Paper Citing NAMD - Abstract
Feng, Jie; Pandey, Ras B.; Berry, Rajiv J.; Farmer, Barry L.; Naik, Rajesh R.; Heinz, Hendrik
Adsorption mechanism of single amino acid and surfactant molecules to Au {111} surfaces in aqueous solution: design rules for metal-binding molecules
SOFT MATTER, 7:2113-2120, 2011
The adsorption mechanism of twenty amino acids and four surfactants was examined on a {111} surface of gold in dilute aqueous solution using molecular dynamics simulation with a broadly applicable intermolecular potential CHARMM-METAL. All molecules are attracted to the surface between -3 and -26 kcal mol(-1). The adsorption strength correlates with the degree of coordination of polarizable atoms (O, N, C) to multiple epitaxial sites. Therefore, the molecular size and geometry rather than the specific chemistry determine the adsorption energy. Large molecules with planar sp(2) hybridized groups (Arg, Trp, Gln, Tyr, Asn, and PPh3) adsorb most strongly, followed by molecules with polar sp(3) hybridized groups, and short molecules with sp(3) hybridized alkyl groups exhibit least attraction. Conformationally flexible, extended molecules such as hexadecyltrimethylammonium bromide (CTAB) also showed significant attraction to the metal surface related to accommodation in epitaxial grooves and coordination with numerous epitaxial sites. Computational results are consistent with combinatorial binding experiments, observations in the growth and stabilization of metal nanoparticles, and ab initio data. The mechanism of adsorption conforms to soft epitaxy observed for peptides on metal surfaces (H. Heinz et al., J. Am. Chem. Soc., 2009, 131, 9704) and enables the de novo design of molecules for binding to a given metal surface. In addition to soft epitaxy, contributions to adsorption are possible by covalent bonding and induced charges.
