Hybrid-DFT study on electronic structures of the active site of sweet potato purple acid phosphatase: The origin of stronger antiferromagnetic couplings than other purple acid phosphatases

Journal of Physical Chemistry A

Volumn 113, Issue 17, 2009, Pages 5099-5104

  Koizumi, Kenichi ^a,b   Yamaguchi, Kizashi ^b   Nakamura, Haruki ^b   Takano, Yu ^b  

^a Japan Biological Information Research Center   (Japan)

^b OSAKA UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

ACIDIC CONDITIONS; ACTIVE SITE; ANTIFERROMAGNETIC COUPLING; BINUCLEAR METAL CENTER; BRIDGING LIGANDS; BRIDGING OXYGEN; CHEMICAL INDICES; DFT STUDY; HYBRID DFT METHOD; MAGNETIC INTERACTIONS; NATURAL ORBITALS; PHOSPHATE ESTERS; PURPLE ACID PHOSPHATASE; REACTION MECHANISM; SPIN DELOCALIZATION; SPIN DENSITY DISTRIBUTIONS; SWEET POTATO;

ACIDS; ANTIFERROELECTRICITY; ANTIFERROMAGNETIC MATERIALS; ANTIFERROMAGNETISM; ELECTRONIC PROPERTIES; ELECTRONIC STRUCTURE; ESTERS; IRON COMPOUNDS; LIGANDS; MAGNETIC COUPLINGS; MANGANESE; OXYGEN; PROBABILITY DENSITY FUNCTION; SPIN DYNAMICS;

MANGANESE COMPOUNDS;

ACID PHOSPHATASE; ACID PHOSPHATASE TARTRATE RESISTANT ISOENZYME; FERROUS ION; GLYCOPROTEIN; LIGAND; MANGANESE DERIVATIVE;

ARTICLE; CATALYSIS; CHEMICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; ELECTRON; ENZYME ACTIVE SITE; ENZYMOLOGY; HYDROLYSIS; MAGNETISM; METABOLISM; SWEET POTATO;

ACID PHOSPHATASE; CATALYSIS; CATALYTIC DOMAIN; COMPUTER SIMULATION; ELECTRONS; FERROUS COMPOUNDS; GLYCOPROTEINS; HYDROLYSIS; IPOMOEA BATATAS; LIGANDS; MAGNETICS; MANGANESE COMPOUNDS; MODELS, CHEMICAL; MOLECULAR STRUCTURE;

EID: 65649113960     PISSN: 10895639     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp8090123     Document Type: Article

References (44)

1. Lindqvist, Y.; Johansson, E.; Kaija, H.; Vihko, P.; Schneider, G. J. Mol. Biol. 1999, 291, 135.
2. Guddat, L. W.; McAlpine, A. S.; Hume, D.; Hamilton, S.; de Jarsey, J.; Martin, J. L. Structure 1999, 7, 757.
3. Strater, N.; Jasper, B.; Scholte, M.; Krabs, B.; Duff, A. P.; Langley, D. B.; Han, R.; Averill, B. A.; Freeman, H. C.; Guss, J. M. J. Mol. Biol. 2005, 351, 233.
4. Klabunde, T.; Strater, N.; Frohich, R.; Witzel, H.; Krebs, B. J. Mol. Biol. 1996, 259, 737.
5. Schenk, G.; Gahan, L. R.; Carrington, L. E.; Mitic, N.; Valizadeh, M.; Hamilton, S. E.; de Jersey, J.; Guddat, L. W Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 273.
6. Schenk, G.; Boutchard, C. L.; Carrington, L. E.; Noble, C. J.; Moubaraki, B.; Murray, K. S. J. Biol. Chem. 2001, 276, 19084.
7. Wilcox, D. E. Chem. Rev. 1996, 96, 2435.
8. Maruno, Y.; Shoji, M.; Koizumi, K.; Nishiyama, Y.; Kitagawa, Y.; Kawakami, T.; Okumura, M.; Yamaguchi, K. Polyhedron 2005, 24, 2778.
9. Smoukov, S. K.; Quaroni, L.; Wang, X.; Doan, P. E.; Hoffman, B. M.; Que, L. J. Am. Chem. Soc. 2002, 124, 2595.
10. Averill, B. A.; Davis, J. C.; Burman, S. J.; Sanders-Loehr, J.; Loeher, T. M.; Sage, T. J.; Debrunner, P. G. J. Am. Chem. Soc. 1987, 109, 3760.
11. Antanaitis, B. C.; Aisen, P.; Lilienthal, H. R. J. Biol. Chem. 1983, 258, 3166.
12. Lauffer, R. B.; Antanaitis, B. C.; Aisen, P.; Que, L., Jr. J. Biol. Chem. 1983, 258, 14212.
13. Day, E. P.; David, S. S.; Peterson, J.; Dunham, W. R.; Bonvoisin, J. J.; Sands, R. H.; Que, L., Jr. J. Biol. Chem. 1988, 263, 15561.
14. Koizumi, K.; Shoji, M.; Kitagawa, Y.; Ohoyama, H.; Kasai, T.; Yamaguchi, K. Eur. Phys. J. D 2006, 38, 193.
15. Shoji, M.; Isobe, H.; Takano, Y.; Kitagawa, Y.; Yamanaka, S.; Okumura, Y.; Yamaguchi, K. Int. J. Quantum Chem. 2007, 107, 3250.
16. (a) Siegbahn, P. E. M.; Crabtree, R. H. J. Am. Chem. Soc. 1997, 119, 3113.
17. (b) Siegbahn, P. E. M Inorg. Chem. 1999, 38, 2880.
18. (c) Siegbahn, P. E. M. Chem. Phys. Lett. 2002, 351, 311.
19. Yoon, Y.; Liboiron, B. D.; Sarangi, R.; Hodgson, K. O.; Hedman, B.; Solomon, E. I. Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 13609.
20. Noodleman, L.; Peng, C. Y.; Case, D. A.; Mouesca, J.-M. Coord. Chem. Rev. 1995, 144, 199.
21. Shoji, M.; Hamamoto, T.; Koizumi, K.; Isobe, H.; Kitagawa, Y.; Takano, Y.; Yamanaka, S.; Yamaguchi, K. Polyhedron 2005, 24, 2701.
22. Takano, Y.; Isobe, H.; Yamaguchi, K. Bull. Chem. Soc. Jpn. 2008, 81, 91.
23. Itoh, K.; Kinoshita, M., Eds. Molecular Magnetism: New Magnetic Materials; Kodansha-Godon and Breach: Tokyo, Japan, 2000.
24. Kahn, O., Ed. Magnetism: A Supramolecular Function; NATO ASI Series C; Kluwer Academic Publishers: Dordrecht, The Netherlands, 1996; Vol.484.
25. Yamaguchi, K.; Takahara, Y.; Fueno, T. In Applied Quantum Chemistry; Smith, V. H., Schaefer, H. F., III., Morokuma, K., Eds.; Reidal: Boston, MA, 1986.
26. Parr, R. G.; Young, W. Density Functional Theory of Atoms and Molecules; Oxford University Press: Oxford, UK, 1989.
27. Trickey, S. B., Ed. Density Functional Theory of Many Fermion Systems; Advances in Quantum Chemistry, Vol.21; Academic Press: San Diego, CA, 1990.
28. Becke, A. D. Phys. Rev.A1988, 38, 3098.
29. Vosko, S. H.; Wilk, L.; Nusair, M. Can. J. Phys 1980, 58, 785.
30. Lee, C.; Yang, W.; Parr, R. G. Phys. Rev. B1988, 37, 785.
31. Becke, A. D. J. Chem. Phys. 1993, 98, 5648.
32. (a) Takano, Y.; Kitagawa, Y.; Onishi, T.; Yoshioka, Y.; Yamaguchi, K.; Koga, N.; Iwamura, H. J. Am. Chem. Soc. 2002, 124, 450.
33. (b) Takano, Y.; Soda, T.; Kitagawa, Y.; Yoshioka, Y.; Yamaguchi, K. Chem. Phys. Lett. 1999, 301, 309.
34. (c) Takano, Y.; Soda, T.; Kitagawa, Y.; Onishi, T.; Yoshioka, Y.; Yamaguchi, K. Int. J. Quantum Chem. 2000, 80, 681.
35. Isobe, H.; Takano, Y.; Kitagawa, Y.; Kawakami, T.; Yamanaka, S.; Yamaguchi, K.; Houk, K. N. Mol. Phys. 2002, 100, 717.
36. Mitani, M.; Yamaki, D.; Takano, Y.; Kitagawa, Y.; Yoshioka, Y.; Yamaguchi, K. J. Chem. Phys. 2000, 113, 10486.
37. Tatewaki, H.; Huzinaga, S. J. Chem. Phys. 1980, 72, 339.
38. Hariharan, P. J.; Pople, J. A. Theor. Chem. Acta 1973, 28, 213.
39. Hehre, W. J.; Ditchfild, R.; Pople, J. A. J. Chem. Phys. 1972, 56, 2257.
40. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R., Montgomery, J. A., Jr.; Vreven, T.; Kudin, K. N.; Burant, J. C.; Millam, J. M.; Iyenger, S. S.; Tomasi, J.; Barone, V.; Mennucci, B.; Cossi, M.; Scalmani, G.; Rega, N.; Petersson, G. A.; Nakatsuji, H.; Hada, M.; Ehara, M.; Toyota, K.; Fukuda, R.; Hasegawa, J.; Ishida, M.; Nakajima, T.; Honda, Y.; Kitao, O.; Nakai, H.; Klene, M.; Li, X.; Knox, J. E.; Hratchian, H. P.; Cross, J. B.; Bakken, V.; Adamo, C.; Jaramillo, J.; Gomperts, R.; Startmann, R. E.; Yazyev, O.; Austin, A. J.; Cammi, R.; Pomelli, C.; Ochterski, J. W.; Ayala, P. Y.; Morokuma, K.; Voth, G. A.; Salvador, P.; Dannenberg, J. J.; Zakrzewski, V. G.; Dapprich, S.; Daniels, A. D.; Strain, M. C.; Farkas, O.; Malick, D. K.; Rabuck, A. D.; Raghavachari, K.; Foresman, J. B.; Ortiz, J. V.; Cui, Q.; Baboul, A. G.; Clifford, S.; Cioslowski, J.; Stefanov, B. B.; Liu, G.; Liashenko, A.; Piskorz, P.; Komaromi, I.; Martin, R. L.; Fox, D. J.; Keith, T.; Al-Laham, M. A.; Peng, C. Y.; Nanayakkara, A.; Challacombe, M.; Gill, P. M. W.; Johnson, B.; Chen, W.; Wong, M. W.; Gonzalez, C.; Pople, J. A. Gaussian 03, Revision C.02; Gaussian, Inc., Wallingford, CT, 2004.
41. Brunold, T. C.; Solomon, E. I. J. Am. Chem. Soc. 1999, 121, 8277.
42. Kitagawa, Y.; Saito, T.; Ito, M.; Shoji, M.; Koizumi, K.; Yamanaka, S.; Kawakami, T.; Okumura, M.; Yamaguchi, K. Chem. Phys. Lett. 2007, 442, 445.
43. Wirstam, M.; Lippard, S. J.; Friesner, R. A. J. Am. Chem. Soc. 2003, 125, 3987.
44. Koizumi, K.; Shoji, M.; Nishiyama, Y.; Maruno, Y.; Kitagawa, Y.; Soda, K.; Yamanaka, S.; Okumura, M.; Yamaguchi, K. Int. J. Quantum Chem. 2004, 100, 943.