Adsorption of Amino Acids on Graphene: Assessment of Current Force Fields

Abstract

We compare the free energies of adsorption (∆A ads ) and the structural preferences of amino acids obtained using the 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 ∆A ads differ between the force fields, the trends in the free energy of adsorption with amino acids are similar across the studied force fields. ∆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 while the thermodynamics of adsorption of proteins and peptides would be described consistently across different force fields, the structural preferences of peptides and proteins on graphene will be force field dependent.

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

“…This is true especially because ∆A ads of larger proteins is generally not the simple sum of the ∆A ads of individual amino acids. [70,80] The free energies of adsorption of amino acids on graphene are not reported by wet-laboratory experiments to date for validating any of the studied force fields. Indirect validations can be performed by comparing the binding preferences of amino acids on graphene with the corresponding observations from ab initio, simulations, and wet-laboratory studies.…”

Molecular thermodynamics for amino‐acid adsorption at inorganic surfaces

“…Complementary to experimental investigations, molecular modeling offers valuable details to bridge the knowledge gap between microscopic and macroscopic observations. Whereas atomistic models can be used to describe amino-acid adsorption through molecular dynamics (MD) simulation, [15][16][17] coarse-grained models are often more convenient for the development of analytical methods. By capturing the essential features of intermolecular interactions and surface forces, coarse-grained models are able to provide quantitative predictions in good agreement with experimental observations.…”

Thermal Selection of Aqueous Molecular Conformations for Tailored Energetics of Peptide Assemblies at Solid Interfaces

“…Using these potential molecular contacts, a ballpark energetic estimate of the binding energy of the peptides was calculated based on MD determined free energies of adsorption available in the literature, provided in Table 1. 50 As the IFA energies were determined on dried peptide monolayers, there may be some inherent error in the binding energy estimates as they are based on aqueous MD. Despite this potential discrepancy, we believe the error to be acceptable for the stated goal of providing a plausible molecular interpretation of our experimental energies, as (i) the peptide monolayers are likely still hydrated considering experimental challenge in removing water from thin films with hydrogen bonding, and (ii) MD free energy values found in the literature have a range of a few kcal/ mol.…”

“…a Range of energies determined by Dasetty et al for various forcefields 50. Values rounded to the nearest kcal/mol.…”