Partial charges by multipole constraint. Application to the amino acids

Gruschus, James M.; Kuski, Atsuo

doi:10.1002/jcc.540110810

Cited by 15 publications

(4 citation statements)

References 34 publications

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“…90 (The general idea to constrain atom-centered point charges to exactly reproduce the molecular dipole moment is impossible for planar molecules placed in an electric eld perpendicular to the molecule's plane. A point-charge only model includes the rst term in eqn (102) but neglects the atomic dipole terms.…”

Section: Electrostatic Potential Expansion: Atomic Multipole Moments mentioning

confidence: 99%

“…Unless a pointcharge only model is explicitly dened to reproduce m (or higher order multipole) exactly, it will generally reproduce m (or higher order multipole) only approximately except in cases where m (or higher order multipole) is zero by symmetry. 90 (The general idea to constrain atom-centered point charges to exactly reproduce the molecular dipole moment is impossible for planar molecules placed in an electric eld perpendicular to the molecule's plane. For this reason, we abandon the idea to constrain atom-centered point charges to exactly reproduce the system's dipole moment.)…”

Section: Electrostatic Potential Expansion: Atomic Multipole Moments ...mentioning

confidence: 99%

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Introducing DDEC6 atomic population analysis: part 1. Charge partitioning theory and methodology

2016

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Net atomic charges (NACs) are widely used in all chemical sciences to concisely summarize key information about the partitioning of electrons among atoms in materials. The objective of this article is to develop an atomic population analysis method that is suitable to be used as a default method in quantum chemistry programs irrespective of the kind of basis sets employed. To address this challenge, we introduce a new atoms-in-materials method with the following nine properties: (1) exactly one electron distribution is assigned to each atom, (2) core electrons are assigned to the correct host atom, (3) NACs are formally independent of the basis set type because they are functionals of the total electron distribution, (4) the assigned atomic electron distributions give an efficiently converging polyatomic multipole expansion, (5) the assigned NACs usually follow Pauling scale electronegativity trends, (6) NACs for a particular element have good transferability among different conformations that are equivalently bonded, (7) the assigned NACs are chemically consistent with the assigned atomic spin moments, (8) the method has predictably rapid and robust convergence to a unique solution, and (9) the computational cost of charge partitioning scales linearly with increasing system size. We study numerous materials as examples: (a) a series of endohedral C 60 complexes, (b) high-pressure compressed sodium chloride crystals with unusual stoichiometries, (c) metal-organic frameworks, (d) large and small molecules, (e) organometallic complexes, (f) various solids, and (g) solid surfaces. Due to non-nuclear attractors, Bader's quantum chemical topology could not assign NACs for some of these materials. We show for the first time that the Iterative Hirshfeld and DDEC3 methods do not always converge to a unique solution independent of the initial guess, and this sometimes causes those methods to assign dramatically different NACs on symmetry-equivalent atoms. By using a fixed number of charge partitioning steps with well-defined reference ion charges, the DDEC6 method avoids this problem by always converging to a unique solution. These characteristics make the DDEC6 method ideally suited for use as a default charge assignment method in quantum chemistry programs. † Electronic supplementary information (ESI) available: Summary of alternative charge partitioning algorithms considered; summary of integration routines; iterative algorithm for computing the Convex functional NACs; ow diagrams for the DDEC6 method; and .xyz les (which can be read using any text editor or the free Jmol visualization program downloadable from http://jmol.sourceforge.net) containing geometries, net atomic charges, atomic dipoles and quadrupoles, tted tail decay exponents, and ASMs. See

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Section: Electrostatic Potential Expansion: Atomic Multipole Moments mentioning

confidence: 99%

Section: Electrostatic Potential Expansion: Atomic Multipole Moments ...mentioning

confidence: 99%

Introducing DDEC6 atomic population analysis: part 1. Charge partitioning theory and methodology

2016

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“…Accordingly, implementation of this strategy in stochastic molecular dynamics of biomacromolecules would allow expanding sensibly the simulation time by nearly 2 orders of magnitude. The successful application of this approach, nevertheless, can be modulated by several factors, among which the proper balance between solute−solvent and intrasolute polarization effects, the conformational dependence of charges, and their transferability between related functional groups must be considered. The limitations of the atomic charges to give a good description of the electrostatic contribution in all conformations can be overcome, at least partially, by using charges derived from the electrostatic potential and field for each molecular conformation weighting according to the appropriate Boltzmann population …”

Section: Resultsmentioning

confidence: 99%

Semiclassical-Continuum Approach to the Electrostatic Free Energy of Solvation

Luque

Orozco

1997

J. Phys. Chem. B

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A new semiclassical continuum approach for computation of the electrostatic contribution to the free energy of solvation is presented. The method is based on a first-order perturbation treatment of the linear response approximation for the solvent effect. The expression for the electrostatic free energy of solvation afforded by the perturbative approach is formally similar to the classical continuum algorithm reported by Miertus, Scrocco, and Tomasi. Nevertheless, the semiclassical approach allows an accurate, inexpensive treatment of polarization effects, which relies on the use of two sets of partial charges for description of the solute-solvent interactions. The two sets of charges reflect the charge distribution of the solute in the gas phase and fully relaxed in solution. Particular attention is paid to the parametrization of the partial charges. The results determined by using the semiclassical approach for a series of prototypical neutral polar molecules, for selected amino acid residues in neutral and zwitterionic states, and for several test calculations on peptides are very close to the values determined from quantum mechanical self-consistent reaction field calculations. These encouraging results allow us to examine the potential application of the semiclassical treatment as a fast procedure for the inclusion of solvent polarization effects in force-field-derived methods.

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“…In a similar manner, the electrostatic interactions between the rings were computed using potentials from Ref. 31. Again, the interactions, on average, favored the 310 forms slightly.…”

Section: Resultsmentioning

confidence: 99%

Conformational preferences of oligopeptides rich in α‐aminoisobutyric acid. I. Observation of a 3₁₀/α‐helical transition upon sequence permutation

1991

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The solution conformation of peptides rich in the alpha, alpha-dialkylated amino acid Aib has proven to be a subtle problem, not because of helix/coil transitions, but rather because of alpha-helical/3(10)-helical competition. A special series of peptides containing 75% Aib has been synthesized that feature identical amino acid composition but differing sequences; they are sequence permutation isomers. Nuclear magnetic resonance hydrogen-bonding studies reveal that there is a sequence permutation induced transition between the two alternative helical forms within this set. The implications for the design and conformational prediction of helical Aib-rich peptides are discussed.

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Partial charges by multipole constraint. Application to the amino acids

Cited by 15 publications

References 34 publications

Introducing DDEC6 atomic population analysis: part 1. Charge partitioning theory and methodology

Introducing DDEC6 atomic population analysis: part 1. Charge partitioning theory and methodology

Semiclassical-Continuum Approach to the Electrostatic Free Energy of Solvation

Conformational preferences of oligopeptides rich in α‐aminoisobutyric acid. I. Observation of a 3₁₀/α‐helical transition upon sequence permutation

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Partial charges by multipole constraint. Application to the amino acids

Cited by 15 publications

References 34 publications

Introducing DDEC6 atomic population analysis: part 1. Charge partitioning theory and methodology

Introducing DDEC6 atomic population analysis: part 1. Charge partitioning theory and methodology

Semiclassical-Continuum Approach to the Electrostatic Free Energy of Solvation

Conformational preferences of oligopeptides rich in α‐aminoisobutyric acid. I. Observation of a 310/α‐helical transition upon sequence permutation

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Conformational preferences of oligopeptides rich in α‐aminoisobutyric acid. I. Observation of a 3₁₀/α‐helical transition upon sequence permutation