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 language | English |
|---|---|
| Pages (from-to) | 2560-2567 |
| Number of pages | 8 |
| Journal | Unknown Journal |
| Volume | 9 |
| Issue number | 10 |
| DOIs | |
| Publication status | Published - 2018 May 17 |
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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 journal › Article
}
TY - JOUR
T1 - A Direct, Quantitative Connection between Molecular Dynamics Simulations and Vibrational Probe Line Shapes
AU - Xu, Rosalind J.
AU - Blasiak, Bartosz
AU - Cho, Minhaeng
AU - Layfield, Joshua P.
AU - Londergan, Casey H.
PY - 2018/5/17
Y1 - 2018/5/17
N2 - 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.
AB - 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.
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U2 - 10.1021/acs.jpclett.8b00969
DO - 10.1021/acs.jpclett.8b00969
M3 - Article
VL - 9
SP - 2560
EP - 2567
JO - The BMJ
JF - The BMJ
SN - 0730-6512
IS - 10
ER -