Dataset Information


Simulation optimization of spherical non-polar guest recognition by deep-cavity cavitands.

ABSTRACT: Biomimetic deep-cavity cavitand hosts possess unique recognition and encapsulation properties that make them capable of selectively binding a range of non-polar guests within their hydrophobic pocket. Adamantane based derivatives which snuggly fit within the pocket of octa-acid deep cavity cavitands exhibit some of the strongest host binding. Here we explore the roles of guest size and attractiveness on optimizing guest binding to form 1:1 complexes with octa-acid cavitands in water. Specifically we simulate the water-mediated interactions of the cavitand with adamantane and a range of simple Lennard-Jones guests of varying diameter and attractive well-depth. Initial simulations performed with methane indicate hydrated methanes preferentially reside within the host pocket, although these guests frequently trade places with water and other methanes in bulk solution. The interaction strength of hydrophobic guests increases with increasing size from sizes slightly smaller than methane to Lennard-Jones guests comparable in size to adamantane. Over this guest size range the preferential guest binding location migrates from the bottom of the host pocket upwards. For guests larger than adamantane, however, binding becomes less favorable as the minimum in the potential-of-mean force shifts to the cavitand face around the portal. For a fixed guest diameter, the Lennard-Jones well-depth is found to systematically shift the guest-host potential-of-mean force to lower free energies, however, the optimal guest size is found to be insensitive to increasing well-depth. Ultimately our simulations show that adamantane lies within the optimal range of guest sizes with significant attractive interactions to match the most tightly bound Lennard-Jones guests studied.


PROVIDER: S-EPMC3880382 | BioStudies | 2013-01-01

REPOSITORIES: biostudies

Similar Datasets

2008-01-01 | S-EPMC2765558 | BioStudies
1000-01-01 | S-EPMC5890788 | BioStudies
1000-01-01 | S-EPMC6222714 | BioStudies
2015-01-01 | S-EPMC6272763 | BioStudies
2010-01-01 | S-EPMC2945708 | BioStudies
2016-01-01 | S-EPMC4792523 | BioStudies
2017-01-01 | S-EPMC5574188 | BioStudies
2015-01-01 | S-EPMC5588781 | BioStudies
2019-01-01 | S-EPMC6362660 | BioStudies
2012-01-01 | S-EPMC3315598 | BioStudies