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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 Molecular beam scattering of neon from flat jets of cold salty water

Molecular beam scattering of neon from flat jets of cold salty water

(2025)

Molecular beam scattering experiments are carried out to study collisions between Ne atoms (E i = 24.3 kJ mol-1) and the surface of a cold salty water (8 m LiBr(aq), 230 K) flat jet. Translational energy distributions are collected as a function of scattering angle using a rotatable mass spectrometer. Impulsive scattering and thermal desorption contribute to the overall scattering distributions, but impulsive scattering dominates at all three incidence angles explored. Highly super-specular scattering is observed in the impulsive scattering channel that is attributed to anisotropic momentum transfer to the liquid surface. The thermal desorption channel exhibits a cos θ angular distribution. Compared to Ne scattering from dodecane, fractional energy loss in the impulsive scattering channel is much larger across a wide range of deflection angles. A soft-sphere model is applied to investigate the kinematics of energy transfer between the scatterer and liquid surface. Fitting to this model yields an effective surface mass of 250-60 +100 amu and internal excitation of 11.8 ± 1.6 kJ mol-1, both of which are considerably larger than for Ne/dodecane. It thus appears that energy transfer to cold salty water is more efficient than to a dodecane liquid surface, a result attributed to the extensive hydrogen-bonded network of liquid water and roughness of the liquid surface.

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Cover page of Capturing Ring Opening in Photoexcited Enolic Acetylacetone upon Hydrogen Bond Dissociation by Ultrafast Electron Diffraction

Capturing Ring Opening in Photoexcited Enolic Acetylacetone upon Hydrogen Bond Dissociation by Ultrafast Electron Diffraction

(2025)

Photoinduced biological and chemical reactions are often based on key structural transformations of a molecule driven across multiple electronic states. Acetylacetone (AcAc) is a prototypical system for complex chemical pathways involving several conical intersections (CI) and singlet-triplet intersystem crossings (ISC) characterized by distinct geometries. In the gas phase, AcAc is predominantly in a planar ring-like enolic form stabilized by a strong intramolecular O-H···O hydrogen bond. Following excitation into the S2 (ππ*) state at 266 nm, acetylacetone undergoes rapid internal conversion followed by intersystem crossing. Such relaxation pathways are associated with structural changes including ring opening, deplanarization, and bond elongation. In this work, ultrafast electron diffraction (UED) at the SLAC MeV-UED setup is employed as a direct structural probe with a time resolution of 160 fs. Together with trajectory surface hopping simulations, analysis of the UED data provides a new perspective on the early time nuclear dynamics in acetylacetone. Specifically, AcAc is observed to undergo ring opening, deplanarization, and bond elongation all within the first 700 fs after photoexcitation. The monitored dynamics is associated mainly with the nuclear motion on the S1 potential energy surface, formed after very rapid transfer from S2 to S1, allowing AcAc to reach the conical intersection to intersystem crossing. Such time scales of nuclear motion are contrasted with the time scales of electronic transitions in AcAc that were previously characterized with spectroscopic methods, specifically internal conversion (<100 fs) and intersystem crossing (∼1.5 ps).

Cover page of The conundrum of diffuse basis sets: A blessing for accuracy yet a curse for sparsity

The conundrum of diffuse basis sets: A blessing for accuracy yet a curse for sparsity

(2025)

Diffuse atomic orbital basis sets have proven to be essential to obtain accurate interaction energies, especially in regard to non-covalent interactions. However, they also have a detrimental impact on the sparsity of the one-particle density matrix (1-PDM), to a degree stronger than the spatial extent of the basis functions alone could explain. This is despite the fact that the matrix elements of the 1-PDM of insulators (systems with significant highest occupied molecular orbital-lowest unoccupied molecular orbital gaps) are expected to decay exponentially with increasing real-space distance from the diagonal. The observed low sparsity of the 1-PDM appears to be independent of representation and even persists after projecting the 1-PDM onto a real-space grid, leading to the conclusion that this "curse of sparsity" is solely a basis set artifact, which, counterintuitively, becomes worse for larger basis sets, seemingly contradicting the notion of a well-defined basis set limit. We show that this is a consequence of the low locality of the contra-variant basis functions as quantified by the inverse overlap matrix S-1 being significantly less sparse than its co-variant dual. Introducing the model system of an infinite non-interacting chain of helium atoms, we are able to quantify the exponential decay rate to be proportional to the diffuseness as well as local incompleteness of the basis set, meaning small and diffuse basis sets are affected the most. Finally, we propose one solution to the conundrum in the form of the complementary auxiliary basis set singles correction in combination with compact, low l-quantum-number basis sets, showing promising results for non-covalent interactions.

Cover page of Tuning the free energy of host–guest encapsulation by cosolvent

Tuning the free energy of host–guest encapsulation by cosolvent

(2025)

Supramolecular hosts create unique microenvironments which enable the tuning of reactions via steric confinement and electrostatics. It has been shown that "solvent shaping inside hydrophobic cavities" is an important thermodynamic driving force for guest encapsulation in the nanocage host. Here, we show that even small (5%) changes in the solvent composition can have a profound impact on the free energy of encapsulation. In a combined THz, NMR and ab initio MD study, we reveal that the preferential residing of a single DMSO molecule in the cavity upon addition of ≥5% DMSO results in a considerable change of ΔS from 63-76 cal mol-1 K-1 to 23-24 cal mol-1 K-1. This can be rationalized by reduction of the cavity volume due to the DMSO molecule which resides preferentially in the cavity. These results provide novel insights into the guest-binding interactions, emphasizing that the entropic driving force is notably influenced by even small changes in the solvent composition, irrespective of changes in metal ligand vertices. Having demonstrated that the local solvent composition within the cage is essential for regulating catalytic efficiency, solvent tuning might enable novel applications in supramolecular chemistry in catalysis and chemical separation.

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.

Cover page of Emissive Chalcogenide Perovskite Nanowires

Emissive Chalcogenide Perovskite Nanowires

(2025)

Efficient and stable one-dimensional semiconductor nanowires are critical for the development of next-generation on-chip optoelectronics. Here, we report a synthetic approach to produce high-quality nanowires based on chalcogenide perovskite via a vapor phase reaction inside a sealed ampule. An epitaxial vapor-phase growth mechanism is proposed. The nanowires are shown to be single crystalline and highly structurally stable, with a preferential growth along the [010] direction. Red and green photoluminescence (PL) is observed from BaZrS3 and SrHfS3 nanowires, respectively, and the emission is shown to be tunable with varying compositions. PL lifetime is measured by fitting the decay curve with a biexponential model. The longer radiative recombination lifetime component is on the time scale of nanoseconds, indicating good nanowire sample quality with a promising potential for optoelectronic applications.

Cover page of Annihilation-limited long-range exciton transport in high-mobility conjugated copolymer films

Annihilation-limited long-range exciton transport in high-mobility conjugated copolymer films

(2025)

A combination of ultrafast, long-range, and low-loss excitation energy transfer from the photoreceptor location to a functionally active site is essential for cost-effective polymeric semiconductors. Delocalized electronic wavefunctions along π-conjugated polymer (CP) backbone can enable efficient intrachain transport, while interchain transport is generally thought slow and lossy due to weak chain-chain interactions. In contrast to the conventional strategy of mitigating structural disorder, amorphous layers of rigid CPs, exemplified by highly planar poly(indacenodithiophene-co-benzothiadiazole) (IDT-BT) donor-accepter copolymer, exhibit trap-free transistor performance and charge-carrier mobilities similar to amorphous silicon. Here, we report long-range exciton transport in HJ-aggregated IDTBT thin-film, in which the competing exciton transport and exciton-exciton annihilation (EEA) dynamics are spectroscopically separated using a phase-cycling-based scheme and shown to depart from the classical diffusion-limited and strong-coupling regime. In the thin film, we find an annihilation-limited mechanism with ≪100% per-encounter annihilation probability, facilitating the minimization of EEA-induced excitation losses. In contrast, excitons on isolated IDTBT chains diffuse over 350 nm with 0.56 cm2 s-1 diffusivity, before eventually annihilating with unit probability on first contact. We complement the pump-probe studies with temperature-dependent photocurrent and EEA measurements from 295 K to 77 K and find a remarkable correspondence of annihilation rate and photocurrent activation energies in the 140 K to 295 K temperature range.

Cover page of Probing exciton diffusion dynamics in photosynthetic supercomplexes via exciton–exciton annihilation

Probing exciton diffusion dynamics in photosynthetic supercomplexes via exciton–exciton annihilation

(2025)

Photosynthesis converts solar energy into chemical energy through coordinated energy transfer between light-harvesting complexes and reaction centers (RCs). Understanding exciton motion, particularly the exciton diffusion length, is essential for optimizing energy efficiency in photosystems. In this work, we combine intensity-cycling transient absorption spectroscopy with kinetic Monte Carlo (kMC) simulation to investigate exciton motion in the C2S2 photosystem II supercomplex of spinach. Using exciton-exciton annihilation, revealed in the fifth-order response, we experimentally estimate an exciton diffusion length of 10.9 nm based on a 3D normal diffusion model, suggesting the ability of excitons to traverse the supercomplex. However, kMC simulations reveal that exciton motion is sub-diffusive because of spatial constraints and the strong RC traps. An anomalous diffusion model analysis of the experimental data yields a diffusion length of 9.7 nm, while the simulated diffusion length is 7.4 nm. The variable exciton residence time across subunits, partly influenced by their connectivity to the trap, indicates inhomogeneous annihilation probability and suggests how plants balance efficient light harvesting with photoprotection. We also explore the influence of specific assumptions in the annihilation simulation, which are challenging to access in more complex environments, such as the thylakoid membrane. Our study provides a framework for studying exciton dynamics using exciton-exciton annihilation, which can be extended to understand the light-harvesting efficiencies of larger, more complex photosynthetic assemblies.

Cover page of Precursor Identity and Surfactant Concentration Influence Shape of UO2 Nanoparticles

Precursor Identity and Surfactant Concentration Influence Shape of UO2 Nanoparticles

(2025)

A fundamental step toward studying the unique properties of actinide nanomaterials is control over the shape of actinide nanoparticles. Toward this goal, this work demonstrates the effects of precursor identity and surfactant concentration on the shape of uranium dioxide (UO2) nanoparticles. UO2 nanoparticles were synthesized by thermal decomposition of different precursors in the presence of oleylamine and oleic acid as surfactants. The size, shape, phase, and chemical composition of the nanoparticles was evaluated using transmission electron microscopy (TEM), energy dispersive X-ray spectroscopy (EDS), electron diffraction (ED), and U L3-edge X-ray absorption fine-structure (XAFS) spectroscopy. Anisotropic UO2 nanocubes of ∼ 4 nm were obtained only with low surfactant concentrations, while increasing the surfactant concentration resulted in formation of nanoparticles with an isotropic, sphere morphology. The importance of precursor identity was also investigated by employing U(hfa)4, U(acac)4, UO2(acac)2, and UO2(hfa)2·H2O (where hfa = hexafluoracetylacetone and acac = acetylacetone) as precursors. The nanocube morphology was only observed when U(hfa)4 was used as a precursor. XAS allowed for comparison of the disorder in anisotropic vs isotropic UO2 nanoparticles.

Cover page of Key Intermediate Nanostructures in the Self-Assembly of Amphiphilic Polypeptoids Revealed by Cryo-TEM

Key Intermediate Nanostructures in the Self-Assembly of Amphiphilic Polypeptoids Revealed by Cryo-TEM

(2025)

Amphiphilic copolypeptoids are known to form a variety of nanostructures (fibers, tubes, sheets, etc.), but the assembly mechanisms and key intermediates remain underexplored. This study investigates the intermediate structures formed during the early stages of self-assembly in diblock copolypeptoids using cryo-transmission electron microscopy (cryo-TEM). We focused on two diblock copolypeptoids, one with a free N-terminus and the other with a capped N-terminus, which ultimately form less-ordered nanofibers and well-ordered nanosheets, respectively. Through cryo-TEM imaging of vitrified solutions at various time points during the self-assembly process, the study identified micelles and vesicles as key intermediate structures. Notably, the formation of vesicles as intermediates is unusual in crystallization-driven self-assembly and suggests a unique pathway in polypeptoid self-assembly. The study provides direct imaging evidence of key intermediates in polypeptoid self-assembly, advancing the understanding of their self-assembly mechanisms.