Density Functional Theory Study of Biomolecule Adsorption to Graphene and Modified Graphene: Molecular Insights into Biofilm Formation and Adhesion

Author: Sourav Verma, Department of Chemical & Biological Engineering

Mentor: Dr. Kenneth Benjamin, Department of Chemical & Biological Engineering

Despite their prevalence in natural and engineered systems, the exact mechanisms and forces controlling biofilm formation and adhesion are relatively unknown. Moreover, most modeling studies to date have focused more on continuum or macroscopic film behavior. While those studies are important and necessary for biofilm engineering, investigations at the molecular level are needed, too.

Recent work has hypothesized that biofilm formation and adhesion may be related to the adsorption of key, early protein molecules including exopolysaccharides (EPS) to surfaces. As a first step towards exploring this hypothesis, we have studied the adsorption of amino acids, the building blocks of proteins, to graphene and copper-modified graphene surfaces using molecular modeling and simulation.

Specifically, the Adsorption Locator module within Biovia Materials Studio was used to sample adsorption configurational space through Monte Carlo simulation, using Universal classical force fields. After identifying the most energetically stable physisorption configurations, these same configurations were used as starting structures for subsequent density functional theory (DFT) quantum chemical calculations. DFT calculations are conducted using the DMOL3 module within Materials Studio. The generalized gradient approximation with PBE functional, Grimme’s DFT-D dispersion correction, and a DNP basis set are used for all calculations. In addition to vacuum calculations, we have also studied the effect of liquid water solvent on adsorption by implementing the COSMO continuum solvation model.