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.

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 Host–guest binding in water, salty water, and biofluids: general lessons for synthetic, bio-targeted molecular recognition

2021 ◽  
Vol 50 (8) ◽  
pp. 4812-4832
Author(s):  
Meagan A. Beatty ◽  
Fraser Hof
Keyword(s):  
Molecular Recognition ◽  
Biological Targets ◽  
Salty Water ◽  
Guest Binding ◽  
Guest Chemistry

For host–guest chemistry, working on biological targets starts with learning how to make systems that work in warm, salty water.

SAMPL7 TrimerTrip Host-Guest Binding Poses and Binding Affinities from Spherical-Coordinates-Biased Simulations

2020 ◽  
Author(s):  
Zhaoxi Sun
Keyword(s):  
Free Energy ◽  
Computational Modelling ◽  
Free Energy Calculations ◽  
Energy Estimates ◽  
Binding Affinities ◽  
Spherical Coordinates ◽  
Collective Variables ◽  
Guest Binding ◽  
Starting Point ◽  
Sampl Challenge

Host-guest binding remains a major challenge in modern computational modelling. The newest 7<sup>th</sup> statistical assessment of the modeling of proteins and ligands (SAMPL) challenge contains a new series of host-guest systems. The TrimerTrip host binds to 16 structurally diverse guests. Previously, we have successfully employed the spherical coordinates as the collective variables coupled with the enhanced sampling technique metadynamics to enhance the sampling of the binding/unbinding event, search for possible binding poses and predict the binding affinities in all three host-guest binding cases of the 6<sup>th</sup> SAMPL challenge. In this work, we employed the same protocol to investigate the TrimerTrip host in the SAMPL7 challenge. As no binding pose is provided by the SAMPL7 host, our simulations initiate from randomly selected configurations and are proceeded long enough to obtain converged free energy estimates and search for possible binding poses. The predicted binding affinities are in good agreement with the experimental reference, and the obtained binding poses serve as a nice starting point for end-point or alchemical free energy calculations.

A Three-Dimensional Tetraphenylethylene-Based Fluorescence Covalent Organic Framework for Molecular Recognition

2020 ◽  
Author(s):  
Junxia Ren ◽  
Yaozu Liu ◽  
Xin Zhu ◽  
Yangyang Pan ◽  
Yujie Wang ◽  
...  
Keyword(s):  
Molecular Recognition ◽  
Fluorescence Probe ◽  
Three Dimensional ◽  
Hazardous Substances ◽  
Covalent Organic Framework ◽  
Highly Sensitive ◽  
Volatile Organic ◽  
Polycyclic Aromatic ◽  
Better Than ◽  
Organic Framework

<p><a></a><a></a><a></a><a></a><a></a><a></a><a></a><a>The development of highly-sensitive recognition of </a><a></a><a></a><a></a><a></a><a>hazardous </a>chemicals, such as volatile organic compounds (VOCs) and polycyclic aromatic hydrocarbons (PAHs), is of significant importance because of their widespread social concerns related to environment and human health. Here, we report a three-dimensional (3D) covalent organic framework (COF, termed JUC-555) bearing tetraphenylethylene (TPE) side chains as an aggregation-induced emission (AIE) fluorescence probe for sensitive molecular recognition.<a></a><a> </a>Due to the rotational restriction of TPE rotors in highly interpenetrated framework after inclusion of dimethylformamide (DMF), JUC-555 shows impressive AIE-based strong fluorescence. Meanwhile, owing to the large pore size (11.4 Å) and suitable intermolecular distance of aligned TPE (7.2 Å) in JUC-555, the obtained material demonstrates an excellent performance in the molecular recognition of hazardous chemicals, e.g., nitroaromatic explosives, PAHs, and even thiophene compounds, via a fluorescent quenching mechanism. The quenching constant (<i>K</i><sub>SV</sub>) is two orders of magnitude better than those of other fluorescence-based porous materials reported to date. This research thus opens 3D functionalized COFs as a promising identification tool for environmentally hazardous substances.</p>

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