(592f) Density Functional Theory Study of Biomolecule Adsorption to Graphene and Modified Graphene: Molecular Insights into Biofilm Formation and Adhesion

Authors: 
Verma, S., South Dakota School of Mines & Technology
Benjamin, K. M., South Dakota School of Mines and Technology
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 molecules including exopolysaccharides (EPS) to surfaces.[1] To explore this hypothesis, we have studied the adsorption of mannose and glucuronic acid 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 the COMPASS and Universal classical force fields.[2-4] 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.[5] The generalized gradient approximation with PBE functional, Grimme’s DFT-D dispersion correction, and a DNP basis set are used for all calculations.[6-8] In addition to vacuum calculations, we have also studied the effect of liquid water solvent on adsorption by implementing the COSMO continuum solvation model.[9]

[1] Wang, J., Exopolysaccharides from a thermophilic bacterium Geobacillus sp. WSUCF1 – production, characterization, bioactivities and mechanisms, Ph.D. Thesis, South Dakota School of Mines and Technology, 2019.

[2] https://www.3dsbiovia.com/products/datasheets/adsorption-locator.pdf

[3] Sun, H., J. Phys. Chem. B, 102, 7338 (1998).

[4] Rappé, A. K., Casewit, C. J., Colwell, K. S., Goddard III, W. A., and Skiff, W. M., J. Am. Chem. Soc., 114, 10024 (1992).

[5] Delley, B., J. Chem. Phys., 113, 7756 (2000).

[6] Perdew, J. P., Burke, K., and Ernzerhof, M., Phys. Rev. Lett., 77, 3865 (1996).

[7] Grimme, S., Antony, J., Ehrlich, S., and Krieg, H., J. Chem. Phys., 132, 154104 (2010).

[8] Delley, B., J. Chem. Phys., 92, 508 (1990).

[9] Eckert, F. and Klamt, A., AIChE J., 48, 369 (2002).