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Open Access Publications from the University of California
Cover page of Back Matter

Back Matter

(1974)

[No abstract]

Cover page of Using advanced X-ray spectroscopy to reveal molecular level insights into water treatment

Using advanced X-ray spectroscopy to reveal molecular level insights into water treatment

(2025)

Water treatment technologies separate relevant solutes from water resources for water reuse, valuable resource recovery, and increasing the equity and availability of clean water worldwide. Although a variety of treatment methods exist, their performance needs to be improved to enable selective separation with increased durability and fouling resistance. To achieve this, we need to gain a better understanding of how molecular-level physics and chemistry impact integrated systems. Regarding current research on water treatment techniques, there is a clear need to study such systems under realistic environmental conditions. In this review, we aim to show that X-ray spectroscopic techniques are uniquely positioned to provide such information by obtaining detailed molecular insight into phenomena relevant to water research. By doing so, we hope to accelerate the rational design of novel treatment materials and processes. Specifically, a deeper understanding of the complex and interconnected phenomena that impact multilevel water treatment processes will lead to the successful development of next-generation water purification technologies.

Unraveling the Unique Behavior of Atomically Dispersed Pt on Zeolite Fe-DeAlBEA for Catalyzing Propane Dehydrogenation with Cofed Hydrogen.

(2025)

Propene, used on a large scale to manufacture polypropylene and several commodity chemicals, is increasingly produced by catalytic propane dehydrogenation (PDH). Atomically dispersed Pt has emerged as a promising candidate catalyst for PDH; however, stabilizing atomically dispersed Pt at high temperatures is challenging. Here, we demonstrate the use of dealuminated zeolite beta with a high Fe content as a host for stabilizing isolated Pt, which is anchored strongly to the zeolite support by Pt-Fe bonds. The isolated Pt-Fe sites exhibit promising PDH performance, including a high apparent forward rate coefficient for propene formation (404.8-26.4 mol propene/mol Pt·bar·s) and a high selectivity (≥96%) at 823 K in the presence of H2. Kinetics data characterizing the rate of PDH with a range of Pt loadings show that atomically dispersed Pt catalyzes propene formation at rates independent of H2 partial pressure, whereas metallic Pt clusters, formed at high Pt loadings, catalyze the reaction with a slightly negative dependence on H2 partial pressure. The shift in Pt speciation with Pt loading, confirmed by infrared spectroscopy of adsorbed CO, X-ray absorption spectroscopy, and high-angle angular dark field scanning transmission electron microscopy, suggests that the observed change in kinetics with Pt dispersion is a consequence of a change in the reaction mechanism.

Cover page of PyCPETComputing Heterogeneous 3D Protein Electric Fields and Their Dynamics

PyCPETComputing Heterogeneous 3D Protein Electric Fields and Their Dynamics

(2025)

Electrostatic preorganization is an exciting mode to understand the catalytic function of enzymes, yet limited tools exist to computationally analyze it. In particular, no methods exist to interpret the geometry, dynamics, and fundamental components of 3D electric fields, E⃗(r), in protein active sites. To address this, we present PyCPET (Python Computation of Electric Field Topologies), a comprehensive, open-source toolbox to analyze E⃗(r) in enzymes. We designed it around computational efficiency and user friendliness with both CPU- and GPU-accelerated codes. Our aim is to provide a set of functions for rich, descriptive analysis of enzyme systems including dynamics, benchmarking, distribution of streamlines analysis in 3D E⃗(r), computation of point E⃗(r), principal component analysis, and 3D E⃗(r) visualization. Finally, we demonstrate its versatility by exploring the nature of electrostatic preorganization and dynamics in three cases: Cytochrome C, Co-substituted Liver Alcohol Dehydrogenase, and HIV Protease. These test systems, along with previous work, establish PyCPET as an essential toolkit for the in-depth analysis and visualization of electric fields in enzymes, unlocking new avenues for understanding electrostatic contributions to enzyme catalysis.

Cover page of HEPOM: Using Graph Neural Networks for the Accelerated Predictions of Hydrolysis Free Energies in Different pH Conditions.

HEPOM: Using Graph Neural Networks for the Accelerated Predictions of Hydrolysis Free Energies in Different pH Conditions.

(2025)

Hydrolysis is a fundamental family of chemical reactions where water facilitates the cleavage of bonds. The process is ubiquitous in biological and chemical systems, owing to water's remarkable versatility as a solvent. However, accurately predicting the feasibility of hydrolysis through computational techniques is a difficult task, as subtle changes in reactant structure like heteroatom substitutions or neighboring functional groups can influence the reaction outcome. Furthermore, hydrolysis is sensitive to the pH of the aqueous medium, and the same reaction can have different reaction properties at different pH conditions. In this work, we have combined reaction templates and high-throughput ab initio calculations to construct a diverse data set of hydrolysis free energies. The developed framework automatically identifies reaction centers, generates hydrolysis products, and utilizes a trained graph neural network (GNN) model to predict ΔG values for all potential hydrolysis reactions in a given molecule. The long-term goal of the work is to develop a data-driven, computational tool for high-throughput screening of pH-specific hydrolytic stability and the rapid prediction of reaction products, which can then be applied in a wide array of applications including chemical recycling of polymers and ion-conducting membranes for clean energy generation and storage.

Cover page of Water structure and electric fields at the interface of oil droplets

Water structure and electric fields at the interface of oil droplets

(2025)

Interfacial water exhibits rich and complex behaviour1, playing an important part in chemistry, biology, geology and engineering. However, there is still much debate on the fundamental properties of water at hydrophobic interfaces, such as orientational ordering, the concentration of hydronium and hydroxide, improper hydrogen bonds and the presence of large electric fields2-5. This controversy arises from the challenges in measuring interfacial systems, even with the most advanced experimental techniques and theoretical approaches available. Here we report on an in-solution, interface-selective Raman spectroscopy method using multivariate curve resolution6,7 to probe hexadecane-in-water emulsions, aided by a monomer-field theoretical model for Raman spectroscopy8. Our results indicate that oil-water emulsion interfaces can exhibit reduced tetrahedral order and weaker hydrogen bonding, along with a substantial population of free hydroxyl groups that experience about 95 cm-1 redshift in their stretching mode compared with planar oil-water interfaces. Given the known electrostatic zeta potential characteristic of oil droplets9, we propose the existence of a strong electric field (about 50-90 MV cm-1) emanating from the oil phase. This field is inferred indirectly but supported by control experiments and theoretical estimates. These observations are either absent or opposite in the molecular hydrophobic interface formed by small solutes or at planar oil-water interfaces. Instead, water structural disorder and enhanced electric fields emerge as unique features of the mesoscale interface in oil-water emulsions, potentially contributing to the accelerated chemical reactivity observed at hydrophobic-water interfaces10-13.

Cover page of Material needs for power-to-X systems for CO2 utilization require a life cycle approach.

Material needs for power-to-X systems for CO2 utilization require a life cycle approach.

(2025)

The worlds transition from a fossil-fuel-driven society to a future net-zero or negative carbon dioxide emission society will require a significant scale-up of Power-to-X technologies to capture and convert CO2 to low carbon intensity fuels and chemicals. The deployment of Power-to-X technologies at gigawatt scales necessary to impact CO2 emissions and replace existing fossil-fuel-dependent processes will require vast quantities of raw materials and minerals. Many of the materials required in Power-to-X systems, such as rare earth metal yttrium and iridium, differ from those used to construct and operate petroleum-hydrocarbon-based processes for the last 100 years. Thus, electrolyzer manufacturers and mineral producers face significant challenges in matching supply to the growing demand. In this Perspective, we identify critical materials needed for Power-to-X electrolyzers and analyze the impacts and risks of these materials existing global supply chains. We then provide an overview of methodologies for Environmental Life Cycle Assessment (LCA) and Social Life Cycle Assessment (SLCA) that we encourage scientific communities to adopt early in the research process to evaluate the multidimensional socio-environmental impacts throughout a products life cycle, from raw material extraction and processing to manufacturing, use, and end-of-life disposal. We advocate that life cycle thinking is crucial for the informed, just and ethical development of disruptive technologies and systems such as Power-to-X technologies.

Cover page of Humidity Disrupts Structural and Chiroptical Properties of Chiral 2D Perovskites

Humidity Disrupts Structural and Chiroptical Properties of Chiral 2D Perovskites

(2025)

Chiral two-dimensional (2D) hybrid organic-inorganic metal halide perovskite semiconductors have emerged as an exceptional material platform with many design opportunities for spintronic applications. However, a comprehensive understanding of changes to the crystal structure and chiroptical properties upon exposure to atmospheric humidity has not been established. We demonstrate phase degradation to the 1D (MBA)PbI3 (MBA = methylbenzylammonium) and the hypothetical (MBA)3PbI5·H2O hydrate phases, accompanied by a reduction and disappearance of the chiroptical response. First-principle simulations show that water molecules preferentially locate at the interface between the organic cations and the inorganic framework, thereby disrupting the hydrogen bonding, impacting both the structural chirality and stability of the material. These findings provide critical insights into phase degradation mechanisms and their impact on chiroptical activity in chiral 2D perovskites.

Cover page of Fabrication of Functional 3D Nanoarchitectures via Atomic Layer Deposition on DNA Origami Crystals.

Fabrication of Functional 3D Nanoarchitectures via Atomic Layer Deposition on DNA Origami Crystals.

(2025)

While DNA origami is a powerful bottom-up fabrication technique, the physical and chemical stability of DNA nanostructures is generally limited to aqueous buffer conditions. Wet chemical silicification can stabilize these structures but does not add further functionality. Here, we demonstrate a versatile three-dimensional (3D) nanofabrication technique to conformally coat micrometer-sized DNA origami crystals with functional metal oxides via atomic layer deposition (ALD). In addition to depositing homogeneous and conformal nanometer-thin ZnO, TiO2, and IrO2 (multi)layers inside SiO2-stabilized crystals, we establish a method to directly coat bare DNA crystals with ALD layers while maintaining the crystal integrity, enabled by critical point drying and low ALD process temperatures. As a proof-of-concept application, we demonstrate electrocatalytic water oxidation using ALD IrO2-coated DNA origami crystals, resulting in improved performance relative to that of planar films. Overall, our coating strategy establishes a tool set for designing custom-made 3D nanomaterials with precisely defined topologies and material compositions, combining the unique advantages of DNA origami and atomically controlled deposition of functional inorganic materials.

Cover page of The role of the droplet interface in controlling the multiphase oxidation of thiosulfate by ozone.

The role of the droplet interface in controlling the multiphase oxidation of thiosulfate by ozone.

(2025)

Predicting reaction kinetics in aqueous microdroplets, including aerosols and cloud droplets, is challenging due to the probability that the underlying reaction mechanism can occur both at the surface and in the interior of the droplet. Additionally, few studies directly measure the surface activities of doubly charged anions, despite their prevalence in the atmosphere. Here, deep-UV second harmonic generation spectroscopy is used to probe surface affinities of the doubly charged anions thiosulfate, sulfate, and sulfite, key species in the thiosulfate ozonation reaction mechanism. Thiosulfate has an appreciable surface affinity with a measured Gibbs free energy of adsorption of -7.3 ± 2.5 kJ mol-1 in neutral solution, while sulfate and sulfite exhibit negligible surface propensity. The Gibbs free energy is combined with data from liquid flat jet ambient pressure X-ray photoelectron spectroscopy to constrain the concentration of thiosulfate at the surface in our model. Stochastic kinetic simulations leveraging these novel measurements show that the primary reaction between thiosulfate and ozone occurs at the interface and in the bulk, with the contribution of the interface decreasing from ∼65% at pH 5 to ∼45% at pH 13. Additionally, sulfate, the major product of thiosulfate ozonation and an important species in atmospheric processes, can be produced by two different pathways at pH 5, one with a contribution from the interface of >70% and the other occurring predominantly in the bulk (>98%). The observations in this work have implications for mining wastewater remediation, atmospheric chemistry, and understanding other complex reaction mechanisms in multiphase environments. Future interfacial or microdroplet/aerosol chemistry studies should carefully consider the role of both surface and bulk chemistry.