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Efficient Physics-Based Polarizable Charges: from Organic Compounds to Proteins
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.ORCID iD: 0000-0002-1129-6041
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational Biology and Bioinformatics.
(English)Manuscript (preprint) (Other academic)
National Category
Theoretical Chemistry
Identifiers
URN: urn:nbn:se:uu:diva-380342OAI: oai:DiVA.org:uu-380342DiVA, id: diva2:1299321
Available from: 2019-03-26 Created: 2019-03-26 Last updated: 2019-04-01
In thesis
1. Alexandria: A General Drude Polarizable Force Field with Spherical Charge Density
Open this publication in new window or tab >>Alexandria: A General Drude Polarizable Force Field with Spherical Charge Density
2019 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Molecular-mechanical (MM) force fields are mathematical functions that map the geometry of a molecule to its associated energy. MM force fields have been extensively used for an atomistic view into the dynamic and thermodynamics of large molecular systems in their condensed phase. Nevertheless, the grand challenge in force field development—which remains to be addressed—is to predict­­­­ properties of materials with different chemistries and in all their physical phases. 

Force fields are, in principle, derived through supervised machine learning methods. Therefore, the first step toward more accurate force fields is to provide high-quality reference data from which the force fields can learn. Thus, we benchmarked quantum-mechanical methods—at different levels of theory—in predicting of molecular energetics and electrostatic properties. As the result, the Alexandria library was released as an open access database of molecular properties.  

The second step is to use potential functions describing interactions between molecules accurately. For this, we incorporated electronic polarization and charge penetration effects into the Alexandria force field. The Drude model was used for the explicit inclusion of electronic polarization. The distribution of the atomic charges was described by either a 1s-Gaussian or an ns-Slater density function to account for charge penetration effects. Moreover, the 12-6 Lennard-Jones (LJ) potential function, commonly used in force fields, was replaced by the Wang-Buckingham (WBK) function to describe the interaction of two particles at very short distances.  In contrast to the 12-6 LJ function, the WBK function is well behaved at short distances because it has a finite limit as the distance between two particles approaches zero. 

The third step is free and open source software (FOSS) for systematic optimization of the built-in force field parameters. For this, we developed the Alexandria chemistry toolkit that is currently part of the GROMACS software package. 

With these three steps, the Alexandria force field was developed for alkali halides and for organic compounds consisting of (H, C, N, O, S, P) and halogens (F, Cl, Br, I). We demonstrated that the Alexandria force field described alkali halides in gas, liquid, and solid phases with an overall performance better than the benchmarked reference force fields. We also showed that the Alexandria force field predicted the electrostatics of isolated molecules and molecular complexes in agreement with the density functional theory at the B3LYP/aug-cc-pVTZ level of theory. 

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2019. p. 69
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 1793
Keywords
Molecular mechanics, Force field, Drude oscillator model, Alexandria library, GROMACS
National Category
Theoretical Chemistry Biophysics
Research subject
Physics with specialization in Biophysics
Identifiers
urn:nbn:se:uu:diva-380687 (URN)978-91-513-0624-7 (ISBN)
Public defence
2019-05-27, Room B21, Uppsala Biomedical Centre, Husargatan 3, Uppsala, 09:15 (English)
Opponent
Supervisors
Available from: 2019-05-02 Created: 2019-04-01 Last updated: 2019-06-17

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Van der Spoel, David

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