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1. Highly Strained para-Phenylene-Bridged Macrocycles from Unstrained 1,4-Diketo Macrocycles

   https://doi.org/10.1055/s-0036-1589081  

   Mitra, Nirmal ; Merryman, Caroline ; Merner, Bradley ( October 2017 , Synlett)

   The conversion of macrocyclic 1,4-diketones to highly strained para-phenylene rings has recently been reported by our laboratory. This synthetic strategy represents a non-cross-coupling-based approach to arene-bridged macrocycles, and an alternative to palladium- and nickel-mediated processes. In this Synpacts article we discuss the development of endgame aromatization protocols for the synthesis of increasingly strained arene systems, as well as potential advantages of the macrocyclic 1,4-diketone approach to selectively functionalized benzenoid macrocycles for future complexity building reactions. 1 Introduction 2 A Non-Cross-Coupling-Based Approach to Arene-Bridged Macro cycles 3 Macrocyclic 1,4-Diketones: Streamlined Synthesis and Size-­Dependent Diastereoselective Grignard Reactions 4 Dehydrative Aromatization Reactions: Amore »Powerful Tool for Synthesizing Highly Strained para-Phenylene Units 5 Conclusion« less
2. Selective host–guest chemistry, self-assembly and conformational preferences of m -xylene macrocycles probed by ion-mobility spectrometry mass spectrometry

   https://doi.org/10.1039/C9CP06938K  

   Link, Benjamin A. ; Sindt, Ammon J. ; Shimizu, Linda S. ; Do, Thanh D. ( May 2020 , Physical Chemistry Chemical Physics)

   We demonstrated ion-mobility spectrometry mass spectrometry (IMS-MS) as a powerful tool for interrogating and preserving selective chemistry including non-covalent and host–guest complexes of m -xylene macrocycles formed in solution. The technique readily revealed the unique favorability of a thiourea-containing macrocycle MXT to Zn 2+ to form a dimer complex with the cation in an off-axis sandwich structure having the Zn–S bonds in a tetrahedral coordination environment. Replacing thiourea with urea generates MXU which formed high-order oligomerization with weak binding interactions to neutral DMSO guests detected at every oligomer size. The self-assembly pathway observed for this macrocycle is consistent with themore »crystalline assembly. Further transformation of urea into squaramide produces MXS, a rare receptor for probing sulfate in solution. Tight complexes were observed for both monomeric and dimeric of MXS in which HSO 4 − bound stronger than SO 4 2− to the host. The position of HSO 4 − at the binding cavity is a 180° inversion of the reported crystallographic SO 4 2− . The MXS dimer formed a prism-like shape with HSO 4 − exhibiting strong contacts with the 8 amine protons of two MXS macrocycles. By eliminating intermolecular interferences, we detected the low energy structures of MXS with collisional cross section (CCS) matching cis – trans and cis – cis squaramides-amines, both were not observed in crystallization trials. The experiments collectively unravel multiple facets of macrocycle chemistry including conformational flexibility, self-assembly and ligand binding; all in one analysis. Our findings illustrate an inexpensive and widely applicable approach to investigate weak but important interactions that define the shape and binding of macrocycles.« less
3. Synthesis and characterization of 3- O -esters of N -acetyl- d -glucosamine derivatives as organogelators

   https://doi.org/10.1039/c9nj00630c  

   Chen, Anji ; Samankumara, Lalith P. ; Garcia, Consuelo ; Bashaw, Kristen ; Wang, Guijun ( May 2019 , New Journal of Chemistry)

   Carbohydrate derived low molecular weight organogelators are interesting compounds with many potential applications. Selective functionalization of the different hydroxyl substituents on d -glucose and d -glucosamine resulted in small molecular gelators. Previously we have found that the C-2 acylated derivatives including esters and carbamates of 4,6- O -benzylidene protected glucose and glucosamine derivatives have shown remarkable applications as molecular gelators. In this research, in order to probe the structural influence of sugar derivatives on molecular self-assembly, we introduced acylation functional groups to the 3-hydroxyl group of 4,6- O -benzylidene acetal protected N -acetyl glucosamine derivatives. A library of fourteen estermore »derivatives was synthesized and characterized. The ester derivatives typically formed gels in pump oil and aqueous mixtures of dimethyl sulfoxide or ethanol. The resulting gels were characterized using optical microscopy, and rheology, etc. All alkyl ester derivatives were gelators for pump oil. A short chain ester derivative was able to form gels in a few different oils and the corresponding oil water mixtures phase selectively. The compound was also used to trap naproxen sodium and formed a stable co-gel. The controlled release of the drug from the gel to the aqueous phase was analyzed using UV-vis spectroscopy. These results show that the functionalization at the 3-OH position of the N -acetyl glucosamine derivative is a feasible strategy in designing new classes of organogelators.« less
4. Rigid foldability is NP-hard

   Akitaya, Hugo A ; Demaine, Erik D ; Horiyama, Takashi ; Hull, Thomas C ; Ku, Jason S ; Tachi, Tomohiro ( January 2020 , Journal of computational geometry)

   In this paper, we show that the rigid-foldability of a given crease pattern using all creases is weakly NP-hard by a reduction from the partition problem, and that rigid-foldability with optional creases is NP-hard by a reduction from the 1-in-3 SAT problem. Unlike flat-foldabilty of origami or flexibility of other kinematic linkages, whose complexity originates in the complexity of the layer ordering and possible self-intersection of the material, rigid foldabilltiy from a planar state is hard even though there is no potential self-intersection. In fact, the complexity comes from the combinatorial behavior of the different possible rigid folding configurations atmore »each vertex. The results underpin the fact that it is harder to fold from an unfolded sheet of paper than to unfold a folded state back to a plane, frequently encountered problem when realizing folding-based systems such as self-folding matters and reconfigurable robots.« less
5. Shape changes and cooperativity in the folding of the central domain of the 16S ribosomal RNA

   https://doi.org/10.1073/pnas.2020837118  

   Hori, Naoto ; Denesyuk, Natalia A. ; Thirumalai, D. ( March 2021 , Proceedings of the National Academy of Sciences)

   Both the small and large subunits of the ribosome, the molecular machine that synthesizes proteins, are complexes of ribosomal RNAs (rRNAs) and a number of proteins. In bacteria, the small subunit has a single 16S rRNA whose folding is the first step in its assembly. The central domain of the 16S rRNA folds independently, driven either by Mg²⁺ions or by interaction with ribosomal proteins. To provide a quantitative description of ion-induced folding of the ∼350-nucleotide rRNA, we carried out extensive coarse-grained molecular simulations spanning Mg²⁺concentration between 0 and 30 mM. The Mg²⁺dependence of the radius of gyration shows that globallymore »the rRNA folds cooperatively. Surprisingly, various structural elements order at different Mg²⁺concentrations, indicative of the heterogeneous assembly even within a single domain of the rRNA. Binding of Mg²⁺ions is highly specific, with successive ion condensation resulting in nucleation of tertiary structures. We also predict the Mg²⁺-dependent protection factors, measurable in hydroxyl radical footprinting experiments, which corroborate the specificity of Mg²⁺-induced folding. The simulations, which agree quantitatively with several experiments on the folding of a three-way junction, show that its folding is preceded by formation of other tertiary contacts in the central junction. Our work provides a starting point in simulating the early events in the assembly of the small subunit of the ribosome.

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