Adsorption of amino acids on graphene: assessment of current force fields

Soft Matter
Siva DasettySapna Sarupria

Abstract

We compare the free energies of adsorption (ΔAads) and the structural preferences of amino acids on graphene obtained using the non-polarizable force fields-Amberff99SB-ILDN/TIP3P, CHARMM36/modified-TIP3P, OPLS-AA/M/TIP3P, and Amber03w/TIP4P/2005. The amino acid-graphene interactions are favorable irrespective of the force field. While the magnitudes of ΔAads differ between the force fields, the relative free energy of adsorption across amino acids is similar for the studied force fields. ΔAads positively correlates with amino acid-graphene and negatively correlates with graphene-water interaction energies. Using a combination of principal component analysis and density-based clustering technique, we grouped the structures observed in the graphene adsorbed state. The resulting population of clusters, and the conformation in each cluster indicate that the structures of the amino acid in the graphene adsorbed state vary across force fields. The differences in the conformations of amino acids are more severe in the graphene adsorbed state compared to the bulk state for all the force fields. Our findings suggest that the force fields studied will give qualitatively consistent relative strength of adsorption across proteins but diff...Continue Reading

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Citations

Nov 12, 2019·Physical Chemistry Chemical Physics : PCCP·Zhongwang FuZheng Liu
Jan 23, 2021·Physical Chemistry Chemical Physics : PCCP·Bin Li, Changwen Mi
Mar 5, 2021·The Journal of Physical Chemistry. B·Siva Dasetty, Sapna Sarupria
Dec 13, 2019·Langmuir : the ACS Journal of Surfaces and Colloids·Tyler D JorgensonRené M Overney
Jul 6, 2019·Langmuir : the ACS Journal of Surfaces and Colloids·Mounika GosikaPrabal K Maiti

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Software Mentioned

OPLS
GRAPPA
house Perl script
GROMACS
Python script
in
Amber14
CHARMM22
CHARMM
Umbrella

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