A Novel Approach for Deriving Force Field Torsion Angle Parameters Accounting for Conformation-Dependent Solvation Effects

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Authors	ZGARBOVÁ Marie JAVIER LUQUE F. ŠPONER Jiří OTYEPKA Michal JUREČKA Petr
Year of publication	2012
Type	Article in Periodical
Magazine / Source	Journal of Chemical Theory and Computation
MU Faculty or unit	Central European Institute of Technology
Citation
web	http://pubs.acs.org/doi/abs/10.1021/ct3001987
Doi	http://dx.doi.org/10.1021/ct3001987
Field	Biophysics
Keywords	MOLECULAR-ORBITAL METHODS; NUCLEIC-ACIDS; FREE-ENERGY; ANISOTROPIC DIELECTRICS; CONTINUUM MODEL; IONIC-SOLUTIONS; ATOMIC CHARGES; RESP MODEL; BASIS-SETS; PARAMETRIZATION
Attached files	JCTC.pdf
Description	A procedure for deriving force field torsion parameters including certain previously neglected solvation effects is suggested. In contrast to the conventional in vacuo approaches, the dihedral parameters are obtained from the difference between the quantum-mechanical self-consistent reaction field and Poisson-Boltzmann continuum solvation models. An analysis of the solvation contributions shows that two major effects neglected when torsion parameters are derived in vacuo are (i) conformation-dependent solute polarization and (ii) solvation of conformation-dependent charge distribution. Using the glycosidic torsion as an example, we demonstrate that the corresponding correction for the torsion potential is substantial and important. Our approach avoids double counting of solvation effects and provides parameters that may be used in combination with any of the widely used nonpolarizable discrete solvent models, such as TIPnP or SPC/E, or with continuum solvent models. Differences between our model and the previously suggested solvation models are discussed. Improvements were demonstrated for the latest AMBER RNA chi(OL3) parameters derived with inclusion of solvent effects in a previous publication (Zgarbova et al. J. Chem. Theory Comput. 2011, 7, 2886). The described procedure may help to provide consistently better force field parameters than the currently used parametrization approaches.
Related projects:	Biochemie na rozcestí mezi in silico a in vitro CEITEC - Central European Institute of Technology