From Decades to Minutes: Steps Toward the Structure of Strychnine 1910–1948 and the Application of Today's Technology

Highly Accurate Prediction of NMR Chemical Shifts from Low-Level Quantum Mechanics Calculations Using Machine Learning

Theoretical predictions of NMR chemical shifts from first-principles can greatly facilitate experimental interpretation and structure identification of molecules in gas, solution, and solid-state phases. However, accurate prediction of chemical shifts using the gold-standard coupled cluster with singles, doubles, and perturbative triple excitations [CCSD(T)] method with a complete basis set (CBS) can be prohibitively expensive. By contrast, machine learning (ML) methods offer inexpensive alternatives for chemical shift predictions but are hampered by generalization to molecules outside the original training set. Here, we propose several new ideas in ML of the chemical shift prediction for H, C, N, and O that first introduce a novel feature representation, based on the atomic chemical shielding tensors within a molecular environment using an inexpensive quantum mechanics (QM) method, and train it to predict NMR chemical shieldings of a high-level composite theory that approaches the accuracy of CCSD(T)/CBS. In addition, we train the ML model through a new progressive active learning workflow that reduces the total number of expensive high-level composite calculations required while allowing the model to continuously improve on unseen data. Furthermore, the algorithm provides an error estimation, signaling potential unreliability in predictions if the error is large. Finally, we introduce a novel approach to keep the rotational invariance of the features using tensor environment vectors (TEVs) that yields a ML model with the highest accuracy compared to a similar model using data augmentation. We illustrate the predictive capacity of the resulting inexpensive shift machine learning (iShiftML) models across several benchmarks, including unseen molecules in the NS372 data set, gas-phase experimental chemical shifts for small organic molecules, and much larger and more complex natural products in which we can accurately differentiate between subtle diastereomers based on chemical shift assignments.

Revolutions in Chemistry: Assessment of Six 20th Century Candidates (The Instrumental Revolution; Hückel Molecular Orbital Theory; Hückel's 4n + 2 Rule; the Woodward-Hoffmann Rules; Quantum Chemistry; and Retrosynthetic Analysis)

Six 20th century candidates for revolutions in chemistry are examined, using a definitional scheme published recently by the author. Six groupings of 13 characteristics of revolutions in science are considered: causes and birthings of revolutions, relationships between the old and the new, conceptual qualities of the candidate revolutions, instrumental and methodological functions, social construction of knowledge and practical considerations, and testimonials. The Instrumental Revolution was judged to be a revolution in chemistry because of the enormous increase in community-wide knowledge provided by the new instruments and the intentionality in the identification of specific target instruments, in the mindfulness in their design, manufacture, testing, use, and ultimately commercialization. The Woodward-Hoffmann rules were judged to precipitate the Quantum Chemistry Revolution because of theoretical, practical, and social construction of knowledge characteristics. Neither Hückel molecular orbital theory nor Hückel's 4n + 2 rule was considered an initiator of a revolution in chemistry but rather participants in the Quantum Chemistry Revolution. Retrosynthetic analysis was not judged to initiate a revolution in chemistry.

Brucine-Induced Neurotoxicity by Targeting Caspase 3: Involvement of PPARγ/NF-κB/Apoptosis Signaling Pathway

Brucine, a weak alkaline indole alkaloid, is one of the main bioactive and toxic constituents of Strychnos nux-vomica L., which exerts multiple pharmacological activities, such as anti-tumor, anti-inflammatory, and analgesic effect. However, its potential toxic effects limited its clinical application, especially central nervous system toxicity. The present study was designed to investigate the neurotoxicity and mechanism of brucine. Our results showed that brucine significantly induced Neuro-2a cells and primary astrocyte death, as evidenced by MTT assay and LDH release. Moreover, transcriptome analysis indicated that PPAR/NF-κB and apoptosis signaling pathways were involved in the brucine-induced cytotoxicity in Neuro-2a cells. Subsequently, in fact, brucine evidently inhibited PPARγ and promoted phosphorylation of NF-κB. Furthermore, PPARγ inhibitor aggravated the neurotoxicity, while NF-κB inhibitor substantially reversed brucine-induced neurotoxicity. Moreover, brucine also significantly induced neuronal apoptosis and triggered increase in ratio of Bax/Bcl-2 and level of cleaved caspase 3, as well as its activity as evidenced by TUNEL staining and Western blot. Furthermore, molecular docking analysis predicted that brucine directly bound to caspase 3. Intriguingly, a caspase 3 inhibitor (Z-DEVE-FMK) largely abolished the neurotoxicity of brucine. Our results reveal that brucine-induced neurotoxicity via activation of PPARγ/NF-κB/caspase 3-dependent apoptosis pathway. These findings will provide a novel strategy against brucine-induced neurotoxicity.

Pitfalls in the structural elucidation of small molecules. A critical analysis of a decade of structural misassignments of marine natural products

Covering: July 2010 to August 2021This article summarizes more than 200 cases of misassigned marine natural products reported between July 2010 and August 2021, sorting out errors according to the structural elements. Based on a comparative analysis of the original and the revised structures, major pitfalls still plaguing the structural elucidation of small molecules were identified, emphasizing the role of total synthesis, crystallography, as well as chemical- and biosynthetic logic to complement spectroscopic data. Distinct "trends" in natural product misassignment are evident between compounds of marine and plant origin, with an overall much lower incidence of "impossible" structures within misassigned marine natural products.

"For Its Size, the Most Complex Natural Product Known." Who Deserves Credit for Determining the Structure of Strychnine?

In this paper, the following question is explored: Who should be given credit for a discovery of a scientific phenomenon?

Strychnine and its mono- and dimeric analogues: a pharmaco-chemical perspective

Covering: up to November 2021Since its isolation in 1818, strychnine has attracted the attention of a plethora of chemists and pharmacologists who have established its structure, developed total syntheses, and examined its complex pharmacology. While numerous reviews on structure elucidation and total synthesis of strychnine are available, reports on structure-activity relationships (SARs) of this fascinating alkaloid are rare. In this review, we present and discuss structures, synthetic approaches, metabolic transformations, and the diverse pharmacological actions of strychnine and its mono- and dimeric analogues. Particular attention is given to its SARs at glycine receptors (GlyRs) in light of recently published high-resolution structures of strychnine-GlyR complexes. Other pharmacological actions of strychnine and its derivatives, such as their antagonistic properties at nicotinic acetylcholine receptors (nAChRs), allosteric modulation of muscarinic acetylcholine receptors as well as anti-cancer and anti-plasmodial effects are also critically reviewed, and possible future developments in the field are discussed.

An Asymmetric Synthesis of (+)-Isostrychnine Based on Catalytic Asymmetric Tandem Double Michael Addition

Herein, a concise asymmetric synthesis of (+)-isostrychnine is achieved in nine longest-linear steps with a 16% overall yield. The key features of this synthesis include the catalytic asymmetric tandem double Michael addition of a tryptamine-derived oxindole to an alkynone to facilely forge the A/B/C ring framework, a one-pot intramolecular dehydrative condensation/lactamization reaction to efficiently establish the E/G ring system, and an allylic diazene rearrangement to introduce the pivotal olefin for the subsequent intramolecular Heck reaction.

The Relationship of William Henry Perkin, Jr. and Sir Robert Robinson: Teacher and Student, then Student and Teacher

William Henry Perkin, Jr. FRS, the son of the inventor of mauve and other commercial dyes and credited for initiating the industrialization of chemistry, was himself a notable chemist. He was the Professor of Organic Chemistry at Manchester from 1892-1912 and then was the Waynflete Professor of Chemistry at Oxford and the first Head of the Dyson Perrins Laboratory from 1912-1929. One of Perkin's graduate students and research assistants at Manchester was Robert Robinson, subsequently Sir Robert Robinson, FRS and recipient of the 1947 Nobel Prize in Chemistry. Perkin and Robinson had perhaps the most productive and broad collaboration between a professor and one's student. Together, during and after Robinson's student days, they had 71 joint publications, 25 of which involved just the two of them, 17 of which involved the structure determination of strychnine, and eight of which were published after Perkin's death in 1929. Upon Perkin's early death, Robinson succeeded him as the fourth Waynflete Professor of Chemistry at the Dyson Perrins Laboratory, Oxford University. This Essay will examine the professional relationship of Perkin, Jr. and Robinson as revealed in their joint publications on the structure of strychnine.