Developments in synthesis,characterization, and self-assembly of polycarbodiimide systems

Described herein is a comprehensive survey on the most recent advancements in polycarbodiimide synthetic methodologies, structure determination, property design, and self-assembly. In particular, the ¹⁵N-isotopic enrichment of polycarbodiimides is detailed along with the use of ¹⁵N NMR to identify the regioregularity and mechanism of chiroptical switching in polycarbodiimides. Furthermore, the new Ni(II) mediated “living” polymerization is explained along with its utilization in the incorporation of polycarbodiimides into block copolymers, graft copolymers, and star polymers. Finally, we review the recent discoveries focusing on the highly tunable self-assembly behaviors of polycarbodiimide homopolymers and copolymers. © 2017 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2017 , 55, 2915–2934     

Automated discovery of noncovalent inhibitors of SARS-CoV-2 main protease by consensus Deep Docking of 40 billion small molecules

Recent explosive growth of ‘make-on-demand’ chemical libraries brought unprecedented opportunities but also significant challenges to the field of computer-aided drug discovery. To address this expansion of the accessible chemical universe, molecular docking needs to accurately rank billions of chemical structures, calling for the development of automated hit-selecting protocols to minimize human intervention and error. Herein, we report the development of an artificial intelligence-driven virtual screening pipeline that utilizes Deep Docking with Autodock GPU, Glide SP, FRED, ICM and QuickVina2 programs to screen 40 billion molecules against SARS-CoV-2 main protease (Mpro). This campaign returned a significant number of experimentally confirmed inhibitors of Mpro enzyme, and also enabled to benchmark the performance of twenty-eight hit-selecting strategies of various degrees of stringency and automation. These findings provide new starting scaffolds for hit-to-lead optimization campaigns against Mpro and encourage the development of fully automated end-to-end drug discovery protocols integrating machine learning and human expertise.

Deep learning-accelerated docking coupled with computational hit selection strategies enable the identification of inhibitors for the SARS-CoV-2 main protease from a chemical library of 40 billion small molecules.     

Mannose‐based graft polyesters with tunable binding affinity to concanavalin A

Glycopolymers have been widely used to understand the interactions between carbohydrates and lectins, which facilitate the diagnosis and detection of disease and pathogens as well as the development of vaccines. While studies have been focused on the correlation of glycopolymer structure and their binding to lectins, graft‐type glycopolyesters are uncommon. Herein, we report the design and synthesis of mannose‐based graft polyesters by “grafting‐from” method and investigate their interactions with Concanavalin A (Con A). As confirmed by ¹H NMR spectroscopy and sulfuric acid‐UV method, graft polyesters with different lengths of mannose graft were successfully synthesized. Our results from turbidimetry binding assay showed that graft polyesters with longer mannose graft exhibit higher initial binding rate (k_i). Isothermal titration calorimetry measurements of these graft polyesters with Con A showed that polymers exhibit higher binding affinity (k_a) with the number of side chain mannose. This study provides understanding of the interaction between Con A and mannose‐based graft polyesters, which can be employed for the development of glycopolymeric therapeutics. © 2017 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2017 , 55, 3908–3917     

1H NMR patterns of antiaromatic systems: Paratropic displacement dependence upon LUMO-HOMO energy gap

¹H NMR chemical shifts of antiaromatic species reveal an enhanced paratropic displacement. The high-field shifts exhibited by doubly charged benzenoid polycycles were shown to be strongly related to the LUMO-HOMO energy gaps in these antiaromatic systems. As the gap decreases, a larger paratropic shift was observed.     

Approaches to charge calculations in molecular mechanics

Alternative methods of estimating atomic charges in haloalkanes are presented, derived from quantum mechanical and classical treatments. A scheme based on a breakdown of the transmission of charge by polar atoms into one-bond, two-bond, and three-bond additive contributions is given, in which the one-bond effect is proportional to the difference in the electronegativities of the bonded atoms, and the two- and three-bond effects functions of the atomic electronegativity and polarizability. Suitable developments of the basic scheme, including an iterative self-consistent process, give calculated dipole moments for a variety of haloalkanes in good agreement with the observed values. The atomic charges obtained by this scheme are compared with other estimates of these charges. They are similar to those derived from a simple LCAO –MO scheme but differ from those obtained by population analysis of more refined quantum mechanical calculations.     

Functionalization of polystyrene. III. Synthesis of polymeric thiol reagents

The synthesis of polymer-bound thiol reagents, supported on macroporous 4% divinylbenzene co-polymer (Amberlite XE-305), via three synthetic approaches is described: (i) Alkylation or acylation of XE-305 with 3-nitro-4-halogen-substituted benzyl chloride or benzoyl halide yielding 3-nitro-4-halobenzene-bound species, followed by substitution of the activated polymeric halogen atom with sulfur (see Scheme 1). (ii) Formation of a thiol ether by a direct substitution of an active polymeric halogen by reaction with benzylthiol, followed by chlorination, thiolation, and reduction (see Scheme 2). (iii) Attachment of a prepared tailor-made disulfide to aminomethyl function of a polymeric support, followed by reduction (see Scheme 3). The polymers were tested for their free-thiol content by 5, 5′-dithiobis(2-nitrobenzoic acid) (Ellman's reagent¹²) in DMF. Their thiolytic activity was investigated in the removal of 2-nitrophenylsulphenyl (Nps) group from Nps-protected amino acid (Scheme 4). Site-site interaction between the polymer-bound thiol with its activated halide precursor to yield polymeric sulfide during displacement reaction, and the interconversion of the polymeric thiols into polymeric disulfides at equilibrium or during reaction with Nps-amino acids, observed, and is attributed to the flexibility of the polymeric matrices.     

The NMR spectra of porphyrins—19: 13C and proton NMR spectra of metal-free porphyrins with the Type-IX substituent orientation,and of their zinc(II) complexes

The ¹³C and proton NMR spectra of six porphyrins bearing the substituent orientation characteristic of the natural “Type-IX” arrangement are reported and assigned. Significant concentration effects in the spectra of the free base porphyrins, together with the broadening of the C_α (and occasionally C_β) carbon resonances due to NH tautomerism caused a significant loss of data in these spectra. However, the spectra of the corresponding zinc(II) porphyrins (with addition of excess pyrrolidine) show that both these extraneous effects are completely removed to give well-resolved spectra with accurately reproducible chemical shifts. These spectra are assigned and an analysis of the chemical shifts allows the deduction of substituent chemical shift (SCS) parameters for the peripheral substituents at the beta and meso carbons. There is no global effect of these beta substituents, the beta carbon SCS being confined to the immediate pyrrole ring, and the meso carbon SCS to the two adjacent pyrrole rings. The SCS parameters are analyzed and it is shown how they can be used to predict the peripheral and meso carbon chemical shifts of any porphyrin bearing the substituents discussed.     

Electron transfer from dibenzo[b,f]-1-azapentalene dianion: Attempted synthesis of dibenzo[b,f]-1-azapentalene

When dibenzo[b,f]-1-azapentalene dianion (3) was allowed to react with either iron (III) chloride or ethylene bromide, a one-electron transfer from3 took place readily to give the radical anion11. Further electron transfer from11 did not occur presumably due to the antiaromatic character of dibenzo[b,f]-1-azapentalene (1) that would have resulted. The radical anion11 underwent further transformation by hydrogen abstraction from the solvent to give 5,10-dihydroindeno[1,2-b]indole (2) and by dimerization to themeso and (R,S) isomers of 5,5,10,10-tetrahydro-10,10-biindeno[1,2-b]indole (4 a and4 b) respectively.

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Elektronentransfer von Dibenzo[b,f]-1-azapentalen-Dianion: Ein Versuch zur Synthese von Dibenzo[b,f]-1-azapentalen

Zusammenfassung Die Reaktion von Dibenzo[b,f]-1-azapentalen-Dianion (3) mit Eisen (III) oder Ethylenbromid ergab einen Ein-Elektronentransfer zum Radikalanion11. Ein weiterer Elektronentransfer fand nicht statt, vermutlich wegen des antiaromatischen Charakters von Dibenzo[b,f]-1-azapentalen (1), das dabei entstehen müßte. Das Radikalanion11 ergab unter Wasserstoffentzug aus dem Lösungsmittel 5,10-Dihydroindeno[1,2-b]indol (2), das weiter zummeso- bzw. (R,S)-5,5,10,10-tetrahydro-10,10-biindeno[1,2-b]indol (4 a bzw.4 b) dimerisierte.

     

Anomalous dehydration of 2-phenylindole-3-carboxamide to 2-phenylindole-3-carbonitrile by lithium aluminum hydride

Steric factors have been shown to be responsible for the anomalous dehydration of 2-phenylindole-3-carboxamide (1) to 2-phenylindole-3-carbonitrile (3) by lithium aluminum hydride. This steric effect was also reflected in the reactions of 2-phenylindole (4) and its derivatives.

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Anomale Dehydratisierung von 2-Phenylindol-3-carbonsäureamid zu 2-Phenyl-indol-3-carbonitril mit Lithiumaluminiumhydrid (Kurze Mitteilung)

Zusammenfassung Es wird gezeigt, daß für die anomale Dehydratisierung von 2-Phenylindol-3-carbonsäureamid (1) zum entsprechenden Nitril3 durch Lithiumaluminiumhydrid sterische Faktoren verantwortlich sind. Dieser sterische Effekt zeigt sich auch bei Reaktionen von 2-Phenylindol (4) und seiner Derivate.

     

Nitration of 2-substituted pyrimidine-4,6-diones,structure and reactivity of 5,5-gem-dinitropyrimidine-4,6-diones

Nitration of some 2-substituted pyrimidine-4,6-diones in sulfuric acid was studied, which afforded previously unknown 5,5-gem-dinitropyrimidine-4,6-diones in high yields. The gem-dinitro products were easily attacked by nucleophiles with concomitant formation of gem-dinitroacetyl derivatives, which in turn could be further hydrolyzed to salts of dinitromethane and triureas.