Experimental and Computational Study of BODIPY Dye-Labeled Cavitand Dynamics

Abstract

Understanding the distance distribution and dynamics between moieties attached to the walls of a resorcin [4]arene cavitand, which is switchable between an expanded kite and a contracted vase form, might enable the use of this molecular system for the study of fundamental distance-dependent interactions. Toward this goal, a combined experimental and molecular dynamics (MD) simulation study on donor/acceptor borondipyrromethene (BODIPY) dyelabeled cavitands present in the vase and kite forms was performed. Direct comparison between anisotropy decays calculated from MD simulations with experimental fluorescence anisotropy data showed excellent agreement, indicating that the simulations provide an accurate representation of the dynamics of the system. Distance distributions between the BODIPY dyes were established by comparing time-resolved Forster resonance energy transfer experiments and MD simulations. Fluorescence intensity decay curves emulated on the basis of the MD trajectories showed good agreement with the experimental data, suggesting that the simulations present an accurate picture of the distance distributions and dynamics in this molecular system and provide an important tool for understanding the behavior of extended molecular systems and designing future applications.

Vase‐Kite Equilibrium of Resorcin[4]arene Cavitands Investigated Using Molecular Dynamics Simulations with Ball‐and‐Stick Local Elevation Umbrella Sampling

“…[134] The application of experimental methods with a higher sensitivity to intermediates could provide crucial evidence for elucidating the mechanism in the future. These could include in particular photoluminescence spectroscopy (PL) or Förster resonance energy transfer (FRET) experiments applied to specifically functionalized resorcin [4] arene systems, [73] as well as molecular-design ap-…”

“…Previous quantum mechanics [57] [66 -70] (QM) and molecular dynamics [44] [71 -73] (MD) studies of resorcin [4]arene systems have mainly focused on the host-guest complexation [44][69] [71] and on the calculation of flap-flap distance distributions. [73] To our knowledge, the VASE-KITE transition was never observed directly in a computer simulation, and the free-energy difference between VASE and KITE was never explicitly calculated. In the present work, classical atomistic MD simulation is used to investigate the VASE-KITE equilibrium position and interconversion mechanism of two resorcin [4]arenes.…”

Light Harvesting with Guide-Slide Superabsorbing Condensed-Matter Nanostructures

“…⊗: Silicon vacancy centres [55][56][57]. ⊕: Phosphorous defects [58][59][60].♣: BODIPY dye [61][62][63][64]. †: Porphyrin rings [25,65,66].…”

Evaluation of DFT Methods and Implicit Solvation Models for Anion‐Binding Host‐Guest Systems

“…In addition, François Diederich's work on host-guest complexation with synthetic cyclophane receptors in a variety of solvents, including aqueous, played a pivotal role in understanding the important features of molecular recognition such as hydrophobic effect, complementarity, and preorganization. [18][19][20][21][22] In host-guest systems, host molecules bind to their guests using a variety of noncovalent interactions. Hydrogen bonding interactions in particular are ubiquitous and potent in molecular recognition.…”