The time scale of recombination rate evolution in great apes

We present three linkage-disequilibrium (LD)-based recombination maps generated using whole-genome sequence data from 10 Nigerian chimpanzees, 13 bonobos, and 15 western gorillas, collected as part of the Great Ape Genome Project (Prado-Martinez J, et al. 2013. Great ape genetic diversity and population history. Nature 499:471-475). We also identified species-specific recombination hotspots in each group using a modified LDhot framework, which greatly improves statistical power to detect hotspots at varying strengths. We show that fewer hotspots are shared among chimpanzee subspecies than within human populations, further narrowing the time scale of complete hotspot turnover. Further, using species-specific PRDM9 sequences to predict potential binding sites (PBS), we show higher predicted PRDM9 binding in recombination hotspots as compared to matched cold spot regions in multiple great ape species, including at least one chimpanzee subspecies. We found that correlations between broad-scale recombination rates decline more rapidly than nucleotide divergence between species. We also compared the skew of recombination rates at centromeres and telomeres between species and show a skew from chromosome means extending as far as 10-15Mb from chromosome ends. Further, we examined broad-scale recombination rate changes near a translocation in gorillas and found minimal differences as compared to other great ape species perhaps because the coordinates relative to the chromosome ends were unaffected. Finally, on the basis of multiple linear regression analysis, we found that various correlates of recombination rate persist throughout the African great apes including repeats, diversity, and divergence. Our study is the first to analyze within- And between-species genome-wide recombination rate variation in several close relatives

Assessing Ryanodine Receptor Inhibition and Antioxidant Ability of Carvedilol and its Abilities

The antioxidant ability of the commonly prescribed antiarrhythmic medication carvedilol was assessed using two distinct assays. The first assay monitored the depletion of the stable radical DPPH via hydrogen atom abstraction utilizing UV-VIS spectrophotometry. The second assay involved monitoring the inhibition of a radical chain reaction initiated by UV light. Three metabolites of carvedilol were synthesized and assessed in each assay along with carvedilol and several benchmark antioxidants to ensure assay validity. It was determined that carvedilol possessed negligible antioxidant ability in both assays, while the metabolites possessed moderate-high antioxidant strength. It is therefore concluded that the antioxidant ability of carvedilol originates from the phenolic metabolites and not from carvedilol itself. The primary function of carvedilol to regulate calcium handling in cardiac myocytes was also assessed for each metabolite using a mutant embryonic cell line. It was determined that metabolic deactivation via hydroxylation pathways is minimal

Leveraging automation to elucidate reaction mechanisms

Understanding chemical processes facilitates reaction optimization to make synthetic procedures more efficient while also enabling reaction discovery. Temporal profiling of chemical reactions provides the gold standard for increasing mechanistic understanding. Unfortunately, obtaining time-course information reproducibly, accurately, and also minimizing analyst intervention is a significant challenge. Combining in situ spectroscopic methods with automated sampling techniques provides a robust method to generate kinetic profiles enabling increased mechanistic understanding. This thesis explores the development and application of online HPLC as an analytical technique to obtain concentration data while minimizing workload for the analyst. By utilizing commercially available laboratory equipment and software we have created a sampling device capable of automatically monitoring both homogeneous and heterogeneous reactions, as well as those performed under an inert atmosphere. The ability of the platform to sample, dilute, mix, and analyze reaction aliquots reproducibly has been validated, thereby ensuring accuracy of acquired time-course data. This automated reaction monitoring device has been used to delineate reaction mechanisms for a series of chemically distinct transformations. The Kinugasa reaction for the synthesis of beta-lactams was investigated. A novel retrocycloaddition step accounts mechanistically for byproducts associated with the transformation. A telescoped synthesis yielding cyanoimidazoles via combining an imidazole forming condensation annulation with a functional group conversion was also investigated. A series of Buchwald-Hartwig aminations performed within a glovebox using various aryl halide components were explored. Lastly, the mechanism of a synthetic procedure to synthesize Spiro-OMeTAD, a state-of-the-art organic material used in modern solar cells, was probed. By leveraging automated reaction monitoring devices, mechanistic understanding for each transformation was increased, ultimately making these transformations more efficient.Science, Faculty ofChemistry, Department ofGraduat

Online HPLC Analysis of Buchwald-Hartwig Aminations from Within an Inert Environment

We have developed a reaction monitoring platform capable of automated sampling and online HPLC analysis to generate temporal profiles for reactions performed from within a glovebox. The device allows for facile reaction progress analysis to aid in mechanistic studies of air-sensitive chemical transformations. The platform has demonstrated high reproducibility regarding sample mixing, dilution, delivery, and analysis. We employed the sampling platform to acquire temporal profiles for a series of Buchwald-Hartwig aminations. Parallel coupling reactions using iodobenzene and bromobenzene both exhibit complex kinetics. A competition reaction including both aryl halides demonstrated high selectivity for iodobenzene indicative of catalyst monopoly. The temporal profile for the difunctionalized substrate 1,4-iodobromobenzene was unexpected based a priori and is indicative of a distinct underlying mechanism. We attribute this unanticipated reactivity to intramolecular catalysts transfer through the π system as seen in “living” polymerization transfer catalyst systems. This automated sampling platform has greatly increased mechanistic understanding by performing only a small subset of experiments

A Revised Mechanism for the Kinugasa Reaction

Detailed kinetic analysis for the Cu­(I)-catalyzed Kinugasa reaction forming β-lactams has revealed an anomalous overall zero-order reaction profile, due to opposing positive and negative orders in nitrone and alkyne, respectively. Furthermore, the reaction displays a second-order dependence on the catalyst, confirming the critical involvement of a postulated bis-Cu complex. Finally, reaction progress analysis of multiple byproducts has allowed a new mechanism, involving a common ketene intermediate to be delineated. Our results demonstrate that β-lactam synthesis through the Kinugasa reaction proceeds via a cascade involving (3 + 2) cycloaddition, (3 + 2) cycloreversion, and finally (2 + 2) cycloaddition. Our new mechanistic understanding has resulted in optimized reaction conditions to dramatically improve the yield of the target β-lactams and provides the first consistent mechanistic model to account for the formation of all common byproducts of the Kinugasa reaction

Enantioselective Sulfonimidamide Acylation via a Cinchona Alkaloid-Catalyzed Desymmetrization: Scope, Data Science, and Mechanistic Investigation.

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