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Developing an Undergraduate Research Laboratory for Experimental Physical Chemistry [Book Chapter]

Embarking on a faculty career in physical chemistry at a primarily undergraduate institution (PUI) is exciting, but also overwhelming. Becoming both an effective teacher and a productive researcher requires a good plan, hard work and support from others who understand what it takes to be successful. The phrase, “building a laboratory,” calls to mind the physical construction of a research instrument, but beginning a career at a PUI involves much more than assembling equipment. Funding for the lab must be secured, students must be recruited and mentored, and the lab must be overseen to keep things running on a daily basis. While many of these tasks would also be part of starting a career at a doctoral level institution, there are many special considerations that must be taken into account when working with undergraduate students because their laboratory experience and chemical knowledge are still within those beautiful but nascent stages. Here, this unique aspect makes building a research program challenging, but also very rewarding. Exposing young minds to the wonders of physical chemistry and building personal relationships through the mentoring process can be immensely gratifying. This chapter is a compilation of holistic advice for building an experimental physical chemistry research laboratory for undergraduates, reflecting a typical experience found in the United States.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

The physical chemistry of solar fuels catalysis

The demonstration of effective light-driven electrochemical water splitting at the surface of a TiO 2 electrode in the seminal 1972 Honda–Fujishima publication spurred global research efforts to understand this effect and design advanced systems for solar H 2 generation from water as a carbon-free and sustainable fuel. In the 50+ years since that discovery, research investigating approaches toward the catalytic generation of the so-called “solar fuels,” i.e., not only H 2 from water but also CO 2 reduction products and NH 3 from N 2 , has expanded dramatically in scope and scale. The development of new experimental and computational methods and construction and commissioning of large-scale facilities have paved the way for important insights into the machinery of natural photosynthesis, leading to a greater understanding of the complexity of light-to-chemical energy conversion with an exquisite temporal and spatial resolution. Finally, these studies have provided the foundation for biologically inspired molecular and hybrid designs with the goal to promote the photochemical steps critical to solar fuels generation while avoiding unproductive or unnecessary pathways.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Dataset for "Resistance of Boron Nitride Nanotubes to Radiation-Induced Oxidation" as published in The Journal of Physical Chemistry C

We present unprecedented results on the damage thresholds and pathways for boron nitride nanotubes (BNNT) under the influence of energetic electrons in an oxidative gas environment, using an environmental aberration-corrected electron microscope over a range of oxygen pressures. We observe a damage cascade process that resists damage until a higher electron dose, compared with carbon nanotubes, initiating at defect-free BNNT sidewalls and proceeding through the conversion from crystalline nanotubes to amorphous boron nitride (BN), resisting oxidation throughout. We compare with prior results on the oxidation of carbon nanotubes and present a model that attributes the onset of damage in both cases to a physisorbed oxygen layer that reduces the threshold for damage onset. Surprisingly, increased temperatures offer protection against damage, as do electron dose rates that significantly exceed the oxygen dose rates, and our model attributes both effects to a physisorbed oxygen population.

Adsorption↗

Ultrafast Spectroscopy and Dynamics of Photoredox Catalysis

Photoredox catalysis has emerged as a powerful platform for chemical synthesis, utilizing chromophore excited states as selective energy stores to surmount chemical activation barriers toward making desirable products. Developments in this field have pushed synthetic chemists to design and discover new photocatalysts with novel and impactful photoreactivity but also with uncharacterized excited states and only an approximate mechanistic understanding. This review highlights specific instances in which ultrafast spectroscopies dissected the photophysical and photochemical dynamics of new classes of photoredox catalysts and their photochemical reactions. After briefly introducing the photophysical processes and ultrafast spectroscopic methods central to this topic, the review describes selected recent examples that evoke distinct classes of photoredox catalysts with demonstrated synthetic utility and ultrafast spectroscopic characterization. Furthermore, this review cements the significant role of ultrafast spectroscopy in modern photocatalyzed organic transformations and institutionalizes the developing intersection of synthetic organic chemistry and physical chemistry.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Phase Transitions in Organic and Organic/Inorganic Aerosol Particles

The phase state of aerosol particles can impact numerous atmospheric processes, including new particle growth, heterogeneous chemistry, cloud condensation nucleus formation, and ice nucleation. In this article, the phase transitions of inorganic, organic, and organic/inorganic aerosol particles are discussed, with particular focus on liquid-liquid phase separation (LLPS). The physical chemistry that determines whether LLPS occurs, at what relative humidity it occurs, and the resultant particle morphology is explained using both theoretical and experimental methods. The known impacts of LLPS on aerosol processes in the atmosphere are discussed. Finally, potential evidence for LLPS from field and chamber studies is presented. By understanding the physical chemistry of the phase transitions of aerosol particles, we will acquire a better understanding of aerosol processes, which in turn impact human health and climate.

Chemistry↗

Physics and chemistry from parsimonious representations: image analysis via invariant variational autoencoders

Electron, optical, and scanning probe microscopy methods are generating ever increasing volume of image data containing information on atomic and mesoscale structures and functionalities. This necessitates the development of the machine learning methods for discovery of physical and chemical phenomena from the data, such as manifestations of symmetry breaking phenomena in electron and scanning tunneling microscopy images, or variability of the nanoparticles. Variational autoencoders (VAEs) are emerging as a powerful paradigm for the unsupervised data analysis, allowing to disentangle the factors of variability and discover optimal parsimonious representation. Here, we summarize recent developments in VAEs, covering the basic principles and intuition behind the VAEs. The invariant VAEs are introduced as an approach to accommodate scale and translation invariances present in imaging data and separate known factors of variations from the ones to be discovered. We further describe the opportunities enabled by the control over VAE architecture, including conditional, semi-supervised, and joint VAEs. Several case studies of VAE applications for toy models and experimental datasets in Scanning Transmission Electron Microscopy are discussed, emphasizing the deep connection between VAE and basic physical principles. Python codes and datasets discussed in this article are available at https://github.com/saimani5/VAE-tutorials and can be used by researchers as an application guide when applying these to their own datasets.

36 MATERIALS SCIENCE↗

Tribute to José N. Onuchic

This Festschrift Virtual Special Issue in The Journal of Physical Chemistry B is dedicated to the scientific contributions of Prof. José Nelson Onuchic. It serves as a celebration of his years of service, mentorship, and leadership to the biological physics, theoretical chemistry, and computational biology communities. This collection of more than 60 articles has been compiled from an extensive network of scientists that have, in distinct ways, been impacted by the scientific legacy of Prof. Onuchic. It is a written testament to how his work has influenced many areas related to the physics and chemistry of biological systems. In conclusion, this Festschrift provides a good sample of the areas in that Professor Onuchic has had a direct impact via collaboration, mentorship, and scientific dissemination of his research.

99 GENERAL AND MISCELLANEOUS↗

Hiding in plain sight: The prevalence and impact of trions and Fermi polarons in transient absorption spectroscopy experiments of 2D semiconductors

Transient absorption (TA) spectroscopy is one of the most popular experimental methods to measure the excited state lifetimes and charge carrier recombination mechanisms in two dimensional (2D) semiconductors. This fundamental information is essential for designing and optimizing the next generation of ultrathin and lightweight 2D semiconductor-based optoelectronic devices. However, the interpretation of TA spectroscopy data varies across the community. The community lacks a unifying physical explanation for how and why experimental variables such as incident light intensity, sample-substrate interactions, and/or applied bias affect TA spectral data. This Perspective (1) compares the physical chemistry TA literature to nanomaterial physics literature from a historical perspective, (2) reviews multiple physical explanations that the TA community developed to explain spectral features and experimental trends, (3) provides a unifying explanation for how and why trions—and, more generally, Fermi polarons—contribute to TA spectra, and (4) quantifies the extent to which various physical interpretations and data analysis procedures yield different timescales and mechanisms for the same set of experimental results. We highlight the importance of considering trions/Fermi polarons in TA measurements and their implications for advancing our understanding of 2D material properties.

2D materials↗

40th Eastern Regional Photosynthesis Conference

Photosynthesis has shaped global biochemistry and geochemistry in its production of almost all atmospheric oxygen, and almost every electron that supports the processes of life on Earth was extracted from water by the light-dependent reactions, many of which were then used to fix carbon in the dark reactions. To humans, that fixed carbon is the originator of all fossil fuels and a critical step in conversion of solar photons to human-usable energy. The Eastern Regional Photosynthesis Conference (ERPC) serves as a forum for advancement of science in this field. As a regional-level conference, it specializes in providing developmental opportunities for early-career researchers from undergraduates to pre-tenure professors, as well as broadening the field in terms of participating scholars and research approaches to produce new interdisciplinary collaborations. Funding from the Department of Energy is used to mitigate registration and attendance costs for junior (non-PI) researchers. The ERPC is one of the three regional conferences in the field of photosynthesis research in the United States, alongside the Western Photosynthesis Conference (currently in California) and the Midwestern Photosynthesis Conference (Turkey Run, Indiana). A longstanding incubator for scientific discourse, discovery, and collaborations, this conference has spawned many collaborations which led to Department of Energy-funded projects and brought two full generations of scientists into the field. In 2023 the landmark 40th such conference was held at the Woods Hole Marine Biological Laboratory in Massachusetts. The conference was held April 14th-16th, 2023. The majority of the total attendees are traditionally undergraduates, graduate students, and postdoctoral researchers, whose scientific development greatly benefits from conferences like these. Almost all talks besides the ones given by invited speakers were given by young scientists who benefited from this award. Many posters presented at this conference were also the work of junior scientists. This conference is many young scientists' first exposure to the photosynthesis research community and its primary goal is to provide a positive atmosphere for those attendees, as exemplified by the three poster sessions and dedicated interactions between senior and junior scientists. Additionally, this was the first year of a successful equitable outreach and speaker recruitment plan to provide fair representation at the conference in line with Department of Energy policies and mission. The central focus of the ERPC is the understanding of energy flow from photons to usable chemical products in both natural and artificial photosynthesis. We support the DOE-BES aim of understanding of the biochemical/biophysical processes of photosynthesis to inform new technology development and field applications. This year’s theme, “Photosynthesis Across Scales,” reflected the scope of work being done from the individual exciton to the crop scale. This research encompasses applied biology, chemistry, physics, and materials engineering. The aim of this conference is to present new discoveries, techniques, and questions which can be sourced from any of these disciplines and provide an audience which is broadly qualified to use or respond to these developments.

08 HYDROGEN↗

A fresh perspective on the role of band bending, and related contributors, in light-driven production of electricity and chemicals

It is widely known that semiconductor-based solar energy conversion could power our planet. This is in part because high-quality semiconductor structures are unrivalled in their ability to separate photogenerated electrons and holes. One effective approach to achieving this photoinduced charge separation relies on a phenomenon known as “band bending”. But details to justify why band bending results in photoinduced charge separation are more complex than often appreciated. This underappreciation is an impediment to the rational, hypothesis-driven design of next-generation approaches to solar energy conversion. Herein we show, by means of derivations rooted in physical chemistry, that several phenomena – not just band bending – can facilitate photoinduced charge separation, and that each is influenced by nonequilibrium species concentration and a parameter, such as diffusion coefficient or rate coefficient, that introduces dynamics. To help visualize the impact of each phenomenon, we introduce plots that depict their contributions as free energy, force, flux, force constant, and rate. We reveal that spatial dopant distributions that define band bending are predictors of initial photogenerated species transport rates. But charge separation alone does not guarantee high-efficiency operation. A photogenerated change in energy that is freely available to do useful work is also essential, and is strongly dependent on semiconductor optical properties and reaction kinetics. Notably, this information reveals that specificity of interfacial chemical reactions – even when they are not preceded by charge separation elsewhere – can result in efficient solar energy conversion. We expect that this tutorial will guide researchers in their pursuit to uncover new mechanisms for light to perform useful work.

14 SOLAR ENERGY↗

Electric fields imbue enzyme reactivity by aligning active site fragment orbitals

It is broadly recognized that intramolecular electric fields, produced by the protein scaffold and acting on the active site, facilitate enzymatic catalysis. This field effect can be described by several theoretical models, each of which is intuitive to varying degrees. In this contribution, we show that a fundamental effect of electric fields is to generate electrostatic potentials that facilitate the energetic alignment of reactant frontier orbitals. We apply this model to demystify the impact of electric fields on high-valent iron–oxo heme proteins: catalases, peroxidases, and peroxygenases/monooxygenases. Specifically, we show that this model easily accounts for the observed field-induced changes to the spin distribution within peroxidase active sites and explains the transition between epoxidation and hydroxylation pathways seen in Cytochrome P450 active site models. Thus, for the intuitive interpretation of the chemical effect of the field, the strategy involves analyzing the response of the orbitals of active site fragments, and their energetic alignment. We note that the energy difference between fragment orbitals involved in charge redistribution acts as a measure for the chemical hardness/softness of the reactive complex. This measure, and its sensitivity to electric fields, offers a single parameter model from which to quantitatively assess the effects of electric fields on reactivity and selectivity. Thus, the model provides an additional perspective to describe electrostatic preorganization and offers ways for its manipulation.

59 BASIC BIOLOGICAL SCIENCES↗

Teaching Nonradiative Transitions with MATLAB and Python

Nonradiative transitions are changes in energy states of atoms, ions, or molecules that do not involve the emission or absorption of photons. Despite their importance in understanding luminescent properties and photochemical reaction mechanisms, nonradiative transitions are rarely given more than a qualitative overview in undergraduate and even graduate physical chemistry curricula. To supplement the coverage of nonradiative transition topics, we provide here a set of active learning exercises to help students develop an intuitive understanding of the factors that determine the rate of nonradiative transitions. Here, we start by outlining the theoretical background through the formulations of the Franck–Condon factor and its relation to the rate of nonradiative transition. We then introduce three teaching modules, with associated MATLAB and Python codes, to explore how (1) the excited state nuclear displacement, (2) the electronic energy gap between excited and ground state and (3) the excited/ground state vibrational mode frequencies affect the magnitude of the Franck–Condon factor and thereby the rate of nonradiative transitions. The wave function overlap plots that accompany all teaching modules provide direct visualization of the effect of input parameters on the magnitude of Franck–Condon overlap integral.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Soft x-ray spectroscopy of ammonium sulfate aerosols at varied pH conditions

Aqueous aerosols are useful model systems for understanding the physical chemistry that takes place in the Earth’s atmosphere, as well as the chemistry of other solar system objects. Ammonium sulfate aerosols are impacted by anthropogenic sources such as farming and shipping and are understood to be important seeds of cloud nucleation in the atmosphere, affecting climate. X-ray photoelectron spectroscopy and near edge x-ray absorption fine structure spectroscopy were used in tandem to probe the surface and bulk properties of aqueous (NH 4 ) 2 SO 4 , respectively. Aerosolized solutions of (NH 4 ) 2 SO 4 , some altered with NaOH to modify pH, were introduced via an aerodynamic lens to a velocity map imaging instrument for detection. The results show that as pH and sodium cation concentration increase, sulfate anion and ammonia become more prevalent at the surface, and the aerosol surface appears to become drier. However, most of the aerosol remains aqueous, with ion concentrations insensitive to the addition of NaOH. Density functional theory calculations were also performed to probe the coordination environment at the aerosol surfaces to understand the underlying phenomena. Finally, the changes seen on the surface of the aerosol underscore the importance of pH in regulating the structure and chemical properties of atmospherically relevant aerosols.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Electrochemical Reaction Engineering: A Lost (and Found) Art

The heart (or, perhaps more appropriately, the stomach) of any chemical manufacturing process is the reactor, where chemical and physical transformations occur under precisely controlled conditions. For non-electrochemical industrial processes, the design, optimization and operation of chemical reactors are extremely well developed, drawing upon the principles of chemistry, physics, calculus and economics. However, electrolytic processes face a dearth of well documented reaction engineering principles and design practices. This tutorial-style poster presentation introduces electrochemistry students and industrial practitioners to the "lost art" of reaction engineering and its organic extensions to electrochemical devices. Electrochemical reactor fundamentals and illustrative design equations are presented alongside a proposed five-step generalizable methodology for electrochemical reactor scale-up. Overall, this contribution seeks to educate electrochemistry researchers on practical means of reducing laboratory technologies to commercial practice.

electrochemistry↗

Molecules Functionalized with Cycling Centers for Quantum Information Science

The ability for a single molecule to produce enough laser-induced fluorescence to control and detect its quantum state is known as optical cycling. This property has been used to great effect in atoms, where the relatively small number of states promotes their ability to repeatedly fluoresce, for applications such as laser cooling, precision measurement, atomic clocks, and quantum information processing. The extension of this capability to molecular species, however, has been difficult, primarily due to their propensity to become vibrationally excited during illumination. This project brought together experts from atomic physics, physical chemistry, and computational quantum chemistry to develop means to create molecules capable of optical cycling. In particular, this program sought to produce an optical cycling center (OCC), a quantum functional group capable of chemical attachment to a wide variety of molecular hosts while retaining (and thereby furnishing to its host) the ability to optically cycle. Following our team’s theoretical identification of promising species, including alkaline-earth phenoxides, we then created these species and in many cases confirmed their optical cycle closure. We now not only know of the existence of a handful of large, molecular species that can be deployed for applications in quantum technologies and measurement, but have improved our knowledge of the molecular mechanisms leading to this discovery, which will enable generalization in the future. The extension of these ideas for informed chemical design of cycling molecules with bespoke properties is now being pursued by multiple groups.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗