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J Phys Chem A. 2009 Feb 19;113(7):1335-42. doi: 10.1021/jp8071525.

Understanding the role of intra- and intermolecular interactions in the formation of single- and double-helical structures of aromatic oligoamides: a computational study.

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Institute of Theoretical and Computational Chemistry, Key Laboratory of Mesoscopic Chemistry of Ministry of Education, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210093, PR China.


The generalized energy-based fragmentation (GEBF) approach has been implemented to extend the applications of density function theory (DFT) with empirical van der Waals (vdW) correction (Wu, Q.; Yang, W. T. J. Chem. Phys. 2002, 116, 515.) to large supramolecular systems with extensive pi-pi stacking interactions. This mixed approach, DFT(vdW)-GEBF, is applied to investigate the energies and structures of several aromatic oligoamide foldamers. Our calculations show that the formation of single helical structures is mainly driven by the stacking interaction between neighboring aromatic rings, further stabilized by the intramolecular hydrogen bonds of the backbone. The dimerization of two single helical strands to form the double helical structure is an energetically favorable process, which is mainly driven by extensive interstrand aromatic-aromatic interactions. However, the dimerization energy tends to decrease significantly for longer oligomeric strands.

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