scholarly journals Supramolecular chemistry: from aromatic foldamers to solution-phase supramolecular organic frameworks

2015 ◽  
Vol 11 ◽  
pp. 2057-2071 ◽  
Author(s):  
Zhan-Ting Li
Keyword(s):  
Hydrogen Bonding ◽  
Supramolecular Chemistry ◽  
Radical Cations ◽  
Secondary Structures ◽  
Solution Phase ◽  
Aromatic Stacking ◽  
Research Activities ◽  
Donor Acceptor

This mini-review covers the growth, education, career, and research activities of the author. In particular, the developments of various folded, helical and extended secondary structures from aromatic backbones driven by different noncovalent forces (including hydrogen bonding, donor–acceptor, solvophobicity, and dimerization of conjugated radical cations) and solution-phase supramolecular organic frameworks driven by hydrophobically initiated aromatic stacking in the cavity of cucurbit[8]uril (CB[8]) are highlighted.

scholarly journals Structural relation matching: an algorithm to identify structural patterns into RNAs and their interactions

2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Michela Quadrini
Keyword(s):  
Hydrogen Bonding ◽  
Secondary Structure ◽  
Nucleotide Sequence ◽  
Thermus Thermophilus ◽  
Three Dimensional ◽  
Secondary Structures ◽  
Structural Effect ◽  
Biological Processes ◽  
Structural Pattern ◽  
Rna Molecules

Abstract RNA molecules play crucial roles in various biological processes. Their three-dimensional configurations determine the functions and, in turn, influences the interaction with other molecules. RNAs and their interaction structures, the so-called RNA–RNA interactions, can be abstracted in terms of secondary structures, i.e., a list of the nucleotide bases paired by hydrogen bonding within its nucleotide sequence. Each secondary structure, in turn, can be abstracted into cores and shadows. Both are determined by collapsing nucleotides and arcs properly. We formalize all of these abstractions as arc diagrams, whose arcs determine loops. A secondary structure, represented by an arc diagram, is pseudoknot-free if its arc diagram does not present any crossing among arcs otherwise, it is said pseudoknotted. In this study, we face the problem of identifying a given structural pattern into secondary structures or the associated cores or shadow of both RNAs and RNA–RNA interactions, characterized by arbitrary pseudoknots. These abstractions are mapped into a matrix, whose elements represent the relations among loops. Therefore, we face the problem of taking advantage of matrices and submatrices. The algorithms, implemented in Python, work in polynomial time. We test our approach on a set of 16S ribosomal RNAs with inhibitors of Thermus thermophilus, and we quantify the structural effect of the inhibitors.

scholarly journals Deciphering the Role of π-Interactions in Polyelectrolyte Complexes Using Rationally Designed Peptides

Polymers ◽  
2021 ◽  
Vol 13 (13) ◽  
pp. 2074
Author(s):  
Sara Tabandeh ◽  
Cristina Elisabeth Lemus ◽  
Lorraine Leon
Keyword(s):  
Hydrogen Bonding ◽  
Phase Separation ◽  
Liquid Phase ◽  
Charge Density ◽  
Secondary Structures ◽  
Liquid Phase Separation ◽  
Polyelectrolyte Complexes ◽  
Π Interactions ◽  
Liquid Liquid Phase Separation

Electrostatic interactions, and specifically π-interactions play a significant role in the liquid-liquid phase separation of proteins and formation of membraneless organelles/or biological condensates. Sequence patterning of peptides allows creating protein-like structures and controlling the chemistry and interactions of the mimetic molecules. A library of oppositely charged polypeptides was designed and synthesized to investigate the role of π-interactions on phase separation and secondary structures of polyelectrolyte complexes. Phenylalanine was chosen as the π-containing residue and was used together with lysine or glutamic acid in the design of positively or negatively charged sequences. The effect of charge density and also the substitution of fluorine on the phenylalanine ring, known to disrupt π-interactions, were investigated. Characterization analysis using MALDI-TOF mass spectroscopy, H NMR, and circular dichroism (CD) confirmed the molecular structure and chiral pattern of peptide sequences. Despite an alternating sequence of chirality previously shown to promote liquid-liquid phase separation, complexes appeared as solid precipitates, suggesting strong interactions between the sequence pairs. The secondary structures of sequence pairs showed the formation of hydrogen-bonded structures with a β-sheet signal in FTIR spectroscopy. The presence of fluorine decreased hydrogen bonding due to its inhibitory effect on π-interactions. π-interactions resulted in enhanced stability of complexes against salt, and higher critical salt concentrations for complexes with more π-containing amino acids. Furthermore, UV-vis spectroscopy showed that sequences containing π-interactions and increased charge density encapsulated a small charged molecule with π-bonds with high efficiency. These findings highlight the interplay between ionic, hydrophobic, hydrogen bonding, and π-interactions in polyelectrolyte complex formation and enhance our understanding of phase separation phenomena in protein-like structures.

Solution Phase Measurement of Both Weak σ and C−H···X−Hydrogen Bonding Interactions in Synthetic Anion Receptors

2008 ◽  
Vol 130 (33) ◽  
pp. 10895-10897 ◽  
Author(s):  
Orion B. Berryman ◽  
Aaron C. Sather ◽  
Benjamin P. Hay ◽  
Jeffrey S. Meisner ◽  
Darren W. Johnson
Keyword(s):  
Hydrogen Bonding ◽  
Phase Measurement ◽  
Solution Phase ◽  
Anion Receptors ◽  
Hydrogen Bonding Interactions

Degradation of Cytosine Radical Cations in 2′-Deoxycytidine and in i-Motif DNA: Hydrogen-Bonding Guided Pathways

2019 ◽  
Vol 141 (5) ◽  
pp. 1970-1979 ◽  
Author(s):  
Yinghui Wang ◽  
Hongmei Zhao ◽  
Chunfan Yang ◽  
Jialong Jie ◽  
Xiaojuan Dai ◽  
...  
Keyword(s):  
Hydrogen Bonding ◽  
Radical Cations

Synthesis of Complementary Hydrogen Bonding Cyclotriveratrylenes

2002 ◽  
Vol 2002 (8) ◽  
pp. 359-360 ◽  
Author(s):  
Magali Darzac ◽  
Stéphanie Montésinos ◽  
André Collet ◽  
Jean-Pierre Dutasta
Keyword(s):  
Hydrogen Bonding ◽  
Cyanuric Acid ◽  
Donor Acceptor

Two new cyclotriveratrylenes CTV-1 and CTV-2 bearing complementary H-bond donor-acceptor substituents were prepared from 4-hydroxy-3-methoxybenzyl alcohol following a multistep strategy to introduce melamine or cyanuric acid substituents.

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