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Alexandria: A General Drude Polarizable Force Field with Spherical Charge Density
Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi. (Computational Biology and Bioinformatics)ORCID-id: 0000-0002-1129-6041
2019 (Engelska)Doktorsavhandling, sammanläggning (Övrigt vetenskapligt)
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. 

Ort, förlag, år, upplaga, sidor
Uppsala: Acta Universitatis Upsaliensis, 2019. , s. 69
Serie
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 1793
Nyckelord [en]
Molecular mechanics, Force field, Drude oscillator model, Alexandria library, GROMACS
Nationell ämneskategori
Teoretisk kemi Biofysik
Forskningsämne
Fysik med inriktning mot biofysik
Identifikatorer
URN: urn:nbn:se:uu:diva-380687ISBN: 978-91-513-0624-7 (tryckt)OAI: oai:DiVA.org:uu-380687DiVA, id: diva2:1300961
Disputation
2019-05-27, Room B21, Uppsala Biomedical Centre, Husargatan 3, Uppsala, 09:15 (Engelska)
Opponent
Handledare
Tillgänglig från: 2019-05-02 Skapad: 2019-04-01 Senast uppdaterad: 2020-03-25
Delarbeten
1. Large-scale calculations of gas phase thermochemistry: Enthalpy of formation, standard entropy, and heat capacity
Öppna denna publikation i ny flik eller fönster >>Large-scale calculations of gas phase thermochemistry: Enthalpy of formation, standard entropy, and heat capacity
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2016 (Engelska)Ingår i: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 145Artikel i tidskrift (Refereegranskat) Published
Abstract [en]

Large scale quantum calculations for molar enthalpy of formation (ΔfH0), standard entropy (S0), and heat capacity (CV) are presented. A large data set may help to evaluate quantum thermochemistry tools in order to uncover possible hidden shortcomings and also to find experimental data that might need to be reinvestigated, indeed we list and annotate approximately 200 problematic thermochemistry measurements. Quantum methods systematically underestimate S0 for flexible molecules in the gas phase if only a single (minimum energy) conformation is taken into account. This problem can be tackled in principle by performing thermochemistry calculations for all stable conformations [Zheng et al., Phys. Chem. Chem. Phys. 13, 10885–10907 (2011)], but this is not practical for large molecules. We observe that the deviation of composite quantum thermochemistry recipes from experimental S0 corresponds roughly to the Boltzmann equation (S = RlnΩ), where R is the gas constant and Ω the number of possible conformations. This allows an empirical correction of the calculated entropy for molecules with multiple conformations. With the correction we find an RMSD from experiment of ≈13 J/mol K for 1273 compounds. This paper also provides predictions of ΔfH0, S0, and CV for well over 700 compounds for which no experimental data could be found in the literature. Finally, in order to facilitate the analysis of thermodynamics properties by others we have implemented a new tool obthermo in the OpenBabel program suite [O’Boyle et al., J. Cheminf. 3, 33 (2011)] including a table of reference atomization energy values for popular thermochemistry methods.

Nationell ämneskategori
Teoretisk kemi
Identifikatorer
urn:nbn:se:uu:diva-380330 (URN)10.1063/1.4962627 (DOI)
Tillgänglig från: 2019-03-26 Skapad: 2019-03-26 Senast uppdaterad: 2020-03-02Bibliografiskt granskad
2. The Alexandria library, a quantum-chemical database of molecular properties for force field development
Öppna denna publikation i ny flik eller fönster >>The Alexandria library, a quantum-chemical database of molecular properties for force field development
2018 (Engelska)Ingår i: Scientific Data, E-ISSN 2052-4463, Vol. 5, artikel-id 180062Artikel i tidskrift (Refereegranskat) Published
Abstract [en]

Data quality as well as library size are crucial issues for force field development. In order to predict molecular properties in a large chemical space, the foundation to build force fields on needs to encompass a large variety of chemical compounds. The tabulated molecular physicochemical properties also need to be accurate. Due to the limited transparency in data used for development of existing force fields it is hard to establish data quality and reusability is low. This paper presents the Alexandria library as an open and freely accessible database of optimized molecular geometries, frequencies, electrostatic moments up to the hexadecupole, electrostatic potential, polarizabilities, and thermochemistry, obtained from quantum chemistry calculations for 2704 compounds. Values are tabulated and where available compared to experimental data. This library can assist systematic development and training of empirical force fields for a broad range of molecules.

Nationell ämneskategori
Teoretisk kemi
Identifikatorer
urn:nbn:se:uu:diva-380335 (URN)10.1038/sdata.2018.62 (DOI)000429522800001 ()29633987 (PubMedID)
Forskningsfinansiär
Vetenskapsrådet, 2013-5947Swedish National Infrastructure for Computing (SNIC), SNIC2015-16-33Swedish National Infrastructure for Computing (SNIC), SNIC2016-34-44
Tillgänglig från: 2019-03-26 Skapad: 2019-03-26 Senast uppdaterad: 2020-02-05Bibliografiskt granskad
3. Polarizable Drude Model with s‑Type Gaussian or Slater Charge Density for General Molecular Mechanics Force Fields
Öppna denna publikation i ny flik eller fönster >>Polarizable Drude Model with s‑Type Gaussian or Slater Charge Density for General Molecular Mechanics Force Fields
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2018 (Engelska)Ingår i: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, nr 11, s. 5553-5566Artikel i tidskrift (Refereegranskat) 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.

Nationell ämneskategori
Teoretisk kemi
Identifikatorer
urn:nbn:se:uu:diva-380336 (URN)10.1021/acs.jctc.8b00430 (DOI)
Tillgänglig från: 2019-03-26 Skapad: 2019-03-26 Senast uppdaterad: 2020-02-28Bibliografiskt granskad
4. Phase-Transferable Force Field for Alkali Halides
Öppna denna publikation i ny flik eller fönster >>Phase-Transferable Force Field for Alkali Halides
2018 (Engelska)Ingår i: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 14, nr 11, s. 5933-5948Artikel i tidskrift (Refereegranskat) 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.

Nationell ämneskategori
Teoretisk kemi
Identifikatorer
urn:nbn:se:uu:diva-380340 (URN)10.1021/acs.jctc.8b00507 (DOI)000450695200042 ()30300552 (PubMedID)
Forskningsfinansiär
Vetenskapsrådet, 2013-5947Swedish National Infrastructure for Computing (SNIC), SNIC2017-12-41eSSENCE - An eScience Collaboration
Tillgänglig från: 2019-03-26 Skapad: 2019-03-26 Senast uppdaterad: 2020-02-05Bibliografiskt granskad
5. Small Molecule Thermochemistry: A Tool for Empirical Force Field Development
Öppna denna publikation i ny flik eller fönster >>Small Molecule Thermochemistry: A Tool for Empirical Force Field Development
2018 (Engelska)Ingår i: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 122, nr 45, s. 8982-8988Artikel i tidskrift (Refereegranskat) 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.

Ort, förlag, år, upplaga, sidor
American Chemical Society (ACS), 2018
Nationell ämneskategori
Teoretisk kemi
Identifikatorer
urn:nbn:se:uu:diva-380341 (URN)10.1021/acs.jpca.8b09867 (DOI)000451101200020 ()30362355 (PubMedID)
Forskningsfinansiär
Vetenskapsrådet, 2013-5947
Tillgänglig från: 2019-03-26 Skapad: 2019-03-26 Senast uppdaterad: 2020-02-05Bibliografiskt granskad
6. Efficient Physics-Based Polarizable Charges: from Organic Compounds to Proteins
Öppna denna publikation i ny flik eller fönster >>Efficient Physics-Based Polarizable Charges: from Organic Compounds to Proteins
(Engelska)Manuskript (preprint) (Övrigt vetenskapligt)
Nationell ämneskategori
Teoretisk kemi
Identifikatorer
urn:nbn:se:uu:diva-380342 (URN)
Tillgänglig från: 2019-03-26 Skapad: 2019-03-26 Senast uppdaterad: 2019-04-01

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