Amide I vibrational frequencies of alpha-helical peptides based upon ONIOM and density functional theory (DFT) studies

The Journal of Physical Chemistry. B
Robert Wieczorek, J J Dannenberg

Abstract

We present ONIOM and pure DFT calculations on infrared spectra of alpha-helical-capped polyalanines. The calculations used two-layer ONIOM (B3LYP/D95**:AM1) calculations of the amide I vibrational frequencies for acetyl(ala)NNH2 (N=8, 10, 12-18) whose structures have been previously completely optimized by the same method. These are the first such calculations based upon structures of alpha-helical peptides that are completely optimized using DFT or molecular orbital methods. As the peptide becomes longer, the amide I band becomes both more intense and more red shifted. However, the individual absorptions that contribute most to the band vary between three patterns: one very intense absorption, two absorptions of similar intensity, and two strong absorptions where one is roughly twice as intense as the other. This pattern appears to be related to the relative number of H bonds in the individual H-bonding chains; however, there is one exception. Using 14C=O's to selectively decouple specific C=O's, we found that the couplings between the C=O's within each of the three individual H-bonding chains within the helices follow the same pattern previously reported for planar H-bonding chains of formamides. The coupling between the H-bo...Continue Reading

References

Sep 27, 2001·Journal of the American Chemical Society·R Schweitzer-StennerK Griebenow
Jan 8, 2004·Journal of the American Chemical Society·Qingyi LuSridhar Komarneni
May 6, 2004·Journal of the American Chemical Society·Cynthia PaulPaul H Axelsen
May 21, 2005·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Lars IsmerJörg Neugebauer
Apr 25, 2006·Physical Chemistry Chemical Physics : PCCP·Wutharath ChinMichel Mons
Jul 1, 2006·The Journal of Organic Chemistry·Marcin PalusiakMiquel Solà
Jul 21, 2006·The Journal of Physical Chemistry. B·Aleksandr V Mikhonin, Sanford A Asher
Jan 27, 2007·The Journal of Organic Chemistry·Roman I ZubatyukJerzy Leszczynski
Mar 31, 2007·The Journal of Physical Chemistry. B·Nataliya S Myshakina, Sanford A Asher
Sep 1, 2006·Journal of Chemical Theory and Computation·Keiji MorokumaThom Vreven

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Citations

Mar 13, 2010·Journal of Molecular Modeling·Angamuthu Abiram, Ponmalai Kolandaivel
Jan 30, 2010·International Journal of Molecular Sciences·Shiru JiaYuhua Qi
Feb 4, 2016·Chemical Reviews·A Subha Mahadevi, G Narahari Sastry
Apr 9, 2015·Chemical Reviews·Lung Wa ChungKeiji Morokuma
Jul 12, 2016·Physical Chemistry Chemical Physics : PCCP·Waldemar HoffmannKevin Pagel
Dec 18, 2013·The Journal of Physical Chemistry. B·Timothy ZekoMatthew A Kubasik
Jun 29, 2013·The Journal of Physical Chemistry. a·Sergey A KatsyubaTimur I Burganov
Jul 16, 2011·Physical Chemistry Chemical Physics : PCCP·A Subha MahadeviG Narahari Sastry
Oct 24, 2008·The Journal of Physical Chemistry. a·Yves BouteillerJean Pierre Schermann
Jun 23, 2009·The Journal of Physical Chemistry. a·Jean-Christophe PoullyJean-Pierre Schermann
Apr 5, 2008·The Journal of Physical Chemistry. B·Raji Viswanathan, J J Dannenberg

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