Browse > Article

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

Kwon, Ki-Deok D. (Geochemistry Department, Earth Sciences Division, Lawrence Berkeley National Laboratory)
Sposito, Garrison (Geochemistry Department, Earth Sciences Division, Lawrence Berkeley National Laboratory)
Publication Information
Journal of the Mineralogical Society of Korea / v.23, no.2, 2010 , pp. 161-170 More about this Journal
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.
Keywords
biogenic manganese oxide; density functional theory; metal adsorption; photoreactivity; vacancy;
Citations & Related Records
연도 인용수 순위
  • Reference
1 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.   DOI   ScienceOn
2 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.   DOI   ScienceOn
3 Villalobos, M., Bargar, J., and Sposito, G. (2005) Mechanisms of Pb(II) sorption on a biogenic manganese oxide. Env. Sci. Technol., 39, 569-576.   DOI   ScienceOn
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.   DOI   ScienceOn
5 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.   DOI   ScienceOn
6 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.   DOI   ScienceOn
7 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.   DOI   ScienceOn
8 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.   DOI   ScienceOn
9 Sposito G. (2008) The Chemistry of Soils. Oxford University Press, New York, 329p.
10 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.   DOI
11 Cramer, C.J. (2003) Essentials of Computational Chemistry. John Wiley & Sons Ltd, Chichester, 542p.
12 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.   DOI   ScienceOn
13 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.   DOI   ScienceOn
14 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.   DOI   ScienceOn
15 Spiro, T.G., Bargar, J.R., Sposito, G., and Tebo, B.M. (2010) Bacteriogenic manganese oxides. Acc. Chem. Res., 43, 2-9.   DOI   ScienceOn
16 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.
17 Sposito G. (2004) The Surface Chemistry of Natural Particles. Oxford University Press, New York, 242p.
18 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.   DOI   ScienceOn
19 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.   DOI   ScienceOn
20 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.   DOI   ScienceOn
21 Perdew, J.P., Burke, K., and Ernzerhof, M. (1996) Generalized gradient approximation made simple, Phys. Rev. Lett., 77, 3865-3868.   DOI   ScienceOn
22 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.
23 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.   DOI   ScienceOn
24 Pinaud, B.A. and Jaramillo, T.F. (2010) Manganese oxide thin film for photoelectrochemical hydrogen production. The Electrochemical Society meeting abstract, 1001, 1348.
25 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.   DOI   ScienceOn
26 Post, J.E. (1999) Manganese oxide minerals: Crystal structures and economic and environmental significance. Proc. Natl. Acad. Sci. U.S.A., 96, 3447-3454.   DOI   ScienceOn
27 Armstrong, A.R. and Bruce, P.G. (1996) Synthesis of layered LiMnO2 as an electrode for rechargeable lithium batteries. Nature, 381, 499-500.   DOI   ScienceOn
28 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.
29 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.   DOI   ScienceOn
30 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.   DOI   ScienceOn
31 Morgan, J.J. (2005) Kinetics of reaction between $O_2$ and Mn(II) species in aqueous solutions. Geochim. Cosmochim. Acta, 69, 35-48.   DOI   ScienceOn
32 김수진 (1990) 7 A 층상구조형 산화망간광물의 결정화학, 광물학회지, 3, 34-43.
33 최헌수, 장세원, 이성록 (2000) 망간단괴 미세조직에 따른 광물조성과 화학조성의 상관관계, 광물학회지, 13, 205-220.
34 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.   DOI   ScienceOn
35 Peacock, C.L., and Sherman, D.M. (2007) Sorption of Ni by birnessite: Equilibrium controls on Ni in seawater.Chem. Geol., 238, 94-106.   DOI   ScienceOn
36 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.
37 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.   DOI   ScienceOn
38 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.
39 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.   DOI   ScienceOn
40 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.   DOI
41 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.   DOI   ScienceOn
42 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.   DOI   ScienceOn
43 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.   DOI   ScienceOn
44 Martin, R.M. (2004) Electronic Structure: Basic Theory and Practical Methods. Cambridge University Press, Cambridge, 624 p.
45 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.   DOI   ScienceOn
46 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.   DOI   ScienceOn
47 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.   DOI   ScienceOn
48 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.   DOI   ScienceOn
49 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.   DOI   ScienceOn
50 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.   DOI   ScienceOn
51 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.   DOI   ScienceOn
52 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.
53 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.   DOI   ScienceOn
54 Kohn, W. and Sham, L.J. (1965) Self-consistent equations including exchange and correlation effects. Phys. Rev., 140, A1133-A1138.   DOI
55 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.   DOI   ScienceOn
56 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.   DOI   ScienceOn
57 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.   DOI   ScienceOn
58 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.   DOI   ScienceOn
59 Kang, K. and Cder, S. (2006) Factors that affect Li mobility in layered lithium transition metal oxides. Phys. Rev. B, 74, 094105.   DOI   ScienceOn