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Cyanohydrins are compounds that contain –CN and –OH groups on the same carbon atom. They are formed by the nucleophilic addition of the cyanide ions to the carbonyl group. Cyanide ions are highly basic and nucleophilic and can be generated from HCN under aqueous conditions. However, since HCN is a weak acid, the number of cyanide ions generated is very small. Hence, a small amount of base or KCN/NaCN is added to HCN to increase the concentration of the cyanide ions in the reaction...
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Noncovalent Helicene Structure between Nucleic Acids and Cyanuric Acid.

Asem Alenaizan1,2,3, Kévin Fauché3,4, Ramanarayanan Krishnamurthy3,4

  • 1School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332-0400, USA.

Chemistry (Weinheim an Der Bergstrasse, Germany)
|November 11, 2020
PubMed
Summary

Researchers explored the self-assembly of cyanuric acid (CA) and poly(adenine). Molecular dynamics simulations suggest a novel noncovalent helicene structure, challenging the hexameric rosette model for these supramolecular fibers.

Keywords:
molecular dynamicsnoncovalent helicenesnucleic acidsself-assembly

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Area of Science:

  • Supramolecular Chemistry
  • Materials Science
  • Computational Chemistry

Background:

  • Cyanuric acid (CA) is a triazine heterocycle widely used in noncovalent self-assembly.
  • Previous studies proposed a hexameric rosette structure for poly(adenine) and CA assemblies.
  • Recent experimental data prompted a reevaluation of this proposed structure.

Purpose of the Study:

  • To investigate the structural motif of poly(adenine) and cyanuric acid (CA) fibers.
  • To evaluate the validity of the hexameric rosette model versus a proposed helicene model.
  • To elucidate the noncovalent interactions driving the self-assembly process.

Main Methods:

  • Utilized molecular dynamics simulations.
  • Analyzed hydrogen-bonding networks.
  • Compared simulation results with experimental observations.

Main Results:

  • Molecular dynamics simulations indicate the hexad model is unlikely.
  • A novel noncovalent helicene geometry is proposed as a more probable structural motif.
  • An extended helical hydrogen-bond network between adenine and CA bases was identified.

Conclusions:

  • The noncovalent helicene structure is a more likely motif for poly(adenine)-CA assemblies.
  • This finding challenges the previously proposed hexameric rosette model.
  • Noncovalent helicene compounds hold potential for DNA nanotechnology and helicene chemistry.