scholarly journals Atomic Charges and Electron Density Partitioning

1985 ◽  
Vol 38 (3) ◽  
pp. 273 ◽  
Author(s):  
EN Maslen ◽  
MA Spackman
Keyword(s):  
Electron Density ◽  
Diffraction Data ◽  
Diatomic Molecules ◽  
Dipole Moments ◽  
Atomic Charges ◽  
Crystalline Solids ◽  
Partitioning Methods

Atomic charges are derived from two dissimilar methods of partitioning the electron density of diatomic molecules. The results given by both methods are similar, with the exception of those for molecules containing lithium; factors responsible for this discrepancy are explored. The charges derived are correlated closely with electronegativity differences and with dipole moments. They follow chemically sensible trends and have reasonable magnitudes. The partitioning methods used in the derivation can also be applied to the analysis of diffraction data for crystalline solids.

Topological analysis of the experimental electron density

1996 ◽  
Vol 74 (6) ◽  
pp. 1171-1179 ◽  
Author(s):  
Vladimir G. Tsirelson
Keyword(s):  
Key Words ◽  
Electron Density ◽  
Diffraction Data ◽  
Topological Analysis ◽  
Crystalline Solids ◽  
X Ray Diffraction ◽  
X Ray ◽  
Experimental Electron Density

Methods of topological analysis of the experimental electron density reconstructed from X-ray diffraction data are described. Their advantages and drawbacks are discussed and the results for organic and inorganic crystalline solids are presented. Key words: topological analysis, experimental electron density.

Atomic charges, dipole moments, and Fukui functions using the Hirshfeld partitioning of the electron density

2002 ◽  
Vol 23 (12) ◽  
pp. 1198-1209 ◽  
Author(s):  
F. De Proft ◽  
C. Van Alsenoy ◽  
A. Peeters ◽  
W. Langenaeker ◽  
P. Geerlings
Keyword(s):  
Electron Density ◽  
Dipole Moments ◽  
Atomic Charges ◽  
Fukui Functions

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>

SAMPL6 Octanol-Water Partition Coefficients from Alchemical Free Energy Calculations with MBIS Atomic Charges

2019 ◽  
Author(s):  
Maximiliano Riquelme ◽  
Esteban Vöhringer-Martinez
Keyword(s):  
Free Energy ◽  
Electron Density ◽  
Free Energy Calculations ◽  
Basis Set ◽  
Energetic Cost ◽  
Atomic Charges ◽  
Free Energies ◽  
Energy Calculations ◽  
Alchemical Free Energy ◽  
Alchemical Free Energy Calculations

In molecular modeling the description of the interactions between molecules forms the basis for a correct prediction of macroscopic observables. Here, we derive atomic charges from the implicitly polarized electron density of eleven molecules in the SAMPL6 challenge using the Hirshfeld-I and Minimal Basis Set Iterative Stockholder(MBIS) partitioning method. These atomic charges combined with other parameters in the GAFF force field and different water/octanol models were then used in alchemical free energy calculations to obtain hydration and solvation free energies, which after correction for the polarization cost, result in the blind prediction of the partition coefficient. From the tested partitioning methods and water models the S-MBIS atomic charges with the TIP3P water model presented the smallest deviation from the experiment. Conformational dependence of the free energies and the energetic cost associated with the polarization of the electron density are discussed.

scholarly journals Crystallographic features of ammonium fluoroelpasolites: dynamic orientational disorder in crystals of (NH4)3HfF7 and (NH4)3Ti(O2)F5

2017 ◽  
Vol 73 (1) ◽  
pp. 1-9 ◽  
Author(s):  
Anatoly A. Udovenko ◽  
Alexander A. Karabtsov ◽  
Natalia M. Laptash
Keyword(s):  
Single Crystal ◽  
Electron Density ◽  
Diffraction Data ◽  
Central Atom ◽  
X Ray Diffraction ◽  
Dynamic Nature ◽  
Orientational Disorder ◽  
High Quality ◽  
Structural Units ◽  
X Ray

A classical elpasolite-type structure is considered with respect to dynamically disordered ammonium fluoro-(oxofluoro-)metallates. Single-crystal X-ray diffraction data from high quality (NH4)3HfF7 and (NH4)3Ti(O2)F5 samples enabled the refinement of the ligand and cationic positions in the cubic Fm \bar 3 m (Z = 4) structure. Electron-density atomic profiles show that the ligand atoms are distributed in a mixed (split) position instead of 24e. One of the ammonium groups is disordered near 8c so that its central atom (N1) forms a tetrahedron with vertexes in 32f. However, a center of another group (N2) remains in the 4b site, whereas its H atoms (H2) occupy the 96k positions instead of 24e and, together with the H3 atom in the 32f position, they form eight spatial orientations of the ammonium group. It is a common feature of all ammonium fluoroelpasolites with orientational disorder of structural units of a dynamic nature.

scholarly journals X-ray phase determination by the principle of minimum charge

1999 ◽  
Vol 55 (3) ◽  
pp. 489-499 ◽  
Author(s):  
Veit Elser
Keyword(s):  
Electron Density ◽  
Diffraction Data ◽  
Global Minimum ◽  
Unit Cell ◽  
Electronic Charge ◽  
Total Charge ◽  
Phase Determination ◽  
X Ray ◽  
Average Electron Density ◽  
Average Electron

When the electron density in a crystal or a quasicrystal is reconstructed from its Fourier modes, the global minimum value of the density is sensitively dependent on the relative phases of the modes. The set of phases that maximizes the value of the global minimum corresponds, by positivity of the density, to the density having the minimum total charge that is consistent with the measured Fourier amplitudes. Phases that minimize the total electronic charge (i.e. the average electron density) have the additional property that the lowest minima of the electron density become exactly degenerate and proliferate within the unit cell. The large number of degenerate minima have the effect that density maxima are forced to occupy ever smaller regions of the unit cell. Thus, by minimization of the electronic charge, the atomicity of the electron density is enhanced as well. Charge minimization applied to simulated crystalline and quasicrystalline diffraction data successfully reproduces the correct phases starting from random initial phases.

Structure and electron density of oxysulfide Sm2Ti2S2O4.9, a visible-light-responsive photocatalyst

2008 ◽  
Vol 64 (3) ◽  
pp. 291-298 ◽  
Author(s):  
Masatomo Yashima ◽  
Kiyonori Ogisu ◽  
Kazunari Domen
Keyword(s):  
Dft Calculations ◽  
Visible Light ◽  
Valence Band ◽  
Electron Density ◽  
Diffraction Data ◽  
Density Functional ◽  
Oxygen Deficiency ◽  
Covalent Bonds ◽  
Synchrotron Powder Diffraction ◽  
Visible Wavelengths

We report the crystal structure and electron density of samarium titanium oxysulfide, Sm2Ti2S2O4.9, photocatalyst obtained through the Rietveld analysis, maximum-entropy method (MEM) and MEM-based pattern fitting of the high-resolution synchrotron powder diffraction data taken at 298.7 K. The Sm2Ti2S2O4.9 has a tetragonal structure with the space group I4/mmm. Refined occupancy factors at the `equatorial' O1 and `apical' O2 sites were 0.994 (3) and 0.944 (12), respectively, which strongly suggest oxygen deficiency at the O2 site. Electron-density analyses based on the synchrotron diffraction data of Sm2Ti2S2O4.9 in combination with density-functional theory (DFT) calculations of stoichiometric Sm2Ti2S2O5 reveal covalent bonds between Ti and O atoms, while the Sm and S atoms are more ionic. The presence of S 3p and O 2p orbitals results in increased dispersion of the valence band, raising the top of the valence band and making the material active at visible wavelengths. The present DFT calculations of stoichiometric Sm2Ti2S2O5 indicate the possibility of overall splitting of water, although Sm2Ti2S2O4.9 works as a visible-light-responsive photocatalyst in aqueous solutions only in the presence of sacrificial electron donors or acceptors. The oxygen deficiency and cocatalyst seem to be factors affecting the catalytic activity.

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