JAOA • Vol 105 • No 1 • January 2005 • 21-
A Theoretical Study of Polarization Effects on a Model Peptide Bond
Que Huong T. Nguyen, BS
Of the many aspects that govern the structure, stability, and functionality
of proteins, interactions involving peptide and hydrogen bonds often play a
very important role. Peptide bonds are present in proteins between amino acid
residues, covalently linking them together, and hydrogen bonds are present at,
among other locations, the substrate binding sites of enzymes, as well as the
structures such as the alpha helixes and beta confirmations. In order to
understand the fundamental aspects of peptide and hydrogen bonds in proteins,
three systems of N-methylacetamide (NMA) have been established and studied
from a theoretical perspective. Through the use of ab initio
molecular dynamics simulations, the structure of NMA in solution, as well as
in the gas and crystal phases, was computed and analyzed. From this, the
structural changes of NMA going from the gas to the crystal phase along with
the changes of the NMA vibrational spectra in differing chemical environments
were discussed and compared to available experimental data. In addition, the
dipole moment of water as induced by the presence of NMA was calculated in
order to quantify polarization effects present in NMA solution. Overall, the
results of this study coincide those of available experimental data and can be
used as the foundation for studying more complex systems involving
proteins.
Footnotes
A Best Poster Presentation Award Recipient
Western University of Health Sciences College of Osteopathic Medicine of
the Pacific, Pomona, Calif; Research conducted at the University of
California, Irvine through the Department of Chemistry
