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

• Published in: Soft matter 2019-03, Vol.15 (11), p.2359-2372
• Main Authors: Dasetty, Siva, Barrows, John K, Sarupria, Sapna
• Format: Article
• Language: English
• Subjects: Adsorption; Amino acids; Clustering; Conformation; Correlation analysis; Free energy; Graphene; Principal components analysis; Proteins
• ISSN: 1744-683X; 1744-6848
• DOI: 10.1039/c8sm02621a

We compare the free energies of adsorption (Δ A ads ) 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 Δ A ads differ between the force fields, the relative free energy of adsorption across amino acids is similar for the studied force fields. Δ A ads 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 different structural preferences in the graphene adsorbed state. We thoroughly investigate the differences in free energy of adsorption and the structures of the amino acids adsorbed on graphene with force fields.