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

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Quantum Systems in Chemistry and Physics

Part of the book series: Progress in Theoretical Chemistry and Physics ((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.

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References

  1. Fersht A (1999) Structure and mechanism in protein science. W. H. Freeman and Co, New York

    Google Scholar 

  2. Lippard SJ, Berg JM (1994) Principles of bioinorganic chemistry. University Science, Mill Valley

    Google Scholar 

  3. Solomon EI, Scott RA, King RB (eds) (2009) Computational inorganic and bioinorganic chemistry. Wiley, New York

    Google Scholar 

  4. Signorini GF, Chelli R, Procacci P, Schettino V (2004) J Phys Chem B 108:12252–12257

    Article  CAS  Google Scholar 

  5. Nilsson K, Ryde U (2004) J Inorg Biochem 98:1539–1546

    Article  CAS  Google Scholar 

  6. Koizumi K, Yamaguchi K, Nakamura H, Takano Y (2009) J Phys Chem A 113:5099–5104

    Article  CAS  Google Scholar 

  7. Shoji M, Nishiyama Y, Maruno Y, Koizumi K, Kitagawa T, Yamanaka S, Kawakami T, Okumura M, Yamaguchi K (2004) Int J Quantum Chem 100:887–906

    Article  CAS  Google Scholar 

  8. Ames W, Pantazis DA, Krewald V, Cox N, Messinger J, Lubitz W, Neese F (2011) J Am Chem Soc 133:19743–19757

    Article  CAS  Google Scholar 

  9. Umena Y, Kawakami K, Shen J-R, Kamiya N (2011) Nature 473:55–61

    Article  CAS  Google Scholar 

  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 506:98–103

    Article  CAS  Google Scholar 

  11. Manchanda R, Brudvig GW, Crabtree RH (1995) Coord Chem Rev 144:1–38

    Article  CAS  Google Scholar 

  12. Wiechen M, Berends H-M, Kurz P (2012) Dalton Trans 41:21–31

    Article  CAS  Google Scholar 

  13. Yagi M, Kaneko M (2001) Chem Rev 101:21–35

    Article  CAS  Google Scholar 

  14. Dismukes GC, Brimblecombe R, Felton GAN, Pryadun RS, Sheats JE, Spiccia L, Swiegers GF (2009) Acc Chem Res 42:1935–1943

    Article  CAS  Google Scholar 

  15. Michaud-Soret I, Jacquamet L, Debaecker-Petit N, Le Pape L, Barynin VV, Latour J-M (1998) Inorg Chem 37:3874–3876

    Article  CAS  Google Scholar 

  16. Siegbahn PEM (2001) Theor Chem Acc 105:197–206

    Article  CAS  Google Scholar 

  17. Teutloff C, Schäfer K-O, Sinnecker S, Barynin W, Bittl R, Wieghardt K, Lendzian F, Lubitz W (2005) Magn Reson Chem 43:551–564

    Article  Google Scholar 

  18. Wu AJ, Penner-Hahn JE, Pecoraro VL (2004) Chem Rev 104:903–938

    Article  CAS  Google Scholar 

  19. Larson EJ, Riggs PJ, Penner-Han JE, Pecorro VL (1992) J Chem Soc Chem Commun 116:102–103

    Article  Google Scholar 

  20. Baldwin MJ, Stemmler TL, Xia YM, Riggs-Gelasco PJ, Kirk ML, Penner-Han JE, Pecorro VL (1994) J Am Chem Soc 116:11349–11356

    Article  CAS  Google Scholar 

  21. Gohdes JW, Armstrong WH (1992) Inorg Chem 31:368–373

    Article  CAS  Google Scholar 

  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

    Article  CAS  Google Scholar 

  23. Srnec M, Aquiilante F, Ryde U, Rulisek L (2009) J Phys Chem B 113:6074–6086

    Article  CAS  Google Scholar 

  24. Cox N, Ames W, Epel B, Kulik LV, Rapatskiy L, Neese F, Messinger J, Wieghardt K, Lubitz W (2011) Inorg Chem 59:8238–8251

    Article  Google Scholar 

  25. Pantazis DA, Krewald V, Orio M, Neese F (2010) Dalton Trans 39:4959–4967

    Article  CAS  Google Scholar 

  26. Cramer CJ, Truhlar DG (2009) Phys Chem Chem Phys 11:10757–10816

    Article  CAS  Google Scholar 

  27. Yamanaka S, Kanda K, Saito T, Kitagawa Y, Kawakami T, Ehara M, Okumura M, Nakamura H, Yamaguchi K (2011) Chem Phys Lett 519–520:134–140

    Google Scholar 

  28. Yamanaka S, Kanda K, Saito T, Ehara M, Okumura M, Nakamura H, Yamaguchi K (to be published).

    Google Scholar 

  29. Reiher M, Salomon O, Hess BA (2001) Theor Chem Acc 107:48–55

    Article  CAS  Google Scholar 

  30. Phillips JJ, Peralta JE (2011) J Chem Phys 134:034108

    Article  Google Scholar 

  31. Becke AD (1993) J Chem Phys 98:5648–5652

    Article  CAS  Google Scholar 

  32. Becke AD (1988) Phys Rev A 38:3098–3100

    Article  CAS  Google Scholar 

  33. Perdew JP (1986) Phys Rev B 33:8822–8824

    Article  Google Scholar 

  34. Sproviero EM, Gascon JA, McEvoy JP, Brudvig GW, Batista VS (2006) J Inorg Biochem 100:786–800

    Article  CAS  Google Scholar 

  35. Grimme S (2006) J Comput Chem 27:1787–1799

    Article  CAS  Google Scholar 

  36. Iikura H, Tsuneda T, Yanai T, Hirao K (2001) J Chem Phys 115:3540–3544

    Article  CAS  Google Scholar 

  37. Vydrov OA, Scuseria GE (2006) J Chem Phys 125:234109

    Article  Google Scholar 

  38. Yamaguchi K, Jensen F, Dorigo A, Houk KN (1988) Chem Phys Lett 149:537–542

    Article  CAS  Google Scholar 

  39. Yamanaka S, Kawakami T, Nagao H, Yamaguchi K (1994) Chem Phys Lett 231:25–33

    Article  CAS  Google Scholar 

  40. Shoji M, Koizumi K, Kitagawa Y, Kawakami T, Yamanaka S, Okumura M, Yamaguchi K (2006) Chem Phys Lett 432:343–347

    Article  CAS  Google Scholar 

  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., Wallingford

    Google Scholar 

  42. Vydrov OA, Scuseria GE, Perdew JP (2007) J Chem Phys 126(15):154109

    Article  Google Scholar 

  43. Yoshida K (1966) Theory of magnetism. Springer, Berlin

    Google Scholar 

Download references

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.

Author information

Authors and Affiliations

  1. Graduate School of Science, Osaka University, Toyonaka, 560-0043, Japan

    S. Yamanaka, K. Kanda, T. Saito, Y. Kitagawa, T. Kawakami & M. Okumura

  2. Institute for Molecular Science, Myodaiji, Okazaki, 444-8585, Japan

    M. Ehara

  3. Protein Institute, Osaka University, Suita, 560-0871, Japan

    H. Nakamura

  4. TOYOTA Physical and Chemical Research Institute, Nagakute, Aichi, Japan

    K. Yamaguchi

  5. Graduate School of Science, Osaka University, Toyonaka, Osaka, Japan

    K. Yamaguchi

Authors
  1. S. Yamanaka
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  2. K. Kanda
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  3. T. Saito
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  4. Y. Kitagawa
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  5. T. Kawakami
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  6. M. Ehara
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  7. M. Okumura
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  8. H. Nakamura
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  9. K. Yamaguchi
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Corresponding author

Correspondence to S. Yamanaka .

Editor information

Editors and Affiliations

  1. , Division of Mathem. and Physical Science, Kanazawa University, Kanazawa, 920-1192, Japan

    Kiyoshi Nishikawa

  2. Laboratoire de Chimie Physique, rue Pierre et Marie Curie 11, Paris, 75005, France

    Jean Maruani

  3. Dept. Quantum Chemistry, Uppsala University, Uppsala, Sweden

    Erkki J. Brändas

  4. Inst. Matemáticas y Física, Fundamental (IMAFF), CSIC Madrid, C/ Serrano 123, Madrid, 28006, Spain

    Gerardo Delgado-Barrio

  5. Dept. Chemistry, Michigan State University, Chemistry Building, East Lansing, 48824, Michigan, USA

    Piotr Piecuch

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© 2012 Springer Science+Business Media Dordrecht

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Yamanaka, S. et al. (2012). Density Functional Study of Manganese Complexes: Protonation Effects on Geometry and Magnetism. In: Nishikawa, K., Maruani, J., Brändas, E., Delgado-Barrio, G., Piecuch, P. (eds) Quantum Systems in Chemistry and Physics. Progress in Theoretical Chemistry and Physics, vol 26. Springer, Dordrecht. https://doi.org/10.1007/978-94-007-5297-9_26

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