A QM/MM molecular dynamic simulation and vibrational spectroscopic study of 6-azaCytidine and cytidine

TL;DR

This study uses QM/MM molecular dynamics and vibrational spectroscopy to analyze the conformational stability and spectral properties of 6-azaCytidine and Cytidine in different environments, revealing structural differences.

Contribution

It provides a detailed computational analysis of conformational stability and vibrational spectra of 6-azaCytidine and Cytidine in gas and aqueous phases, including solvation effects.

Findings

Conformational stability order changes from gas to solution.

Simulated Raman spectra match experimental data.

Structural differences influence vibrational spectra.

Abstract

The conformational and vibrational properties of 6-azaCytidine (6-azaC) and Cytidine (Cyt) have been studied in gas phase and aqueous environment. The two most stable conformers of each molecule have been identified and investigated in more details. The stability order of the two most stable conformers of both molecules is changing going from gas phase to solution. The first solvation shell of both molecules has been studied using QM/MM-MD (Quantum Mechanics/Molecular Mechanics-Molecular Dynamic) simulations. The Raman vibrational spectra in gas phase and aqueous solution have been simulated and compared with the available experimental data. The two molecules exhibit certain differences reflected in their spectra as a result of structural and conformational differences.