Site-specific hydrogen-bonding interaction between N-acetylproline amide and protic solvent molecules: Comparisons of IR and VCD measurements with MD simulations

Kwang Im Oh, Jaebeom Han, Kyung Koo Lee, Seungsoo Hahn, Hogyu Han, Minhaeng Cho

Research output: Contribution to journalArticle

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Abstract

The effects of solute - solvent interactions on solution structures of small peptides have been paid a great deal of attention. To study the effect of hydrogen-bonding interactions on peptide solution structures, we measured the amide I IR and VCD spectra of N-acetylproline amide (AP) in various protic solvents, i.e., D2O, MeOD, EtOD, and PrOD, and directly compared them with theoretically simulated ones. The numbers of protic solvent molecules hydrogen-bonded to the two peptide bonds in the AP were quantitatively determined by carrying out the molecular dynamics (MD) simulations and then compared with the spectral analyses of the experimentally measured amide I bands. The two peptides in the AP have different propensities of forming H-bonds with protic solvent molecules, and the H-bond population distribution is found to be strongly site-specific and solvent-dependent. However, it is found that adoption of the polyproline II (PII) conformation by AP in protic solvents does not strongly depend on the hydrogen bond network-forming ability of protic solvents nor on the solvent polarity. We present a brief discussion on the validity as well as limitation of the currently available force field parameters used for the present MD simulation study.

Original languageEnglish
Pages (from-to)13355-13365
Number of pages11
JournalJournal of Physical Chemistry A
Volume110
Issue number50
DOIs
Publication statusPublished - 2006 Dec 21

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Molecular Dynamics Simulation
Hydrogen Bonding
Amides
amides
Molecular dynamics
Hydrogen bonds
molecular dynamics
Molecules
Computer simulation
hydrogen
peptides
molecules
simulation
interactions
Peptides
Hydrogen
Population distribution
N-acetylproline
field theory (physics)
Conformations

ASJC Scopus subject areas

  • Physical and Theoretical Chemistry

Cite this

Site-specific hydrogen-bonding interaction between N-acetylproline amide and protic solvent molecules : Comparisons of IR and VCD measurements with MD simulations. / Oh, Kwang Im; Han, Jaebeom; Lee, Kyung Koo; Hahn, Seungsoo; Han, Hogyu; Cho, Minhaeng.

In: Journal of Physical Chemistry A, Vol. 110, No. 50, 21.12.2006, p. 13355-13365.

Research output: Contribution to journalArticle

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