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Alexandria: A General Drude Polarizable Force Field with Spherical Charge Density
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology. (Computational Biology and Bioinformatics)ORCID iD: 0000-0002-1129-6041
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 [en]
Molecular mechanics, Force field, Drude oscillator model, Alexandria library, GROMACS
National Category
Theoretical Chemistry Biophysics
Research subject
Physics with specialization in Biophysics
Identifiers
URN: urn:nbn:se:uu:diva-380687ISBN: 978-91-513-0624-7 (print)OAI: oai:DiVA.org:uu-380687DiVA, id: diva2:1300961
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
List of papers
1. Large-scale calculations of gas phase thermochemistry: Enthalpy of formation, standard entropy, and heat capacity
Open this publication in new window or tab >>Large-scale calculations of gas phase thermochemistry: Enthalpy of formation, standard entropy, and heat capacity
Show others...
2016 (English)In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 145Article in journal (Refereed) Published
National Category
Theoretical Chemistry
Identifiers
urn:nbn:se:uu:diva-380330 (URN)10.1063/1.4962627 (DOI)
Available from: 2019-03-26 Created: 2019-03-26 Last updated: 2019-04-01
2. The Alexandria library, a quantum-chemical database of molecular properties for force field development
Open this publication in new window or tab >>The Alexandria library, a quantum-chemical database of molecular properties for force field development
2018 (English)In: Scientific Data, E-ISSN 2052-4463Article in journal (Refereed) Published
National Category
Theoretical Chemistry
Identifiers
urn:nbn:se:uu:diva-380335 (URN)10.1038/sdata.2018.62 (DOI)
Available from: 2019-03-26 Created: 2019-03-26 Last updated: 2019-04-01
3. Polarizable Drude Model with s‑Type Gaussian or Slater Charge Density for General Molecular Mechanics Force Fields
Open this publication in new window or tab >>Polarizable Drude Model with s‑Type Gaussian or Slater Charge Density for General Molecular Mechanics Force Fields
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2018 (English)In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626Article in journal (Refereed) Published
National Category
Theoretical Chemistry
Identifiers
urn:nbn:se:uu:diva-380336 (URN)10.1021/acs.jctc.8b00430 (DOI)
Available from: 2019-03-26 Created: 2019-03-26 Last updated: 2019-04-01
4. Phase-Transferable Force Field for Alkali Halides
Open this publication in new window or tab >>Phase-Transferable Force Field for Alkali Halides
2018 (English)In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626Article in journal (Refereed) Published
Abstract [en]

A longstanding goal of computational chemistry is to predict the state of materials in all phases with a single model. This is particularly relevant for materials that are difficult or dangerous to handle or compounds that have not yet been created. Progress toward this goal has been limited, as most work has concentrated on just one phase, often determined by particular applications. In the framework of the development of the Alexandria force field, we present here new polarizable force fields for alkali halides with Gaussian charge distributions for molecular dynamics simulations. We explore different descriptions of the van der Waals interaction, like the commonly applied 12–6 Lennard-Jones (LJ), and compare it to “softer” ones, such as the 8–6 LJ, Buckingham, and a modified Buckingham potential. Our results for physicochemical properties of the gas, liquid, and solid phases of alkali halides are compared to experimental data and calculations with reference polarizable and nonpolarizable force fields. The new polarizable force field that employs a modified Buckingham potential predicts the tested properties for gas, liquid, and solid phases with a very good accuracy. In contrast to reference force fields, this model reproduces the correct crystal structures for all alkali halides at low and high temperature. Seeing that experiments with molten salts may be tedious due to high temperatures and their corrosive nature, the models presented here can contribute significantly to our understanding of alkali halides in general and melts in particular.

National Category
Theoretical Chemistry
Identifiers
urn:nbn:se:uu:diva-380340 (URN)10.1021/acs.jctc.8b00507 (DOI)
Available from: 2019-03-26 Created: 2019-03-26 Last updated: 2019-09-03Bibliographically approved
5. Small Molecule Thermochemistry:: A Tool for Empirical Force Field Development
Open this publication in new window or tab >>Small Molecule Thermochemistry:: A Tool for Empirical Force Field Development
2018 (English)In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 122, no 45, p. 8982-8988Article in journal (Refereed) Published
Abstract [en]

Spectroscopic analysis of compounds is typically combined with density functional theory, for instance, for assigning vibrational frequencies, limiting application to relatively small compounds. Accurate classical force fields could, in principle, complement these quantum-chemical tools. A relatively simple way to validate vibrational frequencies is by computing thermochemical properties. We present such a validation for over 1800 small molecules using the harmonic approximation. Two popular empirical force fields (GAFF and CGenFF) are compared to experimental data and results from Gaussian-4 quantum-chemical calculations. Frequency scaling factors of 1.035 (CGenFF) and 1.018 (GAFF) are derived from the zero-point energies. The force field calculations have larger deviation from experiment than the G4 method for standard entropy, but for heat capacity the results are comparable. For internal thermal energy and zero-point energy the deviations from G4 are relatively small. The work suggests that with some tuning force fields could indeed complement DFT in spectroscopical applications.

National Category
Theoretical Chemistry
Identifiers
urn:nbn:se:uu:diva-380341 (URN)10.1021/acs.jpca.8b09867 (DOI)
Available from: 2019-03-26 Created: 2019-03-26 Last updated: 2019-09-03Bibliographically approved
6. Efficient Physics-Based Polarizable Charges: from Organic Compounds to Proteins
Open this publication in new window or tab >>Efficient Physics-Based Polarizable Charges: from Organic Compounds to Proteins
(English)Manuscript (preprint) (Other academic)
National Category
Theoretical Chemistry
Identifiers
urn:nbn:se:uu:diva-380342 (URN)
Available from: 2019-03-26 Created: 2019-03-26 Last updated: 2019-04-01

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