Advertisement

OH oxidation of methionine in the presence of discrete water molecules: DFT, QTAIM and valence bond analyses

  • Jacqueline BergèsEmail author
  • Dominik Domin
  • Julien PilméEmail author
  • Benoît Braïda
  • Chantal Houée-Levin
Original Research
  • 22 Downloads

Abstract

The first steps of the oxidation process of amino acid methionine (Met, CAS 63-68-3) by OH radicals, leading to Met-OH adduct and then to Met radical cation, were investigated theoretically over the last few years considering the aqueous environment as a continuum. In this work, following the same procedure that we used for the oxidation of dimethyl sulfide as reported by Domin et al. (J Phys Chem B, 121:9321), discrete water molecules, as well as relative positions, of the OH radical to Met were taken from molecular dynamics calculations. The presence of water molecules strongly modifies the relative energies of Met-OH adducts and cations when water is properly modeled. Depending on the terminal functional groups and on the position of the OH radical, several stable structures were found; however, the most stable radical is the N-centered or the S∴N radical cation. QTAIM analysis and valence bond (VB) treatment allowed for the characterization of the 2c∴3e nature of S∴N and S∴OH bonds. VB analysis estimated the probability of the heterolytic rupture of the OH adduct that is modified by the presence of water molecules.

Graphical abstract

Oxidation of amino acid methionine by OH radicals in the presence of discrete water molecules.

Keywords

Oxidation of methionine by OH radicals Explicit water molecules DFT calculation QTAIM VB analysis Two center-three electron bonded radical 

Notes

Compliance with ethical standards

Conflict of interest

The authors declare that they have no competing interests.

Supplementary material

11224_2019_1438_MOESM1_ESM.docx (39 kb)
Table S1 (DOCX 38 kb)

References

  1. 1.
    Asmus KD, Janata E (1982). In: Baxendale JH, Busi F, Reidel D (ed) The study of fast processes and transient species by Electron Pulse Radiolysis Publishing Company Dordrecht, pp 115-128Google Scholar
  2. 2.
    Asmus KD (2001) In: Jonah CD, BMSR R (eds) Radiation chemsitry: present status and future trends. Elsevier, New York, pp 341–393CrossRefGoogle Scholar
  3. 3.
    Bobrowski K, Hug GL, Pogocki D, Marciniak B, Schoneich C (2007). J Phys Chem B111:9608CrossRefGoogle Scholar
  4. 4.
    Bobrowski K, Houée Levin C, Marciniak B (2008). Chimia 62:728CrossRefGoogle Scholar
  5. 5.
    Ignasiak M, Marciniak B, Houée Levin C (2014). Isr J Chem 54:225CrossRefGoogle Scholar
  6. 6.
    Ignasiak M, Scuderi D, de Oliveira P, Pedzinski T, Rayah Y, Houée Levin C (2011). Chem Phys Lett 502:29CrossRefGoogle Scholar
  7. 7.
    Ignasiak M, de Oliveira P, Houée Levin C, Scuderi D (2013). Chem Phys Lett 590:35CrossRefGoogle Scholar
  8. 8.
    Ignasiak M, Pedzinski T, Rusconi F, Filipiak P, Bobrowski K, Houée-Levin C, Marciniak B (2014). J Phys Chem B 118:8549CrossRefGoogle Scholar
  9. 9.
    Buxton G, Greenstock CL, Helman WP, Ross AB (1988). J Phys Chem 17:513Google Scholar
  10. 10.
    Archirel P, Bergès J, Houée-Levin C (2016). J Phys Chem B 120:9875CrossRefGoogle Scholar
  11. 11.
    Bergès J, de Oliveira P, Fourré I, Houée-Levin C (2012). J Phys Chem B 116:9352CrossRefGoogle Scholar
  12. 12.
    Bergès J, Kamar A, de Oliveira P, Pilmé J, Luppi E, Houée-Levin C (2015). J Phys Chem B 119:6885CrossRefGoogle Scholar
  13. 13.
    Fourré I, Bergès J, Houée-Levin C (2010). J Phys Chem A 114:7359CrossRefGoogle Scholar
  14. 14.
    Fourré I, Bergès J, Braïda B, Houée Levin C (2008). Chem Phys Lett 467:164CrossRefGoogle Scholar
  15. 15.
    Scuderi D, Bergès J, de Oliveira P, Houée-Levin C (2016). Radiat Phys Chem 128:103CrossRefGoogle Scholar
  16. 16.
    Scuderi D, Ignasiak M, Serfaty X, de Oliveira P, Houée Levin C (2015). PhysChem Chem Phys 17:25998Google Scholar
  17. 17.
    Perdivara I, Deterding LJ, Przybylski M, Tomer KB (2010). J Amer Soc Mass Spect 21:1114CrossRefGoogle Scholar
  18. 18.
    Pilmé J, Luppi E, Bergès J, Houée-Levin C, de la Lande A (2014). J Mol Model 20:2368CrossRefGoogle Scholar
  19. 19.
    Xipsiti C, Nicolaides AV (2013). Comput Theor Chem 1009:24CrossRefGoogle Scholar
  20. 20.
    Uranga J, Mujika JI, Matxain JM (2015). J Phys Chem B 119:15430CrossRefGoogle Scholar
  21. 21.
    Chu JW, Brooks BR, Trout BLJ (2004). J Am Chem Soc 126:16601CrossRefGoogle Scholar
  22. 22.
    Marino T, Soriano-Correa C, Russo N (2012). J Phys Chem B 116:5349CrossRefGoogle Scholar
  23. 23.
    Domin D, Braïda B, Bergès J (2017). J Phys Chem B 121:9321CrossRefGoogle Scholar
  24. 24.
    Shaik S, Braïda B, Wu W, Hiberty PC (2016). In: Mingos, DMP (ed) Chemical bond II: 100 years old and getting stronger, Springer: Switzerland 170, pp 169Google Scholar
  25. 25.
    Danovich D, Foroutan-Nejad C, Hiberty PC, Shaik S (2018). J Phys Chem A 122:1873CrossRefGoogle Scholar
  26. 26.
    Jorgensen WL, Chandrasekhar J, Madura JD (1983). J Chem Phys 79:926CrossRefGoogle Scholar
  27. 27.
    MacKerell Jr AD, Bashford D, Bellott M et al (1998). J Phys Chem B 102:3586CrossRefGoogle Scholar
  28. 28.
    Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Scalmani G, Barone V, Mennucci B, Petersson GA, Nakatsuji H, Caricato M, Li X, Hratchian HP, IzmaylovAF, Bloino J, Zheng G, Sonnenberg JL, Hada M, Ehara M,Toyota K, Fukuda R, Hasegawa J, Ishida M, Nakajima T, HondaY, Kitao O, Nakai H, Vreven T, Montgomery JA Jr, Peralta JE,Ogliaro F, Bearpark M, Heyd JJ, Brothers E, Kudin KN, Staroverov VN, Kobayashi R, Normand J, Raghavachari K,Rendell A, Burant JC, Iyengar SS, Tomasi J, Cossi M, Rega N,Millam JM, Klene M, Knox JE, Cross JB, Bakken V, Adamo C,Jaramillo J, Gomperts R, Stratmann RE, Yazyev O, Austin AJ,Cammi R, Pomelli C, Ochterski JW, Martin RL, Morokuma K, Zakrzewski VG, Voth GA, Salvador P, Dannenberg JJ, Dapprich S, Daniels AD, Farkas Ö, Foresman JB, Ortiz JV, Cioslowski J, Fox (2009) Gaussian 09. vol D.01. Wallingford CTGoogle Scholar
  29. 29.
    Bader RFW (1991). Chem Rev 91:893CrossRefGoogle Scholar
  30. 30.
    Bader RFW, Stephens ME (1975). J Amer Chem Soc 97:7391CrossRefGoogle Scholar
  31. 31.
    Fradera X, Austen MA, Bader RFW (1998). J Phys Chem A 103:304CrossRefGoogle Scholar
  32. 32.
    Braïda B, Hiberty PC, Savin A (1998). J Phys Chem A 102:7872CrossRefGoogle Scholar
  33. 33.
    Braïda B, Hiberty PC (2000). J Phys Chem A 104:4618CrossRefGoogle Scholar
  34. 34.
    Braïda B, Lauvergnat D, Hiberty PC (2001). J Chem Phys 115:90CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Laboratoire de Chimie ThéoriqueSorbonne UniversitéParisFrance
  2. 2.Faculty of Biotechnology, Chemistry and Environmental Engineering, Phenikaa Institute for Advanced Study (PIAS)Phenikaa UniversityHanoiVietnam
  3. 3.Laboratoire de Chimie PhysiqueUniversité Paris Sud, Université Paris SaclayOrsayFrance

Personalised recommendations