scholarly journals Chiral 1,5-disubstituted 1,2,3-triazoles – versatile tools for foldamers and peptidomimetic applications

2020 ◽  
Vol 18 (10) ◽  
pp. 1957-1967
Author(s):  
Anna Said Stålsmeden ◽  
Andrew J. Paterson ◽  
Imola Cs. Szigyártó ◽  
Linda Thunberg ◽  
Johan R. Johansson ◽  
...  
Keyword(s):  
Quantum Chemistry ◽  
Building Blocks ◽  
Conformational Properties

Eight chiral triazoles, for use as peptidomimetic building blocks, were prepared using the ruthenium-catalyzed click (RuAAC) reaction and their conformational properties evaluated by quantum chemistry.

scholarly journals Locked nucleic acid building blocks as versatile tools for advanced G-quadruplex design

2020 ◽  
Vol 48 (18) ◽  
pp. 10555-10566 ◽  
Author(s):  
Linn Haase ◽  
Klaus Weisz
Keyword(s):  
Nucleic Acid ◽  
Detailed Analysis ◽  
Building Blocks ◽  
Locked Nucleic Acid ◽  
Structural Element ◽  
Hybrid Type ◽  
G Quadruplex ◽  
Conformational Properties ◽  
Neighboring Site ◽  
Potential Use

Abstract A hybrid-type G-quadruplex is modified with LNA (locked nucleic acid) and 2′-F-riboguanosine in various combinations at the two syn positions of its third antiparallel G-tract. LNA substitution in the central tetrad causes a complete rearrangement to either a V-loop or antiparallel structure, depending on further modifications at the 5′-neighboring site. In the two distinct structural contexts, LNA-induced stabilization is most effective compared to modifications with other G surrogates, highlighting a potential use of LNA residues for designing not only parallel but various more complex G4 structures. For instance, the conventional V-loop is a structural element strongly favored by an LNA modification at the V-loop 3′-end in contrast with an alternative V-loop, clearly distinguishable by altered conformational properties and base-backbone interactions as shown in a detailed analysis of V-loop structures.

Intrinsic Folding Proclivities in Cyclic β-Peptide Building Blocks: Configuration and Heteroatom Effects Analyzed by Conformer-Selective Spectroscopy and Quantum Chemistry

2015 ◽  
Vol 21 (46) ◽  
pp. 16479-16493 ◽  
Author(s):  
Mohammad Alauddin ◽  
Eric Gloaguen ◽  
Valérie Brenner ◽  
Benjamin Tardivel ◽  
Michel Mons ◽  
...  
Keyword(s):  
Quantum Chemistry ◽  
Building Blocks

scholarly journals Building blocks of topological quantum chemistry: Elementary band representations

2018 ◽  
Vol 97 (3) ◽  
Author(s):  
Jennifer Cano ◽  
Barry Bradlyn ◽  
Zhijun Wang ◽  
L. Elcoro ◽  
M. G. Vergniory ◽  
...  
Keyword(s):  
Quantum Chemistry ◽  
Building Blocks ◽  
Topological Quantum ◽  
Elementary Band

scholarly journals Understanding the Sequence Preference of Recurrent RNA Building Blocks Using Quantum Chemistry: The Intrastrand RNA Dinucleotide Platform

2011 ◽  
Vol 8 (1) ◽  
pp. 335-347 ◽  
Author(s):  
Arnošt Mládek ◽  
Judit E. Šponer ◽  
Petr Kulhánek ◽  
Xiang-Jun Lu ◽  
Wilma K. Olson ◽  
...  
Keyword(s):  
Quantum Chemistry ◽  
Building Blocks ◽  
Sequence Preference

scholarly journals High-throughput dissection of the thermodynamic and conformational properties of a ubiquitous class of RNA tertiary contact motifs

2021 ◽  
Vol 118 (33) ◽  
pp. e2109085118
Author(s):  
Steve L. Bonilla ◽  
Sarah K. Denny ◽  
John H. Shin ◽  
Aurora Alvarez-Buylla ◽  
William J. Greenleaf ◽  
...  
Keyword(s):  
High Throughput ◽  
Conformational Changes ◽  
Building Blocks ◽  
Conformational Behavior ◽  
Rna Motifs ◽  
Tertiary Structures ◽  
Conformational Properties ◽  
Functional Rnas ◽  
The Universe ◽  
Folding Thermodynamics

Despite RNA’s diverse secondary and tertiary structures and its complex conformational changes, nature utilizes a limited set of structural “motifs”—helices, junctions, and tertiary contact modules—to build diverse functional RNAs. Thus, in-depth descriptions of a relatively small universe of RNA motifs may lead to predictive models of RNA tertiary conformational landscapes. Motifs may have different properties depending on sequence and secondary structure, giving rise to subclasses that expand the universe of RNA building blocks. Yet we know very little about motif subclasses, given the challenges in mapping conformational properties in high throughput. Previously, we used “RNA on a massively parallel array” (RNA-MaP), a quantitative, high-throughput technique, to study thousands of helices and two-way junctions. Here, we adapt RNA-MaP to study the thermodynamic and conformational properties of tetraloop/tetraloop receptor (TL/TLR) tertiary contact motifs, analyzing 1,493 TLR sequences from different classes. Clustering analyses revealed variability in TL specificity, stability, and conformational behavior. Nevertheless, natural GAAA/11ntR TL/TLRs, while varying in tertiary stability by ∼2.5 kcal/mol, exhibited conserved TL specificity and conformational properties. Thus, RNAs may tune stability without altering the overall structure of these TL/TLRs. Furthermore, their stability correlated with natural frequency, suggesting thermodynamics as the dominant selection pressure. In contrast, other TL/TLRs displayed heterogenous conformational behavior and appear to not be under strong thermodynamic selection. Our results build toward a generalizable model of RNA-folding thermodynamics based on the properties of isolated motifs, and our characterized TL/TLR library can be used to engineer RNAs with predictable thermodynamic and conformational behavior.

Photochemical Evolution of Interstellar/Precometary Organic Material

1997 ◽  
Vol 161 ◽  
pp. 23-47 ◽  
Author(s):  
Louis J. Allamandola ◽  
Max P. Bernstein ◽  
Scott A. Sandford
Keyword(s):  
Origin Of Life ◽  
Building Blocks ◽  
Complex Species ◽  
Infrared Observations ◽  
Interstellar Ice ◽  
Polycyclic Aromatic ◽  
Ultraviolet Photolysis ◽  
The Origin Of Life ◽  
Simple Molecules ◽  
Complex Organic

AbstractInfrared observations, combined with realistic laboratory simulations, have revolutionized our understanding of interstellar ice and dust, the building blocks of comets. Since comets are thought to be a major source of the volatiles on the primative earth, their organic inventory is of central importance to questions concerning the origin of life. Ices in molecular clouds contain the very simple molecules H2O, CH3OH, CO, CO2, CH4, H2, and probably some NH3and H2CO, as well as more complex species including nitriles, ketones, and esters. The evidence for these, as well as carbonrich materials such as polycyclic aromatic hydrocarbons (PAHs), microdiamonds, and amorphous carbon is briefly reviewed. This is followed by a detailed summary of interstellar/precometary ice photochemical evolution based on laboratory studies of realistic polar ice analogs. Ultraviolet photolysis of these ices produces H2, H2CO, CO2, CO, CH4, HCO, and the moderately complex organic molecules: CH3CH2OH (ethanol), HC(= O)NH2(formamide), CH3C(= O)NH2(acetamide), R-CN (nitriles), and hexamethylenetetramine (HMT, C6H12N4), as well as more complex species including polyoxymethylene and related species (POMs), amides, and ketones. The ready formation of these organic species from simple starting mixtures, the ice chemistry that ensues when these ices are mildly warmed, plus the observation that the more complex refractory photoproducts show lipid-like behavior and readily self organize into droplets upon exposure to liquid water suggest that comets may have played an important role in the origin of life.

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