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

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.

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 Influence of Copper(I) Halides on the Reactivity of Aliphatic Carbodiimides

2020 ◽  
Vol 3 (1) ◽  
pp. 20
Author(s):  
Valentina Ferraro ◽  
Marco Bortoluzzi
Keyword(s):  
Density Functional Theory ◽  
Electronic Structure ◽  
General Formula ◽  
Electron Density ◽  
Density Functional ◽  
Functional Theory ◽  
Fukui Functions ◽  
Bond Lengths ◽  
Linear Complexes ◽  
Nitrogen Bond

The influence of copper(I) halides CuX (X = Cl, Br, I) on the electronic structure of N,N′-diisopropylcarbodiimide (DICDI) and N,N′-dicyclohexylcarbodiimide (DCC) was investigated by means of computational DFT (density functional theory) methods. The coordination of the considered carbodiimides occurs by one of the nitrogen atoms, with the formation of linear complexes having a general formula of [CuX(carbodiimide)]. Besides varying the carbon–nitrogen bond lengths, the thermodynamically favourable interaction with Cu(I) reduces the electron density on the carbodiimides and alters the energies of the (NCN)-centred, unoccupied orbitals. A small dependence of these effects on the choice of the halide was observable. The computed Fukui functions suggested negligible interaction of Cu(I) with incoming nucleophiles, and the reactivity of carbodiimides was altered by coordination mainly because of the increased electrophilicity of the {NCN} fragments.

Electrostatically embedded many-body method for dipole moments, partial atomic charges, and charge transfer

2012 ◽  
Vol 14 (21) ◽  
pp. 7669 ◽  
Author(s):  
Hannah R. Leverentz ◽  
Katie A. Maerzke ◽  
Samuel J. Keasler ◽  
J. Ilja Siepmann ◽  
Donald G. Truhlar
Keyword(s):  
Charge Transfer ◽  
Dipole Moments ◽  
Atomic Charges ◽  
Many Body ◽  
Partial Atomic Charges ◽  
Body Method

Benchmarking Electronic Structure Methods for Accurate Fixed-Charge Electrostatic Models

2019 ◽  
Author(s):  
Alex Zhou ◽  
Michael Schauperl ◽  
Paul Nerenberg
Keyword(s):  
Electronic Structure ◽  
Gas Phase ◽  
Condensed Phase ◽  
Force Fields ◽  
Dipole Moments ◽  
Fixed Charge ◽  
Basis Set ◽  
Atomic Charges ◽  
Molecular Dipole ◽  
Partial Atomic Charges

<p>The accuracy of classical molecular mechanics (MM) force fields used for condensed phase molecular simulations depends strongly on the accuracy of modeling nonbonded interactions between atoms, such as electrostatic interactions. Some popular fixed-charge MM force fields use partial atomic charges derived from gas phase electronic structure calculations using the Hartree-Fock method with the relatively small 6-31G* basis set (HF/6-31G*). It is generally believed that HF/6-31G* generates fortuitously overpolarized electron distributions, as would be expected in the higher dielectric environment of the condensed phase. Using a benchmark set of 47 molecules we show that HF/6-31G* overpolarizes molecules by just under 10% on average with respect to experimental gas phase dipole moments. The overpolarization of this method/basis set combination varies significantly though and, in some cases, even leads to molecular dipole moments that are lower than experimental gas phase measurements. We further demonstrate that using computationally inexpensive density functional theory (DFT) methods, together with appropriate augmented basis sets and a continuum solvent model, can yield molecular dipole moments that are both more strongly and more uniformly overpolarized. These data suggest that these methods – or ones similar to them – should be adopted for the derivation of accurate partial atomic charges for next-generation MM force fields.<br></p>

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.

Sign in / Sign up

Export Citation Format

Share Document