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Allopurinol (AL) was investigated in the isolated state, solid state, and in the hydrated form through an exhaustive quantum-chemical analysis. Full geometry optimization and energy calculations of the 11 most stable tautomers in the isolated state were performed. The most stable one corresponds to AL-15 at all the levels of computation. Several weak bands of the experimental spectrum in Ar-matrix were tentatively assigned to tautomer AL-25. The crystal unit cell of the solid state was simulated by a heptamer form. Comparisons with the experimental values confirm that only tautomer AL-15 appears in the solid state. The hydration of the two most stable tautomers: AL-15 and AL-25 was carried out. Solvent effects were considered using the Tomasi's polarized continuum model (PCM) and by the explicit model (EM) including a variable number of water molecules surrounding the base to simulate the first and second hydration shells. In this second hydration shell the calculated difference in the free energy between both tautomers is so small, that both tautomers can coexist in bull water. Some of the most important conclusions on the effects of the hydration on the molecular structure were presented. The deformation and interaction energies were corrected for basis set superposition error (BSSE) using the counterpoise (CP) procedure. [ABSTRACT FROM AUTHOR]

The experimental FT-IR and FT-Raman spectra of 2,5-dichlorobenzonitrile molecule were recorded at room temperature, and the results compared with quantum chemical theoretical values using MP2 and DFT methods. Molecular geometry, vibrational wavenumbers and thermodynamic parameters were calculated. With the help of specific scaling procedures for the computed wavenumbers, the experimentally observed FTIR and FT-Raman bands were analyzed and assigned to different normal modes of the molecule. Most of the modes have wavenumbers in the expected range and the error obtained was in general very low. Several general conclusions were deduced. The NBO analysis has been done and Molecular Electrostatic Potential (MEP) has been plotted. [ABSTRACT FROM AUTHOR]

Highlights: [•] The assignment of the wavenumbers using a scaling equation procedure improves the accuracy. [•] The DFT calculations lead to agree with the experimental vibrational spectra. [•] HOMO–LUMO energy gap is slightly lower than that of Benzonitrile molecule. [ABSTRACT FROM AUTHOR]

Highlights: [•] The spectra of 5-BrC in the solid and in the isolated state were simulated. [•] In the IR Ar matrix spectrum were identified the bands related to the two tautomers. [•] The scaled wavenumbers of our tetramer model are in accordance to the experimental. [•] The effect of the Br atom is more notorious in 5-BrC than in 5-bromouracil. [•] All the cytosine tautomers have relative energies lower than those in uracil. [Copyright &y& Elsevier]

Highlights: [•] An accurate assignment of vibrational modes was performed in 5-ClU. [•] The agreement between the scaled and exp. wavenumbers seems reasonable. [•] Our tetramer simulation of the solid state is adequate. [•] The effect of the substituents on the different normal modes is described. [Copyright &y& Elsevier]

Abstract: The Raman and IR spectra of the biomolecule 5-aminoorotic acid in the solid state were simulated by a dimer and tetramer forms, with the special interest in the interactions that involve the NH and NH2 groups. The unit cell expected in the crystal was simulated as a tetramer form by density functional calculations. They were performed to clarify wavenumber assignments of the experimentally observed bands in the spectra. Correlations with the molecule of uracil were made, and accurate scaling procedures deduced by us were employed in the calculated wavenumbers of 5-aminoorotic acid. Good reproduction of the experimental wavenumbers is obtained and the % error is very small in the majority of cases. This fact confirms our simplified solid state model. The scaling leads to a reassignment of the IR and Raman experimental bands. The NBO atomic charges and several thermodynamic parameters were also calculated. [Copyright &y& Elsevier]

Abstract: A comprehensive theoretical conformational analysis of the anti-HIV AZT 5′-aminocarbonylphosphonate prodrug was carried out, due to this prodrug has noticeable advantage over approved drugs AZT and Nikavir. The whole conformational parameters (χ, γ, β, α, δ, ε, τ, P, ν max) were analysed as well as the NBO Natural atomic charges. The calculations were carried out by means of B3LYP/6-31G∗∗ and B3LYP/6-311++G(3df,pd) DFT levels of theory with full relaxation of all geometrical parameters. The search located at least 86 stable structures, 6 of which are within a 1kcal/mol electronic energy range of the global minimum and 11 conformers are within a 1kcal/mol Gibbs energy range. The global minimum with the 6-311++G(3df,pd) basis set corresponds to the calculated values of the exocyclic torsional angles χ =−121.6°, β =153.0°, γ =−152.0° and α =−74.1°. The results obtained are in accordance to those found in related anti-HIV nucleoside Analogs. Comparisons of the conformers with those determined in the common anti-HIV drug AZT were carried out. Several correlations and general conclusions were emphasized. [Copyright &y& Elsevier]

Four new potential agents muscarinic (allosteric modulators) were synthesized and studied by using the B3LYP density functional method. The optimum conformation and geometry structure of these compounds were determined and analyzed. Solvent effects were considered including a variable number (1-15) of explicit water molecules surrounding the compound in order to simulate the first hydration shell, as well as using the Tomasi's polarized continuum model (PCM). A similar simultaneous analysis of the potents W84 and DUO-3O allosteric modulator of muscarinic receptors was also carried out. The effect of the hydration on the total atomic charges and several intermolecular distances of interest were also discussed. The biological activity against acetylcholine of our four synthesized bispyridinium salts was determined. Relationships/tendencies structure-activity were established. Several general conclusions were underlined. [ABSTRACT FROM AUTHOR]

Abstract: The unit cell found in the crystal was simulated as a tetramer form by density functional calculations (DFT). They were performed to clarify wavenumber assignments of the experimental observed bands in the biomolecule 2,4-dihydroxy-5-iodopyrimidine (5-iodouracil). Comparisons with the gas phase data were also carried out. Correlations with the molecule of uracil were made, and specific scale factors were deduced and employed in the predicted wavenumbers of 5-iodouracil. The scaled wavenumbers were used in the assignment of the IR and Raman experimental spectra. Good reproduction of the experimental wavenumbers is obtained and the % error is very small in the majority of cases. Comparisons were also performed with other 5-substituted uracil derivatives. The NBO atomic charges and several thermodynamic parameters were also calculated. Several linear relationships were established. [Copyright &y& Elsevier]

Abstract: Density functional calculations (DFT) by various methods were performed to clarify wavenumber assignments of the experimental observed bands. A comparison with the molecule of uracil was made, and specific scale factors were deduced and employed in the predicted wavenumbers of 5-IU. Comparisons were also performed with other halo-uracil derivatives. The scaled wavenumbers were compared with IR and Raman experimental data. Good reproduction of the experimental wavenumbers is obtained and the % error is very small in the majority of cases. The equilibrium geometry of 5-IU was also calculated at several levels, as well as the atomic charges and several thermodynamic parameters. All the tautomer forms of 5-iodouracil were determined and optimized. Several general conclusions were underlined. [Copyright &y& Elsevier]

Abstract: FT-IR and FT-Raman spectra of the biomolecule 5-aminouracil were recorded in the regions 400–4000cm−1 and 10–3500cm−1, respectively. The observed vibrational wavenumbers were analyzed and assigned to different normal modes of vibration of the molecule. Density functional calculations were performed to support wavenumber assignments of the observed bands. A comparison with the molecule of uracil was made, and specific scale factors were employed in the predicted wavenumbers of 5-aminouracil. With the purpose of study the important molecule 5-aminouracil, its equilibrium geometry and harmonic wavenumbers were calculated for the first time by the B3LYP DFT method. The vibrational wavenumbers were compared with IR and Raman experimental data. Also good reproduction of the experimental wavenumbers is obtained and the % error is very small. All the tautomeric forms of 5-aminouracil were determined and optimized. The dimer forms were also simulated. The energy, atomic charges and dipole moments were discussed and several general conclusions were underlined. [Copyright &y& Elsevier]