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VIBRATIONAL ANALYSIS AND HYDROGEN-BONDING EFFECTS ON THE VIBRATIONAL MODES OF ZWITTERIONIC DL-TRYPTOPHAN: IR SPECTROSCOPY AND DFT CALCULATIONS

Yıl 2019, Cilt: 37 Sayı: 4, 1180 - 1198, 01.12.2019

Öz

The vibrational behavior of zwitterionic DL-tryptophan has been investigated using infra-red spectroscopy and density functional theory calculations. In order to study the hydrogen bonding effects on the molecular structure and vibrational normal modes of the under-investigated amino acid, both the solid state and aqueous solution calculations have been presented. The three dimensional molecular structure optimized by the solid state calculations shows the best agreement with that previously published using X-Ray diffraction technique. In addition, the calculated and experimentally observed wavenumbers have been compared. However, only the calculations performed in the solid state allowed us to attribute the band observed at around 2532 cm-1 to the N-H stretching vibration. Because some normal modes are strongly affected by the extensive hydrogen bonding network present in DL-tryptophan crystal, the solid state model is the most suitable for interpreting the experimental infra-red spectrum.

Kaynakça

  • [1] Boldyreva E., (2008) Crystalline amino acids: a link between chemistry, materials science and biology. Springer: Dordrecht 167-192.
  • [2] Wu G., (2009) Amino acids: metabolism, functions, and nutrition. Amino acids 37, 1-17.
  • [3] Lamzin V.S., Dauter Z., Wilson K. S., (1995) How nature deals with stereoisomers. Current opinion in structural biology 5(6), 830-836.
  • [4] Hegstrom R. A., Kondepudi D. K., (1990) The handedness of the universe. Scientific American 262(1), 108-115.
  • [5] Blackmond D. G., (2010) The origin of biological homochirality. Cold Spring Harb. Perspect. Biol a002147.
  • [6] Smith C., (1929) The ultra-violet absorption spectra of certain aromatic amino-acids, and of the serum proteins. Proc. R. Soc. Lond. B 104, 198-205.
  • [7] Goodwin T. W., Morton R. A., (1946) The spectrophotometric determination of tyrosine and tryptophan in proteins. Biochem. J 40(5-6), 628-632.
  • [8] Ivanova B. B., (2006) IR-LD spectroscopic characterization of L-Tryptophan containing dipeptides. Spectroc. Acta A 64, 931-938.
  • [9] Çakır S., Biçer E., (2010) Synthesis, spectroscopic and electrochemical characteristics of a novel Schiff-base from saccharin and tryptophan. J. Iran. Chem. Soc 7, 394-404.
  • [10] Cao X., Fischer G., (1999) Infrared spectral, structural, and conformational studies of zwitterionic L-tryptophan. J. Phys. Chem. A 103, 9995-10003.
  • [11] Bakke Ø., Mostad A., (1980) The structure and conformation of tryptophan in the crystal of the pure racemic compound and the hydrogen oxalate. Acta Chem Scand B 34, 559-570.
  • [12] Hübschle C. B., Messerschmidt M., Luger P., (2004) Crystal structure of DL‐Tryptophan at 173K. Cryst. Res. Technol 39, 274-278.
  • [13] Görbitz H., Törnroos K. W., Day G. M., (2012) Single-crystal investigation of l-tryptophan with Z′= 16. Acta Cryst B 68, 549-557.
  • [14] Zhou T., Wu Y., Cao J., Zou L., Yuan J., Yao Z., Xu G., (2017) Research on the Terahertz Absorption Spectra of Histidine Enantiomer (L) and its Racemic Compound (DL). Appl. Spectrosc 71(2), 194-202.
  • [15] Minkov V. S., Chesalov Yu. A., Boldyreva E. V., (2010) A study of the temperature effect on the IR spectra of crystalline amino acids, dipeptids, and polyamino acids. VI. L-alanine and dl-alanine. Journal of Structural Chemistry 51, 1052-1063.
  • [16] Jarmelo S., Reva I., Carey P. R., Fausto R., (2007) Infrared and Raman spectroscopic characterization of the hydrogen-bonding network in L-serine crystal. Vib. Spectrosc 43(2), 395-404.
  • [17] Jarmelo S., Reva I., Rozenberg M., Carey P. R., Fausto R., (2006) Low-temperature infrared spectra and hydrogen bonding in polycrystalline DL-serine and deuterated derivatives. Vib. Spectrosc 41(1), 73-82.
  • [18] Gronert S., O'Hair R. A., (1995) Ab initio studies of amino acid conformations. 1. The conformers of alanine, serine, and cysteine. J. Am. Chem. Soc 117(7), 2071-2081.
  • [19] Contreras C. D., Ledesma A. E., Lanús H. E., Zinczuk J., Brandán S. A., (2011) Hydration of l-tyrosine in aqueous medium. An experimental and theoretical study by mixed quantum mechanical/molecular mechanics methods. Vib. Spectrosc 57(1), 108-115.
  • [20] Cao X., Fischer G., (2000) The infrared spectra and molecular structure of zwitterionic L-β-phenylalanine. J. Mol. Struct 519(1-3), 153-163.
  • [21] Cao X., Fischer G., (1999) New infrared spectra and the tautomeric studies of purine and αL-alanine with an innovative sampling technique. Spectroc. Acta A 55(11), 2329-2342.
  • [22] Neese F., ( 2012) The ORCA program system. WIREs Comput Mol Sci 2, 73–78.
  • [23] Becke A. D., (1993) Density‐functional thermochemistry. III. The role of exact exchange. J. Chem. Phys 98, 5648- 5652.
  • [24] 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, 785-789.
  • [25] Schafer A., Horn H., Ahlrichs R., (1992) Fully optimized contracted Gaussian basis sets for atoms Li to Kr. J. Chem. Phys 97, 2571-2577.
  • [26] Weigend F., Ahlrichs R., (2005) Balanced basis sets of split valence, triple zeta valence and quadruple zeta valence quality for H to Rn: Design and assessment of accuracy. Phys. Chem. Chem. Phys 7, 3297-3305.
  • [27] Kossmann S., Neese F., (2010) Efficient structure optimization with second-order many-body perturbation theory: The RIJCOSX-MP2 method. J. Chem. Theory Comput 6, 2325–2338.
  • [28] Izsàk R., Neese F., (2013) Speeding up spin-component-scaled third-order pertubation theory with the chain of spheres approximation: the COSX-SCS-MP3 method. Molecular Physics 111, 1190–1195.
  • [29] Osaki T., Soejima E., (2010) Quadratic scaling functions for obtaining normal vibrational wavenumbers from the B3LYP calculation. Res. Bull. Fukuoka Inst. Tech 42(2), 129-134.
  • [30] Yoshida H., Ehara A., Matsuura H., (2000) Density functional vibrational analysis using wavenumber-linear scale factors.Chem. Phys. Lett 325, 477–483.
  • [31] Perdew J. P., Burke K., Ernzerhof M., (1996) Generalized gradient approximation made simple. Phys. Rev. Lett 77, 3865.
  • [32] Clark S. J., Segall M. D., Pickard C. J., Hasnip P. J., Probert M. I., Refson K., Payne M.C., (2005) First principles methods using CASTEP. Z. Kristallog 220, 567-570.
  • [33] Refson K., Tulip P. R., Clark S. J., (2006) Variational density-functional perturbation theory for dielectrics and lattice dynamics.Phys Rev B 73(15), 155114.
  • [34] Min’kov V. S., Chesalov Y. A., Boldyreva E. V., (2008) Study of the temperature effect on IR spectra of crystalline amino acids, dipeptides, and polyamino acids. IV. L-cysteine and DL-cysteine. Journal of Structural Chemistry 49(6), 1022-1034.
  • [35] Petrosyan A. M., (2007) Vibrational spectra of L-histidine perchlorate and L-histidine tetrafluoroborate.Vib. Spectrosc 43(2), 284-289.
  • [36] Chowdhry B. Z., Dines T. J., Jabeen S., Withnall R., (2008) Vibrational spectra of α-amino acids in the zwitterionic state in aqueous solution and the solid state: DFT calculations and the influence of hydrogen bonding.J. Phys. Chem. A 112, 10333-10347.
  • [37] Pawlukojć A., Hołderna-Natkaniec K., Bator G., Natkaniec I., (2014) INS, IR, RAMAN, 1H NMR and DFT investigations on dynamical properties of l-asparagine. Vib. Spectrosc 72, 1-7.
  • [38] Parker S. F., (2013) Assignment of the vibrational spectrum of L-cysteine. Chemical Physics 424, 75-79.
  • [39] Mostad A. R. V. I. D., Romming C., (1973) Crystal-structure of DL-tyrosin. Acta Chem. Scand 27, 401-410.
  • [40] Frey M. N., Koetzle T. F., Lehmann M. S., Hamilton W. C., (1973) Precision neutron diffraction structure determination of protein and nucleic acid components. X. A comparison between the crystal and molecular structures of L‐tyrosine and L‐tyrosine hydrochloride. J. Chem. Phys 58(6), 2547-2556.
  • [41] Edington P., Harding M. M., (1974) The crystal structure of DL-histidine. Acta Cryst B 30(1), 204-206.
Yıl 2019, Cilt: 37 Sayı: 4, 1180 - 1198, 01.12.2019

Öz

Kaynakça

  • [1] Boldyreva E., (2008) Crystalline amino acids: a link between chemistry, materials science and biology. Springer: Dordrecht 167-192.
  • [2] Wu G., (2009) Amino acids: metabolism, functions, and nutrition. Amino acids 37, 1-17.
  • [3] Lamzin V.S., Dauter Z., Wilson K. S., (1995) How nature deals with stereoisomers. Current opinion in structural biology 5(6), 830-836.
  • [4] Hegstrom R. A., Kondepudi D. K., (1990) The handedness of the universe. Scientific American 262(1), 108-115.
  • [5] Blackmond D. G., (2010) The origin of biological homochirality. Cold Spring Harb. Perspect. Biol a002147.
  • [6] Smith C., (1929) The ultra-violet absorption spectra of certain aromatic amino-acids, and of the serum proteins. Proc. R. Soc. Lond. B 104, 198-205.
  • [7] Goodwin T. W., Morton R. A., (1946) The spectrophotometric determination of tyrosine and tryptophan in proteins. Biochem. J 40(5-6), 628-632.
  • [8] Ivanova B. B., (2006) IR-LD spectroscopic characterization of L-Tryptophan containing dipeptides. Spectroc. Acta A 64, 931-938.
  • [9] Çakır S., Biçer E., (2010) Synthesis, spectroscopic and electrochemical characteristics of a novel Schiff-base from saccharin and tryptophan. J. Iran. Chem. Soc 7, 394-404.
  • [10] Cao X., Fischer G., (1999) Infrared spectral, structural, and conformational studies of zwitterionic L-tryptophan. J. Phys. Chem. A 103, 9995-10003.
  • [11] Bakke Ø., Mostad A., (1980) The structure and conformation of tryptophan in the crystal of the pure racemic compound and the hydrogen oxalate. Acta Chem Scand B 34, 559-570.
  • [12] Hübschle C. B., Messerschmidt M., Luger P., (2004) Crystal structure of DL‐Tryptophan at 173K. Cryst. Res. Technol 39, 274-278.
  • [13] Görbitz H., Törnroos K. W., Day G. M., (2012) Single-crystal investigation of l-tryptophan with Z′= 16. Acta Cryst B 68, 549-557.
  • [14] Zhou T., Wu Y., Cao J., Zou L., Yuan J., Yao Z., Xu G., (2017) Research on the Terahertz Absorption Spectra of Histidine Enantiomer (L) and its Racemic Compound (DL). Appl. Spectrosc 71(2), 194-202.
  • [15] Minkov V. S., Chesalov Yu. A., Boldyreva E. V., (2010) A study of the temperature effect on the IR spectra of crystalline amino acids, dipeptids, and polyamino acids. VI. L-alanine and dl-alanine. Journal of Structural Chemistry 51, 1052-1063.
  • [16] Jarmelo S., Reva I., Carey P. R., Fausto R., (2007) Infrared and Raman spectroscopic characterization of the hydrogen-bonding network in L-serine crystal. Vib. Spectrosc 43(2), 395-404.
  • [17] Jarmelo S., Reva I., Rozenberg M., Carey P. R., Fausto R., (2006) Low-temperature infrared spectra and hydrogen bonding in polycrystalline DL-serine and deuterated derivatives. Vib. Spectrosc 41(1), 73-82.
  • [18] Gronert S., O'Hair R. A., (1995) Ab initio studies of amino acid conformations. 1. The conformers of alanine, serine, and cysteine. J. Am. Chem. Soc 117(7), 2071-2081.
  • [19] Contreras C. D., Ledesma A. E., Lanús H. E., Zinczuk J., Brandán S. A., (2011) Hydration of l-tyrosine in aqueous medium. An experimental and theoretical study by mixed quantum mechanical/molecular mechanics methods. Vib. Spectrosc 57(1), 108-115.
  • [20] Cao X., Fischer G., (2000) The infrared spectra and molecular structure of zwitterionic L-β-phenylalanine. J. Mol. Struct 519(1-3), 153-163.
  • [21] Cao X., Fischer G., (1999) New infrared spectra and the tautomeric studies of purine and αL-alanine with an innovative sampling technique. Spectroc. Acta A 55(11), 2329-2342.
  • [22] Neese F., ( 2012) The ORCA program system. WIREs Comput Mol Sci 2, 73–78.
  • [23] Becke A. D., (1993) Density‐functional thermochemistry. III. The role of exact exchange. J. Chem. Phys 98, 5648- 5652.
  • [24] 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, 785-789.
  • [25] Schafer A., Horn H., Ahlrichs R., (1992) Fully optimized contracted Gaussian basis sets for atoms Li to Kr. J. Chem. Phys 97, 2571-2577.
  • [26] Weigend F., Ahlrichs R., (2005) Balanced basis sets of split valence, triple zeta valence and quadruple zeta valence quality for H to Rn: Design and assessment of accuracy. Phys. Chem. Chem. Phys 7, 3297-3305.
  • [27] Kossmann S., Neese F., (2010) Efficient structure optimization with second-order many-body perturbation theory: The RIJCOSX-MP2 method. J. Chem. Theory Comput 6, 2325–2338.
  • [28] Izsàk R., Neese F., (2013) Speeding up spin-component-scaled third-order pertubation theory with the chain of spheres approximation: the COSX-SCS-MP3 method. Molecular Physics 111, 1190–1195.
  • [29] Osaki T., Soejima E., (2010) Quadratic scaling functions for obtaining normal vibrational wavenumbers from the B3LYP calculation. Res. Bull. Fukuoka Inst. Tech 42(2), 129-134.
  • [30] Yoshida H., Ehara A., Matsuura H., (2000) Density functional vibrational analysis using wavenumber-linear scale factors.Chem. Phys. Lett 325, 477–483.
  • [31] Perdew J. P., Burke K., Ernzerhof M., (1996) Generalized gradient approximation made simple. Phys. Rev. Lett 77, 3865.
  • [32] Clark S. J., Segall M. D., Pickard C. J., Hasnip P. J., Probert M. I., Refson K., Payne M.C., (2005) First principles methods using CASTEP. Z. Kristallog 220, 567-570.
  • [33] Refson K., Tulip P. R., Clark S. J., (2006) Variational density-functional perturbation theory for dielectrics and lattice dynamics.Phys Rev B 73(15), 155114.
  • [34] Min’kov V. S., Chesalov Y. A., Boldyreva E. V., (2008) Study of the temperature effect on IR spectra of crystalline amino acids, dipeptides, and polyamino acids. IV. L-cysteine and DL-cysteine. Journal of Structural Chemistry 49(6), 1022-1034.
  • [35] Petrosyan A. M., (2007) Vibrational spectra of L-histidine perchlorate and L-histidine tetrafluoroborate.Vib. Spectrosc 43(2), 284-289.
  • [36] Chowdhry B. Z., Dines T. J., Jabeen S., Withnall R., (2008) Vibrational spectra of α-amino acids in the zwitterionic state in aqueous solution and the solid state: DFT calculations and the influence of hydrogen bonding.J. Phys. Chem. A 112, 10333-10347.
  • [37] Pawlukojć A., Hołderna-Natkaniec K., Bator G., Natkaniec I., (2014) INS, IR, RAMAN, 1H NMR and DFT investigations on dynamical properties of l-asparagine. Vib. Spectrosc 72, 1-7.
  • [38] Parker S. F., (2013) Assignment of the vibrational spectrum of L-cysteine. Chemical Physics 424, 75-79.
  • [39] Mostad A. R. V. I. D., Romming C., (1973) Crystal-structure of DL-tyrosin. Acta Chem. Scand 27, 401-410.
  • [40] Frey M. N., Koetzle T. F., Lehmann M. S., Hamilton W. C., (1973) Precision neutron diffraction structure determination of protein and nucleic acid components. X. A comparison between the crystal and molecular structures of L‐tyrosine and L‐tyrosine hydrochloride. J. Chem. Phys 58(6), 2547-2556.
  • [41] Edington P., Harding M. M., (1974) The crystal structure of DL-histidine. Acta Cryst B 30(1), 204-206.
Toplam 41 adet kaynakça vardır.

Ayrıntılar

Birincil Dil İngilizce
Bölüm Research Articles
Yazarlar

Abdelali Boukaoud Bu kişi benim 0000-0003-2190-9152

Younes Chıba Bu kişi benim 0000-0003-0560-5212

Mourad Dehbaouı Bu kişi benim 0000-0001-8681-5099

Nacir Guechı Bu kişi benim 0000-0001-9328-8362

Yayımlanma Tarihi 1 Aralık 2019
Gönderilme Tarihi 15 Nisan 2019
Yayımlandığı Sayı Yıl 2019 Cilt: 37 Sayı: 4

Kaynak Göster

Vancouver Boukaoud A, Chıba Y, Dehbaouı M, Guechı N. VIBRATIONAL ANALYSIS AND HYDROGEN-BONDING EFFECTS ON THE VIBRATIONAL MODES OF ZWITTERIONIC DL-TRYPTOPHAN: IR SPECTROSCOPY AND DFT CALCULATIONS. SIGMA. 2019;37(4):1180-98.

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