Copper-Catalyzed Decarboxylative Trifluoromethylation of Allylic Bromodifluoroacetates

The development of new synthetic fluorination reactions has important implications in medicinal, agricultural and materials chemistries. Given the prevalence and accessibility of alcohols, methods to convert alcohols to trifluoromethanes are desirable. However, this transformation typically requires four-step processes, specialty chemicals, and/or stoichiometric metals to access the trifluoromethyl-containing product. A two-step copper-catalyzed decarboxylative protocol for converting allylic alcohols to trifluoromethanes is reported. Preliminary mechanistic studies distinguish this reaction from previously reported Cu-mediated reactions

Copper-Catalyzed Decarboxylative Trifluoromethylation of Propargyl Bromodifluoroacetates

The development of efficient methods for accessing fluorinated functional groups is desirable. Herein, we report a two-step method that utilizes catalytic Cu for the decarboxylative trifluoromethylation of propargyl bromodifluoroacetates. This protocol affords a mixture of propargyl trifluoromethanes and trifluoromethyl allenes

Recent advances in copper- and palladium-catalyzed carbon-heteroatom and carbon-carbon bond-formation

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 2008.Vita.Includes bibliographical references.Metal-catalyzed nucleophilic substitution reactions of aryl halides have become one of the most valuable and useful classes of reactions developed in the last 30 years. Foremost among these processes are the classes of palladium- and copper-catalyzed reactions, which employ heteroatom-based nucleophiles. Herein, newly designed catalyst systems are presented for the palladium- and/or copper-catalyzed nucleophilic substitution reactions of aryl halides with a variety of nucleophiles, including (benz)imidazoles, oxindoles, 2-, 3- and 4-hydroxypyridines, anilines, and aliphatic, benzylic, allylic and propargylic alcohols. In many cases, catalyst optimization and ligand structure are discussed and evaluated. Where applicable, the palladiumand copper-based catalyst systems are contrasted to demonstrate the complementary relationships between the employment of these two metals. Chapter One Chapter Two Chapter Three Chapter Four Chapter Five. Palladium- and Copper-catalyzed Reactions of Imidazoles and Benzimidazoles with Aryl Halides. Orthogonal Selectivity in Copper- and Palladium-catalyzed Reactions of Aryl Halides with Oxindoles. Copper-catalyzed Reactions of Hydroxypyridines and Related Compounds with Aryl Halides. Pyrrole-2-carboxylic Acid as a Ligand for the Copper-catalyzed Reactions of Primary Anilines with Aryl Halides. An Improved Copper-based Catalyst System for the Reactions of Aryl Halides with Aliphatic Alcohols.y Ryan A. Altman.Ph.D

Fluorination Enables a Ligand-Controlled Regiodivergent Palladium-Catalyzed Decarboxylative Allylation Reaction to Access α,α-Difluoroketones

This is the peer reviewed version of the following article: Yang, M., Orsi, D. L., & Altman, R. A. (2015). Fluorination Enables a Ligand-Controlled Regiodivergent Palladium-Catalyzed Decarboxylative Allylation Reaction to Access α,α-Difluoroketones. Angewandte Chemie (International Ed. in English), 54(8), 2361–2365. http://doi.org/10.1002/anie.201410039, which has been published in final form at doi.org/10.1002/anie.201410039. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-Archiving.α,α-Difluoroketones possess unique physicochemical properties that are useful for developing therapeutics and probes for chemical biology. In order to access the α-allyl-α,α-difluoroketone substructure, complementary Pd-catalyzed decarboxylative allylation reactions were developed to provide linear and branched α-allyl-α,α-difluoroketones. For these orthogonal processes, the regioselectivity was uniquely controlled by fluorination of the substrate and the structure of ligand

Agreement between methods of measurement with multiple observations per individual

Limits of agreement provide a straightforward and intuitive approach to agreement between different methods for measuring the same quantity. When pairs of observations using the two methods are independent, i.e., on different subjects, the calculations are very simple and straightforward. Some authors collect repeated data, either as repeated pairs of measurements on the same subject, whose true value of the measured quantity may be changing, or more than one measurement by one or both methods of an unchanging underlying quantity. In this paper we describe methods for analysing such clustered observations, both when the underlying quantity is assumed to be changing and when it is not

Decarboxylative Fluorination Strategies for Accessing Medicinally-relevant Products

Fluorinated organic compounds have a long history in medicinal chemistry, and synthetic methods to access target fluorinated compounds are undergoing a revolution. One powerful strategy for the installation of fluorine-containing functional groups includes decarboxylative reactions. Benefits of decarboxylative approaches potentially include: 1) readily available substrates or reagents 2) mild reaction conditions; 3) simplified purification. This focus review highlights the applications of decarboxylation strategies for fluorination reactions to access compounds with biomedical potential. The manuscript highlights on two general strategies, fluorination by decarboxylative reagents and by decarboxylation of substrates. Where relevant, examples of medicinally useful compounds that can be accessed using these strategies are highlighted

Safety of the Deferral of Coronary Revascularization on the Basis of Instantaneous Wave-Free Ratio and Fractional Flow Reserve Measurements in Stable Coronary Artery Disease and Acute Coronary Syndromes.

OBJECTIVES: The aim of this study was to investigate the clinical outcomes of patients deferred from coronary revascularization on the basis of instantaneous wave-free ratio (iFR) or fractional flow reserve (FFR) measurements in stable angina pectoris (SAP) and acute coronary syndromes (ACS). BACKGROUND: Assessment of coronary stenosis severity with pressure guidewires is recommended to determine the need for myocardial revascularization. METHODS: The safety of deferral of coronary revascularization in the pooled per-protocol population (n = 4,486) of the DEFINE-FLAIR (Functional Lesion Assessment of Intermediate Stenosis to Guide Revascularisation) and iFR-SWEDEHEART (Instantaneous Wave-Free Ratio Versus Fractional Flow Reserve in Patients With Stable Angina Pectoris or Acute Coronary Syndrome) randomized clinical trials was investigated. Patients were stratified according to revascularization decision making on the basis of iFR or FFR and to clinical presentation (SAP or ACS). The primary endpoint was major adverse cardiac events (MACE), defined as the composite of all-cause death, nonfatal myocardial infarction, or unplanned revascularization at 1 year. RESULTS: Coronary revascularization was deferred in 2,130 patients. Deferral was performed in 1,117 patients (50%) in the iFR group and 1,013 patients (45%) in the FFR group (p < 0.01). At 1 year, the MACE rate in the deferred population was similar between the iFR and FFR groups (4.12% vs. 4.05%; fully adjusted hazard ratio: 1.13; 95% confidence interval: 0.72 to 1.79; p = 0.60). A clinical presentation with ACS was associated with a higher MACE rate compared with SAP in deferred patients (5.91% vs. 3.64% in ACS and SAP, respectively; fully adjusted hazard ratio: 0.61 in favor of SAP; 95% confidence interval: 0.38 to 0.99; p = 0.04). CONCLUSIONS: Overall, deferral of revascularization is equally safe with both iFR and FFR, with a low MACE rate of about 4%. Lesions were more frequently deferred when iFR was used to assess physiological significance. In deferred patients presenting with ACS, the event rate was significantly increased compared with SAP at 1 year.info:eu-repo/semantics/publishedVersio

Reporting of loss to follow-up information in randomised controlled trials with time-to-event outcomes: a literature survey

<p>Abstract</p> <p>Background</p> <p>To assess the reporting of loss to follow-up (LTFU) information in articles on randomised controlled trials (RCTs) with time-to-event outcomes, and to assess whether discrepancies affect the validity of study results.</p> <p>Methods</p> <p>Literature survey of all issues of the BMJ, Lancet, JAMA, and New England Journal of Medicine published between 2003 and 2005. Eligible articles were reports of RCTs including at least one Kaplan-Meier plot. Articles were classified as "assessable" if sufficient information was available to assess LTFU. In these articles, LTFU information was derived from Kaplan-Meier plots, extracted from the text, and compared. Articles were then classified as "consistent" or "not consistent". Sensitivity analyses were performed to assess the validity of study results.</p> <p>Results</p> <p>319 eligible articles were identified. 187 (59%) were classified as "assessable", as they included sufficient information for evaluation; 140 of 319 (44%) presented consistent LTFU information between the Kaplan-Meier plot and text. 47 of 319 (15%) were classified as "not consistent". These 47 articles were included in sensitivity analyses. When various imputation methods were used, the results of a chi²-test applied to the corresponding 2 × 2 table changed and hence were not robust in about half of the studies.</p> <p>Conclusions</p> <p>Less than half of the articles on RCTs using Kaplan-Meier plots provide assessable and consistent LTFU information, thus questioning the validity of the results and conclusions of many studies presenting survival analyses. Authors should improve the presentation of both Kaplan-Meier plots and LTFU information, and reviewers of study publications and journal editors should critically appraise the validity of the information provided.</p

Stepwise O atom Transfer in Heme-Based Tryptophan Dioxygenase: Role of Substrate Ammonium in Epoxide Ring Opening

This document is the Accepted Manuscript version of a Published Work that appeared in final form in Journal of the American Chemical Society, copyright © American Chemical Society after peer review and technical editing by the publisher. To access the final edited and published work see http://doi.org/10.1021/jacs.8b00262.Heme-based tryptophan dioxygenases are established immunosuppressive metalloproteins with significant biomedical interest. Here, we synthesized two mechanistic probes to specifically test if the α-amino group of the substrate directly participates in a critical step of the O atom transfer during catalysis in human tryptophan 2,3-dioxygenase (TDO). Substitution of the nitrogen atom of the substrate to a carbon (probe 1) or oxygen (probe 2) slowed the catalytic step following the first O atom transfer such that transferring the second O atom becomes less likely to occur, although the dioxygenated products were observed with both probes. A monooxygenated product was also produced from probe 2 in a significant quantity. Analysis of this new product by HPLC coupled UV–vis spectroscopy, high-resolution mass spectrometry, 1H NMR, 13C NMR, HSQC, HMBC, and infrared (IR) spectroscopies concluded that this monooxygenated product is a furoindoline compound derived from an unstable epoxyindole intermediate. These results prove that small molecules can manipulate the stepwise O atom transfer reaction of TDO and provide a showcase for a tunable mechanism by synthetic compounds. The product analysis results corroborate the presence of a substrate-based epoxyindole intermediate during catalysis and provide the first substantial experimental evidence for the involvement of the substrate α-amino group in the epoxide ring-opening step during catalysis. This combined synthetic, biochemical, and biophysical study establishes the catalytic role of the α-amino group of the substrate during the O atom transfer reactions and thus represents a substantial advance to the mechanistic comprehension of the heme-based tryptophan dioxygenases

Normalized Affymetrix expression data are biased by G-quadruplex formation

Probes with runs of four or more guanines (G-stacks) in their sequences can exhibit a level of hybridization that is unrelated to the expression levels of the mRNA that they are intended to measure. This is most likely caused by the formation of G-quadruplexes, where inter-probe guanines form Hoogsteen hydrogen bonds, which probes with G-stacks are capable of forming. We demonstrate that for a specific microarray data set using the Human HG-U133A Affymetrix GeneChip and RMA normalization there is significant bias in the expression levels, the fold change and the correlations between expression levels. These effects grow more pronounced as the number of G-stack probes in a probe set increases. Approximately 14 of the probe sets are directly affected. The analysis was repeated for a number of other normalization pipelines and two, FARMS and PLIER, minimized the bias to some extent. We estimate that ∼15 of the data sets deposited in the GEO database are susceptible to the effect. The inclusion of G-stack probes in the affected data sets can bias key parameters used in the selection and clustering of genes. The elimination of these probes from any analysis in such affected data sets outweighs the increase of noise in the signal. © 2011 The Author(s)