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Study of optical absorption cross-section spectra and high-order harmonic generation of thymine, thymine glycol, and thymine dimer molecules

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Abstract

The last two decades have witnessed advances in femtosecond and sub-femtosecond physics which have made accessible the study of phenomena with atomic and subatomic resolution. In particular, developments in laser physics and high-order harmonic generation have enabled tracking and investigating molecular reaction dynamics and the actual dynamics of electrons in chemical reactions, as well as investigating the structure of molecules. High-order harmonic generation has proved to be an ideal means for generating autosecond pulses. Time-dependent density functional theory provides an invaluable tool for the theoretical study of high-order harmonic generation. In this article, an exact study of the optical absorption cross-section spectra and high-order harmonic generation of thymine and its damage forms (thymine glycol and thymine dimer) has been performed using the time dependent density functional theory via the octopus code. The spectra have been characterized with the aim of distinguishing thymine from its damaged forms. The discrepancies in the optical absorption spectra of thymine and its damaged forms have been elucidated. The effects of laser pulse intensity and pulse profile on the high-order harmonic spectra of these molecules has been investigated, showing the possibility to distinguish between thymine and its damaged forms using high-order harmonic generation. In particular, it is demonstrated that high-order harmonic generation corresponding to a laser pulse with a cosinusoidal envelope and intensity \(3.47\times {10}^{14}\frac{\mathrm{W}}{{\mathrm{cm}}^{2}}\) clearly differentiates thymine from its damaged forms. This laser could potentially be applied to discern damage in more complex DNA material.

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References

  1. Zewail AH (2000) Femtochemistry: atomic-scale dynamics of the chemical bond using ultrafast lasers. Chem Int Ed 39:2586–2631. https://doi.org/10.1002/1521-3773(20000804)39:15%3C2586::AID-ANIE2586%3E3.0.CO;2-O

    Article  CAS  Google Scholar 

  2. Zewail AH (2000) Femtochemistry: atomic-scale dynamics of the chemical bond. J Phys Chem A 104:5660–5694. https://doi.org/10.1021/jp001460h

    Article  CAS  Google Scholar 

  3. Baker S, Robinson JS, Haworth CA, Teng H, Smith RA, Chirila CC, Lein M, Tisch JWG, Marangos JP (2006) Probing proton dynamics in molecules on an attosecond time scale. Science 312:424–427. https://doi.org/10.1126/science.1123904

    Article  CAS  Google Scholar 

  4. Worner HJ, Bertrand JB, Kartashov DV, Corkum PB, Villeneuve DM (2010) Following a chemical reaction using high-harmonic interferometry. Nature 466:604–607. https://doi.org/10.1038/nature09185

    Article  CAS  Google Scholar 

  5. Li W, Zhou W, Li X, Lock R, Patchkovskii S, Stolow A, Kapteyn HC, Murnane MM (2010) Time resolved dynamics in N2O4 probed using high harmonic generation. Science 322:1207–1211. https://doi.org/10.1126/science.1163077

    Article  CAS  Google Scholar 

  6. McPherson A, Gibson G, Jara H, Johann U, Luk TS, McIntyre IA, Boyer K, Rhodes CK (1987) Studies of multiphoton production of vacuum-ultraviolet radiation in the rare gases. J Opt Soc Am B 4:595–601. https://doi.org/10.1364/JOSAB.4.000595

    Article  CAS  Google Scholar 

  7. Corkum PB (1993) Plasma perspective on strong field multiphoton ionization. Phys Rev Lett 71:1994–1997. https://doi.org/10.1103/PhysRevLett.71.1994

    Article  CAS  Google Scholar 

  8. Krause JL, Schafer KJ, Kulander KC (1992) High-order harmonic generation from atoms and ions in the high intensity regime. Phys Rev Lett 68:3535–3538. https://doi.org/10.1103/PhysRevLett.68.3535

    Article  CAS  Google Scholar 

  9. Marangos JP (2016) Development of high harmonic generation spectroscopy of organic molecules and biomolecules. J Phys B At Mol Opt Phys 49:132001. https://doi.org/10.1088/0953-4075/49/13/132001

    Article  CAS  Google Scholar 

  10. Li J, Lu J, Chew A, Han S, Li J, Wu Y, Wang H, Ghimire S, Chang Z (2020) Attosecond science based on high harmonic generation from gases and solids. Nat Commun 11:2748. https://doi.org/10.1038/s41467-020-16480-6

    Article  CAS  Google Scholar 

  11. Varsano D, Di Felice R, Marques MAL, Rubio A (2006) A TDDFT study of the excited states of DNA bases and their assemblies. J Phys Chem B 110:7129–7138. https://doi.org/10.1021/jp056120g

    Article  CAS  Google Scholar 

  12. Nguyen TH, Hoang VH, Hoang-Do NT, Le VH (2012) Possibility of tracking imino–amino tautomerism of cytosine by ultra-short laser pulses using high-order harmonic generation. Comput Theor Chem 988:92–97. https://doi.org/10.1016/j.comptc.2012.02.037

    Article  CAS  Google Scholar 

  13. Hoang VH, Le CT, Nguyen NT, Le VH (2014) Possibility of distinguishing DNA bases and of tracking the keto–enol tautomerism by using high-order harmonic generation. Comput Theor Chem 1043:31–37. https://doi.org/10.1016/j.comptc.2014.05.011

    Article  CAS  Google Scholar 

  14. Kozak CR, Kistler KA, Lu Z, Matsika S (2010) Excited-state energies and electronic couplings of DNA base dimers. J Phys Chem B 114:1674–1683. https://doi.org/10.1021/jp9072697

    Article  CAS  Google Scholar 

  15. Kraemer KH (1997) Sunlight and skin cancer: another link revealed. Proc Natl Acad Sci USA 94:11–14. https://doi.org/10.1073/pnas.94.1.11

    Article  CAS  Google Scholar 

  16. Pryor WA (ed) (1976–1982) Free radicals in biology, Vols. 1–5. Academic press, New York

  17. Halliwell B, Gutteridge JM (1984) Oxygen toxicity, oxygen radicals, transition metals and disease. Biochem J 219:1–14. https://doi.org/10.1042/bj2190001

    Article  CAS  Google Scholar 

  18. Nygaard DF, Simic MG (eds) (1983) Radioprotectors and anticarcinogens. Academic press, New York

    Google Scholar 

  19. Ames BN (1983) Dietary carcinogens and anticarcinogens: oxygen radicals and degenerative diseases. Science 221:1256–1264. https://doi.org/10.1126/science.6351251

    Article  CAS  Google Scholar 

  20. Chance B, Sies H, Boveris A (1979) Hydroperoxide metabolism in mammalian organs. Phys Rev 59:527–605. https://doi.org/10.1152/physrev.1979.59.3.527

    Article  CAS  Google Scholar 

  21. Watson JD, Baker TA, Bell SP, Gann A, Levine M, Losick RM (2013) Molecular biology of the gene, 7th edn. Pearson, New York

    Google Scholar 

  22. Yatsui T, Yamaguchi M, Nobusada K (2017) Nano-scale chemical reactions based on non-uniform optical near-fields and their applications. Prog Quantum Electron 55:166–194. https://doi.org/10.1016/j.pquantelec.2017.06.001

    Article  Google Scholar 

  23. Tate N, Yatsui T (2019) Visible light-induced thymine dimerization based on large localized field gradient by non-uniform optical near-field. Sci Rep 9:18383. https://doi.org/10.1038/s41598-019-54661-6

    Article  CAS  Google Scholar 

  24. Shoseyov O, Levy I (ed) (2008) NanoBioTechnology: BioInspired devices and materials of the future. Humana Press, New Jersey

  25. Runge E, Gross EKU (1984) Density-functional theory for time-dependent systems. Phys Rev Lett 52:997. https://doi.org/10.1103/PhysRevLett.52.997

    Article  CAS  Google Scholar 

  26. Marques MAL, Maitra NT, Nogueira FMS, Gross EKU, Rubio A (eds) (2012) Fundamentals of time-dependent density functional theory (Lecture Notes in Physics, Vol 837), Springer, Berlin

  27. Marques MAL, Gross EKU (2004) Time-dependent density functional theory. Ann Rev Phys Chem 55:427–455. https://doi.org/10.1146/annurev.physchem.55.091602.094449

    Article  CAS  Google Scholar 

  28. Marques MAL, Castro A, Bertsch GF, Rubio A (2003) octopus: a first-principles tool for excited electron–ion dynamics. Comput Phys Commun 151:60. Octopus version 11.3 released 2021-11-25 Available at: https://octopus-code.org/wiki/Main_Page

  29. Onida G, Reining L, Rubio A (2002) Electronic excitations: density-functional versus many-body Green’s-function approaches. Rev Mod Phys 74:601. https://doi.org/10.1103/RevModPhys.74.601

    Article  CAS  Google Scholar 

  30. Costero A, Rubio A, Gross EKU (2015) Enhancing and controlling single-atom high-harmonic generation spe0ctra: a time-dependent density-functional scheme. Eur Phys J B 88:191. https://doi.org/10.1140/epjb/e2015-50889-7

    Article  CAS  Google Scholar 

  31. Sundaram B, Milonni PW (1990) High-order harmonic generation: Simplified model and relevance of single-atom theories to experiment. Phys Rev A 41:6571–6573. https://doi.org/10.1103/physreva.41.6571

    Article  CAS  Google Scholar 

  32. Schwerdtfeger P (2011) The pseudopotential approximation in electronic structure theory. Chemphyschem 12:3143–3155. https://doi.org/10.1002/cphc.201100387

    Article  CAS  Google Scholar 

  33. Pickett WE (1989) Pseudopotential methods in condensed matter applications. Comput Phys Rep 9:115. https://doi.org/10.1016/0167-7977(89)90002-6

    Article  Google Scholar 

  34. Troullier N, Martins JL (1991) Efficient pseudopotentials for plane-wave calculations. Phys Rev B 43:1993. https://doi.org/10.1103/PhysRevB.43.1993

    Article  CAS  Google Scholar 

  35. Kohn W, Sham LJ (1965) Self-consistent equations including exchange and correlation effects. Phys Rev 140:A1133. https://doi.org/10.1103/PhysRev.140.A1133

    Article  Google Scholar 

  36. Perdew JP, Zunger A (1981) Self-interaction correction to density-functional approximations for many-electron systems. Phys Rev B 23:5048. https://doi.org/10.1103/PhysRevB.23.5048

    Article  CAS  Google Scholar 

  37. Tsolakidis A, Kaxiras E (2005) A TDDFT study of the optical response of DNA bases, base pairs, and their tautomers in the gas phase. J Phys Chem A 109:2373–2380. https://doi.org/10.1021/jp044729w

    Article  CAS  Google Scholar 

  38. Shukla MK, Leszczynski J (2004) TDDFT investigation on nucleic acid bases: comparison with experiments and standard approach. J Comput Chem 25:768–778. https://doi.org/10.1002/jcc.20007

    Article  CAS  Google Scholar 

  39. Lorentzon J, Fulscher MP, Roos BO (1995) Theoretical study of the electronic spectra of uracil and thymine. J Am Chem Soc 117:9265–9273. https://doi.org/10.1021/ja00141a019

    Article  CAS  Google Scholar 

  40. Wallace SS (2002) Biological consequences of free radical-damaged DNA bases. Free Radic Biol Med 33:1–14. https://doi.org/10.1016/s0891-5849(02)00827-4

    Article  CAS  Google Scholar 

  41. Okahashi Y, Iwamoto T, Suzuki N, Shibutani S, Sugiura S, Itoh S, Nishiwaki T, Ueno S, Mori T (2010) Quantitative detection of 4-hydroxyequilenin-DNA adducts in mammalian cells using an immunoassay with a novel monoclonal antibody. Nucleic Acids Res 38:E133. https://doi.org/10.1093/nar/gkq233

    Article  CAS  Google Scholar 

  42. Barnes JL, Zubair M, John K, Poirier MC, Martin FL (2018) Carcinogens and DNA damage. Biochem Soc Trans 46:1213–1224. https://doi.org/10.1042/BST20180519

    Article  CAS  Google Scholar 

  43. Kumar A, Sevilla MD (2019) Excited states of one-electron oxidized guanine-cytosine base pair radicals: a time dependent density functional theory study. J Phys Chem A 123:3098–3108. https://doi.org/10.1021/acs.jpca.9b00906

    Article  CAS  Google Scholar 

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Author information

Authors and Affiliations

  1. Faculty of Chemistry, Islamic Azad University Tehran North Branch, Tehran, Iran

    Fatemeh Mohammadtabar & Reza Rajaie Khorasani

  2. Department of Chemistry, Yazd University, P.O. Box 89195-741, Yazd, Iran

    Hossein Mohammadi-Manesh

  3. Department of Physics, Payame Noor University, PO BOX 119395-3697, Tehran, Iran

    Ali Kazempour

  4. Nano Structured Coatings Institute of Yazd Payame Noor University, Yazd, PO Code: 89431-74559, Iran

    Ali Kazempour

Authors
  1. Fatemeh Mohammadtabar
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  4. Ali Kazempour
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Contributions

F. Mohammatabar had the idea, performed the computations, interpreted the results, and prepared the first draft of the manuscript. R. Rajaie Khorasani contributed to interpretation of the results, edited the manuscript, and wrote the final draft and supervised. H. Mohamadi-Manesh contributed to interpretation of the results and co-supervised. A. Kazempour contributed to interpretation of the results. All the authors have contributed to the study conception. All authors have read and approved the manuscript.

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Correspondence to Reza Rajaie Khorasani.

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Mohammadtabar, F., Rajaie Khorasani, R., Mohammadi-Manesh, H. et al. Study of optical absorption cross-section spectra and high-order harmonic generation of thymine, thymine glycol, and thymine dimer molecules. J Mol Model 28, 402 (2022). https://doi.org/10.1007/s00894-022-05388-1

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