ZGARBOVÁ, Marie, F. JAVIER LUQUE, Jiří ŠPONER, Michal OTYEPKA and Petr JUREČKA. A Novel Approach for Deriving Force Field Torsion Angle Parameters Accounting for Conformation-Dependent Solvation Effects. Journal of Chemical Theory and Computation. WASHINGTON: AMER CHEMICAL SOC, 2012, vol. 8, No 9, p. 3232-3242. ISSN 1549-9618. doi:10.1021/ct3001987.
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Basic information
Original name A Novel Approach for Deriving Force Field Torsion Angle Parameters Accounting for Conformation-Dependent Solvation Effects
Authors ZGARBOVÁ, Marie (203 Czech Republic), F. JAVIER LUQUE (724 Spain), Jiří ŠPONER (203 Czech Republic, guarantor, belonging to the institution), Michal OTYEPKA (203 Czech Republic) and Petr JUREČKA (203 Czech Republic).
Edition Journal of Chemical Theory and Computation, WASHINGTON, AMER CHEMICAL SOC, 2012, 1549-9618.
Other information
Original language English
Type of outcome Article in a journal
Field of Study 10610 Biophysics
Country of publisher United States of America
Confidentiality degree is not subject to a state or trade secret
WWW URL
Impact factor Impact factor: 5.389
RIV identification code RIV/00216224:14740/12:00057886
Organization unit Central European Institute of Technology
Doi http://dx.doi.org/10.1021/ct3001987
UT WoS 000308830700027
Keywords in English MOLECULAR-ORBITAL METHODS; NUCLEIC-ACIDS; FREE-ENERGY; ANISOTROPIC DIELECTRICS; CONTINUUM MODEL; IONIC-SOLUTIONS; ATOMIC CHARGES; RESP MODEL; BASIS-SETS; PARAMETRIZATION
Tags ok, rivok
Tags International impact, Reviewed
Changed by Changed by: Olga Křížová, učo 56639. Changed: 6. 4. 2013 06:12.
Abstract
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.
Links
ED1.1.00/02.0068, research and development projectName: CEITEC - central european institute of technology
GD203/09/H046, research and development projectName: Biochemie na rozcestí mezi in silico a in vitro
Investor: Czech Science Foundation
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