Vibrational spectroscopic and theoretical studies of urea derivatives with biochemical interest

N,N'-dimethylurea, N,N,N',N'-tetramethylurea, and N,N'-dimethylpropyleneurea

J. Mink, László Hajba, I. Pápai, J. Mihály, Csaba Neméth, Mikhail Yu Skripkin, Magnus Sandström

Research output: Contribution to journalArticle

4 Citations (Scopus)

Abstract

Mid-infrared, far-infrared, and Raman vibrational spectroscopic studies were combined with density functional theory (DFT) calculations and normal coordinate force field analyses for N,N'-dimethylurea (DMU), N,N,N',N'-tetramethylurea (TMU), and N,N'-dimethylpropyleneurea (DMPU: IUPAC name 1,3-dimethyltetrahydropyrimidin-2(1H)-one). The equilibrium molecular geometry of DMU (all three conformers), TMU, and DMPU and the frequencies, intensities, and depolarization ratios of their fundamental infrared (IR) and Raman vibrational transitions were obtained by DFT calculations. The vibrational spectra were fully analyzed by normal coordinate methods as well. A starting force field for DMPU was obtained by adapting corresponding force constants for DMU and TMU, resulting after refinements in the stretching force constants C=O (7.69, 7.30, 7.68 N·cm-1), C-N (5.16, 5.55, 5.05N·cm-1), and C-Me (5.93, 4.00, 4.22 N·cm -1) for DMU, TMU, and DMPU, respectively. The dominating conformer of liquid DMU was identified as trans-trans, strong intermolecular hydrogen bonding was verified in solid DMU, and weak dipole-dipole association was found in liquid TMU and in DMPU. Special attention was paid to analyzing the methyl group frequencies, which revealed deviations from local C3v symmetry. A linear correlation was found between the CH stretching force constants and the inverse of the CH bond lengths (1/r2). The averaged NH stretching frequencies of gaseous, dissolved, and solid urea and of DMU, with variations for hydrogen bonding of different strength, are linearly correlated to the NH stretching force constants. Characteristic skeletal vibrations were assigned for a broad variety of urea derivatives and also for pyrimidine derivatives, which all contain the N2C=O entity. The very strong IR bands of C=O stretching (1,676 ± 40 cm-1) and asymmetric CN2 stretching (1,478 ± 60 cm-1), and the very intense Raman feature of symmetric CN2 stretching or ring breathing (757 80 cm-1), can be recognized as fingerprint bands also for the pyrimidine derivatives cytosine, thymine, and uracil, which all are nucleobases in DNA and RNA nucleotides.

Original languageEnglish
Pages (from-to)274-326
Number of pages53
JournalApplied Spectroscopy Reviews
Volume45
Issue number4
DOIs
Publication statusPublished - Jul 2010

Fingerprint

ureas
Urea
Stretching
Derivatives
Infrared radiation
pyrimidines
field theory (physics)
Density functional theory
Hydrogen bonds
methylidyne
dipoles
density functional theory
uracil
Thymine
Uracil
thymine
Cytosine
nucleotides
Depolarization
Liquids

Keywords

  • equilibrium geometry
  • hydrogen bonding
  • N,N'-dimethylpropyleneurea
  • N,N'-dimethylurea
  • N,N,N',N'-tetramethylurea
  • theoretical calculations
  • urea
  • Vibrational spectra

ASJC Scopus subject areas

  • Spectroscopy
  • Instrumentation

Cite this

Vibrational spectroscopic and theoretical studies of urea derivatives with biochemical interest : N,N'-dimethylurea, N,N,N',N'-tetramethylurea, and N,N'-dimethylpropyleneurea. / Mink, J.; Hajba, László; Pápai, I.; Mihály, J.; Neméth, Csaba; Skripkin, Mikhail Yu; Sandström, Magnus.

In: Applied Spectroscopy Reviews, Vol. 45, No. 4, 07.2010, p. 274-326.

Research output: Contribution to journalArticle

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abstract = "Mid-infrared, far-infrared, and Raman vibrational spectroscopic studies were combined with density functional theory (DFT) calculations and normal coordinate force field analyses for N,N'-dimethylurea (DMU), N,N,N',N'-tetramethylurea (TMU), and N,N'-dimethylpropyleneurea (DMPU: IUPAC name 1,3-dimethyltetrahydropyrimidin-2(1H)-one). The equilibrium molecular geometry of DMU (all three conformers), TMU, and DMPU and the frequencies, intensities, and depolarization ratios of their fundamental infrared (IR) and Raman vibrational transitions were obtained by DFT calculations. The vibrational spectra were fully analyzed by normal coordinate methods as well. A starting force field for DMPU was obtained by adapting corresponding force constants for DMU and TMU, resulting after refinements in the stretching force constants C=O (7.69, 7.30, 7.68 N·cm-1), C-N (5.16, 5.55, 5.05N·cm-1), and C-Me (5.93, 4.00, 4.22 N·cm -1) for DMU, TMU, and DMPU, respectively. The dominating conformer of liquid DMU was identified as trans-trans, strong intermolecular hydrogen bonding was verified in solid DMU, and weak dipole-dipole association was found in liquid TMU and in DMPU. Special attention was paid to analyzing the methyl group frequencies, which revealed deviations from local C3v symmetry. A linear correlation was found between the CH stretching force constants and the inverse of the CH bond lengths (1/r2). The averaged NH stretching frequencies of gaseous, dissolved, and solid urea and of DMU, with variations for hydrogen bonding of different strength, are linearly correlated to the NH stretching force constants. Characteristic skeletal vibrations were assigned for a broad variety of urea derivatives and also for pyrimidine derivatives, which all contain the N2C=O entity. The very strong IR bands of C=O stretching (1,676 ± 40 cm-1) and asymmetric CN2 stretching (1,478 ± 60 cm-1), and the very intense Raman feature of symmetric CN2 stretching or ring breathing (757 80 cm-1), can be recognized as fingerprint bands also for the pyrimidine derivatives cytosine, thymine, and uracil, which all are nucleobases in DNA and RNA nucleotides.",
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AU - Hajba, László

AU - Pápai, I.

AU - Mihály, J.

AU - Neméth, Csaba

AU - Skripkin, Mikhail Yu

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