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Issue 5, 2004
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Calculating vibrational frequencies of amides: From formamide to concanavalin A

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Abstract

The infrared (IR) is an information rich region of molecular spectra. From characteristic absorptions it is possible to determine much structural information about molecules. This has been used to a large degree in the study of protein structure as a complementary technique to circular dichroism, X-ray crystallography and NMR. However, the current understanding of protein IR spectra is predicated largely on empirical structure–spectra relationships that are not infallible. Providing a theoretical basis for protein spectra will help to reduce these problems. In this paper, we review our recent work on accurate and computationally efficient small molecule gas phase calculations and examine how point charge environments can mimic features of proteins. We then develop a general automated strategy for applying the transition dipole coupling method for computing the IR spectra of proteins. Finally, we study the effect of conformational dynamics on the amide I band of concanavalin A.

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Publication details

The article was received on 01 Oct 2003, accepted on 26 Nov 2003 and first published on 19 Dec 2003


Article type: Paper
DOI: 10.1039/B312181J
Citation: Phys. Chem. Chem. Phys., 2004,6, 998-1005
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    Calculating vibrational frequencies of amides: From formamide to concanavalin A

    T. M. Watson and J. D. Hirst, Phys. Chem. Chem. Phys., 2004, 6, 998
    DOI: 10.1039/B312181J

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