Structural study and characterization of the dipeptide 2-[[5-amino-5-oxo-2-(phenylmethoxycarbonylamino) pentanoyl] amino] acetic acid by vibrational spectroscopy and DFT calculations

• Published in: Journal of molecular structure Vol. 1031; no. 16; pp. 110 - 118
• Main Authors: Leyton, Patricio, Paipa, Carolina, Berrios, Andrés, Zárate, Antonio, Castillo, María Victoria, Brandán, Silvia Antonia
• Format: Journal Article
• Language: English
• Published: Elsevier B.V 16-01-2013
• Subjects: 2-[[5-amino-5-oxo-2-(phenylmethoxycarbonylamino) pentanoyl] amino] acetic acid; Acetic acid; Band spectra; Bands; DFT calculations; Electronics; Force constants; Force field; Infrared; Mathematical analysis; Molecular structure; spectroscopy; topology; vibration; vibrational properties; Vibrational spectra; Wavenumber; Force field; Force constants; 2-[[5-amino-5-oxo-2-(phenylmethoxycarbonylamino) pentanoyl] amino] acetic acid; Molecular structure; Vibrational spectra; DFT calculations
• ISSN: 0022-2860; 1872-8014
• DOI: 10.1016/j.molstruc.2012.07.042

► The dipeptide was characterized by IR and Raman spectroscopies. ► The neutral and zwitterionic forms of the dipeptide were studied by B3LYP calculations. ► A complete assignment of the spectral features is proposed. ► Both structures of the dipeptide were analyzed by NBO and AIM analysis.
We have studied 2-[[5-amino-5-oxo-2-(phenylmethoxycarbonylamino) pentanoyl] amino] acetic acid and characterized it by infrared and Raman spectroscopies in the solid phase. The Density Functional Theory (DFT) method and Pople’s basis set have been used to study its structure and vibrational properties. These calculations have given us a precise understanding of the normal modes of vibration, taking into account the neutral and zwitterionic forms of the compound. The harmonic vibrational wavenumbers for the optimized geometries of both structures were calculated at the B3LYP/6-31G*and B3LYP/6-311G** levels for an isolated molecule. For a complete assignment of the vibrational spectra, DFT calculations were combined with Pulay´s Scaled Quantum Mechanics Force Field (SQMFF) methodology to fit the theoretical and experimental wavenumber values. In this context, an assignment of the observed spectral features is proposed. Four intense bands in the infrared spectrum at 3332, 1734, 1654 and 1534cm−1 and three bands in the Raman spectrum at 3332, 2928 and 985cm−1 are reported to characterize both forms of the compound. The theoretical vibrational calculations allowed us to obtain a set of scaled force constants. A Natural Bond Orbital (NBO) study revealed the characteristics of the electronic delocalization of both structures, while the corresponding topological properties of electronic charge density were analyzed by employing Bader’s Atoms in the Molecules theory (AIM).