Predictions of Pattern Formation in Amino Acid Adlayers at the In Vacuo Graphene Interface: Influence of Termination State.

Controlled self-assembly of biomolecules on graphene offers a pathway for realizing its full potential in biological applications. Microscopy has revealed the self-assembly of amino acid adlayers into dimer rows on nonreactive substrates. However, neither the spontaneous formation of these patterns, nor the influence of amino acid termination state on the formation of patterns has been directly resolved to date. Molecular dynamics simulations, with the ability to reveal atomic level details and exert full control over the termination state, are used here to model initially disordered adlayers of neutral, zwitterionic, and neutral-zwitterionic mixtures for two types of amino acids, tryptophan and methionine, adsorbed on graphene in vacuo. The simulations of the zwitterion-containing adlayers exhibit the spontaneous emergence of dimer row ordering, mediated by charge-driven intermolecular interactions. In contrast, adlayers containing only neutral species do not assemble into ordered patterns. It is also found that the presence of trace amounts of water reduces the interamino acid interactions in the adlayers, but does not induce or disrupt pattern formation. Overall, the findings reveal the balance between the lateral interamino acid interactions and amino acid-graphene interactions, providing foundational insights for ultimately realizing the predictable pattern formation of biomolecules adsorbed on unreactive surfaces.

A density functional theory study of arsenic immobilization by the Al(III)-modified zeolite clinoptilolite.

We present density functional theory calculations of the adsorption of arsenic acid (AsO(OH)3) and arsenous acid (As(OH)3) on the Al(III)-modified natural zeolite clinoptilolite under anhydrous and hydrated conditions. From our calculated adsorption energies, we show that adsorption of both arsenic species is favorable (associative and exothermic) under anhydrous conditions. When the zeolite is hydrated, adsorption is less favourable, with the water molecules causing dissociation of the arsenic complexes, although exothermic adsorption is still observed for some sites. The strength of interaction of the arsenic complexes is shown to depend sensitively on the Si/Al ratio in the Al(III)-modified clinoptilolite, which decreases as the Si/Al ratio increases. The calculated large adsorption energies indicate the potential of Al(iii)-modified clinoptilolite for arsenic immobilization.

Side-chain effects on the co-existence of emergent nanopatterns in amino acid adlayers on graphene.

The spontaneous tendency of amino acid adlayers to self-assemble into ordered patterns on non-reactive surfaces is thought to be chiefly influenced by amino acid termination state. Experiments have shown that different side chains can produce different patterns, with a distinction drawn between side chains that can support hydrogen bonds or electrostatic interactions, and those that are hydrophobic. However, as is demonstrated in this work, this distinction is not clear cut, implying that there is currently no way to predict in advance what type of pattern will be formed. Here, we use molecular dynamics simulations of amino acid adlayers in neutral, zwitterion, and neutral-zwitterion states for two types of amino acids, either histidine or alanine, adsorbed at the in-vacuo graphene interface. In contrast to earlier studies on adlayers of tryptophan and methionine on graphene that reveal the presence of only a single type of pattern motif, the canonical dimer row, here we find that emergent patterns of histidine and alanine adlayers supported the co-existence of several different types of motifs, influenced by the different side-chain characteristics. For alanine, the compact side-chain does not support hydrogen bonding and engages weakly with the surface, leading to the emergence of a new dimer row configuration in addition to the canonical dimer row motif. On the contrary, for histidine, the side-chain supports hydrogen bonding, leading to the emergence of a dimer row motif different from the canonical dimer row, co-existing with several different monomer row motifs. On this basis, we propose that emergent canonical dimer row patterns are more likely for amino acids with side-chains that are non-compact and that also lack extensive hydrogen bonding capacity, and that engage strongly with the underlying substrate. These findings provide a fundamental basis to rationally guide the design of desired self-assembled nanostructures on planar surfaces.