RDCanon: A Python Package for Canonicalizing the Order of Tokens in SMARTS Queries

SMARTS is a widely used language in cheminformatics for defining substructural queries for database lookups, reaction templates for chemical transformations, and other applications. As an extension to SMILES, many SMARTS patterns can represent the same query. Despite this, no canonicalization algorithm invariant of the line notation sequence or atomic numbering is publicly available. Here, we introduce RDCanon, an open-source Python package that can be used to standardize SMARTS queries. RDCanon is designed to ensure that the sequence of atomic queries remains consistent for all graphs representing the same substructure query and to ensure a canonical sequence of primitives within each individual atom query; furthermore, the algorithm can be applied to canonicalize the order of reactants, agents, and products and their atom map numbers in reaction SMARTS templates. As part of its canonicalization algorithm, RDCanon provides a mechanism in which the canonicalized SMARTS is optimized for speed against specific molecular databases. Several case studies are provided to showcase improved efficiency in substructure matching and retrosynthetic analysis.

The (±)-5-Aza[1.0]triblattane Skeleton via Azetine Cycloaddition

The first synthesis of the 5-aza[1.0]triblattane skeleton was achieved through a [4 + 2] cycloaddition approach using a suitably protected azetine and cyclopentadiene. A series of azetines were synthesized to explore both stability and suitable N-protection. The key step following cycloaddition utilized a noninitiated protonated aminyl radical cyclization to install the final 5-azatriblattane bond, but it was found to be considerably more unstable than the 6-aza isomer under acidic conditions.

SynRoute: A Retrosynthetic Planning Software

Computer-assisted synthetic planning has seen major advancements that stem from the availability of large reaction databases and artificial intelligence methodologies. SynRoute is a new retrosynthetic planning software tool that uses a relatively small number of general reaction templates, currently 263, along with a literature-based reaction database to find short, practical synthetic routes for target compounds. For each reaction template, a machine learning classifier is trained using data from the Pistachio reaction database to predict whether new computer-generated reactions based on the template are likely to work experimentally in the laboratory. This reaction generation methodology is used together with a vectorized Dijkstra-like search of top-scoring routes organized by synthetic strategies for easy browsing by a synthetic chemist. SynRoute was able to find routes for an average of 83% of compounds based on selection of random subsets of drug-like compounds from the ChEMBL database. Laboratory evaluation of 12 routes produced by SynRoute, to synthesize compounds not from the previous random subsets, demonstrated the ability to produce feasible overall synthetic strategies for all compounds evaluated.

Microwave-Aided Reactions of Aniline Derivatives with Formic Acid: Inquiry-Based Learning Experiments

The synthesis of amides belongs to traditional experimental tasks not only in organic chemistry exercises at universities but also at chemically focused secondary schools or in special practices at general high schools. An example of such a synthesis may be the preparation of acetanilide via reaction of aniline with acetic acid or acetic anhydride. However, both of these reactions are associated with a rather long reaction time and certain hazards that limit their straightforward use in pedagogical practice. Conveniently, the reaction of aniline with acetic acid may be significantly optimised if it is performed under solvent-free conditions in the presence of microwaves, which reduces considerably the reaction time and provides very good yield, compared to traditional heating by a heating nest. In this study, the main pedagogical aim of the experimental design is elucidation of the influence of the structure of the amines on the course of the reaction with formic acid through inquiry-based learning. Specifically, the proposed experiments consist in investigation of the chemical yield achieved in microwave assisted reactions of aniline and its derivatives with formic acid in such a way that is adequate for constructive learning of undergraduate chemistry students. The selected series of amines involves aniline, 4-methoxyaniline, 4-chloroaniline, and 4-nitroaniline. In accordance with the chemical reactivity principles, students gradually realise that the influence of the substituent is reflected in the reaction yield, which grows in the following order: N-(4-nitrophenyl)formamide ˂ N-(4-chlorophenyl)formamide ˂ N-phenylformamide ˂ N-(4-methoxyphenyl)formamide. Therefore, the results of the experiments enable students to discover that stronger basicity of the amine increases the yield of the amide. In order to deepen the students’ chemical knowledge and skills, the concept of the experiments was transformed to support inquiry-based student learning. The proposed experiments are intended for experimental learning in universities educating future chemistry teachers, but they may be also utilised in the form of workshops for students at secondary schools of a general educational nature.

Small molecules and their impact in drug discovery: A perspective on the occasion of the 125th anniversary of the Bayer Chemical Research Laboratory

The year 2021 marks the 125th anniversary of the Bayer Chemical Research Laboratory in Wuppertal, Germany. A significant number of prominent small-molecule drugs, from aspirin to Xarelto, have emerged from this research site. In this review, we shed light on historic cornerstones of small-molecule drug research, discussing current and future trends in drug discovery as well as providing a personal outlook on the future of drug research with a focus on small molecules.

The (±)-6-Aza[1.0]triblattane Skeleton: Contraction beyond the Wilder-Culberson Ring System

Synthesis of the 6-aza[1.0]triblattane skeleton and the unexpected construction of the 7-azatetracyclo[4.2.1.0^2,5.0^3,7]nonane framework are reported, as inspired by the Wilder-Culberson 1-aza[1.1]triblattane ring system. The key steps to assess the 6-aza[1.0]triblattane include accessing the 1,6-cycloaddition product from reaction of chlorosulfonyl isocyanate with cyclohept-1,3,5-triene followed by intramolecular electrocyclization and aminium radical cyclization.

Tandem Oxidation-Dehydrogenation of (Hetero)Arylated Primary Alcohols via Perruthenate Catalysis

Tandem oxidative-dehydrogenation of primary alcohols to give α,β-unsaturated aldehydes in one pot are rare transformations in organic synthesis, with only two methods currently available. Reported herein is a novel method using the bench-stable salt methyltriphenylphosphonium perruthenate (MTP3), and a new co-oxidant NEMO·PF6 (NEMO = N-ethyl-N-hydroxymorpholinium) which provides unsaturated aldehydes in low to moderate yields. The Ley-Griffith oxidation of (hetero)arylated primary alcohols with N-oxide co-oxidants NMO (NMO = N-methylmorpholine N-oxide)/NEMO, is expanded by addition of the N-oxide salt NEMO·PF6 to convert the intermediate saturated aldehyde into its unsaturated counterpart. The discovery, method development, reaction scope, and associated challenges of this method are highlighted. The conceptual value of late-stage dehydrogenation in natural product synthesis is demonstrated via the synthesis of a polyene scaffold related to auxarconjugatin B.