Literature DB >> 19655857

The electronegativity equalization method and the split charge equilibration applied to organic systems: parametrization, validation, and comparison.

Toon Verstraelen1, Veronique Van Speybroeck, Michel Waroquier.   

Abstract

An extensive benchmark of the electronegativity equalization method (EEM) and the split charge equilibration (SQE) model on a very diverse set of organic molecules is presented. These models efficiently compute atomic partial charges and are used in the development of polarizable force fields. The predicted partial charges that depend on empirical parameters are calibrated to reproduce results from quantum mechanical calculations. Recently, SQE is presented as an extension of the EEM to obtain the correct size dependence of the molecular polarizability. In this work, 12 parametrization protocols are applied to each model and the optimal parameters are benchmarked systematically. The training data for the empirical parameters comprise of MP2/Aug-CC-pVDZ calculations on 500 organic molecules containing the elements H, C, N, O, F, S, Cl, and Br. These molecules have been selected by an ingenious and autonomous protocol from an initial set of almost 500,000 small organic molecules. It is clear that the SQE model outperforms the EEM in all benchmark assessments. When using Hirshfeld-I charges for the calibration, the SQE model optimally reproduces the molecular electrostatic potential from the ab initio calculations. Applications on chain molecules, i.e., alkanes, alkenes, and alpha alanine helices, confirm that the EEM gives rise to a divergent behavior for the polarizability, while the SQE model shows the correct trends. We conclude that the SQE model is an essential component of a polarizable force field, showing several advantages over the original EEM.

Entities:  

Year:  2009        PMID: 19655857     DOI: 10.1063/1.3187034

Source DB:  PubMed          Journal:  J Chem Phys        ISSN: 0021-9606            Impact factor:   3.488


  9 in total

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Review 2.  Metal Ion Modeling Using Classical Mechanics.

Authors:  Pengfei Li; Kenneth M Merz
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3.  Scalable Evaluation of Polarization Energy and Associated Forces in Polarizable Molecular Dynamics: II.Towards Massively Parallel Computations using Smooth Particle Mesh Ewald.

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Journal:  J Chem Theory Comput       Date:  2014-02-28       Impact factor: 6.006

4.  Fractional nuclear charge approach to isolated anion densities for Hirshfeld partitioning methods.

Authors:  Farnaz Heidar-Zadeh; Paul W Ayers; Patrick Bultinck
Journal:  J Mol Model       Date:  2017-11-21       Impact factor: 1.810

5.  Molecular Interactions From the Density Functional Theory for Chemical Reactivity: The Interaction Energy Between Two-Reagents.

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Journal:  Front Chem       Date:  2022-06-13       Impact factor: 5.545

6.  Charge profile analysis reveals that activation of pro-apoptotic regulators Bax and Bak relies on charge transfer mediated allosteric regulation.

Authors:  Crina-Maria Ionescu; Radka Svobodová Vařeková; Jochen H M Prehn; Heinrich J Huber; Jaroslav Koča
Journal:  PLoS Comput Biol       Date:  2012-06-14       Impact factor: 4.475

7.  Evaluating Charge Equilibration Methods To Generate Electrostatic Fields in Nanoporous Materials.

Authors:  Daniele Ongari; Peter G Boyd; Ozge Kadioglu; Amber K Mace; Seda Keskin; Berend Smit
Journal:  J Chem Theory Comput       Date:  2018-12-04       Impact factor: 6.006

8.  AtomicChargeCalculator: interactive web-based calculation of atomic charges in large biomolecular complexes and drug-like molecules.

Authors:  Crina-Maria Ionescu; David Sehnal; Francesco L Falginella; Purbaj Pant; Lukáš Pravda; Tomáš Bouchal; Radka Svobodová Vařeková; Stanislav Geidl; Jaroslav Koča
Journal:  J Cheminform       Date:  2015-10-22       Impact factor: 5.514

9.  Minimally Empirical Double-Hybrid Functionals Trained against the GMTKN55 Database: revDSD-PBEP86-D4, revDOD-PBE-D4, and DOD-SCAN-D4.

Authors:  Golokesh Santra; Nitai Sylvetsky; Jan M L Martin
Journal:  J Phys Chem A       Date:  2019-06-12       Impact factor: 2.944

  9 in total

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