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Performance of Particle Swarm Optimization in Predicting the Orientation of π-Conjugated Molecules Inside Carbon Nanotubes Compared with Density Functional Theory Calculations.

Shuta FukuuraYohei NishidateTakashi Yumura
Published in: The journal of physical chemistry. A (2024)
Particle swarm optimization (PSO) was employed to obtain the global minimum of host-guest structures consisting of a triiodobenzene molecule (BzI 3 ) inside an armchair ( m , m ) nanotube (BzI 3 @( m , m )), whose host-guest interactions are approximated by Lennard-Jones (LJ) potentials. The host-guest structures obtained using the PSO-LJ method were then compared with those obtained through dispersion-corrected density functional theory (DFT) calculations to evaluate the performance of the PSO-LJ approach in predicting the guest orientation inside a tube. When the inner space of the host tube is limited for guest encapsulation, the PSO-LJ method can reproduce the DFT results of BzI 3 @( m , m ) in terms of the guest orientation. Conversely, in nanotubes with a sufficiently large space to allow a guest to freely move, corresponding to weak tube confinement, the PSO-LJ method yields guest orientations that are different from those obtained through DFT calculations; however, both methods obtain energetically close guest orientations. Accordingly, PSO-LJ method-assisted DFT calculations can quickly provide energetically stable guest orientations in BzI 3 @( m , m ) in weak tube confinement, which can be ignored in DFT calculations, where a single initial geometry is typically used.
Keyphrases
  • density functional theory
  • molecular dynamics
  • water soluble
  • carbon nanotubes
  • photodynamic therapy
  • mass spectrometry
  • molecular dynamics simulations
  • molecular docking