A density functional theory study for the hydrogen-bonded nucleic acid base pair: cytosine dimer

Area of Science:

• Computational Chemistry
• Molecular Biophysics
• Quantum Chemistry

Background:

• Nucleic acid base pairing is fundamental to DNA and RNA structure and function.
• Understanding the stability and properties of base dimers is crucial for molecular biology.
• Cytosine, a key nucleobase, can form various dimer structures through tautomerization.

Purpose of the Study:

• To theoretically investigate the geometric, energetic, and vibrational properties of cytosine dimers.
• To identify the most stable cytosine dimer isomers using computational methods.
• To analyze the electronic and bonding characteristics of the most stable dimer.

Main Methods:

• Density Functional Theory (DFT) was employed for all calculations.
• Geometric optimizations, energy calculations, and vibrational frequency analyses were performed.
• Basis set superposition error correction was applied to binding energy calculations.

Main Results:

• The planar cytosine dimer (K-K3) formed from nonplanar keto tautomers is the most thermodynamically stable.
• K-K3 exhibits the highest binding energy of 19.51 kcal/mol.
• Vibrational frequency analysis indicates a significant red shift for the hydrogen bonds in K-K3.

Conclusions:

• The K-K3 isomer represents the most stable configuration for cytosine dimers.
• Detailed electronic and charge distribution analyses provide insights into the dimer's stability.
• These findings contribute to a deeper understanding of nucleic acid base pairing mechanisms.