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Force Field Optimization using Dynamics and Ensemble Averaged Data : Vibrational Spectra and Relaxation in Bound MbCO

Devereux, M. and Meuwly, M.. (2010) Force Field Optimization using Dynamics and Ensemble Averaged Data : Vibrational Spectra and Relaxation in Bound MbCO. Journal of Chemical Information and Modeling, 50. pp. 349-357.

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Official URL: http://edoc.unibas.ch/dok/A5842405

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Abstract

Force field parameters are ingredients for realistic atomistic simulations of gas- and condensed-phase systems. Here we discuss the effect of including averaged data from explicit MD simulations in optimizing potential energy functions. It is shown that vibrational frequencies (FeC and CO stretch and FeCO bend) and CO vibrational relaxation times ((v = 1) → (v = 0) (T10) and (v = 2) → (v = 1) (T21)) in the active site of CO-bound myoglobin (MbCO) can be well represented with a single set of force field parameters. It is further demonstrated that parameters fitted in a subsystem of MbCO comprising the CO ligand, heme group and proximal histidine, are transferable to investigating the full protein and to providing quantitatively correct results. In particular, it is possible to calculate the CO and FeC stretch and the FeCO bending frequency to within ≈5%; the relaxation time of the first vibrationally excited state including quantum corrections of T10 ≈25 ps is calculated close to the experimental value (17 ps), and the ratio T10/T21 ≈2 agrees favorably with experimental estimates. In contrast, following the more traditional approach of fitting frequencies from analyzing the Hessian matrix leads to a force field that captures frequencies correctly but not relaxation of vibrations.
Faculties and Departments:05 Faculty of Science > Departement Chemie > Chemie > Physikalische Chemie (Meuwly)
UniBasel Contributors:Meuwly, Markus
Item Type:Article, refereed
Article Subtype:Research Article
Publisher:American Chemical Society
ISSN:0095-2338
Note:Publication type according to Uni Basel Research Database: Journal article
Identification Number:
Last Modified:07 Dec 2016 13:47
Deposited On:14 Sep 2012 06:59

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