Abstract
Using Gaussian and Orca, UV and fluorescence spectra of three amino acids (Tyr: Tyrosine, Trp: Tryptophan, Phe: Phenylalanine) were calculated by different functionals (B3LYP, BP86, wB97X). The spectra calculated by BP86 are consistent with the experiments. UV spectra peak of Tyr is 255 nm (Exp. 275 nm, Δλ = 20 nm), Trp is 279 nm (Exp. 277 nm, Δλ = 2 nm), and Phe is 275 nm (Exp. 257 nm, Δλ = 18 nm). Fluorescence spectra peak of Trp is 341 nm (Exp. 350 nm, Δλ = 9 nm), Tyr is 295 nm (Exp. 306 nm, Δλ = 11 nm), and Phe is 285 nm (Exp. 302 nm, Δλ = 17 nm). Moreover, a theoretical model for calculating the excited states of biomolecules is established. Compared with Gaussian’s results, Orca is more quickly and effectively for calculating excited state spectra with the same accuracy.
Similar content being viewed by others
References
Cohen AJ, Mori-Sánchez P, Yang W (2011) Challenges for density functional theory. Chem Rev 112(1):289–320. https://doi.org/10.1021/cr200107z
Runge E, Gross EKU (1984) Density-functional theory for time-dependent systems. Phys Rev Lett 52(12):997–1000. https://doi.org/10.1103/PhysRevLett.52.997
Yang H, Watts HD, Gibilterra V, Weiss TB, Petridis L, Cosgrove DJ, Kubicki JD (2019) Quantum calculations on plant cell wall component interactions. Interdiscip Sci, Comput Life Sci 11(3):485–495. https://doi.org/10.1007/s12539-018-0293-4
Grimme S, Bannwarth C (2016) Ultra-fast computation of electronic spectra for large systems by tight-binding based simplified Tamm-Dancoff approximation (sTDA-xTB). J Chem Phys 145(5):054103. https://doi.org/10.1063/1.4959605
Becke AD (1992) Density-functional thermochemistry. II. The effect of the Perdew-Wang generalized-gradient correlation correction. J Chem Phys 97(12):9173–9177. https://doi.org/10.1063/1.463343
Adamo C, Barone V (1999) Toward reliable density functional methods without adjustable parameters: the PBE0 model. J Chem Phys 110(13):6158–6170. https://doi.org/10.1063/1.478522
Ernzerhof M, Scuseria GE (1999) Assessment of the Perdew–Burke–Ernzerhof exchange-correlation functional. J Chem Phys 110(11):5029–5036. https://doi.org/10.1063/1.478401
Zhao Y, Truhlar DG (2007) The M06 suite of density functionals for main group thermochemistry, thermochemical kinetics, noncovalent interactions, excited states, and transition elements: two new functionals and systematic testing of four M06-class functionals and 12 other functionals. Theoret Chem Acc 120(1–3):215–241. https://doi.org/10.1007/s00214-007-0310-x
Dierksen M, Grimme S (2004) The vibronic structure of electronic absorption spectra of large molecules: a time-dependent density functional study on the influence of “Exact” Hartree-Fock exchange. J Phys Chem A 108(46):10225–10237. https://doi.org/10.1021/jp047289h
Teale FWJ, Weder G (1957) Ultraviolet fluorescence of the aromatic amino acids. Biochem J 65(3):476–482. https://doi.org/10.1042/bj0650476
Su Y, Liao XW, Li SW, Liang XQ, Zou Q, Li H (2003) Quantum chemistry study on fluorescence spectra of Three kinds of amino acids. Spectrosc Spectral Anal 23(1):137–139 (in Chinese)
Ghisaidoobe AB, Chung SJ (2014) Intrinsic tryptophan fluorescence in the detection and analysis of proteins: a focus on Forster resonance energy transfer techniques. Int J Mol Sci 15(12):22518–22538. https://doi.org/10.3390/ijms151222518
Franck J, Dymond EG (1926) Elementary processes of photochemical reactions. Trans Faraday Soc 21(February):536. https://doi.org/10.1039/tf9262100536
Adamo C, Jacquemin D (2013) The calculations of excited-state properties with time-dependent density functional theory. Chem Soc Rev 42(3):845–856. https://doi.org/10.1039/c2cs35394f
Hirata S, Head-Gordon M (1999) Time-dependent density functional theory within the Tamm-Dancoff approximation. Chem Phys Lett 314(3–4):291–299. https://doi.org/10.1016/S0009-2614(99)01149-5
Dreuw A, Head-Gordon M (2005) Single-reference ab initio methods for the calculation of excited states of large molecules. Chem Rev 105(11):4009–4037. https://doi.org/10.1021/cr0505627
de Souza B, Neese F, Izsak R (2018) On the theoretical prediction of fluorescence rates from first principles using the path integral approach. J Chem Phys 148(3):034104. https://doi.org/10.1063/1.5010895
Frisch M, Trucks G, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Scalmani G, Barone V, Mennucci B, Petersson G (2009) gaussian 09, Revision d. 01, Gaussian. Inc, Wallingford CT 201
Neese F (2011) The ORCA program system. WIREs Comput Mol Sci 2(1):73–78. https://doi.org/10.1002/wcms.81
Neese F (2017) Software update: the ORCA program system, version 40. WIREs Comput Mol Sci. https://doi.org/10.1002/wcms.1327
Becke AD (1988) Density-functional exchange-energy approximation with correct asymptotic behavior. Phys Rev A 38(6):3098–3100. https://doi.org/10.1103/physreva.38.3098
Perdew JP (1986) Density-functional approximation for the correlation energy of the inhomogeneous electron gas. Phys Rev B 33(12):8822–8824. https://doi.org/10.1103/PhysRevB.33.8822
Chai JD, Head-Gordon M (2008) Long-range corrected hybrid density functionals with damped atom-atom dispersion corrections. Phys Chem ChemPhys 10(44):6615–6620. https://doi.org/10.1039/b810189b
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 ChemPhys 7(18):3297–3305. https://doi.org/10.1039/b508541a
Weigend F (2006) Accurate Coulomb-fitting basis sets for H to Rn. Phys Chem ChemPhys 8(9):1057–1065. https://doi.org/10.1039/b515623h
Hellweg A, Hättig C, Höfener S, Klopper W (2007) Optimized accurate auxiliary basis sets for RI-MP2 and RI-CC2 calculations for the atoms Rb to Rn. Theoret Chem Acc 117(4):587–597. https://doi.org/10.1007/s00214-007-0250-5
Dunlap BI, Connolly JWD, Sabin JR (1979) On some approximations in applications ofXα theory. J Chem Phys 71(8):3396–3402. https://doi.org/10.1063/1.438728
Vahtras O, Almlöf J, Feyereisen M (1993) Integral approximations for LCAO-SCF calculations. Chem Phys Lett 213(5–6):514–518. https://doi.org/10.1016/0009-2614(93)89151-7
Eichkorn K, Weigend F, Treutler O, Ahlrichs R (1997) Auxiliary basis sets for main row atoms and transition metals and their use to approximate Coulomb potentials. Theoret Chem Acc 97(1–4):119–124. https://doi.org/10.1007/s002140050244
Lu T, Chen F (2012) Multiwfn: a multifunctional wavefunctionanalyzer. J Comput Chem 33(5):580–592. https://doi.org/10.1002/jcc.22885
Author information
Authors and Affiliations
Corresponding authors
Ethics declarations
Conflict of interest
The authors declare no conflicts of interest.
Rights and permissions
About this article
Cite this article
Liu, Y., Xu, J., Han, L. et al. Theoretical Research on Excited States: Ultraviolet and Fluorescence Spectra of Aromatic Amino Acids. Interdiscip Sci Comput Life Sci 12, 530–536 (2020). https://doi.org/10.1007/s12539-020-00395-3
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s12539-020-00395-3