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Theoretical studies of the excited states of p-cyanophenylalanine and comparisons with the natural amino acids phenylalanine and tyrosine


The absorption and fluorescence properties of the non-natural amino acid p-cyanophenylalanine (PheCN) were examined using high-level ab initio methods and were compared to those of natural amino acids phenylalanine and tyrosine. Single-reference and multireference methods were surveyed for their accuracy in predicting the excited state energies and transition dipole moments of the chromophores and the corresponding amino acids. The excitation energies were found to be very similar between the chromophores and the various conformers of the amino acids for all three amino acids studied here, but the transition dipole moments and consequently the radiative lifetimes were very sensitive to conformation. In agreement with experimental data, PheCN is predicted to have increased fluorescence intensity compared to phenylalanine and the amino acid group is partly responsible for this effect.

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  1. 1.

    Abo-Riziq A, Grace L, Crews B, Callahan MP, van Mourik T, de Vries MS (2011) Conformational structure of tyrosine, tyrosyl-glycine, and 2 tyrosyl-glycyl-glycine by double resonance spectroscopy. J. Phys. Chem. A 115:6077–6087

    CAS  Article  Google Scholar 

  2. 2.

    Berkeley L, Field M (1997) A diagnostic for the applicability of the CIS and CIS(D) excitation energy methods. Chem. Phys. Lett. 279:151–157

    Article  Google Scholar 

  3. 3.

    Bode BM, Gordon MS (1998) MacMolPlt: a graphical user interface for GAMESS. J. Mol. Graphics Modell. 16(133—-8):164

    Google Scholar 

  4. 4.

    Chen RF (1967) Fluorescence Quantum Yields of Tryptophan and Tyrosine. Anal. Lett. 1:35–42

    CAS  Article  Google Scholar 

  5. 5.

    Chen Y, Berkley MD (1998) Toward understanding tryptophan fluorescence in proteins. Biochemistry 37:9976–82

    CAS  Article  Google Scholar 

  6. 6.

    Chipman DM (2000) Reaction field treatment of charge penetration. J. Chem. Phys. 112:5558

    CAS  Article  Google Scholar 

  7. 7.

    Cohen R, Brauer B, Nir E, Grace L, de Vries MS (2000) Resonance-enhanced multiphoton ionization spectroscopy of dipeptides. J. Phys. Chem. A 104:6351–6355

    CAS  Article  Google Scholar 

  8. 8.

    Cossi M, Barone V, Cammi R, Tomasi J (1996) Ab initio study of solvated molecules: a new implementation of the polarizable continuum model. Chem. Phys. Lett. 255:327–335

    CAS  Article  Google Scholar 

  9. 9.

    Dewar MJS, Zoebisch EG, Healy EF, Stewart JJP (1985) AM1: A New General Purpose Quantum Mechanical Molecular Model. J. Am. Chem. Soc. 107:3902–3909

    CAS  Article  Google Scholar 

  10. 10.

    Fleming I (1976) Frontier Orbitals and Organic Chemical Reactions. John Wiley & Sons Ltd, New York

    Google Scholar 

  11. 11.

    Foreman JB, Frisch MJ (1992) Toward a Systematic Molecular Orbital Theory for Excited States. J. Phys. Chem. 96:135–149

    Article  Google Scholar 

  12. 12.

    Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Montgomery Jr. JA, Vreven T, Kudin KN, Burant JC, Millam JM, Iyengar SS, Tomasi J, Barone V, Mennucci B, Cossi M, Scalmani G, Rega N, Peter GA, Pople JA (2003) Gaussian 03

  13. 13.

    Getahun Z, Huang CY, Wang T, De León B, DeGrado WF, Gai F (2003) Using nitrile-derivatized amino acids as infrared probes of local environment. J. Am. Chem. Soc. 125:405–11

    CAS  Article  Google Scholar 

  14. 14.

    Hashimoto T, Takasu Y, Yamada Y, Ebata T (2006) Anomalous conformer dependent S1 lifetime of l-phenylalanine. Chem. Phys. Lett. 421:227–231

    CAS  Article  Google Scholar 

  15. 15.

    Huang CY, Wang T, Gai F (2003) Temperature dependence of the CN stretching vibration of a nitrile-derivatized phenylalanine in water. Chem. Phys. Lett. 371:731–738

    CAS  Article  Google Scholar 

  16. 16.

    Huang Z, Yu W, Lin Z (2006) Exploration of the full conformational landscapes of gaseous aromatic amino acid phenylalanine: An ab initio study. Journal of Molecular Structure: THEOCHEM 758:195–202

    CAS  Article  Google Scholar 

  17. 17.

    Inokuchi Y, Kobayashi Y, Ito T, Ebata T (2007) Conformation of L-tyrosine studied by fluorescence-detected UV-UV and IR-UV double-resonance spectroscopy. J. Phys. Chem. A 111:3209–3215

    CAS  Article  Google Scholar 

  18. 18.

    Kawashima Y, Nakano H, Jung J, Ten-no S (2011) A combined quantum mechanical and molecular mechanical method using modified generalized hybrid orbitals: implementation for electronic excited states. Phys. Chem. Chem. Phys. 13:11,731–11,738

    CAS  Article  Google Scholar 

  19. 19.

    Krylov AI (2008) Equation-of-Motion Coupled-Cluster Methods for Open-Shell and Electronically Excited Species: The Hitchhiker’s Guide to Fock Space. Annu. Rev. Phys. Chem. 59:433–462

    CAS  Article  Google Scholar 

  20. 20.

    Kushwaha P, Mishra P (2000) Electronic spectra, excited-state geometries and molecular electrostatic potentials of aromatic amino acids. J. Photochem. Photobiol., A 137:79–86

    CAS  Article  Google Scholar 

  21. 21.

    Laikov D Priroda: An Electronic Structure Code

  22. 22.

    Laikov D, Matsika S (2007) Inclusion of second-order correlation effects for the ground and singly-excited states suitable for the study of conical intersections: The CIS(2) model. Chem. Phys. Lett. 448:132–137

    CAS  Article  Google Scholar 

  23. 23.

    Lakowicz JR (2006) Principles of Fluorescence Spectroscopy, 6th edn. Springer, Baltimore, USA

    Book  Google Scholar 

  24. 24.

    Lee KT, Sung J, Lee KJ, Park YD, Kim SK (2002) Conformation-dependent ionization energies of L-phenylalanine. Angew. Chem. 41:4114–7

    CAS  Article  Google Scholar 

  25. 25.

    Link A, Mock M, Tirrell D (2003) Non-canonical amino acids in protein engineering. Current Opinion in Biotechnology 14:603–609

    CAS  Article  Google Scholar 

  26. 26.

    Marazzi M, Sancho U, Castano O, Domcke W (2010) Manuel Frutos, L.: Photoinduced Proton Transfer as a Possible Mechanism for Highly Efficient Excited-State Deactivation in Proteins. J. Phys. Chem. Lett. 1(1):425–428

    CAS  Article  Google Scholar 

  27. 27.

    Marek P, Gupta R, Raleigh DP (2008) The fluorescent amino acid p-cyanophenylalanine provides an intrinsic probe of amyloid formation. ChemBioChem 9:1372–1374

    CAS  Article  Google Scholar 

  28. 28.

    Martinez SJ, Alfano JC, Levy DH (1992) The Electronic Spectroscopy of the Amino Acids Tyrosine and Phenylalanine in a Supersonic Jet. J. Mol. Spectrosc. 430:421–430

    Article  Google Scholar 

  29. 29.

    Matsika S, Krause P (2011) Nonadiabatic Events and Conical Intersections. Annu. Rev. Phys. Chem. 62:621–643

    CAS  Article  Google Scholar 

  30. 30.

    Nakano H (1993) Quasidegenerate perturbation theory with multiconfigurational self-consistent-field reference functions. J. Chem. Phys. 99:7983. doi:10.1063/1.465674

    CAS  Article  Google Scholar 

  31. 31.

    Rogers D, Hirst J (2003) Ab initio study of aromatic side chains of amino acids in gas phase and solution. J. Phys. Chem. A 107

  32. 32.

    Rogers JMG, Lippert LG, Gai F (2010) Non-natural amino acid fluorophores for one- and two-step fluorescence resonance energy transfer applications. Anal. Biochem. 399:182–9

    CAS  Article  Google Scholar 

  33. 33.

    Royer CA (2006) Probing protein folding and conformational transitions with fluorescence. Chem. Rev. 106:1769–84

    CAS  Article  Google Scholar 

  34. 34.

    Schmidt MW, Baldridge KK, Boatz JA, Elbert ST, Gordon MS, Jensen JH, Koseki S, Matsunaga N, Nguyen KA, Shyjun SU, Dupuis M, Montgomery JA (1993) General Atomic and Molecular Electronic Structure System. J. Comput. Chem. 14:1347–1363

    CAS  Article  Google Scholar 

  35. 35.

    Serrano AL, Troxler T, Tucker MJ, Gai F (2010) Photophysics of a Fluorescent Non-natural Amino Acid: p-Cyanophenylalanine. Chem. Phys. Lett. 487:303–306

    CAS  Article  Google Scholar 

  36. 36.

    Serrano AL, Waegele MM, Gai F (2012) Spectroscopic studies of protein folding: linear and nonlinear methods. Protein Sci. 21:157–170

    CAS  Article  Google Scholar 

  37. 37.

    Shao Y, Molnar LF, Jung Y, Kussmann J, Ochsenfeld C, Brown ST, Gilbert ATB, Slipchenko LV, Levchenko SV, O’Neill DP (2006) DiStasio, R.a., Lochan, R.C., Wang, T., Beran, G.J.O., Besley, N.a., Herbert, J.M., Lin, C.Y., Van Voorhis, T., Chien, S.H., Sodt, A., Steele, R.P., Rassolov, V.a., Maslen, P.E., Korambath, P.P., Adamson, R.D., Austin, B., Baker, J., Byrd, E.F.C., Dachsel, H., Doerksen, R.J., Dreuw, A., Dunietz, B.D., Dutoi, A.D., FOPTurlani, T.R., Gwaltney, S.R., Heyden, A., Hirata, S., Hsu, C.P., Kedziora, G., Khalliulin, R.Z., Klunzinger, P., Lee, A.M., Lee, M.S., Liang, W., Lotan, I., Nair, N., Peters, B., Proynov, E.I., Pieniazek, P.a., Rhee, Y.M., Ritchie, J., Rosta, E., Sherrill, C.D., Simmonett, A.C., Subotnik, J.E., Woodcock, H.L., Zhang, W., Bell, A.T., Chakraborty, A.K., Chipman, D.M., Keil, F.J., Warshel, A., Hehre, W.J., Schaefer, H.F., Kong, J., Krylov, A.I., Gill, P.M.W., Head-Gordon, M.: Advances in methods and algorithms in a modern quantum chemistry program package. Phys. Chem. Chem. Phys. 8:3172–91

    CAS  Article  Google Scholar 

  38. 38.

    Shemesh D, Domcke W (2011) Effect of the Chirality of Residues and gamma-Turns on the Electronic Excitation Spectra, Excited-State Reaction Paths and Conical Intersections of Capped Phenylalanine-Alanine Dipeptides. ChemPhysChem 12:1833–1840

    CAS  Article  Google Scholar 

  39. 39.

    Shimozono Y, Yamada K (2013) Ishiuchi, S.i., Tsukiyama, K., Fujii, M.: Revised conformational assignments and conformational evolution of tyrosine by laser desorption supersonic jet laser spectroscopy. Phys. Chem. Chem. Phys. 15(14):5163–5175

    CAS  Article  Google Scholar 

  40. 40.

    Sinkeldam RW, Greco NJ, Tor Y (2010) Fluorescent analogs of biomolecular building blocks: design, properties, and applications. Chem. Rev. 110:2579–619

    CAS  Article  Google Scholar 

  41. 41.

    Snoek L, Robertson E, Kroemer R, Simons J (2000) Conformational landscapes in amino acids: infrared and ultraviolet ion-dip spectroscopy of phenylalanine in the gas phase. Chem. Phys. Lett. 321:49

    CAS  Article  Google Scholar 

  42. 42.

    Sobolewski AL, Domcke W, Dedonder-Lardeux C, Jouvet C (2002) Excited-state hydrogen detachment and hydrogen transfer driven by repulsive \(^1\pi \sigma ^*\) states: a new paradigm for nonradiative decay in aromatic biomolecules. Phys. Chem. Chem. Phys. 4:1093–1100

    CAS  Article  Google Scholar 

  43. 43.

    Sobolewski AL, Shemesh D, Domcke W (2009) Computational Studies of the Photophysics of Neutral and Zwitterionic Amino Acids in an Aqueous Environment: Tyrosine-(H2O)(2) and Tryptophan-(H2O)(2) Clusters. J. Phys. Chem. A 113(3):542–550

    CAS  Article  Google Scholar 

  44. 44.

    Stanton JF, Bartlett RJ (1993) The equation of motion coupled-cluster method. A systematic biorthogonal approach to molecular excitation energies, transition probabilities, and excited state properties. J. Chem. Phys. 98:7029

    CAS  Article  Google Scholar 

  45. 45.

    Taskent-Sezgin H, Chung J, Patsalo V, Miyake-Stoner SJ, Miller AM, Brewer SH (2009) Mehl, R.a., Green, D.F., Raleigh, D.P., Carrico, I.: Interpretation of p-cyanophenylalanine fluorescence in proteins in terms of solvent exposure and contribution of side-chain quenchers: a combined fluorescence, IR and molecular dynamics study. Biochemistry 48:9040–9046

    CAS  Article  Google Scholar 

  46. 46.

    Taskent-Sezgin H, Marek P, Thomas R, Goldberg D, Chung J, Carrico I, Raleigh DP (2010) Modulation of p-cyanophenylalanine fluorescence by amino acid side chains and rational design of fluorescence probes of alpha-helix formation. Biochemistry 49:6290–6295

    CAS  Article  Google Scholar 

  47. 47.

    Tucker MJ, Oyola R (2006) A Novel Fluorescent Probe for Protein Binding and Folding Studies: p-Cyano-Phenylalanine. Biopolymers 83:571–576

    CAS  Article  Google Scholar 

  48. 48.

    Twine SM, Szabo AG (2003) Fluorescent amino acid analogs. Methods Enzymol. 360:104–127

    CAS  Article  Google Scholar 

  49. 49.

    Wavefunction (2010) spartan 10; wavefunction, inc

  50. 50.

    Zhang M, Huang Z, Lin Z (2005) Systematic ab initio studies of the conformers and conformational distribution of gas-phase tyrosine. J. Chem. Phys. 122:134, 313

    Article  Google Scholar 

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Support by the National Science Foundation under grant CHE-1213614 is acknowledged. SM thanks the Alexander von Humboldt Foundation for support during a visit to Germany where part of this paper was written. SLM thanks the Undergraduate Research Program of the College of Science and Technology at Temple University for partial support.

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Correspondence to Spiridoula Matsika.

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Dedicated to the memory of Professor Isaiah Shavitt and published as part of the special collection of articles celebrating his many contributions.

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Meloni, S.L., Matsika, S. Theoretical studies of the excited states of p-cyanophenylalanine and comparisons with the natural amino acids phenylalanine and tyrosine. Theor Chem Acc 133, 1497 (2014).

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  • Excited states
  • Fluorescence
  • Amino acids
  • Cyanophenylalanine
  • Tyrosine
  • Phenylalanine
  • Radiative lifetime