A Direct, Quantitative Connection between Molecular Dynamics Simulations and Vibrational Probe Line Shapes

Rosalind J. Xu, Bartosz Blasiak, Minhaeng Cho, Joshua P. Layfield, Casey H. Londergan

Research output: Contribution to journalArticle

7 Citations (Scopus)

Abstract

A quantitative connection between molecular dynamics simulations and vibrational spectroscopy of probe-labeled systems would enable direct translation of experimental data into structural and dynamical information. To constitute this connection, all-atom molecular dynamics (MD) simulations were performed for two SCN probe sites (solvent-exposed and buried) in a calmodulin-target peptide complex. Two frequency calculation approaches with substantial nonelectrostatic components, a quantum mechanics/molecular mechanics (QM/MM)-based technique and a solvatochromic fragment potential (SolEFP) approach, were used to simulate the infrared probe line shapes. While QM/MM results disagreed with experiment, SolEFP results matched experimental frequencies and line shapes and revealed the physical and dynamic bases for the observed spectroscopic behavior. The main determinant of the CN probe frequency is the exchange repulsion between the probe and its local structural neighbors, and there is a clear dynamic explanation for the relatively broad probe line shape observed at the "buried" probe site. This methodology should be widely applicable to vibrational probes in many environments.

Original languageEnglish
Pages (from-to)2560-2567
Number of pages8
JournalUnknown Journal
Volume9
Issue number10
DOIs
Publication statusPublished - 2018 May 17

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Molecular dynamics
Computer simulation
Molecular mechanics
Quantum theory
Calmodulin
Vibrational spectroscopy
Peptides
Infrared radiation
Atoms
Experiments

ASJC Scopus subject areas

  • Materials Science(all)

Cite this

A Direct, Quantitative Connection between Molecular Dynamics Simulations and Vibrational Probe Line Shapes. / Xu, Rosalind J.; Blasiak, Bartosz; Cho, Minhaeng; Layfield, Joshua P.; Londergan, Casey H.

In: Unknown Journal, Vol. 9, No. 10, 17.05.2018, p. 2560-2567.

Research output: Contribution to journalArticle

Xu, Rosalind J. ; Blasiak, Bartosz ; Cho, Minhaeng ; Layfield, Joshua P. ; Londergan, Casey H. / A Direct, Quantitative Connection between Molecular Dynamics Simulations and Vibrational Probe Line Shapes. In: Unknown Journal. 2018 ; Vol. 9, No. 10. pp. 2560-2567.
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