Polarized Protein-Specific Charges from Atoms-in-Molecule Electron Density Partitioning
| Autor: | Daniel J. Cole, Louis P. Lee, Chris-Kriton Skylaris, Mike C. Payne, William L. Jorgensen |
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| Rok vydání: | 2013 |
| Předmět: |
Physics
Electron density 010304 chemical physics Ab initio Nanotechnology Charge (physics) 010402 general chemistry 01 natural sciences Article 0104 chemical sciences Computer Science Applications Molecular dynamics Partial charge Chemical physics 0103 physical sciences Molecule Density functional theory Physical and Theoretical Chemistry Quantum |
| Zdroj: | Journal of Chemical Theory and Computation |
| ISSN: | 1549-9626 1549-9618 |
| DOI: | 10.1021/ct400279d |
| Popis: | Atomic partial charges for use in traditional force fields for biomolecular simulation are often fit to the electrostatic potentials of small molecules and, hence, neglect large-scale electronic polarization. On the other hand, recent advances in atoms-in-molecule charge derivation schemes show promise for use in flexible force fields but are limited in size by the underlying quantum mechanical calculation of the electron density. Here, we implement the density derived electrostatic and chemical charges method in the linear-scaling density functional theory code ONETEP. Our implementation allows the straightforward derivation of partial atomic charges for systems comprising thousands of atoms, including entire proteins. We demonstrate that the derived charges are chemically intuitive, reproduce ab initio electrostatic potentials of proteins and are transferable between closely related systems. Simulated NMR data derived from molecular dynamics of three proteins using force fields based on the ONETEP charges are in good agreement with experiment. |
| Databáze: | OpenAIRE |
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