scholarly journals Protein side chain modeling with orientation‐dependent atomic force fields derived by series expansions

2011 ◽  
Vol 32 (8) ◽  
pp. 1680-1686 ◽  
Author(s):  
Shide Liang ◽  
Yaoqi Zhou ◽  
Nick Grishin ◽  
Daron M. Standley
Keyword(s):  
Force Fields ◽  
Side Chain ◽  
Series Expansions ◽  
Atomic Force

How accurately do force fields represent protein side chain ensembles?

2018 ◽  
Vol 86 (9) ◽  
pp. 935-944 ◽  
Author(s):  
Dušan Petrović ◽  
Xue Wang ◽  
Birgit Strodel
Keyword(s):  
Force Fields ◽  
Side Chain

Evaluating the London Dispersion Coefficients of Protein Force Fields Using the Exchange-Hole Dipole Moment Model

2018 ◽  
Author(s):  
Evan T. Walters ◽  
Mohamad Mohebifar ◽  
Erin R. Johnson ◽  
Christopher Rowley
Keyword(s):  
Dipole Moment ◽  
Force Fields ◽  
Higher Order ◽  
Side Chain ◽  
Dispersion Interactions ◽  
Dispersion Coefficients ◽  
Hydration Energies ◽  
London Dispersion ◽  
Higher Order Dispersion ◽  
Order Dispersion

<div>London dispersion is one of the fundamental intermolecular interactions involved in protein folding and dynamics. The popular CHARMM36, Amber ff14sb, and OPLS-</div><div>AA force fields represent these interactions through the C6 /r 6 term of the Lennard-Jones potential. The C6 parameters are assigned empirically, so these parameters are</div><div>not necessarily a realistic representation of the true dispersion interactions. In this work, dispersion coefficients of all three force fields were compared to corresponding</div><div>values from quantum-chemical calculations using the exchange-hole dipole moment (XDM) model. The force field values were found to be roughly 50% larger than the XDM values for protein backbone and side-chain models. The CHARMM36 and Amber OL15 force fields for nucleic acids were also found to exhibit this trend. To explore how these elevated dispersion coefficients affect predicted properties, the hydration energies of the side-chain models were calculated using the staged REMD-TI method of Deng and Roux for the CHARMM36, Amber ff14sb, and OPLS-AA force fields. Despite having large C 6 dispersion coefficients, these force fields predict side-chain hydration energies that are in generally good agreement with the experimental values, including for hydrocarbon residues where the dispersion component is the dominant attractive solute–solvent interaction. This suggests that these force fields predict the correct total strength of dispersion interactions, despite C6 coefficients that are considerably larger than XDM predicts. An analytical expression for the water–methane dispersion energy using XDM dispersion coefficients shows that that higher-order dispersion terms(i.e., C 8 and C 10 ) account for roughly 37.5% of the hydration energy of methane. This suggests that the C 6 dispersion coefficients used in contemporary force fields are</div><div>elevated to account for the neglected higher-order terms. Force fields that include higher-order dispersion interactions could resolve this issue.</div>

scholarly journals On the ability of molecular dynamics force fields to recapitulate NMR derived protein side chain order parameters

2016 ◽  
Vol 25 (6) ◽  
pp. 1156-1160 ◽  
Author(s):  
Evan S. O'Brien ◽  
A. Joshua Wand ◽  
Kim A. Sharp
Keyword(s):  
Molecular Dynamics ◽  
Force Fields ◽  
Order Parameters ◽  
Side Chain ◽  
Chain Order

scholarly journals Influence of methyl group in a quinoline moiety on optical and light-induced properties of side-chain azo-polymers

2021 ◽  
Author(s):  
D. Chomicki ◽  
O. Kharchenko ◽  
L. Skowronski ◽  
J. Kowalonek ◽  
V. Smokal ◽  
...  
Keyword(s):  
Thin Films ◽  
Side Chain ◽  
Photochromic Properties ◽  
Azo Polymers ◽  
Force Microscopy ◽  
Atomic Force ◽  
Responsive Behavior ◽  
Quinoline Moiety

AbstractWe present the optical and photochromic properties as well as surface quality of thin films of the methacrylic copolymers containing 2-methylquinoline and quinoline azo-dyes in side chain. The extinction coefficient and refractive index were determined using spectroscopic ellipsometry combined with transmittance measurements. Photo-responsive behavior was investigated by determination of trans–cis photoisomerization rates under irradiation with unpolarized 365 nm light. We found that optical properties as well as photoisomerization rates of investigated polymers are dependent on the presence of a methyl substituent in the 2nd position of the quinoline moiety. The quality of the thin films was examined using Atomic Force Microscopy measurements.

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