Biomolecular springs: Low-frequency collective helical vibrations of Ace-Gly(n)-NHMe (n=3-8). A DFT study employing the PW91(XC) functional

 
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2004 (EN)
Biomolecular springs: Low-frequency collective helical vibrations of Ace-Gly(n)-NHMe (n=3-8). A DFT study employing the PW91(XC) functional (EN)

Papamokos, G. V. (EN)

Πανεπιστήμιο Ιωαννίνων. Σχολή Θετικών Επιστημών. Τμήμα Χημείας (EL)
Papamokos, G. V. (EN)

The collective helical vibrations of the Ace-Gly(n)-NHMe (n = 3, 4, 5, 6, 7, 8) series of molecules were studied. The computational vibration analysis at the DFT PW91(XC)/6-31+G* level of theory confirmed the kinds of vibrations that were previously described for helical polysulfanes. The, vibrations resembling the motion of (a) a transverse wave, (b) a longitudinal wave, and (c) a transformation of the cylindrical shape to a breathing pulse, to an ellipsoidal-hyperboloidal, or to a cone were also located in helical oligopeptides of glycine. The precursors of both the transverse and the longitudinal wave are C-C and C-N torsional vibrations while the origin of the cylindrical transformation is attributed to bond angle bending vibrations. The helical stretch 1r was located in all molecules but helical stretches 2r and 3r were not located in any molecule. Also, it was observed that helical twist is present, and mixed with helical bend. These collective motions are known to be interesting for their biological functions. They can also play an important role in the new field of nanomechanics as properties of molecular springs. Two additional computational experiments were carried out: (a) A 50-peptide alpha-helix consisting of consecutive dipeptides of gly-ala, was also studied employing molecular mechanics (AMBER force field). The motion of the helix is better observed in this helical peptide because of its length. (b) 310 helical Ace-Ala(4)-NHMe employing the PW91(XC)/6-31+G* was also studied to assess the use of glycine as a model. The sensitivity of the frequencies, intensities, and modes to grid quality was also assessed. (EN)

poly-l-alanine (EN)

Πανεπιστήμιο Ιωαννίνων (EL)
University of Ioannina (EN)

Journal of Physical Chemistry A (EN)

English

2004

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