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Vibrational spectroscopic studies of the structure and conformation of cyclic di-amino acid peptides

Vibrational spectroscopic studies of the structure and conformation of cyclic di-amino acid peptides

Mendham, Andrew P. (2006) Vibrational spectroscopic studies of the structure and conformation of cyclic di-amino acid peptides. PhD thesis, University of Greenwich.

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Abstract

The aim of the studies reported in this investigation was to examine (from both a theoretical and experimental perspective) the effect of the change in structure and conformation of the diketopiperazine (DKP) ring and the cis amide geometry of the peptide bond, in relation to the vibrational spectra of a series of cyclic di-amino acid peptides (CDAPs). Experimental Raman and infra-red spectra have been recorded for the following CDAPs: cyclo(Gly-Gly), cyclo(L-Ala-L-Ala), cyclo(L-Ala-Gly), cyclo(L-Met-L-Met), cyclo(L-Ser-LSer), cyclo(L-Asp-L-Asp), and cyclo(L-Glu-L-Glu). The Raman and infra-red spectra of the aforementioned CDAPs were recorded using solid state samples (protonated and N-deuteriated), and where possible in the aqueous solution state. Ab initio calculations have also been conducted on all the CDAPs examined experimentally in order to determine their energy minimized, i.e. geometry optimised, structures (based on single isolated molecule in the gaseous state). Normal coordinate calculations have provided vibrational assignments for fundamental modes, including their potential energy distributions. Single crystal X-ray structures have been determined for cyclo(L-Met-L-Met) and two polymorphs of cyclo(L-Glu-L-Glu). Cyclo(L-Met-L-Met) forms triclinic crystals, with one molecule per unit cell and occupies space group P1. The crystalline polymorphs of cyclo(L-Glu-L-Glu) are both monoclinic, with two molecules per unit cell, but form 1 occupies space group P21 and crystallises as hydrogen bonded layers and form 2 occupies space group C2 and crystallises as hydrogen bonded chains.

The work reported herein demonstrates that the cis amide vibrations of CDAPs have radically different potential energy distribution to those of the trans amide vibrations of peptides and proteins. The cis amide I vibrational bands of the CDAPs examined occur between ~1640 and 1690 cm-1, in a similar region to the trans amide I band which has been reported to appear at in the 1630-1700 cm-1 range. However, all the cis amide I modes investigated show a downward shift on N-deuteriation, of the order of ~30cm-1, indicating that the C=O stretch is significantly coupled to the N-H bend. In stark contrast, this coupling is greater than that found in trans amide peptides, which have been reported to show deuterium shifts in the order of 10-15cm-1. The cis amide II vibrational modes of the CDAPs, occur between ~1480 and 1525 cm-1, in a lower wavenumber region than the trans amide II band which has been reported in the 1510-1570cm-1 range. All the cis amide II modes investigated show a downward shift of N-deuteriation, of the order of about 10 to 30 cm-1. This mode is, apparently, mainly an out of phase Ca-C-N stretch with a lower degree of contribution from the N-H in plane bend than in the trans amide II mode.

Item Type: Thesis (PhD)
Additional Information: uk.bl.ethos.438714
Uncontrolled Keywords: covalent chemical bond, peptide bond, cyclic di-amino acid peptides, CDAPs, Raman spectroscopy, infra-red spectra, electromagnetics,
Subjects: Q Science > QC Physics
Q Science > QD Chemistry
Faculty / Department / Research Group: Faculty of Engineering & Science > Department of Pharmaceutical, Chemical & Environmental Sciences
Last Modified: 17 Oct 2016 09:11
URI: http://gala.gre.ac.uk/id/eprint/6251

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