A comparative study of the hydrogen-bonding patterns and prototropism in solid 2-thiocytosine (potential antileukemic agent) and cytosine, as studied by 1H-14N NQDR and QTAIM/ DFT

Resonance Raman spectroscopic and density functional theoretical study on microsolvated 2-Thiocytosine clusters with polar solvents

Microsolvation effects on the excited state deactivation dynamics of 2-thiocytosine (2tC) were studied in hydrogen-bonded 2tC clusters with protic solvents using resonance Raman, FT-IR, FT-Raman, UV-vis spectroscopy combining with density functional theoretical calculation. Two protic solvents, water (H₂O) and methanol (MeOH), and one aprotic solvent, acetonitrile (MeCN), were used to investigate the 2tC(H₂O)_1-5, 2tC(MeOH)_1-5, and 2tC(MeCN)_1-3 microsolvated clusters. In CH₃OH and H₂O solvents, most of the Raman shifts were due to the vibration modes of 2tC(solvent)_n (solvent = H₂O, CH₃OH; n = 1-4) clusters via intermolecular NH⋯O hydrogen bonds (HB). The intermolecular >NH⋯O hydrogen bond interactions, which are the key constituents of stable thione structure of 2tC, revealed the spectra difference of 2tC in CH₃CN, CH₃OH and H₂O. With the aid of electronic structural and vibration frequency calculations, the observed Raman spectra were assigned to the low energy isomers of 2tC(solvent)₂ (solvent = H₂O, CH₃OH) clusters in water and methanol and 2tC(CH₃CN) in acetonitrile solvents. 2tC(solvent)₂ clusters in water and methanol may prohibit or promote excited state proton transfer reaction from sulfur atom to neighbor nitrogen atom due to the hydrogen bonding chain between 2tC and protic solvent molecules. Our experimental and theoretical studies confirmed that the hydrogen bond sites were located on the specified functional group SCNH of 2tC with solvent molecules.

Solvatochromic Effects on the Absorption Spectrum of 2-Thiocytosine

The solvatochromic effects of six different solvents on the UV absorption spectrum of 2-thiocytosine have been studied by a combination of experimental and theoretical techniques. The steady-state absorption spectra show significant shifts of the absorption bands, where in more polar solvents the first absorption maximum shifts to higher transition energies and the second maximum to lower energies. The observed solvatochromic shifts have been rationalized using three popular solvatochromic scales and with high-level multireference quantum chemistry calculations including implicit and explicit solvent effects. It has been found that the dipole moments of the excited states account for some general shifts in the excitation energies, whereas the explicit solvent interactions explain the differences in the spectra recorded in the different solvents.

Contrasting reactions of hydrated electron and formate radical with 2-thio analogues of cytosine and uracil

2-thiocytosine (TC) and 2-thiouracil (TU) were found to react with formate radical via reductive and oxidative pathways simultaneously.

Metal coordination study at Ag and Cd sites in crown thioether complexes through DFT calculations and hyperfine parameters

Structural and electronic properties of [C12H24S6X], [C13H26S6OX], and [C14H28S6OX] (X: Ag(+), Cd(2+)) crown thioether complexes were investigated within the framework of the density functional theory (DFT) using the projector augmented wave (PAW) method. The theoretical results were compared with time-differential perturbed γ-γ angular correlations (TDPAC) experiments reported in the literature using the (111)Ag→(111)Cd probe. In the case of X=Ag(+), a refinement of the structure was performed and the predicted equilibrium structures compared with available X-ray diffraction experimental data. Structural distortions induced by replacing Ag(+) with Cd(2+) were investigated as well as the electric-field gradient (EFG) tensor at the Cd(2+) sites. Our results suggest that the EFG at Cd(2+) sites corresponds to the Ag(+) coordination sphere structure, i.e., before the structural relaxations of the molecule with X=Cd(2+) are completed. The results are discussed in terms of the characteristics of the TDPAC (111)Ag→(111)Cd probe and the time window of the measurement, and provide an interesting tool with which to probe molecular relaxations.

Modeling the effect of H-bonding interactions and molecular packing on the molecular structure of [Ag(ethylnicotinate)(2)]NO (3) complex

The gas phase molecular structure of a single isolated molecule of [Ag(Etnic)(2)NO(3)];1 where Etnic = Ethylnicotinate was calculated using B3LYP method. The H-bonding interaction between 1 with one (complex 2) and two (complex 3) water molecules together with the dimeric formula [Ag(Etnic)(2)NO(3)](2);4 and the tetrameric formula [Ag(Etnic)(2)NO(3)](4);5 were calculated using the same level of theory to model the effect of intermolecular interactions and molecular packing on the molecular structure of the titled complex. The H-bond dissociation energies of complexes 2 and 3 were calculated to be in the range of 12.220-14.253 and 30.106-31.055 kcal mol(-1), respectively, indicating the formation of relatively strong H-bonds between 1 and water molecules. The calculations predict bidentate nitrate ligand in the case of 1 and 2, leading to distorted tetrahedral geometry around the silver ion with longer Ag-O distances in case of 2 compared to 1, while 3 has a unidentate nitrate ligand leading to a distorted trigonal planar geometry. The packing of two [Ag(Etnic)(2)NO(3)] complex units; 4 does not affect the molecular geometry around Ag(I) ion compared to 1. In the case of 5, the two asymmetric units of the formula [Ag(Etnic)(2)NO(3)] differ in the bonding mode of the nitrate group, where the geometry around the silver ion is distorted tetrahedral in one unit and trigonal planar in the other. The calculations predicted almost no change in the charge densities at the different atomic sites except at the sites involved in the C-H⋯O interactions as well as at the coordinated nitrogen of the pyridine ring.

Theoretical study of the interaction between 5-methylcytosine and acrylamide

The hydrogen-bonded complexes between 5-methylcytosine and acrylamide have been investigated using the density function theory (DFT) method. Five stable complexes have been found with no imaginary frequencies. Complex C3 is the most stable one with interaction energies of -69.01 kJ mol(-1) corrected for basis set superposition error (BSSE). The charge change in the process of these complexes formation has also been examined. The atoms in molecules (AIM) theory and natural bond orbital (NBO) method have been performed to investigate the hydrogen bonds involved in all the complexes. The electron density and its corresponding Laplacian at the bond and ring critical points have been analyzed. In C3 complex, there is the largest stabilization energy (18.17 kJ mol(-1)) between N11-H12 antibonding orbital and lone electron pair of O17. It can be seen that the hydrogen bonds play a crucial role in the stability of all the complexes between 5-methylcytosine and acrylamide. The theoretical results could provide helpful information for other researchers in further work.