Cite this article as:
Ten G. N., Glukhova O. Е., Slepchenkov M. М., Shcherbakova N. Е., Baranov V. I. Modeling of Vibrational Spectra of L-tryptophan in Condensed States. Izvestiya of Saratov University. New series. Series Physics, 2017, vol. 17, iss. 1, pp. 20-32. DOI: https://doi.org/10.18500/1817-3020-2017-17-1-20-32
Modeling of Vibrational Spectra of L-tryptophan in Condensed States
Background and Objectives: This work is devoted to the interpretation of IR and Raman spectra of Trp in the condensed states. For this purpose, we calculated the complexes in the zwitterionic form of Trp with the water molecules. Obtained results allow us to determine the influence of hydrogen bonds on the vibrational spectra of Trp in the aqueous solution and solid state. Materials and Methods: The calculation of the normal modes and intensities of IR and Raman spectra of Trp was performed using Gaussian 09 software package based on the DFT method with the use of the B3LYP/6-311++G(d,p) functional. We used the reaction field model SCRF (the dielectric constant ε=78.39). As the structural models, we considered the complexes of Trp with one and four water molecules. Results: The calculation results and comparison with experiment showed that for the simulation of the vibrational spectra of Trp in the zwitterionic form in the aqueous solution the most appropriate for application was the complex of Trp with the single water molecule positioned between bipolar groups, and for the simulation of the spectra in the solid state – the complex of Trp with four water molecules. Conclusion: It is shown that the lengths of the hydrogen bonds in the complex of Trp with one water molecule for N+H… Ow and OwH… O are equal to 2.82 and 2.68 Å correspondingly, and the energy of the hydrogen bond – 5.65 kcal/mol; the length of the hydrogen bonds in the complex of Trp with four water molecules vary in the range from 2.77 to 2.92 Å. The forming of the hydrogen bonds between the ionic groups of Trp in the zwitterion form and water molecules leads to an increase in the frequency of the valence vibration of N+H bond at ~30–200 cm-1.
1. Ris A., Sternberg M. Ot kletok k atomam [From Cells to Atoms]. Moscow, Mir Publ., 1988. 144 p. (in Russian).
2. Musil Ja., Novakova O., Kunc K. Sovremennaja biohimija v shemah [Modern biochemistry in schemes]. Moscow, Mir Publ., 1981. 216 p. (in Russian).
3. Gurskaja G. V. Struktury aminokislot [Structure of amino acids]. Moscow, Nauka Publ., 1966. 160 p. (in Russian).
4. Cao X., Fischer G. Infrared Spectral, Structural, and Conformational Studies of Zwitterionic L-Tryptophan. J. Phys. Chem. A, 1999, vol. 103, pp. 9995–10003. DOI: https://doi.org/10.1021/jp992421c
5. Snoek L. C., Kroemer R. T., Simons J. P. A spectroscopic and computational exploration of tryptophan-water cluster structures in the gas phase. Phys. Chem. Chem. Phys., 2002, vol. 4, pp. 2130–2139. DOI: https://doi.org/10.1039/b200059h
6. Blom M. N., Compagnon I., Polfer N. C., von Helden G., Meijer G., Suhai S., Paizs B., Oomens J. Stepwise Solvation of Amino Acid: The Appearance of Zwitterionic Structures. J. Phys. Chem. A, 2007, vol. 111, pp. 7309–7316. DOI: https://doi.org/10.1021/jp070211r
7. Chuang C.-H., Chen Y.-T. Raman scattering of L-tryptophan enhanced by surface plasmon of silver nanoparticles: vibrational assignment and structural determination. J. Raman Spectrosc., 2008, vol. 40, pp. 150–156. DOI: https://doi.org/10.1002/jrs.2097
8. Kim S. K., Kim M. S., Suh S. W. Surface-enhanced Raman scattering (SERS) of aromatic amino acides and their glycyl dipeptides in silver sol. J. Raman Spectrosc., 1987, vol. 18, pp. 171–175. DOI: https://doi.org/10.1002/jrs.1250180305
9. Lee H. I., Suh S. W., Kim M. S. Raman spectroscopy of L-tryptophan-containing peptides adsorbed on a silver surface. J. Raman Spectrosc., 1988, vol. 19, pp. 491–495. DOI: https://doi.org/10.1002/jrs.1250190710
10. Wong M. W., Wiberg K. B., Frisch M. J. Hartree-Fock Second Derivatives and Electric Field Properties in a Solvent Reaction Field-theory and Application. J. Chem. Phys., 1991, vol. 95, pp. 8991–8998. DOI: https://doi.org/10.1063/1.461230
11. Jeffrey G. A., Saenger W. Hydrogen Bonding in Biological Structures. Berlin, Germany, Springer, 1991. 569 p.
12. Derbel N., Hernández B., Pfl üger F., Liquier J., Geinguenaud F., Jaidane N., Lakhdar Y. B., Ghomi M. Vibrational analysis of amino acids and short peptides in hydrated media. I. L-glycine and L-leucine. J. Phys. Chem. B, 2007, vol. 111, pp. 1470–1477. DOI: https://doi.org/10.1021/jp0633953
13. Ten G. N., Kadrov D. M., Baranov V. I. Hydrophobic radical infl uence on the structure and vibrational spectra of zwitterionic glycine and alanine in the condensed states. J. Appl. Spectr., 2014, vol. 81, no. 2, pp. 174–182. DOI: https://doi.org/10.1007/s10812-014-9906-9
14. Ten G. N., Jakovleva A. A., Baranov V.I. Theoretical study of hydrophobicity and hydrophilicity of indole, skatole, and ethanol. J. Struct. Chem., 2013, vol. 54, no. 6, pp.1018–1028. DOI: https://doi.org/10.1134/S0022476613060048
15. Ten G. N., Kadrov D. M., Baranov V. I. Model’nye potencialy mezhmolekuljarnogo vzaimodejstvija piridina, skatola i pirrola s vodoj [Model potentials of intermolecular interaction of pyridine, skatole and pyrrole with water]. Izv. Saratov Univ. (N. S.), Ser. Physics, 2014, vol. 14, iss.1, pp. 5–11 (in Russian).
16. Frisch M. J., Trucks G. W., Schlegel H. B., Scuseria G. E., Robb M. A., Cheeseman J. R., Scalmani G., Barone V., Mennucci B., Petersson G. A., Nakatsuji H., Caricato M., Li X., Hratchian H. P., Izmaylov A. F., Bloino J., Zheng G., Sonnenberg J. L., Hada M., Ehara M., Toyota K., Fukuda R., Hasegawa J., Ishida M., Nakajima T., Honda Y., Kitao O., Nakai H., Vreven T., Montgomery J., Peralta J. E., Ogliaro F., Bearpark M., Heyd J. J., Brothers E., Kudin K. N., Staroverov V. N., Kobayashi R., Normand J., Raghavachari K., Rendell A., Burant J. C., Iyengar S. S., Tomasi J., Cossi M., Rega N., Millam J. M., Klene M., Knox J. E., 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., Martin R. L., Morokuma K., Zakrzewski V. G., Voth G. A., Salvador P., Dannenberg J. J., Dapprich S., Daniels A. D., Farkas Ö., Foresman J. B., Ortiz J. V., Cioslowski J., Fox D. J. Gaussian 09. Gaussian Inc., Wallingford CT, 2009. 394 р.
17. Kon V. Electronic structure of matter – wave functions and density functionals. Usp. Fiz. Nauk (UFN), 2002, vol. 172, no. 3, pp. 336–348. DOI: https://doi.org/10.3367/UFNr.0172.200203e.0336
18. Pople J. Quantum chemical models. Usp. Fiz. Nauk (UFN), 2002, vol. 172, no. 3, pp. 349–356. DOI: https://doi.org/10.3367/UFNr.0172.200203f.0349
19. Ten G. N., Yakovleva A. A., Burova T. G., Berezin V. I., Baranov V. I. Modeling vibrational spectra of indole in water. J. Appl. Spectr., 2010, vol. 77, iss. 4, pp. 542–549. DOI: https://doi.org/10.1007/s10812-010-9360-2
20. Majoube M., Vergoten G. Vibrational spectra of indole and assignments on the basis of ab initio force fi elds. J. Raman Spectrosc., 1992, vol. 23, pp. 431–444. DOI: https://doi.org/10.1002/jrs.1250230803
21. Rosado M. T. S., Duarte M. L. R. S., Fausto R. Vibrational spectra (FI-IR, Raman and MI-IR) of α- and β-alanine. J. Mol. Struct., 1997, vol. 410–411, pp. 343–348. DOI: https://doi.org/10.1016/S0022-2860(96)09695-0
22. Butyrskaya E. V., Nechaeva L. S., SHaposhnik V. A., Selemenev V. F. Otnesenie polos v IK-spektrah vodnyh rastvorov alanina na osnove kvantovo-himicheskogo raschjota [Assignment of bands in IR-spectra of aqueous solutions alanine on basis of quantum-chemical calculation]. Proceedings of Voronezh State Univ., Series: Chemistry. Biology. Pharmacy, 2014, no. 2, pp. 9–16 (in Russian).
23. Cao X., Fischer G. New infrared spectra and the tautomeric studies of purine and alpha L-alanine with an innovative sampling technique. Spectrochim. Acta PT A-Mol. Biolog., 1999, vol. 55, pp. 2329–2342. DOI: https://doi.org/10.1016/S1386-1425(99)00133-X
