Chemical Terms : Charge Functions

This set of functions deal with polarizability and partial charges.

Example

Compute charge for each atom in the given molecule:


charge()

The calculation returns the following numbers: 0; -0.15; -0.15; -0.15; -0.15; -0.15; 0; -0.15

List of Charge Functions

Click here for the complete list of charge functions.
Name License Description Return value Parameters Examples
atomicPolarizability
atomPol
pol
polarizability		 Charge Plugin Group calculates atomic polarizability the polarizability values
  • the atom index / MolAtom object,
  • the major microspecies pH (takes the input molecule itself if omitted)
 Molecule Context (All)
atomicPolarizability(0) returns the polarizability of atom  0 of the input molecule  atomicPolarizability(2, "7.4")returns the polarizability of atom  2 of the major microspecies taken at pH  7.4
Reaction Context (All)
averagePolarizability
averagePol
avgPol		 Charge Plugin Group calculates average molecular polarizability component considering 3D geometry the polarizability value
  • the major microspecies pH (takes the input molecule itself if omitted)
 Molecule Context (All)
averagePolarizability() returns the average polarizability component of the input molecule  averagePolarizability("7.4")returns the average polarizability component of the major microspecies taken at pH  7.4
Reaction Context (All)
axxPol Charge Plugin Group calculates principal component of polarizability tensor (a(xx), a(yy), a(zz)) the principal component of polarizability tensor
  • the major microspecies pH (takes the input molecule itself if omitted)
 Molecule Context (All)
axxPol() returns the principal component  a(xx) of polarizability tensor of the input molecule  axxPol("7.4") returns the principal component  a(xx) of polarizability tensor of the major microspecies taken at pH  7.4
Reaction Context (All)
ayyPol Charge Plugin Group calculates principal component of polarizability tensor (a(xx), a(yy), a(zz)) the principal component of polarizability tensor
  • the major microspecies pH (takes the input molecule itself if omitted)
 Molecule Context (All)
ayyPol() returns the principal component  a(yy) of polarizability tensor of the input molecule  ayyPol("7.4") returns the principal component  a(yy) of polarizability tensor of the major microspecies taken at pH  7.4
Reaction Context (All)
azzPol Charge Plugin Group calculates principal component of polarizability tensor (a(xx), a(yy), a(zz)) the principal component of polarizability tensor
  • the major microspecies pH (takes the input molecule itself if omitted)
 Molecule Context (All)
azzPol() returns the principal component  a(zz) of polarizability tensor of the input molecule  azzPol("7.4") returns the principal component  a(zz) of polarizability tensor of the major microspecies taken at pH  7.4
Reaction Context (All)
charge Charge Plugin Group calculates partial charges on atoms
for result types "aromaticsystem" / "aromaticring", calculates the sum of partial charges of the atoms in the aromatic system / smallest aromatic ring containing the atom		 the charge values
  • the atom index / MolAtom object,
  • the result type ("total" (default), "pi", "sigma", "aromaticsystem", "aromaticsystemsigma", "aromaticsystempi", "aromaticring", "aromaticringsigma", "aromaticringpi"),
  • the major microspecies pH (takes the input molecule itself if omitted)
 Molecule Context (All)
charge(0) returns the partial charge on atom  0 of the input molecule  charge(2, "pi", "7.4") returns the partial "pi" charge on atom  2 of the major microspecies taken at pH  7.4
Reaction Context (All)
molecularPolarizability
molPol		 Charge Plugin Group calculates molecular polarizability the polarizability value
  • the major microspecies pH (takes the input molecule itself if omitted)
 Molecule Context (All)
molecularPolarizability() returns the molecular polarizability of the input molecule  molecularPolarizability("7.4")returns the molecular polarizability of the major microspecies taken at pH  7.4
Reaction Context (All)
piOrbitalElectronegativity
pOEN		 Charge Plugin Group calculates atomic pi orbital electronegativity the pi orbital electronegativity values
  • the atom index / MolAtom object,
  • the major microspecies pH (takes the input molecule itself if omitted)
 Molecule Context (All)
piOrbitalElectronegativity(0)returns the pi orbital electronegativity of atom  0 of the input molecule  piOrbitalElectronegativity(2, "7.4")returns the pi orbital electronegativity of atom  2 of the major microspecies taken at pH  7.4
Reaction Context (All)
resonantCharge Charge Plugin Group calculates partial charges on atoms considering resonance effect
for result types "aromaticsystem" / "aromaticring", calculates the sum of partial charges of the atoms in the aromatic system / smallest aromatic ring containing the atom		 the charge values
  • the atom index / MolAtom object,
  • the result type ("total" (default), "pi", "sigma", "aromaticsystem", "aromaticsystemsigma", "aromaticsystempi", "aromaticring", "aromaticringsigma", "aromaticringpi"),
  • the major microspecies pH (takes the input molecule itself if omitted)
 Molecule Context (All)
resonantCharge(0) returns the partial charge on atom  0 of the input molecule considering resonance effect resonantCharge(2, "pi", "7.4")returns the partial "pi" charge on atom  2 of the major microspecies taken at pH  7.4considering resonance effect
Reaction Context (All)
sigmaOrbitalElectronegativity
sOEN		 Charge Plugin Group calculates atomic sigma orbital electronegativity the sigma orbital electronegativity values
  • the atom index / MolAtom object,
  • the major microspecies pH (takes the input molecule itself if omitted)
 Molecule Context (All)
sigmaOrbitalElectronegativity(0)returns the sigma orbital electronegativity of atom  0 of the input molecule  sigmaOrbitalElectronegativity(2, "7.4")returns the sigma orbital electronegativity of atom  2 of the major microspecies taken at pH  7.4
Reaction Context (All)