This manual gives you a walk-through on how to use the Polarizability Plugin:
Polarizability is the relative tendency of an electron cloud (a charge distribution) of a molecule to be distorted by an external electric field. The more stable an ionized (charged) site is the more polarizable its vicinity is. This is why atomic polarizability is an important factor in the determination of pKa and why it is considered in our pKa Plugin. Atomic polarizability is altered by partial charges of atoms. The Polarizability Plugin is able to calculate the atomic and molecular polarizability values.
We use two methods to calculate polarizability: one of the calculations is based on the atomic parameters in Miller et al., while the other is based on the parameters in Jensen et al.
The calculation result appears in a new (2D display or 3D display) window, displaying on each atom its polarizability contribution (its dimension is Å3) .
Fig. 1 Displayed atomic polarizability values in 2D
Fig. 2 Displayed atomic polarizability values in 3D
In the Polarizability 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 type of the calculation (molecular or atomic polarizability)
- Take 3D geometry (Thole): calculates the polarization tensor values.
- Take major microspecies: the polarizability of major microspecies at the given pH is calculated
Fig. 3 Polariizability Options panel
- Miller, K. J.; Savchik, J. A., J. Am. Chem. Soc., 1979, 101, 7206-7213; doi
- Jensen, L.; Åstrand, P.-O.; Osted, A.; Kongsted, J.; Mikkelsen, K.V. J. Chem. Phys., 2002, 116, 4001-4010; doi