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Polarizable Drude Model with s‑Type Gaussian or Slater Charge Density for General Molecular Mechanics Force Fields
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, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
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2018 (English)In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, no 11, p. 5553-5566Article in journal (Refereed) Published
Abstract [en]

Gas-phase electric properties of molecules can be computed routinely using wave function methods or density functional theory (DFT). However, these methods remain computationally expensive for high-throughput screening of the vast chemical space of virtual compounds. Therefore, empirical force fields are a more practical choice in many cases, particularly since force field methods allow one to routinely predict the physicochemical properties in the condensed phases. This work presents Drude polarizable models, to increase the physical realism in empirical force fields, where the core particle is treated as a point charge and the Drude particle is treated either as a 1s-Gaussian or a ns-Slater (n = 1, 2, 3) charge density. Systematic parametrization to large high-quality quantum chemistry data obtained from the open access Alexandria Library (https://doi.org/10.5281/zenodo.1004711) ensures the transferability of these parameters. The dipole moments and isotropic polarizabilities of the isolated molecules predicted by the proposed Drude models are in agreement with experiment with accuracy similar to DFT calculations at the B3LYP/aug-cc-pVTZ level of theory. The results show that the inclusion of explicit polarization into the models reduces the root-mean-square deviation with respect to DFT calculations of the predicted dipole moments of 152 dimers and clusters by more than 50%. Finally, we show that the accuracy of the electrostatic interaction energy of the water dimers can be improved systematically by the introduction of polarizable smeared charges as a model for charge penetration.

Place, publisher, year, edition, pages
2018. no 11, p. 5553-5566
National Category
Theoretical Chemistry
Identifiers
URN: urn:nbn:se:uu:diva-380336DOI: 10.1021/acs.jctc.8b00430OAI: oai:DiVA.org:uu-380336DiVA, id: diva2:1299312
Available from: 2019-03-26 Created: 2019-03-26 Last updated: 2020-02-28Bibliographically approved
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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Ghahremanpour, Mohammad MehdiCaleman, CarlVan der Spoel, David

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