The keto–amino/enol tautomerism of cytosine in aqueous solution. A theoretical study using combined discrete/self-consistent reaction field models

Structure and Stability of Molecular Crystals with Many-Body Dispersion-Inclusive Density Functional Tight Binding

Accurate prediction of structure and stability of molecular crystals is crucial in materials science and requires reliable modeling of long-range dispersion interactions. Semiempirical electronic structure methods are computationally more efficient than their ab initio counterparts, allowing structure sampling with significant speedups. We combine the Tkatchenko-Scheffler van der Waals method (TS) and the many-body dispersion method (MBD) with third-order density functional tight-binding (DFTB3) via a charge population-based method. We find an overall good performance for the X23 benchmark database of molecular crystals, despite an underestimation of crystal volume that can be traced to the DFTB parametrization. We achieve accurate lattice energy predictions with DFT+MBD energetics on top of vdW-inclusive DFTB3 structures, resulting in a speedup of up to 3000 times compared with a full DFT treatment. This suggests that vdW-inclusive DFTB3 can serve as a viable structural prescreening tool in crystal structure prediction.

DNA spontaneous mutation and its role in the evolution of GC-content: assessing the impact of the genetic sequence

We use theoretical tools to investigate the possible role played by a DNA sequence in the base pair tautomerization phenomena.

Molecular modeling study of dihydrofolate reductase inhibitors. Molecular dynamics simulations, quantum mechanical calculations, and experimental corroboration

A molecular modeling study on dihydrofolate reductase (DHFR) inhibitors was carried out. By combining molecular dynamics simulations with semiempirical (PM6), ab initio, and density functional theory (DFT) calculations, a simple and generally applicable procedure to evaluate the binding energies of DHFR inhibitors interacting with the human enzyme is reported here, providing a clear picture of the binding interactions of these ligands from both structural and energetic viewpoints. A reduced model for the binding pocket was used. This approach allows us to perform more accurate quantum mechanical calculations as well as to obtain a detailed electronic analysis using the quantum theory of atoms in molecules (QTAIM) technique. Thus, molecular aspects of the binding interactions between inhibitors and the DHFR are discussed in detail. A significant correlation between binding energies obtained from DFT calculations and experimental IC₅₀ values was obtained, predicting with an acceptable qualitative accuracy the potential inhibitor effect of nonsynthesized compounds. Such correlation was experimentally corroborated synthesizing and testing two new inhibitors reported in this paper.

Gas-phase hydration thermochemistry of sodiated and potassiated nucleic acid bases

Hydration reactions of sodiated and potassiated nucleic acid bases (uracil, thymine, cytosine, and adenine) produced by electrospray have been studied in a gas phase using the pulsed ion-beam high-pressure mass spectrometer. The thermochemical properties, ΔH(o)(n), ΔS(o)(n), and ΔG(o)(n), for the hydrated systems were obtained from hydration equilibrium measurement. The structural aspects of the hydrated complexes are discussed in conjunction with available literature data. The correlation between water binding energies in the hydrated complexes and the corresponding metal ion affinities of nucleobases suggests that a significant (if not dominant) amount of the canonical structure of cytosine undergoes tautomerization during electrospray ionization, and the thermochemical values for cationized cytosine probably correspond to a mixture of tautomeric complexes.

Theoretical study of the tautomerism in the one-electron oxidized guanine-cytosine base pair

Ionizing radiation on DNA mainly generates one-electron oxidized guanine-cytosine base pair (G(+·):C), and in the present paper we study all possible tautomers of G(+·):C by using ab initio approaches. Our calculations reveal that the tautomeric equilibrium follows a peculiar path, characterized by a stepwise mechanism: first the proton in the central hydrogen bond N1(G)-H1-N3(C) migrates from guanine to cytosine, and then the cytosine cation releases one proton from its amino group. During this second step, water acts as a proton acceptor, localizing the positive charge on one of the water molecules interacting with the guanine radical. In agreement with experimental findings, the computed energy barriers show that the deprotonation of the cytosine cation is the speed-limiting step in the tautomeric equilibrium. The influence of the number of water molecules incorporated in the theoretical model is analyzed in detail. The evolution of electronic properties along the reaction path is also discussed on the basis of partial atomic charges and spin density distributions. This work demonstrates that water indeed plays a crucial role in the tautomeric equilibra of base pairs.

Infrared spectra of protonated uracil, thymine and cytosine

The gas-phase structures of protonated uracil, thymine, and cytosine are probed by using mid-infrared multiple-photon dissociation (IRMPD) spectroscopy performed at the Free Electron Laser facility of the Centre Laser Infrarouge d'Orsay (CLIO), France. Experimental infrared (IR) spectra are recorded for ions that were generated by electrospray ionization, isolated, and then irradiated in a quadrupole ion trap; the results are compared to the calculated infrared absorption spectra of the different low-lying isomers (computed at the B3LYP/6-31++G(d,p) level). For each protonated base, the global energy minimum corresponds to an enolic tautomer, whose infrared absorption spectrum matched very well with the experimental IRMPD spectrum, with the exception of a very weak IRMPD signal observed at about 1800 cm(-1) in the case of the three protonated bases. This signal is likely to be the signature of the second-energy-lying oxo tautomer. We thus conclude that within our experimental conditions, two tautomeric ions are formed which coexist in the quadrupole ion trap.

Ca, Cd, Zn, and Their Ions Interacting with Cytosine: A Theoretical Study

Metal atoms play a major role in the chemical behavior of biological systems. In this work, known issues of the metal-base interactions, such as the stabilization of different tautomers of cytosine that could be incompatible with the DNA double helix, are researched using DFT methods. Ca-, Zn-, and Cd-cytosine in neutral and ionic forms were studied at the B3LYP/LANL2DZ level. Several neutral and ionic isomers were found within an interval of 10 kcal/mol of relative stability, with the most stable isomer in each group being a compound derived from the canonical isomer of cytosine, except for the dications where two iso-energetic isomers were found. Interatomic lengths from each metal atom to the nearest atoms in cytosine's ring were larger than 2 A, discouraging the possibility of a covalent interaction, as supported by additional evidence from molecular orbitals. The interaction between metal and cytosine, electrostatic in nature, is reinforced with the increase of the metal's nuclear charge. Additionally, the ionization energies of the metal-cytosine compounds exhibit a significant reduction (below 6 eV) compared with that of plain cytosine (8.7 eV), posing an interesting possibility with respect to the experimental determination of the photoelectron spectra of these compounds. Analyses of the energetics of the global reactions to form cationic species show that metal cations bind more strongly to neutral cytosine than to neutral metals. Metal dications form the most stable compounds with neutral cytosine, and the stabilities of these systems decrease as (Zn-cyt)2+ > (Cd-cyt)2+ > (Ca-cyt)2+. Aromaticities computed via the HOMA indexes also support the observation regarding the greater affinity of cytosine for metal cations.

Potential energy surfaces of the microhydrated guanine...cytosine base pair and its methylated analogue

A complete scan of the potential and free-energy surfaces of monohydrated and dihydrated guanine...cytosine and 9-methylguanine...1-methylcytosine base pairs was realized by the molecular dynamics/quenching technique using the force field of Cornell et al. implemented in the AMBER7 program. The most stable and populated structures localized were further fully reoptimized at the correlated ab initio level employing the resolution of identity Møller-Plesset method with a large basis set. A systematic study of microhydration of these systems using a high-level correlated ab initio approach is presented for the first time. The different behavior of guanine...cytosine and adenine...thymine complexes is also discussed. These studies of nucleic acid base pairs are important for finding binding sites of water molecules around bases and for better understanding of the influence of the solvent on the stability of the structure of DNA.

Hydrogen-bonded nucleic acid base pairs containing unusual base tautomers: complete basis set calculations at the MP2 and CCSD(T) levels

The total interaction energies of altogether 15 hydrogen-bonded nucleic acid base pairs containing unusual base tautomers were calculated. The geometry properties of all selected adenine-thymine and guanine-cytosine hydrogen-bonded base pairs enable their incorporation into DNA. Unusual base pairing patterns were compared with Watson-Crick H-bonded structures of the adenine-thymine and guanine-cytosine pairs. The complete basis set (CBS) limit of the MP2 interaction energy and the CCSD(T) correction term, determined as the difference between the CCSD(T) and MP2 interaction energies, was evaluated. Extrapolation to the MP2 CBS limit was done using the aug-cc-pVDZ and aug-cc-pVTZ results, and the CCSD(T) correction term was determined with the 6-31G*(0.25) basis set. Final interaction energies were corrected while taking into account both tautomeric penalization determined at the CBS level and solvation/desolvation free energies. The situation for the adenine-thymine pairs is straightforward, and tautomeric pairs are significantly less stable than the Watson-Crick pair consisting of the canonical forms. In the case of the guanine-cytosine pair, the Watson-Crick structure made by canonical forms is again the most stable. The other two structures are, however, energetically rather similar (by 5 and 6 kcal/mol), which provides a very small but non-negligible chance of detecting these structures in the DNA double helix (1:5000). Due to the fact that DNA bases and base pairs incorporated into DNA are solvated less favorably than in isolated systems, this probability represents the very upper limit. The results clearly show how precisely the canonical building blocks of DNA molecules were chosen and how well their stability is maintained.

Hydration and stability of nucleic acid bases and base pairs

Empirical, quantum chemical calculations and molecular dynamics simulations of the role of a solvent on tautomerism of nucleic acid bases and structure and properties of nucleic acid base pairs are summarized. Attention was paid to microhydrated (by one and two water molecules) complexes, for which structures found by scanning of empirical potential surfaces were recalculated at a correlated ab initio level. Additionally, isolated as well as mono- and dihydrated H-bonded, T-shaped and stacked structures of all possible nucleic acid base pairs were studied at the same theoretical levels. We demonstrate the strong influence of a solvent on the tautomeric equilibrium between the tautomers of bases and on the spatial arrangement of the bases in a base pair. The results provide clear evidence that the prevalence of either the stacked or hydrogen-bonded structures of the base pairs in the solvent is not determined only by its bulk properties, but rather by specific hydrophilic interactions of the base pair with a small number of solvent molecules.

Na+, Mg2+, and Zn2+ Binding to All Tautomers of Adenine, Cytosine, and Thymine and the Eight Most Stable Keto/Enol Tautomers of Guanine: A Correlated ab Initio Quantum Chemical Study

Interactions of adenine, cytosine, guanine, and thymine with Na(+), Mg(2+), and Zn(2+) cations were studied using an approximate resolution of identity correlated second-order MP2 (RI-MP2) method with the TZVPP ([5s3p2d1f/3s2p1d]) basis set. All existing tautomers of adenine, cytosine, and thymine and the eight most stable keto/enol tautomers of guanine were considered. Cations bind mostly in a bidentate manner, and stabilization energies of these complexes are larger than those in the case when cations bind in a unidentate manner. The cation...Y (Y equal to N or O) distances for divalent metals are shorter than those for Na(+) and for Zn(2+) are mostly shorter than the Mg(2+)...Y distance. The intermolecular distances between the cation and the base for complexes containing adenine and cytosine are systematically shorter than those for complexes containing guanine and thymine. Only for cytosine the canonical keto/amino tautomer structure with ions represents the global minimum. For guanine, the metalated canonical form is again the most stable, but its stabilization energy is within less than 5% of the stabilization energies of the two other rare tautomers, which indicates that the canonical form and these two rare tautomers could coexist. The canonical structures of adenine and thymine in the presence of ions are considerably less stable (by more than 10%) than the complexes of the rare tautomers. It can be concluded that the interaction of Na(+), Mg(2+), and Zn(2+) cations with cytosine in the gas phase will not induce the change of the canonical form to the rare tautomeric form. In the case of isolated guanine, the equilibrium of the canonical form with rare tautomers can be found. For isolated adenine and thymine the presence of rare tautomers is highly probable.

Computational Study of the Deamination Reaction of Cytosine with H2O and OH-

The mechanism for the deamination reaction of cytosine with H(2)O and OH(-) to produce uracil was investigated using ab initio calculations. Optimized geometries of reactants, transition states, intermediates, and products were determined at RHF/6-31G(d), MP2/6-31G(d), and B3LYP/6-31G(d) levels and for anions at the B3LYP/6-31+G(d) level. Single-point energies were also determined at B3LYP/6-31+G(d), MP2/GTMP2Large, and G3MP2 levels of theory. Thermodynamic properties (DeltaE, DeltaH, and DeltaG), activation energies, enthalpies, and free energies of activation were calculated for each reaction pathway that was investigated. Intrinsic reaction coordinate analysis was performed to characterize the transition states on the potential energy surface. Two pathways for deamination with H(2)O were found, a five-step mechanism (pathway A) and a two-step mechanism (pathway B). The activation energy for the rate-determining steps, the formation of the tetrahedral intermediate for pathway A and the formation of the uracil tautomer for pathway B, are 221.3 and 260.3 kJ/mol, respectively, at the G3MP2 level of theory. The deamination reaction by either pathway is therefore unlikely because of the high barriers that are involved. Two pathways for deamination with OH(-) were also found, and both of them are five-step mechanisms. Pathways C and D produce an initial tetrahedral intermediate by adding H(2)O to deprotonated cytosine which then undergoes three conformational changes. The final intermediate dissociates to product via a 1-3 proton shift. Deamination with OH(-), through pathway C, resulted in the lowest activation energy, 148.0 kJ/mol, at the G3MP2 level of theory.

Prototropic tautomerism of imidazolone in aqueous solution: a density functional approach using the combined discrete/self-consistent reaction field (SCRF) models

A systematic investigation of the proton transfer in the keto-amino/enol tautomerization of imidazolone was undertaken. Calculations in aqueous solution were performed using both combined discrete/self-consistent reaction field (SCRF) and SCRF methods. Complexes containing one to three water molecules around the hydrophilic site of imidazolone were used for the combined discrete/SCRF calculations. The DFT results predict that the barrier height for non-water-assisted intramolecular proton transfer is very high (214.8 kJmol(-1)). Hydrogen bonding between imidazolone and the water molecule(s) will dramatically lower the barrier by a concerted multiple proton transfer mechanism. The proton transfer process through a eight-member ring formed by imidazolone and two water molecules is found to be more efficient and the calculated barrier height is ca. 61 kJmol(-1).

Hydration Gibbs Energies of Nucleic Acid Bases Determined by Gibbs Energy Perturbation, Continuous and Hybrid Approaches

The hydration Gibbs energies of adenine, cytosine, guanine, thymine, uracil and isoguanine are determined by the molecular dynamics-thermodynamic integration method (MD-TI) and using continuous COSMO and hybrid models. The role of solvents in the COSMO model is described by permittivity and by combining the permittivity and specific hydration of single water molecules placed on the energetically most probable position in the hybrid model. The hybrid model describes hydration similarly to the COSMO model; both the continuous methods are in good agreement with the MD-TI method. Differences are small and the use of both models can be recommended.

Correlated ab initio study of nucleic acid bases and their tautomers in the gas phase, in a microhydrated environment and in aqueous solution. guanine: surprising stabilization of rare tautomers in aqueous solution

Altogether eight keto and enol tautomers of guanine were studied theoretically in the gas phase, in a microhydrated environment (1 and 2 water molecules) and in bulk water. The structures of isolated, as well as mono- and dihydrated tautomers were determined by means of the RI-MP2 method using the extended TZVPP (5s3p2d1f/3s2p1d) basis set. The relative energies of isolated tautomers included the correction to higher correlation energy terms evaluated at the CCSD(T)/aug-cc-pVDZ level. The relative enthalpies at 0 K and relative free energies at 298 K were based on the above-mentioned relative energies and zero-point vibration energies, temperature-dependent enthalpy terms and entropies evaluated at the MP2/6-31G level. The keto form having hydrogen atom at N7 is the global minimum while the canonical form having hydrogen atom at N9 represents the first local minimum at all theoretical levels in vacuo and in the presence of 1 and 2 water molecules. All three unusual rare tautomers having hydrogens at N3 and N7, at N3 and N9, and also at N9 and N7 are systematically considerably less stable and can be hardly detected in the gas phase. The theoretical predictions fully agree with existing theoretical as well as experimental results. The effect of bulk solvent on the relative stability of guanine tautomers was studied by self-consistent reaction field and molecular dynamics free energy calculations using the thermodynamic integration method. Bulk solvent, surprisingly, strongly favored these three rare tautomers over all remaining low-energy tautomers and probably only these forms can exist in water phase. The global minimum (tautomer with hydrogens at N3 and N7) is by 13 kcal/mol more stable than the canonical form (3rd local minimum). Addition of one or two water molecules does not change the relative stability order of isolated guanine tautomers but the respective trend clearly supports the surprising stabilization of three rare forms.