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At least 73 records · Page 4

The TPR domain of PgaA is a multifunctional scaffold that binds PNAG and modulates PgaB-dependent polymer processing

The synthesis of exopolysaccharides as biofilm matrix components by pathogens is a crucial factor for chronic infections and antibiotic resistance. Many periplasmic proteins involved in polymer processing and secretion in Gram-negative synthase dependent exopolysaccharide biosynthetic systems have been individually characterized. The operons responsible for the production of PNAG, alginate, cellulose and the Pel polysaccharide each contain a gene that encodes an outer membrane associated tetratricopeptide repeat (TPR) domain containing protein. While the TPR domain has been shown to bind other periplasmic proteins, the functional consequences of these interactions for the polymer remain poorly understood. Herein, we show that the C-terminal TPR region of PgaA interacts with the de-N-acetylase domain of PgaB, and increases its deacetylase activity. Additionally, we found that when the two proteins form a complex, the glycoside hydrolase activity of PgaB is also increased. To better understand structure-function relationships we determined the crystal structure of a stable TPR module, which has a conserved groove formed by three repeat motifs. Tryptophan quenching, mass spectrometry analysis and molecular dynamics simulation studies suggest that the crystallized TPR module can bind PNAG/dPNAG via its electronegative groove on the concave surface, and potentially guide the polymer through the periplasm towards the porin for export. Our results suggest a scaffolding role for the TPR domain that combines PNAG/dPNAG translocation with the modulation of its chemical structure by PgaB.

59 BASIC BIOLOGICAL SCIENCES↗

16S and ITS Amplicon Sequencing Fastq files and metadata from PARCHED Panama Tropical Forest soils, 2019-2020,

Model projections predict tropical forests will experience longer periods of drought and more intense precipitation cycles under a changing climate. Such transitions have implications for structure-function relationships within microbial communities. We examine how chronic drying might reshape prokaryotic and fungal communities across four lowland forests in Panama with a wide variation in mean annual precipitation and soil fertility. Four sites were established across a 1000 mm span in mean annual precipitation (2335 to 3300 mm). We expected microbial communities at sites with lower MAP to be less sensitive to chronic drying than sites with higher MAP; while fungal communities to be more resistant to disturbance than prokaryotes. At each location, partial throughfall exclusion structures were established over 10 x 10 m plots to reduce direct precipitation input. Raw demultiplexed sequences (bacteria, archaea, fungal) from soil samples taken from PARCHED Panama Tropical Forest throughfall exclusion experiments. Files that contain 16S are sequences from prokaryotes, ITS indicates sequences from fungi. Compressed fastq files are contained in Field_PARCHED_ITS_fastq_2020.zip, Field_PARCHED_ITS_fastq_2019.zip, Field_PARCHED_16S_fastq_2020.zip, Field_PARCHED_16S_fastq_2019.zip.There are four sites across the isthmus of Panama, each with 4 control and 4 exclusion plots. Throughfall exclusion shelters were built to intercept 50% of throughfall precipitation that hits the soil. Samples were taken on May 2019 and Jan 2020 from 0-10 cm and 10-20 cm depth approximately 9 and 18 months after shelter installation. Metadata and sample IDs for fastq files for 2019 sampling are within Field_PARCHED_Metadata_2019_ITS.csv and Field_PARCHED_Metadata_2019_16S.csv. The metadata for both 16S and ITS fastq files for January 2020 is included in Field_PARCHED_Metadata_2020.csv. No data processing or QA/QC was done on the raw data. Data processing example provided in R notebook file.

54 ENVIRONMENTAL SCIENCES↗

Biological Electron Transfer and Catalysis Energy Frontier Research Center

The overarching objective of the BETCy EFRC project is to investigate the mechanisms and structural basis controlling electron bifurcation, electron-ion coupling, and redox catalysis in model enzymes. This detailed understanding of how biological systems control and exploit electron flow will be used to develop modular biochemical conversions for the production of hydrocarbon and hydrogen biofuels. This project will conduct an in-depth study of metalloenzyme structure-function relationships that enable retuning of catalytic sites, electron-transfer thermodynamics, and the evolution of tailor-designed chemical reactions involving two model enzymes: hydrogenase and nitrogenase. The center is organized into three major thrust areas: Thrust 1. Energy conservation and electron flow; Thrust 2. ATP-coupled electron transfer; and Thrust 3. Atomic level determinants of enzymatic redox properties and their relationship to catalytic bias. We will develop a collective knowledge in metalloenzymes by applying physical science and computational tools to characterize biochemical reactions catalyzed specifically by multi-subunit enzymes harboring iron-sulfur clusters and flavin cofactors, as models for redox reactions throughout biology. Understanding these mechanisms is central to overcoming the key thermodynamic barriers currently limiting production of reduced products and biofuels. The research plan of the BETCy EFRC has been designed to provide the basis to exploit unique biochemical mechanisms that have yet to be explored substantively in the context of bioenergy but have the potential for game-changing advancement. The successful outcome of this research will be a collection of fundamental principles that serve as a blueprint to enable the tailored re-design of biological systems and enzymes to control matter and energy at the level of electrons and molecules to provide the foundations to create new energy technologies.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Mechanistic Studies to Enable Aerobic Oxidation of C-H Bonds by Manganese Catalysts (Final Report)

The project Mechanistic Studies to Enable Aerobic Oxidation of C-H Bonds by Manganese Catalysts provided fundamental new insight into the factors affecting hydrocarbon oxidation reactions by manganese-oxo complexes. These insights stem from the development of a structure-function relationship, whereby particular molecular properties of manganese(IV)-oxo complexes were shown to correlate to their efficacy in hydrocarbon oxidation reactions. This work is important, as manganese oxidation catalysts have seen increasing use in synthetic transformations, including reactions relevant to the synthesis of pharmaceuticals and other value-added chemicals. The desirability of developing new manganese catalysts stems from the inexpensive nature and low toxicity of the metal manganese, which contrasts with the high cost and toxicity of many other metals. The work carried out by this project was disseminated to the scientific community in the form of 14 peer-reviewed publications and over twenty presentations. In addition, the research results were incorporated into graduate and undergraduate courses at the University of Kansas, providing additional means of dissemination.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Surface Charge at an Oil/Water Interface Promoting the Enhancement and Assignment of Water Combination Bands

Given the different polarities and distinct chemical structures, it is no wonder that oil and water are incompatible neighbors. They can be forced to cooperate if provided sufficient energy or a suitable intermediary. Emulsions are the result of such a cooperation, where an emulsifying agent (the intermediary) in the form of a surfactant or a cocktail of surface stabilizing compounds allows for the ‘mixing’ of oil and water. Surfactant stabilized emulsions that are nanoscale in size (nanoemulsions) have caught the attention of many because of their newly discovered use in the synthesis of nanomaterials, oil recovery, drug delivery, and food science. Unlike smaller emulsions (e.g. microemulsions with 2-20 nm diameters), very little is known about the molecular level properties of nanoemulsions (NEs) whose diameters are in the 100-500 nm range. One thing that is well known is the macroscopic properties of droplets from these two size regimes are dramatically different, often for reasons not yet fully understood. Nanoemulsions do not form spontaneously and require an external shear beyond ordinary procedures used to create micelles. This shear is required to overcome the effects of surface tension and create droplets in the nanoscale regime. Once formed, however, they can be stable for long periods of time, making them very attractive for commercial and pharmaceutical products requiring a long shelf life. What is not well known is the interfacial molecular processes that lead to the formation and stability of nanoemulsions including those stabilized by surfactants and/or polymers. Such knowledge is important in understanding the molecular structure-function relationship that assists in predicting what additives and solvents are necessary for a specific application. Key to advancing nanoemulsion utility is to develop the needed molecular-level understanding of the structure and bonding interactions present at the surface of these soft nanoparticles.

36 MATERIALS SCIENCE↗

A Bottom-Up Approach to Rational Design of Crystalline Materials: Investigation of Vibronic Coherences Underlying Exciton Dynamics in Semiconductors

In this project we uncovered structure-function relationships of donor-acceptor co-crystals used to develop next-generation optoelectronic devices. Unraveling the photodynamics of molecular crystalline materials poses many challenges for spectroscopy due to broad, overlapping features representing numerous underlying dynamical processes. This leads researchers to make many assumptions about the dynamics of a system in choosing an appropriate kinetic fitting model. Computationally, electronic structure methods are either prohibitively expensive or underdeveloped for computing the excited state structure of molecular materials, especially states that exhibit charge transfer. Researchers must therefore perform calculations of excited electronic states using truncated models of molecular materials. Here we present a joint experimental-theoretical approach to bridging the gap between the photodynamics of a molecular material and its constituent molecules. We focus our efforts on quantifying the timescales and mechanisms of photoexcitation in donor-acceptor co-crystals and donor-acceptor dimers where the lowest-lying excited state is characterized by charge transfer from the donor to the acceptor. We employ ultrafast UV pump, UV-Vis probe transient absorption spectroscopy to unravel the time-resolved spectroscopic signatures of the photodynamics in both the crystalline material and donor-acceptor dimers in solution. We perform electronic structure and excited state dynamics calculations of the dimers to inform kinetic fitting models and assign the spectral features. The photodynamics of the crystal vs. dimer systems have many similarities, enabling unprecedented insights into the formation and evolution of charge transfer excitons in the crystalline systems.

36 MATERIALS SCIENCE↗

Cross-species analysis of FcγRIIa/b (CD32a/b) polymorphisms at position 131: structural and functional insights into the mechanism of IgG- mediated phagocytosis in human and macaque

Introduction Antibodies play a critical role in immunity in part by mediating clearance of pathogens and infected cells by antibody-dependent cellular phagocytosis (ADCP) through engagement of Fc gamma receptors (FcγRs) on innate immune cells. Among these, FcγRIIa (CD32a) is a key activating receptor expressed on macrophages, dendritic cells, and other antigen-presenting cells. Its affinity for IgG and ability to mediate ADCP is influenced by allelic polymorphisms. In humans, a single amino acid polymorphism at position 131, where histidine (H) is substituted with arginine (R), leads to decreased IgG1 and IgG2 subclass binding affinity and, consequently, lower efficiency of phagocytic responses. Rhesus macaques ( Macaca mulatta ), which are widely used as nonhuman primate models, exhibit a similar polymorphism at position 131 of FcγRIIa, but with arginine replaced by proline (P). Here, we investigated structure-function relationships associated with the FcγRIIa polymorphism at position 131 in both species, specifically with respect to IgG1 and IgG2. Methods We determined the structures of complexes formed by each variant with IgG1 Fc and those formed by the higher affinity variant with IgG2 Fc for both species by x-ray crystallography and linked these structures to affinity and activity using SPR and an ADCP assay. We also determined the structure of human inhibitory FcγRIIb (CD32b) in complex with IgG1 Fc by x-ray crystallography. Results Through analysis of these structures, our studies reveal that FcγRIIa engagement is minimally influenced by Fc glycan composition, distinguishing it from FcγRIIIa whose affinity is strongly influenced by glycan-composition. Comparative structures of human and macaque FcγRIIa variants demonstrate species- and allele-specific differences in Fc binding, but our functional assays showed only minimal allele-specific effects in humans. In contrast, allele-specific effects in macaques were highly significant; the macaque P 131 variant showing uniformly reduced IgG affinity. Conclusion These insights highlight fundamental interspecies and allelic distinctions that are critical for interpreting FcγRIIa-mediated effector functions in macaque models and for optimizing translational antibody and vaccine design.

Tolbert, William D.↗

BETO 2021 Peer Review - Inverse Bioproduct Design Through Machine Learning and Molecular Simulation

This work aims to identify performance advantaged bioproducts (PABPs) through property prediction, which will guide experimental synthesis. The impact of this work will be faster market adoption of bioproducts with greater performance relative to incumbent products. We have identified >106 bioproduct candidates, but only some will have superior performance to create a market pull. High-throughput property prediction, enabled by machine learning, and elucidation of structure-function relationships, enabled by molecular simulation, provide a hypothesis driven approach for down selection of candidate biomolecules to pursue experimentally. To enable machine learning and molecular simulation for bioproduct discovery, automated structure generation and embedding must capture relevant features for prediction, databases must cover domains applicable to biobased products, and best practices for simulation of polymer systems must be developed. To address these challenges, we have established bioproduct relevant datasets, developed high-throughput polymer structure generation, and built end-to-end neural networks that have predicted 8 properties for >1.4 x 106 biopolymers. A molecular simulation pipeline for building, running, and analyzing polymers and polymer additives is being used to predict performance and develop design principles of biobased products. In collaboration with the PABP synthesis project, these computational tools are guiding synthesis and informing design of PABPs.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

Aminopolycarboxylates in trivalent f-element separations

Aminopolycarboxylate reagents strongly bind a variety of metal ions. Trivalent f-elements are no exception. The formed complexes are very stable, especially when aminopolycarboxylate structure contains multiple aminoacetate groups. The efficient coordination of trivalent f-elements by these reagents prompted decades of research and development efforts devoted to separation and purification of f-block metal ions. This chapter overviews the fundamental and applied aspects of aminopolycarboxylate use in trivalent f-element separations. First, a brief synopsis on how the chemical properties of 4f and 5f metal ions determine their similar solution behavior is followed by a discussion of aqueous complexation as means to perturb it. The synthetic methodologies for preparation of aminopolycarboxylate complexants are discussed next. Fundamental features of trivalent f-element complexation by aminopolycarboxylates are summarized, focusing on a variety of structure-function relationships demonstrated for this class of chelators and theoretical efforts to accurately describe such coordination environments. Finally, historical accounts of aminopolycarboxylate use in 4f and 5f element separations are supplemented by recent advances in those research fields.

Jansone-Popova, Santa↗

PersGNN: Applying Topological Data Analysis and Geometric Deep Learning to Structure-Based Protein Function Prediction

Understanding protein structure-function relationships is a key challenge in computational biology, with applications across the biotechnology and pharmaceutical industries. While it is known that protein structure directly impacts protein function, many functional prediction tasks use only protein sequence. In this work, we isolate protein structure to make functional annotations for proteins in the Protein Data Bank in order to study the expressiveness of different structure-based prediction schemes. We present PersGNN - an end-to-end trainable deep learning model that combines graph representation learning with topological data analysis to capture a complex set of both local and global structural features. While variations of these techniques have been successfully applied to proteins before, we demonstrate that our hybridized approach, PersGNN, outperforms either method on its own as well as a baseline neural network that learns from the same information. PersGNN achieves a 9.3% boost in area under the precision recall curve (AUPR) compared to the best individual model, as well as high F1 scores across different gene ontology categories, indicating the transferability of this approach.

Swenson, Nicolas↗

Determining the Role of Synthesis and Reaction Conditions on the Exposed Surface and Shape of ..beta..-Mo2C Catalysts

The production of drop-in quality biofuels typically can be achieved through catalytic fast pyrolysis (CFP) of biomass, followed by hydrodeoxygenation (HDO) of the vapor-phase product to reduce the oxygen content and stabilize the bio-oil product. To favor selectivity toward desired deoxygenation products, bifunctional catalysts with both acidic and hydrogenation sites are often employed. Due to both its oxophilicity and its ability to promote hydrogenation reactions, molybdenum carbide catalysts have shown promise for promoting the HDO of CFP vapors. However, the surface structure and composition of carbide catalyst particles are not well understood, precluding the establishment of fundamental structure-function relationships needed for the rational development of molybdedum carbide for HDO, as well as other reactions. For orthorhombic ..beta..-Mo2C, the (100) facet is largely studied for computational surface-reaction analyses, possibly due to its similarities with the close-packed (111) facet of noble-metal catalysts. However, it has previously been postulated through ab initio thermodynamic studies that the (111), (110), and (011) facets are most stable, though there is no consensus. Furthermore, while a majority of previous surface stability analyses of ..beta..-Mo2C focus on bulk terminations, the highly carburizing synthesis conditions and the use of ..beta..-Mo2C in carbon-containing reaction applications could introduce non-stoichiometric coverages of surface carbon. As such, this study uses ab initio thermodynamics calculations to assess the relative surface stability of the low-index facets of ..beta..-Mo2C, including consideration of varying the coverage of surface carbon. From this information, Wulff constructions are utilized to predict the synthesis and reaction condition-dependent shape and surface carbon composition of ..beta..-Mo2C catalyst particles.

BIOMASS FUELS,INORGANIC, ORGANIC, PHYSICAL, AND AN↗

Toward More Efficient Organic Solar Cells: A Detailed Study of Loss Pathway and Its Impact on Overall Device Performance in Low‐Offset Organic Solar Cells

Abstract Low‐offset organic solar cell systems have attracted great interest since nonfullerene acceptors came into the picture. While numerous studies have focused on the charge generation process in these low‐offset systems, only a few studies have focused on the details of each loss channel in the charge generation process and their impact on the overall device performance. Here, several nonfullerene acceptors are blended with the same polymer donor to form a series of low‐offset organic solar cell systems where significant variation in device performance is observed. Through detailed analyses of loss pathways, it is found that: i) the donor:acceptor interfaces of PM6:Y6 and PM6:TPT10 are close to the optimum energetic condition, ii) energetics at the donor:acceptor interface are the most important factor to the overall device performance, iii) exciton dissociation yield can be field‐dependent owing to the sufficiently small energetic offset at the donor:acceptor interface, and iv) the change in substituents in the terminal group of Y‐series acceptors in this work mainly affects energetics at the donor:acceptor interface instead of the interface density in the active layer. In general, this work presents a path toward more efficient organic solar cells.

14 SOLAR ENERGY↗

Current understanding of Oxidative Coupling of Methane (OCM) reaction over supported Mn-Na 2 WO 4 catalysts

This perspective reviews the current understanding of the Oxidative Coupling of Methane (OCM) reaction over the supported Mn-Na 2 WO 4 /SiO 2 catalyst, with a focus on recent insights gained from state-of-the-art in-situ and operando spectroscopic characterization and chemical probe experiments under controlled environments. The supported Mn-Na 2 WO 4 /SiO 2 catalyst exhibits dynamic structural changes during the OCM reaction, involving multiple reactive lattice and adsorbed oxygen species, each associated with different oxide phases. These oxygen species play distinct roles in various steps of the OCM mechanism. The catalytic active sites for activation of CH 4 are associated with isolated surface Na-WO x sites on the SiO 2 support and the role of surface MnO x sites on SiO 2 is to oxidatively dehydrogenate C 2 H 6 to C 2 H 4 . Furthermore, this paper provides a detailed discussion of these roles and also introduces new experimental data from Temporal Analysis of Products (TAP) studies to clarify the ongoing debate in the literature regarding the contributions of lattice versus adsorbed oxygen species in OCM reaction product formation. Additionally, recommendations are offered for optimizing the performance of supported Mn-Na 2 WO 4 /SiO 2 catalysts to enhance CH 4 activation and C 2 product selectivity.

03 - NATURAL GAS↗

Chitosan as a Canvas for Studies of Macromolecular Controls on CaCO 3 Biological Crystallization

A mechanistic understanding of how macromolecules, typically as an organic matrix, nucleate and grow crystals to produce functional biomineral structures remains elusive. Advances in structural biology indicate that polysaccharides (e.g., chitin) and negatively charged proteoglycans (due to carboxyl, sulfate, and phosphate groups) are ubiquitous in biocrystallization settings and play greater roles than currently recognized. This review highlights studies of CaCO 3 crystallization onto chitinous materials and demonstrates that a broader understanding of macromolecular controls on mineralization has not emerged. With recent advances in biopolymer chemistry, it is now possible to prepare chitosan-based hydrogels with tailored functional group compositions. By deploying these characterized compounds in hypothesis-based studies of nucleation rate, quantitative relationships between energy barrier to crystallization, macromolecule composition, and solvent structuring can be determined. Finally, this foundational knowledge will help researchers understand composition-structure-function controls on mineralization in living systems and tune the designs of new materials for advanced applications.

15 GEOTHERMAL ENERGY↗

Critical Role of Sc Substitution in Modulating Ferroelectricity in Multiferroic LuFeO 3

Understanding how individual dopants or substitutional atoms interact with host lattices enables us to manipulate, control, and improve the functionality of materials. However, because of the intimate coupling among various degrees of freedom in multiferroics, the atomic-scale influence of individual foreign atoms has remained elusive. Here, we unravel the critical roles of individual Sc substitutional atoms in modulating ferroelectricity at the atomic scale of typical multiferroics, Lu 1–x Sc x FeO 3 , by combining advanced microscopy and theoretical studies. Atomic variations in polar displacement of intriguing topological vortex domains stabilized by Sc substitution are directly correlated with Sc atom-mediated local chemical and electronic fluctuations. The local FeO 5 trimerization magnitude and Lu/Sc–O hybridization strength are found to be significantly reinforced by Sc, clarifying the origin of the strong dependence of improper ferroelectricity on Sc content. We find that this study could pave the way for correlating dopant-regulated atomic-scale local structures with global properties to engineer emergent functionalities of numerous chemically doped functional materials.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Thermally Stable Co@C3N4 Single-Atom Catalysts for CO Oxidation: Atomic-Level Insights into Structure and Activity

Single Co atoms supported on C3N4 (Co@C3N4) have demonstrated high activity and selectivity in photocatalysis. However, the investigation of structure–function relationships and reaction mechanisms under photocatalytic conditions is very challenging due to the complex conditions of light absorption, charge transfer, and catalysis. In this study, we employed thermal CO oxidation as a prototypical probe reaction to benchmark the intrinsic catalytic performance and track the active-site evolution of Co@C3N4. Single Co atoms were identified and shown to be the catalytically active sites for CO oxidation based on control experiments and isotope-labeling experiments. The Co sites remained atomically dispersed before, during, and after the reaction with temperatures up to 400 °C, as established by in situ X-ray absorption fine structure (XAFS) combined with density functional theory (DFT), FDMNES simulations, and dynamic-time-warping (DTW)-assisted X-ray absorption near edge structure (XANES) matching. Together with theoretical calculations, the integrated analysis reveals a stable coordination environment under reaction conditions, which correlates with sustained activity, establishing Co@C3N4 single-atom catalysts as thermally stable CO oxidation catalysts. Beyond these findings, the current study provides a workflow for unambiguously assigning active sites in Co@C3N4 for thermal CO oxidation. This workflow will aid the understanding of their behavior in photocatalysis in the future, where light-driven dynamics obscure direct structure–function links. Notably, this study provides fundamental insights for the rational design of robust single-atom catalysts and a foundation for the broader application of Co@C3N4 catalysts in oxidation reactions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Structure–Function Relationships in Sequence-Controlled Copolymers for Rare Earth Element Chelation

The ability to tune material function through primary sequence is a defining feature of biological macromolecules, allowing precise control over structure and target interactions in complex aqueous environments. However, translating sequence–structure–function relationships to synthetic macromolecules is challenging due to their dispersity in sequence, conformation, and composition. Here, we report systematic studies of amphiphilic polymer chelators designed to probe how composition and patterning influence binding affinity and selectivity for rare earth elements (REEs), a series of technologically relevant metals with challenging separation profiles. A library of copolymers varying hydrophobic monomer composition and patterning was synthesized via reversible addition–fragmentation chain transfer (RAFT) polymerization, spanning statistical, gradient, and block architectures. REE binding was quantified using a high-throughput colorimetric assay, and reconstruction of polymer ensembles using kinetic stochastic simulations enabled quantitative comparisons of sequence heterogeneity, linking local monomer colocalization to emergent REE binding. Further, we investigated the role of different hydrophobic comonomers in tuning metal coordination, with binding trends linked to structural features that influence binding site desolvation. Complementary dynamic light scattering (DLS) and small-angle X-ray scattering (SAXS) measurements showed that both polymer and monomer architecture modulate metal-induced conformational changes, and that multichain assembly behavior emerges beyond critical hydrophobic thresholds. Sequence control also altered REE selectivity, with nonmonotonic differences observed across compositionally identical polymers with different sequence architectures. Together, these findings establish design principles that connect polymer sequence and structure to binding performance, guiding the design of macromolecular chelators with enhanced affinity and selectivity for applications in separations, sensing, and catalysis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗