Hydrogen bonding in Watson–Crick, reversed Watson–Crick, Hoogestein, reversed Hoogestein and other configurations of adenine–thymine base pairs have been studied with theoretical methods. In order to determine the optimized geometries, energies, dipole moments, atomic charges, thermo chemical analysis and other properties of hydrogen bonding in A–T base pairs, we have performed quantum chemical ab initio and density functional calculations at HF/6-31G (d,p), B3LYP/6-31G (d) and B3LYP/6-31G (d,p) levels in gas phase and solution. The solvent effect is taken into account via the self-consistent reaction field (SCRF) method. We optimized the geometries of A–T base pairs in various solvents (water, methanol, ethanol and acetone) with Polarized Continuum Model (PCM). Best agreement with available gas phase experimental A–T bond enthalpies (−12.1 kcal mol−1) is obtained at the B3LYP/6-31G (d,p) level, which (for 298 K) yields −12.44 kcal mol−1, deviating by as little as −0.34 kcal mol−1 from experimental. Bond enthalpies of A–T (1) base pair in various solvents at the B3LYP/6-31G (d) level are −2.30, −2.64, −3.03 and −8.06 kcal mol−1 in water, methanol, ethanol and acetone, respectively, these results show that with increasing dielectric constant of solvent the bond enthalpies of A–T base pairs decrease. The bond enthalpy of A–T (9) model is larger than other models in gas phase and various solvents. In addition for further correction about interaction energies between A and T, the basis set super position error (BSSE), has been computed. In Watson–Crick base pair, A–T (1), the distances for (N2⋯H23–N19), (N8–H13⋯O24) and (C1⋯O18) obtained from B3LYP/6-31G (d,p) level are 2.84, 2.94 and 3.63 A, respectively, in agreement with experimental results (2.82, 2.98 and 3.52 A). Also, we use natural bond orbital (NBO) method to identify principle delocalizing acceptor orbital associated with each donor NBO and their topological relationship to this NBO and donor–acceptor interaction perturbation theory energy analysis, for different configurations of A–T base pairs in gas phase and solution. The effect of solvent on charge distribution of acceptor and donor atoms show that with decreasing of dielectric constant of solvent, the acceptor atom charges decreasing and for proton atoms charges increase further. In acetone, changes in distance of N–H and C O bonds in different orientations of A–T base pairs are further than other solvents. This means that with decreasing dielectric constant of solvent, hydrogen bond to be stronger. To identify any artifacts in the Mulliken population analysis, a natural bond orbital (NBO) was examined.

Theoretical investigation of hydrogen bonding in Watson–Crick, Hoogestein and their reversed and other models: comparison and analysis for configurations of adenine–thymine base pairs in 9 models

Monte Carlo computer simulations were performed on dilute aqueous solutions of thymine, cytosine, uracil, adenine, guanine, the dimethyl phosphate anion in the gauche-gauche conformation and a ribose and deoxyribose derivative. The aqueous hydration of each molecule was analysed in terms of quasi-component distribution functions based on the Proximity Criterion, and partitioned into hydrophobic, hydrophilic and ionic contributions. Color stereo views of selected hydration complexes are also presented. A preliminary discussion of the transferability of functional group coordination numbers is given. The results enable to comment on two current problems related to the hydration of nucleic acids: a) the theory of Dickerson and coworkers on the role of water in the relative stability of the A and B forms of DNA and b) the idea of water bridges and filaments emerging from the computer simulation results on the hydration of DNA fragments by Clementi.

Aqueous Hydration of Nucleic Acid Constituents: Monte Carlo Computer Simulation Studies

The results of a Monte Carlo simulation of the hydration of uracil and thymine molecules, their stacked dimers and hydrogen-bonded base pairs are presented. Simulations have been performed in a cluster approximation. The semiempirical atom-atom potential functions have been used (cluster consisting of 200 water molecules). It has been shown that the stacking interactions of uracil and thymine molecules in water arise mainly due to the increase in the water-water interaction during the transition from monomers to dimer. It has been found out that stacked base associates are more preferable than base pairs in water. This preference is mainly due to the energetically more favourable structure of water around the stack.

Nature of the stacking of nucleic acid bases in water: a Monte Carlo simulation.

An extensive computer simulation of nucleic acid bases and Watson-Crick base pairs in a water cluster and DMSO cluster is performed by the Monte Carlo method. It is demonstrated that the unfavorable energetics of pair formation in a water cluster is determined by the significant destabilizing contribution of solvent to the energy of complex formation. It is shown that the formation of coplanar base pairs in a DMSO cluster is favorable. The DMSO cluster stabilizes A-U and A-T base pairs and the insignificant destabiliza'tion of the G-C base pair by a DMSO cluster is much less than the stabilization which occurs due to the attraction between bases.

The Study of the Stability of Watson-Crick Nucleic Acid Base Pairs in Water and Dimethyl Sulfoxide: Computer Simulation by the Monte Carlo Method

In this study, the anticancer properties of a series of synthesized indolyl-oxazoles drugs 1–6 and their interactions with DNA base pairs were investigated. The quantum molecular descriptors (chemical potential, hardness, and electrophilicity) for studied drugs and their complexes with DNA base pairs were calculated. The reaction enthalpies (BDE and IP) of HAT and SET-PT mechanism of anticancer action of drugs 1–6 were calculated. Results reveal that interactions of indolyl-oxazole drugs with DNA base pairs are energetically favorable and solvent increase the binding energies in comparison with gas phase. The binding energies of drugs 4–6 DNA base pairs complexes are more negative than corresponding values for drugs 1–3. The obtained binding energy and reaction enthalpy (BDE and IP) trends for drugs 1–6 confirm pervious experimental anticancer activity trends. IC50 scale has been used as a benchmark for measuring the anticancer activity. Based on theoretical and published experimental scales, drugs 4, 5, and 6 have higher anticancer activity among drugs 1–6. Finally, according to the obtained results, drugs 7–10 can consider as novel drugs with higher anticancer activity than drug 1. Results show that binding energies of drugs 7–10 with DNA base pairs were more negative than corresponding values for drugs 1–6. The BDE and IP values of drugs 4–10 were lower than corresponding values of drug 1. For drugs 1–10, results indicated that the SET-PT and HAT mechanisms represent the thermodynamically preferred mechanism in solvent and gas phase, respectively.

Theoretical study of anticancer properties of indolyl-oxazole drugs and their interactions with DNA base pairs in gas phase and solvent

https://febs.onlinelibrary.wiley.com/doi/pdf/10.1016/0014-5793%2884%2980135-0

Nature of the stacking interaction of nucleotide bases in water: a Monte Carlo study of the hydration of uracil molecule associates

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Nature of the stacking interaction of nucleotide bases in water: a Monte Carlo study of the hydration of uracil molecule associates