N. Iza

The hydration effect on the uracil frequencies: an experimental and quantum chemical study

This work describes the performance of different quantum chemical theoretical methods in calculating the vibrational frequencies of uracil and some derivatives, and the effect of hydration on the uracil frequencies. The Raman spectra of polycristalline uracil with different water contents are discussed. To correct the deficiency of the theoretical quantum chemical methods, several procedures are described in detail. Two of them are new. For these new procedures, scaling factors and scaling equations were determined at different levels. With them, a significant reduction in the error of the predicted frequencies was obtained over the one-factor scaling standard procedure. A comparison of the cost/effective method and procedure of scaling was carried out on uracil molecule. Scale factors transferred from uracil to related molecules provided an a priori prediction of fundamental frequencies and intensities, permitting several corrections to be proposed for earlier assignments.

Simulation of the First Hydration Shell of Nucleosides D4T and Thymidine: Structures Obtained Using MP2 and DFT Methods

A comparative theoretical analysis on the effect of the solvent on the molecular structure and energetics of the most stable conformers of the nucleoside analogue D4T (stavudine) and of the natural nucleoside thymidine (Thy) was carried out. Solvent effects were considered using the Tomasis polarized continuum model (PCM) and including a variable number (1-13) of explicit water molecules surrounding the nucleoside in order to simulate the first hydration shell. More than 200 cluster structures with water were analyzed. B3LYP and MP2 quantum chemical methods were used. The CP-corrected interaction energies for D4T and water molecules were computed. For cases where literature data are available, the computed values were in good agreement with previous experimental and theoretical studies. In the isolated state, conformer I (anti-gg-gg) appears the most stable for D4T molecule and conformer II (anti-gg-gt) for Thy molecule. In D4T with eight water molecules, conformer II changes to conformer I. Thus, conformer I seems preferred when water molecules are situated in the first hydration shell. However, in hydrated thymidine conformer Ia (anti-gg-tg) is the more stable one, and the first hydration shell is more extended than in D4T molecule. The effect of the hydration on the total atomic charges and intermolecular distances were also discussed. Several general conclusions on hydrogen bonds network and involved interaction energies were underlined.

Accuracy and Linearity in UV Spectrophotometry with a Liquid Absorbance Standard

Estimations of the uncertainty of eight significant values (λ = 235, 257, 313, 322, 323, 345, 346, and 350 nm) of apparent molar absorptivities in the UV region have been obtained for acidic potassium dichromate solutions at pH 2.21–2.25, recommended as Standard Reference Materials (SRMs). The uncertainties include all the usual sources of possible systematic error in a commercial microprocessor-controlled spectrophotometer. The comparison of these values with those provided by the National Bureau of Standards (U.S.A.) indicates that a precision of ±0.40% has been obtained throughout the absorptivity range. Likewise, the uncertainty in the linearity of experimental absorbances for the eight wavelengths has been estimated, and a table has been drawn up of the absorptivity values and their uncertainties at 10-nm increments over the wavelength range of 200 to 500 nm.

Identification of ionic and tautomeric species of uracil by second derivative UV absorption spectroscopy.

Abstract The individual UV absorption spectra of ionic and tautomeric species of uracil and eight derivatives have been determined by second derivative spectroscopy. Second derivative bands have been ascribed to different species by taking into account the proportion of each molecular species at each pH value and the tautomer fixed for derivatives. Theoretical results in the literature are in good agreement with the observed λ Min (D 2nd ) positions of both N(1)- and N(3)- uracil monoanion and dianion. Neutral uracil species (diketo form) presents six second derivative bands (two in normal spectra). For the three higher electronic transition energies, the discrepancy between calculated and experimental values does not exceed 0.05 e V. Literature assignment from normal spectra for the N(3)- anion are ππ* transitions but our results show that n π* are possible too.

FT-IR and 13C-NMR Correlations for Some N-Substituted Azoles and Benzazoles

The FT-IR (in carbon tetrachloride) and 13C-NMR (in deuterochloroform) spectra of six p-substituted aniline derivatives, as reference compounds, and nine 1-p-aminophenyl-azoles and benzazoles were recorded. The measured spectral parameters from FT-IR were symmetric, vs(NH2), and antisymmetric, vas(NH2), stretching fundamentals and their band intensity ratio, A(vas)/A(vs), while the corresponding 13C-NMR parameters were C-1 to C-4 chemical shifts of 1-p-aminophenyl carbons. Different IR and 13C-NMR spectral parameters and Hammett constants σp (or σp-) were correlated, and statistic analysis of the results permitted an estimation of σp values of the nine (azol-1-yl) substituents. An empirical equation to calculate the Hammett constants of new azoles and benzazoles is proposed.

A study of anthracene-metallic cation interactions by UV-Vis spectroscopy.

Abstract Normal, first and second derivative UV-Visible absorption spectra for anthracene, some metallic chlorides (Li, K, Rb, Mg, Ca, Fe, Ni, Co, Mn, Cu, Sn, Cd and Hg) and their mixtures in ethanolic solutions, have been recorded at low concentrations. Comparison of intensity changes of β and p anthracene bands for mixtures, with the spectra of original solutions, suggested anthracene - cation interactions for all studied metallic chlorides. The results obtained for these solutions via second derivative spectra are in agreement with the data from normal UV-Vis spectra. Hypo-and hyper-chromic effects in anthracene absorption bands show a strong dependence on the nature and concentration of the metallic cations, due to modification of the anthracene-anthracene complex arrangement. Cu 2+ ions show the greatest hyperchromic effect in second derivative spectra of anthracene p bands . The band asymmetry parameter, ϱ, varies with cation nature, whereas the spectral width, Δλ, and the minimum position, λ Min , remain almost invariable. All these spectral changes are related to cation concentration and ionic radii, and are interpreted as variations in molecular arrangement.

Amide resonance and FT-IR spectra of some β-lactam derivatives: application of resolution enhancement procedures in Fourier space

Abstract Fourier Transform infrared (FT-IR) spectra of five 4-acyl-β-lactam derivatives in three organic solvents (carbon tetrachloride, benzene and chloroform) have been registered. Nominal spectral resolution was 1 cm −1 and a Happ-Genzel function was used to apodize the interferograms. Fourier self-deconvolutions were done using standard software based on the algorithm of Kauppinen (1981). The digitalized FT-IR spectra were converted into second and fourth derivatives in Fourier domain using a standard software package supplied for the purpose and based on the technique developed by the N.R.C.C. group. The inherent enhancement resolution of Fourier self-deconvolution and derivatives in Fourier Space have permitted resolution of the characteristic “amide I” bands of the β-lactam ring. The ν(CO) band splitting in the “amide I” region is due to solvent and ring substitution influences on amide resonance and not to H-bonding association. Simultaneous application of both apparent resolution enhancement procedures has allowed us to identify true bands and mathematical artifacts.

Intermolecular associations of some biologically interesting pyrimidines in aqueous solution: caffeine-uracil

Ultraviolet absorption spectra of aqueous solutions of caffeine-uracil mixtures at CT=0.004 M have been obtained. An apparent hyperchromic effect has been observed for both bases at two bands. The hyperchromic effect attributed solely to caffeine has been evaluated at 290 nm, where uracil absorption is minimum. From this value, uracil contribution has been determinated. It results about 10% relative hyperchromism for caffeine and about −7, 5% relative hypochromism for uracil. The data obtained indicate the presence of complexes having caffeine-uracil ratio of 1:1 and higher complexes. The association constant K (CAF-U) is found to be 76± 12 M−1 from an equation where K (CAF-CAF) = 102± 6 M−1 and K (U-U) = =68±5 M−1, have been enclosed.

Integrated intensities and band shapes in infrared and uv-visible absorption bands

Abstract The infrared integrated intensity and the shape of absorption bands corresponding to three compounds in solution phase have been carefully determined using a original procedure. The isolated broad UV-Visible absorption band of I 2 in a Cl 4 C solution was examined by means of the same method. In all these bands, the experimental band shape is adjusted with a Cauchy-Gauss product function. A parameter P, which defines the percentages of Lorentzian profile (Cauchy character). makes it possible to determine the apparent integrated intensity. Furthemore, a procedure of wing corrections is applied. The accuracy of the results has been evaluated by comparison with reference values obtained for a total integration of six half-band widths. The goodness of fit is discussed, and some practical applications of the method are suggested.

Vibrational study of 3-methyluracil

The molecule of 3-methyluracil (3-MeU) (Fig. 1) is one simple and well-studied uracil derivative. A good understanding of the vibrational spectra of nucleic bases and their derivatives is essential to analyze the spectra of more complex and related compounds, like nucleosides, nucleotides and their polymers [1]. The FT-IR spectra of 3-MeU have been studied by matrix isolation technique [2], and the equilibrium geometries have been determinated by theoretical methods in a recent study [3].