Minimal Basis Iterative Stockholder: Atoms in Molecules for Force-Field Development.

@article{Verstraelen2016MinimalBI,
  title={Minimal Basis Iterative Stockholder: Atoms in Molecules for Force-Field Development.},
  author={Toon Verstraelen and Steven Vandenbrande and Farnaz Heidar-Zadeh and Louis Vanduyfhuys and V{\'e}ronique Van Speybroeck and Michel Waroquier and Paul W. Ayers},
  journal={Journal of chemical theory and computation},
  year={2016},
  volume={12 8},
  pages={
          3894-912
        }
}
Atomic partial charges appear in the Coulomb term of many force-field models and can be derived from electronic structure calculations with a myriad of atoms-in-molecules (AIM) methods. More advanced models have also been proposed, using the distributed nature of the electron cloud and atomic multipoles. In this work, an electrostatic force field is defined through a concise approximation of the electron density, for which the Coulomb interaction is trivially evaluated. This approximate "pro… 

Comment on "Minimal Basis Iterative Stockholder: Atoms in Molecules for Force-Field Development"

Verstraelen et al. (J. Chem. Theory Comput. 12 (2016) 3894-3912) recently introduced a new method for partitioning the electron density of a material into constituent atoms. Their approach falls

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References

SHOWING 1-10 OF 139 REFERENCES

Direct computation of parameters for accurate polarizable force fields.

TLDR
This model is a generalization of the Atom-Condensed Kohn-Sham Density Functional Theory, approximated to second order and can now be defined with any underlying variational theory and it can include atomic multipoles and off-center basis functions.

Towards a force field based on density fitting.

TLDR
The results show very good agreement with density functional theory calculations, reproducing the individual CSOV energy contributions for a given interaction as well as the B3LYP total interaction energies with errors below kBT at room temperature.

A General Quantum Mechanically Derived Force Field (QMDFF) for Molecules and Condensed Phase Simulations.

  • S. Grimme
  • Chemistry
    Journal of chemical theory and computation
  • 2014
TLDR
Initial results suggest QMDFF as a routine tool for the computation of a wide range of properties and systems (e.g., for molecular dynamics of isolated molecules, explicit solvation, self-solvation (melting) or even for molecular crystals) in particular when standard parametrizations are unavailable.

Biomolecular Force Field Parameterization via Atoms-in-Molecule Electron Density Partitioning

TLDR
The proposed methods significantly reduce the number of empirical parameters needed to construct molecular mechanics force fields, naturally include polarization effects in charge and Lennard-Jones parameters, and scale well to systems comprised of thousands of atoms, including proteins.

A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu.

TLDR
The revised DFT-D method is proposed as a general tool for the computation of the dispersion energy in molecules and solids of any kind with DFT and related (low-cost) electronic structure methods for large systems.

General Model for Treating Short-Range Electrostatic Penetration in a Molecular Mechanics Force Field

TLDR
This empirical penetration model significantly improves agreement between point multipole and quantum mechanical electrostatic energies across the set of dimers and distances, while using only a limited set of parameters for each chemical element.

Improved Atoms-in-Molecule Charge Partitioning Functional for Simultaneously Reproducing the Electrostatic Potential and Chemical States in Periodic and Nonperiodic Materials.

TLDR
Comparisons to a variety of other charge assignment methods show that the DDEC/c3 net atomic charges are well-suited for constructing flexible force-fields for atomistic simulations.

Generalization of the Gaussian electrostatic model: extension to arbitrary angular momentum, distributed multipoles, and speedup with reciprocal space methods.

TLDR
The Coulomb and exchange components of the force field are extended to auxiliary basis sets of arbitrary angular momentum and the issue of computational speed is investigated by reciprocal space based formalisms which include the particle mesh Ewald (PME) and fast Fourier-Poisson (FFP) methods.

A test of the Hirshfeld definition of atomic charges and moments

TLDR
The Hirshfeld population analysis scheme which carves the molecular density into atomic density contributions is tested and, when the molecular deformation density converges to the true solution, the computed net charges will necessarily converge.

Screened Electrostatic Interactions in Molecular Mechanics.

TLDR
This work presents a scheme involving radial screened Coulomb potentials that reproduces the accurate electrostatics much more accurately than point-charge electrostatic interactions and chooses a more conservative parametrization that systematically underestimates the screening and only occasionally overestimates it.
...