M. Alcolea Palafox

3,5-Difluorobenzonitrile: ab initio calculations, FTIR and Raman spectra

Geometry, vibrational wavenumbers and several thermodynamic parameters were calculated using ab initio quantum chemical methods for the 3,5-difluorobenzonitrile molecule. The results were compared with the experimental values. With the help of three specific scaling procedures, the observed vibrational wavenumbers in FTIR and Raman spectra were analysed 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. Using PEDs the contributions were determined for the different modes to each wavenumber. From the PED, it is apparent that the frequency corresponding to C[triple bond]N stretching contains 87% contribution from the C[triple bond]N stretching force constant and it mixes with the C-CN stretching mode 13 to the extent of 12%. Other general conclusions were also deduced.

Accurate scaling of the vibrational spectra of aniline and several derivatives

The structure of aniline was studied by quantum chemical methods. Complete geometry optimization of the minimum energy structure and of the transition states for internal rotation and inversion of the amino group was carried out using several levels. The performance of the different methods in calculating and describing the vibrational wavenumbers of aniline was determined. The normal modes were characterized by the magnitude and direction of the displacement vectors. Three procedures were used to obtain the scaled wavenumbers, two of them new, using specific scale factors and scaling equations from benzene molecule. The errors obtained were compared with those calculated through other standard procedures. A reassignment of several bands was made. A comparison of the cost/effective method and procedure of scaling was carried out. Specific scale factors and scale equations were determined for the amino group to be used in large aromatic amines.

Vibrational frequencies and structure of 2-thiouracil by Hartree/Fock, post-Hartree/Fock and density functional methods

Vibrational study of the biomolecule 2-thiouracil was carried out. Ab initio and density functional calculations were performed to assign the experimental spectra. A comparison with the uracil molecule was made, and specific scale factors were deduced and employed in the predicted frequencies of 2-thiouracil. Several scaling procedures were used. The geometry structure of the molecule was determined. The effect of sulfur substitution at C2 position in the uracil molecule, on the N1-H and N3-H frequencies and intensities reflects changes in proton donor abilities of these groups. Calculations with the 6-31 G** basis set with HF and DFT methods appear in general to be useful for interpretation of the general features of the IR and Raman spectra of the molecule. Using specific scale factors a very small error was obtained. The use of these specific scale factors resolve and correct some of the controversial assignments in the literature.

Relationships observed in the structure and spectra of uracil and its 5-substituted derivatives.

The effects on the geometry structure, atomic charges and vibrational wavenumbers of the main different substituents in the 5th position of the uracil ring were analysed, and relationships were established. The 5-monosubstituted derivatives studied were 5-XU (X=F, Cl, Br, I, CH(3), NH(2), NO(2)). The geometry and vibrational wavenumbers were determined in these molecules. The FT-IR and Raman spectra were studied with the support of B3LYP calculations using several basis sets. Several general conclusions were underlined.

A comparative study of the vibrational frequencies and intensities in benzocaine by means of semiempirical methods : AM1, MINDO/3 and MNDO

Abstract AM1, MINDO/3 and MNDO calculations were carried out to obtain the frequencies and intensities of the normal modes in benzocaine. The optimized parameters: bond lengths, bond and torsional angles were also computed. The values calculated with the three methods are compared with one another and with experimental data by means of correlation coefficients vcalc./vexp.. Some general conclusions are drawn.

FTIR and FT-Raman spectra of 5-methyluracil (thymine)

FTIR and FT-Raman spectra of 5-methyluracil (thymine) were recorded in the regions 400–4000 cm−1 and 50–4000 cm−1, respectively. The observed wavenumbers were analysed and assigned to different normal modes of vibration of the molecule. Ab initio and density functional calculations were performed to support the assignments of the observed wavenumbers. The geometry structure was determined and a comparison with the uracil molecule was made. Good reproducibility of the experimental wavenumbers was obtained at the B3LYP level and the percentage error was very small, less than 1% in most cases. Copyright

Structure and spectral characteristics of o-aminobenzoic acid by AM1

Abstract The geometry of the o -aminobenzoic acid (anthranilic acid) molecule in two stable conformations was obtained with the AM1 semiempirical method. All geometric parameters, torsional angles included, were fully optimized by means of a quantum mechanic program package. The frequency and intensity of the vibrational bands were calculated and related to the IR and Raman spectra through several scaling coefficients used to improve the theoretical spectra. The total atomic charges, electron density, dipole moment and several thermodynamic and structural parameters were also computed.

Molecular structure differences between the antiviral Nucleoside Analogue 5-iodo-2′-deoxyuridine and the natural nucleoside 2′-deoxythymidine using MP2 and DFT methods: conformational analysis, crystal simulations, DNA pairs and possible behaviour

5-iodo-2′-deoxyuridine Nucleoside Analogue (IUdR) was the first selective antiviral nucleoside against herpes simplex virus type 1 and 2, and it was also a meaningful anticancer drug. Within a full study of this drug and its possible behaviour, previously, a comprehensive theoretical conformational analysis by MP2 and B3LYP was carried out, and all the possible stable structures were determined with full relaxation of all geometrical parameters. The search located 45 stable structures, and in all them, the whole conformational parameters (, , , , , P, max) were analyzed as well as the NBO natural atomic charges. Comparisons of the conformers with those of the natural Nucleoside 2′-deoxythymidine (dT) were carried out, and the main differences between IUdR and dT were analyzed. The accuracy of the methods used was probed with the simulation of the X-ray crystal data by a tetramer form. Watson-Crick (WC) IUdR/dT···2′-deoxyadenosine pairs were analyzed for the first time using quantum chemical calculations, as well as the mispairing IUdR/dT···2′-deoxyguanosine. As result, it is observed that IUdR give rises to a slightly stronger WC pair and weaker mispairing than those with dT, therefore deforming slightly the DNA axis and difficulting the growth of the DNA virus and consequently, killing it.

Vibrational spectra, tautomerism and thermodynamics of anticarcinogenic drug: 5-fluorouracil.

The FT-IR and FT-Raman spectra of 5-Fluorouracil were recorded in the solid phase in the regions 400-4000 cm(-1) and 50-4000 cm(-1), respectively. The vibrational spectra were analysed and the observed fundamentals were assigned to different normal modes of vibration. The experimental wavenumbers were compared with the scaled vibrational values using DFT methods: the Ar matrix data were related to gas phase calculations, while the values of the solid state spectra were compared to those with dimer simulations. The study indicates that some features that are characteristic of vibrational spectra of uracil and its derivatives are retained in the spectrum of 5-fluorouracil and it exists in ketonic form in the solid phase. The tautomerism was also studied and the spectra of the two most stable forms were simulated. The calculated wavenumbers have been employed to yield thermodynamic properties.

Inter-relationships between the geometrical parameters of the amino group in several para-substituted anilines

Abstract Several theoretical methods were used to obtain the relationships between the geometric parameters of the amino group in para -substituted anilines. Several equations were established. These relations were found in the majority of the cases as linear or slightly parabolic with a correlation coefficient close to the value one. The study was extended to the stretching frequencies of the amino group. Some general conclusions were drawn.