QM energy, gradient and hessian and those calculated from the FFs.…”