Homodimers of Cytosine and 1-MethylCytosine. A DFT study of geometry, relative stability and H-NMR shifts in gas-phase and selected solvents

Abstract

Dimers of cytosine and its N¹-methylated counterpart were investigated in gas-phase and in various solvents including chloroform, dimethylsulfoxide, and water. The studies were performed at DFT/M06-2X/6-31+G(d,p) level of theory. Relative stabilities of tautomers of cytosine solvated explicitly by a small number of solvent molecules were evaluated. Further solvation effect calculations for homodimers were carried out with conductor-like polarizable continuum model (CPCM). H-NMR shifts and IR frequencies for optimized structures were calculated and compared with available experimental data.

Theoretical and experimental NMR studies on muscimol from fly agaric mushroom (Amanita muscaria)

“…1 H and 13 C NMR spectroscopy in DMSO-d6 solution of muscimol was selected as source of experimental information of muscimol molecular structure in solution. The current approach is partly similar to recent theoretical and experimental 1 H NMR studies on GABA 51 , as well as cytosine and 1-methylcytosine in solution 54 . However, in our study the analysis of the observed NMR data was supported by high-level DFT calculations combined with fairly complete basis sets and using both equilibrium and rovibrationally averaged geometry [59][60][61][62] .…”

“…The further complication is due to a possibility of migration of hydrogen atom from a hydroxyl group to nitrogen atom in isoxazole ring (Scheme 1B). In fact, the two latter forms resemble the canonic keto (CK) and enol, or aminohydroxy (CE) forms of cytosine which is dominating in solution [54][55][56][57] . Recently, the structure and charge distribution of GABA and muscimol in the gas phase and solution was studied in details theoretically by Serdaroglu 58 .…”

Using Density Functional Theory To Study Neutral and Ionized Stacked Thymine Dimers

“…π stacking is crucial for functioning of biological systems: it is essential not only for molecular recognition processes but also for structure, stability, and dynamics of biological macromolecules (DNA, RNA, various proteins), which prompted their extensive analysis in the last two decades. − Stacking interactions are also important in material science. For example, they are significant for the stability of nanostructres formed by discotic liquid crystals, which are used in organic electronics, or for host–guest chemistry. − These large systems are particularly intriguing because their properties are often governed by weak interactions that might be ignored in small systems .…”

“…Significantly less demanding approaches include Møller–Plesset perturbation theory, MP2, ,,− ,,, as well as density functional theory, DFT. The latter approach either relies on functionals with dispersion corrections ,,, or is based on new functionals that account for dispersion effects. , DFT methods are employed for analysis of large systems that cannot be studied with wave function-based methods. This was demonstrated by Kim and co-workers who studied adsorption of nucleobases on graphene, as well as electronic and magnetic properties of graphene-based devices .…”

“…For that reason, we have chosen this system as a case study for analysis of stacking interactions. It has already been demonstrated that derivatives of DNA base pairs with substituted benzyl hydrogen atoms generally exhibit stronger stacking interactions than the nonsubstituted analogues, ,, except in cytosine where methylation (1-methylcytosine) weakens intermolecular interactions . In this contribution we analyze thymine (T)-stacked dimers (neutral and ionized forms), as well as the influence of methylation on binding energies through investigation of neutral 1-methylthymine (1 mT) homodimers.…”