Effect of protonation and hydrogen bonding on 2, 4, 6-substituted pyrimidine and its salt complex-experimental and theoretical evidence.

Journal of molecular modeling

PubMedID: 24567157

Pillai CN, Chellapan J. Effect of protonation and hydrogen bonding on 2, 4, 6-substituted pyrimidine and its salt complex-experimental and theoretical evidence. J Mol Model. 2014;20(3):2139.
Quantum molecular simulations of chemical systems can provide detailed information that is often inaccessible to direct experimental measurement. Pyrimidine is an interesting p-electron heterocyclic aromatic system which acts as the building block of many nucleic acid bases. The hydrogen bonds associated with the 2, 4, and 6-substituted pyrimidine and its hydrogen sulfate anion are considered for this current work. The experimental and computational evidence for the strength of these intra and intermolecular hydrogen are determined using vibrational spectra and quantum chemical calculations. Thus the effect of hydrogen bonding on the title compound is studied using its geometrical parameters, interaction energies, and vibrational spectra. Aromaticity and charge transfer studies have been performed to ascertain the aromatic behavior of the molecule. The PES scan studies have been done by varying the bond length to ascertain the protonation process of the compound. The IR spectral red shift (~100 cm(-1)), blue shift (~97 cm(-1)) and broadening of the polar stretching peaks shows the inter and intramolecular hydrogen bonding strength. Bond length alternation of proton donors along with the enormous interaction energies (~0.5-150 kJ mol(-1)) between the lone pair and proton donors provides clear evidence for this hydrogen bonding. The charge transfer due to the methyl substitutions which enhances the possibility of hydrogen bonding has been discussed. The main scope of this work is to study the protonation and hydrogen bonding associated with charge transfer which has great effect on the 2-amino-4, 6-dimethyl pyrimidinium hydrogen sulfate (ADHS) molecule.