Advertisement

Density Functional Study of Manganese Complexes: Protonation Effects on Geometry and Magnetism

  • S. Yamanaka
  • K. Kanda
  • T. Saito
  • Y. Kitagawa
  • T. Kawakami
  • M. Ehara
  • M. Okumura
  • H. Nakamura
  • K. Yamaguchi
Conference paper
Part of the Progress in Theoretical Chemistry and Physics book series (PTCP, volume 26)

Abstract

Protonation processes are ubiquitous in various biochemical reactions such as the water-oxidizing reaction in photosystem II and detoxications of active oxygen species in Mn catalase and Mn superoxide dismutase. In order to investigate them, experiments to probe protons often need supplementary computational results to support the experimental spectra, for which reliable DFT methods are required for description of protonation processes. In this study, we investigated manganese complexes, [Mn(IV)2O2Hn(salpn)2] n+ (n = 0,1,2), of which geometries and magnetism show systematic changes due to protonations to bridged oxygen anions. We examined the performance of B3LYP, B3LYP-D, BP86, BP86-D, and LC-ωPBE on these changes. With all methods, the observed changes during protonation processes can be reproduced, and the quantitatively best procedure is found to be LC-ωPBE/LACVP* for geometry optimization calculations and LC-ωPBE/chem for calculations of magnetic interactions. This conclusion is expected to be a numerical foundation for theoretical investigation of reaction centers in manganese-containing proteins.

Keywords

Electron Spin Resonance Magnetic Interaction Spin Orbital Dispersion Correction Manganese Complex 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Notes

Acknowledgment

We acknowledge financial support by the Ministry of Education, Culture, Sports, Science and Technology (MEXT) (Grant-in-Aid for Scientific Research C No. 23550016 and B No. 23350064), and by Research and Development of the Next-Generation Integrated Simulation of Living Matter, as a part of the Development and Use of the Next-Generation Supercomputer Project. A part of the calculations were carried out on computer systems in the Institute for Molecular Science Computer Center.

References

  1. 1.
    Fersht A (1999) Structure and mechanism in protein science. W. H. Freeman and Co, New YorkGoogle Scholar
  2. 2.
    Lippard SJ, Berg JM (1994) Principles of bioinorganic chemistry. University Science, Mill ValleyGoogle Scholar
  3. 3.
    Solomon EI, Scott RA, King RB (eds) (2009) Computational inorganic and bioinorganic chemistry. Wiley, New YorkGoogle Scholar
  4. 4.
    Signorini GF, Chelli R, Procacci P, Schettino V (2004) J Phys Chem B 108:12252–12257CrossRefGoogle Scholar
  5. 5.
    Nilsson K, Ryde U (2004) J Inorg Biochem 98:1539–1546CrossRefGoogle Scholar
  6. 6.
    Koizumi K, Yamaguchi K, Nakamura H, Takano Y (2009) J Phys Chem A 113:5099–5104CrossRefGoogle Scholar
  7. 7.
    Shoji M, Nishiyama Y, Maruno Y, Koizumi K, Kitagawa T, Yamanaka S, Kawakami T, Okumura M, Yamaguchi K (2004) Int J Quantum Chem 100:887–906CrossRefGoogle Scholar
  8. 8.
    Ames W, Pantazis DA, Krewald V, Cox N, Messinger J, Lubitz W, Neese F (2011) J Am Chem Soc 133:19743–19757CrossRefGoogle Scholar
  9. 9.
    Umena Y, Kawakami K, Shen J-R, Kamiya N (2011) Nature 473:55–61CrossRefGoogle Scholar
  10. 10.
    Kanda K, Yamanaka S, Saito T, Umena Y, Kawakami K, Shen J-R, Kamiya N, Okumura M, Nakamura H, Yamaguchi K (2011) Chem Phys Lett 506:98–103CrossRefGoogle Scholar
  11. 11.
    Manchanda R, Brudvig GW, Crabtree RH (1995) Coord Chem Rev 144:1–38CrossRefGoogle Scholar
  12. 12.
    Wiechen M, Berends H-M, Kurz P (2012) Dalton Trans 41:21–31CrossRefGoogle Scholar
  13. 13.
    Yagi M, Kaneko M (2001) Chem Rev 101:21–35CrossRefGoogle Scholar
  14. 14.
    Dismukes GC, Brimblecombe R, Felton GAN, Pryadun RS, Sheats JE, Spiccia L, Swiegers GF (2009) Acc Chem Res 42:1935–1943CrossRefGoogle Scholar
  15. 15.
    Michaud-Soret I, Jacquamet L, Debaecker-Petit N, Le Pape L, Barynin VV, Latour J-M (1998) Inorg Chem 37:3874–3876CrossRefGoogle Scholar
  16. 16.
    Siegbahn PEM (2001) Theor Chem Acc 105:197–206CrossRefGoogle Scholar
  17. 17.
    Teutloff C, Schäfer K-O, Sinnecker S, Barynin W, Bittl R, Wieghardt K, Lendzian F, Lubitz W (2005) Magn Reson Chem 43:551–564CrossRefGoogle Scholar
  18. 18.
    Wu AJ, Penner-Hahn JE, Pecoraro VL (2004) Chem Rev 104:903–938CrossRefGoogle Scholar
  19. 19.
    Larson EJ, Riggs PJ, Penner-Han JE, Pecorro VL (1992) J Chem Soc Chem Commun 116:102–103CrossRefGoogle Scholar
  20. 20.
    Baldwin MJ, Stemmler TL, Xia YM, Riggs-Gelasco PJ, Kirk ML, Penner-Han JE, Pecorro VL (1994) J Am Chem Soc 116:11349–11356CrossRefGoogle Scholar
  21. 21.
    Gohdes JW, Armstrong WH (1992) Inorg Chem 31:368–373CrossRefGoogle Scholar
  22. 22.
    Sheng Y, Stich TA, Barnese K, Gralla EB, Cascio D, Britt RD, Cabelli DE, Valentine JS (2011) J Am Chem Soc 133(51):20878–20889. doi: 10.1021/ja2077476 CrossRefGoogle Scholar
  23. 23.
    Srnec M, Aquiilante F, Ryde U, Rulisek L (2009) J Phys Chem B 113:6074–6086CrossRefGoogle Scholar
  24. 24.
    Cox N, Ames W, Epel B, Kulik LV, Rapatskiy L, Neese F, Messinger J, Wieghardt K, Lubitz W (2011) Inorg Chem 59:8238–8251CrossRefGoogle Scholar
  25. 25.
    Pantazis DA, Krewald V, Orio M, Neese F (2010) Dalton Trans 39:4959–4967CrossRefGoogle Scholar
  26. 26.
    Cramer CJ, Truhlar DG (2009) Phys Chem Chem Phys 11:10757–10816CrossRefGoogle Scholar
  27. 27.
    Yamanaka S, Kanda K, Saito T, Kitagawa Y, Kawakami T, Ehara M, Okumura M, Nakamura H, Yamaguchi K (2011) Chem Phys Lett 519–520:134–140Google Scholar
  28. 28.
    Yamanaka S, Kanda K, Saito T, Ehara M, Okumura M, Nakamura H, Yamaguchi K (to be published).Google Scholar
  29. 29.
    Reiher M, Salomon O, Hess BA (2001) Theor Chem Acc 107:48–55CrossRefGoogle Scholar
  30. 30.
    Phillips JJ, Peralta JE (2011) J Chem Phys 134:034108CrossRefGoogle Scholar
  31. 31.
    Becke AD (1993) J Chem Phys 98:5648–5652CrossRefGoogle Scholar
  32. 32.
    Becke AD (1988) Phys Rev A 38:3098–3100CrossRefGoogle Scholar
  33. 33.
    Perdew JP (1986) Phys Rev B 33:8822–8824CrossRefGoogle Scholar
  34. 34.
    Sproviero EM, Gascon JA, McEvoy JP, Brudvig GW, Batista VS (2006) J Inorg Biochem 100:786–800CrossRefGoogle Scholar
  35. 35.
    Grimme S (2006) J Comput Chem 27:1787–1799CrossRefGoogle Scholar
  36. 36.
    Iikura H, Tsuneda T, Yanai T, Hirao K (2001) J Chem Phys 115:3540–3544CrossRefGoogle Scholar
  37. 37.
    Vydrov OA, Scuseria GE (2006) J Chem Phys 125:234109CrossRefGoogle Scholar
  38. 38.
    Yamaguchi K, Jensen F, Dorigo A, Houk KN (1988) Chem Phys Lett 149:537–542CrossRefGoogle Scholar
  39. 39.
    Yamanaka S, Kawakami T, Nagao H, Yamaguchi K (1994) Chem Phys Lett 231:25–33CrossRefGoogle Scholar
  40. 40.
    Shoji M, Koizumi K, Kitagawa Y, Kawakami T, Yamanaka S, Okumura M, Yamaguchi K (2006) Chem Phys Lett 432:343–347CrossRefGoogle Scholar
  41. 41.
    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, Izmaylov AF, Bloino J, Zheng G, Sonnenberg JL, Hada M, Ehara M, Toyota K, Fukuda R, Hasegawa J, Ishida M, Nakajima T, Honda Y, 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 NJ, 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 DJ (2010) Gaussian 09. Revision B.01. Gaussian, Inc., WallingfordGoogle Scholar
  42. 42.
    Vydrov OA, Scuseria GE, Perdew JP (2007) J Chem Phys 126(15):154109CrossRefGoogle Scholar
  43. 43.
    Yoshida K (1966) Theory of magnetism. Springer, BerlinGoogle Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2012

Authors and Affiliations

  • S. Yamanaka
    • 1
  • K. Kanda
    • 1
  • T. Saito
    • 1
  • Y. Kitagawa
    • 1
  • T. Kawakami
    • 1
  • M. Ehara
    • 2
  • M. Okumura
    • 1
  • H. Nakamura
    • 3
  • K. Yamaguchi
    • 4
    • 5
  1. 1.Graduate School of ScienceOsaka UniversityToyonakaJapan
  2. 2.Institute for Molecular ScienceOkazakiJapan
  3. 3.Protein InstituteOsaka UniversitySuitaJapan
  4. 4.TOYOTA Physical and Chemical Research InstituteNagakuteJapan
  5. 5.Graduate School of ScienceOsaka UniversityToyonakaJapan

Personalised recommendations