Infrared and NMR spectra, tautomerism, vibrational assignment, normal coordinate analysis, and quantum mechanical calculations of 4-amino-5- pyrimidinecarbonitrile

Mahmoud S. Afifi, Rabei S. Farag, Ibrahim A. Shaaban, Lee D. Wilson, Wajdi M. Zoghaib, Tarek A. Mohamed

Research output: Contribution to journalArticle

7 Citations (Scopus)

Abstract

The infrared (4000-200 cm-1) spectrum for 4-amino-5- pyrimidinecarbonitrile (APC, C5H4N4) was acquired in the solid phase. In addition, the 1H and 13C NMR spectra of APC were obtained in DMSO-d6 along with its mass spectrum. Initially, six isomers were hypothesized and then investigated by means of DFT/B3LYP and MP2(full) quantum mechanical calculations using a 6-31G(d) basis set. Moreover, the 1H and 13C NMR chemical shifts were predicted using a GIAO approximation at the 6-311+G(d,p) basis set and the B3LYP method with (and without) solvent effects using PCM method. The correlation coefficients showed good agreement between the experimental/ theoretical chemical shift values of amino tautomers (1 and 2) rather than the eliminated imino tautomers (3-6), in agreement with the current quantum mechanical calculations. Structures 3-6 are less stable than the amino tautomers (1 and 2) by about 5206-8673 cm-1 (62.3-103.7 kJ/mol). The MP2(full)/6-31G(d) computational results favor the amino structure 1 with a pyramidal NH2 moiety and calculated real vibrational frequencies, however; structure 2 is considered a transition state owing to the calculated imaginary frequency. It is worth mentioning that, the calculated structural parameters suggest a strong conjugation between the amino nitrogen and pyrimidine ring. Aided by frequency calculations, normal coordinate analysis, force constants and potential energy distributions (PEDs), a complete vibrational assignment for the observed bands is proposed herein. Finally, NH2 internal rotation barriers for the stable non-planar isomer (1) were carried out using MP2(full)/6-31G(d) optimized structural parameters. Our results are discussed herein and compared to structural parameters for similar molecules whenever appropriate.

Original languageEnglish
Pages (from-to)277-289
Number of pages13
JournalSpectrochimica Acta - Part A: Molecular and Biomolecular Spectroscopy
Volume111
DOIs
Publication statusPublished - Jul 2013

Fingerprint

tautomers
Vibrational spectra
vibrational spectra
infrared spectra
Nuclear magnetic resonance
Chemical shift
Infrared radiation
Isomers
nuclear magnetic resonance
chemical equilibrium
isomers
Pulse code modulation
pyrimidines
Dimethyl Sulfoxide
Potential energy
conjugation
Discrete Fourier transforms
correlation coefficients
mass spectra
solid phases

Keywords

  • 4-Aminopyrimidine-5-carbonitrile
  • Infrared
  • MP2 and DFT calculations
  • NMR and mass spectra
  • Vibrational assignment

ASJC Scopus subject areas

  • Instrumentation
  • Atomic and Molecular Physics, and Optics
  • Analytical Chemistry
  • Spectroscopy

Cite this

Infrared and NMR spectra, tautomerism, vibrational assignment, normal coordinate analysis, and quantum mechanical calculations of 4-amino-5- pyrimidinecarbonitrile. / Afifi, Mahmoud S.; Farag, Rabei S.; Shaaban, Ibrahim A.; Wilson, Lee D.; Zoghaib, Wajdi M.; Mohamed, Tarek A.

In: Spectrochimica Acta - Part A: Molecular and Biomolecular Spectroscopy, Vol. 111, 07.2013, p. 277-289.

Research output: Contribution to journalArticle

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abstract = "The infrared (4000-200 cm-1) spectrum for 4-amino-5- pyrimidinecarbonitrile (APC, C5H4N4) was acquired in the solid phase. In addition, the 1H and 13C NMR spectra of APC were obtained in DMSO-d6 along with its mass spectrum. Initially, six isomers were hypothesized and then investigated by means of DFT/B3LYP and MP2(full) quantum mechanical calculations using a 6-31G(d) basis set. Moreover, the 1H and 13C NMR chemical shifts were predicted using a GIAO approximation at the 6-311+G(d,p) basis set and the B3LYP method with (and without) solvent effects using PCM method. The correlation coefficients showed good agreement between the experimental/ theoretical chemical shift values of amino tautomers (1 and 2) rather than the eliminated imino tautomers (3-6), in agreement with the current quantum mechanical calculations. Structures 3-6 are less stable than the amino tautomers (1 and 2) by about 5206-8673 cm-1 (62.3-103.7 kJ/mol). The MP2(full)/6-31G(d) computational results favor the amino structure 1 with a pyramidal NH2 moiety and calculated real vibrational frequencies, however; structure 2 is considered a transition state owing to the calculated imaginary frequency. It is worth mentioning that, the calculated structural parameters suggest a strong conjugation between the amino nitrogen and pyrimidine ring. Aided by frequency calculations, normal coordinate analysis, force constants and potential energy distributions (PEDs), a complete vibrational assignment for the observed bands is proposed herein. Finally, NH2 internal rotation barriers for the stable non-planar isomer (1) were carried out using MP2(full)/6-31G(d) optimized structural parameters. Our results are discussed herein and compared to structural parameters for similar molecules whenever appropriate.",
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AU - Afifi, Mahmoud S.

AU - Farag, Rabei S.

AU - Shaaban, Ibrahim A.

AU - Wilson, Lee D.

AU - Zoghaib, Wajdi M.

AU - Mohamed, Tarek A.

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AB - The infrared (4000-200 cm-1) spectrum for 4-amino-5- pyrimidinecarbonitrile (APC, C5H4N4) was acquired in the solid phase. In addition, the 1H and 13C NMR spectra of APC were obtained in DMSO-d6 along with its mass spectrum. Initially, six isomers were hypothesized and then investigated by means of DFT/B3LYP and MP2(full) quantum mechanical calculations using a 6-31G(d) basis set. Moreover, the 1H and 13C NMR chemical shifts were predicted using a GIAO approximation at the 6-311+G(d,p) basis set and the B3LYP method with (and without) solvent effects using PCM method. The correlation coefficients showed good agreement between the experimental/ theoretical chemical shift values of amino tautomers (1 and 2) rather than the eliminated imino tautomers (3-6), in agreement with the current quantum mechanical calculations. Structures 3-6 are less stable than the amino tautomers (1 and 2) by about 5206-8673 cm-1 (62.3-103.7 kJ/mol). The MP2(full)/6-31G(d) computational results favor the amino structure 1 with a pyramidal NH2 moiety and calculated real vibrational frequencies, however; structure 2 is considered a transition state owing to the calculated imaginary frequency. It is worth mentioning that, the calculated structural parameters suggest a strong conjugation between the amino nitrogen and pyrimidine ring. Aided by frequency calculations, normal coordinate analysis, force constants and potential energy distributions (PEDs), a complete vibrational assignment for the observed bands is proposed herein. Finally, NH2 internal rotation barriers for the stable non-planar isomer (1) were carried out using MP2(full)/6-31G(d) optimized structural parameters. Our results are discussed herein and compared to structural parameters for similar molecules whenever appropriate.

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