International Journal of Research and Scientific Innovation (IJRSI) |Volume X, Issue I, January 2023|ISSN 2321-2705
Quantum Chemical Study of Hydrogen Bonded Guanine-Water Complexes
Brijesh Kumar Sharma1, Achchhe Lal2 and *Devendra Kumar Singh1
1Department of Physics, Udai Pratap (Autonomous) College, Varanasi-221002, India
2Department of Physics, Harishchndra P G College, Varanasi-221002, India
Abstract: – The Optimized geometries of all the four isomers of Guanine-water complexes have been obtained at B3LYP/6-311++G(d,p), X3LYP/6-311++G(d,p), B3PW91/6-311++G(d,p) levels. Structural parameters of the optimized geometries, total energies and the APT charges of guanine-water complex have been computed. Frequency calculations are carried out on each optimized structure and their IR and Raman spectra have been discussed. The calculated frequencies of the guanine are found to be in good agreement with the experimental values in the most of the cases.
Key words: MP2, DFT, B3LYP, Optimized geometry.
I. Introduction
Guanine is one of the five main nucleobases found in the nucleic acids DNA and RNA. Guanine is a derivative of purine, consisting of a fused pyrimidine-imidazole ring system with conjugated double bonds. Being unsaturated, the bicyclic molecule is planar. The guanine nucleoside is called guanosine.The first isolation of guanine was reported in 1844 by the German chemist Julius Bodo Unger (1819–1885), who obtained it as a mineral formed from the excreta of sea birds, which is known as guano and which was used as a source of fertilizer; guanine was named in 1846. In both DNA and RNA, guanine is one of the most important nucleic acid bases. In addition to being the largest nucleic acid bases, it has also the most complex tautomeric equilibria [1-3]. The property of amino tautomers of guanine has been discussed in several recent works [4–8]. The interaction between guanine and one water molecules [9] or two [10] can influence the NH2-nonplanarity phenomena and this has been discussed for the cyclic complex where water acts as a proton donor towards the carbonyl bond while accepting a proton from the vicinal NH bond of guanine. In a recent work [11], the optimized geometries, harmonic vibrational frequencies and energies of four cyclic structures of monohydrated guanine have been computed using density functional theory (DFT) combined with the 6-311G(d,p) basis set. In these calculations, only the amino group hydrogen atoms were considered as having a nonplanar structure. In the present work, the same parameters are calculated with geometry optimization and vibrational assignment using density functional theory (DFT) B3LYP, X3LYP and B3PW91 method employing 6-311++G (d,p) as the basis set.
II. Computational methods
The ground state geometries and vibrational spectra for free guanine and its hydrogen-bonded complexes with molecules of water have been optimized. The total energies, structural parameters of the optimized geometries parameters (bond length and bond angles) the APT charges, IR intensity, Raman activity and ring breathing vibration of have been computed using density functional theory (DFT) B3LYP, X3LYP and B3PW91 method employing 6-311++G (d,p) as the basis set. For theoretical study, we have used GAUSSIAN 09 [12] package of programs. The geometries were optimized by minimizing the energies without imposing any constraint on the geometry. It has well known that this level of theory is sufficient to reliably predict molecular geometries hydrogen bonded systems. The geometry of the free guanine and guanine -water complex have been fully optimized by the density functional theory (DFT) B3LYP, X3LYP and B3PW91 method employing 6-311++G (d,p) as the basis set for the first time. The optimized geometrical parameters (bond length and bond angles), total energies [13], ring breathing vibration ʋ1, IR intensity, Raman activity and dipole moment have been calculated for guanine and guanine -water complexes and compared. The optimized structure of free guanine and guanine -water isomers at B3LYP/6-311++ G (d,p) along with atomic numbering have been shown in Figure 1and Figure 2 (I-IV) respectively.