Category Archives: Israel Journal of Chemistry

Quasicrystal Structure Prediction: A Review

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Quasicrystal Structure Prediction: A Review


Abstract

Predicting quasicrystal structures is a multifaceted problem that can involve predicting a previously unknown phase, predicting the structure of an experimentally observed phase, or predicting the thermodynamic stability of a given structure. We survey the history and current state of these prediction efforts with a focus on methods that have improved our understanding of the structure and stability of known metallic quasicrystal phases. Advances in the structural modeling of quasicrystals, along with first principles total energy calculation and statistical mechanical methods that enable the calculation of quasicrystal thermodynamic stability, are illustrated by means of cited examples of recent work.

A Quantitative Sequencing Method for 5‐Formylcytosine in RNA

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A Quantitative Sequencing Method for 5-Formylcytosine in RNA


Abstract

5-Formylcytosine (f5C) modification is present in human mitochondrial methionine tRNA (mt-tRNAMet) and cytosolic leucine tRNA (ct-tRNALeu), with their formation mediated by NSUN3 and ALKBH1. f5C has also been detected in yeast mRNA and human tRNA, but its transcriptome-wide distribution in mammals has not been studied. Here we report f5C-seq, a quantitative sequencing method to map f5C transcriptome-wide in HeLa and mouse embryonic stem cells (mESCs). We show that f5C in RNA can be reduced to dihydrouracil (DHU) by pic-borane, and DHU can be exclusively read as T during reverse transcription (RT) reaction, allowing the detection and quantification of f5C sites by a unique C-to-T mutation signature. We validated f5C-seq by identifying and quantifying the two known f5C sites in tRNA, in which the f5C modification fractions dropped significantly in ALKBH1-depleted cells. By applying f5C-seq to chromatin-associated RNA (caRNA), we identified several highly modified f5C sites in HeLa and mouse embryonic stem cells (mESC).

The Cellular Environment Guides Self‐Assembly and Structural Conformations of Microtubule‐Associated Protein Tau (MAPT)

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The Cellular Environment Guides Self-Assembly and Structural Conformations of Microtubule-Associated Protein Tau (MAPT)


Abstract

In neurodegenerative tauopathies, such as Alzheimer's disease (AD), microtubule-associated protein tau (MAPT/tau) transitions from a soluble form to insoluble, filamentous lesions inside affected neurons. During this process, tau adopts a range of physical configurations: from misfolded monomers to higher-order oligomers and fibrils. Tau aggregation is also associated with changes in post-translational modifications (PTMs), such as ubiquitination, oxidation, glycation, hyper-phosphorylation and acetylation, which collectively produce an impressive range of possible tau proteoforms. Many of these tau proteoforms are highly cationic and unlikely to self-assemble without neutralization of their charges. Indeed, tau fibrils from patients contain anionic biomacromolecules and bound proteins, suggesting that cytosolic components contribute to fibrilligenesis. Here, we review what is known about how the cytosol impacts tau's aggregation pathways. We also speculate that the composition of each brain region (e. g., redox state, tau proteoforms, levels of permissive polyanions, etc.) might play an active role in shaping the structure of the resulting tau fibrils. Although much remains to be discovered, a greater understanding of the role of the cytosol on tau self-assembly might lead to identification of new therapeutic targets.

Enantioselective Synthesis of [5]Helicenes Containing Two Additional Chiral Axes

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Enantioselective Synthesis of [5]Helicenes Containing Two Additional Chiral Axes


Abstract

A Au-catalyzed protocol for the enantioselective synthesis of molecular architectures containing an internal [5]helicene and two peripherical axial stereogenic elements is described. While the diasteroselectivity of the double alkyne hydroarylation sequence is not optimal, and mixtures that contain similar amounts of two of the four possible diasteromeric products are obtained (one C2 and one non-symmetric), the assembly of the C2-symmetric isomer often occurs with high enantioselectivity (up to 98 % ee). The absolute configurations of the products obtained were determined by X-ray crystallography. Studies on the thermal racemization of the internal [5]helicene moiety in the C2-symmetric isomers determined the half-life of this element to be approximately 3 h at 50 °C.

Cationic Complexes with Au→Ge Bonds – Synthesis and Carbophilic Reactivity

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Cationic Complexes with Au→Ge Bonds – Synthesis and Carbophilic Reactivity


Abstract

As part of our efforts to interface late transition metals with Lewis acidic main group fragments, we have decided to investigate gold complexes bearing halogermanes as Z-type ligands. Toward this end, we have synthesized complexes of general formula [(o-(Ph2P)C6H4)2(Ph)(X)GeAuCl] (X = F, Cl). Experimental and computational analyses indicate the presence of an Au→Ge interaction in both cases. Chloride abstraction reactions have also been investigated. In the case of X = Cl, double chloride abstraction with AgSbF6 affords a putative dication that gradually abstracts fluoride from its counterion. This putative dication is also significantly more active as a catalyst than its monocationic analog in alkyne hydroamination reactions.

Transition Metal‐Catalyzed Rearrangement and Cycloisomerization Reactions Toward Hedonic Materials

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Transition Metal-Catalyzed Rearrangement and Cycloisomerization Reactions Toward Hedonic Materials


Abstract

Over the last century, the fragrance industry had relied on the synthetic chemists for the development of new odors, but also for the replacement of some known materials due to allergy or toxicity. Transition metal-catalyzed transformations have allowed atom economy and synthetic efficiency for several transformations and they caught the attention of fragrance industrials. The metal-catalyzed cyclization reactions have been particularly successful toward the synthesis of key skeletons. This review highlights the developments of selected hedonic materials according to transition metal-catalyzed according to cycloisomerization reactions and related rearrangements.

Fused Polycyclic NHC Ligands in Gold Catalysis: Recent Advances

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Fused Polycyclic NHC Ligands in Gold Catalysis: Recent Advances


Abstract

Thanks to their appealing properties, N-heterocyclic carbene (NHC) ligands gained considerable significance as highly powerful ancillary ligands in gold catalysis. While NHC-gold catalysis is still dominated by the classical imidazole-derived NHC ligands, annelated NHC systems, which feature fused aromatic rings to the carbenic heterocycle, have drawn wider attention over the last few years thanks to their unique structural and electronic properties. Fused polyaromatic NHCs are indeed versatile platforms that offer unique stereoelectronic tuning possibilities to exhibit superior activity and/or selectivity in NHC-gold catalysis. But their polycyclic scaffolds also provide further scope for functionalization and the introduction of chirality, stimuli-responsiveness, or cooperativity within the NHC-gold systems. In this review, the recent advances in this area are discussed and a particular attention is drawn on the unique role of the annelation.

Chiral Ligands for Au(I), Au(III), and Au(I)/Au(III) Redox Catalysis

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Chiral Ligands for Au(I), Au(III), and Au(I)/Au(III) Redox Catalysis


Abstract

Gold catalysis has emerged as an efficient tool for the selective functionalisation of C−C multiple bonds. Despite significant progress in this field, the potential of asymmetric gold catalysis has not been fully explored to date. A historical retrospect on the progress in this area reveals that enantioselective gold catalysis is based on three pillars: Au(I) catalysis, Au(III) catalysis, and Au(I)/Au(III) redox catalysis. Irrespective of the mode of catalysis being operative, the design of new ligands is crucial for the development of gold-catalysed organic transformations. This minireview summarizes the progress made in the development of ligand design for enantioselective Au(I) catalysis, Au(III) catalysis, and Au(I)/Au(III) redox catalysis focusing on the ligands which were specially designed for gold catalysis.

DFT Studies of Au(I) Catalysed Reactions: Anion Effects and Reaction Selectivity

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DFT Studies of Au(I) Catalysed Reactions: Anion Effects and Reaction Selectivity


Abstract

Density functional theory (DFT) is a powerful tool that can aid in the exploration and development of synthetic chemistry, and its use is often applied in the chemistry of gold(I) catalysis. In this review, we discuss two different facets of these calculations – namely, the exploration and explanation of anion effects, and the regioselectivity and speciation of gold(I)-catalysed reactions. The research described herein clearly shows the importance of including the anion in DFT studies of Au(I)-catalysed reactions, especially when using low polarity solvents, or where hydrogen-bonding is prevalent. Additionally, we show that whilst using DFT to study the selectivity of reactions can be successful, benchmarking the computational results against experimental data is vitally important for ensuring that the model is accurately describing the observed results.