Predicting the Limit of Intramolecular Hydrogen Bonding with Classical Molecular Dynamics

Abstract

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Weak functional group interactions revealed through metal-free active template rotaxane synthesis

“…Active template synthesis, essentially the use of catalysis to form and kinetically trap an unstable assembly, should prove to be a generally applicable tool for revealing weak functional group interactions. The difficulties in characterizing weak interactions was recently highlighted by Colizzi et al 84 : "…intramolecular hydrogen bonds are widespread in biological molecules and are crucial in the design of new drugs and materials, including supramolecular machines… Unfortunately, the characterization of intramolecular H-bonds (and their utilization) is still limited, most likely as a consequence of the complexities that hamper the interpretation of experimental data obtained for large and flexible entities." The ability to kinetically stabilize modest strength hydrogen bonding modes is another noteworthy consequence of the mechanical bond 3 .…”

Quantifying Interactions and Solvent Effects Using Molecular Balances and Model Complexes

“…Molecular modelling subsequently determined that the sharp drop in stability of the intramolecular H-bond was explained by a proportionately large entropic penalty of ~3 kJ mol −1 per rotor associated forming an intramolecular hydrogen bond. 38…”

The importance of intramolecular hydrogen bonds on the translocation of the small drug piracetam through a lipid bilayer

“…21 Due to the intrinsic exibility that is granted by IMHB, their experimental characterization is still limited. 22 In this regard, computational simulations have provided important information on these interactions extending the limits of current experiments. 18,22 Molecular dynamics (MD) simulations, for instance, can offer a practical solution to efficiently sample the conformational space of molecules that are able to form IMHBs, and that can display different sets of conformations depending on the properties of the surrounding media.…”

“…22 In this regard, computational simulations have provided important information on these interactions extending the limits of current experiments. 18,22 Molecular dynamics (MD) simulations, for instance, can offer a practical solution to efficiently sample the conformational space of molecules that are able to form IMHBs, and that can display different sets of conformations depending on the properties of the surrounding media. 23 This work attempts to get a ner, atomic-level understanding of the inuence of IMHB on the membrane translocation with MD simulations.…”