Modeling vibrational spectra of amino acid side chains in proteins: Effects of chloride and bromide counterions on ethylguanidino vibrational frequencies

Carl Trindle, Mark S Braiman, Amy Beth Prager

Research output: Contribution to journalArticle

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Abstract

Ethylguanidinium salts in nonpolar medium offer a model of arginine side chains in halorhodopsin, a chloride transport agent. Identification of halide-sensitive vibrational modes may make possible a more detailed understanding of the environments of the arginine in biological systems. We report studies of the effects on the structure and vibrational spectra of the guanidinium cation arising from alkyl substitution, the presence of the counterion, and immersion in a polarizable medium. We used restricted Hartree-Fock and the Becke-Perdew 86 implementation of density functional theory, expressed in a 6-31 Gaussian basis, which give slightly differing accounts of the strength of interaction with the counterion and the structural consequences of the counterion on the guanidino core. We represented the solvent by the Onsager self-consistent reaction field, a cavity-continuum model. The medium moderated the counterion effects in a plausible way. We carried out density functional calculations on the vibrational spectrum of ethylguanidinium chloride and bromide and isotopic variants. Calculated frequencies for ethylguanidinium chloride and bromide closely match experimental data on C - N stretching modes and approximate the small observed shifts arising from halogen substitution. Frequencies for isotopically substituted species reflect the direction and relative magnitudes of known substituted species. Our estimates of 2D-and 15N-isotopic shifts suggest that there are vibrational modes which, for suitably substituted arginine systems, will be usefully diagnostic of their environment.

Original languageEnglish (US)
Pages (from-to)291-297
Number of pages7
JournalInternational Journal of Quantum Chemistry
Volume74
Issue number3
StatePublished - 1999
Externally publishedYes

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ASJC Scopus subject areas

  • Physical and Theoretical Chemistry

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