Browse > Article
http://dx.doi.org/10.4491/KSEE.2017.39.7.426

Reviews in Infrared Spectroscopy and Computational Chemistry to Reveal Rhizospheric Interactions among Organic Acids, Oxyanions and Metal oxides: Fundamental Principles and Spectrum Processing  

Han, Junho (Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University)
Ro, Hee-Myong (Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University)
Publication Information
Abstract
This review summarizes advantage and limitation in infrared spectroscopy and computational chemistry to understand rhizospheric interaction among organic acids, oxyanions and metal oxides. Since organic acids and metal oxides determine dynamics of oxyanions in the soil environment, knowledge of fundamental mechanisms is a prerequisite for understanding the interactions at soil-water interface. Attenuated total reflectance-fourier transform infrared spectroscopy (ATR-FTIR) is a powerful tool to measure the interfacial reactions. However, the ATR-FTIR measurements are abstruse, because the optical characteristics for measurements are variable depending on the experimental setup. In addition, spectral overlapping is a primary obstacle to the analysis of the interfacial reaction; thus, it is essential to detect and to deconvolute bands for signal interpretation. In this review, we expained the fundamental principle for spectrum processing, and four band identification methods, such as derivative spectroscopy, two-dimension correlation spectroscopy, multivariate curve resolution, and computational chemistry with example of aqueous phosphate speciation. As a result, spectrum processing and computational chemistry improved interpretation and spectral deconvolution of overlapped spectra in relatively simple systems, but it was still unsatisfactory for the problems in more complexed system like nature. Nevertheless, we believed that our challenge would contribute practically to develop adequate analytical procedure, signal processing and protocols that could help to improve interpretation and to understand the interfacial interactions of oxyanions in natural systems.
Keywords
Infrared Spectroscopy; Computational Spectroscopy; Attenuated Total Reflectance; Organic Acid; Oxyanion; Metal Oxide;
Citations & Related Records
연도 인용수 순위
  • Reference
1 Griffiths, T. R. and Hubbard, H. V. S. A., "Absorption Spectrum of Single-crystal $UO_2$: Identification of and Effect of Temperature on the Peak Positions of Essentially All Optical Transitions in the Visible to Near Infrared Regions Using Derivative Spectroscopy," J. Nucl. Mater., 185, 243-259(1991).   DOI
2 Noda, I., Dowrey, A. E., Marcoli, C., Story, G. M. and Ozaki, Y., "Generalized Two-Dimensional Correlation Spectroscopy," Spectrosc., 54(7), 236A-248A(2000).   DOI
3 Pazderka, T. and Kopecky, Jr, V., "2D Correlation Spectroscopy and its Application in Vibrational Spectroscopy Using Matlab," (2008).
4 Noda, I., "Techniques of Two-dimensional (2D) Correlation Spectroscopy Useful in Life," Biomed. Spectrosc. Imaging, 4, 109-127(2015).
5 Planinsek, O., Planinsek, D. and Zega, A., "Surface Analysis of Powder Binary Mixtures with ATR FTIR Spectroscopy," Int. J. Pharm., 319, 13-19(2006).   DOI
6 de Juan, A. and Tauler, R., "Multivariate Curve Resolution (MCR) from 2000: Progress in Concepts and Applications," Crit. Rev. Anal. Chem., 36, 163-176(2006).   DOI
7 Ruckebusch, C., Duponchel, L., Huvenne, J. P. and Saurina, J., "Multivariate Curve Resolution of Step-scan FTIR Spectral Data," Vib. Spectrosc., 35, 21-26(2004).   DOI
8 Kessler, W. and Kessler, R. W., "Multivariate Curve Resolution: A Method of Evaluating the Kinetics of Biotechnological Reactions," Anal. Bioanal. Chem., 384, 1087-1095(2006).   DOI
9 Ruckebusch, C. and Blanchet, L., "Multivariate Curve Resolution: A Review of Advanced and Tailored Applications and Challenges," Anal. Chim. Acta, 765, 28-36(2013).   DOI
10 Johnson, D. L., "Simultaneous Determination of Arsenate and Phosphate in Natural Waters," Environ. Sci. Technol., 5, 411-414(1971).   DOI
11 Sparks, D. L., "New Frontiers in Elucidating The Kinetics and Mechanisms of Metal and Oxyanion Sorption at the Soil Mineral/water Interface," J. Plant Nutr. Soil Sci., 163, 563-570(2000).   DOI
12 Jackson, B. P. and Bertsch, P. M., "Determination of Arsenic Speciation in Poultry Wastes By IC-ICP-MS," Environ. Sci. Technol., 35, 4868-4873(2001).   DOI
13 Mir, K. A., Rutter, A., Koch, I., Smith, P., Reimer, K. J. and Poland, J. S., "Extraction and Speciation of Arsenic in Plants Grown on Arsenic Contaminated Soils," Talanta, 72, 1507-1518(2007).   DOI
14 Rudolph D. I. and Gert, W. W. F., "Vibrational Spectroscopic Studies and Density Functional Theory Calculations of Speciation in the $CO_2$-Water System," Appl. Spectrosc., 60, 130-144(2006).   DOI
15 Jaumot, J., de Juan, A. and Tauler, R., "MCR-ALS GUI 2.0: New Features and Applications," Chemom. Intell. Lab. Syst., 140, 1-12(2015).   DOI
16 Felten, J., Hall, H., Jaumot, J., Tauler, R., de Juan, A. and Gorzsas, A., "Vibrational Spectroscopic Image Analysis of Biological Material Using Multivariate Curve Resolution-alternating Least Squares (MCR-ALS)," Nat. Protoc., 10, 217-240(2015).   DOI
17 Klahn, M., Mathias, G., Kotting, C., Nonella, M., Schlitter, J., Gerwert, K. and Tavan, P., "IR Spectra of Phosphate Ions in Aqueous Solution : Predictions of a DFT / MM Approach Compared with Observations," J. Phys. Chem. A, 108, 6186-6194(2004).
18 Hanwell, M. D. Lonie, D. C., Vandermeersch, T., Zurek, E. and Hutchison, G. C. D. E., "Avogadro: An Advanced Semantic Chemical Editor, Visualisation, and Analysis Platform," J. Chem. Informatics, 4, 1-17(2012).
19 Bhandari, N., Hausner, D. B., Kubicki, J. D. and Strongin, D. R., "Photodissolution of Ferrihydrite in the Presence of Oxalic Acid: An in Situ ATR-FTIR/DFT Study," Langmuir, 26, 16246-16253(2010).   DOI
20 Yaguchi, M., Uchida, T., Motobayashi, K. and Osawa, M., "Speciation of Adsorbed Phosphate at Gold Electrodes: A Combined Surface-Enhanced Infrared Absorption Spectroscopy and DFT Study," J. Phys. Chem. Lett., 7, 3097-3102(2016).   DOI
21 Goh, K. H. and Lim, T. T., "Geochemistry of Inorganic Arsenic and Selenium in a Tropical Soil: Effect of Reaction Time, PH, and Competitive Anions on Arsenic and Selenium Adsorption," Chemosphere, 55, 849-859(2004).   DOI
22 Szekeres, M. and Tombacz, E., "Surface Charge Characterization of Metal Oxides by Potentiometric Acid-base Titration, Revisited Theory and Experiment," Colloids Surf., A, 414, 302-313(2012).   DOI
23 Su, C. and Suarez, D. L., "Selenate and Selenite Sorption on Iron Oxides," Soil Sci. Soc. Am. J., 64, 101(2000).   DOI
24 Wei, S., Tan, W., Liu, F., Zhao, W. and Weng, L., "Surface Properties and Phosphate Adsorption of Binary Systems Containing Goethite and Kaolinite," Geoderma, 213, 478-484(2014).   DOI
25 Bucher, M., "Functional Biology of Plant Phosphate Uptake at Root and Mycorrhiza Interfaces," New Phytol., 173, 11-26(2007).   DOI
26 Parker, J. L. and Newstead, S., "Molecular Basis of Nitrate Uptake by the Plant Nitrate Transporter NRT1.1," Nature, 507, 68-72(2014).   DOI
27 Ariz, I., Cruz, C., Moran, J. F., Gonzalez-Moro, M. B., Garcia-Olaverri, C., Gonzalez-Murua, C., Martins-Loucao, M. a and Aparicio-Tejo, P. M., "Depletion of the Heaviest Stable N Isotope is Associated with $NH_4{^+}/NH_3$ Toxicity in $NH_4{^+}$-fed Plants," BMC Plant Biol., 11, 83(2011).   DOI
28 Arai, Y. and Sparks, D., "Phosphate Reaction Dynamics in Soils and Soil Components: A Multiscale Approach," Adv. Agron., 94, 135-179(2007).
29 Aufort, J., Segalen, L., Gervais, C., Brouder, C. and Balan, E., "Modeling the Attenuated Total Reflectance Infrared (ATR-FTIR) Spectrum of Apatite," Phys. Chem. Miner.,(2016).
30 Lopez-Arredondo, D. L., Leyva-Gonzalez, M. A., Gonzalez-Morales, S. I., Lopez-Bucio, J. and Herrera-Estrella, L., "Phosphate Nutrition: Improving Low-phosphate Tolerance in Crops," Annu. Rev. Plant Biol., 65, 95-123(2014).   DOI
31 Andrew, S., Bob, F. and Paul, W., "Practical and Innovative Measures for the Control of Agricultural Phosphorus Losses To Water," J. Environ. Qual., 29, 1-9(2000).
32 Zamparas, M. and Zacharias, I., "Restoration of Eutrophic Freshwater by Managing Internal Nutrient Loads. a Review," Sci. Total Environ., 496, 551-562(2014).   DOI
33 Riley, W., Ortiz-Monasterio, I. and Matson, P., "Nitrogen Leaching and Soil Nitrate, Nitrite, and Ammonium Levels Under Irrigated Wheat in Northern Mexico," Nutr. Cycl. Agroecosys., 61, 223-236(2001).   DOI
34 Zhang, H. and Selim, H. M., "Colloid Mobilization and Arsenite Transport in Soil Columns: Effect of Ionic Strength," J. Environ. Qual., 36, 1273-1280(2007).   DOI
35 Gadd, G. M., "Metals, Minerals and Microbes: Geomicrobiology and Bioremediation," Microbiol., 156, 609-643(2010).   DOI
36 Bais, H. P., Weir, T. L., Perry, L. G., Gilroy, S. and Vivanco, J. M., "The role of Root Exudates in Rhizosphere Interactions with Plants and Other Organisms," Annu. Rev. Plant Biol., 57, 233-266(2006).   DOI
37 Kim, K., Owens, G. and Naidu, R., "Effect of Root-induced Chemical Changes on Dynamics and Plant Uptake of Heavy Metals In Rhizosphere Soils," Pedosphere, 20, 494-504(2010).   DOI
38 Baetz, U. and Martinoia, E., "Root Exudates: The Hidden Part of Plant Defense," Trends Plant Sci., 19, 90-98(2014).   DOI
39 Fan, J. X., Wang, Y. J., Liu, C., Wang, L. H., Yang, K., Zhou, D. M., Li, W. and Sparks, D. L., "Effect of Iron Oxide Reductive Dissolution on the Transformation and Immobilization of Arsenic in Soils: New Insights from X-ray Photoelectron and X-ray Absorption Spectroscopy," J. Hazard. Mater., 279, 212-219(2014).   DOI
40 McGeehan, S. L., Fendorf, S. E. and Naylor, D. V, "Alteration of Arsenic Sorption in Flooded-dried Soils," Soil Sci. Soc. Am. J., 62, 828-833(1998).   DOI
41 Hind, A. R., Bhargava, S. K. and McKinnon, A., "At The Solid/liquid Interface: FTIR/ATR - the Tool of Choice," Adv. Colloid Interface Sci., 93, 91-114(2001).   DOI
42 Mudunkotuwa, I. A, Minshid, A. Al and Grassian, V. H., "ATR-FTIR Spectroscopy as a Tool to Probe Surface Adsorption on Nanoparticles at the Liquid-solid Interface in Environmentally and Biologically Relevant Media," Analyst., 139, 870-881(2014).   DOI
43 Shi, Q.-T. and Yan, W., "Adsorption of Arsenate on Lanthanum-impregnated Activated Alumina: In Situ ATR-FTIR and Two-dimensional Correlation Analysis Study," Chinese Chem. Lett., 26, 200-204(2014).
44 Max, J.-J. and Chapados, C., "Isotope Effects in Liquid Water by Infrared Spectroscopy. III. $H_2O$ and $D_2O$ Spectra from 6000 To 0 Cm(-1)," J. Chem. Phys., 131, 184505 (2009).   DOI
45 Kubicki, J., Paul, K., Kabalan, L. and Zhu, Q., "ATR-FTIR and Density Functional Theory Study of the Structures, Energetics, and Vibrational Spectra of Phosphate Adsorbed onto Goethite," Langmuir,(2012).
46 Watts, H., Tribe, L. and Kubicki, J., "Arsenic Adsorption onto Minerals: Connecting Experimental Observations with Density Functional Theory Calculations," Minerals, 4, 208-240(2014).   DOI
47 Blinder, S., "Basic Concepts of Self-consistent-field Theory," Am. J. Phys., 33, 431(1965).   DOI
48 Carabante, I. and Grahn, M., "In Situ ATR-FTIR Studies on the Competitive Adsorption of Arsenate and Phosphate on Ferrihydrite," J. Colloid Interface Sci., 351, 523-531(2010).   DOI
49 Schrodinger, E., "An Undulatory Theory of The Mechanics of Atoms and Molecules," Phys. Rev., 28, 1049-1070(1926).   DOI
50 Kim, N., Yoon, S. and Park, G., "Introduction to Computational Chemistry Namseok," KIC News, 15, 23-27(2012).
51 Gunnarsson, M., "Surface Complexation at the Iron Oxide/Water Interface," Doctoral dissertation, (2002).
52 VandeVondele, J., Troster, P., Tavan, P. and Mathias, G., "Vibrational Spectra of Phosphate Ions in Aqueous Solution Probed by First-principles Molecular Dynamics," J. Phys. Chem. A, 116, 2466-2474(2012).   DOI
53 Becke, A. D., "Density-functional Thermochemistry. III. The Role of Exact Exchange," J. Chem. Phys., 98, 5648-5652(1993).   DOI
54 Stephens, P. J., Devlin, F. J., Chabalowski, C. F. and Frisch, M. J., "Ab Initio Calculation of Vibrational Absorption and Circular Dichroism Spectra Using Density Functional Force Fields," J. Phys. Chem., 98, 11623-11627(1994).   DOI
55 Violante, A., "Elucidating Mechanisms of Competitive Sorption at the Mineral/water Interface," Adv. Agron., 118, 111-176(2013).
56 Selim, H. M. and Zhang, H., "Modeling Approaches of Competitive Sorption and Transport of Trace Metals and Metalloids in Soils: A Review," J. Environ. Qual., 42, 640-653(2013).   DOI
57 Cerkez, E. B., Bhandari, N., Reeder, R. J. and Strongin, D. R., "Coupled Redox Transformation of Chromate and Arsenite on Ferrihydrite," Environ. Sci. Technol., 49, 2858-2866(2015).   DOI
58 Hwang, Y. S. and Lenhart, J. J., "Adsorption of $C_4$-dicarboxylic Acids at the Hematite/water Interface," Langmuir, 24, 13934-13943(2008).   DOI
59 Lefevre, G., "In Situ Fourier-transform Infrared Spectroscopy Studies of Inorganic Ions Adsorption on Metal Oxides and Hydroxides," Adv. Colloid Interface Sci., 107, 109-123(2004).   DOI
60 Froese Fischer, C., "General Hartree-Fock Program," Comput. Phys. Commun., 43, 355-365(1987).   DOI
61 Hamers, R. J., Stavis, C., Pokhrel, A., Franking, R., Ruther, R. E., Wang, X., Cooperrider, M. C., Zheng, H., Carlisle, J. A. and Butler, J. E., "Characterization of Molecular and Biomolecular Layers on Diamond Thin Films by Infrared Reflection-absorption Spectroscopy," Diam. Relat. Mater., 20, 733-742(2011).   DOI
62 Bekiaris, G., Bruun, S., Peltre, C., Houot, S. and Jensen, L. S., "FTIR-PAS: A Powerful Tool for Characterising the Chemical Composition and Predicting the Labile C Fraction of Various Organic Waste Products," Waste Manag., 39, 45-56(2015).   DOI
63 Amma, S. I., Luo, J., Pantano, C. G. and Kim, S. H., "Specular Reflectance (SR) and Attenuated Total Reflectance (ATR) Infrared (IR) Spectroscopy of Transparent Flat Glass Surfaces: A Case Study for Soda Lime Float Glass," J. Non. Cryst. Solids, 428, 189-196(2015).   DOI
64 Hebert, G. N., Odom, M. A., Bowman, S. C. and Strauss, S. H., "Attenuated Total Reflectance FTIR Detection and Quantification of Low Concentrations of Aqueous Polyatomic Anions," Anal. Chem., 76, 781-787(2004).   DOI
65 Udo, S. and Rochelle, M. C., "Iron Oxides in the Laboratory. Preparation and Characterization," Wiley-vch(2008).
66 Hase, M., Scheffelmaier, R., Hayden, S. and Rivera, D., "Quantitative in Situ Attenuated Total Internal Reflection Fourier Transform Infrared Study of the Isotherms of Poly (sodium 4-styrene Sulfonate) Adsorption to a $TiO_2$ Surface over a Range of Cetylpyridinium Bromide Monohydrate Concentration," Langmuir, 26, 5534-5543(2010).   DOI
67 Fang, V., Kennedy, J., Futter, J. and Manning, J., "A Review of Near Infrared Reflectance Properties of Metal Oxide Nanostructures," GNS Science Report, 39, 1-23(2013).
68 Parikh, S. J., Lafferty, B. J. and Sparks, D. L., "An ATR-FTIR Spectroscopic Approach for Measuring Rapid Kinetics at the Mineral/water Interface," J. Colloid Interface Sci., 320, 177-185(2008).   DOI
69 Taga, K., Kellner, R., Kainz, U. and Sleytr, U., "In Situ Attenuated Total Reflectance FT-IR Analysis of an Enzyme-Modified Mid-Infrared Fiber Surface Using Crystalline Bacterial Surface Proteins," Anal. Chem., 66, 35-39(1994).   DOI
70 Madejova, J., "FTIR Techniques in Clay Mineral Studies," Vib. Spectrosc., 31, 1-10(2003).   DOI
71 Muller, K. and Lefevre, G., "Vibrational Characteristics of Outer-sphere Surface Complexes: Example of Sulfate Ions Adsorbed onto Metal (Hydr)oxides," Langmuir, 27, 6830-6835(2011).   DOI
72 Glotch, T. D. and Rossman, G. R., "Mid-infrared Reflectance Spectra and Optical Constants of Six Iron Oxide/oxyhydroxide Phases," Icarus, 204, 663-671(2009).   DOI
73 Wijnja, H. and Schulthess, C., "Vibrational Spectroscopy Study of Selenate and Sulfate Adsorption Mechanisms on Fe and Al (Hydr)oxide Surfaces," J. Colloid Interface Sci., 229, 286-297(2000).   DOI
74 Rakshit, S., Sallman, B., Davantes, A. and Lefevre, G., "Tungstate (VI) Sorption on Hematite: an in Situ ATR-FTIR Probe on the Mechanism," Chemosphere, 168, 685-691(2017).   DOI
75 Tofan-Lazar, J. and Al-Abadleh, H., "Kinetic ATR-FTIR Studies on Phosphate Adsorption on Iron(Oxyhydr)oxides in the Absence and Presence of Surface Arsenic: Molecular-Level Insights into the Ligand Exchange Mechanism," J. Phys. Chem. A, 116, 10143-10149(2012).   DOI
76 Kira, O., Linker, R. and Shaviv, A., "A Novel Method Combining FTIR-ATR Spectroscopy and Stable Isotopes to Investigate the Kinetics of Nitrogen Transformations in Soils," Soil Sci. Soc. Am. J., 78, 54(2014).   DOI
77 Du, J., Jing, C., Duan, J., Zhang, Y. and Hu, S., "Removal of Arsenate with Hydrous Ferric Oxide Coprecipitation: Effect of Humic Acid," J. Environ. Sci. (China), 26, 240-247(2014).   DOI
78 Brechbuhl, Y. and Christl, I., "Competitive Sorption of Carbonate and Arsenic to Hematite: Combined ATR-FTIR and Batch Experiments," J. Colloid Interface Sci., 377, 313-321(2012).   DOI
79 Lindegren, M. and Persson, P., "Competitive Adsorption between Phosphate and Carboxylic Acids: Quantitative Effects and Molecular Mechanisms," Eur. J. Soil Sci., 60, 982-993(2009).   DOI
80 Waiman, C. V, Avena, M. J., Regazzoni, A. E. and Zanini, G. P., "Journal of Colloid and Interface Science a Real Time in Situ ATR-FTIR Spectroscopic Study of Glyphosate Desorption From Goethite as Induced by Phosphate Adsorption : Effect of Surface Coverage," J. Colloid Interface Sci., 394, 485-489(2013).   DOI
81 Sabur, M. A. and Al-Abadleh, H. A., "Surface Interactions of Monomethylarsonic Acid With Hematite Nanoparticles Studied Using ATR-FTIR : Adsorption and Desorption Kinetics," Can. J. Chem., 93, 1297-1304(2015).   DOI
82 Elzinga, E. J. and Sparks, D. L., "Phosphate Adsorption onto Hematite: An in Situ ATR-FTIR Investigation of the Effects of PH and Loading Level on The Mode of Phosphate Surface Complexation," J. Colloid Interface Sci., 308, 53-70(2007).   DOI
83 Elzinga, E. J., Huang, J.-H., Chorover, J. and Kretzschmar, R., "ATR-FTIR Spectroscopy Study of the Influence of PH and Contact Time on the Adhesion of Shewanella Putrefaciens Bacterial Cells to the Surface of Hematite," Environ. Sci. Technol., 46, 12848-12855(2012).   DOI
84 Kuan, D. T., Sawchuk, A. A., Strand, T. C. and Chavel, P., "Adaptive Noise Smoothing Filter for Images with Signal-dependent Noise," IEEE Trans. Pattern Anal. Mach. Intell., 7, 165-177(1985).
85 Rieppo, L., Saarakkala, S., Narhi, T., Helminen, H. J., Jurvelin, J. S. and Rieppo, J., "Application of Second Derivative Spectroscopy for Increasing Molecular Specificity of Fourier Transform Infrared Spectroscopic Imaging of Articular Cartilage," Osteoarthritis Cartilage, 20, 451-459(2012).   DOI
86 Huang, J. B. and Urban, M. W., "Evaluation and Analysis of Attenuated Total Reflectance FT-IR Spectra Using Kramers-Kronig Transforms," Appl. Spectrosc., 46, 1666-1672(1992).   DOI