Polarizable force fields

A new classical empirical potential is proposed for water. The model uses a polarizable atomic multipole description of electrostatic interactions. Multipoles through the quadrupole are assigned to each atomic center based on a distributed multipole analysis (DMA) derived from large basis set molecular orbital calculations on the water monomer. Polarization is treated via self-consistent induced atomic dipoles. A modified version of Thole's interaction model is used to damp induction at short range. Repulsion-dispersion (vdW) effects are computed from a buffered 14-7 potential. In a departure from most current water potentials, we find that significant vdW parameters are necessary on hydrogen as well as oxygen. The new potential is fully flexible and has been tested versus a variety of experimental data and quantum calculations for small clusters, liquid water, and ice. Overall, excellent agreement with experimental and high level ab initio results is obtained for numerous properties, including cluster structures and energetics and bulk thermodynamic and structural measures. The parametrization scheme described here is easily extended to other molecular systems, and the resulting water potential should provide a useful explicit solvent model for organic solutes and biopolymer modeling. IntroductionEmpirical potential energy functions derived from classical molecular mechanics are central to computational modeling at the atomic level. Molecular mechanics has long enjoyed great success in application to many classes of isolated, gas-phase organic compounds. 1 Beginning with the pioneering work of Bernal and Fowler, 2 water has probably been the target of more potential energy models than any other substance. An interesting overview and historical perspective on the development of water models was recently presented by Finney. 3 Simple nonpolarizable pairwise-additive models that describe the average structure and energetics of liquid water have been in wide use for many years (e.g., TIP3P 4 and SPC 5 ). The recently developed TIP5P potential exhibits excellent agreement with the experimental internal energy, density, and O‚‚‚O radial distribution at room temperature. 6 These models typically use fixed atom-based partial charges to model electrostatics and include polarization response to the environment only in an averaged, mean-field sense. As a result, nonpolarizable potentials that provide excellent descriptions of the homogeneous bulk phase are poor models for gas phase clusters and for nonpolar solutes in polar solvents. For example, the gas phase binding energy of the water dimer is overestimated by more than 30% in the TIP5P model. In application to large biomolecular systems, there is concern that such models cannot correctly account for situations where the same nonpolarizable moiety is exposed to different electrostatic environments, either within a single large static structure or during a course of simulation. In addition, there is an inherent inconsistency in most nonpolarizable models related to thei...

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“…8,9 Water has been the focus of many such studies due to its highly polarizable, hydrogen bonded nature, and obvious biological importance.…”

Section: Introductionmentioning

confidence: 99%

Polarizable Atomic Multipole Water Model for Molecular Mechanics Simulation

Ren¹,

2003

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“…It is well-known that the molecularmechanics force fields employed in many of these methods have a limited accuracy, e.g. owing to the primitive treatment of electrostatic interactions [7,8]. Therefore, there has recently been much interest in using quantum mechanical (QM) calculations to improve binding affinities [9,10,11,12,13].…”

Section: Introductionmentioning

confidence: 99%

Free-energy perturbation and quantum mechanical study of SAMPL4 octa-acid host–guest binding energies

Mikulskis

Cioloboc

Andrejić

et al. 2014

J Comput Aided Mol Des

220

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Free-energy perturbation and quantum mechanical study of SAMPL4 octa-acid hostguest binding energies. Link to publication Citation for published version (APA): Mikulskis, P., Cioloboc, D., Andrejić, M., Khare, S., Brorsson, J., Genheden, S., ... Ryde, U. (2014). Free-energy perturbation and quantum mechanical study of SAMPL4 octa-acid host-guest binding energies. Journal of Computer-Aided Molecular Design, 28(4), 375-400. DOI: 10.1007/s10822-014-9739-x General rights Copyright and moral rights for the publications made accessible in the public portal are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights.• Users may download and print one copy of any publication from the public portal for the purpose of private study or research.• You may not further distribute the material or use it for any profit-making activity or commercial gain • You may freely distribute the URL identifying the publication in the public portal AbstractWe have estimated free energies for the binding of nine cyclic carboxylate guest molecules to the octa-acid host in the SAMPL4 blind-test challenge with four different approaches. First, we used standard free-energy perturbation calculations of relative binding affinities, performed at the molecular-mechanics (MM) level with TIP3P waters, the GAFF force field, and two different sets of charges for the host and the guest, obtained either with the restrained electrostatic potential or AM1-BCC methods. Both charge sets give good and nearly identical results, with a mean absolute deviation (MAD) of 4 kJ/mol and a correlation coefficient (R 2 ) of 0.8 compared to experimental results. Second, we tried to improve these predictions with 28 800 density-functional theory (DFT) calculations for selected snapshots and the non-Boltzmann Bennett acceptance-ratio method, but this led to much worse results, probably because of a too large difference between the MM and DFT potential-energy functions. Third, we tried to calculate absolute affinities using minimised DFT structures. This gave intermediate-quality results with MADs of 5-9 kJ/mol and R 2 = 0.6-0.8, depending on how the structures were obtained. Finally, we tried to improve these results using local coupled-cluster calculations with single and double excitations, and non-iterative perturbative treatment of triple excitations (LCCSD(T0)), employing the polarisable multipole interactions with supermolecular pairs approach. Unfortunately, this only degraded the predictions, probably because a mismatch between the solvation energies obtained at the DFT and LCCSD(T0) levels.Key Words: binding affinities, host-guest, free-energies perturbation, density-functional calculations, CCSD(T), polarisable multipole interactions. 2 IntroductionOne of the largest challenges of computational chemistry is to predict the binding affinity of a small ligand to a larger receptor molecule, e.g. a drug candidate to its receptor prot...

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“…9 The PE method requires at least polarizabilities to describe the effects of polarization both in the ground state and upon electronic excitation, so force fields based on fixed partial charges only cannot be used. Many different polarizable force fields exist, [10][11][12][13] but none of these has been developed specifically for the present purpose, i.e., molecular property calculations of solutes in solvents with solvent-specific isotropic parameters for an embedding method based on induced dipoles.…”

Section: Introductionmentioning

confidence: 99%

Averaged Solvent Embedding Potential Parameters for Multiscale Modeling of Molecular Properties

Beerepoot

Steindal

List

et al. 2016

J. Chem. Theory Comput.

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We derive and validate averaged solvent parameters for embedding potentials to be used in polarizable embedding quantum mechanics/molecular mechanics (QM/MM) molecular property calculations of solutes in organic solvents. The parameters are solvent-specific atom-centered partial charges and isotropic polarizabilities averaged over a large number of geometries of solvent molecules. The use of averaged parameters 1 reduces the computational cost to obtain the embedding potential, which can otherwise be a rate-limiting step in calculations involving large environments. The parameters are evaluated by analyzing the quality of the resulting molecular electrostatic potentials with respect to full QM potentials. We show that a combination of geometry-specific parameters for solvent molecules close to the QM region and averaged parameters for solvent molecules further away allows for efficient polarizable embedding multiscale modeling without compromising the accuracy. The results are promising for the development of general embedding parameters for biomolecules, where the reduction in computational cost can be considerable.

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Polarizable force fields

Cited by 478 publications

References 56 publications

Polarizable Atomic Multipole Water Model for Molecular Mechanics Simulation

Polarizable Atomic Multipole Water Model for Molecular Mechanics Simulation

Free-energy perturbation and quantum mechanical study of SAMPL4 octa-acid host–guest binding energies

Averaged Solvent Embedding Potential Parameters for Multiscale Modeling of Molecular Properties

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