TD-DFT insight into photodissociation of the Co-C bond in coenzyme B12

Frontiers in Chemistry

Volumn 1, Issue FEB, 2014, Pages 1-12

  Liu, Hui ^a   Kornobis, Karina ^a   Lodowski, Piotr ^b   Jaworska, Maria ^b   Kozlowski, Pawel M ^a  

^a UNIVERSITY OF LOUISVILLE   (United States)

^b UNIVERSITY OF SILESIA   (Poland)

Author keywords

Co C bond; coenzyme B12; Photodissociation; Ribosylcobalamin; Time dependent density functional theory

Indexed keywords

EID: 84986887439     PISSN: None     EISSN: 22962646     Source Type: Journal    
DOI: 10.3389/fchem.2013.00041     Document Type: Article

References (73)

1. Ahlrichs R., Bär M., Häser M., Horn H., Kölmel C. (1989). Electronic structure calculations on workstation computers: the program system turbomole. Chem. Phys. Lett. 162, 165-169 10.1016/0009-2614(89)85118-8
2. 12. J. Chem. Phys. 131, 105105 10.1063/1.3190326
3. Banerjee R. (1997). The Yin-Yang of cobalamin biochemistry. Chem. Biol. 4, 175-186 10.1016/S1074-5521(97)90286-6
4. 12. New York, NY: John Wiley and Sons
5. 12-dependent enzymes. Biochemistry 40, 6191-6198 10.1021/bi0104423
6. Banerjee R. (2003). Radical carbon skeleton rearrangements: catalysis by coenzyme b12-dependent mutases. Chem. Rev. 103, 2083-2094 10.1021/cr0204395
7. 12: catalysis by cobalamin-dependent enzymes. Annu. Rev. Biochem. 72, 209-247 10.1146/annurev.biochem.72.121801.161828
8. Becke A. D. (1993). Density-functional thermochemistry. III. The role of exact exchange. J. Chem. Phys. 98, 5648-5652 10.1063/1.464913
9. 12. Chem. Rev. 105, 2075-2149 10.1021/cr030720z
10. Cammi R., Tomasi J. (1995). Remarks on the use of the apparent surface charges (ASC) methods in solvation problems: iterative versus matrix-inversion procedures and the renormalization of the apparent charges. J. Comput. Chem. 16, 1449-1458 10.1002/jcc.540161202
11. 12 enzymes. J. Am. Chem. Soc. 115, 12152-12157 10.1021/ja00078a063
12. 12. Quantum yields and spectral dynamics. J. Biol. Chem. 265, 12987-12994
13. Chen E., Chance M. R. (1993). Continuous-wave quantum yields of various cobalamins are influenced by competition between geminate recombination and cage escape. Biochemistry 32, 1480-1487 10.1021/bi00057a011
14. 12 coenzymes: a comparison of the primary photolysis mechanism in methyl-, ethyl-, n-propyl-, and 5'-deoxyadenosylcobalamin. J. Am. Chem. Soc. 124, 434-441 10.1021/ja011628s
15. 12. New York, NY: Wiley-Interscience
16. Endicott J. F., Ferraudi G. J. (1977). A flash photolytic investigation of low energy homolytic processes in methylcobalamin. J. Am. Chem. Soc. 99, 243-245 10.1021/ja00443a043
17. Endicott J. F., Netzel T. L. (1979). Early events and transient chemistry in the photohomolysis of alkylcobalamins. J. Am. Chem. Soc. 101, 4000-4002 10.1021/ja00508a066
18. Frisch M. J., Trucks G. W., Schlegel H. B., Scuseria G. E., Robb M. A., Cheeseman J. R., et al. (2009). Gaussian 09, Revision A.1. Wallingford, CT: Gaussian, Inc
19. Furche F., Ahlrichs R. (2002). Adiabatic time-dependent density functional methods for excited state properties. J. Chem. Phys. 117, 7433-7447 10.1063/1.1508368
20. Furche F., Rappoport D. (2005). Density functional methods for excited states: equilibrium structure and electronic spectra computational photochemistry, in Theoretical and Computational Chemistry, Vol. 16, Chapter III, ed Olivucci M., editor. (Amsterdam: Elsevier; ), 93-128
21. Galezowski W., Kuta J., Kozlowski P. M. (2008). DFT study of Co-C bond cleavage in the neutral and one-electron-reduced alkyl-cobalt(iii) phthalocyanines. J. Phys. Chem. B 112, 3177-3183 10.1021/jp0769678
22. 12, enzymatic reactions: the photolysis of methyl cob(III)alamin. Z. Phys. Chem. 182, 181-188 10.1524/zpch.1993.182.Part_1_2.181
23. Harris D. A., Stickrath A. B., Carroll E. C., Sension R. J. (2007). Influence of environment on the electronic structure of Cob(III)alamins: time-resolved absorption studies of the S1 state spectrum and dynamics. J. Am. Chem. Soc. 129, 7578-7585 10.1021/ja066197y
24. Jaworska M., Kozibut G., Lodowski P. (2005). Electronic spectrum of cobalt-free corrins calculated by TDDFT method. J. Phys. Chem. A 107, 1339-1347 10.1021/jp021261t
25. Jaworska M., Lodowski P. (2003). Electronic spectrum of Co-corrin calculated with the TDDFT method. J. Mol. Struct. THEOCHEM 631, 209-223 10.1016/S0166-1280(03)00249-5
26. Jaworska M., Lodowski P., Andruniow T., Kozlowski P. M. (2007). Photolysis of methylcobalamin: identification of the relevant excited states involved in Co-C bond scission. J. Phys. Chem. B. 111, 2419-2422 10.1021/jp0685840
27. Jensen K., Ryde U. (2009). Cobalamins uncovered by modern electronic structure calculations. Coord. Chem. Rev. 253, 769-778 10.1016/j.ccr.2008.04.015
28. Jensen K. P., Ryde U. (2003). Theoretical prediction of the Co-C bond strength in cobalamins. J. Phys. Chem. A 107, 7539-7545 10.1021/jp027566p
29. Kornobis K., Kumar N., Lodowski P., Jaworska M., Piecuch P., Lutz J. J., et al. (2013). Electronic structure of the S1 state in methylcobalamin: insight from CASSCF/MC-XQDPT2, EOM-CCSD, and TD-DFT calculations. J. Comput. Chem. 34, 987-1004 10.1002/jcc.23204
30. 12: benchmark calculations including time-dependent density functional theory and correlated ab initio methods. J. Phys. Chem. A 115, 1280-1292 10.1021/jp110914y
31. Kozlowski P. M., Kumar M., Piecuch P., Li W., Bauman N. P., Hansen J. A., et al. (2012). The cobalt-methyl bond dissociation in methylcobalamin: new benchmark analysis based on density functional theory and completely renormalized coupled-cluster calculations. J. Chem. Theor. Comput. 8, 1870-1894 10.1021/ct300170y
32. Kozlowski P. M., Kuta J., Galezowski W. (2007). Reductive cleavage mechanism of methylcobalamin: elementary steps of Co-C bond breaking. J. Phys. Chem. B 111, 7638-7645 10.1021/jp066972w
33. 12 Proteins. New York, NY: Wiley-VCH; 10.1002/9783527612192
34. 12 model compounds suggesting that C-Co bond homolysis occurs from the singlet state. Inorg. Chem. 36, 758-759 10.1021/ic960562c
35. Kumar M., Kozlowski P. M. (2012). Why hydroxocobalamin is photocatalytically active? Chem. Phys. Lett. 543, 133-136 10.1016/j.cplett.2012.06.007
36. Kumar N., Kozlowski P. M. (2013). Mechanistic insights for formation of an organometallic co-C bond in the methyl transfer reaction catalyzed by methionine synthase. J. Chem. Phys. B 117, 16044-16057 10.1021/jp4093145
37. Kumar N., Jaworska M., Lodowski P., Kumar M., Kozlowski P. M. (2011a). Electronic structure of cofactor-substrate reactant complex involved in the methyl transfer reaction catalyzed by cobalamin-dependent methionine synthase. J. Phys. Chem. B 115, 6722-6731 10.1021/jp200945a
38. Kumar N., Alfonso-Prieto M., Rovira C., Lodowski P., Jaworska M., Kozlowski P. M. (2011b). Role of the axial base in the modulation of the cob(I)alamin electronic properties: insight from QM/MM, DFT, and CASSCF calculations. J. Chem. Theory Comput. 7, 1541-1551 10.1021/ct200065s
39. Kumar N., Kuta J., Galezowski W., Kozlowski P. M. (2013). Electronic structure of one-electron-oxidized form of the methylcobalamin cofactor: spin density distribution and pseudo-jahn-teller effect. Inorg. Chem. 52, 1762-1771 10.1021/ic3013443
40. 12-tyrosine complex in adenosylcobalamin-dependent methylmalonyl-CoA mutase enzyme. J. Phys.Chem. Lett. 3, 1035-1038 10.1021/jz300102s
41. Kuta J., Patchkovskii S., Zgierski M. Z., Kozlowski P. M. (2006). Performance of DFT in modeling electronic and structural properties of cobalamins. J. Comput. Chem. 27, 1429-1437 10.1002/jcc.20454
42. Kuta J., Wuerges J., Randaccio L., Kozlowski P. M. (2009). Axial bonding in alkylcobalamins: DFT analysis of the inverse versus normal trans influence. J. Phys. Chem. A 113, 11604-11612 10.1021/jp901397p
43. 12 cofactor. J. Am. Chem. Soc. 128, 9144-9156 10.1021/ja061433q
44. Lodowski P., Jaworska M., Andruniow T., Kumar M., Kozlowski P. M. (2009). Photodissociation of Co-C bond in methyl- and ethylcobalamin: an insight from TD-DFT calculations. J. Phys. Chem. B. 113, 6898-6909 10.1021/jp810223h
45. 12. J. Phys. Chem. B. 115, 13304-13319 10.1021/jp200911y
46. Lott W. B., Chagovetz A. M., Grissom C. B. (1995). Alkyl radical geometry controls geminate cage recombination in alkylcobalamins. J. Am. Chem. Soc. 117, 12194-12201 10.1021/ja00154a020
47. 12-dependent enzymes. Annu. Rev. Biochem. 66, 269-313 10.1146/annurev.biochem.66.1.269
48. 12 cofactors: Influence of the trans Nitrogen ligand on homolytic and heterolytic processes, Bioinorganic Catalysis, eds Reedijk J., Bouwman E., editors. (New York, NY: Marcel Dekker; ), 423-468 10.1201/9780203908457.ch13
49. Matthews R. G. (2001). Cobalamin-dependent methyltransferases. Acc. Chem. Res. 34, 681-689 10.1021/ar0000051
50. Miertuš S., Scrocco E., Tomasi J. (1981). Electrostatic interaction of a solute with a continuum. A direct utilizaion of AB initio molecular potentials for the prevision of solvent effects. Chem. Phys. 55, 117-129 10.1016/0301-0104(81)85090-2
51. Natarajan E., Grissom C. B. (1996). The origin of magnetic field dependent recombination in alkylcobalamin radical pairs. Photochem. Photobiol. 64, 286-295 10.1111/j.1751-1097.1996.tb02460.x
52. Ouyang L., Rulis P., Ching G., Nardin L., Randaccio L. (2004). Accurate redetermination of the X-ray structure and electronic bonding in adenosylcobalamin. Inorg. Chem. 43, 1235-1241 10.1021/ic0348446
53. Perdew J. P. (1986). Density-functional approximation for the correlation energy of the inhomogeneous electron gas. Phys. Rev. B 33, 8822-8824 10.1103/PhysRevB.33.8822
54. Randaccio L., Geremia S., Nardin G., Wuerges J. (2006). X-ray structural chemistry of cobalamins. Coord. Chem. Rev. 250, 1332-1350 10.1016/j.ccr.2005.12.005
55. 12 proteins. J. Organomet. Chem. 692, 1198-1215 10.1016/j.jorganchem.2006.11.040
56. Rao D. N. R., Symons M. C. R. (1982). Effects of ionizing radiation and photolysis on methyl-cobalamin in low temperature matrices: an e.s.r. study. J. Chem. Soc. Chem. Commun. 954-955 10.1039/C39820000954
57. Rovira C., Biarnes X., Kunc K. (2004). Structure-energy relations in methylcobalamin with and without bound axial base. Inorg. Chem. 43, 6628-6632 10.1021/ic049810s
58. 12. Crystal packing forces effect on axial bond lengths. J. Phys. Chem. B 111, 3251-3257 10.1021/jp0660029
59. Sakaguchi Y., Hayashi H., I'Haya Y. J. (1990). Fast formation of methyl radical from methylaquocobaloxime as studied by time-resolved optical and ESR techniques. J. Phys. Chem. 94, 291-293 10.1021/j100364a048
60. Sension R. J., Cole A. G., Harris A. D., Fox C. C., Woodbury N. W., Lin S., et al. (2004). Photolysis and recombination of adenosylcobalamin bound to glutamate mutase. J. Am. Chem. Soc. 126, 1598-1599 10.1021/ja0396910
61. Sension R. J., Harris A. D., Stickrath A., Cole A. G., Fox C. C., Marsh E. N. G. (2005a). Time-resolved measurements of the photolysis and recombination of adenosylcobalamin bound to glutamate mutase. J. Phys. Chem. B. 109, 18146-18152 10.1021/jp052492d
62. 12 coenzymes: comparison of the influence of solvent on the primary photolysis mechanism and geminate recombination of methyl-, ethyl-, n-propyl-, and 5'-deoxyadenosylcobalamin. J. Phys. Chem. B. 109, 21954-21962 10.1021/jp053202w
63. 12). J. Am. Chem. Soc. 133, 2148-2150 10.1021/ja111585c
64. 12 and related cob(III)alamins. J. Am. Chem. Soc. 128, 801-808 10.1021/ja054374
65. 12 coenzymes: the photolysis of methylcobalamin is wavelength dependent. J. Phys. Chem. B. 103, 10532-10539 10.1021/jp992358r
66. 12 cofactors and biologically relevant precursors. J. Am. Chem. Soc. 125, 5897-5914 10.1021/ja029328d
67. Stich T. R., Buan N. R., Brunold T. C. (2004). Spectroscopic and computational studies of Co2+corrinoids: spectral and electronic properties of the biologically relevant base-on and base-off forms of Co2+cobalamin. J. Am. Chem. Soc. 126, 9735-9749 10.1021/ja0481631
68. 12 enzymes: structure, mechanism, inactivation, and reactivation of diol and glycerol dehydratases. Cell. Mol. Life Sci. 57, 106-127 10.1007/s000180050502
69. 12-dependent isomerization (eliminating) reactions. Chem. Rev. 103, 2095-2127 10.1021/cr020428b
70. Treutler O., Ahlrichs R. (1995). Efficient molecular numerical integration schemes. J. Chem. Phys. 102, 346-354 10.1063/1.469408
71. 12 coenzymes: the identification of a metastable cob(III)alamin photoproduct in the photolysis of methylcobalamin. J. Am. Chem. Soc. 120, 3597-3603 10.1021/ja974024q
72. 12 coenzymes: the photolysis and geminate recombination of adenosylcobalamin. J. Am. Chem. Soc. 120, 7286-7292 10.1021/ja981029u
73. Yoder L. M., Cole A. G., Walker L. A. II., Sension R. J. (2001). Time-resolved spectroscopic studies of b12 coenzymes: influence of solvent on the photolysis of adenosylcobalamin. J. Phys. Chem. B. 105, 12180-12188 10.1021/jp012157z