Properties of atoms in molecules. V. Easy procedure for estimating atomic charges from calculated core-electron energies

1973 ◽  
Vol 95 (17) ◽  
pp. 5450-5455 ◽  
Author(s):  
Peter. Politzer ◽  
Alfred. Politzer
Keyword(s):  
Atoms In Molecules ◽  
Atomic Charges ◽  
Core Electron

The correspondence between Hückel theory and ab initio atomic charges in allyl ions

1988 ◽  
Vol 66 (11) ◽  
pp. 2961-2962 ◽  
Author(s):  
Tom S. Slee ◽  
Preston J. MacDougall
Keyword(s):  
Quantum Theory ◽  
Ab Initio ◽  
Atoms In Molecules ◽  
Atomic Charges ◽  
Allyl Cation ◽  
Hückel Theory ◽  
The Difference

Atomic charges for the allyl cation and anion are reported, as defined by the quantum theory of atoms in molecules. An interesting feature of these charges is that they differ considerably from expectations based on simple π orbital models. The reasons for the difference are investigated and it is shown that the charges are both compatible with and understandable in terms of simple orbital models.

Core Electron Energies, Infrared Intensities, and Atomic Charges

1997 ◽  
Vol 119 (18) ◽  
pp. 4224-4231 ◽  
Author(s):  
Paulo H. Guadagnini ◽  
Anselmo E. Oliveira ◽  
Roy E. Bruns ◽  
Benicio de Barros Neto
Keyword(s):  
Atomic Charges ◽  
Core Electron ◽  
Infrared Intensities

Integration of Core-Edge Spectroscopy Methods for the Study of Polymers

1996 ◽  
Vol 54 ◽  
pp. 154-155
Author(s):  
E. G. Rightor
Keyword(s):  
Excited State ◽  
Polymer Blends ◽  
Gas Phase ◽  
Spatial Resolution ◽  
High Spatial Resolution ◽  
Electronic States ◽  
Core Electron ◽  
Bulk Solids ◽  
Development Application

Core edge spectroscopy methods are versatile tools for investigating a wide variety of materials. They can be used to probe the electronic states of materials in bulk solids, on surfaces, or in the gas phase. This family of methods involves promoting an inner shell (core) electron to an excited state and recording either the primary excitation or secondary decay of the excited state. The techniques are complimentary and have different strengths and limitations for studying challenging aspects of materials. The need to identify components in polymers or polymer blends at high spatial resolution has driven development, application, and integration of results from several of these methods.

CORE ELECTRON SPECTROSCOPY OF SURFACE LAYERS ON LIQUID SUBSTRATES

1987 ◽  
Vol 48 (C9) ◽  
pp. C9-955-C9-959 ◽  
Author(s):  
S. HOLMBERG ◽  
R. MOBERG ◽  
O. BOHMAN ◽  
H. SIEGBAHN
Keyword(s):  
Electron Spectroscopy ◽  
Surface Layers ◽  
Core Electron

Hydration Free Energies of Organic Molecules in the FreeSolv Database Calculated with Polarized Atom In Molecules Atomic Charges and the GAFF Force Field.

2018 ◽  
Author(s):  
Maximiliano Riquelme ◽  
Alejandro Lara ◽  
David L. Mobley ◽  
Toon Vestraelen ◽  
Adelio R Matamala ◽  
...  
Keyword(s):  
Force Field ◽  
Functional Groups ◽  
Electrostatic Interactions ◽  
Organic Molecules ◽  
Force Fields ◽  
Chemical Elements ◽  
Atomic Charges ◽  
Free Energies ◽  
Molecular Systems ◽  
Solvent Model

<div>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.</div><div>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 MBIS atomic charge method, including the solvent polarization, with a root mean square error of 2.0 kcal mol<sup>-1</sup> for the 613 organic molecules studied. The largest deviation was observed for phosphor-containing molecules and the molecules with amide, ester and amine functional groups.</div>

Partition Coefficients of Methylated DNA Bases Obtained from Free Energy Calculations with Molecular Electron Density Derived Atomic Charges.

2018 ◽  
Author(s):  
Alejandro Lara ◽  
Maximiliano Riquelme ◽  
Esteban Vöhringer-Martinez
Keyword(s):  
Electron Density ◽  
Partition Coefficients ◽  
Dna Bases ◽  
Atomic Charges ◽  
Free Energies ◽  
Solvation Model ◽  
Minimal Basis ◽  
Methylated Dna ◽  
Implicit Solvation Model ◽  
Good Agreement

<div> <div> <div> <p>Partition coefficients serve in various areas as pharmacology and environmental sciences to predict the hydrophobicity of different substances. Recently, they have been also used to address the accuracy of force fields for various organic compounds and specifically the methylated DNA bases. In this study atomic charges were derived by different partitioning methods (Hirshfeld and Minimal Basis Iterative Stockholder) directly from the electron density obtained by electronic structure calculations in vac- uum, with an implicit solvation model or with explicit solvation taking the dynamics of the solute and the solvent into account. To test the ability of these charges to describe electrostatic interactions in force fields for condensed phases the original atomic charges of the AMBER99 force field were replaced with the new atomic charges and combined with different solvent models to obtain the hydration and chloroform solvation free energies by molecular dynamics simulations. Chloroform-water partition coefficients derived from the obtained free energies were compared to experimental and previously reported values obtained with the GAFF or the AMBER-99 force field. The results show that good agreement with experimental data is obtained when the polarization of the electron density by the solvent has been taken into account deriving the atomic charges of polar DNA bases and when the energy needed to polarize the electron den- sity of the solute has been considered in the transfer free energy. These results were further confirmed by hydration free energies of polar and aromatic amino acid side chain analogues. Comparison of the two partitioning methods Hirsheld-I and Minimal Basis Iterative Stockholder (MBIS) revealed some deficiencies in the Hirshfeld-I method related to nonexistent isolated anionic nitrogen pro-atoms used in the method. Hydration free energies and partitioning coefficients obtained with atomic charges from the MBIS partitioning method accounting for polarization by the implicit solvation model are in good agreement with the experimental values. </p> </div> </div> </div>

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