Solid state simulation of tetramer form of 5-aminoorotic acid: The vibrational spectra and molecular structure study by using MP2 and DFT calculations

doi:10.1016/j.saa.2012.06.048

Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy

Volume 97, November 2012, Pages 948-962

https://doi.org/10.1016/j.saa.2012.06.048 Get rights and content

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.

Graphical abstract

Highlights

► The Raman and IR spectra of 5-aminoorotic acid in the solid state were simulated. ► The simulation was carried out by a dimer and tetramer forms. ► Two accurate scaling procedures was used to improve the calculated wavenumbers. ► The solid state scaled values are in good accordance to the experimental. ► The analysis of the spectra lead to a reassignment of several fundamentals.

Introduction

5-Aminouracil (5-AU) is an important pyrimidine nucleobase used in the synthesis of other pyrimidines [1], [2], and in other chemical applications [3], [4]. It appears also in the biochemistry of DNA [5], [6].

The orotic acid (uracil-6-carboxylic acid) or vitamin B13, is an important biological molecule, which has been extensively used in crystal engineering [7], [8], [9] and play an important role in biological systems as precursors of pyrimidine nucleosides.

5-Aminoorotic acid (HAOA), Fig. 1, also plays an important role in chemistry and biochemistry. As example, HAOA (5-amino-2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid) inhibits the metabolism of the cardioprotective drug dexrazoxane [10]. However from the spectroscopy point of view it has been studied very less. The complexes of HAOA with zinc(II) [11], La(III) [12], [13], [14], Ce(III) and Nd(III) [15], [16], and with Pt(II) [17] metals have been studied due to that they show cytotoxic activity. Studies appear also for their derivatives, in special with a bromacetamido substitution, due to their antibacterial properties [18], [19]. However, in the spectra in the solid state of HAOA appear doubts, and the assignment of several bands is not enough accurate. Therefore, in the present study we try to clarify the matter with the use of accurate scaling procedures and with the simulation of the crystal by a tetramer form. Thus, a reassignment of the vibrational spectra of HAOA was carried out, improving the results obtained. The assignment was performed following the notation of the normal modes of the uracil molecule [20], [21].

Section snippets

Computational methods

The calculations were carried out using ab initio MP2 and Density Functional methods (DFT) [22], including the Becke’s three-parameter exchange functional (B3) [23] in combination with the correlational functional of Lee, Yang and Parr (LYP) [24]. B3LYP represents the most cost-effective method [25] and therefore, it was the only one used in the present manuscript. B3LYP was chosen because different studies have shown that the data obtained with it were in better agreement than those obtained

Experimental

The sample of HAOA (solid) with spectroscopic purity was obtained from M/S Sigma Chemical Co., St Louis, MO, USA) and used as such without any further purification.

The FT-IR spectrum of the compound in the solid form was recorded in the range 400–4000 cm⁻¹ with a Bruker IFS66 Fourier transform spectrometer equipped with a Global source, Ge/KBr beam splitter and a TGS detector. For the spectrum, 50 interferograms were collected at 1.0 cm⁻¹ resolution.

Geometry optimization in the isolated state

Two possible locations for the carboxylic proton appear in HAOA, according to the value of dihedral angle N1–C6–C12–O16 is 0.0° or 180.0°. Thus, two stable conformers designated for convenience as 1 and 2, were found, Fig. 1. The most stable one, conformer 1 is stabilized by a stronger intramolecular H-bond than conformer 2. The difference of energy between both forms is very small, 5.4 kJ/mol, in agreement with the value of 6.0 kJ/mol reported at the B3LYP/6-31G^∗ level in the orotic acid [8].

Other molecular properties

Calculated wavenumbers were also used to yield thermodynamic properties, which are collected in Table 1S (of Electronic Supplementary Material). The theoretical data are employed to correct experimental thermochemical information at 0 K, and as well as for the effect of the zero-point vibrational energy (ZPVE). For the ZPVE, scaling factors can be used [42] to improve their overestimation.

To observe the convergence of the energy and thus to analyze the quality of the theoretical results, several

Summary and conclusion

The most important findings of this study are the following:

(1)
The equilibrium geometries obtained using the MP2 and B3LYP methods with various basis sets, were determined and the harmonic wavenumbers, compared and analyzed. The results obtained appear as the most accurate today. The effect of the –NH₂ and –COOH substituents on the ring structure was determined.
(2)
To improve the calculated wavenumbers was used two accurate scaling procedures developed by us: the linear scaling equation procedure, and

Acknowledgements

S.O. and M.A.P. wish to thank to the MCI through CTQ2010-18564 (subprogram BQU). V.K.R. is thankful to Prof. Rakesh Kumar, HoD Physics and to Sri V.C. Goel, Vice Chancellor, CCS University, Meerut for motivation and encouragement during the revised draft of the manuscript.

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¹: Present address: Aryan Institute of Technology, 13th km Stone, NH-24, Jindal Nagar, Ghaziabad 201 002, India.

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Solid state simulation of tetramer form of 5-aminoorotic acid: The vibrational spectra and molecular structure study by using MP2 and DFT calculations

Abstract

Graphical abstract

Highlights

Introduction

Section snippets

Computational methods

Experimental

Geometry optimization in the isolated state

Other molecular properties

Summary and conclusion

Acknowledgements

J. Inorg. Biochem.

Corros. Sci.

Biol. Cell

Chem. Phys.

Spectrochim. Acta

J. Mol. Struct. (Theochem.)

Chem. Phys.

Chem. Phys.

J. Comput.-Aided Mol. Des.

J. Phys. Chem. B

Asian Chem. Lett.

Int. J. Quant. Chem.

J. Chem. Soc. Dalton Trans.

J. Chem. Soc., Dalton Trans.

Nucleic Acids Res.

Inorg. Chem.

J. Chem. Soc. Dalton Trans.

Eur. J. Inorg. Chem.

Drug Metab.: Dispos.

J. Chem. Soc. Dalton Trans.

J. Raman Spectrosc.

Archiv Pharmazie

Med. Chem.

Appl. Organomet. Chem.