Combined spectroscopic and computational analysis of the vibrational properties of vitamin B12 in its Co3+, Co2+, and Co1+ oxidation states

Journal of Physical Chemistry B

Volumn 117, Issue 18, 2013, Pages 5397-5410

  Park, Kiyoung ^a,b   Brunold, Thomas C ^a  

^a UNIVERSITY OF WISCONSIN MADISON   (United States)

^b NONE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DENSITY FUNCTIONAL THEORY; ELECTRONIC STRUCTURE; LASER EXCITATION;

COMPUTATIONAL ANALYSIS; COMPUTATIONAL METHODOLOGY; DENSITY FUNCTIONAL THEORY CALCULATIONS; ELECTRONIC TRANSITION; EXPERIMENTAL OBSERVATION; NORMAL MODES OF VIBRATION; RESONANCE RAMAN SPECTRA; VIBRATIONAL PROPERTIES;

EXCITED STATES;

EID: 84877722114     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp309392u     Document Type: Article

References (81)

1. The Nomenclature of Corrinoids (1973 recommendations). IUPAC-IUB Commission on Biochemical Nomenclature. Biochemistry 1974, 13, 1555-1560.
2. 12 Nature 1956, 178, 64-66
3. 12 Nature 1955, 176, 325-328
4. 12 Coenzyme at 15 K-Structure Analysis and Comparison with the Structure at 279 K Acta Crystallogr., Sect. B 1993, 49, 79-89
5. Randaccio, L.; Furlan, M.; Geremia, S.; Slouf, M.; Srnova, I.; Toffoli, D. Similarities and Differences between Cobalamins and Cobaloximes. Accurate Structural Determination of Methylcobalamin and of LiCl-and KCl-Containing Cyanocobalamins by Synchrotron Radiation Inorg. Chem. 2000, 39, 3403-3413
6. 12: Catalysis by Cobalamin-Dependent Enzymes Annu. Rev. Biochem. 2003, 72, 209-247
7. Buan, N. R.; Suh, S. J.; Escalante-Semerena, J. C. The EutT Gene of Salmonella enterica Encodes an Oxygen-Labile, Metal-Containing ATP: Corrinoid Adenosyltransferase Enzyme J. Bacteriol. 2004, 186, 5708-5714
8. 12-Dependent Methylmalonyl-CoA Mutase Biochemistry 2000, 39, 7998-8006
9. Johnson, C. L. V.; Pechonick, E.; Park, S. D.; Havemann, G. D.; Leal, N. A.; Bobik, T. A. Functional Genomic, Biochemical, and Genetic Characterization of the Salmonella pduO Gene, an ATP:Cob(I)alamin Adenosyltransferase Gene J. Bacteriol. 2001, 183, 1577-1584
10. Marsh, E. N. G.; Ballou, D. P. Coupling of Cobalt-Carbon Bond Homolysis and Hydrogen Atom Abstraction in Adenosylcobalamin-Dependent Glutamate Mutase Biochemistry 1998, 37, 11864-11872
11. Thoma, N. H.; Evans, P. R.; Leadlay, P. F. Protection of Radical Intermediates at the Active Site of Adenosylcobalamin-Dependent Methylmalonyl-CoA Mutase Biochemistry 2000, 39, 9213-9221
12. 12 at Physiological Temperatures: Activation Parameters for Cobalt-Carbon Bond Homolysis and a Quantitative Analysis of the Perturbation of the Homolysis Equilibrium by the Ribonucleoside Triphosphate Reductase from Lactobacillus leichmannii J. Inorg. Biochem. 1999, 77, 185-195
13. Gerfen, G. J.; Licht, S.; Willems, J. P.; Hoffman, B. M.; Stubbe, J. Electron Paramagnetic Resonance Investigations of a Kinetically Competent Intermediate Formed in Ribonucleotide Reduction: Evidence for a Thiyl Radical-Cob(II)alamin Interaction J. Am. Chem. Soc. 1996, 118, 8192-8197
14. Matthews, R. G. Cobalamin-Dependent Methyltransferases Acc. Chem. Res. 2001, 34, 681-689
15. 12-Dependent Mutases Chem. Rev. 2003, 103, 2083-2094
16. Giorgetti, M.; Ascone, I.; Berrettoni, M.; Conti, P.; Zamponi, S.; Marassi, R. In Situ X-ray Absorption Spectroelectrochemical Study of Hydroxocobalamin J. Biol. Inorg. Chem. 2000, 5, 156-166
17. 12 and Its Derivatives S. Afr. J. Sci. 2004, 100, 368-380
18. 12 Intermediate-Implications for Enzyme Catalysis Biophys. J. 1992, 63, 412-417
19. 12): Synthesis and Biological Significance Annu. Rev. Microbiol. 1996, 50, 137-181
20. 12) Nat. Prod. Rep. 2002, 19, 390-412
21. 12 J. Am. Chem. Soc. 1987, 109, 1238-1240
22. Randaccio, L.; Geremia, S.; Nardin, G.; Wuerges, J. X-ray Structural Chemistry of Cobalamins Coord. Chem. Rev. 2006, 250, 1332-1350
23. 12-Dependent Rearrangements Science 1985, 227, 869-875
24. Hay, B. P.; Finke, R. G. Thermolysis of the Co-C Bond in Adenosylcorrins. 3. Quantification of the Axial Base Effect in Adenosylcobalamin by the Synthesis and Thermolysis of Axial Base-Free Adenosylcobinamide-Insights into the Energetics of Enzyme-Assisted Cobalt Carbon Bond Homolysis J. Am. Chem. Soc. 1987, 109, 8012-8018
25. Pett, V. B.; Liebman, M. N.; Murrayrust, P.; Prasad, K.; Glusker, J. P. Conformational Variability of Corrins-Some Methods of Analysis J. Am. Chem. Soc. 1987, 109, 3207-3215
26. 12; Dolphin, D., Ed.; Wiley-Interscience: New York, 1982.
27. 12 Cofactor J. Am. Chem. Soc. 2006, 128, 9144-9156
28. 12 Cofactors and Biologically Relevant Precursors J. Am. Chem. Soc. 2003, 125, 5897-5914
29. 2+ Cobalamin J. Am. Chem. Soc. 2004, 126, 9735-9749
30. 12-Dependent Enzymes: Cryogenic Resonance Raman Studies of Methylmalonyl-Coenzyme A Mutase J. Am. Chem. Soc. 1999, 121, 7063-7070
31. 12 Binding to Methylmalonyl-Coenzyme A Mutase Changes the Corrin Ring Conformation but Leaves the Co-C Bond Essentially Unaffected J. Am. Chem. Soc. 1998, 120, 9947-9948
32. Huhta, M. S.; Chen, H. P.; Hemann, C.; Hille, C. R.; Marsh, E. N. G. Protein-Coenzyme Interactions in Adenosylcobalamin-Dependent Glutamate Mutase Biochem. J. 2001, 355, 131-137
33. 12) Appl. Spectrosc. 1973, 27, 390-391
34. 12 and Some Cobalt Corrinoid Derivatives J. Chem. Soc., Faraday Trans. 1973, 69, 1350-1358
35. Mayer, E.; Gardiner, D. J.; Hester, R. E. The Selective Enhancement of Band Intensities in Resonance Raman Spectra of Cobalt Corrinoids Mol. Phys. 1973, 26, 783-787
36. 12 Derivatives with a Rapid-Flow Technique J. Raman Spectrosc. 1977, 6, 57-60
37. Galluzzi, F.; Garozzo, M.; Ricci, F. F. Resonance Raman Scattering and Vibronic Coupling in Aquo-and Cyano-Cobalamin J. Raman Spectrosc. 1974, 2, 351-362
38. Andruniow, T.; Zgierski, M. Z.; Kozlowski, P. M. Vibrational Analysis of Methylcobalamin J. Phys. Chem. A 2002, 106, 1365-1373
39. 12 and Other Cobalamins and of Imidazole and Imidazolate Methylcobinamide Derivatives in Aqueous Solution Inorg. Chem. 1996, 35, 4656-4662
40. Blout, E. R.; Fields, M.; Karplus, R. Absorption Spectra. VI. The Infrared Spectra of Certain Compounds Containing Conjugated Double Bonds J. Am. Chem. Soc. 1948, 70, 194-198
41. Gavin, R. M., Jr.; Rice, S. A. Correlation of Pi-Electron Density with Vibrational Frequencies of Linear Polyenes J. Chem. Phys. 1971, 55, 2675-2681
42. 12 J. Pharm. Pharmacol. 1950, 2, 944-955
43. 12, 2.Mitteilung Helv. Chim. Acta 1951, 34, 1356-1361
44. 12. 3. Proton Magnetic Resonance Spectra of Some Cobalamins J. Chem. Soc. 1965, 2859-2865
45. 12 Chemistry-the Crystal and Molecular Structure of Cob(II)alamin J. Am. Chem. Soc. 1989, 111, 8936-8938
46. ADF2008.01; SCM: Theoretical Chemistry, Vrije Universiteit, Amsterdam, The Netherlands.
47. Perdew, J. P.; Burke, K.; Ernzerhof, M. Generalized Gradient Approximation Made Simple Phys. Rev. Lett. 1996, 77, 3865-3868
48. Vosko, S. H.; Wilk, L.; Nusair, M. Accurate Spin-Dependent Electron Liquid Correlation Energies for Local Spin-Density Calculations-a Critical Analysis Can. J. Phys. 1980, 58, 1200-1211
49. Berces, A.; Dickson, R. M.; Fan, L. Y.; Jacobsen, H.; Swerhone, D.; Ziegler, T. An Implementation of the Coupled Perturbed Kohn-Sham Equations: Perturbation due to Nuclear Displacements Comput. Phys. Commun. 1997, 100, 247-262
50. Guerra, C. F.; Snijders, J. G.; te Velde, G.; Baerends, E. J. Towards an Order-N DFT Method Theor. Chem. Acc. 1998, 99, 391-403
51. Jacobsen, H.; Berces, A.; Swerhone, D. P.; Ziegler, T. Analytic Second Derivatives of Molecular Energies: A Density Functional Implementation Comput. Phys. Commun. 1997, 100, 263-276
52. Velde, G. T.; Bickelhaupt, F. M.; Baerends, E. J.; Guerra, C. F.; Van Gisbergen, S. J. A.; Snijders, J. G.; Ziegler, T. Chemistry with ADF J. Comput. Chem. 2001, 22, 931-967
53. Wolff, S. K. Analytical Second Derivatives in the Amsterdam Density Functional Package Int. J. Quantum Chem. 2005, 104, 645-659
54. Neese, F.; Petrenko, T.; Ganyushin, D.; Olbrich, G. Advanced Aspects of Ab Initio Theoretical Optical Spectroscopy of Transition Metal Complexes: Multiplets, Spin-Orbit Coupling and Resonance Raman Intensities Coord. Chem. Rev. 2007, 251, 288-327
55. Neugebauer, J.; Baerends, E. J.; Efremov, E. V.; Ariese, F.; Gooijer, C. Combined Theoretical and Experimental Deep-UV Resonance Raman Studies of Substituted Pyrenes J. Phys. Chem. A 2005, 109, 2100-2106
56. 2 J. Chem. Phys. 2004, 121, 6155-6166
57. Neugebauer, J.; Baerends, E. J.; Nooijen, M. Vibronic Structure of the Permanganate Absorption Spectrum from Time-Dependent Density Functional Calculations J. Phys. Chem. A 2005, 109, 1168-1179
58. Nooijen, M. First-Principles Simulation of the UV Absorption Spectrum of Ketene Int. J. Quantum Chem. 2003, 95, 768-783
59. ORCA-An Ab Initio, DFT and Semiempirical Electronic Structure Package, version 2.6.4 ed.; 2007.
60. Neese, F.; Olbrich, G. Efficient Use of the Resolution of the Identity Approximation in Time-Dependent Density Functional Calculations with Hybrid Density Functionals Chem. Phys. Lett. 2002, 362, 170-178
61. Baerends, E. J.; Ellis, D. E.; Ros, P. Self-Consistent Molecular Hartree-Fock-Slater Calculations-I. The Computational Procedure Chem. Phys. 1973, 2, 41-51
62. Dunlap, B. I.; Connolly, J. W. D.; Sabin, J. R. Some Approximations in Applications of X-Alpha Theory J. Chem. Phys. 1979, 71, 3396-3402
63. Eichkorn, K.; Treutler, O.; Ohm, H.; Haser, M.; Ahlrichs, R. Auxiliary Basis Sets to Approximate Coulomb Potentials Chem. Phys. Lett. 1995, 240, 283-289
64. Eichkorn, K.; Weigend, F.; Treutler, O.; Ahlrichs, R. Auxiliary Basis Sets for Main Row Atoms and Transition Metals and Their Use to Approximate Coulomb Potentials Theor. Chem. Acc. 1997, 97, 119-124
65. Kendall, R. A.; Fruchtl, H. A. The Impact of the Resolution of the Identity Approximate Integral Method on Modern Ab Initio Algorithm Development Theor. Chem. Acc. 1997, 97, 158-163
66. Vanalsenoy, C. Ab Initio Calculations on Large Molecules-The Multiplicative Integral Approximation J. Comput. Chem. 1988, 9, 620-626
67. Whitten, J. L. Coulombic Potential-Energy Integrals and Approximations J. Chem. Phys. 1973, 58, 4496-4501
68. Godbout, N.; Salahub, D. R.; Andzelm, J.; Wimmer, E. Optimization of Gaussian-Type Basis-Sets for Local Spin-Density Functional Calculations 0.1. Boron through Neon, Optimization Technique and Validation Can. J. Chem. 1992, 70, 560-571
69. Schafer, A.; Horn, H.; Ahlrichs, R. Fully Optimized Contracted Gaussian-Basis Sets for Atoms Li to Kr J. Chem. Phys. 1992, 97, 2571-2577
70. Hirata, S.; Head-Gordon, M. Time-Dependent Density Functional Theory within the Tamm-Dancoff Approximation Chem. Phys. Lett. 1999, 314, 291-299
71. Bergman, D. L.; Laaksonen, L.; Laaksonen, A. Visualization of Solvation Structures in Liquid Mixtures J. Mol. Graphics Modell. 1997, 15, 301-306
72. Laaksonen, L. A Graphics Program for the Analysis and Display of Molecular-Dynamics Trajectories J. Mol. Graphics 1992, 10, 33-34
73. Laaksonen, L. gOpenMol, 3.00 ed.; 2005.
74. 12 Models J. Chem. Phys. 2001, 115, 7522-7533
75. 12; Banerjee, R., Ed.; John Wiley & Sons, Inc.: New York, 1999; pp 239-260.
76. Czernuszewicz, R. S.; Spiro, T. G. IR, Raman, and Resonance Raman Spectroscopy. In Inorganic Electronic Structure and Spectroscopy; Solomon, E. I.; Lever, A. B. P., Eds.; John Wiley & Sons, Inc.: New York, 1999; Vol. 1, pp 353-441.
77. 12 and Related Cob(III)alamins J. Am. Chem. Soc. 2006, 128, 801-808
78. 12 J. Phys. Chem. B 2011, 115, 13304-13319
79. 12 Compound Containing No Cobalt Proc. Natl. Acad. Sci. U.S.A. 1965, 54, 934-942
80. Shorygin, P. P. Raman Scattering of Light near and far from Resonance Sov. Phys. Usp. 1973, 16, 99-120
81. Jensen, K. P. Electronic Structure of Cob(I)alamin: The Story of an Unusual Nucleophile J. Phys. Chem. B 2005, 109, 10505-10512