The conformational sensitivity of iterative stockholder partitioning schemes

Verstraelen, Toon; Ayers, Paul W.; Speybroeck, Véronique Van; Waroquier, Michel

doi:10.1016/j.cplett.2012.07.028

Cited by 45 publications

(67 citation statements)

References 34 publications

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“…Within A-SAPT0, the sensitivity of the result to the choice of ISA atomic density fields should certainly be investigated. It is possible that another atomic charge model such as the Gaussian ISA variant, 109 Hirshfeld-I, 100 or Atoms-In-Molecules 80, 81 might provide more universal or intuitive visualizations than ISA. Additionally, more advanced visualization techniques should be developed to aid in the understanding of the electrostatics terms in systems with net charges, which exhibit physically correct but distracting electrostatic contributions of opposite signs, which largely cancel in the net.…”

Section: Discussionmentioning

confidence: 99%

Spatial assignment of symmetry adapted perturbation theory interaction energy components: The atomic SAPT partition

Parrish

Sherrill

2014

The Journal of Chemical Physics

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We develop a physically-motivated assignment of symmetry adapted perturbation theory for intermolecular interactions (SAPT) into atom-pairwise contributions (the A-SAPT partition). The basic precept of A-SAPT is that the many-body interaction energy components are computed normally under the formalism of SAPT, following which a spatially-localized two-body quasiparticle interaction is extracted from the many-body interaction terms. For electrostatics and induction source terms, the relevant quasiparticles are atoms, which are obtained in this work through the iterative stockholder analysis (ISA) procedure. For the exchange, induction response, and dispersion terms, the relevant quasiparticles are local occupied orbitals, which are obtained in this work through the Pipek-Mezey procedure. The local orbital atomic charges obtained from ISA additionally allow the terms involving local orbitals to be assigned in an atom-pairwise manner. Further summation over the atoms of one or the other monomer allows for a chemically intuitive visualization of the contribution of each atom and interaction component to the overall noncovalent interaction strength. Herein, we present the intuitive development and mathematical form for A-SAPT applied in the SAPT0 approximation (the A-SAPT0 partition). We also provide an efficient series of algorithms for the computation of the A-SAPT0 partition with essentially the same computational cost as the corresponding SAPT0 decomposition. We probe the sensitivity of the A-SAPT0 partition to the ISA grid and convergence parameter, orbital localization metric, and induction coupling treatment, and recommend a set of practical choices which closes the definition of the A-SAPT0 partition. We demonstrate the utility and computational tractability of the A-SAPT0 partition in the context of side-on cation-π interactions and the intercalation of DNA by proflavine. A-SAPT0 clearly shows the key processes in these complicated noncovalent interactions, in systems with up to 220 atoms and 2845 basis functions.

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Section: Discussionmentioning

confidence: 99%

Spatial assignment of symmetry adapted perturbation theory interaction energy components: The atomic SAPT partition

Parrish

Sherrill

2014

The Journal of Chemical Physics

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“…Hirshfeld-I charges are considerably larger in magnitude than Hirshfeld charges, they reproduce electrostatic potentials of organic molecules reasonably well 29 and they have a much lower conformational sensitivity than RESP charges 30 . However, in some corner cases, most notably metal-oxides, 51 Hirshfeld-I charges become ill-defined. For example, the oxygen dianion is unstable in gas phase and there exists no ground state density of this isolated dianion.…”

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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“…91 The other extreme is ISA, 90 in which the sphericity of the atoms is optimized at the expense of their locality. 115,116 In our experience, Hirshfeld-I partitioning provides a reasonable compromise.…”

Section: Therefore 4πr 2fmentioning

confidence: 99%