Biological and Catalytic Conversion of Sugars and Lignin Publications

2016

Base-Catalyzed Depolymerization of Biorefinery Lignins, ACS Sustainable Chemistry & Engineering

Lignin Depolymerization with Nitrate-Intercalated Hydrotalcite Catalysts, ACS Catalysis

Pyrolysis Reaction Networks for Lignin Model Compounds: Unraveling Thermal Deconstruction of β-O-4 and α-O-4 Compounds, Green Chemistry

Simulations of Cellulose Translocation in the Bacterial Cellulose Synthase Suggest a Regulatory Mechanism for the Dimeric Structure of Cellulose, Chemical Science

Succinic Acid Production on Xylose-Enriched Biorefinery Streams by Actinobacillus succinogenes in Batch Fermentation, Biotechnology for Biofuels

2015

Glycosylation of Cellusales: Engineering Better Enzymes for Biofuels, Advances in Carbohydrate Chemistry and Biochemistry

Lignocellulose Degradation Mechanisms across the Tree of Life, Current Opinion in Chemical Biology

Carbocation Stability in H-ZSM5 at High Temperature, Journal of Physical Chemistry A

Continuous Succinic Acid Production by Actinobacillus succinogenes on Xylose-Enriched Hydrolysate, Biotechnology for Biofuels

Molecular-Scale Features that Govern the Effects of O-Glycosylation on a Carbohydrate-Binding Module, Chemical Science

O-Glycosylation Effects on Family 1 Carbohydrate-Binding Module Solution Structures, FEBS Journal

Towards Lignin Consolidated Bioprocessing: Simultaneous Lignin Depolymerization and Co-Product Generation by Bacteria, Green Chemistry

Alkaline Pretreatment of Switchgrass, ACS Sustainable Chemistry & Engineering

Effects of Lytic Polysaccharide Monooxygenase Oxidation on Cellulose Structure and Binding of Oxidized Cellulose Oligomers to Cellulases, Journal of Physical Chemistry B

Electronic Coupling through Natural Amino Acids, Journal of Chemical Physics

Ethanol Dehydration in HZSM-5 Studied by Density Functional Theory: Evidence for a Concerted Process, Journal of Physical Chemistry A

Fungal Cellulases, Chemical Reviews

Aromatic Catabolic Pathway Selection for Optimal Production of Pyruvate and Lactate from Lignin, Metabolic Engineering

Nucleation Rate Analysis of Methane Hydrate from Molecular Dynamics Simulations, Faraday Discussions

Adipic Acid Production from Lignin, Energy & Environmental Science

2014

The Alpha-Bet(a) of Salty Glucose Pyrolysis: Computational Investigations Reveal Carbohydrate Pyrolysis Catalytic Action by Sodium Ions, ACS Catalysis

Reaction Coordinate of Incipient Methane Clathrate Hydrate Nucleation, Journal of Physical Chemistry B

Lignin Valorization through Integrated Biological Funneling and Chemical Catalysis, Proceedings of the National Academy of Sciences

Carbohydrate-Protein Interactions that Drive Processive Polysaccharide Translocation in Enzymes Revealed from a Computational Study of Cellobiohydrolase Processivity, Journal of the American Chemical Society

Lignin Valorization: Improving Lignin Processing in the Biorefinery, Science

Specificity of O-Glycosylation in Enhancing the Stability and Cellulose Binding Affinity of Family 1 Carbohydrate-Binding Modules, Proceedings of the National Academy of Sciences

Structural and Electronic Snapshots during the Transition from a Cu(II) to Cu(I) Metal Center by X-Ray Photo-Reduction, Journal of Biological Chemistry

Clean Fractionation Pretreatment Reduces Enzyme Loadings for Biomass Saccharification and Reveals the Mechanism of Free and Cellulosomal Enzyme Synergy, ACS Sustainable Chemistry & Engineering

Evaluation of Clean Fractionation Pretreatment for the Production of Renewable Fuels and Chemicals from Corn Stover, ACS Sustainable Chemistry & Engineering

The Alpha-Bet(a) of Glucose Pyrolysis: Computational and Experimental Investigations of 5-Hydroxymethylfurfural and Levoglucosan Formation Reveal Implications for Cellulose Pyrolysis, ACS Sustainable Chemistry & Engineering

Alkaline Pretreatment of Corn Stover: Bench-Scale Fractionation and Stream Characterization, ACS Sustainable Chemistry & Engineering

Two-Component Order Parameter for Quantifying Clathrate Hydrate Nucleation and Growth, Journal of Chemical Physics

Crystal Structure of Glycoside Hydrolase Family 127 β-L-Arabinofuranosidase from Bifidobacterium longum, Biochemical and Biophysical Research Communications

Charge Engineering of Cellulases Improves Ionic Liquid Tolerance and Reduces Lignin Inhibition, Biotechnology and Bioengineering

How Sugars Pucker: Electronic Structure Calculations Map the Kinetic Landscape of Five Biologically Paramount Monosaccharides and Their Implications for Enzymatic Catalysis, Journal of the American Chemical Society

Quantum Mechanical Calculations Suggest that Lytic Polysaccharide Monooxygenases Employ a
Copper-Oxyl, Oxygen-Rebound Mechanism, Proceedings of the National Academy of Sciences

The Mechanism of Cellulose Hydrolysis by a Two-Step, Retaining Cellobiohydrolases Elucidated by Structural and Transition Path Sampling Studies, Journal of the American Chemical Society

Towards a Molecular-Level Theory of Carbohydrate Processivity in Glycoside Hydrolases, Current Opinion in Chemical Biology

Sodium Ion Interactions with Aqueous Glucose: Insights from Quantum Mechanics, Molecular Dynamics, and Experiment, Journal of Physical Chemistry B

Lignin Depolymerisation by Nickel Supported Layered-Double Hydroxide Catalysts, Green Chemistry

A Perspective on Oxygenated Species in the Refinery Integration of Pyrolysis Oil, Green Chemistry

The Complete Mitochondrial Genome of Limnoria quadripunctata Holthuis (Isopoda: Limnoriidae), Mitochondrial DNA

A Mechanistic Investigation of Acid-Catalyzed Cleavage of Aryl-Ether Linkages: Implications for Lignin Depolymerization in Acidic Environments, ACS Sustainable Chemistry & Engineering

2013

Glycoside Hydrolase Processivity is Directly Related to Oligosaccharide Binding Free Energy, Journal of the American Chemical Society

Process Design and Economics for the Conversion of Lignocellulosic Biomass to Hydrocarbons: Dilute-Acid Prehydrolysis and Enzymatic Hydrolysis Deconstruction of Biomass to Sugars and Biological Conversion of Sugars to Hydrcarbons, NREL Technical Report

Loop Motions Important to Product Expulsion in the Thermobifida fusca Glycoside Hydrolase Family 6 Cellobiohydrolase from Structural and Computational Studies, Journal of Biological Chemistry

Impact of alg3 Gene Deletion on Growth, Development, Pigment Production, Protein Secretion, and Functions of Recombinant Trichoderma reesei Cellobiohydrolases in Aspergillus niger, Fungal Genetics and Biology

Endoglucanase Peripheral Loops Facilitate Complexation of Glucan Chains on Cellulose via Adaptive Coupling to the Emergent Substrate Structures, Journal of Physical Chemistry B

Glycosylated Linkers in Multimodular Lignocellulose-Degrading Enzymes Dynamically Bind to Cellulose, Proceedings of the National Academy of Sciences

3D Electron Tomography of Pretreated Biomass Informs Atomic Modeling of Cellulose Microfibrils, ACS Nano

Structural Characterization of a Unique Marine Animal Family 7 Cellobiohydrolase Suggests a Mechanism of Cellulase Salt Tolerance, Proceedings of the National Academy of Sciences

Fungal Cellulases and Complexed Cellulosomal Enzymes Exhibit Synergistic Mechanisms in Cellulose Deconstruction, Energy & Environmental Science

Mechanistic Study of a Ru-Xantphos Catalyst for Tandem Alcohol Dehydrogenation and Reductive Aryl-Ether Cleavage, ACS Catalysis

Binding Site Dynamics and Aromatic-Carbohydrate Interactions in Processive and Non-Processive Family 7 Glycoside Hydrolases, Journal of Physical Chemistry B

Crystal Structure and Computational Characterization of the Lytic Polysaccharide Monooxygenase GH61D from the Basidiomycota Fungus Phanerochaete chrysosporium, Journal of Biological Chemistry

Computational Investigation of the pH Dependence of Loop Flexibility and Catalytic Function in Glycoside Hydrolases, Journal of Biological Chemistry

Structural, Biochemical, and Computational Characterization of the Glycoside Hydrolase Family 7 Cellobiohydrolase of the Tree-Killing Fungus Heterobasidion irregulare, Journal of Biological Chemistry

Initial Recognition of a Cellodextrin Chain in the Cellulose-Binding Tunnel May Affect Cellobiohydrolase Directional Specificity, Biophysical Journal

2012

Cellulase Linkers are Optimized Based on Domain Type and Function: Insights from Sequence Analysis, Biophysical Measurements, and Molecular Simulation, PLOS ONE

Hallmarks of Processivity in Glycoside Hydrolases from Crystallographic and Computational Studies of the Serratia marcescens Chitinases, Journal of Biological Chemistry

Product Binding Varies Dramatically between Processive and Nonprocessive Cellulase Enzymes, Journal of Biological Chemistry

Binding Preferences, Surface Attachment, Diffusivity, and Orientation of a Family 1 Carbohydrate-Binding Module on Cellulose, Journal of Biological Chemistry

Uncertainty in Techno-Economic Estimates of Cellulosic Ethanol Production due to Experimental Measurement Uncertainty, Biotechnology for Biofuels

Comparison of Cellulose Iβ Simulations with Three Carbohydrate Force Fields, Journal of Chemical Theory and Computation

Harnessing Glycosylation to Improve Cellulase Activity, Current Opinion in Chemical Biology

Computational Investigation of Glycosylation Effects on a Family 1 Carbohydrate-Binding Module, Journal of Biological Chemistry

2011

Multiple Functions of Aromatic-Carbohydrate Interactions in a Processive Cellulase Examined with Molecular Simulation, Journal of Biological Chemistry

The Cages, Dynamics, and Structuring of Incipient Methane Clathrate Hydrates, Physical Chemistry Chemical Physics

Computational Study of Bond Dissociation Enthalpies for a Large Range of Native and Modified Lignins, Journal of Physical Chemistry Letters

Methane Hydrate Nucleation Rates from Molecular Dynamics Simulations: Effects of Aqueous Methane Concentration, Interfacial Curvature, and System Size, Journal of Physical Chemistry C

Protein Allostery at the Solid-Liquid Interface: Endoglucanase Attachment to Cellulose Affects Glucan Clenching in the Binding Cleft, Journal of the American Chemical Society

Coarse-Grain Model for Glucose, Cellobiose, and Cellotetraose in Water, Journal of Chemical Theory and Computation

Decrystallization of Oligosaccharides from the Cellulose Iβ Surface with Molecular Simulation, Journal of Physical Chemistry Letters

Probing Carbohydrate Product Expulsion from a Processive Cellulase with Multiple Absolute Binding Free Energy Methods, Journal of Biological Chemistry

Optimizing Nucleus Size Metrics for Liquid–Solid Nucleation from Transition Paths of Near-Nanosecond Duration, Journal of Physical Chemistry Letters

Examination of the α-Chitin Structure and Decrystallization Thermodynamics at the Nanoscale, Journal of Physical Chemistry B

Molecular-Level Origins of Biomass Recalcitrance: Decrystallization Free Energies for Four Common Cellulose Polymorphs, Journal of Physical Chemistry B

Modeling the Self-Assembly of the Cellulosome Enzyme Complex, Journal of Biological Chemistry

High-Temperature Behavior of Cellulose I, Journal of Physical Chemistry B

Deconstruction of Lignocellulosic Biomass to Fuels and Chemicals, Annual Review of Chemical and Biomolecular Engineering

Applications of Computational Science for Understanding Enzymatic Deconstruction of Cellulose, Current Opinion in Chemical Biology

2010

The O-Glycosylated Linker from the Trichoderma reesei Family 7 Cellulase Is a Flexible, Disordered Protein, Biophysical Journal

Identification of Amino Acids Responsible for Processivity for a Family 1 Carbohydrate-Binding Module from a Fungal Cellulase, Journal of Physical Chemistry B

2009

The Energy Landscape for the Interaction of the Family 1 Carbohydrate-Binding Module and the Cellulose Surface is Altered by Hydrolyzed Glycosidic Bonds, Journal of Physical Chemistry B

Probing the Role of N-linked Glycans in the Stability and Activity of Fungal Cellobiohydrolases by Mutational Analysis, Cellulose