Peptide-Carbon Nanotube Hybrids under Confinement: Structure and Stability from Atomistic Simulations

The interaction between peptides and carbon nanotubes (CNTs) represents a promising route for developing biofunctional nanomaterials that couple structural flexibility to superior electronic performance. In this work, we investigate the structural and energetic behavior of A₆D peptides confined inside a single-walled CNT using classical molecular dynamics simulations. The system consists of a 2 nm-radius CNT containing 35 A₆D peptides and an equivalent number of counterions, fully solvated in water. Analyses of hydrogen-bond dynamics, Coulombic and van der Waals energies, and Ramachandran distributions reveal that peptide-solvent interactions dominate peptide-peptide aggregation, maintaining high flexibility within the confined environment. The alanine residues exhibit strong hydrophobic attraction to the CNT surface, while aspartic acid residues form extensive hydrogen bonds with water, resulting in a balanced solvation-stabilization regime. The confined peptides preferentially adopt α-helical conformations compatible with the cylindrical geometry of the nanotube, suggesting the potential formation of an internal peptide-membrane-like structure. These findings provide molecular-level insights into how electrostatic (peptide-peptide) and dispersion forces (peptide-peptide and peptide-CNT) govern organization and stability under nanoscale confinement. The results highlight the potential of peptide-coated CNTs as building blocks for bioelectronic interfaces, selective molecular transport systems, and controlled-release nanocarriers, bridging biomolecular self-assembly with advanced carbon nanotechnology.