College of Chemistry

History of Chemical Engineering (Chemical and Biomolecular Engineering) at the University of California, Berkeley including establishment of department within the College of Chemistry. The department has an unusual history among chemical engineering programs in the United States and also has become one of the most respected departments in that area. Although not unique, only a few chemical engineering programs sit outside of engineering departments in the United States.

History of Chemical Engineering (Chemical and Biomolecular Engineering) at the University of California, Berkeley including establishment of department within the College of Chemistry. The department has an unusual history among chemical engineering programs in the United States and also has become one of the most respected departments in that area. Although not unique, only a few chemical engineering programs sit outside of engineering departments in the United States.

We recently reported the discovery of phenylacetate decarboxylase (PhdB), representing one of only ten glycyl-radical-enzyme reaction types known, and a promising biotechnological tool for first-time biochemical synthesis of toluene from renewable resources. Here, we used experimental and computational data to evaluate the plausibility of three candidate PhdB mechanisms, involving either attack at the phenylacetate methylene carbon or carboxyl group [via H-atom abstraction from COOH or single-electron oxidation of COO^- (Kolbe-type decarboxylation)]. In vitro experimental data included assays with F-labeled phenylacetate, kinetic studies, and tests with site-directed PhdB mutants; computational data involved estimation of reaction energetics using density functional theory (DFT). The DFT results indicated that all three mechanisms are thermodynamically challenging (beyond the range of many known enzymes in terms of endergonicity or activation energy barrier), reflecting the formidable demands on PhdB for catalysis of this reaction. Evidence that PhdB was able to bind α,α-difluorophenylacetate but was unable to catalyze its decarboxylation supported the enzyme's abstraction of a methylene H atom. Diminished activity of H327A and Y691F mutants was consistent with proposed proton donor roles for His327 and Tyr691. Collectively, these and other data most strongly support PhdB attack at the methylene carbon.

Sustainable fertilizer production is a pressing challenge due to a growing human population. The manufacture of synthetic nitrogen fertilizer involves intensive emissions of greenhouse gases. The synthetic nitrogen that ends up in biowaste such as animal waste perturbs the nitrogen cycle through significant nitrogen losses in the form of ammonia volatilization, a major human health and environmental hazard. Low-temperature air-plasma treatment of animal waste holds promise for sustainable fertilizer production on farmlands by enabling nitrogen fixation via ionization, forming nitrogen oxyacids. Although the formation of nitrogen oxyacids in plasma treatment of water is well-established, the extent of nitrogen oxyanion enrichment in animal waste and its downstream effects on acidifying the waste remain elusive because many compounds found in complex biowaste media may interfere with absorbed NO_x species. This work aims to establish that plasma treatment of dairy manure can suppress ammonia loss by volatilization via acidification of animal waste while enriching the waste in total nitrogen due to nitrogen retained in ammonia as well as adding nitrogen oxyacids by reacting NO_x with the aqueous slurry. To this end, air-plasma effluent containing NO_x is bubbled through dairy manure, which is then analyzed for changes in the nitrogen oxyanion content and pH. Increasing the plasma treatment time results in more acidic manure, reduced ammonium content in the downstream acid trap, and increased nitrogen oxyanion content, where the yield of nitrogen oxyanion from absorbed NO_x species is approximately 100%. Increased plasma treatment also led to an increase in the total Kjeldahl nitrogen and the total nitrogen. These results indicate that plasma treatment of animal waste can significantly suppress ammonia pollution from animal husbandry facilities such as dairy farms while upcycling animal waste as a rich organic source of nitrogen.

In this work we present a detailed analysis of variational quantum phase estimation (VQPE), a method based on real-time evolution for ground and excited state estimation on near-term hardware. We derive the theoretical ground on which the approach stands, and demonstrate that it provides one of the most compact variational expansions to date for solving strongly correlated Hamiltonians. At the center of VQPE lies a set of equations, with a simple geometrical interpretation, which provides conditions for the time evolution grid in order to decouple eigenstates out of the set of time evolved expansion states, and connects the method to the classical filter diagonalization algorithm. Further, we introduce what we call the unitary formulation of VQPE, in which the number of matrix elements that need to be measured scales linearly with the number of expansion states, and we provide an analysis of the effects of noise which substantially improves previous considerations. The unitary formulation allows for a direct comparison to iterative phase estimation. Our results mark VQPE as both a natural and highly efficient quantum algorithm for ground and excited state calculations of general many-body systems. We demonstrate a hardware implementation of VQPE for the transverse field Ising model. Further, we illustrate its power on a paradigmatic example of strong correlation (Cr2 in the SVP basis set), and show that it is possible to reach chemical accuracy with as few as ~50 timesteps.

Carvone is a sustainable and readily available starting material for organic synthesis. Herein, we present the syntheses of various natural product scaffolds that rely on a novel benzannulation involving the α-methyl group (C-10) of carvone to afford a versatile tetralin. The utility of our synthetic approach is highlighted by its application to a short synthesis of the ent-3,4-seco-atisane diterpenoid (-)-crotogoudin. The 13-step enantiospecific synthesis features a regioselective double oxidative dearomatization, a Diels-Alder cycloaddition with ethylene gas (to construct the bicyclo[2.2.2]octane framework), and a final acid-mediated lactonization. The versatility of this benzannulation strategy is demonstrated by its utility in the preparation of the carbon skeleton of ent-3,4-seco-abietane diterpenoids using an intramolecular oxidative dearomatization.

Oncogenic RAS (H-RAS(V12)) induces premature senescence in primary cells by triggering production of reactive oxygen species (ROS), but the molecular role of ROS in senescence remains elusive. We investigated whether inhibition of protein tyrosine phosphatases by ROS contributed to H-RAS(V12)-induced senescence. We identified protein tyrosine phosphatase 1B (PTP1B) as a major target of H-RAS(V12)-induced ROS. Inactivation of PTP1B was necessary and sufficient to induce premature senescence in H-RAS(V12)-expressing IMR90 fibroblasts. We identified phospho-Tyr 393 of argonaute 2 (AGO2) as a direct substrate of PTP1B. Phosphorylation of AGO2 at Tyr 393 inhibited loading with microRNAs (miRNAs) and thus miRNA-mediated gene silencing, which counteracted the function of H-RAS(V12)-induced oncogenic miRNAs. Overall, our data illustrate that premature senescence in H-RAS(V12)-transformed primary cells is a consequence of oxidative inactivation of PTP1B and inhibition of miRNA-mediated gene silencing.