Hydration Free Energies in the FreeSolv Database Calculated with Polarized Iterative Hirshfeld Charges
| Autor: | Adelio R. Matamala, Toon Verstraelen, Alejandro Lara, Esteban Vöhringer-Martinez, Maximiliano Riquelme, David L. Mobley |
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| Rok vydání: | 2018 |
| Předmět: |
Electron density
Databases Factual BLIND PREDICTION Medicinal & Biomolecular Chemistry General Chemical Engineering Computation MOLECULAR SIMULATIONS Library and Information Sciences 010402 general chemistry computer.software_genre Electrochemistry 01 natural sciences Article Force field (chemistry) Databases Medicinal and Biomolecular Chemistry Theoretical and Computational Chemistry Polarizability 0103 physical sciences SOLVATION FREE-ENERGIES Molecule AMINO-ACIDS Physics::Chemical Physics Factual POTENTIAL FUNCTIONS 010304 chemical physics Database Intermolecular force ATOMIC CHARGES Computation Theory and Mathematics General Chemistry Electrostatics 0104 chemical sciences Computer Science Applications Chemistry Physics and Astronomy FORCE-FIELD Thermodynamics EFFICIENT GENERATION BIOMOLECULAR SIMULATION computer ELECTRON-DENSITY |
| Zdroj: | Journal of chemical information and modeling, vol 58, iss 9 JOURNAL OF CHEMICAL INFORMATION AND MODELING |
| ISSN: | 1549-960X 1549-9596 |
| DOI: | 10.1021/acs.jcim.8b00180 |
| Popis: | Computer simulations of biomolecular systems often use force fields, which are combinations of simple empirical atom-based functions to describe the molecular interactions. Even though polarizable force fields give a more detailed description of intermolecular interactions, nonpolarizable force fields, developed several decades ago, are often still preferred because of their reduced computation cost. Electrostatic interactions play a major role in biomolecular systems and are therein described by atomic point charges. In this work, we address the performance of different atomic charges to reproduce experimental hydration free energies in the FreeSolv database in combination with the GAFF force field. Atomic charges were calculated by two atoms-in-molecules approaches, Hirshfeld-I and Minimal Basis Iterative Stockholder (MBIS). To account for polarization effects, the charges were derived from the solute’s electron density computed with an implicit solvent model, and the energy required to polarize the solute was added to the free energy cycle. The calculated hydration free energies were analyzed with an error model, revealing systematic errors associated with specific functional groups or chemical elements. The best agreement with the experimental data is observed for the AM1-BCC and the MBIS atomic charge methods. The latter includes the solvent polarization and presents a root-mean-square error of 2.0 kcal mol–1 for the 613 organic molecules studied. The largest deviation was observed for phosphorus-containing molecules and the molecules with amide, ester and amine functional groups. |
| Databáze: | OpenAIRE |
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