Journal article
Polarizable Atomic Multipole Solutes in a Generalized Kirkwood Continuum
Journal of chemical theory and computation, Vol.3(6), pp.2083-2097
11/2007
DOI: 10.1021/ct7001336
PMCID: PMC4767294
PMID: 26636202
Abstract
The generalized Born (GB) model of continuum electrostatics is an analytic approximation to the Poisson equation useful for predicting the electrostatic component of the solvation free energy for solutes ranging in size from small organic molecules to large macromolecular complexes. This work presents a new continuum electrostatics model based on Kirkwood’s analytic result for the electrostatic component of the solvation free energy for a solute with arbitrary charge distribution.
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Unlike GB, which is limited to monopoles, our generalized Kirkwood (GK) model can treat solute electrostatics represented by any combination of permanent and induced atomic multipole moments of arbitrary degree. Here we apply the GK model to the newly developed Atomic Multipole Optimized Energetics for Biomolecular Applications (AMOEBA) force field, which includes permanent atomic multipoles through the quadrupole and treats polarization via induced dipoles. A derivation of the GK gradient is presented, which enables energy minimization or molecular dynamics of an AMOEBA solute within a GK continuum. For a series of 55 proteins, GK electrostatic solvation free energies are compared to the Polarizable Multipole Poisson-Boltzmann (PMPB) model
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and yield a mean unsigned relative difference of 0.9%. Additionally, the reaction field of GK compares well to that of the PMPB model, as shown by a mean unsigned relative difference of 2.7% in predicting the total solvated dipole moment for each protein in this test set. The CPU time needed for GK relative to vacuum AMOEBA calculations is approximately a factor of three, making it suitable for applications that require significant sampling of configuration space.
Details
- Title: Subtitle
- Polarizable Atomic Multipole Solutes in a Generalized Kirkwood Continuum
- Creators
- Michael J Schnieders - Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO 63130Jay W Ponder - Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110
- Resource Type
- Journal article
- Publication Details
- Journal of chemical theory and computation, Vol.3(6), pp.2083-2097
- DOI
- 10.1021/ct7001336
- PMID
- 26636202
- PMCID
- PMC4767294
- NLM abbreviation
- J Chem Theory Comput
- ISSN
- 1549-9618
- eISSN
- 1549-9626
- Language
- English
- Date published
- 11/2007
- Academic Unit
- Roy J. Carver Department of Biomedical Engineering; Biochemistry and Molecular Biology
- Record Identifier
- 9984025394102771
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