Inter- and intramolecular stacking interaction between indole and adeninium rings

Area of Science:

• Biophysical Chemistry
• Structural Biology
• Molecular Interactions

Background:

• Understanding molecular interactions is crucial for biological processes.
• The stacking of aromatic rings, such as indole and adenine, plays a role in biomolecular recognition and function.
• Methylated or protonated adenine bases can interact with aromatic residues like tryptophan.

Purpose of the Study:

• To investigate the structural and electronic basis of stacking interactions between indole and methylated adenine derivatives.
• To model the interaction between tryptophanyl residues and methylated adenine bases.
• To explore the implications of these stacking interactions in both crystalline and solution states.

Main Methods:

• X-ray crystallography was used to analyze the crystal structures of two model compounds.
• Spectroscopic techniques including absorption, fluorescence, and proton nuclear magnetic resonance were employed.
• Molecular orbital calculations were performed to understand the governing interactions.

Main Results:

• Nearly parallel stacking with an interplanar spacing of approximately 3.4 Å was observed between indole and adeninium rings in both crystal structures.
• A partial charge-transfer interaction was identified in one of the stacking pairs in the 1,9-dimethyladeninium-indole-3-acetate complex.
• Orbital interactions between the indole's highest occupied molecular orbital and the adeninium's lowest unoccupied molecular orbital were found to govern ring orientation.
• Strong coupled dipole-dipole interactions stabilized the ring stacking in the second compound.
• Evidence of stacking interactions was confirmed in aqueous solutions using spectroscopic data.

Conclusions:

• The study elucidates the structural and electronic factors driving indole-adenine stacking.
• Both charge-transfer and dipole-dipole interactions contribute to the stability of these stacked systems.
• The findings suggest that similar stacking interactions may occur in biological systems, with potential functional significance.