scholarly journals Exploiting the mechanical bond for molecular recognition and sensing of charged species

2020 ◽  
Vol 4 (4) ◽  
pp. 1052-1073 ◽  
Author(s):  
Krzysztof M. Bąk ◽  
Kyriakos Porfyrakis ◽  
Jason J. Davis ◽  
Paul D. Beer
Keyword(s):  
Molecular Recognition ◽  
Ion Recognition ◽  
Charged Species ◽  
Guest Binding ◽  
Mechanical Bond ◽  
Synthetic Approaches

This review presents progress in the field of MIM hosts for ion recognition and sensing since 2014, focusing on the synthetic approaches employed and mechanisms of host–guest binding and detection.

scholarly journals High-throughput Computational Evaluation of Low Symmetry Pd2L4 Cages to Aid in System Design

2021 ◽  
Author(s):  
Andrew Tarzia ◽  
James Lewis ◽  
Kim Jelfs
Keyword(s):  
Low Cost ◽  
High Specificity ◽  
Search Space ◽  
Computational Evaluation ◽  
Single Isomer ◽  
Guest Binding ◽  
Computational Workflow ◽  
Different Shapes ◽  
Synthetic Approaches ◽  
Low Symmetry

<p>The use of unsymmetrical components in metallo-supramolecular chemistry allows for low-symmetry architectures with anisotropic cavities toward guest-binding with high specificity and affinity. Unsymmetrical ditopic ligands mixed with Pd(II) have the potential to self-assemble into reduced symmetry Pd<sub>2</sub>L<sub>4</sub> metallo-architectures. Mixtures of isomers can form, however, resulting in potentially undesirable heterogeneity within a system. Therefore it is paramount to be able to design components that preferentially form a single isomer. Previous data suggested that computational methods could predict with reasonable accuracy whether unsymmetrical ligands would preferentially self-assemble into a single isomer under constraints of geometrical mismatch. We successfully apply a collaborative computational and experimental workflow to mitigate costly trial-and-error synthetic approaches. Our low-cost computational workflow rapidly constructs new unsymmetrical ligands (and Pd<sub>2</sub>L<sub>4</sub> cage isomers) and ranks their likelihood for forming <i>cis</i>-Pd<sub>2</sub>L<sub>4</sub> assemblies. From this narrowed search space, we successfully synthesised four new low-symmetry, <i>cis</i>-Pd<sub>2</sub>L<sub>4</sub> cages, with cavities of different shapes and sizes.</p>

Molecular recognition: effect of rotational isomers on host-guest binding

1993 ◽  
Vol 115 (3) ◽  
pp. 879-884 ◽  
Author(s):  
William R. Cannon ◽  
Jeffry D. Madura ◽  
Randolph P. Thummel ◽  
J. Andrew McCammon
Keyword(s):  
Molecular Recognition ◽  
Rotational Isomers ◽  
Guest Binding

scholarly journals Binding Thermodynamics and Kinetics Calculations Using Chemical Host and Guest: A Comprehensive Picture of Molecular Recognition

2017 ◽  
Author(s):  
Zhiye Tang ◽  
Chia-en A. Chang
Keyword(s):  
Molecular Recognition ◽  
Force Fields ◽  
Md Simulations ◽  
Dissociation Rate ◽  
Water Molecules ◽  
Practical Applications ◽  
Guest Binding ◽  
Hydrogen Bond Networks ◽  
Comprehensive Picture ◽  
Dissociation Rate Constants

Understanding the fine balance between changes of entropy and enthalpy and the competition between a guest and water molecules in molecular binding is crucial in fundamental studies and practical applications. Experiments provide measurements. However, illustrating the binding/unbinding processes gives a complete picture of molecular recognition not directly available from experiments, and computational methods bridge the gaps. Here, we investigated guest association/dissociation with β-cyclodextrin (β-CD) by using microsecond-timescale molecular dynamics (MD) simulations, post-analysis and numerical calculations. We computed association and dissociation rate constants, enthalpy, and solvent and solute entropy of binding. All the computed values of kon, koff, ΔH, ΔS, and ΔG using GAFF-CD and q4MD-CD force fields for β-CD could be compared with experimental data directly and agreed reasonably with experiment findings. Both force fields resulted in similar computed ΔG from independently computed kinetics rates, ΔG=-RTln(kon · C° / k off), and thermodynamics properties, ΔG=ΔH – TΔS. The water entropy calculations show that entropy gain of desolvating water molecules are a major driving force, and both force fields have the same strength of non-polar attractions between solutes and β-CD as well. Water molecules play a crucial role in guest binding to β-CD. However, collective water/β-CD motions could contribute to different computed kon and ΔH values by different force fields, mainly because the parameters of β-CD provide different motions of β-CD, hydrogen-bond networks of water molecules in the cavity of free β-CD and the strength of desolvation penalty. As a result, q4MD-CD suggests that guest binding is mostly driven by enthalpy, while GAFF-CD shows that gaining entropy is the major driven force of binding. The study further interprets experiments, deepens our understanding of ligand binding, and suggests strategies for force field parameterization.

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