Reactivity of Biogenic Manganese Oxide for Metal Sequestration and Photochemistry: Computational Solid State Physics Study

전산 고체물리를 이용한 바이오 산화망간 광물의 금속흡착과 광화학 반응도의 이해

  • Kwon, Ki-Deok D. (Geochemistry Department, Earth Sciences Division, Lawrence Berkeley National Laboratory) ;
  • Sposito, Garrison (Geochemistry Department, Earth Sciences Division, Lawrence Berkeley National Laboratory)
  • 권기덕 (로렌스 버클리 국립연구소) ;
  • Received : 2010.05.19
  • Accepted : 2010.06.18
  • Published : 2010.06.30

Abstract

Many microbes, including both bacteria and fungi, produce manganese (Mn) oxides by oxidizing soluble Mn(II) to form insoluble Mn(IV) oxide minerals, a kinetically much faster process than abiotic oxidation. These biogenic Mn oxides drive the Mn cycle, coupling it with diverse biogeochemical cycles and determining the bioavailability of environmental contaminants, mainly through strong adsorption and redox reactions. This mini review introduces recent findings based on quantum mechanical density functional theory that reveal the detailed mechanisms of toxic metal adsorption at Mn oxide surfaces and the remarkable role of Mn vacancies in the photochemistry of these minerals.

많은 미생물들이 수용성 망간이온($Mn^{2+}$)을 불용성인 산화망간($Mn^{4+}$) 광물로 산화 침전시키는데, 이와 같은 생물학적 산화반응은 비생물학적 산화반응보다 훨씬 빠르게 일어난다. 이처럼 미생물에 의해 생성된 바이오 산화망간 광물은 표면의 강한 흡착성과 산화환원 반응을 통해 생지구화학 순환과 환경오염물질의 생물흡수도에 큰 역할을 한다. 본 논평은 양자역학의 밀도범함수 이론에 바탕을 둔 전산모사를 이용하여 산화망간 광물 표면의 독성금속 흡착의 자세한 기작과 망간원자 빈자리의 광화학적 역할을 새롭게 밝힌 최근 연구결과를 소개한다.

Keywords

References

  1. 김수진 (1990) 7 A 층상구조형 산화망간광물의 결정화학, 광물학회지, 3, 34-43.
  2. 최헌수, 장세원, 이성록 (2000) 망간단괴 미세조직에 따른 광물조성과 화학조성의 상관관계, 광물학회지, 13, 205-220.
  3. Armstrong, A.R. and Bruce, P.G. (1996) Synthesis of layered LiMnO2 as an electrode for rechargeable lithium batteries. Nature, 381, 499-500. https://doi.org/10.1038/381499a0
  4. Bargar, J.R., Fuller, C.C., Marcus, M.A., Brearley, A.J., Perez De la Rosa, M., Webb, S.M., and Caldwell, W.A. (2009) Structural characterization of terrestrial microbial Mn oxides from Pinal Creek, AZ. Geochim. Cosmochim. Acta, 73, 889-910. https://doi.org/10.1016/j.gca.2008.10.036
  5. Clark, S.J., Segall, M.D., Pickard, C.J., Hasnip, P.J., Probert, M.J., Refson, K., and Payne, M.C. (2005) First principles methods using CASTEP. Z. Kristallogr., 220, 567-570. https://doi.org/10.1524/zkri.220.5.567.65075
  6. Cramer, C.J. (2003) Essentials of Computational Chemistry. John Wiley & Sons Ltd, Chichester, 542p.
  7. Duckworth, O.W., Bargar, J.R., and Sposito, G. (2008) Sorption of ferric iron from ferrioxamine B to synthetic and biogenic layer type manganese oxides. Geochim. Cosmochim. Acta, 72, 3371-3380. https://doi.org/10.1016/j.gca.2008.04.026
  8. Forrez, I., Carballa, M., Verbeken, K., Vanhaecke, L., sener, M.S., Ternes, T., Boon, N., and Verstraete, W. (2010) Diclofenac oxidation by biogenic manganese oxides. Environ. Sci. Technol., 44, 3449-3454. https://doi.org/10.1021/es9027327
  9. Frisch, M.J., Trucks, G.W., Schlegel, H.B., Scuseria, G. E., Robb, M.A., Cheeseman, J.R., Scalmani, G., Barone, V., Mennucci, B., Petersson, G.A., Nakatsuji, H., Caricato, M., Li, X., Hratchian, H.P., Izmaylov, A.F., Bloino, J., Zheng, G., Sonnenberg, J.L., Hada, M., Ehara, M., Toyota, K., Fukuda, R., Hasegawa, J., Ishida, M., Nakajima, T., Honda, Y., Kitao, O., Nakai, H., Vreven, T., Montgomery, J.A., Jr., Peralta, J.E., Ogliaro, F., Bearpark, M., Heyd, J.J., Brothers, E., Kudin, K.N., Staroverov, V.N., Kobayashi, R., Normand, J., Raghavachari, K., Rendell, A., Burant, J. C., Iyengar, S.S., Tomasi, J., Cossi, M., Rega, N., Millam, J.M., Klene, M., Knox, J.E., Cross, J.B.,Bakken, V., Adamo, C., Jaramillo, J., Gomperts, R., Stratmann, R.E., Yazyev, O., Austin, A.J., Cammi, R., Pomelli, C., Ochterski, J.W., Martin, R.L., Morokuma, K., Zakrzewski, V.G., Voth, G.A., Salvador, P., Dannenberg, J.J., Dapprich, S., Daniels, A.D., Farkas, O., Foresman, J.B., Ortiz, J.V., Cioslowski, J., and Fox, D. J. (2009) Gaussian 09 (Revision A.2). Gaussian, Inc. Wallingford CT.
  10. Hattori, T., Saito, T., Ishida, K., Scheinost, A.C., Tsuneda, T., Nagasaki, S., and Tanaka, S. (2009) The structure of monomeric and dimeric uranyl adsorption complexes on gibbsite: A combined DFT and EXAFS study. Geochim. Cosmochim. Acta, 73, 5975-5988. https://doi.org/10.1016/j.gca.2009.07.004
  11. Hochella, M.F., Moore, J.N., Putnis, C.V., Putnis, A., Kasama, T., and Eberl, D.D. (2005) Direct observation of heavy metal-mineral association from the Clark Fork River Superfund Complex: Implications for metal transport and bioavailability. Geochim. Cosmochim. Acta, 69, 1651-1663. https://doi.org/10.1016/j.gca.2004.07.038
  12. Kang, K. and Cder, S. (2006) Factors that affect Li mobility in layered lithium transition metal oxides. Phys. Rev. B, 74, 094105. https://doi.org/10.1103/PhysRevB.74.094105
  13. Kim, S.H., Kim, S.J., and Oh, S.M. (1999) Preparation of layered $MnO_{2}$ via thermal decomposition of $KMnO_{4}$ and its electrochemical characterizations. Chem. Mater., 11, 557-563. https://doi.org/10.1021/cm9801643
  14. Kohn, W. and Sham, L.J. (1965) Self-consistent equations including exchange and correlation effects. Phys. Rev., 140, A1133-A1138. https://doi.org/10.1103/PhysRev.140.A1133
  15. Kresse, G. and Furthmuller, J. (1996) Efficient iterative schemes for ab initio total-energy calculations using a plane‐wave basis set. Phys. Rev. B, 54, 11169-11186. https://doi.org/10.1103/PhysRevB.54.11169
  16. Kwon, K.D., Green, H., Bjoorn, P., and Kubicki, J.D. (2006) Model bacterial extracellular polysaccharide adsorption onto silica and alumina: Quartz crystal microbalance with dissipation monitoring of dextran adsorption. Environ. Sci. Technol., 40, 7739-7744. https://doi.org/10.1021/es061715q
  17. Kwon, K.D. and Kubicki, J.D. (2004) Molecular orbital theory study on surface complex structures of phosphates to iron hydroxides: Calculation of vibrational frequencies and adsorption energies. Langmuir, 20, 9249-9254. https://doi.org/10.1021/la0487444
  18. Kwon, K.D., Refson, K., and Sposito, G. (2008) Defect‐ induced photoconductivity in layered manganese oxides: A density functional theory study. Phys. Rev. Lett., 100, 146601. https://doi.org/10.1103/PhysRevLett.100.146601
  19. Kwon, K.D., Refson, K., and Sposito, G. (2009a) Zinc surface complexes on birnessite: A density functional theory study. Geochim. Cosmochim. Acta, 73, 1273-1284. https://doi.org/10.1016/j.gca.2008.11.033
  20. Kwon, K.D., Refson, K., and Sposito, G. (2009b) On the role of Mn(IV) vacancies in the photoreductive dissolution of hexagonal birnessite. Geochim. Cosmochim. Acta, 73, 4142-4150. https://doi.org/10.1016/j.gca.2009.04.031
  21. Lanson, B., Marcus, M.A., Fakra, S., Panfili, F., Geoffroy, N., and Manceau, A. (2008) Formation of Zn-Ca phyllomanganate nanoparticles in grass roots. Geochim. Cosmochim. Acta, 72, 2478-2490. https://doi.org/10.1016/j.gca.2008.02.022
  22. Li, W., Feng, J., Kwon, K.D., Kubicki, J.D., and Phillips, B.L. (2010) Surface speciation of phosphate on boehmite ($\gamma$‐AlOOH) determined from NMR spectroscopy. Langmuir, 26, 4753-4761. https://doi.org/10.1021/la903484m
  23. Manceau, A., Lanson, B., and Drits, V.A. (2002) Structure of heavy metal sorbed birnessite. Part III: Results from powder and polarized extended X-ray absorption fine structure spectroscopy. Geochim. Cosmochim. Acta, 66, 2639-2663. https://doi.org/10.1016/S0016-7037(02)00869-4
  24. Manceau, A., Lanson, M., and Geoffroy, N. (2007) Natural speciation of Ni, Zn, Ba, and As in ferromanganese coatings on quartz using X-ray fluorescence, absorption, and diffraction. Geochim. Cosmochim. Acta, 71, 95-128. https://doi.org/10.1016/j.gca.2006.08.036
  25. Martin, R.M. (2004) Electronic Structure: Basic Theory and Practical Methods. Cambridge University Press, Cambridge, 624 p.
  26. Mason, S.E., Iceman, C.R., Tanwar, K.S., Trainor, T.P., and Chaka, A.M. (2009) Pb(II) Adsorption on isostructural hydrated alumina and hematite (0001) surfaces: A DFT study. J. Phys. Chem. C, 113, 2159- 2170. https://doi.org/10.1021/jp807321e
  27. Mattsson, A.E., Schultz, P.A., Desjarlais, M.P., Mattsson, T.R., and Leung, K. (2005) Designing meaningful density functional theory calculations in materials science-a primer. Model. Simul. Mater. Sci. Eng., 13, R1-R31. https://doi.org/10.1088/0965-0393/13/1/R01
  28. Morgan, J.J. (2000) Manganese in natural waters and earth's crust: its availability to organisms. In: Sigel, A. and Sigel, H. (eds.), Metal Ions in Biological Systems, Vol. 37, Marcel Dekker, Inc., New York, 1-34.
  29. Morgan, J.J. (2005) Kinetics of reaction between $O_2$ and Mn(II) species in aqueous solutions. Geochim. Cosmochim. Acta, 69, 35-48. https://doi.org/10.1016/j.gca.2004.06.013
  30. Ogata, A., Komaba, S., Baddour-Hadjean, R., Pereira-Ramos, J.P., and Kumagai, N. (2008) Doping effects on structure and electrode performance of K-birnessitetype manganese dioxides for rechargeable lithium battery. Electrochim. Acta, 53, 3084-3093. https://doi.org/10.1016/j.electacta.2007.11.038
  31. Payne, M.C., Teter, M.P., Allan, D.C., Arias, T.A., and Joannopoulos, J.D. (1992) Iterative minimization techniques for ab initio total-energy calculations: moleculardynamics and conjugate gradients. Rev. Mod. Phys., 64, 1045-1097. https://doi.org/10.1103/RevModPhys.64.1045
  32. Peacock, C.L. (2009) Physiochemical controls on the crystal-chemistry of Ni in birnessite: Genetic implications for ferromanganese precipitates. Geochim. Cosmochim. Acta, 73, 3568-3578. https://doi.org/10.1016/j.gca.2009.03.020
  33. Peacock, C.L., and Sherman, D.M. (2007) Sorption of Ni by birnessite: Equilibrium controls on Ni in seawater.Chem. Geol., 238, 94-106. https://doi.org/10.1016/j.chemgeo.2006.10.019
  34. Pena, J. (2009) Contaminant metal immobilization by biogenic manganese oxide nanoparticles: implications for natural attenuation and bioremediation. Ph. D. Thesis, University of California, Berkeley, California, USA.
  35. Pena, J., Kwon, K.D., Refson, K., Bargar, J.R., and Sposito, G. (2010) Mechanisms of nickel sorption by a bacteriogenic birnessite. Geochim. Cosmochim. Acta, 74, 3076-3089. https://doi.org/10.1016/j.gca.2010.02.035
  36. Perdew, J.P., Burke, K., and Ernzerhof, M. (1996) Generalized gradient approximation made simple, Phys. Rev. Lett., 77, 3865-3868. https://doi.org/10.1103/PhysRevLett.77.3865
  37. Perdow, J.P. and Ruzsinszky, A. (2010) Density functional theory of electronic structure: a short course for mineralogists and geophysicists. In: Wentzcovitch, R. and Stixrude, L. Editors, Theoretical and Computational Methods in Mineral Physics vol. 71, Mineralogical Society of America, Chantilly, VA. pp. 1-18.
  38. Pinaud, B.A. and Jaramillo, T.F. (2010) Manganese oxide thin film for photoelectrochemical hydrogen production. The Electrochemical Society meeting abstract, 1001, 1348.
  39. Post, J.E. (1999) Manganese oxide minerals: Crystal structures and economic and environmental significance. Proc. Natl. Acad. Sci. U.S.A., 96, 3447-3454. https://doi.org/10.1073/pnas.96.7.3447
  40. Post, J.E. and Appleman, D.E. (1988) Chalcophanite, $ZnMn_{3}O_{7}$.$3H_{2}O$ - New crystal-structure determinations. Am. Mineral., 73, 1401-1404.
  41. Russo, F., Johnson, C.J., Johnson, C.J., McKenzie, D., Aiken, J.M., and Pedersen, J.A. (2009) Pathogenic prion protein is degraded by a manganese oxide mineral found in soils. J. Gen. Virol., 90, 275-280. https://doi.org/10.1099/vir.0.003251-0
  42. Sakai, N., Ebina, Y., Takada, K., and Sasaki, T. (2005) Photocurrent generation from semiconducting manganese oxide nanosheets in response to visible light. J. Phys. Chem. B, 109, 9651-9655. https://doi.org/10.1021/jp0500485
  43. Saratovsky, I., Wightman, P.G., Pastén, P.A., Gaillard, J.F., and Poeppelmeier, K.R. (2006) Manganese oxides: Parallels between abiotic and biotic structures. J. Am. Chem. Soc., 128, 11188-11198. https://doi.org/10.1021/ja062097g
  44. Segall, M.D., Lindan, P.J.D., Probert, M.J., Pickard, C.J., Hasnip, P.J., Clark, S.J., and Payne, M.C. (2002) Firstprinciples simulation: ideas, illustrations and the CASTEP code. J. Phys. Condens. Matter., 14, 2717-2744. https://doi.org/10.1088/0953-8984/14/11/301
  45. Sherman, D.M. (2005) Electronic structures of iron(III) and manganese(IV) (hydr)oxide minerals: Thermodynamics of photochemical reductive dissolution in aquatic environments. Geochim. Cosmochim. Acta, 69, 3249-3255. https://doi.org/10.1016/j.gca.2005.01.023
  46. Spiro, T.G., Bargar, J.R., Sposito, G., and Tebo, B.M. (2010) Bacteriogenic manganese oxides. Acc. Chem. Res., 43, 2-9. https://doi.org/10.1021/ar800232a
  47. Sposito G. (2004) The Surface Chemistry of Natural Particles. Oxford University Press, New York, 242p.
  48. Sposito G. (2008) The Chemistry of Soils. Oxford University Press, New York, 329p.
  49. Sunda, W.G., Huntsman, S.A., and Harvey, G.R. (1983) Photoreduction of manganese oxides in seawater and its geochemical and biological implications. Nature, 301, 234-236. https://doi.org/10.1038/301234a0
  50. Takahashi, Y., Manceau, A., Geoffroy, N., Marcus, M.A., and Usui, A. (2007) Chemical and structural control of the partitioning of Co, Ce, and Pb in marine ferromanganese oxides. Geochim. Cosmochim. Acta, 71, 984-1008. https://doi.org/10.1016/j.gca.2006.11.016
  51. Tani, Y., Miyata, N., Ohashi, M., Ohnuki, T., Seyama, H., Iwahori, K., and Soma, M. (2004) Interaction of inorganic arsenic with biogenic manganese oxide produced by a Mn‐oxidizing fungus, strain KR21‐2. Env. Sci. Technol., 38, 6618-6624. https://doi.org/10.1021/es049226i
  52. Tebo, B.M., Bargar, J.R., Clement, B.G., Dick, G.J., Murray, K.J., Parker, D., Verity, R., and Webb, S.M. (2004) Biogenic manganese oxides: Properties and mechanisms of formation. Annu. Rev. Earth Planet. Sci., 32, 287-328. https://doi.org/10.1146/annurev.earth.32.101802.120213
  53. te Velde, G., Bickelhaupt, F.M., Baerends, E.J., Guerra, C.F., van Gisbergen, S.J.A., Snijders, J.G., and Ziegler, T. (2001) Chemistry with ADF. J. Comput. Chem., 22, 931-967. https://doi.org/10.1002/jcc.1056
  54. Toner, B., Manceau, A., Webb, S.M., and Sposito, G. (2006) Zinc sorption to biogenic hexagonal‐birnessite particles within a hydrated bacterial biofilm. Geochim. Cosmochim. Acta, 70, 27-43.
  55. Villalobos, M., Bargar, J., and Sposito, G. (2005) Mechanisms of Pb(II) sorption on a biogenic manganese oxide. Env. Sci. Technol., 39, 569-576. https://doi.org/10.1021/es049434a
  56. Villalobos, M., Lanson, B., Manceau, A., Toner, B., and Sposito, G. (2006) Structural model for the biogenic Mn oxide produced by Pseudomonas putida. Am. Mineral., 91, 489-502. https://doi.org/10.2138/am.2006.1925
  57. Villalobos, M., Toner, B., Bargar, J., and Sposito, G. (2003) Characterization of the manganese oxide produced by Pseudomonas putida strain MnB1. Geochim. Cosmochim. Acta, 67, 2649-2662. https://doi.org/10.1016/S0016-7037(03)00217-5
  58. Waite, T.D., Wrigley, I.C., and Szymczak, R. (1988) Photoassisted dissolution of a colloidal manganese oxide in the presence of fulvic-acid. Env. Sci. Technol., 22, 778-785. https://doi.org/10.1021/es00172a006
  59. Webb, S.M., Tebo, B.M., and Bargat, J.R. (2005) Structural characterization of biogenic Mn oxides produced in seawater by the marine bacillus sp strain SG-1. Am. Mineral., 90, 1342-1357. https://doi.org/10.2138/am.2005.1669