A DFT investigation on effects of hydration on the tautomeric equilibria of hypoxanthine

Investigation of interactions of doxorubicin with purine nucleobases by molecular modeling

Doxorubicin, an anthracycline antibiotic with anti-tumor activity, is produced by the bacterium Streptomyces peucetius. The interactions between doxorubicin and genetic material and the details of the intercalation with DNA have been controversial issues. Thus, the interactions of doxorubicin with purine nucleobases were studied by quantum mechanical methods. Initially, conformer analyses of doxorubicin were performed with Spartan 08 software and 319 different conformers from 422 initial structures for doxorubicin were obtained. Geometry optimizations and frequency analyses were performed for each structure using density functional theory (DFT) at B3LYP/6-31G** level using Gaussian 09 software. The most stable 20 conformers of doxorubicin and tautomers of purine nucleobases were optimized again with ɷB97XD/6-31G** level and their interactions were also analyzed at the same level. The Discovery Studio 3.5 Visualizer was used to draw the initial and optimized structures of investigated geometries. The noncovalent interactions (NCIs) were visualized by calculating reduced density gradient (RDG) with Multiwfn program. The color-filled isosurfaces and RDG scatter maps of most stable interaction geometries were plotted by Visual Molecular Dynamics (VMD) software and Gnuplot 5.3 software, respectively. This study showed that adenine, guanine, and hypoxanthine nucleobases interact with doxorubicin by forming strong hydrogen bonds and π-π interactions. Considering the normal cellular conditions, the effect of solvent (water) on the interaction geometries were also analyzed and when compared to gas phase it was determined that the movements of the molecules were restricted and there was a minimal change between initial and optimized structures in the aqueous phase.

Microhydration of Deprotonated Nucleobases

Hydration reactions of deprotonated nucleobases (uracil, thymine, 5-fluorouracil,2-thiouracil, cytosine, adenine, and hypoxanthine) produced by electrospray have been experimentally studied in the gas phase at 10 mbar using a pulsed ion-beam high-pressure mass spectrometer. The thermochemical data, ΔH (o) , ΔS (o) , and ΔG (o) , for the monohydrated systems were determined. The hydration enthalpies were found to be similar for all studied systems and varied between 39.4 and 44.8 kJ/mol. A linear correlation was found between water binding energies in the hydrated complexes and the corresponding acidities of the most acidic site of nucleobases. The structural and energetic aspects of the precursors for the hydrated complexes are discussed in conjunction with available literature data. Graphical Abstract ᅟ.

The effects of tautomerization and protonation on the adenine-cytosine mismatches: a density functional theory study

In the present work, we demonstrate the results of a theoretical study concerned with the question how tautomerization and protonation of adenine affect the various properties of adenine-cytosine mismatches. The calculations, in gas phase and in water, are performed at B3LYP/6-311++G(d,p) level. In gas phase, it is observed that any tautomeric form of investigated mismatches is more stabilized when adenine is protonated. As for the neutral mismatches, the mismatches containing amino form of cytosine and imino form of protonated adenine are more stable. The role of aromaticity on the stability of tautomeric forms of mismatches is investigated by NICS(1)ZZ index. The stability of mispairs decreases by going from gas phase to water. It can be explained using dipole moment parameter. The influence of hydrogen bonds on the stability of mismatches is examined by atoms in molecules and natural bond orbital analyses. In addition to geometrical parameters and binding energies, the study of the topological properties of electron charge density aids in better understanding of these mispairs.

Theoretical study of valance photoelectron spectra of hypoxanthine, xanthine, and caffeine using direct symmetry-adapted cluster/configuration interaction methodology

UV photoelectron spectra of hypoxanthine, xanthine, and caffeine, up to 20 eV, were calculated and compared with the experimental spectra reported in literature. The calculations were performed using a novel version of the quantum mechanical symmetry-adapted cluster/configuration interaction (SAC-CI) method termed, direct SAC-CI. The Duning/Huzinaga valance double-zeta D95+(d,p) Gaussian basis set was also employed with this method. The ionization energies and intensities were calculated, and the corresponding spectral bands were assigned. Natural bonding orbital (NBO) calculations were employed for better spectral band assignment. The calculated ionization energies and intensities reasonably produced the experimental photoelectron spectra.

Ab initio study of 2,4-substituted azolidines. II. Amino-imino tautomerism of 2-aminothiazolidine-4-one and 4-aminothiazolidine-2-one in water solution

The relative stabilities of the tautomers of 2-aminothiazolidine-4-one and 4-aminothiazolidine-2-one were calculated at the MP2/6-31+G(d,p) level by considering their mono- and trihydrated complexes. Single-point calculations at the MP4/6-31+G(d,p)//MP2/6-31+G(d,p) level of theory were performed to obtain more accurate energies. The values of proton transfer barriers in the isolated, mono- and trihydrated tautomers of 2-aminothiazolidine-4-one (2AT) and 4-aminothiazolidine-2-one (4AT) were calculated for two different mechanisms of tautomerisation. In the absence of water, the process of proton transfer should not occur. Addition of water molecules decreases the barrier making the process faster, as the participation of two water molecules in a proton transfer reaction is more favorable than the participation of only one water molecule. To estimate the effect of the medium (water) on the relative stabilities of the tautomers of the studied compounds we applied the polarizable continuum model (PCM). (13)C NMR chemical shieldings were calculated using the GIAO approach at MP2/6-31+G(d,p) optimized geometries. HF and the DFT B3LYP functional with 6-31+G(d,p) basis set were employed. The quantum chemical results for the chemical shifts in gas phase and in polar solvents (water and DMSO) were compared with experimental data. TD DFT B3LYP/aug-cc-pVTZ calculations were performed to predict the absorption maxima of tautomers A and B of 2AT and 4AT.

A computational characterization of the hydrogen-bonding and stacking interactions of hypoxanthine

The hydrogen-bonding and stacking interactions of hypoxanthine, a potential universal nucleobase, were calculated using a variety of methodologies (CCSD(T), MP2, B3LYP, PWB6K, AMBER). All methods predict that the hydrogen-bonding interaction in the hypoxanthine-cytosine pair is approximately 25 kJ mol(-1) stronger than that in the other dimers. Although the calculations support suggestions from experiments that hypoxanthine preferentially binds with cytosine, the trend in the calculated hydrogen-bond strengths for the remaining natural nucleobases do not show a strong correlation with the experimentally predicted binding preferences. However, our calculations suggest that the stacking interactions of hypoxanthine are similar in magnitude to the hydrogen-bonding interactions at all levels of theory (with the exception of B3LYP, which incorrectly predicts stacked dimers to be unstable). Therefore, stacking interactions should also be considered when analyzing the stability of DNA helices containing hypoxanthine and the use of larger models that account for both hydrogen-bonding and stacking within DNA duplexes will likely result in better agreement with experimental observations. For the majority of the dimers, PWB6K and AMBER provide reasonable binding strengths at reduced computational costs, and therefore will be useful techniques for considering larger models.

UV-Induced Oxo → Hydroxy Unimolecular Proton-Transfer Reactions in Hypoxanthine

Monomers of hypoxanthine isolated in low-temperature Ar matrixes were studied using Fourier transform infrared spectroscopy. Two most stable tautomeric forms of hypoxanthine: oxo-N(9)-H and oxo-N(7)-H as well as a very small amount of the minor hydroxy-N(9)-H tautomer were observed in Ar matrixes directly after their deposition. UV irradiation of the matrixes induced conversion of the oxo-N(9)-H and oxo-N(7)-H tautomers of the compound into the hydroxy-N(9)-H and hydroxy-N(7)-H forms, respectively. Upon exposure of the matrixes to the UV (lambda > 270 nm) light, the oxo-N(9)-H --> hydroxy-N(9)-H phototautomeric reaction dominated strongly over the oxo-N(7)-H --> hydroxy-N(7)-H phototransformation. The latter phototautomeric reaction occurred effectively when matrix-isolated hypoxanthine was irradiated with shorter-wavelength (lambda > 230 nm) UV light. Thanks to this wavelength dependency, it was possible to clearly distinguish the oxo --> hydroxy photoreaction within the N(9)-H tautomers from the analogous phototautomeric process within the N(7)-H tautomers. All of the observed isomers of hypoxanthine (substrates and products of the photoreactions) were identified by comparison of their IR spectra with the spectra calculated at the DFT(B3LYP)/6-31++G(d,p) level of theory.

UV-induced generation of rare tautomers of allopurinol and 9-methylhypoxanthine — A matrix isolation FTIR study

Monomers of allopurinol and 9-methylhypoxanthine were studied using the matrix isolation technique combined with Fourier transform infrared spectroscopy. The oxo tautomeric forms of both compounds were found to dominate in freshly deposited low-temperature argon matrices. For 9-methylhypoxanthine, a small amount of the hydroxy tautomer was also detected in an Ar matrix before any irradiation. Upon exposure of the matrices to the UV (lambda>230 nm or lambda>270 nm) light, a proton transfer photoreaction converting the oxo forms of both compounds into the corresponding hydroxy tautomers occurred. Generation of conjugated ketenes as minor photoproducts was also observed. For 4(3H)-pyrimidinone (a model compound for both allopurinol and 9-methylhypoxanthine), photoreversibility of the UV-induced oxo --> hydroxy transformation was experimentally proven by direct observation of the back hydroxy --> oxo photoreaction. The substrates (oxo tautomers) and products (hydroxy tautomers) of the observed phototransformations were identified by comparison of their IR spectra with the spectra theoretically predicted at the DFT(B3LYP)/6-31++G(d,p) level. The IR bands in the experimental spectra were assigned to the calculated normal modes.

Oxo−Hydroxy Tautomerism of 5-Fluorouracil: Water-Assisted Proton Transfer

Post-Hartree-Fock ab initio quantum chemical calculations were performed for 5-fluorouracil in the gas phase and in a three-water cluster. Full geometry optimizations of the 5-fluorouracil-water complexes were carried out at the MP2/6-31+G(d,p) level of theory. MP4/6-31+G(d,p)//MP2/6-31+G(d,p) and MP4/6-31++G(d,p)//MP2/6-31+G(d,p) single-point calculations were performed to obtain more accurate energies. In water solution, 5-fluorouracil exists mainly in the 2,4-dioxo form (A). We propose that the populations of the 2-hydroxy-4-oxo (B) and 4-hydroxy-2-oxo (D) tautomers are 1 x 10(-4)% and 3.9 x 10(-8)%, respectively, on the basis of the relative stabilities of the tautomers calculated at the MP4/6-31++G(d,p)//MP2/6-31+G(d,p) level of theory. A profound difference between isolated and hydrated 5-fluorouracil is noted for the height of the tautomerization barrier. In the absence of water, the process of proton transfer is very slow. The addition of water molecules decreases the barrier by 2.3 times, making the process much faster. The minimum energy path (MP2/6-31+G(d,p)) for water-assisted proton transfer in trihydrated 5-fluorouracil was followed. CNDO/S-CI calculations predict singlet pi-pi(*) electron transitions at 312 nm for B and at 318 nm for D. The fluorescence spectrum of 5-fluorouracil in water confirms the presence of the hydroxy tautomer.

((15)N(5))-labeled adenine derivatives: synthesis and studies of tautomerism by (15)N NMR spectroscopy and theoretical calculations

Since the nitrogens of nucleosides and nucleotides play an important role in the molecular recognition of these compounds, (15)N NMR became a method of choice in this field. Fully (15)N-labeled adenine, required in the latter studies, was obtained in four synthetic steps, in a good yield. Likewise, ((15)N(5))-2-hexylthioether-adenine and ((15)N(5))-8-Br-adenine were obtained in five synthetic steps from the relatively inexpensive (15)N sources: (15)N-NH(4)Cl, (15)N-NH(4)OH, (15)N-NaNO(2). Full (15)N labeling of these adenine prototypes enabled to obtain high-resolution (15)N NMR spectra of these bases at 60.8 MHz. Furthermore, the spectra suggested the existence of the N3-H species in the tautomeric mixtures of these compounds in solution, in addition to the well-reported N9-H (major) and N7-H (minor) tautomers. These observations were also supported by quantum mechanical calculations of the tautomeric equilibria in the gas phase and in solution of the above-mentioned adenine compounds. The gas-phase tautomeric equilibria were estimated using density functional theory and second-order perturbation theory methods. Solvent effects were included by means of both continuum and discrete solvation models. The observation of the existence of the N3-H tautomer has a clear impact on the possible H-bonding patterns of these adenine prototypes and on their molecular recognition by various biological macromolecules. The above(15)N-labeled analogues are expected to find use as (15)N NMR probes for numerous biochemical studies.