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Crowley, Michael F.

Publications and source records attributed to Crowley, Michael F..

At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Dataset_for_Conserved_macromolecular_architecture_of_Poplar_secondary_cell_walls_revealed_by_ssNMR_and_atomistic_modeling

This dataset contains solid-state 13C NMR data and atomistic molecular dynamics simulation files supporting the study of nanoscale secondary cell wall architecture across 13 genetically diverse Populus trichocarpa genotypes grown under uniform greenhouse conditions in 13C-enriched CO2 atmospheres (~89% 13C enrichment).The dataset contains two collections of solid-state 13C NMR data. (1) 200 MHz data (Bruker Avance III HD, 4 mm HX probe, 10 kHz MAS): raw Bruker TopSpin experiment folders and DMFIT-exported ascii spectra for selective and non-selective 1D 13C-13C spin diffusion experiments (3000 ms mixing) used to quantify inter-polymer spatial proximities, and short-mixing (1 ms) reference spectra used for polymeric abundance quantification by spectral deconvolution. (2) 600 MHz data (Bruker Avance III, 1.6 mm PhoenixNMR HXY probe, 30 kHz MAS): raw Bruker TopSpin experiment folders containing 2D CORD, 2D CP-INADEQUATE, and 13C/1H relaxation (T1, T1rho) experiments for all 13 genotypes, with processed Excel workbooks per experiment type. Molecular dynamics simulation code, coordinate files, and analysis scripts (NAMD/CHARMM/Python) for six atomistic cell wall models are included. Summarized ssNMR data are compiled into a single excel file and subjected to statistical analysis. Multivariate analysis code (PCA, Pearson correlation) and summary data are provided as excel worksheets and Jupyter notebooks (Python 3).

09 BIOMASS FUELS↗
DOE OSTI2025

A Novel Zwitterionic Chromatography Approach to Separate Lithium from Unconventional Resources

Lithium (Li) is a key element for clean energy technologies, and, accordingly, the global lithium demand has been increasing rapidly. Therefore, to meet the Li demand and maintain supply chain stability, it is critical to develop efficient lithium extraction technologies that allow exploitation of unconventional lithium resources, such as geothermal brines and inland brine streams. However, the recovery of Li from these resources is challenging due to low Li concentration, low ratios of Li/Na, Li/Mg, or Li/Ca, and complex feed compositions. To address this, we introduced a new Direct Lithium Extraction (DLE) process using Zwitterionic Chromatography (ZIC) to separate Li from other salts. Since salts are partitioned on ZIC under water elution, no reagent chemicals are needed, and the Li separation is not limited by the adsorption capacity. We prepared 13 different zwitterionic (ZI) resins to investigate the salt retention on various ZI groups and then screened out promising sorbents for efficient Li separation. It was found that salt retention was synergistically affected by the pore size and ZI configurations. Using carboxybetaine (QAC3CA) sorbents, multicomponent separations showed that Li can be partitioned from divalent salts or Na with selectivities of 1.8 or 1.9, respectively. Although the selectivity is relatively low, in real brine tests, Li was separated from Ca and Mg with 79.2 % yield, showing the potential for a continuous process to achieve high productivity and high yield. Simulation studies suggest the salt elution mechanism is related to the hydration reaction energy and the effective hydrated radius of cations.

critical minerals↗
DOE OSTI2024

Atomistic, macromolecular model of the Populus secondary cell wall informed by solid-state NMR

Plant secondary cell walls (SCWs) are composed of a heterogeneous interplay of three major biopolymers: cellulose, hemicelluloses, and lignin. Details regarding specific intermolecular interactions and higher-order architecture of the SCW superstructure remain ambiguous. Here, we use solid-state nuclear magnetic resonance (ssNMR) measurements to infer refined details about the structural configuration, intermolecular interactions, and relative proximity of all three major biopolymers within air-dried Populus wood. To enhance the utility of these findings and enable evaluation of hypotheses in a physics-based environment in silico, the NMR observables are articulated into an atomistic, macromolecular model for biopolymer assemblies within the plant SCW. Through molecular dynamics simulation, we quantitatively evaluate several variations of atomistic models to determine structural details that are corroborated by ssNMR measurements.

09 BIOMASS FUELS↗
DOE OSTI2023

Diffusion in intact secondary cell wall models of plants at different equilibrium moisture content

Secondary plant cell walls are composed of carbohydrate and lignin polymers, and collectively represent a significant renewable resource. Leveraging these resources depends in part on a mechanistic understanding for diffusive processes within plant cell walls. Common wood protection treatments and biomass conversion processes to create biorefinery feedstocks feature ion or solvent diffusion within the cell wall. X-ray fluorescence microscopy experiments have determined that ionic diffusion rates are dependent on cell wall hydration as well as the ionic species through non-linear relationships. In this work, we use classical molecular dynamics simulations to map the diffusion behavior of different plant cell wall components (cellulose, hemicellulose, lignin), ions (Na + , K + , Cu2 + , Cl - ) and water within a model for an intact plant cell wall at various hydration states (3-30 wt% water). From these simulations, we analyze the contacts between different plant cell wall components with each other and their interaction with the ions. Generally, diffusion increases with increasing hydration, with lignin and hemicellulose components increasing diffusion by an order of magnitude over the tested hydration range. Ion diffusion depends on charge. Positively charged cations preferentially interact with hemicellulose components, which include negatively charged carboxylates. As a result, positive ions diffuse more slowly than negatively charged ions. Measured diffusion coefficients are largely observed to best fit piecewise linear trends, with an inflection point between 10 and 15% hydration. These observations shed light onto the molecular mechanisms for diffusive processes within secondary plant cell walls at atomic resolution.

09 BIOMASS FUELS↗
DOE OSTI2022

Lytic polysaccharide monooxygenase increases cellobiohydrolases activity by promoting decrystallization of cellulose surface

Efficient depolymerization of crystalline cellulose requires cooperation between multiple cellulolytic enzymes. Through biochemical approaches, molecular dynamics (MD) simulation, and single-molecule observations using high-speed atomic force microscopy (HS-AFM), we quantify and track synergistic activity for cellobiohydrolases (CBHs) with a lytic polysaccharide monooxygenase (LPMO) from Phanerochaete chrysosporium. Increasing concentrations of LPMO (AA9D) increased the activity of a glycoside hydrolase family 6 CBH, Cel6A, whereas the activity of a family 7 CBH (Cel7D) was enhanced only at lower concentrations of AA9D. MD simulation suggests that the result of AA9D action to produce chain breaks in crystalline cellulose can oxidatively disturb the crystalline surface by disrupting hydrogen bonds. HS-AFM observations showed that AA9D increased the number of Cel7D molecules moving on the substrate surface and increased the processivity of Cel7D, thereby increasing the depolymerization performance, suggesting that AA9D not only generates chain ends but also amorphizes the crystalline surface, thereby increasing the activity of CBHs.

09 BIOMASS FUELS↗
DOE OSTI2022

Molecular simulation of lignin-related aromatic compound permeation through gram-negative bacterial outer membranes

Lignin, an abundant aromatic heteropolymer in secondary plant cell walls, is the single largest source of renewable aromatics in the biosphere. Leveraging this resource for renewable bioproducts through targeted microbial action depends on lignin fragment uptake by microbial hosts and subsequent enzymatic action to obtain the desired product. Recent computational work has emphasized that bacterial inner membranes are permeable to many aromatic compounds expected from lignin depolymerization processes. In this study, we expand on these findings through simulations for 42 lignin-related compounds across a gram-negative bacterial outer membrane model. Unbiased simulation trajectories indicate that spontaneous crossing for the full outer membrane is relatively rare at molecular simulation timescales, primarily due to preferential membrane partitioning and slow diffusion within the lipopolysaccharide layer within the outer membrane. Membrane partitioning and permeability coefficients were determined through replica exchange umbrella sampling simulations to overcome sampling limitations. We find that the glycosylated lipopolysaccharides found in the outer membrane increase the permeation barrier to many lignin-related compounds, particularly the most hydrophobic compounds. However, the effect is relatively modest; at industrially relevant concentrations, uncharged lignin-related compounds will readily diffuse across the outer membrane without the need for specific porins. Together, our results provide insight into the permeability of the bacterial outer membrane for assessing lignin fragment uptake and the future production of renewable bioproducts.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Production of β-ketoadipic acid from glucose in Pseudomonas putida KT2440 for use in performance-advantaged nylons

Biomass-derived chemicals can offer unique chemical functionality relative to petroleum-derived building blocks. To this end, here we report that β-ketoadipic acid (βKA), a C6 diacid with a β-ketone group, can be used as a performance-advantaged replacement for adipic acid in a nylon-6,6 analog. Building on our previous efforts to produce shikimate-derived products from carbohydrates, Pseudomonas putida KT2440 is engineered to produce βKA from glucose, achieving a 26 g/L titer. Following purification, βKA imparts an increase of 69 degrees C above the nylon-6,6 glass transition temperature and 20% reduced water permeability, equivalent to nylon-6,10. Molecular simulations predict that the enhanced thermal properties result from rigidity introduced by the β-ketone. Process analysis predicts that βKA can be produced for US$1.94/kg from sugars, requiring 63% less energy and emitting 43% less greenhouse gases than fossil-based adipic acid. Overall, this study illustrates the potential for βKA to serve as a useful building block for bio-based polymers.

09 BIOMASS FUELS↗
DOE OSTI2022

Towards Elucidating Structure–Spectra Relationships in Rhamnogalacturonan II: Computational Protocols for Accurate 13C and 1H Shifts for Apiose and Its Borate Esters

Apiose is a naturally occurring, uncommon branched-chain pentose found in plant cell walls as part of the complex polysaccharide Rhamnogalacturonan II (RG-II). The structural elucidation of the three-dimensional structure of RG-II by nuclear magnetic resonance (NMR) spectroscopy is significantly complicated by the ability of apiose to cross-link via borate ester linkages to form RG-II dimers. Here, we developed a computational approach to gain insight into the structure–spectra relationships of apio–borate complexes in an effort to complement experimental assignments of NMR signals in RG-II. Our protocol involved structure optimizations using density functional theory (DFT) followed by isotropic magnetic shielding constant calculations using the gauge-invariant atomic orbital (GIAO) approach to predict chemical shifts. We evaluated the accuracy of 23 different functional–basis set (FBS) combinations with and without implicit solvation for predicting the experimental 1 H and 13 C shifts of a methyl apioside and its three borate derivatives. The computed NMR predictions were evaluated on the basis of the overall shift accuracy, relative shift ordering, and the ability to distinguish between dimers and monomers. We demonstrate that the consideration of implicit solvation during geometry optimizations in addition to the magnetic shielding constant calculations greatly increases the accuracy of NMR chemical shift predictions and can correctly reproduce the ordering of the 13 C shifts and yield predictions that are, on average, within 1.50 ppm for 13 C and 0.12 ppm for 1 H shifts for apio–borate compounds.

BASIC BIOLOGICAL SCIENCES,BIOMASS FUELS↗
DOE OSTI2021

Transition Path Sampling Study of the Feruloyl Esterase Mechanism

Serine hydrolases cleave peptide and ester bonds and are ubiquitous in nature, with applications in biotechnology, in materials, and as drug targets. The serine hydrolase two-step mechanism employs a serine–histidine–aspartate/glutamate catalytic triad, where the histidine residue acts as a base to activate poor nucleophiles (a serine residue or a water molecule) and as an acid to allow the dissociation of poor leaving groups. This mechanism has been the subject of debate regarding how histidine shuttles the proton from the nucleophile to the leaving group. To elucidate the reaction mechanism of serine hydrolases, we employ quantum mechanics/molecular mechanics-based transition path sampling to obtain the reaction coordinate using the Aspergillus niger feruloyl esterase A (AnFaeA) as a model enzyme. The optimal reaction coordinates include terms involving nucleophilic attack on the carbonyl carbon and proton transfer to, and dissociation of, the leaving group. During the reaction, the histidine residue undergoes a reorientation on the time scale of hundreds of femtoseconds that supports the “moving histidine” mechanism, thus calling into question the “ring flip” mechanism. We find a concerted mechanism, where the transition state coincides with the tetrahedral intermediate with the histidine residue pointed between the nucleophile and the leaving group. Moreover, motions of the catalytic aspartate toward the histidine occur concertedly with proton abstraction by the catalytic histidine and help stabilize the transition state, thus partially explaining how serine hydrolases enable poor nucleophiles to attack the substrate carbonyl carbon. Rate calculations indicate that the second step (deacylation) is rate-determining, with a calculated rate constant of 66 s –1 . Altogether, these results reveal the pivotal role of active-site dynamics in the catalytic mechanism of AnFaeA, which is likely similar in other serine hydrolases.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

An Adaptive-Mesh-Refinement Based Computational Tool for Simulating Catalysis at Mesoscale

In this work, we present a computational tool for mesoscale applications using open-source exascale- computing compatible adaptive-mesh-refinement (AMR) library, AMReX [2]. AMReX is software library that enables development of application solvers with block-structured Cartesian AMR. Our tool has capabilities to include realistic geometry representation, chemical species transport, reactions and thermodynamics that are critical for capturing mesoscale physics. A significant achievement is the ability of our solver to automatically import electron microscopy data in the form of a stereolithography (STL) or pixelated file format (mrc, tiff) without undergoing the tedious task of unstructured mesh generation. This feature allows for rapid simulation of catalyst particles with complex morphologies using an immersed-boundary formulation. The use of AMR allows for higher resolutions at catalyst surface interfaces, which in turn provides an accurate description of surface reactions and transport. Our solver uses a hybrid distributed and shared memory parallelism (OpenMP/GPU-based) with which strong scaling up to 10,000 processors for realistic catalyst particle simulations have been demonstrated.

BIOMASS FUELS,MATHEMATICS AND COMPUTING↗
DOE OSTI2020

Molecular Lignin Solubility and Structure in Organic Solvents

Lignin, a polymer found in the secondary plant cell wall of terrestrial plants, is the single largest source of renewable aromatics and has attracted considerable attention as a feedstock for potential industrial use. However, the secondary plant cell wall is a crowded environment, and lignin in its native form interacts with other biomass components within a larger network. Application of some organic solvents is known to liberate lignin from this network and creates lignin-rich streams suitable for conversion into target products. Through molecular-scale lignin simulation, we analyze how diverse lignin polymers change their structure in response to varying organic solvent environments. We quantify the relationship between solvent polarity and lignin polymer extension, observing maximum polymer expansion and solvation for solvents with polarity near those of dimethyl sulfoxide. From our observations at the nanoscale, increasing syringyl content within lignin polymers reduces the expansion of the polymer in organic solvent environments and decreases the free energy difference compared to aqueous solvent environments, thereby reducing solubility for high syringyl lignin polymers. The conformational transition rates between lignin polymer shapes increased through a combination of the solvent diffusion constant and polymer extension. The molecular simulations indicate that there is likely no single optimal organic solvent for lignin. Different solvent mixtures have optimal or near-optimal properties in solubilizing lignin polymers, thereby disrupting interactions with other biopolymers.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Mechanism and Reaction Energy Landscape for Apiose Cross-Linking by Boric Acid in Rhamnogalacturonan II

Rhamnogalacturonan II (RG-II)—the most complex polysaccharide known in nature—exists as a borate cross-linked dimer in the plant primary cell wall. Boric acid facilitates the formation of this cross-link on the apiosyl residues of RG-II’s side chain A. Here, we detail the reaction mechanism for the cross-linking process with ab initio calculations coupled with transition state theory. We determine the formation of the first ester linkage to be the rate-limiting step of the mechanism. Our findings demonstrate that the regio- and stereospecific nature of subsequent steps in the reaction itinerary presents four distinct energetically plausible reaction pathways. This has significant implications for the overall structure of the cross-linked RG-II dimer assembly. Finally, our transition state and reaction path analyses reveal key geometric insights that corroborate previous experimental hypotheses on borate ester formation reactions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Coupling and Reactions of Lignols and New Lignin Monomers: A Density Functional Theory Study

This perspective summarizes and compares computational results for the thermodynamics of bond dissociation, coupling, and rearomatization for a number of noncanonical lignin monomer–lignol combinations that have been found to occur experimentally. The noncanonical lignin monomers discussed are tricin, caffeyl alcohol, 5-hydroxyconiferyl alcohol, and piceatannol. Among dimeric combinations, the results for bond dissociation are generally similar, but in cases for which trimers have been reported (tricin-lignol adducts), this value can be quite variable, with stereochemical and structural preferences. Among the adducts examined thus far, the energies associated with quinone methide formation and rearomatization are not dissimilar and would not impede subsequent polymerization. These fundamental studies may help to elucidate how lignin monomers are incorporated into the lignin polymer, provide leads for targeted genetic modification, and be of use in deconstruction for the production of commodity chemicals.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Advances in Multiscale Modeling of Lignocellulosic Biomass

Applications and associated processing technologies of lignocellulosic biomass are becoming more important as we endeavor to meet societal demand for fuels, chemicals, and materials from renewable resources. Meanwhile, the rapidly expanding availability and capabilities of high-performance computing present an unprecedented opportunity to accelerate development of technologies surrounding lignocellulose utilization. In order to realize this potential, suitable modeling frameworks must be constructed that effectively capture the multiscale complexity and tremendous variety exhibited by lignocellulosic materials. In our assessment of previous endeavors towards this goal, several important shortcomings have been identified: (1) the lack of multiscale integration strategies that capture emergent properties and behaviors spanning different length scales, and (2) the inability of many modeling approaches to effectively capture the variability and diversity of lignocellulose that arise from both natural and process-induced sources. In this perspective, we survey previous modeling approaches for lignocellulose and simulations processes involving its chemical and mechanical transformation, and suggest opportunities for future development to enhance the utility of computational tools to address barriers to widespread adoption of a renewable bioeconomy.

09 BIOMASS FUELS↗
DOE OSTI2019

A Quantitative Molecular Atlas for Interactions Between Lignin and Cellulose

Lignin and cellulose are two of the most abundant polymers on Earth, and are found in close proximity within plant cell walls. Despite their ubiquity, relatively little is known quantitatively about their interactions within plants, and by extension how their interaction may affect industrial biomass utilization. Given the inherent heterogeneity of the lignin polymer and the structural complexity of cellulose, quantitative relationships between given cellulose faces and specific lignin chemistries have been challenging to ascertain experimentally. In this study, we use molecular simulation to examine individual combinations of cellulose binding face and lignin chemistry to build a quantitative lignin-cellulose interaction atlas, including contributions from both specific hydrogen bonds observed in simulation and nonspecific interactions between lignin and cellulose driven by solvent considerations. Over all monomeric and dimeric lignin chemistries tested, the hydrophobic 100 face is the preferred cellulose interaction site. Among the hydrophilic crystalline faces, binding of these molecules is strongest to the 110 cellulose face. The chemical composition of lignin monomers and dimers is also found to modulate the binding affinity, with additional methoxy groups increasing the contact area to the cellulose surface, which we hypothesize may protect native cellulose from degradation. Additional methoxylation and monomer linkages that facilitate planar aromatic ring orientations increase the binding affinity between small lignin-related molecules and cellulose, with the planar linkages between guaiacyl-type monomers leading to higher binding affinities. These trends can be extended to larger lignin polymers, where we quantify the relationships between lignin polymer size and binding affinity through replica exchange umbrella sampling simulations. Rather than molecular weight, the binding surface area between the lignin polymer and the cellulose surface dictates the interaction strength. As a result, based on the findings here, we expect there to be abundant and durable interaction between cellulose and lignin, particularly on the hydrophobic face of cellulose where cellulase enzymes typically bind.

09 BIOMASS FUELS↗