Solid-State Conformational Flexibility at Work: Energetic Landscape of a Single Crystal-to-Single Crystal Transformation in a Cyclic Hexapeptoid

Abstract

We describe the energetic landscape beyond the solid-state dynamic behavior of a cyclic hexapeptoid decorated with four propargyl and two methoxyethyl side chains, namely, cyclo-(Nme-Npa2)2, Nme = N-(methoxyethyl)­glycine, Npa = N-(propargyl)­glycine. By increasing the temperature above 40 °C, the acetonitrile solvate form 1A starts to release acetonitrile molecules and undergoes a reversible single crystal-to-single crystal transformation into crystal form 1B with a remarkable conformational change in the macrocycle: two propargyl side chains move by 113° to form an unprecedented “CH-π zipper”. Then, upon acetonitrile adsorption, the “CH-π zipper” opens and the crystal form 1B transforms back to 1A. By conformational energy and lattice energy calculations, we demonstrate that the dramatic side-chain movement is a peculiar feature of the solid-state assembly and is determined by a backbone conformational change that leads to stabilizing CH···OC backbone-to-backbone interactions tightening the framework upon acetonitrile release. Weak interactions as CH···OC and CH-π bonds with the guest molecules are able to reverse the transformation, providing the energy contribution to unzip the framework. We believe that the underlined mechanism could be used as a model system to understand how external stimuli (as temperature, humidity, or volatile compounds) could determine conformational changes in the solid state.

Elaborate Supramolecular Architectures Formed by Co-Assembly of Metal Species and Peptoid Macrocycles

“…To the best of our knowledge, the presence of the same small molecule in three different conformational forms in a crystallographic unit cell, as we found in the crystal lattice of Cyclo-(Ncm 6 )­K 6 (H 2 O) 13 , is a rare observation in diffractometric studies of single crystals and unique in the peptoid field, as also established by the recent contribution from Tedesco et al ,− This occurrence illustrates the conformational variety of cyclohexamer peptoids and their ability to afford unique solid-state assemblies.…”

Heteroatoms (Si, B, N, and P) doped 2D monolayer MoS2for NH3gas detection

“…16,17 Geometry minimization and energy calculations were carried out by employing the hybrid long-range separated empirical-corrected dispersion (ωB97X-D). 18 All the systems studied here were calculated in a vacuum using the genECP method by assigning the 6-311++G(d,p) and the LanL2DZ basis sets to the lighter and heavier atoms, respectively. Geometric parameters, including all the bond lengths before and after interaction, were obtained with the help of Chemcraft 1.6 (ref.…”

Inclusion of Pentamidine in Carboxylated Pillar[5]arene: Late Sequential Crystallization and Diversity of Host–Guest Interactions

“…8 Unfortunately, the experimental crystal structure data highlighting various binding geometries and intermolecular interaction modes between the same host and guest rarely mirror the whole structural host−guest landscape. 9,10 In this work we showcase an artificial supramolecular system as an ensemble of three host−guest complexes where not all interactions occur at the same time.…”

“…Therefore, the protein–ligand complex is better described as a superposition or ensemble of different structures. , The molecular recognition event between a protein and ligand is a delicate balance of multiple attractive and repulsive interactions affected inter alia by solvation/desolvation phenomena and conformational changes of one or both molecular partners. , The same can refer to the simpler supramolecular host–guest systems composed of flexible partners with multiple binding interactions . Unfortunately, the experimental crystal structure data highlighting various binding geometries and intermolecular interaction modes between the same host and guest rarely mirror the whole structural host–guest landscape. , In this work we showcase an artificial supramolecular system as an ensemble of three host–guest complexes where not all interactions occur at the same time.…”