Python tools for structural tasks in chemistry.

In recent decades, the use of computational approaches and artificial intelligence in the scientific environment has become more widespread. In this regard, the popular and versatile programming language Python has attracted considerable attention from scientists in the field of chemistry. It is used to solve a variety of chemical and structural problems, including calculating descriptors, molecular fingerprints, graph construction, and computing chemical reaction networks. Python offers high-quality visualization tools for analyzing chemical spaces and compound libraries. This review is a list of tools for the above tasks, including scripts, libraries, ready-made programs, and web interfaces. Inevitably this manuscript does not claim to be an all-encompassing handbook including all the existing Python-based structural chemistry codes. The review serves as a starting point for scientists wishing to apply automatization or optimization to routine chemistry problems.

Thermal Rearrangement of 5-(2-Hydroxy-6-oxocyclohexyl)-5H-chromeno[2,3-b]pyridines.

Some of the most important transformations in organic chemistry are rearrangement reactions, which play a crucial role in increasing synthetic efficiency and molecular complexity. The development of synthetic strategies involving rearrangement reactions, which can accomplish synthetic goals in a very efficient manner, has been an evergreen topic in the synthetic chemistry community. Xanthenes, pyridin-2(1H)-ones, and 1,6-naphthyridines have a wide range of biological activities. In this work, we propose the thermal rearrangement of 7,9-dihalogen-substituted 5-(2-hydroxy-6-oxocyclohexyl)-5H-chromeno[2,3-b]pyridines in DMSO. Previously unknown 5,7-dihalogenated 5-(2,3,4,9-tetrahydro-1H-xanthen-9-yl)-6-oxo-1,6-dihydropyridines and 10-(3,5-dihalogen-2-hydroxyphenyl)-5,6,7,8,9,10-hexahydrobenzo[b][1,6]naphthyridines were synthesized with excellent yields (90-99%). The investigation of the transformation using 1H-NMR monitoring made it possible to confirm the ANRORC mechanism. The structures of synthesized compounds were confirmed by 2D-NMR spectroscopy.

Oxidative Cyclization of 5H-Chromeno[2,3-b]pyridines to Benzo[b]chromeno[4,3,2-de][1,6]naphthyridines, Their NMR Study and Computer Evaluation as Material for LED.

Oxidative cyclization is one of the most significant reactions in organic synthesis. Naphthyridine derivatives are often used as luminescence materials in molecular recognition because of their rigid planar structure and as new drugs. Organic light-emitting diodes (OLEDs) have rapidly grown as one of the leading technologies for full-color display panels and eco-friendly lighting sources. In this work, we propose the synthesis of previously unknown benzo[b]chromeno[4,3,2-de][1,6]naphthyridines via intermolecular oxidative cyclization of 5-(2-hydroxy-6-oxocyclohexyl)-5H-chromeno[2,3-b]pyridines in formic acid. The investigation of the reaction mechanism using 1H-NMR monitoring made it possible to confirm the proposed mechanism of the transformation. The structure of synthesized benzo[b]chromeno[4,3,2-de][1,6]naphthyridines was confirmed by 2D-NMR spectroscopy. Such a rigid geometry of synthesized compounds is desired to minimize non-radiative energy losses in OLEDs. The quantum chemical calculations are also presented in the study.

One-Pot Solvent-Involved Synthesis of 5-O-Substituted 5H-Chromeno[2,3-b]pyridines.

Chromeno[2,3-b]pyridines are substances demanded in medicinal and material chemistry. PASE (pot, atom, and step economy) and in particular one-pot approaches are key green chemistry techniques that are applied for the synthesis of heterocyclic compounds. In this case, the PASE approach was extended with 'component economy', as solvent was used also as reactant (solvent-involved reaction). This approach was adopted for the one-pot synthesis of previously unknown O-substituted 5-alkoxy-5H-chromeno[2,3-b]pyridines via two-step transformation, namely the reaction of salicylaldehydes and malononitrile dimer, with the subsequent addition of alcohol. The mechanistic studies revealed the possibility of concurrent reaction. The studies aided in optimizing the reaction conditions for the best yields (77-93%). Thus, the one-pot reaction proceeds efficient and quickly, and the work-up procedure (only simple filtering) is very convenient. The structure of synthesized chromeno[2,3-b]pyridines was confirmed by 2D NMR spectroscopy.

Multicomponent Synthesis of 2-(2,4-Diamino-3-cyano-5H-chromeno[2,3-b]pyridin-5-yl)malonic Acids in DMSO.

Dimethyl sulfoxide is a widely used solvent in organic synthesis and in the pharmaceutical industry because of its low cost, stability, and low toxicity. Multicomponent reactions are an advanced approach that has become an efficient, economical, and eco-friendly substitute for the conventional sequential multi-step synthesis of various biologically active compounds. This approach was adopted for the synthesis of previously unknown 2-(2,4-diamino-3-cyano-5H-chromeno[2,3-b]pyridin-5-yl)malonic acids via transformation of salicylaldehydes, malononitrile dimer, and malonic acid. It was shown that the use of DMSO at room temperature makes it possible to synthesize previously unavailable compounds. The investigation of the reaction mechanism using 1H-NMR monitoring made it possible to confirm the proposed mechanism of the transformation. The structure of synthesized 5H-chromeno[2,3-b]pyridines was confirmed by 2D-NMR spectroscopy.

Catalyst-Solvent System for PASE Approach to Hydroxyquinolinone-Substituted Chromeno[2,3-b]pyridines Its Quantum Chemical Study and Investigation of Reaction Mechanism.

The Pot, Atom, and Step Economy (PASE) approach is based on the Pot economy principle and unites it with the Atom and Step Economy strategies; it ensures high efficiency, simplicity and low waste formation. The PASE approach is widely used in multicomponent chemistry. This approach was adopted for the synthesis of previously unknown hydroxyquinolinone substituted chromeno[2,3-b]pyridines via reaction of salicylaldehydes, malononitrile dimer and hydroxyquinolinone. It was shown that an ethanol-pyridine combination is more beneficial than other inorganic or organic catalysts. Quantum chemical studies showed that chromeno[2,3-b]pyridines has potential for corrosion inhibition. Real time 1H NMR monitoring was used for the investigation of reaction mechanism and 2-((2H-chromen-3-yl)methylene)malononitrile was defined as a key intermediate in the reaction.

Pot, atom and step economic (PASE) assembly of salicylaldehydes, malononitrile dimer and 4-hydroxypyridine-2(1H)-ones into medicinally relevant 5H-chromeno[2,3-b]pyridine scaffold.

The new multicomponent reaction (MCR) has been found: one-pot selective and efficient formation of the new 5-(4-hydroxy-2-oxo-1,2-dihydropyridin-3-yl)-substituted 5H-chromeno[2,3-b]pyridines in 61-97% yields directly from simple and easily available salicylaldehydes, malononitrile dimer and 4-hydroxypyridine-2(1H)-ones in small amount of pyridine-ethanol catalyst/solvent system. This complex "domino" transformation includes Knoevenagel condensation of salicylaldehyde with malononitrile dimer, Michael addition of 4-hydroxypyridine-2(1H)-one, double Pinner-type reaction cyclization and isomerization with following protonation. This facile multicomponent process opens a new way to 5-(4-hydroxy-2-oxo-1,2-dihydropyridin-3-yl)-substituted 5H-chromeno[2,3-b]pyridine systems, which are promising compounds for the treatment for human inflammatory TNFα-mediated diseases and different biomedical applications.

One-pot five-component high diastereoselective synthesis of polysubstituted 2-piperidinones from aromatic aldehydes, nitriles, dialkyl malonates and ammonium acetate.

A novel five-component diastereoselective synthesis of polysubstituted 2-piperidinones is reported. The Knoevenagel condensation-Michael addition-Mannich cascade of two equivalents of aromatic aldehydes, nitriles, dialkyl malonates and ammonium acetate or aqueous ammonia in alcohols provides convenient access to alkyl (3SR,4RS,6SR)-5,5-dicyano-2-oxo-4,6-diarylpiperidine-3-carboxylates with three stereocenters in 52-90% or dialkyl (2SR,3RS,4RS,5SR)-2,4-diaryl-3-cyano-6-oxopiperidine-3,5-dicarboxylates with four stereocenters in 38-88%. The formation of products was highly stereoselective, with only one diastereomer formed. Ammonium acetate or aqueous ammonia plays a role both as a catalyst and as a nitrogen source. 2,4,6-triaryl-3,3,5,5-tetracyanopiperidines were obtained as a side products in the reactions with nitro-substituted aldehydes or with ethyl and n-propyl cyanoacetates. A series of 14 2-piperidinones and piperidines was assessed for antimicrobial activity against a panel of five bacteria and two fungi; no significant activity was observed. Two side piperidines with nitro substituents in aromatic ring possess bacteriostatic action against S. aureus ATCC 43300 and A. baumannii ATCC 19606 at 32 ug/mL.

Structural data of phenanthrene-9,10-dicarbonitriles.

In this data article, we present the single-crystal XRD data of phenanthrene-9,10-dicarbonitriles. Detailed structure analysis and photophysical properties were discussed in our previous study, "Intermolecular interactions-photophysical properties relationships in phenanthrene-9,10-dicarbonitrile assemblies" (Afanasenko et al., 2020). The data include the intra- and intermolecular bond lengths and angles.

High diastereoselective amine-catalyzed Knoevenagel-Michael-cyclization-ring-opening cascade between aldehydes, 3-arylisoxazol-5(4H)-ones and 3-aminocyclohex-2-en-1-ones.

A highly diastereoselective three-component cascade reaction among aromatic aldehydes, 3-arylisoxazol-5(4H)-ones and 3-aminocyclohex-2-en-1-ones takes place under the catalysis of triethylamine, providing (3SR,4SR)-4-aryl-3-[(E)-(hydroxyimino)(aryl)methyl]-4,6,7,8-tetrahydroquinoline-2,5(1H,3H)-diones in 45-85% yields. The transformation presumably proceeds through a sequential cascade of Knoevenagel/Michael-addition/cyclization/ring-opening reactions. This process was carried out in green media (EtOH/water, 1:1-1:3) at reflux. Products are crystallized directly from the reaction mixture and their isolation includes only filtration. The structure of (3SR,4SR)-3-[(E)-(hydroxyimino)(phenyl)methyl]-7,7-dimethyl-4-phenyl-4,6,7,8-tetrahydroquinoline-2,5(1H,3H)-dione was confirmed by X-ray diffraction analysis.

Catalysis of Cascade and Multicomponent Reactions of Carbonyl Compounds and CH Acids by Electricity.

This review is concerned with modern trends in the use of electrochemically induced chain reactions in cascade and multicomponent electroorganic synthesis. The review summarizes the data on the use of electrochemically induced chain reactions in cascade and multicomponent organic synthesis, which were published mainly in the last decade.

New way to substitute tetracyanocyclopropanes: one-pot cascade assembling of carbonyls and malononitrile by the only bromine direct action.

THE NEW TYPE OF THE CHEMICAL CASCADE REACTION WAS FOUND: formation of cyclopropanes from carbonyl compounds and CH acid by the only bromine direct action. The action of aqueous bromine on the carbonyl compounds and malononitrile in EtOH-H2O solutions in the presence of NaOAc results in the formation of 3-substituted 1,1,2,2-tetracyanocyclopropanes in 48-93% yields. The latter are well-known precursors for the different bicyclic heterosystems, among them those containing cyclopropane ring and those possessing different types of pharmacological activity.

Electrochemically induced multicomponent assembling of isatins, 4-hydroxyquinolin-2(1H)-one and malononitrile: a convenient and efficient way to functionalized spirocyclic [indole-3,4'-pyrano[3,2-c]quinoline] scaffold.

Electrochemically induced catalytic multicomponent transformation of isatins, 4-hydroxyquinolin-2(1H)-one and malononitrile in ethanol in an undivided cell in the presence of sodium bromide as an electrolyte results in the formation of spirooxindoles with fused functionalized indole-3,4'-pyrano[3,2-c]quinoline] scaffold in 75-91% substance yields and 500-600% current yield. The developed efficient electrocatalytic approach to medicinally relevant [indole-3,4'-pyrano[3,2-c]quinoline] scaffold is beneficial from the viewpoint of diversity-oriented large-scale processes and represents a novel example of facile environmentally benign synthetic concept for electrocatalytic multicomponent reactions.

Electrocatalytic multicomponent assembling of isatins, 3-methyl-2-pyrazolin-5-ones and malononitrile: facile and convenient way to functionalized spirocyclic [indole-3,4'-pyrano[2,3-c]pyrazole] system.

Electrochemically induced catalytic multicomponent transformation of isatins, 3-methyl-2-pyrazolin-5-ones and malononitrile in ethanol in an undivided cell in the presence of sodium bromide as an electrolyte results in the formation of spirooxindoles with fused functionalized pyrano[2,3-c]pyrazole system in 78-99} yields. The developed efficient electrocatalytic approach to medicinally relevant spirocyclic [indole-3,4'-pyrano[2,3-c]pyrazoles] is beneficial from the viewpoint of diversity-oriented large-scale processes and represents a novel example of facile environmentally benign synthetic concept for electrocatalytic multicomponent reaction strategy.