Foldamers, synthetic oligomers that adopt defined, stable secondary structures in solution, have been the focus of intense research efforts. In this study, molecular dynamics (MD) simulations of various arylamide oligomers in chloroform, methanol and aqueous solutions are carried out. Four types of aromatic building blocks, are used to construct oligomers with varying sizes from trimer to dodecamers through several different connection types. The MD simulations utilize the General Amber Force Field (GAFF) with re-parameterized aryl-amide (aryl-Cpeptide or aryl-Npeptide) torsional parameters and RESP charge sets specific to each building block. Quantum mechanical calculations and NMR conformational studies of appropriate model compounds are used in the parameterization and validation of  the above parameters. By studying the conformational preferences of these oligomers of different types and sizes in solution, we gain valuable information on how molecular scaffold, hydrogen bonding substituent, as well as solvent polarity, affect the structures of arylamide oligomers in solution.

Conformational control of aromatic oligoamide foldamers: Predicting oligomer structures in solution through molecular dynamics simulations

244th National Meeting (2012)

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