An ab Initio Post-Hartree−Fock Comparative Study of 5-Azacytosine and Cytosine and Their Dimers with Guanine

A DFT STUDY OF MOLYBDATE-PHOSPHONIC ACID COMPLEX

The relative stability of Molybdate-Phosphonic Acid (MPA) Complex in gas phase has been carried out using Density Functional Theory (DFT) methods. The methods used for calculations are B3LYP, BP86 and B3PW91, with three series of basis sets: D95**, 6-31+G (d,p) and 6-31++G (d,p) for hydrogen and oxygen atoms; LANL2DZ for Mo and Phosphorus. Predicted geometry and relative stability are discussed. Equilibrium geometry in the ground electronic state energy has been calculated for 1:1 complex. The best result for energetic and geometrical ground state was obtained with Becke3LYP calculations. The Basis Set Superposition Error (BSSE) begins to converge for all methods/basis sets. For this complex, most levels of theory seem to give reasonable estimates of the known binding energies, but here, too, the BSSE overwhelms the reliability of the binding energies for these basis sets.

FTIR Spectra of some Pyrimidine Derivatives: AM1, PM3 and Ab Initio Calculations

Abstract. FTIR spectra of some pyrimidine derivatives have been measured experimentally and the observed FTIR vibrational frequencies have been assigned and reported. The different vibrational frequencies have been calculated by the AM1, PM3, and ab initio methods and compared with the experimentally observed frequencies .

Electronic and molecular structure of M-DNA fragments

To study M-DNA molecular structure (such DNA with transition metal ions placed between the nucleic bases is able to conduct the electric current) and its conductivity mechanisms, we carried out ab initio quantum-mechanical calculations of electronic and spatial structures, thermodynamic characteristics of adenine-thymine (АТ) and guanine-cytosine (GC) base pair complexes with Zn(2+) and Ni(2+). To take into account the influence of the alkaline environment, calculations for these complexes were also carried out with hydroxyl and two water molecules. Computations were performed at MP2 level of theory using 6-31+G* basis set. Analogous calculations were carried out for (AC)(TG) stacking dimer of nucleic acid base pairs with two Zn(2+). The calculation of the interaction energy in complexes has shown the preference of locating the metal ion (instead of the imino proton) between bases in M-DNA. The electronic transition energy calculation has revealed the reduction of the first singlet transition energy in АТ and GC complexes with Ni(2+) from 4.5 eV to 0.4 - 0.6 eV. Ni(2+) orbitals take part in the formation of HOMO and LUMO on the complexes investigated. It was shown that charges of metal ions incorporated into complexes with nucleic bases and in dimer decrease significantly.

Comprehensive Conformational Analysis of the Nucleoside Analogue 2‘-β-Deoxy-6-azacytidine by DFT and MP2 Calculations

A comprehensive conformational analysis of isolated 2'-beta-deoxy-6-azacytidine (d6AC), an analogue of therapeutically active 6-azacytidine (6AC), has been performed by means of ab initio calculations at the MP2/6-311++G(2df,pd)//DFT B3LYP/6-31G(d,p) level of theory. Among the 81 conformers located within a 7.83 kcal/mol Gibbs energy range at T = 298.15 K, 38 contain syn-oriented bases with respect to 2'-deoxyribose; the other conformers include anti-oriented bases. Energetic analysis of these conformers shows that conformational equilibrium of isolated d6AC at T = 298.15 K is shifted to syn conformation with a syn/anti ratio estimated as 61.4%:38.6%. As far as the sugar conformation is concerned, 40 conformers contain north (N) (with 0.3 degrees < or = P < or = 40.1 degrees), and the rest possess south (S) (with 157.1 degrees < or = P < or = 207.0 degrees) puckers, where P is the pseudorotational angle of the furanose ring. The S/N occupancy ratio is estimated as 80.2%:19.8% (T = 298.15 K). The two most stable conformers are energetically quasidegenerate and correspond to both C2'-endo/syn conformers differing only by orientation of the O3'H hydroxyl group. They are both stabilized by means of similar intramolecular H-bonds, i.e., O5'H...O2, C2'H2...O2, and C2'H2...O5'. As examined by AIM criteria, from 1 to 3 H-bonds per conformer were identified among 13 possible interactions: O5'H...O2, O5'H...N6, O3'H...O5', O5'H...O3', C1'H...O2, C2'H2...O2, C2'H2...O5', C3'H...O2, C3'H...N6, C5'H1...O2, C5'H2...O2, C5'H1...N6, and C5'H2...N6. The biological effect of d6AC is conceived as an inhibition of replicative DNA polymerase caused by an unusual orientation of the sugar residue against the base in the only A form DNA-like conformer.

Reaction of Hydroxyl Radicals with Azacytosines: A Pulse Radiolysis and Theoretical Study

Pulse radiolysis and density functional theory (DFT) calculations at B3LYP/6-31+G(d,p) level have been carried out to probe the reaction of the water-derived hydroxyl radicals (*OH) with 5-azacytosine (5Ac) and 5-azacytidine (5Acyd) at near neutral and basic pH. A low percentage of nitrogen-centered oxidizing radicals, and a high percentage of non-oxidizing carbon-centered radicals were identified based on the reaction of transient intermediates with 2,2'-azinobis(3-ethylbenzothiazoline-6-sulfonate), ABTS2-. Theoretical calculations suggests that the N3 atom in 5Ac is the most reactive center as it is the main contributor of HOMO, whereas C5 atom is the prime donor for the HOMO of cytosine (Cyt) where the major addition site is C5. The order of stability of the adduct species were found to be C6-OH_5Ac*>C4-OH_5Ac*>N3-OH_5Ac*>N5-OH_5Ac* both in the gaseous and solution phase (using the PCM model) respectively due to the additions of *OH at C6, C4, N3, and N5 atoms. These additions occur in direct manner, without the intervention of any precursor complex formation. The possibility of a 1,2-hydrogen shift from the C6 to N5 in the nitrogen-centered C6-OH_5Ac* radical is considered in order to account for the experimental observation of the high yield of non-oxidizing radicals, and found that such a conversion requires activation energy of about 32 kcal/mol, and hence this possibility is ruled out. The hydrogen abstraction reactions were assumed to occur from precursor complexes (hydrogen bonded complexes represented as S1, S2, S3, and S4) resulted from the electrostatic interactions of the lone pairs on the N3, N5, and O8 atoms with the incoming *OH radical. It was found that the conversion of these precursor complexes to their respective transition states has ample barrier heights, and it persists even when the effect of solvent is considered. It was also found that the formation of precursor complexes itself is highly endergonic in solution phase. Hence, the abstraction reactions will not occur in the present case. Finally, the time dependent density functional theory (TDDFT) calculations predicted an absorption maximum of 292 nm for the N3-OH_5Ac* adduct, which is close to the experimentally observed spectral maxima at 290 nm. Hence, it is assumed that the addition to the most reactive center N3, which results the N3-OH_5Ac* radical, occurs via a kinetically driven process.

The small planarization barriers for the amino group in the nucleic acid bases

The amino group in the nucleic acid bases frequently interacts with other bases or with other molecular systems. Thus any nonplanarity of the amino group may affect the molecular recognition of nucleic acids. Ab initio Hartree-Fock (HF) and second-order Moller-Plesset perturbation (MP2) levels of theory have been used to obtain the equilibrium geometries of the C(l) and C(s) structures for five common nucleic acid bases. The energy barriers between the C(l) and C(s) structures have also been predicted. A series of correlation consistent basis sets up to cc-pCVQZ and aug-cc-pVQZ has been used to systematically study the dependence of the amino group nonplanarity. The equilibrium geometries of the nucleic acid bases with an amino group, including adenine, guanine, and cytosine, are examined carefully. At the MP2 level of theory, larger basis sets decrease the extent of nonplanarity of the amino group, but the decrease slows down when the QZ basis sets are used, demonstrating the intrinsic property of nonplanarity for guanine. For adenine and cytosine the situation is less clear; as the HF limit is approached, these two structures become planar. Addition of core correlation effects or diffuse functions further decreases the degree of nucleic acid base nonplanarity, in comparison to the original cc-pVXZ (X=D, T, and Q) basis sets. The aug-cc-pVXZ basis shows smaller degrees of nonplanarity than the cc-pCVXZ sets. The aug-cc-pVXZ basis is less size dependent than the cc-pVXZ and cc-pCVXZ sets in the prediction of the amino-group-related bond angles and dihedral angles and energy barriers for adenine, guanine, and cytosine. The cc-pCVQZ and aug-cc-pVQZ MP2 results may be regarded as benchmark predictions for the five common bases. The predicted classical barriers to planarization are 0.02 (adenine), 0.74 (guanine), and 0.03(cytosine) kcal mol(-1).

A TDDFT Study of the Optical Response of DNA Bases, Base Pairs, and Their Tautomers in the Gas Phase

We present calculations of the optical response of the DNA bases and base pairs both in their normal and tautomeric forms in the gas phase, using time-dependent density functional theory (TDDFT). These calculations are performed in real time within the adiabatic approximation with a basis of local orbitals. Our results for the individual bases are in good agreement with experiment and computationally more demanding calculations of chemical accuracy. The optical response of base pairs indicates that the differences between normal and tautomeric forms in certain cases are significant enough to provide a means of identification.

Accuracy and efficiency of atomic basis set methods versus plane wave calculations with ultrasoft pseudopotentials for DNA base molecules

Recent results from Preuss et al. (J Comput Chem 2004, 25, 112) on DNA base molecules, obtained by plane wave density functional calculations using ultrasoft pseudopotentials, are compared with calculations using Gaussian basis sets. Bond lengths and angles agree closely, but dihedral angles and vibrational frequencies show significant differences. The Gaussian basis calculations are at least an order of magnitude more efficient than the plane wave/ultrasoft pseudopotential calculations at a similar level of accuracy; the advantage is even larger if the Fourier Transform Coulomb method is used. To obtain definite benchmark values, the geometries of the four DNA bases were optimized at the MP2 level with large basis sets, up to cc-pVQZ and aug-cc-pVTZ.

Ground- and excited-state properties of DNA base molecules from plane-wave calculations using ultrasoft pseudopotentials

We present equilibrium geometries, vibrational modes, dipole moments, ionization energies, electron affinities, and optical absorption spectra of the DNA base molecules adenine, thymine, guanine, and cytosine calculated from first principles. The comparison of our results with experimental data and results obtained by using quantum chemistry methods show that in specific cases gradient-corrected density-functional theory (DFT-GGA) calculations using ultrasoft pseudopotentials and a plane-wave basis may be a numerically efficient and accurate alternative to methods employing localized orbitals for the expansion of the electron wave functions.

Systematic quantum chemical study of DNA-base tautomers

The relative energies of the energetically low-lying tautomers of pyridone, cytosine, uracil, thymine, guanine, and iso-cytosine are studied by a variety of different quantum chemical methods. In particular, we employ density functional theory (DFT) using the six functionals HCTH407, PBE, BP86, B-LYP, B3-LYP, and BH-LYP, and the ab initio methods Hartree-Fock (HF), standard second-order Møller-Plesset perturbation theory (MP2), an improved version of it (SCS-MP2), and quadratic configuration interaction including single and double excitations (QCISD) and perturbative triple corrections [QCISD(T)]. A detailed basis set study is performed for the formamide/formamidic acid tautomeric pair. In general, large AO basis sets of at least valence triple-zeta quality including f-functions (TZV) are employed, which are found to be necessary for an accurate energetic description of the various structures. The performance of the more approximate methods is evaluated with QCISD(T)/TZV(2df,2dp) data taken as reference. In general it is found that DFT is not an appropriate method for the problem. For the tautomers of pyridone and cytosine, most density functionals, including the popular B3-LYP hybrid, predict a wrong energetic order, and only for guanine, the correct sequence of tautomers is obtained with all functionals. Out of the density functionals tested, BH-LYP, which includes a rather large fraction of HF exchange, performs best. A consistent description of the nonaromatic versus aromatic tautomers seems to be a general problem especially for pure, nonhybrid functionals. Tentatively, this could be assigned to the exchange potentials used while the functional itself, including the correlation part, seems to be appropriate. Out of the ab initio methods tested, the new SCS-MP2 approach seems to perform best because it effectively reduces some outliers obtained with standard MP2. It outperforms the much more costly QCISD method and seems to be a very good compromise between computational effort and accuracy.

Network visualization system for computational chemistry

Network Visualization System for Computational Chemistry (NVSCC) is a molecular graphics program designed for the visualization of molecular assemblies. NVSCC accepts the output files from the most popular ab initio quantum chemical programs, GAUSSIAN and GAMESS, and provides visualization of molecular structures based on atomic coordinates. The main differences between NVSCC and other programs are: Network support due to built-in FTP and telnet clients, which allows for the processing of output from and the sending of input to different computer systems and operating systems. The possibility of working with output files in real time mode. The possibility of animation from an output file during all steps of optimization. The quick processing of huge volumes of data. The development of custom interfaces.