Predicting polycyclic aromatic hydrocarbon formation with an automatically generated mechanism for acetylene pyrolysis

Using Reaction Mechanism Generator (RMG), we have automatically constructed a detailed mechanism for acetylene pyrolysis, which predicts formation of polycyclic aromatic hydrocarbons (PAHs) up to pyrene. To improve the data available for formation pathways from naphthalene to pyrene, new high‐pressure limit reaction rate coefficients and species thermochemistry were calculated using a combination of electronic structure data from the literature and new quantum calculations. Pressure‐dependent kinetics for the CH potential energy surface calculated by Zádor et al. were incorporated to ensure accurate pathways for acetylene initiation reactions. After adding these new data into the RMG database, a pressure‐dependent mechanism was generated in a single RMG simulation which captures chemistry from C to C. In general, the RMG‐generated model accurately predicts major species profiles in comparison to plug‐flow reactor data from the literature. The primary shortcoming of the model is that formation of anthracene, phenanthrene, and pyrene are underpredicted, and PAHs beyond pyrene are not captured. Reaction path analysis was performed for the RMG model to identify key pathways. Notable conclusions include the importance of accounting for the acetone impurity in acetylene in accurately predicting formation of odd‐carbon species, the remarkably low contribution of acetylene dimerization to vinylacetylene or diacetylene, and the dominance of the hydrogen abstraction CH addition (HACA) mechanism in the formation pathways to all PAH species in the model. This work demonstrates the improved ability of RMG to model PAH formation, while highlighting the need for more kinetics data for elementary reaction pathways to larger PAHs.     

Does Perdeuteration Increase the Polarity of Janus Face Cycloalkanes?

Stimulated by a suggestion of the late Professor Jack D. Dunitz, that perdeuterated Janus face cycloalkanes may be more polar than their unlabelled forms, the deuterated isotopologue of all cis-1,2,3,4,5,6-hexafluorocyclohexane ([²H₆]- 1a ) and all cis-1,2,3,4-tetrafluorocyclopentane ([²H₆]- 3a ) were prepared. Computation at the B3LYP−D3 level indicated that [²H₆]- 1a is not more polar than its protio form 1, however perdeuterated cyclopentane [²H₆]- 3a may indeed be more polar than 3 , although the magnitude is predicted to be small. None-the-less retention time analysis on a reverse phase GC/MS column of an add-mix of 3 and [²H₆]- 3a gave some indication that the per-deuterated isotopologue 3a was detected marginally before the unlabelled compound consistent with increased polarity associated with perdeuteration.     

SMART: A data reporting standard for mass spectrometry imaging By Ying Xi,Alexandria L. Sohn,Alena N. Joignant,Stephanie M. Cologna,Boone M. Prentice and David C. Muddiman

Mass spectrometry imaging (MSI) is an important analytical technique that simultaneously reports the spatial location and abundance of detected ions in biological, chemical, clinical, and pharmaceutical studies. As MSI grows in popularity, it has become evident that data reporting varies among different research groups and between techniques. The lack of consistency in data reporting inherently creates additional challenges in comparing intra- and inter-laboratory MSI data. In this tutorial, we propose a unified data reporting system, SMART, based on the common features shared between techniques. While there are limitations to any reporting system, SMART was decided upon after significant discussion to more easily understand and benchmark MSI data. SMART is not intended to be comprehensive but rather capture essential baseline information for a given MSI study; this could be within a study (e.g., effect of spot size on the measured ion signals) or between two studies (e.g., different MSI platform technologies applied to the same tissue type). This tutorial does not attempt to address the confidence with which annotations are made nor does it deny the importance of other parameters that are not included in the current SMART format. Ultimately, the goal of this tutorial is to discuss the necessity of establishing a uniform reporting system to communicate MSI data in publications and presentations in a simple format to readily interpret the parameters and baseline outcomes of the data.     

Steric,Electronic and Conformational Synergistic Effects in the Gold(I)-catalyzed α-C−H Bond Functionalization of Tertiary Amines**

Direct C−H bond functionalization is a useful strategy for the straightforward formation of C−C and C−Heteroatom bonds. In the present work, a unique approach for the challenging electrophilic Au-catalyzed α-C−H bond functionalization of tertiary amines is presented. Electronic, steric and conformational synergistic effects exerted by the use of a malonate unit in the substrate were key to the success of this transformation. This new reactivity was applied to the synthesis of tetrahydro-γ-carboline products which, under oxidative conditions, could be converted into valuable structural motifs found in bioactive alkaloid natural products.     

Salt Metathesis: Tetrafluoroborate Anion Rapidly Fluoridates Organoboronic Acids to give Organotrifluoroborates

Tetrafluoroborate (BF₄⁻) has long been used as a spectator counter anion. Herein, we report an unprecedented salt metathesis between a variety of BF₄⁻ salts and a series of organoboronic acids yielding the corresponding organotrifluoroborates. We identified conditions for fast and efficient fluoridation (<1 h) with minimal workup. Fundamentally, this work discloses the proclivity of BF₄⁻ to exchange fluoride atoms with organoboronates, highlighting the lability of BF₄⁻.     

Influence of Potassium Metal-Support Interactions on Dendrite Growth

Combined synchrotron X-ray nanotomography imaging, cryogenic electron microscopy (cryo-EM) and modeling elucidate how potassium (K) metal-support energetics influence electrodeposit microstructure. Three model supports are employed: O-functionalized carbon cloth (potassiophilic, fully-wetted), non-functionalized cloth and Cu foil (potassiophobic, nonwetted). Nanotomography and focused ion beam (cryo-FIB) cross-sections yield complementary three-dimensional (3D) maps of cycled electrodeposits. Electrodeposit on potassiophobic support is a triphasic sponge, with fibrous dendrites covered by solid electrolyte interphase (SEI) and interspersed with nanopores (sub-10 nm to 100 nm scale). Lage cracks and voids are also a key feature. On potassiophilic support, the deposit is dense and pore-free, with uniform surface and SEI morphology. Mesoscale modeling captures the critical role of substrate-metal interaction on K metal film nucleation and growth, as well as the associated stress state.     

Real-time Imaging of Nascent DNA in Live Cells by Monitoring the Fluorescence Lifetime of DNA-Incorporated Thiazole Orange-Modified Nucleotides

A modified 2′-deoxycytidine triphosphate derivative ( dC^TOTP ) bearing a thiazole orange moiety tethered via an oligoethylene glycol linker was designed and synthesized. The nucleotide was incorporated into DNA by DNA polymerases in vitro as well as in live cells. Upon incorporation of dC^TOTP into DNA, the thiazole orange moiety exhibited a fluorescence lifetime that differed significantly from the non-incorporated (i.e. free and non-covalently intercalated) forms of dC^TOTP . When dC^TOTP was delivered into live U-2 OS cells using a synthetic nucleoside triphosphate transporter, it allowed us to distinguish and monitor cells that were actively synthesizing DNA in real time, from the very first moments after the treatment. We anticipate that this probe could be used to study chromatin organization and dynamics.     

On the Extreme Oxidation States of Iridium

It has recently been suggested that the oxidation states of Ir run from the putative ?III in the synthesized solid Na₃[Ir(CO)₃] to the well‐documented +IX in the species IrO₄⁺. Furthermore, [Ir(CO)₃]^3? was identified as an 18‐electron species. A closer DFT study now finds support for this picture: The orbitals spanned by the 6s,6p,5d orbitals of the iridium are all occupied. Although some have considerable ligand character, the deviations from 18 e leave the orbital symmetries unchanged. The isoelectronic systems from Os^?IV to Au^?I behave similarly, suggesting further possible species. To paraphrase Richard P. Feynmann “there is plenty of room at the bottom”.     

Cationic Cobalt(III)‐Catalyzed Aryl and Alkenyl CH Amidation: A Mild Protocol for the Modification of Purine Derivatives

A cationic cobalt(III)‐catalyzed direct C?H amidation of unactivated (hetero)arenes and alkenes by using 1,4,2‐dioxazol‐5‐ones as the amidating reagent has been developed. This transformation proceeds efficiently under external oxidant‐free conditions with a broad substrate scope. Moreover, 6‐arylpurine compounds, which often exhibit high potency in antimycobacterial, cytostatic, and anti‐HCV activities, can be smoothly amidated, thus offering a mild protocol for their late stage functionalization.