College of Chemistry

Attosecond science requires a substantial rethinking of how to make measurements on very short timescales; how to acquire the necessary equipment, technology, and personnel; and how to build a set of laboratories for such experiments. This entails a rejuvenation of the author in many respects, in the laboratory itself, with regard to students and postdocs, and in generating funding for research. It also brings up questions of what it means to do attosecond science, and the discovery of the power of X-ray spectroscopy itself, which complements the short timescales addressed. The lessons learned, expressed in the meanderings of this autobiographical article, may be of benefit to others who try to reinvent themselves. Expected final online publication date for the Annual Review of Physical Chemistry, Volume 75 is April 2024. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

The L_2,3-edge X-ray absorption spectra of late transition metals such as Cu, Ag, and Au exhibit absorption onsets lower in energy for higher oxidation states, which is at odds with the measured spectra of earlier transition metals. Time-dependent density functional theory calculations for Cu²⁺/Cu⁺ reveal a larger 2p core-exciton binding energy for Cu²⁺, overshadowing shifts in single-particle excitation energies with respect to Cu⁺. We explore this phenomenon in a Cu⁺ metal-organic framework with ∼12% Cu²⁺ defects and find that corrections with self-consistent excited-state total energy differences provide accurate XAS peak alignment.

Methods to access chiral sulfur(VI) pharmacophores are of interest in medicinal and synthetic chemistry. We report the desymmetrization of unprotected sulfonimidamides via asymmetric acylation with a cinchona-phosphinate catalyst. The desired products are formed in excellent yield and enantioselectivity with no observed bis-acylation. A data-science-driven approach to substrate scope evaluation was coupled to high throughput experimentation (HTE) to facilitate statistical modeling in order to inform mechanistic studies. Reaction kinetics, catalyst structural studies, and density functional theory (DFT) transition state analysis elucidated the turnover-limiting step to be the collapse of the tetrahedral intermediate and provided key insights into the catalyst-substrate structure-activity relationships responsible for the origin of the enantioselectivity. This study offers a reliable method for accessing enantioenriched sulfonimidamides to propel their application as pharmacophores and serves as an example of the mechanistic insight that can be gleaned from integrating data science and traditional physical organic techniques.

The electrified aqueous/metal interface is critical in controlling the performance of energy conversion and storage devices, but an atomistic understanding of even basic interfacial electrochemical reactions challenges both experiment and computation. We report a combined simulation and experimental study of (reversible) ion-transfer reactions involved in anodic Ag corrosion/deposition, a model system for interfacial electrochemical processes generating or consuming ions. With the explicit modeling of the electrode potential and a hybrid implicit-explicit solvation model, the density functional theory calculations produce free energy curves predicting thermodynamics, kinetics, partial charge profiles, and reaction trajectories. The calculated (equilibrium) free energy barriers (0.2 eV), and their asymmetries, agree with experimental activation energies (0.4 eV) and transfer coefficients, which were extracted from temperature-dependent voltage-step experiments on Au-supported, Ag-nanocluster substrates. The use of Ag nanoclusters eliminates the convolution of the kinetics of Ag+(aq.) generation and transfer with those of nucleation or etch-pit formation. The results indicate that the barrier is controlled by the bias-dependent competition between partial solvation of the incipient ion, metal-metal bonding, and electrostatic stabilization by image charge, with the latter two factors weakened by stronger positive biases. We also report simulations of the bias-dependence of defect generation relevant to nucleating corrosion by removing an atom from a perfect Ag(100) surface, which is predicted to occur via a vacancy-adatom intermediate. Together, these experiments and calculations provide the first validated, accurate, molecular model of the central steps that govern the rates of important dissolution/deposition reactions broadly relevant across the energy sciences.

Variable temperature electrospray mass spectrometry is useful for multiplexed measurements of the thermal stabilities of biomolecules, but the ionization process can be disrupted by aggregation-prone proteins/complexes that have irreversible unfolding transitions. Resistively heating solutions containing a mixture of bovine carbonic anhydrase II (BCAII), a CO₂ fixing enzyme involved in many biochemical pathways, and cytochrome c leads to complete loss of carbonic anhydrase signal and a significant reduction in cytochrome c signal above ∼72 °C due to aggregation. In contrast, when the tips of borosilicate glass nanoelectrospray emitters are heated with a laser, complete thermal denaturation curves for both proteins are obtained in <1 minute. The simultaneous measurements of the melting temperature of BCAII and BCAII bound to bicarbonate reveal that the bicarbonate stabilizes the folded form of this protein by ∼6.4 °C. Moreover, the temperature dependences of different bicarbonate loss pathways are obtained. Although protein analytes are directly heated by the laser for only 140 ms, heat conduction further up the emitter leads to a total analyte heating time of ∼41 s. Pulsed laser heating experiments could reduce this time to ∼0.5 s for protein aggregation that occurs on a faster time scale. Laser heating provides a powerful method for studying the detailed mechanisms of cofactor/ligand loss with increasing temperature and promises a new tool for studying the effect of ligands, drugs, growth conditions, buffer additives, or other treatments on the stabilities of aggregation-prone biomolecules.

Interactions among proteins and peptides are essential for many biological activities including the tailoring of peptide substrates to produce natural products. The first step in the production of the bacterial redox cofactor pyrroloquinoline quinone (PQQ) from its peptide precursor is catalyzed by a radical SAM (rSAM) enzyme, PqqE. We describe the use of hydrogen-deuterium exchange mass spectrometry (HDX-MS) to characterize the structure and conformational dynamics in the protein-protein and protein-peptide complexes necessary for PqqE function. HDX-MS-identified hotspots can be discerned in binary and ternary complex structures composed of the peptide PqqA, the peptide-binding chaperone PqqD, and PqqE. Structural conclusions are supported by size-exclusion chromatography coupled to small-angle X-ray scattering (SEC-SAXS). HDX-MS further identifies reciprocal changes upon the binding of substrate peptide and S-adenosylmethionine (SAM) to the PqqE/PqqD complex: long-range conformational alterations have been detected upon the formation of a quaternary complex composed of PqqA/PqqD/PqqE and SAM, spanning nearly 40 Å, from the PqqA binding site in PqqD to the PqqE active site Fe₄S₄. Interactions among the various regions are concluded to arise from both direct contact and distal communication. The described experimental approach can be readily applied to the investigation of protein conformational communication among a large family of peptide-modifying rSAM enzymes.

Reaction of the ruthenium carbene complex Cp*(IPr)RuCl (1) (IPr = 1,3-bis(Dipp)imidazol-2-ylidene; Dipp = 2,6-diisopropylphenyl) with sodium phosphaethynolate (NaOCP) led to intramolecular dearomatization of one of the Dipp substituents on the Ru-bound carbene to afford a Ru-bound phosphanorcaradiene, 2. Computations by DFT reveal a transition state characterized by a concerted process whereby CO migrates to the Ru center as the P atom adds to the π system of the aryl group. The phosphanorcaradiene possesses ambiphilic properties and reacts with both nucleophilic and electrophilic substrates, resulting in rearomatization of the ligand aryl group with net P atom transfer to give several unusual metal-bound, P-containing main-group moieties. These new complexes include a metallo-1-phospha-3-azaallene (Ru─P═C═NR), a metalloiminophosphanide (Ru─P═N─R), and a metallophosphaformazan (Ru─P(═N─N═CPh2)2). Reaction of 2 with the carbene 2,3,4,5-tetramethylimidazol-2-ylidene (IMe4) produced the corresponding phosphaalkene DippP═IMe4.

The ribosome is a ribonucleoprotein complex found in all domains of life. Its role is to catalyze protein synthesis, the messenger RNA (mRNA)-templated formation of amide bonds between α-amino acid monomers. Amide bond formation occurs within a highly conserved region of the large ribosomal subunit known as the peptidyl transferase center (PTC). Here we describe the step-wise design and characterization of mini-PTC 1.1, a 284-nucleotide RNA that recapitulates many essential features of the Escherichia coli PTC. Mini-PTC 1.1 folds into a PTC-like structure under physiological conditions, even in the absence of r-proteins, and engages small molecule analogs of A- and P-site tRNAs. The sequence of mini-PTC 1.1 differs from the wild type E. coli ribosome at 12 nucleotides that were installed by a cohort of citizen scientists using the on-line video game Eterna. These base changes improve both the secondary structure and tertiary folding of mini-PTC 1.1 as well as its ability to bind small molecule substrate analogs. Here, the combined input from Eterna citizen-scientists and RNA structural analysis provides a robust workflow for the design of a minimal PTC that recapitulates many features of an intact ribosome.

High or enriched-purity O₂ is used in numerous industries and is predominantly produced from the cryogenic distillation of air, an extremely capital- and energy-intensive process. There is significant interest in the development of new approaches for O₂-selective air separations, including the use of metal-organic frameworks featuring coordinatively unsaturated metal sites that can selectively bind O₂ over N₂ via electron transfer. However, most of these materials exhibit appreciable and/or reversible O₂ uptake only at low temperatures, and their open metal sites are also potential strong binding sites for the water present in air. Here, we study the framework Cu^I-MFU-4l (Cu_xZn_5-xCl_4-x(btdd)₃; H₂btdd = bis(1H-1,2,3-triazolo[4,5-b],[4',5'-i])dibenzo[1,4]dioxin), which binds O₂ reversibly at ambient temperature. We develop an optimized synthesis for the material to access a high density of trigonal pyramidal Cu^I sites, and we show that this material reversibly captures O₂ from air at 25 °C, even in the presence of water. When exposed to air up to 100% relative humidity, Cu^I-MFU-4l retains a constant O₂ capacity over the course of repeated cycling under dynamic breakthrough conditions. While this material simultaneously adsorbs N₂, differences in O₂ and N₂ desorption kinetics allow for the isolation of high-purity O₂ (>99%) under relatively mild regeneration conditions. Spectroscopic, magnetic, and computational analyses reveal that O₂ binds to the copper(I) sites to form copper(II)-superoxide moieties that exhibit temperature-dependent side-on and end-on binding modes. Overall, these results suggest that Cu^I-MFU-4l is a promising material for the separation of O₂ from ambient air, even without dehumidification.

Self-assembly of colloidal nanocrystals (NCs) into superlattices (SLs) is an appealing strategy to design hierarchically organized materials with promising functionalities. Mechanistic studies are still needed to uncover the design principles for SL self-assembly, but such studies have been difficult to perform due to the fast time and short length scales of NC systems. To address this challenge, we developed an apparatus to directly measure the evolving phases in situ and in real time of an electrostatically stabilized Au NC solution before, during, and after it is quenched to form SLs using small-angle X-ray scattering. By developing a quantitative model, we fit the time-dependent scattering patterns to obtain the phase diagram of the system and the kinetics of the colloidal and SL phases as a function of varying quench conditions. The extracted phase diagram is consistent with particles whose interactions are short in range relative to their diameter. We find the degree of SL order is primarily determined by fast (subsecond) initial nucleation and growth kinetics, while coarsening at later times depends nonmonotonically on the driving force for self-assembly. We validate these results by direct comparison with simulations and use them to suggest dynamic design principles to optimize the crystallinity within a finite time window. The combination of this measurement methodology, quantitative analysis, and simulation should be generalizable to elucidate and better control the microscopic self-assembly pathways of a wide range of bottom-up assembled systems and architectures.