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Soil Chemical Insights Provided Through Vibrational Spectroscopy Sanjai J

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Soil Chemical Insights Provided Through Vibrational Spectroscopy Sanjai J University of Nebraska - Lincoln DigitalCommons@University of Nebraska - Lincoln U.S. Department of Agriculture: Agricultural Publications from USDA-ARS / UNL Faculty Research Service, Lincoln, Nebraska 2014 Soil Chemical Insights Provided through Vibrational Spectroscopy Sanjai J. Parikh University of California Davis, [email protected] Keith W. Goyne University of Missouri Andrew J. Margenot University of California Davis Fungai N.D. Mukome University of California Davis Francisco J. Calderón USDA-ARS, Central Great Plains Research Station Follow this and additional works at: http://digitalcommons.unl.edu/usdaarsfacpub Parikh, Sanjai J.; Goyne, Keith W.; Margenot, Andrew J.; Mukome, Fungai N.D.; and Calderón, Francisco J., "Soil Chemical Insights Provided through Vibrational Spectroscopy" (2014). Publications from USDA-ARS / UNL Faculty. Paper 1471. http://digitalcommons.unl.edu/usdaarsfacpub/1471 This Article is brought to you for free and open access by the U.S. Department of Agriculture: Agricultural Research Service, Lincoln, Nebraska at DigitalCommons@University of Nebraska - Lincoln. It has been accepted for inclusion in Publications from USDA-ARS / UNL Faculty by an authorized administrator of DigitalCommons@University of Nebraska - Lincoln. CHAPTER ONE Soil Chemical Insights Provided through Vibrational Spectroscopy Sanjai J. Parikh*,1, Keith W. Goyne†, Andrew J. Margenot*, Fungai N.D. Mukome* and Francisco J. Calderón‡ *Department of Land, Air and Water Resources, University of California Davis, Davis, CA, USA †Department of Soil, Environmental and Atmospheric Sciences, University of Missouri, Columbia, MO, USA ‡USDA-ARS, Central Great Plains Research Station, Akron, CO, USA 1Corresponding author: e-mail address: [email protected] Contents 1. Introduction 2 1.1 FTIR Spectroscopy 3 1.2 Raman Spectroscopy 5 2. FTIR Sampling Techniques 8 2.1 Transmission 8 2.2 Diffuse Reflectance Infrared Fourier Transform Spectroscopy 9 2.3 Attenuated Total Reflectance Fourier Transform Infrared Spectroscopy 10 2.4 IR Microspectroscopy 12 2.5 SR-FTIR Spectromicroscopy 13 3. Raman Sampling Techniques 15 3.1 Dispersive Raman Spectroscopy 15 3.2 Fourier Transformed Raman Spectroscopy (FT-Raman) 17 3.3 Raman Microspectroscopy 18 3.4 Surface-Enhanced Raman Scattering Spectroscopy 18 4. Soil Mineral Analysis 20 4.1 Phyllosilicates 21 4.2 Allophane and Imogolite 26 4.3 Metal Oxides, Hydroxides, and Oxyhydroxides 28 4.4 Mineral Weathering and Pedogenesis 34 5. SOM Spectral Components 36 6. Bacteria and Biomolecules 44 7. Soil Amendments 49 7.1 Biochar 49 7.2 Compost 53 7.3 Biosolids 53 8. Molecular-scale Analysis at the Solid–Liquid Interface 54 8.1 Organic Molecule Interactions with Mineral Surfaces 55 8.1.1 Low Molecular Weight Organic Acids 59 8.1.2 Herbicides and Pharmaceuticals 64 Advances in Agronomy, Volume 126 © 2014 Elsevier Inc. ISSN 0065-2113, http://dx.doi.org/10.1016/B978-0-12-800132-5.00001-8 All rights reserved. 1 2 Sanjai J. Parikh et al. 8.2 Inorganic Molecule Interactions with Mineral Surfaces 72 8.3 Bacteria and Biomolecule Adhesion 78 9. Real World Complexity: Soil Analysis for Mineral and Organic Components 85 9.1 Soil Heterogeneity and Mineral Analysis 85 9.2 Differentiating Mineral and Organic Spectral Absorbance 87 10. FTIR Spectroscopy for SOM Analysis 91 10.1 SOM Analysis in Whole Soils 91 10.2 SOM Analysis via Fractions and Extracts 92 10.2.1 Chemical Extracts and Fractionation 93 10.2.2 HS: A Common SOM Extract for FTIR Analyses 93 10.2.3 SOM Analysis Following Physical Fractionation 98 10.3 SOM Analysis via Subtraction Spectra 104 10.4 Spectral Analysis through Addition of Organic Compounds 107 10.5 Quantitative Analysis of Soil Carbon and Nitrogen 109 11. Summary 111 Acknowledgments 112 References 112 Abstract Vibrational spectroscopy techniques provide a powerful approach to the study of environmental materials and processes. These multifunctional analytical tools can be used to probe molecular vibrations of solid, liquid, and gaseous samples for character- izing materials, elucidating reaction mechanisms, and examining kinetic processes. Although Fourier transform infrared (FTIR) spectroscopy is the most prominent type of vibrational spectroscopy used in the field of soil science, applications of Raman spectroscopy to study environmental samples continue to increase. The ability of FTIR and Raman spectroscopies to provide complementary information for organic and inorganic materials makes them ideal approaches for soil science research. In addition, the ability to conduct in situ, real time, vibrational spectroscopy experiments to probe biogeochemical processes at mineral interfaces offers unique and versatile method- ologies for revealing a myriad of soil chemical phenomena. This review provides a comprehensive overview of vibrational spectroscopy techniques and highlights many of the applications of their use in soil chemistry research. 1. INTRODUCTION Fourier transform infrared (FTIR) and Raman spectroscopies pro- vide scientists with powerful analytical tools for studying the organic and inorganic components of soils and sediments. In addition to their utility for investigating sample mineralogy and organic matter (OM) composi- tion, these techniques provide molecular-scale information on metal and organic sorption processes at the solid–liquid interface. As such, both mech- anistic and kinetic studies of important biogeochemical processes can be Soil Chemical Insights Provided through Vibrational Spectroscopy 3 conducted. It is the versatility and accessibility of these vibrational spec- troscopy techniques that make them a critical tool for soil scientists. In this review FTIR and Raman spectroscopy approaches are introduced and a comprehensive discussion of their applications for soil chemistry research is provided. The primary objective of this review is to provide a synopsis of vibra- tional spectroscopy applications with utility for soil chemistry research. In doing so, FTIR and Raman spectroscopy will be presented, their sampling techniques introduced, and relevant studies discussed. Due to the large num- ber of FTIR studies in the field of soil science and related disciplines far exceeding those for Raman, this review is heavily weighted towards FTIR. Additionally, emphasis will be placed on applications of vibrational spec- troscopy for studying soil minerals, soil organic matter (SOM), bacteria and biopolymers, and various soil amendments (i.e. biochar, compost, biosolids). Particular attention is given to the analysis of OM in whole soils, fractions, and extracts. Molecular-scale analysis at the mineral–liquid interface and approaches for analyzing soil samples will also be discussed. Vibrational spectroscopy approaches for studying soil, and the chemical processes occurring within, are some of the most versatile and user-friendly tools for scientists. Today, computer hardware and software capabilities con- tinue to grow and the vast literature of vibrational spectroscopy studies is correspondingly expanding. As highlighted in this review, there is a wealth of information that can be garnered from these analysis techniques and the future of vibrational spectroscopy holds great promise for scientists working in the fields of soil and environmental sciences. 1.1 FTIR Spectroscopy The development of the FTIR spectrometer relied on the prior inven- tion of the Michelson interferometer by Albert Abraham Michelson in 1880 (Livingston, 1973). With the Michelson interferometer it became possible to accurately measure wavelengths of light. Although Jean Bap- tiste Joseph Fourier had previously developed the Fourier transform (FT), the calculations to convert the acquired interferograms to spec- tra remained cumbersome—even following the advent of computers. It was not until the development of the Cooley–Tukey Algorithm in 1965 (Cooley and Tukey, 1965) that computers could rapidly perform FT and modern FTIR spectroscopy became possible. The FTIR spec- trometers that soon developed have remained relatively unchanged in recent decades, though advances in computer science have enabled new 4 Sanjai J. Parikh et al. methods for data collection, processing, and analysis. Today the meth- ods of data acquisition are becoming increasingly sophisticated and the applications for FTIR continue to grow. Specific collection techniques, such as transmission, diffuse reflectance infrared Fourier transform spec- troscopy (DRIFTS), and attenuated total reflectance (ATR) will be dis- cussed later in this review. Infrared microspectroscopy (IRMS) is a FTIR spectroscopy technique that is developing rapidly and providing exciting new experimental capabili- ties for soil scientists. The first documentation of combining infrared (IR) spectroscopy with microscopy are several studies from 1949 where the tech- nique was applied to analyze tissue sections and amino acids (Barer et al., 1949; Blout and Mellors, 1949; Gore, 1949). This promising new technique offered imaging and chemical information of samples at a new level of reso- lution. However, as the two instruments were not integrated and computer technology was still in its infancy, the combination suffered from low signal to noise ratios and slow data processing (Katon, 1996; Shearer and Peters, 1987). Those interested in the early difficulties of these techniques are referred to Messerschmidt and Chase (1989) for details on the theory and causes of design failures in the early instruments. After about two decades, advances in computerization and IR spectroscopy
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