Professor Charles Wyman has devoted most of his career to leading advancement of technology for biological conversion of cellulosic biomass to ethanol and other products that will reduce our excessive dependence on petroleum. A substantial portion of this research is directed at advancing technologies for the most expensive and critical unit operations: pretreatment and cellulose and hemicellulose hydrolysis. Professor Wyman is Chair in Environmental Engineering at the Center for Environmental Research and Technology and Professor in Chemical and Environmental Engineering at the University of California at Riverside.

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• List of Contributors xviiForeword xxiSeries Preface xxiiiPreface xxvAcknowledgements xxvii1 Introduction 1Charles E. Wyman1.1 Cellulosic Biomass: What and Why? 21.2 Aqueous Processing of Cellulosic Biomass into Organic Fuels and Chemicals 31.3 Attributes for Successful Pretreatment 51.4 Pretreatment Options 71.5 Possible Blind Spots in the Historic Pretreatment Paradigm 81.6 Other Distinguishing Features of Pretreatment Technologies 91.7 Book Approach 91.8 Overview of Book Chapters 10Acknowledgements 10References 112 Cellulosic Biofuels: Importance, Recalcitrance, and Pretreatment 17Lee Lynd and Mark Laser2.1 Our Place in History 172.2 The Need for Energy from Biomass 172.3 The Importance of Cellulosic Biomass 182.4 Potential Barriers 182.5 Biological and Thermochemical Approaches to the Recalcitrance Barrier 192.6 Pretreatment 20Acknowledgements 21References 213 Plant Cell Walls: Basics of Structure, Chemistry, Accessibility and the Influence on Conversion 23Brian H. Davison, Jerry Parks, Mark F. Davis and Bryon S. Donohoe3.1 Introduction 233.2 Biomass Diversity Leads to Variability in Cell-wall Structure and Composition 243.3 Processing Options for Accessing the Energy in the Lignocellulosic Matrix 263.4 Plant Tissue and Cell Types Respond Differently to Biomass Conversion 283.5 The Basics of Plant Cell-wall Structure 293.6 Cell-wall Surfaces and Multilamellar Architecture 303.7 Cell-wall Ultrastructure and Nanoporosity 313.8 Computer Simulation in Understanding Biomass Recalcitrance 323.8.1 What Can We Learn from Molecular Simulation? 323.8.2 Simulations of Lignin 333.8.3 Simulations of Cellulose 343.8.4 Simulation of Lignocellulosic Biomass 353.8.5 Outlook for Biomass Simulations 353.9 Summary 35Acknowledgements 36References 364 Biological Conversion of Plants to Fuels and Chemicals and the Effects of Inhibitors 39Eduardo Ximenes, Youngmi Kim and Michael R. Ladisch4.1 Introduction 394.2 Overview of Biological Conversion 404.3 Enzyme and Ethanol Fermentation Inhibitors Released during Pretreatment and/or Enzyme Hydrolysis 424.3.1 Enzyme Inhibitors Derived from Plant Cell-wall Constituents (Lignin, Soluble Phenolics, and Hemicellulose) 434.3.2 Effect of Furfurals and Acetic Acid as Inhibitors of Ethanol Fermentations 484.4 Hydrolysis of Pentose Sugar Oligomers Using Solid-acid Catalysts 504.4.1 Application of Solid-acid Catalysts for Hydrolysis of Sugar Oligomers Derived from Lignocelluloses 504.4.2 Factors Affecting Efficiency of Solid-acid-catalyzed Hydrolysis 514.5 Conclusions 56Acknowledgements 57References 575 Catalytic Strategies for Converting Lignocellulosic Carbohydrates to Fuels and Chemicals 61Jesse Q. Bond, David Martin Alonso and James A. Dumesic5.1 Introduction 615.2 Biomass Conversion Strategies 625.3 Criteria for Fuels and Chemicals 645.3.1 General Considerations in the Production of Fuels and Fuel Additives 645.3.2 Consideration for Specialty Chemicals 665.4 Primary Feedstocks and Platforms 665.4.1 Cellulose 665.4.2 Hemicellulose 675.5 Sugar Conversion and Key Intermediates 685.5.1 Sugar Oxidation 695.5.2 Sugar Reduction (Polyol Production) 705.5.3 Sugar Dehydration (Furan Production) 775.6 Conclusions 91Acknowledgements 92References 926 Fundamentals of Biomass Pretreatment at Low pH 103Heather L. Trajano and Charles E. Wyman6.1 Introduction 1036.2 Effects of Low pH on Biomass Solids 1046.2.1 Cellulose 1046.2.2 Hemicellulose 1056.2.3 Lignin 1066.2.4 Ash 1076.2.5 Ultrastructure 1076.2.6 Summary of Effects of Low pH on Biomass Solids 1086.3 Pretreatment in Support of Biological Conversion 1086.3.1 Hydrolysis of Cellulose to Fermentable Glucose 1086.3.2 Pretreatment for Improved Enzymatic Digestibility 1096.3.3 Pretreatment for Improved Enzymatic Digestibility and Hemicellulose Sugar Recovery 1106.4 Low-pH Hydrolysis of Cellulose and Hemicellulose 1146.4.1 Furfural 1146.4.2 Levulinic Acid 1156.4.3 Drop-in Hydrocarbons 1156.5 Models of Low-pH Biomass Reactions 1166.5.1 Cellulose Hydrolysis 1176.5.2 Hemicellulose Hydrolysis 1186.5.3 Summary of Kinetic Models 1206.6 Conclusions 122Acknowledgements 123References 1237 Fundamentals of Aqueous Pretreatment of Biomass 129Nathan S. Mosier7.1 Introduction 1297.2 Self-ionization of Water Catalyzes Plant Cell-wall Depolymerization 1307.3 Products from the Hydrolysis of the Plant Cell Wall Contribute to Further Depolymerization 1317.4 Mechanisms of Aqueous Pretreatment 1317.4.1 Hemicellulose 1317.4.2 Lignin 1347.4.3 Cellulose 1367.5 Impact of Aqueous Pretreatment on Cellulose Digestibility 1377.6 Practical Applications of Liquid Hot Water Pretreatment 1387.7 Conclusions 140References 1408 Fundamentals of Biomass Pretreatment at High pH 145Rocıo Sierra Ramirez, Mark Holtzapple and Natalia Piamonte8.1 Introduction 1458.2 Chemical Effects of Alkaline Pretreatments on Biomass Composition 1468.2.1 Non-oxidative Delignification 1478.2.2 Non-oxidative Sugar Degradation 1488.2.3 Oxidative Delignification 1508.2.4 Oxidative Sugar Degradation 1518.3 Ammonia Pretreatments 1538.4 Sodium Hydroxide Pretreatments 1558.5 Alkaline Wet Oxidation 1558.6 Lime Pretreatment 1588.7 Pretreatment Severity 1618.8 Pretreatment Selectivity 1618.9 Concluding Remarks 163References 1639 Primer on Ammonia Fiber Expansion Pretreatment 169S.P.S. Chundawat, B. Bals, T. Campbell, L. Sousa, D. Gao, M. Jin, P. Eranki, R. Garlock, F. Teymouri, V. Balan and B.E. Dale9.1 Historical Perspective of Ammonia-based Pretreatments 1699.2 Overview of AFEX and its Physicochemical Impacts 1709.3 Enzymatic and Microbial Activity on AFEX-treated Biomass 1759.3.1 Impact of AFEX Pretreatment on Cellulase Binding to Biomass 1759.3.2 Enzymatic Digestibility of AFEX-treated Biomass 1769.3.3 Microbial Fermentability of AFEX-treated Biomass 1789.4 Transgenic Plants and AFEX Pretreatment 1839.5 Recent Research Developments on AFEX Strategies and Reactor Configurations 1859.5.1 Non-extractive AFEX Systems 1859.5.2 Extractive AFEX Systems 1869.5.3 Fluidized Gaseous AFEX Systems 1869.6 Perspectives on AFEX Commercialization 1869.6.1 AFEX Pretreatment Commercialization in Cellulosic Biorefineries 1869.6.2 Novel Value-added Products from AFEX-related Processes 1909.6.3 AFEX-centric Regional Biomass Processing Depot 1929.7 Environmental and Life-cycle Analyses for AFEX-centric Processes 1939.8 Conclusions 194Acknowledgements 195References 19510 Fundamentals of Biomass Pretreatment by Fractionation 201Poulomi Sannigrahi and Arthur J. Ragauskas10.1 Introduction 20110.2 Organosolv Pretreatment 20210.2.1 Organosolv Pulping 20210.2.2 Overview of Organosolv Pretreatment 20210.2.3 Solvents and Catalysts for Organosolv Pretreatment 20310.2.4 Fractionation of Biomass during Organosolv Pretreatment 20910.3 Nature of Organosolv Lignin and Chemistry of Organosolv Delignification 21010.3.1 Composition and Structure of Organosolv Lignin 21010.3.2 Mechanisms of Organosolv Delignification 21310.3.3 Commercial Applications of Organosolv Lignin 21410.4 Structural and Compositional Characteristics of Cellulose 21410.5 Co-products of Biomass Fractionation by Organosolv Pretreatment 21610.5.1 Hemicellulose 21610.5.2 Furfural 21710.5.3 Hydroxymethylfurfural (HMF) 21810.5.4 Levulinic Acid 21810.5.5 Acetic Acid 21910.6 Conclusions and Recommendations 219Acknowledgements 219References 21911 Ionic Liquid Pretreatment: Mechanism, Performance, and Challenges 223Seema Singh and Blake A. Simmons11.1 Introduction 22311.2 Ionic Liquid Pretreatment: Mechanism 22511.2.1 IL Polarity and Kamlet–Taft Parameters 22611.2.2 Interactions between ILs and Cellulose 22611.2.3 Interactions between ILs and Lignin 22711.3 Ionic Liquid Biomass Pretreatment: Enzymatic Route 22811.3.1 Grasses 22811.3.2 Agricultural Residues 23011.3.3 Woody Biomass 23011.4 Ionic Liquid Pretreatment: Catalytic Route 23111.4.1 Acid-catalyzed Hydrolysis 23211.4.2 Metal-catalyzed Hydrolysis 23211.5 Factors Impacting Scalability and Cost of Ionic Liquid Pretreatment 23311.6 Concluding Remarks 234Acknowledgements 234References 23412 Comparative Performance of Leading Pretreatment Technologies for Biological Conversion of Corn Stover, Poplar Wood, and Switchgrass to Sugars 239Charles E. Wyman, Bruce E. Dale, Venkatesh Balan, Richard T. Elander, Mark T. Holtzapple, Rocıo Sierra Ramirez, Michael R. Ladisch, Nathan Mosier, Y.Y. Lee, Rajesh Gupta, Steven R. Thomas, Bonnie R. Hames, Ryan Warner and Rajeev Kumar12.1 Introduction 24012.2 Materials and Methods 24212.2.1 Feedstocks 24212.2.2 Enzymes 24312.2.3 CAFI Pretreatments 24312.2.4 Material Balances 24412.2.5 Free Sugars and Extraction 24412.3 Yields of Xylose and Glucose from Pretreatment and Enzymatic Hydrolysis 24512.3.1 Yields from Corn Stover 24512.3.2 Yields from Standard Poplar 24712.3.3 Yields from Dacotah Switchgrass 24812.4 Impact of Changes in Biomass Sources 24912.5 Compositions of Solids Following CAFI Pretreatments 25112.5.1 Composition of Pretreated Corn Stover Solids 25212.5.2 Composition of Pretreated Switchgrass Solids 25212.5.3 Composition of Pretreated Poplar Solids 25312.5.4 Overall Trends in Composition of Pretreated Biomass Solids and Impact on Enzymatic Hydrolysis 25312.6 Pretreatment Conditions to Maximize Total Glucose Plus Xylose Yields 25412.7 Implications of the CAFI Results 25512.8 Closing Thoughts 256Acknowledgements 257References 25813 Effects of Enzyme Formulation and Loadings on Conversion of Biomass Pretreated by Leading Technologies 261Rajesh Gupta and Y.Y. Lee13.1 Introduction 26113.2 Synergism among Cellulolytic Enzymes 26213.3 Hemicellulose Structure and Hemicellulolytic Enzymes 26313.4 Substrate Characteristics and Enzymatic Hydrolysis 26413.5 Xylanase Supplementation for Different Pretreated Biomass and Effect of b-Xylosidase 26513.6 Effect of b-Glucosidase Supplementation 26913.7 Effect of Pectinase Addition 26913.8 Effect of Feruloyl Esterase and Acetyl Xylan Esterase Addition 27013.9 Effect of a-L-arabinofuranosidase and Mannanase Addition 27013.10 Use of Lignin-degrading Enzymes (LDE) 27113.11 Effect of Inactive Components on Biomass Hydrolysis 27113.12 Adsorption and Accessibility of Enzyme with Different Cellulosic Substrates 27113.13 Tuning Enzyme Formulations to the Feedstock 27213.14 Summary 273References 27414 Physical and Chemical Features of Pretreated Biomass that Influence Macro-/Micro-accessibility and Biological Processing 281Rajeev Kumar and Charles E. Wyman14.1 Introduction 28114.2 Definitions of Macro-/Micro-accessibility and Effectiveness 28314.3 Features Influencing Macro-accessibility and their Impacts on Enzyme Effectiveness 28414.3.1 Lignin 28414.3.2 Hemicellulose 28614.4 Features Influencing Micro-accessibility and their Impact on Enzymes Effectiveness 28914.4.1 Cellulose Crystallinity (Structure) 28914.4.2 Cellulose Chain Length/Reducing Ends 29114.5 Concluding Remarks 293Acknowledgements 296References 29615 Economics of Pretreatment for Biological Processing 311Ling Tao, Andy Aden and Richard T. Elander15.1 Introduction 31115.2 Importance of Pretreatment 31115.3 History of Pretreatment Economic Analysis 31315.4 Methodologies for Economic Assessment 31415.5 Overview of Pretreatment Technologies 31515.5.1 Acidic Pretreatments 31515.5.2 Alkaline Pretreatments 31515.5.3 Solvent-based Pretreatments 31615.6 Comparative Pretreatment Economics 31615.6.1 Modeling Basis and Assumptions for Comparative CAFI Analysis 31715.6.2 CAFI Project Comparative Data 32015.6.3 Reactor Design and Costing Data 32015.6.4 Comparison of Sugar and Ethanol Yields 32415.6.5 Comparison of Pretreatment Capital Costs 32515.6.6 Comparison of MESP 32615.7 Impact of Key Variables on Pretreatment Economics 32715.7.1 Yield 32715.7.2 Conversion to Oligomers/Monomers (Shift of Burden between Enzymes and Pretreatment) 32815.7.3 Biomass Loading/Concentration 32815.7.4 Chemical Loading/Recovery/Metallurgy 32915.7.5 Reaction Conditions: Pressure, Temperature, Residence Time 33015.7.6 Reactor Orientation: Horizontal/Vertical 33015.7.7 Batch versus Continuous Processing 33015.8 Future Needs for Evaluation of Pretreatment Economics 33115.9 Conclusions 332Acknowledgements 332References 33216 Progress in the Summative Analysis of Biomass Feedstocks for Biofuels Production 335F.A. Agblevor and J. Pereira16.1 Introduction 33516.2 Preparation of Biomass Feedstocks for Analysis 33716.3 Determination of Non-structural Components of Biomass Feedstocks 33816.3.1 Moisture Content of Biomass Feedstocks 33816.3.2 Determination of Ash in Biomass 33816.3.3 Protein Content of Biomass 33816.3.4 Extractives Content of Biomass 33916.4 Quantitative Determination of Lignin Content of Biomass 34016.5 Quantitative Analysis of Sugars in Lignocellulosic Biomass 34216.5.1 Holocellulose Content of Plant Cell Walls 34216.5.2 Monoethanolamine Method for Cellulose Determination 34316.6 Chemical Hydrolysis of Biomass Polysaccharides 34316.6.1 Mineral Acid Hydrolysis 34316.6.2 Trifluoroacetic Acid (TFA) 34416.6.3 Methanolysis 34416.7 Analysis of Monosaccharides 34516.7.1 Colorimetric Analysis of Biomass Monosaccharides 34516.7.2 Gas Chromatographic Sugar Analysis 34516.8 Gas Chromatography-Mass Spectrometry (GC/MS) 34716.9 High-performance Liquid Chromatographic Sugar Analysis 34716.10 NMR Analysis of Biomass Sugars 34916.11 Conclusions 349References 34917 High-throughput NIR Analysis of Biomass Pretreatment Streams 355Bonnie R. Hames17.1 Introduction 35517.2 Rapid Analysis Essentials 35617.2.1 Rapid Spectroscopic Techniques 35717.2.2 Calibration and Validation Samples 35817.2.3 Quality Calibration Data for Each Calibration Sample 35917.2.4 Multivariate Analysis to Resolve Complex Sample Spectra 36217.2.5 Validation of New Methods 36417.2.6 Standard Reference Materials and Protocols for Ongoing QA/QC 36417.3 Summary 366References 36718 Plant Biomass Characterization: Application of Solution- and Solid-state NMR Spectroscopy 369Yunqiao Pu, Bassem Hallac and Arthur J. Ragauskas18.1 Introduction 36918.2 Plant Biomass Constituents 37018.3 Solution-state NMR Characterization of Lignin 37118.3.1 Lignin Sample Preparation 37218.3.2 1 H NMR Spectroscopy 37218.3.3 13 c NMR Spectroscopy 37218.3.4 HSQC Correlation Spectroscopy 37518.3.5 31 P NMR Spectroscopy 37718.4 Solid-state NMR Characterization of Plant Cellulose 38118.4.1 CP/MAS 13 C NMR Analysis of Cellulose 38118.4.2 Cellulose Crystallinity 38318.4.3 Cellulose Ultrastructure 38518.5 Future Perspectives 387Acknowledgements 387References 38719 Xylooligosaccharides Production, Quantification, and Characterization in Context of Lignocellulosic Biomass Pretreatment 391Qing Qing, Hongjia Li, Rajeev Kumar and Charles E. Wyman19.1 Introduction 39119.1.1 Definition of Oligosaccharides 39119.1.2 Types of Oligosaccharides Released during Lignocellulosic Biomass Pretreatment 39219.1.3 The Importance of Measuring Xylooligosaccharides 39219.2 Xylooligosaccharides Production 39419.2.1 Thermochemical Production of XOs 39419.2.2 Production of XOs by Enzymatic Hydrolysis 39619.3 Xylooligosaccharides Separation and Purification 39719.3.1 Solvent Extraction 39719.3.2 Adsorption by Surface Active Materials 39719.3.3 Chromatographic Separation Techniques 39819.3.4 Membrane Separation 39919.3.5 Centrifugal Partition Chromatography 40119.4 Characterization and Quantification of Xylooligosaccharides 40219.4.1 Measuring Xylooligosaccharides by Quantification of Reducing Ends 40219.4.2 Characterizing Xylooligosaccharides Composition 40219.4.3 Direct Characterization of Different DP Xylooligosaccharides 40319.4.4 Determining Detailed Structures of Oligosaccharides by MS and NMR 40819.5 Concluding Remarks 408Acknowledgements 409References 41020 Experimental Pretreatment Systems from Laboratory to Pilot Scale 417Richard T. Elander20.1 Introduction 41720.2 Laboratory-scale Pretreatment Equipment 42120.2.1 Heating and Cooling Capability 42120.2.2 Contacting of Biomass Particles with Water and/or Pretreatment Chemicals 42120.2.3 Mass and Heat Transfer 42220.2.4 Proper Materials of Construction 42320.2.5 Instrumentation and Control Systems 42420.2.6 Translating to Pilot-scale Pretreatment Systems 42420.3 Pilot-scale Batch Pretreatment Equipment 42420.4 Pilot-scale Continuous Pretreatment Equipment 42720.4.1 Feedstock Handling and Size Reduction 42720.4.2 Pretreatment Chemical and Water Addition 42920.4.3 Pressurized Continuous Pretreatment Feeder Equipment 43220.4.4 Pretreatment Reactor Throughput and Residence Time Control 43620.4.5 Reactor Discharge Devices 43820.4.6 Blow-down Vessel and Flash Vapor Recovery 43820.5 Continuous Pilot-scale Pretreatment Reactor Systems 43920.5.1 Historical Development of Pilot-scale Reactor Systems 43920.5.2 NREL Gravity-flow Reactor Systems 44120.6 Summary 445Acknowledgements 446References 44721 Experimental Enzymatic Hydrolysis Systems 451Todd Lloyd and Chaogang Liu21.1 Introduction 45121.2 Cellulases 45221.2.1 Endoglucanase 45221.2.2 Cellobiohydrolase 45321.2.3 b-glucosidase 45321.3 Hemicellulases 45321.4 Kinetics of Enzymatic Hydrolysis 45421.4.1 Empirical Models 45521.4.2 Michaelis–Menten-based Models 45521.4.3 Adsorption in Cellulose Hydrolysis Models 45621.4.4 Rate Limitations and Decreasing Rates with Increasing Conversion 45721.4.5 Summary of Enzyme Reaction Kinetics 45921.5 Experimental Hydrolysis Systems 46021.5.1 Laboratory Protocols 46021.5.2 Considerations for Scale-up of Hydrolysis Processes 46321.6 Conclusion 465References 46522 High-throughput Pretreatment and Hydrolysis Systems for Screening Biomass Species in Aqueous Pretreatment of Plant Biomass 471Jaclyn DeMartini and Charles E. Wyman22.1 Introduction: The Need for High-throughput Technologies 47122.2 Previous High-throughput Systems and Application to Pretreatment and Enzymatic Hydrolysis 47222.3 Current HTPH Systems 47322.4 Key Steps in HTPH Systems 47822.4.1 Material Preparation 47822.4.2 Material Distribution 47922.4.3 Pretreatment and Enzymatic Hydrolysis 48022.4.4 Sample Analysis 48122.5 HTPH Philosophy, Difficulties, and Limitations 48222.6 Examples of Research Enabled by HTPH Systems 48422.7 Future Applications 48522.8 Conclusions and Recommendations 485References 48623 Laboratory Pretreatment Systems to Understand Biomass Deconstruction 489Bin Yang and Melvin Tucker23.1 Introduction 48923.2 Laboratory-scale Batch Reactors 49123.2.1 Sealed Glass Reactors 49123.2.2 Tubular Reactors 49223.2.3 Mixed Reactors 49523.2.4 Zipperclave 49623.2.5 Microwave Reactors 49723.2.6 Steam Reactors 49923.3 Laboratory-scale Continuous Pretreatment Reactors 50123.4 Deconstruction of Biomass with Bench-Scale Pretreatment Systems 50323.5 Heat and Mass Transfer 50523.5.1 Mass Transfer 50623.5.2 Direct and Indirect Heating 50623.6 Biomass Handling and Comminuting 50823.7 Construction Materials 50823.7.1 Overall Considerations 50823.7.2 Materials of Construction 50923.8 Criteria of Reactor Selection and Applications 51023.8.1 Effect of High/Low Solids Concentration on Reactor Choices 51023.8.2 Role of Heat-up and Cool-down Rates in Laboratory Reactor Selection 51023.8.3 Effect of Mixing and Catalyst Impregnation on Reactor Design 51023.8.4 High Temperatures and Short Residence Times Result in High Yields 51123.8.5 Pretreatment Severity: Tradeoffs of Time and Temperature 51123.8.6 Minimizing Construction and Operating Costs 51223.9 Summary 513Acknowledgements 514References 514Index 523

Professor Charles Wyman has devoted most of his career to leading advancement of technology for biological conversion of cellulosic biomass to ethanol and other products that will reduce our excessive dependence on petroleum. A substantial portion of this research is directed at advancing technologies for the most expensive and critical unit operations: pretreatment and cellulose and hemicellulose hydrolysis. Professor Wyman is Chair in Environmental Engineering at the Center for Environmental Research and Technology and Professor in Chemical and Environmental Engineering at the University of California at Riverside.

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• List of Contributors xviiForeword xxiSeries Preface xxiiiPreface xxvAcknowledgements xxvii1 Introduction 1Charles E. Wyman1.1 Cellulosic Biomass: What and Why? 21.2 Aqueous Processing of Cellulosic Biomass into Organic Fuels and Chemicals 31.3 Attributes for Successful Pretreatment 51.4 Pretreatment Options 71.5 Possible Blind Spots in the Historic Pretreatment Paradigm 81.6 Other Distinguishing Features of Pretreatment Technologies 91.7 Book Approach 91.8 Overview of Book Chapters 10Acknowledgements 10References 112 Cellulosic Biofuels: Importance, Recalcitrance, and Pretreatment 17Lee Lynd and Mark Laser2.1 Our Place in History 172.2 The Need for Energy from Biomass 172.3 The Importance of Cellulosic Biomass 182.4 Potential Barriers 182.5 Biological and Thermochemical Approaches to the Recalcitrance Barrier 192.6 Pretreatment 20Acknowledgements 21References 213 Plant Cell Walls: Basics of Structure, Chemistry, Accessibility and the Influence on Conversion 23Brian H. Davison, Jerry Parks, Mark F. Davis and Bryon S. Donohoe3.1 Introduction 233.2 Biomass Diversity Leads to Variability in Cell-wall Structure and Composition 243.3 Processing Options for Accessing the Energy in the Lignocellulosic Matrix 263.4 Plant Tissue and Cell Types Respond Differently to Biomass Conversion 283.5 The Basics of Plant Cell-wall Structure 293.6 Cell-wall Surfaces and Multilamellar Architecture 303.7 Cell-wall Ultrastructure and Nanoporosity 313.8 Computer Simulation in Understanding Biomass Recalcitrance 323.8.1 What Can We Learn from Molecular Simulation? 323.8.2 Simulations of Lignin 333.8.3 Simulations of Cellulose 343.8.4 Simulation of Lignocellulosic Biomass 353.8.5 Outlook for Biomass Simulations 353.9 Summary 35Acknowledgements 36References 364 Biological Conversion of Plants to Fuels and Chemicals and the Effects of Inhibitors 39Eduardo Ximenes, Youngmi Kim and Michael R. Ladisch4.1 Introduction 394.2 Overview of Biological Conversion 404.3 Enzyme and Ethanol Fermentation Inhibitors Released during Pretreatment and/or Enzyme Hydrolysis 424.3.1 Enzyme Inhibitors Derived from Plant Cell-wall Constituents (Lignin, Soluble Phenolics, and Hemicellulose) 434.3.2 Effect of Furfurals and Acetic Acid as Inhibitors of Ethanol Fermentations 484.4 Hydrolysis of Pentose Sugar Oligomers Using Solid-acid Catalysts 504.4.1 Application of Solid-acid Catalysts for Hydrolysis of Sugar Oligomers Derived from Lignocelluloses 504.4.2 Factors Affecting Efficiency of Solid-acid-catalyzed Hydrolysis 514.5 Conclusions 56Acknowledgements 57References 575 Catalytic Strategies for Converting Lignocellulosic Carbohydrates to Fuels and Chemicals 61Jesse Q. Bond, David Martin Alonso and James A. Dumesic5.1 Introduction 615.2 Biomass Conversion Strategies 625.3 Criteria for Fuels and Chemicals 645.3.1 General Considerations in the Production of Fuels and Fuel Additives 645.3.2 Consideration for Specialty Chemicals 665.4 Primary Feedstocks and Platforms 665.4.1 Cellulose 665.4.2 Hemicellulose 675.5 Sugar Conversion and Key Intermediates 685.5.1 Sugar Oxidation 695.5.2 Sugar Reduction (Polyol Production) 705.5.3 Sugar Dehydration (Furan Production) 775.6 Conclusions 91Acknowledgements 92References 926 Fundamentals of Biomass Pretreatment at Low pH 103Heather L. Trajano and Charles E. Wyman6.1 Introduction 1036.2 Effects of Low pH on Biomass Solids 1046.2.1 Cellulose 1046.2.2 Hemicellulose 1056.2.3 Lignin 1066.2.4 Ash 1076.2.5 Ultrastructure 1076.2.6 Summary of Effects of Low pH on Biomass Solids 1086.3 Pretreatment in Support of Biological Conversion 1086.3.1 Hydrolysis of Cellulose to Fermentable Glucose 1086.3.2 Pretreatment for Improved Enzymatic Digestibility 1096.3.3 Pretreatment for Improved Enzymatic Digestibility and Hemicellulose Sugar Recovery 1106.4 Low-pH Hydrolysis of Cellulose and Hemicellulose 1146.4.1 Furfural 1146.4.2 Levulinic Acid 1156.4.3 Drop-in Hydrocarbons 1156.5 Models of Low-pH Biomass Reactions 1166.5.1 Cellulose Hydrolysis 1176.5.2 Hemicellulose Hydrolysis 1186.5.3 Summary of Kinetic Models 1206.6 Conclusions 122Acknowledgements 123References 1237 Fundamentals of Aqueous Pretreatment of Biomass 129Nathan S. Mosier7.1 Introduction 1297.2 Self-ionization of Water Catalyzes Plant Cell-wall Depolymerization 1307.3 Products from the Hydrolysis of the Plant Cell Wall Contribute to Further Depolymerization 1317.4 Mechanisms of Aqueous Pretreatment 1317.4.1 Hemicellulose 1317.4.2 Lignin 1347.4.3 Cellulose 1367.5 Impact of Aqueous Pretreatment on Cellulose Digestibility 1377.6 Practical Applications of Liquid Hot Water Pretreatment 1387.7 Conclusions 140References 1408 Fundamentals of Biomass Pretreatment at High pH 145Rocıo Sierra Ramirez, Mark Holtzapple and Natalia Piamonte8.1 Introduction 1458.2 Chemical Effects of Alkaline Pretreatments on Biomass Composition 1468.2.1 Non-oxidative Delignification 1478.2.2 Non-oxidative Sugar Degradation 1488.2.3 Oxidative Delignification 1508.2.4 Oxidative Sugar Degradation 1518.3 Ammonia Pretreatments 1538.4 Sodium Hydroxide Pretreatments 1558.5 Alkaline Wet Oxidation 1558.6 Lime Pretreatment 1588.7 Pretreatment Severity 1618.8 Pretreatment Selectivity 1618.9 Concluding Remarks 163References 1639 Primer on Ammonia Fiber Expansion Pretreatment 169S.P.S. Chundawat, B. Bals, T. Campbell, L. Sousa, D. Gao, M. Jin, P. Eranki, R. Garlock, F. Teymouri, V. Balan and B.E. Dale9.1 Historical Perspective of Ammonia-based Pretreatments 1699.2 Overview of AFEX and its Physicochemical Impacts 1709.3 Enzymatic and Microbial Activity on AFEX-treated Biomass 1759.3.1 Impact of AFEX Pretreatment on Cellulase Binding to Biomass 1759.3.2 Enzymatic Digestibility of AFEX-treated Biomass 1769.3.3 Microbial Fermentability of AFEX-treated Biomass 1789.4 Transgenic Plants and AFEX Pretreatment 1839.5 Recent Research Developments on AFEX Strategies and Reactor Configurations 1859.5.1 Non-extractive AFEX Systems 1859.5.2 Extractive AFEX Systems 1869.5.3 Fluidized Gaseous AFEX Systems 1869.6 Perspectives on AFEX Commercialization 1869.6.1 AFEX Pretreatment Commercialization in Cellulosic Biorefineries 1869.6.2 Novel Value-added Products from AFEX-related Processes 1909.6.3 AFEX-centric Regional Biomass Processing Depot 1929.7 Environmental and Life-cycle Analyses for AFEX-centric Processes 1939.8 Conclusions 194Acknowledgements 195References 19510 Fundamentals of Biomass Pretreatment by Fractionation 201Poulomi Sannigrahi and Arthur J. Ragauskas10.1 Introduction 20110.2 Organosolv Pretreatment 20210.2.1 Organosolv Pulping 20210.2.2 Overview of Organosolv Pretreatment 20210.2.3 Solvents and Catalysts for Organosolv Pretreatment 20310.2.4 Fractionation of Biomass during Organosolv Pretreatment 20910.3 Nature of Organosolv Lignin and Chemistry of Organosolv Delignification 21010.3.1 Composition and Structure of Organosolv Lignin 21010.3.2 Mechanisms of Organosolv Delignification 21310.3.3 Commercial Applications of Organosolv Lignin 21410.4 Structural and Compositional Characteristics of Cellulose 21410.5 Co-products of Biomass Fractionation by Organosolv Pretreatment 21610.5.1 Hemicellulose 21610.5.2 Furfural 21710.5.3 Hydroxymethylfurfural (HMF) 21810.5.4 Levulinic Acid 21810.5.5 Acetic Acid 21910.6 Conclusions and Recommendations 219Acknowledgements 219References 21911 Ionic Liquid Pretreatment: Mechanism, Performance, and Challenges 223Seema Singh and Blake A. Simmons11.1 Introduction 22311.2 Ionic Liquid Pretreatment: Mechanism 22511.2.1 IL Polarity and Kamlet–Taft Parameters 22611.2.2 Interactions between ILs and Cellulose 22611.2.3 Interactions between ILs and Lignin 22711.3 Ionic Liquid Biomass Pretreatment: Enzymatic Route 22811.3.1 Grasses 22811.3.2 Agricultural Residues 23011.3.3 Woody Biomass 23011.4 Ionic Liquid Pretreatment: Catalytic Route 23111.4.1 Acid-catalyzed Hydrolysis 23211.4.2 Metal-catalyzed Hydrolysis 23211.5 Factors Impacting Scalability and Cost of Ionic Liquid Pretreatment 23311.6 Concluding Remarks 234Acknowledgements 234References 23412 Comparative Performance of Leading Pretreatment Technologies for Biological Conversion of Corn Stover, Poplar Wood, and Switchgrass to Sugars 239Charles E. Wyman, Bruce E. Dale, Venkatesh Balan, Richard T. Elander, Mark T. Holtzapple, Rocıo Sierra Ramirez, Michael R. Ladisch, Nathan Mosier, Y.Y. Lee, Rajesh Gupta, Steven R. Thomas, Bonnie R. Hames, Ryan Warner and Rajeev Kumar12.1 Introduction 24012.2 Materials and Methods 24212.2.1 Feedstocks 24212.2.2 Enzymes 24312.2.3 CAFI Pretreatments 24312.2.4 Material Balances 24412.2.5 Free Sugars and Extraction 24412.3 Yields of Xylose and Glucose from Pretreatment and Enzymatic Hydrolysis 24512.3.1 Yields from Corn Stover 24512.3.2 Yields from Standard Poplar 24712.3.3 Yields from Dacotah Switchgrass 24812.4 Impact of Changes in Biomass Sources 24912.5 Compositions of Solids Following CAFI Pretreatments 25112.5.1 Composition of Pretreated Corn Stover Solids 25212.5.2 Composition of Pretreated Switchgrass Solids 25212.5.3 Composition of Pretreated Poplar Solids 25312.5.4 Overall Trends in Composition of Pretreated Biomass Solids and Impact on Enzymatic Hydrolysis 25312.6 Pretreatment Conditions to Maximize Total Glucose Plus Xylose Yields 25412.7 Implications of the CAFI Results 25512.8 Closing Thoughts 256Acknowledgements 257References 25813 Effects of Enzyme Formulation and Loadings on Conversion of Biomass Pretreated by Leading Technologies 261Rajesh Gupta and Y.Y. Lee13.1 Introduction 26113.2 Synergism among Cellulolytic Enzymes 26213.3 Hemicellulose Structure and Hemicellulolytic Enzymes 26313.4 Substrate Characteristics and Enzymatic Hydrolysis 26413.5 Xylanase Supplementation for Different Pretreated Biomass and Effect of b-Xylosidase 26513.6 Effect of b-Glucosidase Supplementation 26913.7 Effect of Pectinase Addition 26913.8 Effect of Feruloyl Esterase and Acetyl Xylan Esterase Addition 27013.9 Effect of a-L-arabinofuranosidase and Mannanase Addition 27013.10 Use of Lignin-degrading Enzymes (LDE) 27113.11 Effect of Inactive Components on Biomass Hydrolysis 27113.12 Adsorption and Accessibility of Enzyme with Different Cellulosic Substrates 27113.13 Tuning Enzyme Formulations to the Feedstock 27213.14 Summary 273References 27414 Physical and Chemical Features of Pretreated Biomass that Influence Macro-/Micro-accessibility and Biological Processing 281Rajeev Kumar and Charles E. Wyman14.1 Introduction 28114.2 Definitions of Macro-/Micro-accessibility and Effectiveness 28314.3 Features Influencing Macro-accessibility and their Impacts on Enzyme Effectiveness 28414.3.1 Lignin 28414.3.2 Hemicellulose 28614.4 Features Influencing Micro-accessibility and their Impact on Enzymes Effectiveness 28914.4.1 Cellulose Crystallinity (Structure) 28914.4.2 Cellulose Chain Length/Reducing Ends 29114.5 Concluding Remarks 293Acknowledgements 296References 29615 Economics of Pretreatment for Biological Processing 311Ling Tao, Andy Aden and Richard T. Elander15.1 Introduction 31115.2 Importance of Pretreatment 31115.3 History of Pretreatment Economic Analysis 31315.4 Methodologies for Economic Assessment 31415.5 Overview of Pretreatment Technologies 31515.5.1 Acidic Pretreatments 31515.5.2 Alkaline Pretreatments 31515.5.3 Solvent-based Pretreatments 31615.6 Comparative Pretreatment Economics 31615.6.1 Modeling Basis and Assumptions for Comparative CAFI Analysis 31715.6.2 CAFI Project Comparative Data 32015.6.3 Reactor Design and Costing Data 32015.6.4 Comparison of Sugar and Ethanol Yields 32415.6.5 Comparison of Pretreatment Capital Costs 32515.6.6 Comparison of MESP 32615.7 Impact of Key Variables on Pretreatment Economics 32715.7.1 Yield 32715.7.2 Conversion to Oligomers/Monomers (Shift of Burden between Enzymes and Pretreatment) 32815.7.3 Biomass Loading/Concentration 32815.7.4 Chemical Loading/Recovery/Metallurgy 32915.7.5 Reaction Conditions: Pressure, Temperature, Residence Time 33015.7.6 Reactor Orientation: Horizontal/Vertical 33015.7.7 Batch versus Continuous Processing 33015.8 Future Needs for Evaluation of Pretreatment Economics 33115.9 Conclusions 332Acknowledgements 332References 33216 Progress in the Summative Analysis of Biomass Feedstocks for Biofuels Production 335F.A. Agblevor and J. Pereira16.1 Introduction 33516.2 Preparation of Biomass Feedstocks for Analysis 33716.3 Determination of Non-structural Components of Biomass Feedstocks 33816.3.1 Moisture Content of Biomass Feedstocks 33816.3.2 Determination of Ash in Biomass 33816.3.3 Protein Content of Biomass 33816.3.4 Extractives Content of Biomass 33916.4 Quantitative Determination of Lignin Content of Biomass 34016.5 Quantitative Analysis of Sugars in Lignocellulosic Biomass 34216.5.1 Holocellulose Content of Plant Cell Walls 34216.5.2 Monoethanolamine Method for Cellulose Determination 34316.6 Chemical Hydrolysis of Biomass Polysaccharides 34316.6.1 Mineral Acid Hydrolysis 34316.6.2 Trifluoroacetic Acid (TFA) 34416.6.3 Methanolysis 34416.7 Analysis of Monosaccharides 34516.7.1 Colorimetric Analysis of Biomass Monosaccharides 34516.7.2 Gas Chromatographic Sugar Analysis 34516.8 Gas Chromatography-Mass Spectrometry (GC/MS) 34716.9 High-performance Liquid Chromatographic Sugar Analysis 34716.10 NMR Analysis of Biomass Sugars 34916.11 Conclusions 349References 34917 High-throughput NIR Analysis of Biomass Pretreatment Streams 355Bonnie R. Hames17.1 Introduction 35517.2 Rapid Analysis Essentials 35617.2.1 Rapid Spectroscopic Techniques 35717.2.2 Calibration and Validation Samples 35817.2.3 Quality Calibration Data for Each Calibration Sample 35917.2.4 Multivariate Analysis to Resolve Complex Sample Spectra 36217.2.5 Validation of New Methods 36417.2.6 Standard Reference Materials and Protocols for Ongoing QA/QC 36417.3 Summary 366References 36718 Plant Biomass Characterization: Application of Solution- and Solid-state NMR Spectroscopy 369Yunqiao Pu, Bassem Hallac and Arthur J. Ragauskas18.1 Introduction 36918.2 Plant Biomass Constituents 37018.3 Solution-state NMR Characterization of Lignin 37118.3.1 Lignin Sample Preparation 37218.3.2 1 H NMR Spectroscopy 37218.3.3 13 c NMR Spectroscopy 37218.3.4 HSQC Correlation Spectroscopy 37518.3.5 31 P NMR Spectroscopy 37718.4 Solid-state NMR Characterization of Plant Cellulose 38118.4.1 CP/MAS 13 C NMR Analysis of Cellulose 38118.4.2 Cellulose Crystallinity 38318.4.3 Cellulose Ultrastructure 38518.5 Future Perspectives 387Acknowledgements 387References 38719 Xylooligosaccharides Production, Quantification, and Characterization in Context of Lignocellulosic Biomass Pretreatment 391Qing Qing, Hongjia Li, Rajeev Kumar and Charles E. Wyman19.1 Introduction 39119.1.1 Definition of Oligosaccharides 39119.1.2 Types of Oligosaccharides Released during Lignocellulosic Biomass Pretreatment 39219.1.3 The Importance of Measuring Xylooligosaccharides 39219.2 Xylooligosaccharides Production 39419.2.1 Thermochemical Production of XOs 39419.2.2 Production of XOs by Enzymatic Hydrolysis 39619.3 Xylooligosaccharides Separation and Purification 39719.3.1 Solvent Extraction 39719.3.2 Adsorption by Surface Active Materials 39719.3.3 Chromatographic Separation Techniques 39819.3.4 Membrane Separation 39919.3.5 Centrifugal Partition Chromatography 40119.4 Characterization and Quantification of Xylooligosaccharides 40219.4.1 Measuring Xylooligosaccharides by Quantification of Reducing Ends 40219.4.2 Characterizing Xylooligosaccharides Composition 40219.4.3 Direct Characterization of Different DP Xylooligosaccharides 40319.4.4 Determining Detailed Structures of Oligosaccharides by MS and NMR 40819.5 Concluding Remarks 408Acknowledgements 409References 41020 Experimental Pretreatment Systems from Laboratory to Pilot Scale 417Richard T. Elander20.1 Introduction 41720.2 Laboratory-scale Pretreatment Equipment 42120.2.1 Heating and Cooling Capability 42120.2.2 Contacting of Biomass Particles with Water and/or Pretreatment Chemicals 42120.2.3 Mass and Heat Transfer 42220.2.4 Proper Materials of Construction 42320.2.5 Instrumentation and Control Systems 42420.2.6 Translating to Pilot-scale Pretreatment Systems 42420.3 Pilot-scale Batch Pretreatment Equipment 42420.4 Pilot-scale Continuous Pretreatment Equipment 42720.4.1 Feedstock Handling and Size Reduction 42720.4.2 Pretreatment Chemical and Water Addition 42920.4.3 Pressurized Continuous Pretreatment Feeder Equipment 43220.4.4 Pretreatment Reactor Throughput and Residence Time Control 43620.4.5 Reactor Discharge Devices 43820.4.6 Blow-down Vessel and Flash Vapor Recovery 43820.5 Continuous Pilot-scale Pretreatment Reactor Systems 43920.5.1 Historical Development of Pilot-scale Reactor Systems 43920.5.2 NREL Gravity-flow Reactor Systems 44120.6 Summary 445Acknowledgements 446References 44721 Experimental Enzymatic Hydrolysis Systems 451Todd Lloyd and Chaogang Liu21.1 Introduction 45121.2 Cellulases 45221.2.1 Endoglucanase 45221.2.2 Cellobiohydrolase 45321.2.3 b-glucosidase 45321.3 Hemicellulases 45321.4 Kinetics of Enzymatic Hydrolysis 45421.4.1 Empirical Models 45521.4.2 Michaelis–Menten-based Models 45521.4.3 Adsorption in Cellulose Hydrolysis Models 45621.4.4 Rate Limitations and Decreasing Rates with Increasing Conversion 45721.4.5 Summary of Enzyme Reaction Kinetics 45921.5 Experimental Hydrolysis Systems 46021.5.1 Laboratory Protocols 46021.5.2 Considerations for Scale-up of Hydrolysis Processes 46321.6 Conclusion 465References 46522 High-throughput Pretreatment and Hydrolysis Systems for Screening Biomass Species in Aqueous Pretreatment of Plant Biomass 471Jaclyn DeMartini and Charles E. Wyman22.1 Introduction: The Need for High-throughput Technologies 47122.2 Previous High-throughput Systems and Application to Pretreatment and Enzymatic Hydrolysis 47222.3 Current HTPH Systems 47322.4 Key Steps in HTPH Systems 47822.4.1 Material Preparation 47822.4.2 Material Distribution 47922.4.3 Pretreatment and Enzymatic Hydrolysis 48022.4.4 Sample Analysis 48122.5 HTPH Philosophy, Difficulties, and Limitations 48222.6 Examples of Research Enabled by HTPH Systems 48422.7 Future Applications 48522.8 Conclusions and Recommendations 485References 48623 Laboratory Pretreatment Systems to Understand Biomass Deconstruction 489Bin Yang and Melvin Tucker23.1 Introduction 48923.2 Laboratory-scale Batch Reactors 49123.2.1 Sealed Glass Reactors 49123.2.2 Tubular Reactors 49223.2.3 Mixed Reactors 49523.2.4 Zipperclave 49623.2.5 Microwave Reactors 49723.2.6 Steam Reactors 49923.3 Laboratory-scale Continuous Pretreatment Reactors 50123.4 Deconstruction of Biomass with Bench-Scale Pretreatment Systems 50323.5 Heat and Mass Transfer 50523.5.1 Mass Transfer 50623.5.2 Direct and Indirect Heating 50623.6 Biomass Handling and Comminuting 50823.7 Construction Materials 50823.7.1 Overall Considerations 50823.7.2 Materials of Construction 50923.8 Criteria of Reactor Selection and Applications 51023.8.1 Effect of High/Low Solids Concentration on Reactor Choices 51023.8.2 Role of Heat-up and Cool-down Rates in Laboratory Reactor Selection 51023.8.3 Effect of Mixing and Catalyst Impregnation on Reactor Design 51023.8.4 High Temperatures and Short Residence Times Result in High Yields 51123.8.5 Pretreatment Severity: Tradeoffs of Time and Temperature 51123.8.6 Minimizing Construction and Operating Costs 51223.9 Summary 513Acknowledgements 514References 514Index 523

Professor Charles Wyman has devoted most of his career to leading advancement of technology for biological conversion of cellulosic biomass to ethanol and other products that will reduce our excessive dependence on petroleum. A substantial portion of this research is directed at advancing technologies for the most expensive and critical unit operations: pretreatment and cellulose and hemicellulose hydrolysis. Professor Wyman is Chair in Environmental Engineering at the Center for Environmental Research and Technology and Professor in Chemical and Environmental Engineering at the University of California at Riverside.

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• List of Contributors xviiForeword xxiSeries Preface xxiiiPreface xxvAcknowledgements xxvii1 Introduction 1Charles E. Wyman1.1 Cellulosic Biomass: What and Why? 21.2 Aqueous Processing of Cellulosic Biomass into Organic Fuels and Chemicals 31.3 Attributes for Successful Pretreatment 51.4 Pretreatment Options 71.5 Possible Blind Spots in the Historic Pretreatment Paradigm 81.6 Other Distinguishing Features of Pretreatment Technologies 91.7 Book Approach 91.8 Overview of Book Chapters 10Acknowledgements 10References 112 Cellulosic Biofuels: Importance, Recalcitrance, and Pretreatment 17Lee Lynd and Mark Laser2.1 Our Place in History 172.2 The Need for Energy from Biomass 172.3 The Importance of Cellulosic Biomass 182.4 Potential Barriers 182.5 Biological and Thermochemical Approaches to the Recalcitrance Barrier 192.6 Pretreatment 20Acknowledgements 21References 213 Plant Cell Walls: Basics of Structure, Chemistry, Accessibility and the Influence on Conversion 23Brian H. Davison, Jerry Parks, Mark F. Davis and Bryon S. Donohoe3.1 Introduction 233.2 Biomass Diversity Leads to Variability in Cell-wall Structure and Composition 243.3 Processing Options for Accessing the Energy in the Lignocellulosic Matrix 263.4 Plant Tissue and Cell Types Respond Differently to Biomass Conversion 283.5 The Basics of Plant Cell-wall Structure 293.6 Cell-wall Surfaces and Multilamellar Architecture 303.7 Cell-wall Ultrastructure and Nanoporosity 313.8 Computer Simulation in Understanding Biomass Recalcitrance 323.8.1 What Can We Learn from Molecular Simulation? 323.8.2 Simulations of Lignin 333.8.3 Simulations of Cellulose 343.8.4 Simulation of Lignocellulosic Biomass 353.8.5 Outlook for Biomass Simulations 353.9 Summary 35Acknowledgements 36References 364 Biological Conversion of Plants to Fuels and Chemicals and the Effects of Inhibitors 39Eduardo Ximenes, Youngmi Kim and Michael R. Ladisch4.1 Introduction 394.2 Overview of Biological Conversion 404.3 Enzyme and Ethanol Fermentation Inhibitors Released during Pretreatment and/or Enzyme Hydrolysis 424.3.1 Enzyme Inhibitors Derived from Plant Cell-wall Constituents (Lignin, Soluble Phenolics, and Hemicellulose) 434.3.2 Effect of Furfurals and Acetic Acid as Inhibitors of Ethanol Fermentations 484.4 Hydrolysis of Pentose Sugar Oligomers Using Solid-acid Catalysts 504.4.1 Application of Solid-acid Catalysts for Hydrolysis of Sugar Oligomers Derived from Lignocelluloses 504.4.2 Factors Affecting Efficiency of Solid-acid-catalyzed Hydrolysis 514.5 Conclusions 56Acknowledgements 57References 575 Catalytic Strategies for Converting Lignocellulosic Carbohydrates to Fuels and Chemicals 61Jesse Q. Bond, David Martin Alonso and James A. Dumesic5.1 Introduction 615.2 Biomass Conversion Strategies 625.3 Criteria for Fuels and Chemicals 645.3.1 General Considerations in the Production of Fuels and Fuel Additives 645.3.2 Consideration for Specialty Chemicals 665.4 Primary Feedstocks and Platforms 665.4.1 Cellulose 665.4.2 Hemicellulose 675.5 Sugar Conversion and Key Intermediates 685.5.1 Sugar Oxidation 695.5.2 Sugar Reduction (Polyol Production) 705.5.3 Sugar Dehydration (Furan Production) 775.6 Conclusions 91Acknowledgements 92References 926 Fundamentals of Biomass Pretreatment at Low pH 103Heather L. Trajano and Charles E. Wyman6.1 Introduction 1036.2 Effects of Low pH on Biomass Solids 1046.2.1 Cellulose 1046.2.2 Hemicellulose 1056.2.3 Lignin 1066.2.4 Ash 1076.2.5 Ultrastructure 1076.2.6 Summary of Effects of Low pH on Biomass Solids 1086.3 Pretreatment in Support of Biological Conversion 1086.3.1 Hydrolysis of Cellulose to Fermentable Glucose 1086.3.2 Pretreatment for Improved Enzymatic Digestibility 1096.3.3 Pretreatment for Improved Enzymatic Digestibility and Hemicellulose Sugar Recovery 1106.4 Low-pH Hydrolysis of Cellulose and Hemicellulose 1146.4.1 Furfural 1146.4.2 Levulinic Acid 1156.4.3 Drop-in Hydrocarbons 1156.5 Models of Low-pH Biomass Reactions 1166.5.1 Cellulose Hydrolysis 1176.5.2 Hemicellulose Hydrolysis 1186.5.3 Summary of Kinetic Models 1206.6 Conclusions 122Acknowledgements 123References 1237 Fundamentals of Aqueous Pretreatment of Biomass 129Nathan S. Mosier7.1 Introduction 1297.2 Self-ionization of Water Catalyzes Plant Cell-wall Depolymerization 1307.3 Products from the Hydrolysis of the Plant Cell Wall Contribute to Further Depolymerization 1317.4 Mechanisms of Aqueous Pretreatment 1317.4.1 Hemicellulose 1317.4.2 Lignin 1347.4.3 Cellulose 1367.5 Impact of Aqueous Pretreatment on Cellulose Digestibility 1377.6 Practical Applications of Liquid Hot Water Pretreatment 1387.7 Conclusions 140References 1408 Fundamentals of Biomass Pretreatment at High pH 145Rocıo Sierra Ramirez, Mark Holtzapple and Natalia Piamonte8.1 Introduction 1458.2 Chemical Effects of Alkaline Pretreatments on Biomass Composition 1468.2.1 Non-oxidative Delignification 1478.2.2 Non-oxidative Sugar Degradation 1488.2.3 Oxidative Delignification 1508.2.4 Oxidative Sugar Degradation 1518.3 Ammonia Pretreatments 1538.4 Sodium Hydroxide Pretreatments 1558.5 Alkaline Wet Oxidation 1558.6 Lime Pretreatment 1588.7 Pretreatment Severity 1618.8 Pretreatment Selectivity 1618.9 Concluding Remarks 163References 1639 Primer on Ammonia Fiber Expansion Pretreatment 169S.P.S. Chundawat, B. Bals, T. Campbell, L. Sousa, D. Gao, M. Jin, P. Eranki, R. Garlock, F. Teymouri, V. Balan and B.E. Dale9.1 Historical Perspective of Ammonia-based Pretreatments 1699.2 Overview of AFEX and its Physicochemical Impacts 1709.3 Enzymatic and Microbial Activity on AFEX-treated Biomass 1759.3.1 Impact of AFEX Pretreatment on Cellulase Binding to Biomass 1759.3.2 Enzymatic Digestibility of AFEX-treated Biomass 1769.3.3 Microbial Fermentability of AFEX-treated Biomass 1789.4 Transgenic Plants and AFEX Pretreatment 1839.5 Recent Research Developments on AFEX Strategies and Reactor Configurations 1859.5.1 Non-extractive AFEX Systems 1859.5.2 Extractive AFEX Systems 1869.5.3 Fluidized Gaseous AFEX Systems 1869.6 Perspectives on AFEX Commercialization 1869.6.1 AFEX Pretreatment Commercialization in Cellulosic Biorefineries 1869.6.2 Novel Value-added Products from AFEX-related Processes 1909.6.3 AFEX-centric Regional Biomass Processing Depot 1929.7 Environmental and Life-cycle Analyses for AFEX-centric Processes 1939.8 Conclusions 194Acknowledgements 195References 19510 Fundamentals of Biomass Pretreatment by Fractionation 201Poulomi Sannigrahi and Arthur J. Ragauskas10.1 Introduction 20110.2 Organosolv Pretreatment 20210.2.1 Organosolv Pulping 20210.2.2 Overview of Organosolv Pretreatment 20210.2.3 Solvents and Catalysts for Organosolv Pretreatment 20310.2.4 Fractionation of Biomass during Organosolv Pretreatment 20910.3 Nature of Organosolv Lignin and Chemistry of Organosolv Delignification 21010.3.1 Composition and Structure of Organosolv Lignin 21010.3.2 Mechanisms of Organosolv Delignification 21310.3.3 Commercial Applications of Organosolv Lignin 21410.4 Structural and Compositional Characteristics of Cellulose 21410.5 Co-products of Biomass Fractionation by Organosolv Pretreatment 21610.5.1 Hemicellulose 21610.5.2 Furfural 21710.5.3 Hydroxymethylfurfural (HMF) 21810.5.4 Levulinic Acid 21810.5.5 Acetic Acid 21910.6 Conclusions and Recommendations 219Acknowledgements 219References 21911 Ionic Liquid Pretreatment: Mechanism, Performance, and Challenges 223Seema Singh and Blake A. Simmons11.1 Introduction 22311.2 Ionic Liquid Pretreatment: Mechanism 22511.2.1 IL Polarity and Kamlet–Taft Parameters 22611.2.2 Interactions between ILs and Cellulose 22611.2.3 Interactions between ILs and Lignin 22711.3 Ionic Liquid Biomass Pretreatment: Enzymatic Route 22811.3.1 Grasses 22811.3.2 Agricultural Residues 23011.3.3 Woody Biomass 23011.4 Ionic Liquid Pretreatment: Catalytic Route 23111.4.1 Acid-catalyzed Hydrolysis 23211.4.2 Metal-catalyzed Hydrolysis 23211.5 Factors Impacting Scalability and Cost of Ionic Liquid Pretreatment 23311.6 Concluding Remarks 234Acknowledgements 234References 23412 Comparative Performance of Leading Pretreatment Technologies for Biological Conversion of Corn Stover, Poplar Wood, and Switchgrass to Sugars 239Charles E. Wyman, Bruce E. Dale, Venkatesh Balan, Richard T. Elander, Mark T. Holtzapple, Rocıo Sierra Ramirez, Michael R. Ladisch, Nathan Mosier, Y.Y. Lee, Rajesh Gupta, Steven R. Thomas, Bonnie R. Hames, Ryan Warner and Rajeev Kumar12.1 Introduction 24012.2 Materials and Methods 24212.2.1 Feedstocks 24212.2.2 Enzymes 24312.2.3 CAFI Pretreatments 24312.2.4 Material Balances 24412.2.5 Free Sugars and Extraction 24412.3 Yields of Xylose and Glucose from Pretreatment and Enzymatic Hydrolysis 24512.3.1 Yields from Corn Stover 24512.3.2 Yields from Standard Poplar 24712.3.3 Yields from Dacotah Switchgrass 24812.4 Impact of Changes in Biomass Sources 24912.5 Compositions of Solids Following CAFI Pretreatments 25112.5.1 Composition of Pretreated Corn Stover Solids 25212.5.2 Composition of Pretreated Switchgrass Solids 25212.5.3 Composition of Pretreated Poplar Solids 25312.5.4 Overall Trends in Composition of Pretreated Biomass Solids and Impact on Enzymatic Hydrolysis 25312.6 Pretreatment Conditions to Maximize Total Glucose Plus Xylose Yields 25412.7 Implications of the CAFI Results 25512.8 Closing Thoughts 256Acknowledgements 257References 25813 Effects of Enzyme Formulation and Loadings on Conversion of Biomass Pretreated by Leading Technologies 261Rajesh Gupta and Y.Y. Lee13.1 Introduction 26113.2 Synergism among Cellulolytic Enzymes 26213.3 Hemicellulose Structure and Hemicellulolytic Enzymes 26313.4 Substrate Characteristics and Enzymatic Hydrolysis 26413.5 Xylanase Supplementation for Different Pretreated Biomass and Effect of b-Xylosidase 26513.6 Effect of b-Glucosidase Supplementation 26913.7 Effect of Pectinase Addition 26913.8 Effect of Feruloyl Esterase and Acetyl Xylan Esterase Addition 27013.9 Effect of a-L-arabinofuranosidase and Mannanase Addition 27013.10 Use of Lignin-degrading Enzymes (LDE) 27113.11 Effect of Inactive Components on Biomass Hydrolysis 27113.12 Adsorption and Accessibility of Enzyme with Different Cellulosic Substrates 27113.13 Tuning Enzyme Formulations to the Feedstock 27213.14 Summary 273References 27414 Physical and Chemical Features of Pretreated Biomass that Influence Macro-/Micro-accessibility and Biological Processing 281Rajeev Kumar and Charles E. Wyman14.1 Introduction 28114.2 Definitions of Macro-/Micro-accessibility and Effectiveness 28314.3 Features Influencing Macro-accessibility and their Impacts on Enzyme Effectiveness 28414.3.1 Lignin 28414.3.2 Hemicellulose 28614.4 Features Influencing Micro-accessibility and their Impact on Enzymes Effectiveness 28914.4.1 Cellulose Crystallinity (Structure) 28914.4.2 Cellulose Chain Length/Reducing Ends 29114.5 Concluding Remarks 293Acknowledgements 296References 29615 Economics of Pretreatment for Biological Processing 311Ling Tao, Andy Aden and Richard T. Elander15.1 Introduction 31115.2 Importance of Pretreatment 31115.3 History of Pretreatment Economic Analysis 31315.4 Methodologies for Economic Assessment 31415.5 Overview of Pretreatment Technologies 31515.5.1 Acidic Pretreatments 31515.5.2 Alkaline Pretreatments 31515.5.3 Solvent-based Pretreatments 31615.6 Comparative Pretreatment Economics 31615.6.1 Modeling Basis and Assumptions for Comparative CAFI Analysis 31715.6.2 CAFI Project Comparative Data 32015.6.3 Reactor Design and Costing Data 32015.6.4 Comparison of Sugar and Ethanol Yields 32415.6.5 Comparison of Pretreatment Capital Costs 32515.6.6 Comparison of MESP 32615.7 Impact of Key Variables on Pretreatment Economics 32715.7.1 Yield 32715.7.2 Conversion to Oligomers/Monomers (Shift of Burden between Enzymes and Pretreatment) 32815.7.3 Biomass Loading/Concentration 32815.7.4 Chemical Loading/Recovery/Metallurgy 32915.7.5 Reaction Conditions: Pressure, Temperature, Residence Time 33015.7.6 Reactor Orientation: Horizontal/Vertical 33015.7.7 Batch versus Continuous Processing 33015.8 Future Needs for Evaluation of Pretreatment Economics 33115.9 Conclusions 332Acknowledgements 332References 33216 Progress in the Summative Analysis of Biomass Feedstocks for Biofuels Production 335F.A. Agblevor and J. Pereira16.1 Introduction 33516.2 Preparation of Biomass Feedstocks for Analysis 33716.3 Determination of Non-structural Components of Biomass Feedstocks 33816.3.1 Moisture Content of Biomass Feedstocks 33816.3.2 Determination of Ash in Biomass 33816.3.3 Protein Content of Biomass 33816.3.4 Extractives Content of Biomass 33916.4 Quantitative Determination of Lignin Content of Biomass 34016.5 Quantitative Analysis of Sugars in Lignocellulosic Biomass 34216.5.1 Holocellulose Content of Plant Cell Walls 34216.5.2 Monoethanolamine Method for Cellulose Determination 34316.6 Chemical Hydrolysis of Biomass Polysaccharides 34316.6.1 Mineral Acid Hydrolysis 34316.6.2 Trifluoroacetic Acid (TFA) 34416.6.3 Methanolysis 34416.7 Analysis of Monosaccharides 34516.7.1 Colorimetric Analysis of Biomass Monosaccharides 34516.7.2 Gas Chromatographic Sugar Analysis 34516.8 Gas Chromatography-Mass Spectrometry (GC/MS) 34716.9 High-performance Liquid Chromatographic Sugar Analysis 34716.10 NMR Analysis of Biomass Sugars 34916.11 Conclusions 349References 34917 High-throughput NIR Analysis of Biomass Pretreatment Streams 355Bonnie R. Hames17.1 Introduction 35517.2 Rapid Analysis Essentials 35617.2.1 Rapid Spectroscopic Techniques 35717.2.2 Calibration and Validation Samples 35817.2.3 Quality Calibration Data for Each Calibration Sample 35917.2.4 Multivariate Analysis to Resolve Complex Sample Spectra 36217.2.5 Validation of New Methods 36417.2.6 Standard Reference Materials and Protocols for Ongoing QA/QC 36417.3 Summary 366References 36718 Plant Biomass Characterization: Application of Solution- and Solid-state NMR Spectroscopy 369Yunqiao Pu, Bassem Hallac and Arthur J. Ragauskas18.1 Introduction 36918.2 Plant Biomass Constituents 37018.3 Solution-state NMR Characterization of Lignin 37118.3.1 Lignin Sample Preparation 37218.3.2 1 H NMR Spectroscopy 37218.3.3 13 c NMR Spectroscopy 37218.3.4 HSQC Correlation Spectroscopy 37518.3.5 31 P NMR Spectroscopy 37718.4 Solid-state NMR Characterization of Plant Cellulose 38118.4.1 CP/MAS 13 C NMR Analysis of Cellulose 38118.4.2 Cellulose Crystallinity 38318.4.3 Cellulose Ultrastructure 38518.5 Future Perspectives 387Acknowledgements 387References 38719 Xylooligosaccharides Production, Quantification, and Characterization in Context of Lignocellulosic Biomass Pretreatment 391Qing Qing, Hongjia Li, Rajeev Kumar and Charles E. Wyman19.1 Introduction 39119.1.1 Definition of Oligosaccharides 39119.1.2 Types of Oligosaccharides Released during Lignocellulosic Biomass Pretreatment 39219.1.3 The Importance of Measuring Xylooligosaccharides 39219.2 Xylooligosaccharides Production 39419.2.1 Thermochemical Production of XOs 39419.2.2 Production of XOs by Enzymatic Hydrolysis 39619.3 Xylooligosaccharides Separation and Purification 39719.3.1 Solvent Extraction 39719.3.2 Adsorption by Surface Active Materials 39719.3.3 Chromatographic Separation Techniques 39819.3.4 Membrane Separation 39919.3.5 Centrifugal Partition Chromatography 40119.4 Characterization and Quantification of Xylooligosaccharides 40219.4.1 Measuring Xylooligosaccharides by Quantification of Reducing Ends 40219.4.2 Characterizing Xylooligosaccharides Composition 40219.4.3 Direct Characterization of Different DP Xylooligosaccharides 40319.4.4 Determining Detailed Structures of Oligosaccharides by MS and NMR 40819.5 Concluding Remarks 408Acknowledgements 409References 41020 Experimental Pretreatment Systems from Laboratory to Pilot Scale 417Richard T. Elander20.1 Introduction 41720.2 Laboratory-scale Pretreatment Equipment 42120.2.1 Heating and Cooling Capability 42120.2.2 Contacting of Biomass Particles with Water and/or Pretreatment Chemicals 42120.2.3 Mass and Heat Transfer 42220.2.4 Proper Materials of Construction 42320.2.5 Instrumentation and Control Systems 42420.2.6 Translating to Pilot-scale Pretreatment Systems 42420.3 Pilot-scale Batch Pretreatment Equipment 42420.4 Pilot-scale Continuous Pretreatment Equipment 42720.4.1 Feedstock Handling and Size Reduction 42720.4.2 Pretreatment Chemical and Water Addition 42920.4.3 Pressurized Continuous Pretreatment Feeder Equipment 43220.4.4 Pretreatment Reactor Throughput and Residence Time Control 43620.4.5 Reactor Discharge Devices 43820.4.6 Blow-down Vessel and Flash Vapor Recovery 43820.5 Continuous Pilot-scale Pretreatment Reactor Systems 43920.5.1 Historical Development of Pilot-scale Reactor Systems 43920.5.2 NREL Gravity-flow Reactor Systems 44120.6 Summary 445Acknowledgements 446References 44721 Experimental Enzymatic Hydrolysis Systems 451Todd Lloyd and Chaogang Liu21.1 Introduction 45121.2 Cellulases 45221.2.1 Endoglucanase 45221.2.2 Cellobiohydrolase 45321.2.3 b-glucosidase 45321.3 Hemicellulases 45321.4 Kinetics of Enzymatic Hydrolysis 45421.4.1 Empirical Models 45521.4.2 Michaelis–Menten-based Models 45521.4.3 Adsorption in Cellulose Hydrolysis Models 45621.4.4 Rate Limitations and Decreasing Rates with Increasing Conversion 45721.4.5 Summary of Enzyme Reaction Kinetics 45921.5 Experimental Hydrolysis Systems 46021.5.1 Laboratory Protocols 46021.5.2 Considerations for Scale-up of Hydrolysis Processes 46321.6 Conclusion 465References 46522 High-throughput Pretreatment and Hydrolysis Systems for Screening Biomass Species in Aqueous Pretreatment of Plant Biomass 471Jaclyn DeMartini and Charles E. Wyman22.1 Introduction: The Need for High-throughput Technologies 47122.2 Previous High-throughput Systems and Application to Pretreatment and Enzymatic Hydrolysis 47222.3 Current HTPH Systems 47322.4 Key Steps in HTPH Systems 47822.4.1 Material Preparation 47822.4.2 Material Distribution 47922.4.3 Pretreatment and Enzymatic Hydrolysis 48022.4.4 Sample Analysis 48122.5 HTPH Philosophy, Difficulties, and Limitations 48222.6 Examples of Research Enabled by HTPH Systems 48422.7 Future Applications 48522.8 Conclusions and Recommendations 485References 48623 Laboratory Pretreatment Systems to Understand Biomass Deconstruction 489Bin Yang and Melvin Tucker23.1 Introduction 48923.2 Laboratory-scale Batch Reactors 49123.2.1 Sealed Glass Reactors 49123.2.2 Tubular Reactors 49223.2.3 Mixed Reactors 49523.2.4 Zipperclave 49623.2.5 Microwave Reactors 49723.2.6 Steam Reactors 49923.3 Laboratory-scale Continuous Pretreatment Reactors 50123.4 Deconstruction of Biomass with Bench-Scale Pretreatment Systems 50323.5 Heat and Mass Transfer 50523.5.1 Mass Transfer 50623.5.2 Direct and Indirect Heating 50623.6 Biomass Handling and Comminuting 50823.7 Construction Materials 50823.7.1 Overall Considerations 50823.7.2 Materials of Construction 50923.8 Criteria of Reactor Selection and Applications 51023.8.1 Effect of High/Low Solids Concentration on Reactor Choices 51023.8.2 Role of Heat-up and Cool-down Rates in Laboratory Reactor Selection 51023.8.3 Effect of Mixing and Catalyst Impregnation on Reactor Design 51023.8.4 High Temperatures and Short Residence Times Result in High Yields 51123.8.5 Pretreatment Severity: Tradeoffs of Time and Temperature 51123.8.6 Minimizing Construction and Operating Costs 51223.9 Summary 513Acknowledgements 514References 514Index 523