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Open Access Publications from the University of California

College of Chemistry

UC Berkeley

This series is automatically populated with publications deposited by UC Berkeley College of Chemistry Department of Chemistry 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 Sodium Carbonate ion complexes modify water structure at electrode interfaces

Sodium Carbonate ion complexes modify water structure at electrode interfaces

(2024)

Water structure near electrode interfaces may play an important role in controlling CO2 electroreduction. Using plasmon-enhanced vibrational sum frequency generation spectroscopy, we demonstrate the emergence of an interfacial water subpopulation with large electric fields along their OH bonds, when Na2CO3 ions are present near the electrode under applied potential. With molecular dynamics simulations, we show that the approach of aqueous Na2CO3 to electrodes is coupled to the formation of structured and oriented ion complexes, and that the emergent water population is associated with the first solvation shell of these complexes. This water subpopulation is seen even when the sole source of CO32− is its in-situ generation from CO2, indicating that the interfacial species investigated here are likely ubiquitous in CO2 electroreduction contexts.

Cover page of Scanning electrochemical probe microscopy investigation of two-dimensional materials

Scanning electrochemical probe microscopy investigation of two-dimensional materials

(2024)

Research interests in two-dimensional (2D) materials have seen exponential growth owing to their unique and fascinating properties. The highly exposed lattice planes coupled with tunable electronic states of 2D materials have created manifold opportunities in the design of new platforms for energy conversion and sensing applications. Still, challenges in understanding the electrochemical (EC) characteristics of these materials arise from the complexity of both intrinsic and extrinsic heterogeneities that can obscure structure-activity correlations. Scanning EC probe microscopic investigations offer unique benefits in disclosing local EC reactivities at the nanoscale level that are otherwise inaccessible with macroscale methods. This review summarizes recent progress in applying techniques of scanning EC microscopy (SECM) and scanning EC cell microscopy (SECCM) to obtain distinctive insights into the fundamentals of 2D electrodes. We showcase the capabilities of EC microscopies in addressing the roles of defects, thickness, environments, strain, phase, stacking, and many other aspects in the heterogeneous electron transfer, ion transport, electrocatalysis, and photoelectrochemistry of representative 2D materials and their derivatives. Perspectives for the advantages, challenges, and future opportunities of scanning EC probe microscopy investigation of 2D structures are discussed.

Cover page of α-Phenylthioaldehydes for the effective generation of acyl azolium and azolium enolate intermediates.

α-Phenylthioaldehydes for the effective generation of acyl azolium and azolium enolate intermediates.

(2024)

α-Phenylthioaldehydes are readily prepared using a simple multi-step procedure and herein are introduced as a new precursor for the NHC-catalysed generation of acyl azolium and azolium enolate intermediates that are of widespread synthetic interest and utility. Treatment of α-phenylthioaldehydes with an NHC precatalyst and base produces an efficient redox rearrangement via a Breslow intermediate, elimination of thiophenolate, and subsequent rebound addition to the generated acyl azolium to give the corresponding thiol ester. In the presence of an external alcohol, competition between redox rearrangement and redox esterification can be controlled through judicious choice of the N-aryl substituent within the NHC precatalyst and the base used in the reaction. With NEt3 as base, NHCs bearing electron-withdrawing (N-C6F5 or N-C6H2Cl3) substituents favour redox rearrangement, while triazolium precatalysts with electron-rich N-aryl substituents (N-Ph, N-Mes) result in preferential redox esterification. Using DBU, redox esterification is preferred due to transesterification of the initially formed thiol ester product. Additionally, α-phenylthioaldehyde-derived azolium enolates have been used in enantioselective formal [4 + 2]-cycloaddition reactions to access dihydropyridinone heterocycles with high enantioselectivity (up to >95 : 5 dr, 98 : 2 er).

Cover page of Long Duration Energy Storage Using Hydrogen in Metal-Organic Frameworks: Opportunities and Challenges.

Long Duration Energy Storage Using Hydrogen in Metal-Organic Frameworks: Opportunities and Challenges.

(2024)

Materials-based H2 storage plays a critical role in facilitating H2 as a low-carbon energy carrier, but there remains limited guidance on the technical performance necessary for specific applications. Metal-organic framework (MOF) adsorbents have shown potential in power applications, but need to demonstrate economic promises against incumbent compressed H2 storage. Herein, we evaluate the potential impact of material properties, charge/discharge patterns, and propose targets for MOFs deployment in long-duration energy storage applications including backup, load optimization, and hybrid power. We find that state-of-the-art MOF could outperform cryogenic storage and 350 bar compressed storage in applications requiring ≤8 cycles per year, but need ≥5 g/L increase in uptake to be cost-competitive for applications that require ≥30 cycles per year. Existing challenges include manufacturing at scale and quantifying the economic value of lower-pressure storage. Lastly, future research needs are identified including integrating thermodynamic effects and degradation mechanisms.

Cover page of Anion and Cation Migration at 2D/3D Halide Perovskite Interfaces

Anion and Cation Migration at 2D/3D Halide Perovskite Interfaces

(2024)

This study explores the ionic dynamics in 2D/3D perovskite solar cells, which are known for their improved efficiency and stability. The focus is on the impact of halide choice in 3D perovskites treated with phenethylammonium halide salts (PEAX, X = Br and I). Our findings reveal that light and heat drive ionic migration in these structures, with PEA+ species diffusing into the 3D film in PEABr-treated samples. Mixed-halide 3D perovskites show halide interdiffusion, with bromine migrating to the surface and iodine diffusing into the film. Cathodoluminescence microscopy reveals localized 2D phases on the 3D perovskite, which become more evenly distributed after thermal treatment. Both PEAX salts enhance the performance of photovoltaic devices. This improvement is attributed to the passivation capabilities of the salts themselves and their respective Ruddlesden−Popper (RP) phases. Annealed PEAI-treated devices show a better balance between efficiency and statistical distribution of photovoltaic parameters.

Cover page of Utopia Point Bayesian Optimization Finds Condition-Dependent Selectivity for N-Methyl Pyrazole Condensation.

Utopia Point Bayesian Optimization Finds Condition-Dependent Selectivity for N-Methyl Pyrazole Condensation.

(2024)

Utopia Point Bayesian Optimization (UPBO) was used to identify reaction conditions that are highly selective for the formation of N1 and N2-methyl-3-aryl pyrazole constitutional isomers. UPBO was used to explore a wide chemical space and identify basic reaction conditions for a typically acid-catalyzed Knorr pyrazole condensation. These studies revealed that selectivity in the reaction stems from a condition-dependent equilibrium of intermediates prior to dehydration. For the N2-methyl isomer reaction pathway, a hemiaminal intermediate was found to form reversibly under the reaction conditions, enabling a highly selective synthesis of the N2 isomer upon dehydrative workup. UPBO was able to successfully optimize conversion and selectivity simultaneously with search spaces of >1 million potential variable combinations without the need for high-performance computational resources.

Cover page of Nanomedicine Targeting Cuproplasia in Cancer: Labile Copper Sequestration Using Polydopamine Particles Blocks Tumor Growth In Vivo through Altering Metabolism and Redox Homeostasis.

Nanomedicine Targeting Cuproplasia in Cancer: Labile Copper Sequestration Using Polydopamine Particles Blocks Tumor Growth In Vivo through Altering Metabolism and Redox Homeostasis.

(2024)

Copper plays critical roles as a metal active site cofactor and metalloallosteric signal for enzymes involved in cell proliferation and metabolism, making it an attractive target for cancer therapy. In this study, we investigated the efficacy of polydopamine nanoparticles (PDA NPs), classically applied for metal removal from water, as a therapeutic strategy for depleting intracellular labile copper pools in triple-negative breast cancer models through the metal-chelating groups present on the PDA surface. By using the activity-based sensing probe FCP-1, we could track the PDA-induced labile copper depletion while leaving total copper levels unchanged and link it to the selective MDA-MB-231 cell death. Further mechanistic investigations revealed that PDA NPs increased reactive oxygen species (ROS) levels, potentially through the inactivation of superoxide dismutase 1 (SOD1), a copper-dependent antioxidant enzyme. Additionally, PDA NPs were found to interact with the mitochondrial membrane, resulting in an increase in the mitochondrial membrane potential, which may contribute to enhanced ROS production. We employed an in vivo tumor model to validate the therapeutic efficacy of PDA NPs. Remarkably, in the absence of any additional treatment, the presence of PDA NPs alone led to a significant reduction in tumor volume by a factor of 1.66 after 22 days of tumor growth. Our findings highlight the potential of PDA NPs as a promising therapeutic approach for selectively targeting cancer by modulating copper levels and inducing oxidative stress, leading to tumor growth inhibition as shown in these triple-negative breast cancer models.

Cover page of A mitochondrial-targeted activity-based sensing probe for ratiometric imaging of formaldehyde reveals key regulators of the mitochondrial one-carbon pool.

A mitochondrial-targeted activity-based sensing probe for ratiometric imaging of formaldehyde reveals key regulators of the mitochondrial one-carbon pool.

(2024)

Formaldehyde (FA) is both a highly reactive environmental genotoxin and an endogenously produced metabolite that functions as a signaling molecule and one-carbon (1C) store to regulate 1C metabolism and epigenetics in the cell. Owing to its signal-stress duality, cells have evolved multiple clearance mechanisms to maintain FA homeostasis, acting to avoid the established genotoxicity of FA while also redirecting FA-derived carbon units into the biosynthesis of essential nucleobases and amino acids. The highly compartmentalized nature of FA exposure, production, and regulation motivates the development of chemical tools that enable monitoring of transient FA fluxes with subcellular resolution. Here we report a mitochondrial-targeted, activity-based sensing probe for ratiometric FA detection, MitoRFAP-2, and apply this reagent to monitor endogenous mitochondrial sources and sinks of this 1C unit. We establish the utility of subcellular localization by showing that MitoRFAP-2 is sensitive enough to detect changes in mitochondrial FA pools with genetic and pharmacological modulation of enzymes involved in 1C and amino acid metabolism, including the pervasive, less active genetic mutant aldehyde dehydrogenase 2*2 (ALDH2*2), where previous, non-targeted versions of FA sensors are not. Finally, we used MitoRFAP-2 to comparatively profile basal levels of FA across a panel of breast cancer cell lines, finding that FA-dependent fluorescence correlates with expression levels of enzymes involved in 1C metabolism. By showcasing the ability of MitoRFAP-2 to identify new information on mitochondrial FA homeostasis, this work provides a starting point for the design of a broader range of chemical probes for detecting physiologically important aldehydes with subcellular resolution and a useful reagent for further studies of 1C biology.

Cover page of Diborane Reductions of CO2 and CS2 Mediated by Dicopper μ-Boryl Complexes of a Robust Bis(phosphino)-1,8-naphthyridine Ligand.

Diborane Reductions of CO2 and CS2 Mediated by Dicopper μ-Boryl Complexes of a Robust Bis(phosphino)-1,8-naphthyridine Ligand.

(2024)

A dinucleating 1,8-naphthyridine ligand featuring fluorene-9,9-diyl-linked phosphino side arms (PNNPFlu) was synthesized and used to obtain the cationic dicopper complexes 2, [(PNNPFlu)Cu2(μ-Ph)][NTf2]; [NTf2] = bis(trifluoromethane)sulfonimide, 6, [(PNNPFlu)Cu2(μ-CCPh)][NTf2], and 3, [(PNNPFlu)Cu2(μ-OtBu)][NTf2]. Complex 3 reacted with diboranes to afford dicopper μ-boryl species (4, with μ-Bcat; cat = catecholate and 5, with μ-Bpin; pin = pinacolate) that are more reactive in C(sp)-H bond activations and toward activations of CO2 and CS2, compared to dicopper μ-boryl complexes supported by a 1,8-naphthyridine-based ligand with di(pyridyl) side arms. The solid-state structures and DFT analysis indicate that the higher reactivities of 4 and 5 relate to changes in the coordination sphere of copper, rather than to perturbations on the Cu-B bonding interactions. Addition of xylyl isocyanide (CNXyl) to 4 gave 7, [(PNNPFlu)Cu2(μ-Bcat)(CNXyl)][NTf2], demonstrating that the lower coordination number at copper is chemically significant. Reactions of 4 and 5 with CO2 yielded the corresponding dicopper borate complexes (8, [(PNNPFlu)Cu2(μ-OBcat)][NTf2]; 9, [(PNNPFlu)Cu2(μ-OBpin)][NTf2]), with 4 demonstrating catalytic reduction in the presence of excess diborane. Related reactions of 4 and 5 with CS2 provided insertion products 10, {[(PNNPFlu)Cu2]2[μ-S2C(Bcat)2]}[NTf2]2, and 11, [(PNNPFlu)Cu2(μ,κ2-S2CBpin)][NTf2], respectively. These products feature Cu-S-C-B linkages analogous to those of proposed CO2 insertion intermediate.

Cover page of STORM Super-Resolution Visualization of Self-Assembled γPFD Chaperone Ultrastructures in Methanocaldococcus jannaschii

STORM Super-Resolution Visualization of Self-Assembled γPFD Chaperone Ultrastructures in Methanocaldococcus jannaschii

(2024)

Gamma-prefoldin (γPFD), a unique chaperone found in the extremely thermophilic methanogen Methanocaldococcus jannaschii, self-assembles into filaments in vitro, which so far have been observed using transmission electron microscopy and cryo-electron microscopy. Utilizing three-dimensional stochastic optical reconstruction microscopy (3D-STORM), here we achieve ∼20 nm resolution by precisely locating individual fluorescent molecules, hence resolving γPFD ultrastructure both in vitro and in vivo. Through CF647 NHS ester labeling, we first demonstrate the accurate visualization of filaments and bundles with purified γPFD. Next, by implementing immunofluorescence labeling after creating a 3xFLAG-tagged γPFD strain, we successfully visualize γPFD in M. jannaschii cells. Through 3D-STORM and two-color STORM imaging with DNA, we show the widespread distribution of filamentous γPFD structures within the cell. These findings provide valuable insights into the structure and localization of γPFD, opening up possibilities for studying intriguing nanoscale components not only in archaea but also in other microorganisms.