This manual gives you a walk-through on how to use the Orbital Electronegativity Plugin:
Partial charge distribution of the molecule is governed by the orbital electronegativity (orbital EN) of the atoms in the molecule.
The Orbital Electronegativity Plugin is able to calculate the orbital EN values of atoms in a molecule.
Learn more about how the plugin calculates orbital electronegativity here.
The calculation results appear in a new window, displaying on each atom (except hydrogens) the EN value:
The structure field offers a context menu from MarvinView.
Fig, 1 Displayed orbital EN values next to the atoms
In the Orbital Electronegativity Options panel you can set the following options:
Decimal places: setting the number of decimal places with which the result value is given.
Type: setting the type of the calculation. (sigma charge or pi electronegativity components)
Take resonant structures: the average of the charge of the resonant srtuctures will be calculated.
Take major microspecies: the electronegativity of major the microspecies at the given pH is calculated
Fig. 2 Orbital EN Options panel