Vibrational spectroscopic and theoretical studies of urea derivatives with biochemical interest: N,N'-dimethylurea, N,N,N',N'-tetramethylurea, and N,N'-dimethylpropyleneurea

Applied Spectroscopy Reviews

Volumn 45, Issue 4, 2010, Pages 274-326

  Mink, János ^a,b,c   Hajba, László ^b,c   Pápai, Imre ^a   Mihály, Judith ^a   Neméth, Csaba ^a   Skripkin, Mikhail Yu ^c,d   Sandström, Magnus ^c  

^a CHEMICAL RESEARCH CENTER   (Hungary)

^b UNIVERSITY OF PANNONIA   (Hungary)

^c STOCKHOLM UNIVERSITY   (Sweden)

^d ST PETERSBURG STATE UNIVERSITY   (Russian Federation)

Author keywords

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

Indexed keywords

DIMETHYLUREA; EQUILIBRIUM GEOMETRIES; HYDROGEN BONDINGS; N,N,N',N'-TETRAMETHYLUREA; TETRAMETHYLUREA; THEORETICAL CALCULATIONS;

AROMATIC COMPOUNDS; COMPUTATIONAL GEOMETRY; DENSITY FUNCTIONAL THEORY; DISSOLUTION; HYDROCARBONS; HYDROGEN; ISOMERS; LIQUIDS; METABOLISM; RNA; SPECTROSCOPIC ANALYSIS; UREA; VIBRATION ANALYSIS; VIBRATIONAL SPECTRA;

HYDROGEN BONDS;

EID: 77953757322     PISSN: 05704928     EISSN: 1520569X     Source Type: Journal    
DOI: 10.1080/05704928.2010.483670     Document Type: Article

References (71)

1. Carmalt, C.J.; Farrugia, L.J.; Norman, N.C. (1995) Structural Studies on some lodoantimonate and lodobismuthate Anions. Z Anorg. Allg. Chem., 621: 47-56.
2. 3. J. Chem. Soc. Dalton Trans., 16: 2703-2710.
3. Näslund, J.; Lindqvist-Reis, P.; Persson, L.; Sandström, M. (2000) Steric Effects Control the Structure of the Solvated Lanthanum(III) Ion in Aqueous, Dimethyl Sulfoxide, and N,N′- Dimethylpropyleneurea Solution. An EXAFS and Large-Angle X-ray Scattering Study. Inorg. Chem., 39: 4006-4011.
4. Näslund, J.; Persson, I.; Sandström, M. (2000) Solvation of the bismuth(III) ion by water, dimethylsulfoxide, N,N′-dimethylpropyleneurea, and N,N-dimethylthioformamide. An EXAFS, large-angle X-ray scattering, and crystallographic structural study. Inorg. Chem., 39: 4012-4021.
5. Smirnov, P.;Weng, L.; Persson, I. (2001) Determination of the transfer thermodynamic functions for some monovalent ions from water to N,N′-dimethylpropyleneurea. Phys. Chem. Chem. Phys., 3: 5248-5254.
6. Persson, I.; Jalilehvand, F.; Sandström, M. (2002) Structure of the solvated thallium(I) ion in aqueous, dimethyl sulfoxide, N,N′- dimethylpropyleneurea, and N,N-dimethylthioformamide solution. Inorg. Chem., 4: 192-197.
7. Kristiansson, O.; Persson, I.; Bobicz, D.; Xu. D. (2003) A structural study of the hydrated and the dimethylsulfoxide, N,N-dimethylpropyleneurea, acetonitrile, pyridine and N,N′- dimethylthioformamide solvated nickel(II) ion in solution and solid state. Inorg. Chim. Acta, 344: 15-27.
8. Rosdahl, J.; Persson, I.; Kloo, L.; Stahl. K. (2004) On the solvation of the mercury(I) ion. A structural, vibration spectroscopic and quantum chemical study. Inorg. Chim. Acta, 357: 2624-2634.
9. Hagfeldt, C.; Kessler, V.; Persson, I. (2004) Structure of the hydrated, hydrolysed and solvated zirconium(IV) and hafnium(IV) ions in water and aprotic oxygen donor solvents. A crystallographic, EXAFS spectroscopic and large angleX-ray scattering study. Dalton Trans., 2142-2151.
10. Theophanides, T.; Harvey, P.D. (1987) Structural and spectroscopic properties of metal-urea complexes. Coord Chem. Rev., 76: 237-264.
11. Keuleers, R.; Desseyn, H.O.; Rousseau, B.; Van Alsenoy, C. (1999) Vibrational Analysis of Urea. J. Phys. Chem. A, 103: 4621-4630.
12. 18O frequency shift data. Spectrochim. Acta, 27A: 1197-1205.
13. Stewards, J.E. (1957) Infrared Absorption Spectra of Urea, Thiourea, and Some Thiourea-Alkali Halide Complexes. J. Chem. Phys., 26: 248-254.
14. 18O-labelled urea. Spectrochim. Acta, 21: 1487-1494.
15. Saito, Y.; Machida, K.; Uno, T. (1971) Infrared spectra of partially deuterated ureas. Spectrochim. Acta, 27A: 991-1002.
16. 2). J.Mol Struct., 10: 253-264.
17. Yamaguchi, A.; Miyazawa, T.; Shimanouchi, T.; Mizushima, S. (1957) Infrared spectroscopic studies of hydrogen bonding in methanol, ethanol, and t-butanol. Spectrochim Acta, 10: 70-84.
18. Yamaguchi, A. (1957) Infrared and Raman spectra of urea and urea-d4. J. Chem. Soc. Japan, 78: 1465.
19. King, S.T. (1972) Low temperature matrix isolation study of hydrogen-bonded, high-boiling organic compounds-III: Infrared spectra of monomeric acetamide, urea and urea-d4. Spectrochim Acta, 28A: 165-175.
20. Ravindranah, K.; Raminah, K.V. (1976) The normal coordinate analysis of urea, thiourea. Indian J. Pure and Applied Physics, 14: 58.
21. Hadzi, D.; Kidric, J.; Knezevic, Z.V.; Barlic, R. (1976) The normal coordinate analysis of urea, thiourea, and their isotopic analogues in the solid phase and in solution. Spectrochim. Acta, 32A: 693-704.
22. Arenas, J.F.; Marquez, F.; Cardenete, A. (1984) Force Field for out-of-plane Bl vibrations of urea and thiourea. Spectrochim. Acta, 40A: 1033-1035.
23. Li, X.; Stitesbury, J.S.; Jayasooriya, V.A. (1987) Infrared spectra of urea isolated in a solid argon matrix. Spectrochim. Acta, 43A: 1595-1597.
24. Liapis, K.; Jayasooriya, N.A.; Kettle, S.F.A.; Eckert, J.; Goldstone, J.A.; Taylor, A.D. (1985) Solid state studies. 29. Crystalline urea: evidence for vibrational delocalization. J. Phys. Chem., 89: 4560-4565.
25. Derreumaux, P.; Vergoten, G.; Lagant, P. (1990) A vibrational molecular force field of model compounds with biological interest. I. Harmonic dynamics of crystalline urea at 123 K.J. Comput. Chem., 11: 560-568.
26. Vijay, A.; Sathyanarayana, D.N. (1993) Ab initio study of the force field, geometry and vibrational assignment of urea. J. Mol. Struct., 295: 245-258.
27. Umo, T.; Machida, K.; Saito, Y. (1969) Infrared Spectra of Biuret-hydrate and Its Deuterated Compound. Bull. Chem. Soc. Jpn, 6: 1539-1545.
28. Ravindranah, K.; Raminah, K.V. (1977) Infrared spectra of methyl derivatives of urea. Indian J. Pure and Applied Physics, 15: 182-191.
29. Mido, Y.; Tanase, K.; Kido, K. (1989) Vibrational spectra and normal vibrations of N,Ndimethylurea and three deuterated analogues. Spectrochim. Acta, 45A: 397-402.
30. Rao, C.N.R.; Chaturvedi, G.C.; Gasavi, R.K. (1968) Infrared spectra and configurations of alkylurea derivatives: Normal vibrations on N,N′-dimethyl- and tetramethylurea. J. Mol. Spectrosc., 28: 526-535.
31. Schafer, M.; Curran, C. (1966) Infrared Spectra of Complexes of Metal Halides with Tetramethylurea and Tetramethylthiourea. Inorg. Chem., 5: 265-268.
32. Roeges, N.P.G. (1998) A Guide to the Complete Interpretation of Infrared Spectral of Organic Structures, John Wiley & Sons Ltd, Chichester, p. 15 and 246.
33. Gasovi, R.K.; Agarrala, U.; Rao, C.N.R. (1967) Infrared Spectra and Configuration of Alkylthiourea Derivatives. Normal Vibrations of N,N′-Dimethyl- and Tetramethylthiourea. J. Am. Chem. Soc., 89: 235-239.
34. Dwarakanath, K.; Sathyanarayana, D.N. (1979) Vibrational Spectra and Normal Coordinate Analysis of Tioureas. Indian J. Pure and Applied Physics, 17: 171.
35. Dwarakanath, K.; Sathyanarayana, D.N. (1979) Vibrational Spectra and Normal Coordinate Analysis of TV-Methyl Thiourea. Bui. Chem. Soc. Japan, 52: 2084-2087.
36. Schachtschneider, J.H.; Snyder, R.G. (1963) Vibrational analysis of the n-paraffins-II: Normal co-ordinate calculations. Spectrochim. Acta, 19: 117-168.
37. Ray, A.; Sathyanarayana, D.N. (1972) Infrared Spectrum and Normal Vibrations of N,NDimethylthioacetamide. Bui. Chem. Soc. Japan, 45: 2712-2715.
38. Desseyn, H.O.; Van DerVeken, B.J.; Herman,M.A. (1977).Vibrational analysis of the oxamidesthe characteristic pattern of amides in i.r. and Raman spectra. Spectrochim. Acta, 33A: 633-641.
39. Sabatini, A.; Calijano, S. (1960) Infra-red spectra in polarized light of ethylenediamine and ethylenediamine-d4. Spectrochim Acta, 16: 677-688.
40. Segal, L.; Eggerton, F.V. (1961) Infrared Spectra of Aliphatic Normal Mono-Amines and Alpha- Omega Diamines. Appl. Spectrosc., 15: 112-116.
41. Borring, A.-L.; Rasmussen, K. (1975) Infrared and far infrared spectra of normal, C-, N- and per-deuterated 1,2-ethanediamine. Spectrochim. Acta, 31A: 889-893.
42. Omura, Y.; Shimanouchi, T. (1975) Skeletal deformation vibrations and rotational isomerism of ethylenediamine and monoethanolamine. J. Mol. Spectrosc., 57: 480-489.
43. Giorgini,M.; Pellet, M.R.; Paliani,G.; Cataliotti, R.S. (1983)Vibrational spectra and assignments of ethylene-diamine and its deuterated derivatives. J. Raman Spectrosc., 14: 16-21.
44. Sneyder, R.G.; Schachtschneider, J.H. (1965) A valence force field for saturated hydrocarbons. Spectrochim Acta, 21: 169-195.
45. (a) Becke, A.D. (1993) Density-functional thermochemistry. III. The role of exact exchange. J. Chem. Phys, 98: 5648-5652.
46. (b) Lee, C.; Yang, W.; Parr, R.G. (1988) Development of the Colle-Salvetti correlation-energy formula into a functional of the electron-density. Phys. Rev. B, 37: 785-788.
47. (c) Stephens, P.J.; Devlin, F.J.; Chabalowski, C.F.; Frisch, M.J. (1994) Ab Initio Calculation of Vibrational Absorption and Circular Dichroism Spectra Using Density Functional Force Fields. J. Phys. Chem, 98: 11623-11627.
48. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Montgomery, Jr., J. A.; Vreven, T.; Kudin, K. N.; Burant, J. C.; Millam, J. M.; lyengar, S. S.; Tomasi, J.; Barone, V.; Mennucci, B.; Cossi, M.; Scalmani, G.; Rega, N.; Petersson, G. A.; Nakatsuji, H.; Hada, M.; Ehara,M.; Toyota, K.; Fukuda, R.; Hasegawa, J.; Ishida,M.; Nakajima, T.; Honda, Y.; Kitao, O.; Nakai, H.; Klene, M.; Li, X.; Knox, J. E.; Hratchian, H. P.; Cross, J. B.; Bakken, V.; Adamo, C.; Jaramillo, J.; Gomperts, R.; Stratmann, R. E.; Yazyev, O.; Austin, A. J.; Cammi, R.; Pomelli, C.; Ochterski, J. W.; Ayala, P. Y.; Morokuma, K.; Voth, G. A.; Salvador, P.; Dannenberg, J. J.; Zakrzewski, V. G.; Dapprich, S.; Daniels, A. D.; Strain, M. C.; Farkas, O.; Malick, D. K.; Rabuck, A. D.; Raghavachari, K.; Foresman, J. B.; Ortiz, J. V.; Cui, Q.; Baboul, A. G.; Clifford, S.; Cioslowski, J.; Stefanov, B. B.; Liu, G.; Liashenko, A.; Piskorz, P.; Komaromi, I.; Martin, R. L.; Fox, D. J.; Keith, T.; Al-Laham, M. A.; Peng, C. Y.; Nanayakkara, A.; Challacombe, M.; Gill, P. M. W.; Johnson, B.; Chen, W.; Wong, M. W.; Gonzalez, C.; and Pople, J. A.; Gaussian 03, Revision E.01, Gaussian, Inc., Wallingford, CT, 2004.
49. Mink, J.; Mink, L., Computer program system for vibrational analysis of polyatomic molecules (in Lahey-Fujitsu Fortan Win32). Stockholm, 2004. (Self developed program system, available at the working places of the authors by e-mail.).
50. Ṕerez-Folch, J.; Subirana, J.A.; Aymami, J. (1997) Polar structure of N,N′-dimethylurea crystals. J. Chem. Crystallogr., 27: 367-369.
51. Martins, D.M.S.; Spanswick, C.K.; Middlemiss, D.S.; Abbas, N.; Pulham, C.R.; Morrison, C.A. (2009) A New Polymorph of N,N′-Dimethylurea Characterized by X-ray Diffraction and First- Principles Lattice Dynamics Calculations. J. Phys. Chem. A, 113: 5998-6003.
52. Galabov, B.; Ilieva, S.; Hadjieva, B.; Dudev, T. (1997) N H stretching frequencies and the conformation of substituted ureas: an ab initio MO study. J. Mol. Struct., 407: 47-51.
53. Keuleers, R.; Desseyn, H.O.; Rousseau, B.; Van Alsenoy, C. (2000) Solids Modeled by ab Initio Crystal Field Methods. 21. Study of the Structure andVibrational Spectrum of N,N′-Dimethylurea in the Gas Phase and in Its Cc Crystal Phase. J. Phys. Chem. A, 104: 5946-5954.
54. Shukla, A.; Isaacs, E.D.; Hamann, D.R.; Platzman, P.M. (2001) Hydrogen bonding in urea. Phys. Rev. B, 64: 052101.
55. Rousseau, B.; Van Alsenoy, C.; Keuleers, R.; Desseyn, H.O. (1998) SolidsModeled by Ab-Initio Crystal Field Methods. Part 17. Study of the Structure and Vibrational Spectrum of Urea in the Gas Phase and in Its P421m Crystal Phase. J. Phys. Chem. A, 102: 6540-6548.
56. Godfrey, P.D.; Brown, R.D.; Hunter, A.N. (1997) The shape of urea. J. Mol. Struct., 413-414: 405-414.
57. Miao,M.S.; Van Doren, V.E.; Keuleers, R.; Desseyn, H.O.; Van Alsenoy, C.;Martins, J.L. (2000) Density functional calculations of the structure of crystalline urea under high pressure. Chem. Phys. Lett., 316: 297-302.
58. Harnagea, E.I.; Jagodzinski, P.W. (1996) Infrared spectra of cyclic and non-cyclic ureas in solution: structures and interactions. Vib. Spectr., 10: 169-175.
59. Saito, Y.; Maceida, K.; Uno, T. (1975) Vibrational spectra of methylurea. Spectrochim. Acta, 31A: 1237-1244.
60. 15N Isotope Shifts. J. Chem. Phys., 57: 1236-1247.
61. Thomas, G.J., Jr.; Benevides, J.M.; Overman, S.A.; Ueda, T.; Ushizawa, K.; Saitoh, M.; Tsuboi, M. (1995) Polarized Raman spectra of oriented fibres of A DNA and B DNA: anisotropic and isotropic local Raman tensors of base and backbone vibrations. Biophys. J., 68: 1073-1088.
62. 2O Solutions. Bull. Chem. Soc. Japan, 46: 3891-3892.
63. Benevides, J.M.; Tsuboi, M.; Wang, A.H.J.; Thomas, G.J., Jr. (1993) Local Raman tensors of double-helical DNA in the crystal: a basis for determining DNA residue orientations. J. Am. Chem Soc., 115: 5351-5359.
64. Naumann, D. (2001) FT-infrared and FT-Raman spectroscopy in biomedieal research. Appl. Spectr. Rev., 36: 239-298.
65. Les, A.; Adamowicz, L.; Nowak, M.J.; Lapinski, L. (1992) The infrared spectra of matrix isolated uracil and thymine: An assignment based on new theoretical calculations. Spectrochim. Acta, 48A: 1385-1395.
66. Xu, Z.H.; Butler, I.S. (1987) Fourier transform infrared and laser Raman microprobe spectra of uridine. J. Raman Spect., 18: 351-356.
67. Jose, C.I. (1969) Infrared spectra of substituted ureas-I. Alkyl ureas. Spectrochim. Acta, 25A: 111-118.
68. Mido, Y. (1972) Infrared spectra and configurations of dialkylureas. Spectrochim. Acta, 28A: 1503-1518.
69. Susi, H.; Ard, J.S.; Purcell, J.M. (1973) Vibrational spectra of nucleic acid constituents-II: Planar vibrations of cytosine. Spectrochim. Acta, 29A: 725-733.
70. Nishimura, Y.; Tsuboi, M. (1985) In-plane vibrational modes of cytosine from an ab initio MO calculation. Chem. Phys., 98: 71-80.
71. Aida, M.; Kaneko, M.; Dupuis, M.; Ueda, T.; Ushizawa, K.; Ito, G.; Kumakura, A.; Tsuboi, M. (1997) Vibrational modes in thymine molecule from an ab initio MO calculation. Spectrochim. Acta, 53A: 393-407. (Pubitemid 127429023)