I am doing interaction studies of dna-drug. I want to know, what is the difference between distance dependent and distance independent dielectric constant? Also I want to know whether there is a possibility to use distance dependent dielectric constant in the ONIOM technique?
Alexey Nikitin
We can not directly calculate the DNA in a vacuum. It's too rough approximation.
Electrostatic forces break our model. Look at the Fig. 5a and 5b at
http://www.layruoru.com/dokuwiki/doku.php/dna_interaction_with_a_benzimidazole-containing_ligands
The simplest way to keep a reasonable geometry of the model is to make the dielectric constant proportional to the distance (Fig. 5c).
A more sophisticated technique is Generalized Born model (Fig. 5e and 5f).
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