Paper Citing NAMD - Abstract
Karachevtsev, Victor A.; Stepanian, Stepan G.; Glamazda, Alexander Yu.; Karachevtsev, Maksym V.; Eremenko, Victor V.; Lytvyn, Oksana S.; Adamowicz, Ludwik
Noncovalent Interaction of Single-Walled Carbon Nanotubes with 1-Pyrenebutanoic Acid Succinimide Ester and Glucoseoxidase
JOURNAL OF PHYSICAL CHEMISTRY C, 115:21072-21082, NOV 3 2011
Peculiarities of the interface interactions of 1-pyrenebutanoic acid N-hydroxysuccinimide ester (PSE) with single-walled carbon nanotubes (SWCNTs) and enzyme glucoseoxidase (GOX) have been studied with the resonance Raman spectroscopy and theoretical calculations employing the DFT method and the molecular dynamics (MD) simulation. The interaction of a nanotube with PSE leads to a downshift of the band assigned in the Raman spectrum to the tangential mode of the hybrid with respect to the position of this mode in the spectrum of the pristine SWCNT. The MD simulation demonstrates that the direct interaction between SWCNT and GOX is very strong. This interaction can be expected to change the structure of the enzyme and to significantly affect its activity. The MD simulation also shows that only one PSE molecule used as a linker between SWCNT and GOX is enough to keep GOX near the nanotube surface in the water surrounding and to prevent strong interaction between SWCNT and GOX. However, to stabilize this nanobiohybrid in water at least two PSE linkers are needed. The molecular structure of PSE is determined using the density functional theory approach (DFT/B3LYP/6-31++G(d,p). The geometries and the relative stabilities of all possible PSE conformers are characterized in the calculations. High structural flexibility of the PSE molecule is demonstrated. Calculations (at the M05-2X level of theory) have also been performed on the structures and the interaction energies of complexes formed by various SWCNTs with PSE and pyrene. Pyrene interacts strongly with the surface of carbon nanotubes with different chiralities, but the interaction with zigzag nanotubes is stronger than with armchair ones of the same diameter. Increasing the diameter of the SWCNTs leads to a higher adsorption energy, reaching the maximum value for graphene (-20.8 kcal/mol).
