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• W2896588574 endingPage "2695" @default.
• W2896588574 startingPage "2695" @default.
• W2896588574 abstract "Maintaining a proper balance between specific intermolecular interactions and non-specific solvent interactions is of critical importance in molecular simulations, especially when predicting binding affinities or reaction rates in the condensed phase. The most rigorous metric for characterizing solvent affinity are solvation free energies, which correspond to a transfer from the gas phase into solution. Due to the drastic change of the electrostatic environment during this process, it is also a stringent test of polarization response in the model. Here, we employ both the CHARMM fixed charge and polarizable force fields to predict hydration free energies of twelve simple solutes. The resulting classical ensembles are then reweighted to obtain QM/MM hydration free energies using a variety of QM methods, including MP2, Hartree⁻Fock, density functional methods (BLYP, B3LYP, M06-2X) and semi-empirical methods (OM2 and AM1 ). Our simulations test the compatibility of quantum-mechanical methods with molecular-mechanical water models and solute Lennard⁻Jones parameters. In all cases, the resulting QM/MM hydration free energies were inferior to purely classical results, with the QM/MM Drude force field predictions being only marginally better than the QM/MM fixed charge results. In addition, the QM/MM results for different quantum methods are highly divergent, with almost inverted trends for polarizable and fixed charge water models. While this does not necessarily imply deficiencies in the QM models themselves, it underscores the need to develop consistent and balanced QM/MM interactions. Both the QM and the MM component of a QM/MM simulation have to match, in order to avoid artifacts due to biased solute⁻solvent interactions. Finally, we discuss strategies to improve the convergence and efficiency of multi-scale free energy simulations by automatically adapting the molecular-mechanics force field to the target quantum method." @default.
• W2896588574 created "2018-10-26" @default.
• W2896588574 creator A5027168981 @default.
• W2896588574 creator A5056944006 @default.
• W2896588574 creator A5060822545 @default.
• W2896588574 creator A5067610846 @default.
• W2896588574 creator A5073581192 @default.
• W2896588574 creator A5076436548 @default.
• W2896588574 creator A5079782789 @default.
• W2896588574 date "2018-10-19" @default.
• W2896588574 modified "2023-10-05" @default.
• W2896588574 title "A Comparison of QM/MM Simulations with and without the Drude Oscillator Model Based on Hydration Free Energies of Simple Solutes" @default.
• W2896588574 cites W1494326194 @default.
• W2896588574 cites W1573009101 @default.
• W2896588574 cites W157808733 @default.
• W2896588574 cites W1625910593 @default.
• W2896588574 cites W176210329 @default.
• W2896588574 cites W1932588580 @default.
• W2896588574 cites W1958729574 @default.
• W2896588574 cites W1963577981 @default.
• W2896588574 cites W1966363041 @default.
• W2896588574 cites W1966867657 @default.
• W2896588574 cites W1968755416 @default.
• W2896588574 cites W1969432389 @default.
• W2896588574 cites W1970973025 @default.
• W2896588574 cites W1971099220 @default.
• W2896588574 cites W1971617876 @default.
• W2896588574 cites W1971676700 @default.
• W2896588574 cites W1972327332 @default.
• W2896588574 cites W1975996616 @default.
• W2896588574 cites W1979687764 @default.
• W2896588574 cites W1979883283 @default.
• W2896588574 cites W1980705414 @default.
• W2896588574 cites W1980933072 @default.
• W2896588574 cites W1983092879 @default.
• W2896588574 cites W1983731524 @default.
• W2896588574 cites W1984690321 @default.
• W2896588574 cites W1986025575 @default.
• W2896588574 cites W1986411697 @default.
• W2896588574 cites W1991216956 @default.
• W2896588574 cites W1991794210 @default.
• W2896588574 cites W1991952935 @default.
• W2896588574 cites W1994732149 @default.
• W2896588574 cites W1995534005 @default.
• W2896588574 cites W1996420136 @default.
• W2896588574 cites W1997119191 @default.
• W2896588574 cites W1997151511 @default.
• W2896588574 cites W1998870918 @default.
• W2896588574 cites W1999572189 @default.
• W2896588574 cites W1999707298 @default.
• W2896588574 cites W2000219995 @default.
• W2896588574 cites W2000363444 @default.
• W2896588574 cites W2000793695 @default.
• W2896588574 cites W2001384706 @default.
• W2896588574 cites W2001443877 @default.
• W2896588574 cites W2002912579 @default.
• W2896588574 cites W2003939057 @default.
• W2896588574 cites W2005069114 @default.
• W2896588574 cites W2005739967 @default.
• W2896588574 cites W2006228399 @default.
• W2896588574 cites W2007349244 @default.
• W2896588574 cites W2008192323 @default.
• W2896588574 cites W2008437107 @default.
• W2896588574 cites W2008792691 @default.
• W2896588574 cites W2011215428 @default.
• W2896588574 cites W2015517515 @default.
• W2896588574 cites W2016111085 @default.
• W2896588574 cites W2017000223 @default.
• W2896588574 cites W2017544790 @default.
• W2896588574 cites W2018586823 @default.
• W2896588574 cites W2018872041 @default.
• W2896588574 cites W2021832765 @default.
• W2896588574 cites W2023271753 @default.
• W2896588574 cites W2023400093 @default.
• W2896588574 cites W2023812284 @default.
• W2896588574 cites W2025229221 @default.
• W2896588574 cites W2025540327 @default.
• W2896588574 cites W2026467865 @default.
• W2896588574 cites W2027684389 @default.
• W2896588574 cites W2028702957 @default.
• W2896588574 cites W2031888811 @default.
• W2896588574 cites W2031896949 @default.
• W2896588574 cites W2033022456 @default.
• W2896588574 cites W2035460800 @default.
• W2896588574 cites W2035643173 @default.
• W2896588574 cites W2036024373 @default.
• W2896588574 cites W2036050166 @default.
• W2896588574 cites W2037535298 @default.
• W2896588574 cites W2038418805 @default.
• W2896588574 cites W2039537789 @default.
• W2896588574 cites W2039559098 @default.
• W2896588574 cites W2040771733 @default.
• W2896588574 cites W2041638382 @default.
• W2896588574 cites W2041698026 @default.
• W2896588574 cites W2042586818 @default.
• W2896588574 cites W2043429268 @default.
• W2896588574 cites W2044940178 @default.
• W2896588574 cites W2045304149 @default.

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