Automated library generation using sequential microwave-assisted chemistry. Application toward the Biginelli multicomponent condensation

Machine learning-guided strategies for reaction conditions design and optimization

This review surveys the recent advances and challenges in predicting and optimizing reaction conditions using machine learning techniques. The paper emphasizes the importance of acquiring and processing large and diverse datasets of chemical reactions, and the use of both global and local models to guide the design of synthetic processes. Global models exploit the information from comprehensive databases to suggest general reaction conditions for new reactions, while local models fine-tune the specific parameters for a given reaction family to improve yield and selectivity. The paper also identifies the current limitations and opportunities in this field, such as the data quality and availability, and the integration of high-throughput experimentation. The paper demonstrates how the combination of chemical engineering, data science, and ML algorithms can enhance the efficiency and effectiveness of reaction conditions design, and enable novel discoveries in synthetic chemistry.

When Yield Prediction Does Not Yield Prediction: An Overview of the Current Challenges

Machine Learning (ML) techniques face significant challenges when predicting advanced chemical properties, such as yield, feasibility of chemical synthesis, and optimal reaction conditions. These challenges stem from the high-dimensional nature of the prediction task and the myriad essential variables involved, ranging from reactants and reagents to catalysts, temperature, and purification processes. Successfully developing a reliable predictive model not only holds the potential for optimizing high-throughput experiments but can also elevate existing retrosynthetic predictive approaches and bolster a plethora of applications within the field. In this review, we systematically evaluate the efficacy of current ML methodologies in chemoinformatics, shedding light on their milestones and inherent limitations. Additionally, a detailed examination of a representative case study provides insights into the prevailing issues related to data availability and transferability in the discipline.

Polymer-Supported Dioxidovanadium(V) Complex-Based Heterogeneous Catalyst for Multicomponent Biginelli Reaction Producing Biologically Active 3,4-Dihydropyrimidin-2-(1H)-ones

Dioxidovanadium(V) complex [VVO2(sal-aebmz)] (1) (where Hsal-aebmz = Schiff base derived from the condensation of salicylaldehyde and 2-aminoethylbenzimidazole) has been immobilized on chloromethylated polystyrene (PS-Cl) cross-linked with divinylbenzene to obtain [VVO2(sal-aebmz)]@PS (2), a heterogeneous complex. Both complexes, after characterization, have been used as catalysts to explore a single pot multicomponent (benzaldehyde or its derivatives, urea and ethyl acetoacetate) Biginelli reaction producing biologically active 3,4-dihydropyrimidin-2-(1H)-one (DHPM)-based biomolecules under solvent-free conditions in the presence of H2O2 as a green oxidant. Various reaction conditions such as amounts of catalyst and oxidant, temperature, time, and solvent have been optimized to obtain the maximum yield of DHPMs. The polymer-immobilized complex has been found to show excellent catalytic activity, giving ca. 95% yield of DHPMs under the optimized reaction conditions selectively. Oxidant plays an important role in enhancing the yield of DHPMs.

Synthesis of Dihydropyrimidines: Isosteres of Nifedipine and Evaluation of Their Calcium Channel Blocking Efficiency

Hypertension and cardiovascular diseases related to it remain the leading medical challenges globally. Several drugs have been synthesized and commercialized to manage hypertension. Some of these drugs have a dihydropyrimidine skeleton structure, act as efficient calcium channel blockers, and affect the calcium ions' intake in vascular smooth muscle, hence managing hypertension. The synthesis of such moieties is crucial, and documenting their structure-activity relationship, their evolved and advanced synthetic procedures, and future opportunities in this area is currently a priority. Tremendous efforts have been made after the discovery of the Biginelli condensation reaction in the synthesis of dihydropyrimidines. From the specific selection of Biginelli adducts to the variation in the formed intermediates to achieve target compounds containing heterocylic rings, aldehydes, a variety of ketones, halogens, and many other desired functionalities, extensive studies have been carried out. Several substitutions at the C3, C4, and C5 positions of dihydropyrimidines have been explored, aiming to produce feasible derivatives with acceptable yields as well as antihypertensive activity. The current review aims to cover this requirement in detail.

MOF/POM hybrids as catalysts for organic transformations

Insertion of molecular metal oxides, e.g. polyoxometalates (POMs), into metal-organic frameworks (MOFs) opens up new research opportunities in various fields, particularly in catalysis. POM/MOF composites have strong acidity, oxygen-rich surface, and redox capacity due to typical characteristics of POMs and the large surface area, highly organized structures, tunable pore size, and shape are due to MOFs. Such hybrid materials have gained a lot of attention due to astonishing structural features, and hence have potential applications in organic catalysis, sorption and separation, proton conduction, magnetism, lithium-ion batteries, supercapacitors, electrochemistry, medicine, bio-fuel, and so on. The exceptional chemical and physical characteristics of POMOFs make them useful as catalysts in simple organic transformations with high capacity and selectivity. Here, the thorough catalytic study starts with a brief introduction related to POMs and MOFs, and is followed by the synthetic strategies and applications of these materials in several catalytic organic transformations. Furthermore, catalytic conversions like oxidation, condensation, esterification, and some other types of catalytic reactions including photocatalytic reactions are discussed in length with their plausible catalytic mechanisms. The disadvantages of the POMOFs and difficulties faced in the field have also been explored briefly from our perspectives.

The Open Reaction Database

Chemical reaction data in journal articles, patents, and even electronic laboratory notebooks are currently stored in various formats, often unstructured, which presents a significant barrier to downstream applications, including the training of machine-learning models. We present the Open Reaction Database (ORD), an open-access schema and infrastructure for structuring and sharing organic reaction data, including a centralized data repository. The ORD schema supports conventional and emerging technologies, from benchtop reactions to automated high-throughput experiments and flow chemistry. The data, schema, supporting code, and web-based user interfaces are all publicly available on GitHub. Our vision is that a consistent data representation and infrastructure to support data sharing will enable downstream applications that will greatly improve the state of the art with respect to computer-aided synthesis planning, reaction prediction, and other predictive chemistry tasks.

N-Directed Pd-Catalyzed Photoredox-Mediated C–H Arylation for Accessing Phenyl-Extended Analogues of Biginelli/Suzuki-Derived Ethyl 4-Methyl-2,6-diphenylpyrimidine-5-carboxylates

The availability and application of direct, functional group-compatible C–H activation methods for late-stage modification of small-molecule bioactives and other valuable materials remains an ongoing challenge in organic synthesis. In the current study, we demonstrate that a LED-activated, photoredox-mediated, Pd(OAc)2-catalyzed C–H arylation, employing a phenyldiazonium aryl source and either tris(2,2′-bipyridine)ruthenium(II) or (2,2′-bipyridine)bis[3,5-di-fluoro-2-[5-(trifluoromethyl)-2-pyridinyl-kN][phenyl-kC]iridium(III) as photoredox initiator, may successfully produce unprecedented mono- and bis-phenyl derivatives of functionality-rich 2,6-diphenylpyrimidine substrates at room temperature. The series of 19 substrates employed herein, which share the biologically-relevant 4-methyl-2,6-diphenylpyrimidine-5-carboxylate scaffold, were generated via a synthetic route involving (3-component) Biginelli condensation, oxidative dehydrogenation of the obtained 3,4-dihydropyrimidin-2(1H)-one to 2-hydroxypyrimidine, O-sulfonylation, and Suzuki-Miyaura C–C cross-coupling. Submission of these substrates to pyrimidine-N-atom-directed C–H arylation conditions led to regioselective phenylation at the ortho site(s) of the pyrimidine-C2-connected phenyl ring, revealing substituent-dependent electronic and steric effects. A focused library of 18 mono- and 10 bis-phenyl derivatives was generated. Its members exhibit interesting 3D and peripheral substitution features that render them promising for evaluation in drug discovery efforts.

[Development of Efficient Synthetic Method for Tautomeric Dihydropyrimidines and Analysis of Their Functionality]

I here present the results of our studies on the synthesis and functional analysis of tautomeric dihydropyrimidines (DPs) and related compounds in two sections. In the first section, we describe our experimental and theoretical studies on the thermodynamics and properties of 2-substituted 1,4- and 1,6-dihydropyrimidine-5-carboxylates by ¹H NMR measurements and density functional theory (DFT) calculations, respectively. The concentration ratios of tautomers a/b of DPs 1, 2, and 3 were determined under various conditions to determine the effects of temperature, solvent, and concentration on thermodynamics data. The obtained free energy differences (ΔG), enthalpy differences (ΔH), and entropy differences (ΔS) are discussed in terms of the molecular structures, dipole moments (DM), and electrostatic potential maps obtained by DFT calculations to clarify the nature of DPs 4-8. In the second section, an efficient synthetic method developed for 6-unsubstituted 3,4-dihydropyrimidin-2(1H)-thiones 9 and 2-ones 10 is described. The novelties of the synthesis protocol are as follows: 1) the use of Lewis acid-mediated reaction, 2) good to high yields, and 3) its broad scope of applicability to aldehydes and ureas. Hitherto unavailable 6-unsubstituted 2-amino DP 11 and 2-aryl DP 12 were obtained from 9 by a substitution reaction with the amine and the Liebeskind-Srogl reaction, respectively. The compounds 9, 10, and related 6-methyl derivatives 19-21 were assessed for their antiproliferative effect on the human promyelocytic leukemia cell line HL-60. 4,4-Dipropyl derivative 20 showed relatively strong activity with an IC₅₀ value of 341 nM.

An Overview on Steroids and Microwave Energy in Multi-Component Reactions towards the Synthesis of Novel Hybrid Molecules

In recent years, hybrid systems are gaining considerable attention owing to their various biological applications in drug development. Generally, hybrid molecules are constructed from different molecular entities to generate a new functional molecule with improved biological activities. There already exist a large number of naturally occurring hybrid molecules based on both non-steroid and steroid frameworks synthesized by nature through mixed biosynthetic pathways such as, a) integration of the different biosynthetic pathways or b) Carbon- Carbon bond formation between different components derived through different biosynthetic pathways. Multicomponent reactions are a great way to generate efficient libraries of hybrid compounds with high diversity. Throughout the scientific history, the most common factors developing technologies are less energy consumption and avoiding the use of hazardous reagents. In this case, microwave energy plays a vital role in chemical transformations since it involves two very essential criteria of synthesis, minimizing energy consumption required for heating and time required for the reaction. This review summarizes the use of microwave energy in the synthesis of steroidal and non-steroidal hybrid molecules and the use of multicomponent reactions.

Synthesis of Dihydropyrimidinones (DHPMs) and Hexahydro Xanthene Catalyzed by 1,4-Diazabicyclo [2.2.2] Octane Triflate Under Solvent-Free Condition

OBJECTIVE

DABCO salts were evaluated as catalysts for the Biginelli reaction between 4- methoxybenzaldehyde, urea and ethyl acetoacetate under solvent-free conditions. 1,4-Diazabicyclo [2.2.2] octane triflate was found to be a simple, inexpensive, highly efficient catalyst for Biginelli reaction for a variety aromatic aldehyde with urea and ethyl acetoacetate at 80°C afforded corresponding 3,4-dihydropyrimidinones in 50-99% yields after 30-120 minutes. 1,3-Cyclohexadione was used in place of ethyl acetoacetate in the absence of urea this methodology is giving hexahydro xanthene derivatives in good to excellent yields after 3-4 hours.

METHODS

DABCO salt 4 (5 mol%), 4-methoxybenzaldehyde (0.73 mmol) and urea (0.73 mmol) were stirred for 10 minutes at 80°C, then ethyl acetoacetate (1.5 equiv.) was added and reaction mixture was stirred at 80°C for specified time. The resulting solution was stirred continuously and progress of the reaction was followed by TLC. The crude reaction mixture was purified by flash column chromatography on silica gel (hexane/ethyl acetate (1:2)) to give pure desired product.

RESULTS

Reaction conditions of the Biginelli reaction were optimized using 4-methoxybenzaldehyde (0.73 mmol), urea (0.73 mmol), and ethyl acetoacetate (5 equiv.) as model substrates catalyzed by 1,4-Diazabicyclo [2.2.2] octane triflate (5 mol%) in a different solvents, screening of different catalysts and different temperatures. Neat condition was found to be the best for the Biginelli condensation and corresponding 3,4- dihydropyrimidinones was obtained in good to excellent yields. When the reaction was carried out with benzaldehyde derivatives and cyclohexane-1,3-dione in place of ethyl acetoacetate in the absence of urea, solely corresponding hexahydro xanthene derivatives were obtained in 61-91% yields.

CONCLUSION

In conclusion, we have applied salts of 1,4-Diaza-bicyclo [2.2.2] octane as catalysts in the Biginelli condensation and corresponding 3,4-dihydropyrimidinones were obtained in 50- 99% yields under solvent free conditions. This methodology is having advantages like simple work-up; low loading of catalyst and reaction was performed at moderate temperature under solvent-free conditions.

Understanding the Lack of Reactivity of 2,4-Dihydroxybenzaldehyde Towards the Biginelli Adduct Using Density Functional Theory Molecular Modeling

The Biginelli reaction is a multicomponent reaction for obtaining dihydropyrimidinthiones quickly, with multiple substitution patterns. The reaction mechanism remains unclear. Three possible pathways proposed for the reaction are the iminium route, an enamine intermediate, and the Knoevenagel pathway. However, when thiourea was used, no theoretical calculations were reported. Thus, based on the literature, the iminium pathway was used to obtain evidence explaining the lack of reactivity of 2,4-dihydroxybenzaldehyde towards the Biginelli adduct, compared with 4-hydroxybenzaldehyde. This computational study, carried out using the B3LYP/6-31++G(d,p) level of theory, showed an increment of 150 kJ/mol in the activation energy of the slowest pathway, due to the presence of a hydroxyl group in position 2 (ortho) of the aromatic aldehyde, decreasing its reactivity. Natural bond orbital (NBO) calculations suggest that the determinant steps are simultaneous, i.e., the polarization of the carbonyl group and its corresponding protonation by the hydrogen of the SH fragment of the thiourea tautomer. The activation enthalpy values suggest that the nucleophile attack takes place later on the compound 2,4-dihydroxybenzaldehyde compared to 4-hydroxybenzaldehyde-TS, confirming that the OH group in position 2 hinders the condensation reaction.

My Twenty Years in Microwave Chemistry: From Kitchen Ovens to Microwaves that aren't Microwaves

This Personal Account describes the author's involvement in the field of microwave-assisted organic synthesis (MAOS) from the late 1990's starting out with kitchen microwave ovens right through to the development of a reactor in 2016 that - although not using microwave technology - in many ways mimics the performance of a modern laboratory microwave. The reader is taken along a journey that has spanned two decades of intense research on various aspects of microwave chemistry, and, at the same time, was intimately linked to key innovations regarding equipment design and development. A "behind the scenes" approach is taken in this article to share - from a very personal point of view - how specific projects and research ideas were conceived and developed in my research group, and how in general the field of microwave chemistry has progressed in the last two decades.

Effect of N-1 arylation of monastrol on kinesin Eg5 inhibition in glioma cell lines

An original and focused library of two sets of dihydropyrimidin-2-thiones (DHPMs) substituted with N-1 aryl groups derived from monastrol was designed and synthesized in order to discover a more effective Eg5 ligand than the template. Based on molecular docking studies, four ligands were selected to perform pharmacological investigations against two glioma cell lines. The results led to the discovery of two original compounds, called 20h and 20e, with an anti-proliferative effects, achieving IC50 values of about half that of the IC50 of monastrol in both cell lines. As with monastrol, flow cytometry analyses showed that the 20e and 20h compounds induced cell cycle arrest in the G2/M phase, and immunocytochemistry essays revealed the formation of monopolar spindles due to Eg5 inhibition without any toxicity to Caenorhabditis elegans.

FeCl₃∙6H₂O/TMSBr-Catalyzed Rapid Synthesis of Dihydropyrimidinones and Dihydropyrimidinethiones under Microwave Irradiation

An efficient and practical protocol has been developed to synthesize dihydropyrimidinones and dihydropyrimidinethiones through FeCl₃∙6H₂O/TMSBr-catalyzed three-component cyclocondensation under microwave irradiation. This approach features high yields, broad substrate scope, short reaction time, mild reaction conditions, operational simplicity and easy work-up, thus affording a versatile method for the synthesis of dihydropyrimidinones and dihydropyrimidinethiones.

New dihydropyrimidin-2(1H)-one based Hsp90 C-terminal inhibitors

The inhibition of the C-terminal domain of heat shock protein 90 (Hsp90) is emerging as a novel strategy for cancer therapy, therefore the identification of a new class of C-terminal inhibitors is strongly required.

Dihydropyrimidine based hydrazine dihydrochloride derivatives as potent urease inhibitors

Four series of heterocyclic compounds 4-dihydropyrimidine-2-thiones 7-12 (series A), N,S-dimethyl-dihydropyrimidines 13-18 (series B), hydrazine derivatives of dihydropyrimidine 19-24 (series C), and tetrazolo dihydropyrimidine derivatives 25-30 (series D), were synthesized and evaluated for in vitro urease inhibitory activity. The series B-D were first time examined for urease inhibition. Series A and C were found to be significantly active with IC50 values between 34.7-42.9 and 15.0-26.0 μM, respectively. The structure-activity relationship showed that the free S atom and hydrazine moiety are the key pharmacophores against urease enzyme. The kinetic studies of the active series A (7-12) and C (19-24) were carried out to determine their modes of inhibition and dissociation constants Ki. Compounds of series A (7-12) and series C (19-24) showed a mixed-type of inhibition with Ki values ranging between 15.76-25.66 and 14.63-29.42 μM, respectively. The molecular docking results showed that all the active compounds of both series have significant binding interactions with the active sites specially Ni-ion of the urease enzyme. Cytotoxicity of all series A-D was also evaluated against mammalian mouse fibroblast 3T3 cell lines, and no toxicity was observed in cellular model.

Microwave-Assisted Multicomponent Synthesis of Dihydroquinoxalinones on Soluble Polymer Support

A one-pot and two-step reaction of four components, including aldehydes, Fmoc-protected α-amino acid, isocyanide, and soluble polymer-supported 4-fluoro-3-amino benzoate ester, was developed for an efficient synthesis of dihydroquinoxalinones under microwave irradiation. Fmoc deprotection followed by intramolecular cyclization of the diamide gave a facile access to novel bicyclic quinoxalin-2-ones. On the basis of this approach, a new route to synthesize this privileged scaffold from the diamide intermediate was designed and accomplished with high yields. Use of multicomponent reaction (MCR) has been shown to display a good functional group tolerance, while the product isolation and purification is straightforward by precipitation and washings. Current library discusses the synthesis and diversification of 21 compounds produced using this strategy.

Exploration of the dihydropyrimidine scaffold for the development of new potential anti-inflammatory agents blocking prostaglandin E₂ synthase-1 enzyme (mPGES-1)

Agents targeting microsomal prostaglandin E2 synthase-1 (mPGES-1) would inhibit only PGE2 production induced by inflammatory stimuli and thus could represent a valuable alternative to non-steroidal anti-inflammatory drugs (NSAIDs) as they should be free from the severe side effects of the classic anti-inflammatory drugs. Although several mPGES-1 inhibitors have been so far identified, none of them is currently in clinical trials, therefore the discovery of new molecular platforms, able to interfere with this interesting target, is urgently required. Here, we report the results of a focused collection of dyhidropyrimidin-2(1H)-one based molecules projected by Virtual Screening computational techniques. The key interactions with the receptor counterpart were introduced as a qualitative filter for the selection of the most promising compounds. The biological data obtained are consistent with the computer-aided suggestions and disclosed two interesting molecules showing in vitro mPGES-1 inhibitory activity in the low μM range.

Direct synthesis of 5- and 6-substituted 2-aminopyrimidines as potential non-natural nucleobase analogues

A series of 2-aminopyrimidine derivatives, substituted at 5- and 6-positions, were synthesized.

Regioselective synthesis of novel and diverse naphtho[1,2-b]furan-3-carboxamides and benzofuran-3-carboxamides by cascade formal [3 + 2] cycloaddition

The regioselective synthesis of diverse naphtho[1,2-b]furan-3-amides and benzofuran-3-amides was accomplished by the In(OTf)₃-catalyzed cascade formal [3 + 2] cycloaddition of 1,4-naphthoquinones or benzoquinones with β-ketoamides.

Efficient synthesis of dihydropyrimidinones via a three-component Biginelli-type reaction of urea, alkylaldehyde and arylaldehyde

A one-pot three-component synthesis of dihydropyrimidinones via a molecular iodine-catalyzed tandem reaction of simple readily available mono-substituted urea, alkylaldehyde, and arylaldehyde has been developed. The reaction proceeds with high chemo- and regioselectivity to give highly diverse dihydropyrimidinones in reasonable yields under mild reaction conditions. Moreover, the first catalytic enantioselective version of this reaction was also realized by using chiral spirocyclic SPINOL-phosphoric acids.

Regioselective N1-alkylation of 3,4-dihydropyrimidine-2(1H)-ones: screening of their biological activities against Ca(2+)-ATPase

A regioselective N1-alkylation of 3,4-dihydropyrimidin-2(1H)-ones using a very efficient mild base Cs(2)CO(3) and alkyl halides at room temperature has been reported. The selectivity of this methodology is excellent and the yields of the alkylated products are very good. Furthermore inhibitory action of both the 3,4-dihydropyrimidin-2(1H)-ones and the N1-alkylated derivatives were tested on Ca(2+)-ATPase, which revealed that the parent compounds can act as Ca(2+)-ATPase inhibitors whereas the N1-alkylated derivatives are inefficient for this purpose.