Paper Citing NAMD - Abstract
Preat, Julien; Rodriguez-Ropero, Francisco; Torras, Juan; Bertran, Oscar; Zanuy, David; Aleman, Carlos
Parameterization of the Torsional Potential for Calix[4]arene-Substituted Poly(thiophene)s
JOURNAL OF COMPUTATIONAL CHEMISTRY, 31:1741-1751, JUN 2010
Three different strategies have been followed to develop the torsional force-field parameters of the interring dihedral angles for calixt[4]arene-substituted poly(thiophene)s, a family of highly sensitive ion receptors. These procedures, which are based on the rotational profiles calculated using quantum mechanical methods. differ in the complexity of the model compounds and the processing applied to the quantum mechanical energies before the fitting. The performance of the three sets of developed parameters, which are essentially compatible with the General Amber Force Field, has been evaluated by computing the potential of mean forces for the inter-ring rotation of 2,2'-bithiophene, and its substituted analog bearing a calix[4]arene group in different environments. Finally, the ability of the new sets of torsional parameters to describe a calix[4]arene-substituted poly(thiophene) in tetrahydrofuran solution has been checked using Molecular Dynamics simulations. Specifically, the molecular shape, the polymer conformation, and the effects of the Na(+) ions trapped in the cavity of the receptor have been examined. Although the potential derived from unsubstituted 2,2'-bithiophene is able to reproduce the experimental free energies of the minima, the overall results indicate that the parameters derived from the analog bearing a calix[4]arene group provide the best description of the systems under study. This should be attributed to the strong constraints found in complex substituted poly(thiophene)s, which require parameterization strategies able to capture all the interactions and phenomena involved in their inter-ring rotations. (C) 2009 Wiley Periodicals, Inc. J Comput Chem 31: 1741-17.51. 2010
