Paper Citing NAMD - Abstract
Zanuy, David; Preat, Julien; Perpete, Eric A.; Aleman, Carlos
Response of Crown Ether Functionalized Polythiophenes to Alkaline Ions
JOURNAL OF PHYSICAL CHEMISTRY B, 116:4575-4583, APR 19 2012
The sensing response of 15-crown-S-ether functionalized polythiophene to Li+, Na+, and K+ has been investigated at the atomistic level using molecular dynamics simulations. The stability associated with all the identified binding sites has been corroborated by quantum mechanical calculations. Although the cavity of the macrocycle is not the most visited binding site, such receptor is responsible of the selective sensing response of this polythiophene derivative. PF6- counterions reduce the mobility of the alkaline cations, which do not occupy the crown ether cavity of consecutive repeating units due to electrostatic repulsions. Furthermore, the relative entropy for the "free state -> bound state" has been estimated using a procedure based on the covariance matrix atom-positional fluctuations. Evaluation of the entropic contributions allow us to complete the thermodynamics scenario of binding process, which was recently initiated by calculating the enthalpies at quantum mechanical level [Chem. Eur. J. 2009, 15, 4676]. Results indicate an entropycally driven binding preference.
