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 journalArticlepeer-review

24 Citations (Scopus)


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
JournalJournal of Physical Chemistry Letters
Issue number10
Publication statusPublished - 2018 May 17

Bibliographical note

Funding Information:
This work was funded by NSF Career Grant CHE-1150727 and a Henry Dreyfus Teacher-Scholar Award to C.H.L. R.J.X. acknowledges a Velay summer fellowship from the Panaphill/ Uphill foundations. Additional support was provided by IBS Grant IBS-R023-D1 to M.C. C.H.L. also acknowledges helpful discussion with S. Corcelli in framing this manuscript.

Publisher Copyright:
© 2018 American Chemical Society.

ASJC Scopus subject areas

  • General Materials Science
  • Physical and Theoretical Chemistry


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