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Open Access Publications from the University of California

Chemical and Biomolecular Engineering - Open Access Policy Deposits

This series is automatically populated with publications deposited by UC Irvine Samueli School of Engineering Chemical and Biomolecular Engineering researchers in accordance with the University of California’s open access policies. For more information see Open Access Policy Deposits and the UC Publication Management System.

Cover page of Parameter-Fitting-Free Continuum Modeling of Electric Double Layer in Aqueous Electrolyte.

Parameter-Fitting-Free Continuum Modeling of Electric Double Layer in Aqueous Electrolyte.

(2024)

Electric double layers (EDLs) play fundamental roles in various electrochemical processes. Despite the extensive history of EDL modeling, there remain challenges in the accurate prediction of its structure without expensive computation. Herein, we propose a predictive multiscale continuum model of EDL that eliminates the need for parameter fitting. This model computes the distribution of the electrostatic potential, electron density, and species' concentrations by taking the extremum of the total grand potential of the system. The grand potential includes the microscopic interactions that are newly introduced in this work: polarization of solvation shells, electrostatic interaction in parallel plane toward the electrode, and ion-size-dependent entropy. The parameters that identify the electrode and electrolyte materials are obtained from independent experiments in the literature. The model reproduces the trends in the experimental differential capacitance with multiple electrode and nonadsorbing electrolyte materials (Ag(110) in NaF, Ag(110) in NaClO4, and Hg in NaF), which verifies the accuracy and predictiveness of the model and rationalizes the observed values to be due to changes in electron stability. However, our calculation on Pt(111) in KClO4 suggests the need for the incorporation of electrode/ion-specific interactions. Sensitivity analyses confirmed that effective ion radius, ion valence, the electrode's Wigner-Seitz radius, and the bulk modulus of the electrode are significant material properties that control the EDL structure. Overall, the model framework and findings provide insights into EDL structures and predictive capability at low computational cost.

Cover page of Improved synthesis and polymerase recognition of 7-deaza-7-modified α-l-threofuranosyl guanosine analogs.

Improved synthesis and polymerase recognition of 7-deaza-7-modified α-l-threofuranosyl guanosine analogs.

(2024)

Threofuranosyl nucleic acid (TNA), an artificial genetic polymer known for its nuclease resistance and acid stability, has grown in popularity as a genetically-encoded material for applications in synthetic biology and biomedicine. TNA oligonucleotide synthesis requires enzymatic or solid phase synthesis pathways that rely on monomer building blocks that are not commercially available and can only be obtained by chemical synthesis. Here we present a synthetic route to 7-deaza-7-modified tGTP and phosphoramidite analogs that is operationally simpler than our previously described strategy. The new methodology offers an HPLC-free route to tGTP analogs that are recognized by engineered TNA polymerases and can be incorporated with continued TNA synthesis.

Cover page of Direct in-situ imaging of electrochemical corrosion of Pd-Pt core-shell electrocatalysts.

Direct in-situ imaging of electrochemical corrosion of Pd-Pt core-shell electrocatalysts.

(2024)

Corrosion of electrocatalysts during electrochemical operations, such as low potential - high potential cyclic swapping, can cause significant performance degradation. However, the electrochemical corrosion dynamics, including structural changes, especially site and composition specific ones, and their correlation with electrochemical processes are hidden due to the insufficient spatial-temporal resolution characterization methods. Using electrochemical liquid cell transmission electron microscopy, we visualize the electrochemical corrosion of Pd@Pt core-shell octahedral nanoparticles towards a Pt nanoframe. The potential-dependent surface reconstruction during multiple continuous in-situ cyclic voltammetry with clear redox peaks is captured, revealing an etching and deposition process of Pd that results in internal Pd atoms being relocated to external surface, followed by subsequent preferential corrosion of Pt (111) terraces rather than the edges or corners, simultaneously capturing the structure evolution also allows to attribute the site-specific Pt and Pd atomic dynamics to individual oxidation and reduction events. This work provides profound insights into the surface reconstruction of nanoparticles during complex electrochemical processes.

Cover page of X-ray Photoelectron Spectroscopy Analysis of Nafion-Containing Samples: Pitfalls, Protocols, and Perceptions of Physicochemical Properties.

X-ray Photoelectron Spectroscopy Analysis of Nafion-Containing Samples: Pitfalls, Protocols, and Perceptions of Physicochemical Properties.

(2024)

X-ray photoelectron spectroscopy (XPS) is one of the most common techniques used to analyze the surface composition of catalysts and support materials used in polymer electrolyte membrane (PEM) fuel cells and electrolyzers, providing important insights for further improvement of their properties. Characterization of catalyst layers (CLs) is more challenging, which can be at least partially attributed to the instability of ionomer materials such as Nafion during measurements. This work explores the stability of Nafion during XPS measurements, illuminating and addressing Nafion degradation concerns. The extent of Nafion damage as a function of XPS instrumentation, measurement conditions, and sample properties was evaluated across multiple instruments. Results revealed that significant Nafion damage to the ion-conducting sulfonic acid species (>50% loss in sulfur signal) may occur in a relatively short time frame (tens of minutes) depending on the exact nature of the sample and XPS instrument. This motivated the development and validation of a multipoint XPS data acquisition protocol that minimizes Nafion damage, resulting in reliable data acquisition by avoiding significant artifacts from Nafion instability. The developed protocol was then used to analyze both thin film ionomer samples and Pt/C-based CLs. Comparison of PEM fuel cell CLs to Nafion thin films revealed several changes in Nafion spectral features attributed to charge transfer due to interaction with conductive catalyst and support species. This study provides a method to reliably characterize ionomer-containing samples, facilitating fundamental studies of the catalyst-ionomer interface and more applied investigations of structure-processing-performance correlations in PEM fuel cell and electrolyzer CLs.

Cover page of Functionalization and Structural Evolution of Conducting Quasi-One-Dimensional Chevrel-Type Telluride Nanocrystals.

Functionalization and Structural Evolution of Conducting Quasi-One-Dimensional Chevrel-Type Telluride Nanocrystals.

(2024)

Interfacing organic molecular groups with well-defined inorganic lattices, especially in low dimensions, enables synthetic routes for the rational manipulation of both their local or extended lattice structures and physical properties. While appreciably studied in two-dimensional systems, the influence of surface organic substituents on many known and emergent one-dimensional (1D) and quasi-1D (q-1D) crystals has remained underexplored. Herein, we demonstrate the surface functionalization of bulk and nanoscale Chevrel-like q-1D ionic crystals using In2Mo6Te6, a predicted q-1D Dirac semimetal, as the model phase. Using a series of alkyl ammonium (-NR4+; R = H, methyl, ethyl, butyl, and octyl) substituents with varying chain lengths, we demonstrate the systematic expansion of the intrachain c-axis direction and the contraction of the interchain a/b-axis direction with longer chain substituents. Additionally, we demonstrate the systematic expansion of the intrachain c-axis direction and the contraction of the interchain a/b-axis direction as the alkyl chain substituents become longer using a combination of powder X-ray diffraction and Raman experiments. Beyond the structural modulation that the substituted groups can impose on the lattice, we also found that the substitution of ammonium-based groups on the surface of the nanocrystals resulted in selective suspension in aqueous (NH4+-functionalized) or organic solvents (NOc4+-functionalized), imparted fluorescent character (Rhodamine B-functionalized), and modulated the electrical conductivity of the nanocrystal ensemble. Altogether, our results underscore the potential of organic-inorganic interfacing strategies to tune the structural and physical properties of rediscovered Chevrel-type q-1D ionic solids and open opportunities for the development of surface-addressable building blocks for hybrid electronic and optoelectronic devices at the nanoscale.

Cover page of Neural network kinetics for exploring diffusion multiplicity and chemical ordering in compositionally complex materials.

Neural network kinetics for exploring diffusion multiplicity and chemical ordering in compositionally complex materials.

(2024)

Diffusion involving atom transport from one location to another governs many important processes and behaviors such as precipitation and phase nucleation. The inherent chemical complexity in compositionally complex materials poses challenges for modeling atomic diffusion and the resulting formation of chemically ordered structures. Here, we introduce a neural network kinetics (NNK) scheme that predicts and simulates diffusion-induced chemical and structural evolution in complex concentrated chemical environments. The framework is grounded on efficient on-lattice structure and chemistry representation combined with artificial neural networks, enabling precise prediction of all path-dependent migration barriers and individual atom jumps. To demonstrate the method, we study the temperature-dependent local chemical ordering in a refractory NbMoTa alloy and reveal a critical temperature at which the B2 order reaches a maximum. The atomic jump randomness map exhibits the highest diffusion heterogeneity (multiplicity) in the vicinity of this characteristic temperature, which is closely related to chemical ordering and B2 structure formation. The scalable NNK framework provides a promising new avenue to exploring diffusion-related properties in the vast compositional space within which extraordinary properties are hidden.

Cover page of PCMRESP: A Method for Polarizable Force Field Parameter Development and Transferability of the Polarizable Gaussian Multipole Models Across Multiple Solvents

PCMRESP: A Method for Polarizable Force Field Parameter Development and Transferability of the Polarizable Gaussian Multipole Models Across Multiple Solvents

(2024)

The transferability of force field parameters is a crucial aspect of high-quality force fields. Previous investigations have affirmed the transferability of electrostatic parameters derived from polarizable Gaussian multipole models (pGMs) when applied to water oligomer clusters, polypeptides across various conformations, and different sequences. In this study, we introduce PCMRESP, a novel method for electrostatic parametrization in solution, intended for the development of polarizable force fields. We utilized this method to assess the transferability of three models: a fixed charge model and two variants of pGM models. Our analysis involved testing these models on 377 small molecules and 100 tetra-peptides in five representative dielectric environments: gas, diethyl ether, dichloroethane, acetone, and water. Our findings reveal that the inclusion of atomic polarization significantly enhances transferability and the incorporation of permanent atomic dipoles, in the form of covalent bond dipoles, leads to further improvements. Moreover, our tests on dual-solvent strategies demonstrate consistent transferability for all three models, underscoring the robustness of the dual-solvent approach. In contrast, an evaluation of the traditional HF/6-31G* method indicates poor transferability for the pGM-ind and pGM-perm models, suggesting the limitations of this conventional approach.

Cover page of Modulation of Stiffness-Dependent Macrophage Inflammatory Responses by Collagen Deposition

Modulation of Stiffness-Dependent Macrophage Inflammatory Responses by Collagen Deposition

(2024)

Macrophages are innate immune cells that interact with complex extracellular matrix environments, which have varied stiffness, composition, and structure, and such interactions can lead to the modulation of cellular activity. Collagen is often used in the culture of immune cells, but the effects of substrate functionalization conditions are not typically considered. Here, we show that the solvent system used to attach collagen onto a hydrogel surface affects its surface distribution and organization, and this can modulate the responses of macrophages subsequently cultured on these surfaces in terms of their inflammatory activation and expression of adhesion and mechanosensitive molecules. Collagen was solubilized in either acetic acid (Col-AA) or N-(2-hydroxyethyl)piperazine-N'-ethanesulfonic acid (HEPES) (Col-HEP) solutions and conjugated onto soft and stiff polyacrylamide (PA) hydrogel surfaces. Bone marrow-derived macrophages cultured under standard conditions (pH 7.4) on the Col-HEP-derived surfaces exhibited stiffness-dependent inflammatory activation; in contrast, the macrophages cultured on Col-AA-derived surfaces expressed high levels of inflammatory cytokines and genes, irrespective of the hydrogel stiffness. Among the collagen receptors that were examined, leukocyte-associated immunoglobulin-like receptor-1 (LAIR-1) was the most highly expressed, and knockdown of the Lair-1 gene enhanced the secretion of inflammatory cytokines. We found that the collagen distribution was more homogeneous on Col-AA surfaces but formed aggregates on Col-HEP surfaces. The macrophages cultured on Col-AA PA hydrogels were more evenly spread, expressed higher levels of vinculin, and exerted higher traction forces compared to those of cells on Col-HEP. These macrophages on Col-AA also had higher nuclear-to-cytoplasmic ratios of yes-associated protein (YAP) and transcriptional co-activator with PDZ-binding motif (TAZ), key molecules that control inflammation and sense substrate stiffness. Our results highlight that seemingly slight variations in substrate deposition for immunobiology studies can alter critical immune responses, and this is important to elucidate in the broader context of immunomodulatory biomaterial design.

Cover page of Cu Promoted the Dynamic Evolution of Ni-Based Catalysts for Polyethylene Terephthalate Plastic Upcycling.

Cu Promoted the Dynamic Evolution of Ni-Based Catalysts for Polyethylene Terephthalate Plastic Upcycling.

(2024)

Upcycling plastic wastes into value-added chemicals is a promising approach to put end-of-life plastic wastes back into their ecocycle. As one of the polyesters that is used daily, polyethylene terephthalate (PET) plastic waste is employed here as the model substrate. Herein, a nickel (Ni)-based catalyst was prepared via electrochemically depositing copper (Cu) species on Ni foam (NiCu/NF). The NiCu/NF formed Cu/CuO and Ni/NiO/Ni(OH)2 core-shell structures before electrolysis and reconstructed into NiOOH and CuOOH/Cu(OH)2 active species during the ethylene glycol (EG) oxidation. After oxidation, the Cu and Ni species evolved into more reduced species. An indirect mechanism was identified as the main EG oxidation (EGOR) mechanism. In EGOR, NiCu60s/NF catalyst exhibited an optimal Faradaic efficiency (FE, 95.8%) and yield rate (0.70 mmol cm-2 h-1) for formate production. Also, over 80% FE of formate was achieved when a commercial PET plastic powder hydrolysate was applied. Furthermore, commercial PET plastic water bottle waste was employed as a substrate for electrocatalytic upcycling, and pure terephthalic acid (TPA) was recovered only after 1 h electrolysis. Lastly, density functional theory (DFT) calculation revealed that the key role of Cu was significantly reducing the Gibbs free-energy barrier (ΔG) of EGORs rate-determining step (RDS), promoting catalysts dynamic evolution, and facilitating the C-C bond cleavage.

Cover page of Methodology for Assessing Retrofitted Hydrogen Combustion and Fuel Cell Aircraft Environmental Impacts

Methodology for Assessing Retrofitted Hydrogen Combustion and Fuel Cell Aircraft Environmental Impacts

(2024)

Hydrogen (H2) combustion and solid oxide fuel cells (SOFCs) can potentially reduce aviation-produced greenhouse gas emissions compared to kerosene propulsion. This paper outlines a methodology for evaluating performance and emission tradeoffs when retrofitting conventional kerosene-powered aircraft with lower-emissionH2 combustion and SOFC hybrid alternatives. The proposed framework presents a constant-range approach for designing liquid hydrogen fuel tanks, considering insulation, sizing, center of gravity, and power constraints. A lifecycle assessment evaluates greenhouse gas emissions and contrail formation effects for carbon footprint mitigation, while a cost analysis examines retrofit implementation consequences. A Cessna Citation 560XLS+ case study shows a 5% mass decrease for H2 combustion and a 0.4% mass decrease for the SOFC hybrid, at the tradeoff of removing three passengers. The lifecycle analysis of green hydrogen in aviation reveals a significant reduction in CO2 emissions for H2 combustion and SOFC systems, except for natural-gas-produced H2 combustion, when compared to Jet-A fuel. However, this environmental benefit is contrasted by an increase in fuel cost per passenger-km for green H2 combustion and a rise for natural-gas-produced H2 SOFC compared to kerosene. The results suggest that retrofitting aircraft with alternative fuels could lower carbon emissions, noting the economic and passenger capacity tradeoffs.