QM/MM-Based Fitting of Atomic Polarizabilities for Use in Condensed-Phase Biomolecular Simulation

Vosmeer, C. Ruben; Rustenburg, Ariën S.; Rice, Julia E.; Horn, Hans W.; Swope, William C.; Geerke, Daan P.

doi:10.1021/ct300085z

Cited by 19 publications

(55 citation statements)

References 87 publications

(169 reference statements)

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“…Combined with the electric fields at the atoms and assuming linear response, polarizabilities can be calculated. It was shown that the values for the atomic polarizabilities obtained are similar to those previously reported based on empirical optimization, and they could be directly used to guide calibration of a methanol solvent model (CPC) …”

Section: Introductionsupporting

confidence: 71%

“…One of the challenges in calibrating polarizable force fields is assigning appropriate values to the atomic polarizabilities . In the current work, we make profit from a recently proposed QM/MM approach to estimate atomic polarizabilities that are suited for use in condensed‐phase environment . In this approach, solvent configurations around a solute are sampled through MD simulation.…”

Section: Introductionmentioning

confidence: 99%

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A systematic approach to calibrate a transferable polarizable force field parameter set for primary alcohols

et al. 2017

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In this work, parameters are optimized for a charge-on-spring based polarizable force field for linear alcohols. We show that parameter transferability can be obtained using a systematic approach in which the effects of parameter changes on physico-chemical properties calculated from simulation are predicted. Our previously described QM/MM calculations are used to attribute condensed-phase polarizabilities, and starting from the non-polarizable GROMOS 53A5/53A6 parameter set, van der Waals and Coulomb interaction parameters are optimized to reproduce pure-liquid (thermodynamic, dielectric, and transport) properties, as well as hydration free energies. For a large set of models, which were obtained by combining small perturbations of 10 distinct parameters, values for pure-liquid properties of the series methanol to butanol were close to experiment. From this large set of models, we selected 34 models without special repulsive van der Waals parameters to distinguish between hydrogen-bonding and non-hydrogen-bonding atom pairs, to make the force field simple and transparent. © 2017 Wiley Periodicals, Inc.

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Section: Introductionsupporting

confidence: 71%

Section: Introductionmentioning

confidence: 99%

A systematic approach to calibrate a transferable polarizable force field parameter set for primary alcohols

et al. 2017

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“…Then one could use that understanding to develop a proper parameterization scheme and, since the polarizability in condensed phase (even in water pentamer) can significantly differ from that in the gas phase, 128–131 use QM/MM calculations to fit anisotropic atomic polarizabilities in a self-consistent fashion. 132,133 …”

Section: Discussionmentioning

confidence: 99%

Numerical Study on the Partitioning of the Molecular Polarizability into Fluctuating Charge and Induced Atomic Dipole Contributions

Simmonett

Pickard

et al. 2015

J. Phys. Chem. A

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In order to carry out a detailed analysis of the molecular static polarizability, which is the response of the molecule to a uniform external electric field, the molecular polarizability was computed using the finite-difference method for 21 small molecules, using density functional theory. Within nine charge population schemes (Löwdin, Mulliken, Becke, Hirshfeld, CM5, Hirshfeld-I, NPA, CHELPG, MK-ESP) in common use, the charge fluctuation contribution is found to dominate the molecular polarizability, with its ratio ranging from 59.9% with the Hirshfeld or CM5 scheme to 96.2% with the Mulliken scheme. The Hirshfeld-I scheme is also used to compute the other contribution to the molecular polarizability coming from the induced atomic dipoles, and the atomic polarizabilities in 8 small molecules and water pentamer are found to be highly anisotropic for most atoms. Overall, the results suggest that (a) more emphasis probably should be placed on the charge fluctuation terms in future polarizable force field development; (b) an anisotropic polarizability might be more suitable than an isotropic one in polarizable force fields based entirely or partially on the induced atomic dipoles.

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“…This method is based on linear response theory and was proposed by Karamertzanis et al 73 . who showed that under the approximation of linear electronic response, the sum of electrostatic and polarization interactions of a molecule with an external electric field is equal to the electrostatic interaction of a half-polarized molecule with the same field 74 , 75 . This means that atomic multipoles in a non-polarizable force field should be based on a (distributed) multipole expansion of the average of the vacuum and solvated electron densities.…”

Section: Methodsmentioning

confidence: 99%

Hydration Free Energies in the FreeSolv Database Calculated with Polarized Iterative Hirshfeld Charges

Riquelme

Lara

Mobley

et al. 2018

J. Chem. Inf. Model.

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Computer simulations of bio-molecular systems often use force fields, which are combinations of simple empirical atom-based functions to describe the molecular interactions. Even though polarizable force fields give a more detailed description of intermolecular interactions, nonpolarizable force fields, developed several decades ago, are often still preferred because of their reduced computation cost. Electrostatic interactions play a major role in bio-molecular systems and are therein described by atomic point charges. In this work, we address the performance of different atomic charges to reproduce experimental hydration free energies in the FreeSolv database in combination with the GAFF force field. Atomic charges were calculated by two atoms-in-molecules approaches, Hirshfeld-I and Minimal Basis Iterative Stockholder (MBIS). To account for polarization effects, the charges were derived from the solute’s electron density computed with an implicit solvent model and the energy required to polarize the solute was added to the free energy cycle. The calculated hydration free energies were analyzed with an error model, revealing systematic errors associated with specific functional groups or chemical elements. The best agreement with the experimental data is observed for the AM1-BCC and the MBIS atomic charge methods. The latter includes the solvent polarization and present a root mean square error of 2.0 kcal mol−1 for the 613 organic molecules studied. The largest deviation was observed for phosphorus-containing molecules and the molecules with amide, ester and amine functional groups.

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QM/MM-Based Fitting of Atomic Polarizabilities for Use in Condensed-Phase Biomolecular Simulation

Cited by 19 publications

References 87 publications

A systematic approach to calibrate a transferable polarizable force field parameter set for primary alcohols

A systematic approach to calibrate a transferable polarizable force field parameter set for primary alcohols

Numerical Study on the Partitioning of the Molecular Polarizability into Fluctuating Charge and Induced Atomic Dipole Contributions

Hydration Free Energies in the FreeSolv Database Calculated with Polarized Iterative Hirshfeld Charges

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