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Effect of amino acid polarization in force field biomolecular calculations
Author(s) -
Mitin Alexander V.
Publication year - 2011
Publication title -
international journal of quantum chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.484
H-Index - 105
eISSN - 1097-461X
pISSN - 0020-7608
DOI - 10.1002/qua.22692
Subject(s) - biomolecule , chemistry , force field (fiction) , atomic charge , molecule , polarization (electrochemistry) , partial charge , conformational isomerism , chemical physics , amino acid , computational chemistry , quantum , physics , quantum mechanics , organic chemistry , biochemistry
It is well known that an interaction of atoms in molecules leads to their polarization and, in a general case, to changing their partial atomic charges, which depends on atomic coordination. Similar effects for amino acids in biomolecules have been observed in the present theoretical study. These effects are especially important for correct calculations of the total molecular energies based on the molecular force fields. It is shown that the dependences of charges and polarizations of amino acids on their mutual coordination lead to huge errors in the force field relative energies of biomolecular conformers because these effects are not taken into account by the known force field energy functionals. This error proportionally increases with molecular size. To reduce it, a parameterization of amino acid and atomic partial charges in dependence on their mutual coordination is proposed. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011