Prediction of Compound Synthesis Accessibility Based on Reaction Knowledge Graph

With the increasing application of deep-learning-based generative models for de novo molecule design, the quantitative estimation of molecular synthetic accessibility (SA) has become a crucial factor for prioritizing the structures generated from generative models. It is also useful for helping in the prioritization of hit/lead compounds and guiding retrosynthesis analysis. In this study, based on the USPTO and Pistachio reaction datasets, a chemical reaction network was constructed for the identification of the shortest reaction paths (SRP) needed to synthesize compounds, and different SRP cut-offs were then used as the threshold to distinguish a organic compound as either an easy-to-synthesize (ES) or hard-to-synthesize (HS) class. Two synthesis accessibility models (DNN-ECFP model and graph-based CMPNN model) were built using deep learning/machine learning algorithms. Compared to other existing synthesis accessibility scoring schemes, such as SYBA, SCScore, and SAScore, our results show that CMPNN (ROC AUC: 0.791) performs better than SYBA (ROC AUC: 0.76), albeit marginally, and outperforms SAScore and SCScore. Our prediction models based on historical reaction knowledge could be a potential tool for estimating molecule SA.     

A Molecular-Wide and Electron Density-Based Approach in Exploring Chemical Reactivity and Explicit Dimethyl Sulfoxide (DMSO) Solvent Molecule Effects in the Proline Catalyzed Aldol Reaction

Modelling of the proline (1) catalyzed aldol reaction (with acetone 2) in the presence of an explicit molecule of dimethyl sulfoxide (DMSO) (3) has showed that 3 is a major player in the aldol reaction as it plays a double role. Through strong interactions with 1 and acetone 2, it leads to a significant increase of energy barriers at transition states (TS) for the lowest energy conformer 1a of proline. Just the opposite holds for the higher energy conformer 1b. Both the ‘inhibitor’ and ‘catalyst’ mode of activity of DMSO eliminates 1a as a catalyst at the very beginning of the process and promotes the chemical reactivity, hence catalytic ability of 1b. Modelling using a Molecular-Wide and Electron Density-based concept of Chemical Bonding (MOWED-CB) and the Reaction Energy Profile–Fragment Attributed Molecular System Energy Change (REP-FAMSEC) protocol has shown that, due to strong intermolecular interactions, the HN-C-COOH (of 1), CO (of 2), and SO (of 3) fragments drive a chemical change throughout the catalytic reaction. We strongly advocate exploring the pre-organization of molecules from initially formed complexes, through local minima to the best structures suited for a catalytic process. In this regard, a unique combination of MOWED-CB with REP-FAMSEC provides an invaluable insight on the potential success of a catalytic process, or reaction mechanism in general. The protocol reported herein is suitable for explaining classical reaction energy profiles computed for many synthetic processes.     

Decomposition Reaction of Zn-MPA（3-Mercaptopropionic Acid） Complex Under Microwave Irradiation

The thermal decomposition of Zn-MPA complex was investigated under microwave irradiation. ZnO and ZnS nanocrystals could be obtained by decomposing Zn-MPA（3-mercaptopropionic acid） complex under different reaction conditions. It was found that both the pH value of the solution and the molar ratio of Zn2＋ and MPA can play an important role in the formation of ZnO and ZnS nanocrystals. MPA mainly acts as an S source or as a complexing agent. This study provides a new route for the controllable preparation of semiconductor nanocrystals.     

Synthesis and Structure Elucidation of Novel Spirooxindole Linked to Ferrocene and Triazole Systems via [3 + 2] Cycloaddition Reaction

In the present work, a novel heterocyclic hybrid of a spirooxindole system was synthesized via the attachment of ferrocene and triazole motifs into an azomethine ylide by [3 + 2] cycloaddition reaction protocol. The X-ray structure of the heterocyclic hybrid (1″R,2″S,3R)-2″-(1-(3-chloro-4-fluorophenyl)-5-methyl-1H-1,2,3-triazole-4-carbonyl)-5-methyl-1″-(ferrocin-2-yl)-1″,2″,5″,6″,7″,7a″-hexahydrospiro[indoline-3,3″-pyrrolizin]-2-one revealed very well the expected structure, by using different analytical tools (FTIR and NMR spectroscopy). It crystallized in the triclinic-crystal system and the P-1-space group. The unit cell parameters are a = 9.1442(2) Å, b = 12.0872(3) Å, c = 14.1223(4) Å, α = 102.1700(10)°, β = 97.4190(10)°, γ = 99.1600(10)°, and V = 1484.81(7) ų. There are two molecules per unit cell and one formula unit per asymmetric unit. Hirshfeld analysis was used to study the molecular packing of the heterocyclic hybrid. H···H (50.8%), H···C (14.2%), Cl···H (8.9%), O···H (7.3%), and N···H (5.1%) are the most dominant intermolecular contacts in the crystal structure. O···H, N···H, H···C, F···H, F···C, and O···O are the only contacts that have the characteristic features of short and significant interactions. AIM study indicated predominant covalent characters for the Fe–C interactions. Also, the electron density (ρ(r)) at the bond critical point correlated inversely with the Fe–C distances.     

Comparison of betaine and l-stachydrine as phase-transfer catalysts in Michael addition and Darzens reaction

Betaine and l-stachydrine have been tested as phase-transfer catalysts in Michael and Darzens reactions. The catalytic effect of l-stachydrine was found comparable to that of betaine in Michael addition and even higher when considering Darzens reaction. The desired products have been obtained in higher yields in solid-liquid system than under liquid-liquid bi-phase conditions. The influence of microwave irradiation and ultrasound on the reaction rate has been studied.     

Nucleophilic Polymer-supported Tertiaryphosphine Organocatalysis：[3＋2] Annulation Reaction of Alkyl 2-Butynoates with Activated Alkenes

JandaJel resin-supported triphenylphosphine（JJ-TPP）,was used as an effective organocatalyst for the [3＋2] annulation reaction of alkyl 2-butynoates with electron-deficient alkenes to afford the corresponding cyclopentenes in 40％-68％ isolated yields.JJ-TPP was reused after simple filtration and vacuum drying.     

Prediction of the pH‐rate profile for dimethyl sulfide oxidation by hydrogen peroxide: The role of elusive H3O2+ Ion

Experimental kinetics of sulfide oxidation by hydrogen peroxide presents a pH‐dependent profile. In this article, it was carried out a detailed study of the mechanism and kinetics of dimethyl sulfide (DMS) oxidation by H₂O₂ in neutral, acid, and basic aqueous medium using ab initio calculations. The results point out that DMS oxidation in neutral aqueous medium occurs through its direct reaction with H₂O₂. In acid medium, cluster‐continuum model calculations shows that cluster is the best representation of the very reactive species. In basic medium, there is formation of the species. However, the pathway involving this species has high free energy barrier, making this pathway unfeasible. The theoretical pH‐rate profile is in good agreement with the experimental observations. © 2013 Wiley Periodicals, Inc.     

Comparative Study of Catalytic Potential of TBAB,BTEAC, and CTAB in One-Pot Synthesis of 1,4-Dihydropyridines Under Aqueous Medium

Convenient and straightforward tetrabutylammonium bromide (TBAB), benzyltrienthylammonium chloride (BTEAC), and cetyltrimethylammonium bromide (CTAB) catalyzed synthesis of 1,4-dihydropyridines (1,4-DHPs) in water was established for the first time. The catalytic potential of phase-transfer catalysts (PTCs) in three different concentrations was envisioned. Aryl aldehydes and hetero aryl aldehydes afforded good yields of 1,4-DHPs in TBAB and BTEAC reactions. In particular, furfuraldehyde and thienyl-2-carbaldehyde produced excellent yields. Isolation of the products through nonchromatographic methods, good to excellent yields, and benign reaction conditions are the major advantages of this protocol.     

A chromatographic comparison of the pore structure of zirconia high performance liquid chromatographic materials made by the polymerization induced colloidal aggregation and the Oil Emulsion methods

Summary The pore structures of zirconium oxide particles prepared by two different methods (PICA and Oil Emulsion processes) are compared. Nitrogen sorptometry and size exclusion chromatography are used to characterize the two different types of particles. Significant and unexpected differences were found in the accessible pore volumes and the bed packing densities of the two materials. The PICA material was found to have a higher totally included and totally excluded volume than would be normally expected. The chromatographic method provides results which are more useful for the application of these materials to separation sciences.