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Aromatic Hydrocarbon Cations: Structural Overview01:18

Aromatic Hydrocarbon Cations: Structural Overview

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Cycloheptatriene is a neutral monocyclic unsaturated hydrocarbon that consists of an odd number of carbon atoms and an intervening sp3 carbon in the ring. The three double bonds in the ring correspond to 6 π electrons, which is a Huckel number, and therefore satisfies the criteria of 4n + 2 π electrons. However, the intervening sp3 carbon disrupts the continuous overlap of p orbitals. As a result, cycloheptatriene is not aromatic.
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Neutral hydrocarbons like cyclopentadiene with an odd number of carbon atoms and one intervening CH2 group in the ring are not aromatic. Cyclopentadiene with 4 π electrons does not satisfy the 4n + 2 π electron rule. Additionally, the intervening CH2 group is sp3 hybridized and lacks a vacant p orbital, thereby interrupting the overlap of p orbitals in a continuous manner and preventing the delocalization of π electrons throughout the ring.
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Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a...
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The basicity of aromatic amines is much weaker than that of aliphatic amines due to the involvement of the lone pair of electrons over the N atom in resonance with the aryl rings. Generally, the electron-donating ability of any substituents on the aryl ring of aromatic amines increases the basicity of the amine by increasing electron density, and hence the availability of lone pair on the nitrogen. On the other hand, electron-withdrawing functional groups on the aryl ring of amines decrease the...
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Related Experiment Video

Updated: Jul 15, 2025

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions
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Analyzing the cation-aromatic interactions in proteins: Cation-aromatic database V2.0.

Y Bhargav Kumar1,2, Nandan Kumar1, Lijo John1

  • 1Advanced Computation and Data Sciences Division, CSIR-North East Institute of Science and Technology, Jorhat, Assam, India.

Proteins
|October 4, 2023
PubMed
Summary
This summary is machine-generated.

The updated Cation-Aromatic Database (CAD) now includes over 27 million cation-aromatic motifs from protein structures. It details interactions, particularly metal ion binding with histidine, and reveals prevalent motif pairs like HIS-HIS.

Keywords:
amino acidscationcation-aromatic motifsproteins

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Area of Science:

  • Biochemistry
  • Structural Biology
  • Bioinformatics

Background:

  • Cation-aromatic interactions are crucial in protein structure and function.
  • The Cation-Aromatic Database (CAD) previously cataloged these motifs.
  • An updated repository is needed to reflect the growing PDB data.

Purpose of the Study:

  • To update and expand the Cation-Aromatic Database (CAD) with recent protein structure data.
  • To analyze the prevalence and characteristics of cation-aromatic motifs.
  • To identify specific cation-aromatic interaction preferences in proteins.

Main Methods:

  • Retrieval of protein structures from the Protein Data Bank (PDB) as of June 2023.
  • Identification and classification of cation-aromatic motifs using distance parameters (r, d1, d2).
  • Analysis of motif geometry (spherical vs. cylindrical) and specific residue pair interactions.

Main Results:

  • The updated CAD V2.0 contains over 27.26 million cation-aromatic motifs from 193,936 protein structures.
  • Spherical motifs (94.09%) are more common than cylindrical motifs (5.91%).
  • Metal ion interactions are frequent, with 82.08% involving histidine; HIS-HIS and TYR-LYS are prevalent pairs.

Conclusions:

  • The updated CAD provides a comprehensive resource for studying cation-aromatic interactions.
  • Analysis reveals significant roles of histidine in metal ion binding and specific residue preferences.
  • This data aids in understanding the biological functions of cation-aromatic interactions in biomolecules.