Theoretical studies of force fields and IR spectra of isocytosine

Abstract

ABSTRACT:The optimized geometries, complete harmonic force fields, and infrared Ž . intensities of isocytosine tautomers, amino-hydroxy and amino-oxoN 1 H, were calculated at the ab initio Hartree᎐Fock level using the 6-31G* basis set. The theoretical force fields were scaled by empirical scale factors, which were determined by fitting to the IR spectrum of the amino-oxo form and were then transferred to the amino-hydroxy form. The average deviations between experimental and computed frequencies are 7.6 cm y1 for amino-oxo and 9.5 cm y1 for amino-hydroxy, respectively. The assignments of the fundamental frequencies and the transferability of the force constant scale factors are also presented.

Effects of Positive and Negative Ionization on Prototropy in Pyrimidine Bases: An Unusual Case of Isocytosine

“…Depending on the contribution in the tautomeric mixture, individual tautomers can be considered as major (10% < x < 100%), minor (0.1% < x < 10%), or rare forms ( x < 0.1%). The major and minor isomers can be detected experimentally by various spectroscopic techniques, some of them already applied to nucleobases ,− and also to neutral isocytosine. ,,, However, the rare forms possible in the isomeric mixture can only be investigated theoretically. ,,,,,− ,− ,− ,− ,− Quantum-chemical methods applied to all possible isomers of tautomeric system give complete information on tautomeric conversions and on amounts of each isomer in the tautomeric mixture. This kind of information is not accessible on the basis of experimental spectroscopic investigations, particularly for short-lived charged radicals.…”

“…For neutral isocytosine, a change of tautomeric preferences has already been discovered when proceeding from the gas phase to aqueous solution and in the solid state. ,,,,− For investigations, various spectroscopic techniques and quantum-chemical calculations have been applied and the following conclusions reported. The isomer iC3 (Figure ), possessing the canonical tautomeric functions like for G in DNA or RNA (Figure S1 (SI)), is favored in aqueous solution, whereas the isomer iC1 , corresponding to the rare form G *, predominates in the gas phase or apolar environment.…”

An Insight into the Stability Of 3’-(Trifluoromethyl) and 4’-(Trifluoromethyl) Acetophenones Through Molecular Geometry and Charge Transfer Analyses – A Comparative Study

“…The combination of spectroscopic methods with DFT calculations are powerful tools for understanding the fundamental vibrational properties, molecular stability and the electronic structure of the compounds. Quantum chemical calculations were performed on the title molecules by applying DFT method using the Gaussian 09 Program suite [11] at the Becke-3-Lee-Yang-Par [B3LYP] level [12][13], using 6-31G** basis sets. The global minimum energy of the stable conformers of 3 TFMA and 4 TFMA has been determined by energy optimization at the DFT level of theory.…”

Effect of annealing on the structural and optical properties of laser ablated nanostructured barium tungstate thin films

“…The calculations were carried out using the CAM-B3LYP functional [22,23] combined with standard Lanl2Dz basis set.…”