C-H...N and C-H...O intramolecular hydrogen bonding effects in the 1H, 13C and 15N NMR spectra of the configurational isomers of 1-vinylpyrrole-2-carbaldehyde oxime substantiated by DFT calculations

Repurposing 1,2,4-oxadiazoles as SARS-CoV-2 PLpro inhibitors and investigation of their possible viral entry blockade potential

Although vaccines are obviously mitigating the COVID-19 pandemic diffusion, efficient complementary antiviral agents are urgently needed to combat SARS-CoV-2. The viral papain-like protease (PLpro) is a promising therapeutic target being one of only two essential proteases crucial for viral replication. Nevertheless, it dysregulates the host immune sensing response. Here we report repositioning of the privileged 1,2,4-oxadiazole scaffold as promising SARS-CoV-2 PLpro inhibitor with potential viral entry inhibition profile. The design strategy relied on mimicking the general structural features of the lead benzamide PLpro inhibitor GRL0617 with isosteric replacement of its pharmacophoric amide backbone by 1,2,4-oxadiazole core. Inspired by the multitarget antiviral agents, the substitution pattern was rationalized to tune the scaffold's potency against other additional viral targets, especially the spike receptor binding domain (RBD) that is responsible for the viral invasion. The Adopted facial synthetic protocol allowed easy access to various rationally substituted derivatives. Among the evaluated series, the 2-[5-(pyridin-4-yl)-1,2,4-oxadiazol-3-yl]aniline (5) displayed the most balanced dual inhibitory potential against SARS-CoV-2 PLpro (IC50=7.197 μM) and spike protein RBD (IC50 = 8.673 μM), with acceptable ligand efficiency metrics, practical LogP (3.8) and safety profile on Wi-38 (CC50 = 51.78 μM) and LT-A549 (CC50 = 45.77 μM) lung cells. Docking simulations declared the possible structural determinants of activities and enriched the SAR data for further optimization studies.

Computational 1 H and 13 C NMR in structural and stereochemical studies

Present review outlines the advances and perspectives of computational ¹ H and ¹³ C NMR applied to the stereochemical studies of inorganic, organic, and bioorganic compounds, involving in particular natural products, carbohydrates, and carbonium ions. The first part of the review briefly outlines theoretical background of the modern computational methods applied to the calculation of chemical shifts and spin-spin coupling constants at the DFT and the non-empirical levels. The second part of the review deals with the achievements of the computational ¹ H and ¹³ C NMR in the stereochemical investigation of a variety of inorganic, organic, and bioorganic compounds, providing in an abridged form the material partly discussed by the author in a series of parent reviews. Major attention is focused herewith on the publications of the recent years, which were not reviewed elsewhere.

Ambient access to a new family of pyrrole-fused pyrazine nitrones via 2-carbonyl-N-allenylpyrroles

The chemo-, regio- and stereoselective synthesis of pyrrole-fused pyrazine nitrones via the direct reaction of 2-carbonyl-N-allenylpyrroles (readily accessible from the corresponding NH-pyrroles) with hydroxyl amine hydrochloride has been developed.

Synthesis of Pyridylimido Complexes of Tantalum and Niobium by Reductive Cleavage of the N═N Bond of 2,2'-Azopyridine: Precursors for Early-Late Heterobimetallic Complexes

We report the syntheses of 2-pyridylimido complexes of tantalum and niobium by N═N bond cleavage of 2,2'-azopyridine. Reaction of MCl5 (M = Ta and Nb) with 2,2'-azopyridine in the presence of 0.5 equiv of 1-methyl-3,6-bis(trimethylsilyl)-1,4-cyclohexadiene (abbreviated Si-Me-CHD) afforded a dark red solution (for Ta) and a dark blue solution (for Nb) with some insoluble precipitates. After removing the solids, another 0.5 equiv of Si-Me-CHD was added to each solution, giving [M(═Npy)Cl3]n (1a: M = Ta; 1b: M = Nb) through reductive cleavage of the N═N bond of 2,2'-azopyridine. The initial products of the above reactions were determined to be 2,2'-azopyridine-bridged dinuclear complexes, [(MCl4)2(μ-pyNNpy)] (2a: M = Ta; 2b: M = Nb), which were isolated by treating MCl5 with 2,2'-azopyridine and Si-Me-CHD in a 2:1:1 molar ratio. In 2a and 2b, the N═N bond was reduced to a single bond via two-electron reduction. Further reduction of complexes 2a and 2b with 1 equiv of Si-Me-CHD afforded complexes 1a and 1b. An anionic doubly μ-imido-bridged ditantalum complex, [nBu4N][Ta2(μ-Npy)2Cl7] (3a), was generated upon addition of nBu4NCl to complex 1a, while addition of nBu4NCl to niobium complex 1b gave a polymeric terminal imido complex, [nBu4N]n/2[{Nb(═Npy)Cl3}2(μ-Cl)]n/2 (3b). Complexations of 1a and 1b with 1 equiv of 2,2'-bipyridine resulted in the formation of mononuclear 2-pyridylimido complexes, M(═Npy)Cl3(bipy) (4a: M = Ta; 4b: M = Nb), whose main structural feature is intramolecular hydrogen bonding between the ortho hydrogen atom of 2,2'-bipyridine and the nitrogen atom of the pyridyl group on the imido ligand. Isolated 2-pyridylimido complexes 4a and 4b reacted with [RhCl(cod)]2 to produce the corresponding early-late heterobimetallic complexes, (bipy)MCl3(μ-Npy)RhCl(cod) (5a: M = Ta; 5b: M = Nb).

Mechanochemical Synthesis and Isomerization of N-Substituted Indole-3-carboxaldehyde Oximes †

Performing solution-phase oximation reactions with hydroxylamine hydrochloride (NH₂OH·HCl) carries significant risk, especially in aqueous solutions. In the present study, four N-substituted indole-3-carboxaldehyde oximes were prepared from the corresponding aldehydes by solvent-free reaction with NH₂OH·HCl and a base (NaOH or Na₂CO₃) using a mechanochemical approach, thus minimizing the possible risk. In all cases, the conversion to oximes was almost complete. The focus of this work is on 1-methoxyindole-3-carboxaldehyde oxime, a key intermediate in the production of indole phytoalexins with useful antimicrobial properties. Under optimized conditions, it was possible to reach almost 95% yield after 20 min of milling. Moreover, for the products containing electron-donating substituents (-CH₃, -OCH₃), the isomerization from the oxime anti to syn isomer under acidic conditions was discovered. For the 1-methoxy analog, the acidic isomerization of pure isomers in solution resulted in the formation of anti isomer, whereas the prevalence of syn isomer was observed in solid state. From NMR data the syn and anti structures of produced oximes were elucidated. This work shows an interesting and possibly scalable alternative to classical synthesis and underlines environmentally friendly and sustainable character of mechanochemistry.

Theoretical calculations of carbon-hydrogen spin-spin coupling constants

Structural applications of theoretical calculations of carbon-hydrogen spin-spin coupling constants are reviewed covering papers published mainly during the last 10-15 years with a special emphasis on the most notable studies of hybridization, substitution and stereoelectronic effects together with the investigation of hydrogen bonding and intermolecular interactions. The wide scope of different applications of calculated carbon-hydrogen couplings in the structural elucidation of particular classes of organic and bioorganic molecules is reviewed, concentrating mainly on saturated, unsaturated, aromatic and heteroaromatic compounds and their functional derivatives, as well as on natural compounds and carbohydrates. The review is dedicated to Professor Emeritus Michael Barfield in view of his invaluable pioneering contribution to this field.

Estimating the energy of intramolecular hydrogen bonds from 1H NMR and QTAIM calculations

The values of the downfield chemical shift of the bridge hydrogen atom were estimated for a series of compounds containing an intramolecular hydrogen bond O-HO, O-HN, O-HHal, N-HO, N-HN, C-HO, C-HN and C-HHal. Based on these values, the empirical estimation of the hydrogen bond energy was obtained by using known relationships. For the compounds containing an intramolecular hydrogen bond, the DFT B3LYP/6-311++G(d,p) method was used both for geometry optimization and for QTAIM calculations of the topological parameters (electron density ρ^BCP and the density of potential energy V in the critical point of the hydrogen bond). The calculated geometric and topological parameters of hydrogen bonds were also used to evaluate the energy of the hydrogen bond based on the equations from the literature. Comparison of calibrating energies from the ¹H NMR data with the energies predicted by calculations showed that the most reliable are the linear dependence on the topological ρ^BCP and V parameters. However, the correct prediction of the hydrogen bond energy is determined by proper fitting of the linear regression coefficients. To obtain them, new linear relationships were found between the calculated ρ^BCP and V parameters and the hydrogen bond energies obtained from empirical ¹H NMR data. These relationships allow the comparison of the energies of different types of hydrogen bonds for various molecules and biological ensembles.

Calculation of 15N NMR chemical shifts: Recent advances and perspectives

Recent advances in computation of ¹⁵N NMR chemical shifts are reviewed, concentrating mainly on practical aspects of computational protocols and accuracy factors. The review includes the discussion of the level of theory, the choice of density functionals and basis sets together with taking into account solvent effects, rovibrational corrections and relativistic effects. Computational aspects of ¹⁵N NMR are illustrated for the series of neutral and protonated open-chain nitrogen-containing compounds and nitrogen heterocycles, coordination and intermolecular complexes.

Experimental and theoretical study of the intramolecular C-H···N and C-H···S hydrogen bonding effects in the 1H and 13C NMR spectra of the 2-(alkylsulfanyl)-5-amino-1-vinylpyrroles: a particular state of amine nitrogen

In the (1)H NMR spectra of the 1-vinylpyrroles with amino- and alkylsulfanyl groups in 5 and 2 positions, an extraordinarily large difference between resonance positions of the HA and HB terminal methylene protons of the vinyl group is discovered. Also, the one-bond (1)J(C(β),H(B)) coupling constant is surprisingly greater than the (1)J(C(β),H(A)) coupling constant in pyrroles under investigation, while in all known cases, there was a reverse relationship between these coupling constants. These spectral anomalies are substantiated by quantum chemical calculations. The calculations show that the amine nitrogen lone pair is removed from the conjugation with the π-system of the pyrrole ring so that it is directed toward the HB hydrogen. These factors are favorable to the emergence of the intramolecular C-HB •••N hydrogen bonding in the s-cis(N) conformation. On the other hand, the spatial proximity of the sulfur to the HB hydrogen provides an opportunity of the intramolecular C-HB •••S hydrogen bonding in the s-cis(S) conformation. Presence of the hydrogen bond critical points as well as ring critical point for corresponding chelate ring revealed by a quantum theory of atoms in molecules (QTAIM) approach confirms the existence of the weak intramolecular C-H•••N and C-H•••S hydrogen bonding. Therefore, an unusual high-frequency shift of the HB signal and the increase in the (1)J(C(β),H(B)) coupling constant can be explained by the effects of hydrogen bonding.

Structural peculiarities of configurational isomers of 1-styrylpyrroles according to 1Н, 13С and 15N NMR spectroscopy and density functional theory calculations: electronic and steric hindrance for planar structure

Comparative analysis of the (1)Н and (13)С NMR data for a series of the E and Z-1-styrylpyrroles, E and Z-1-(1-propenyl)pyrroles, 1-vinylpyrroles and styrene suggests that the conjugation between the unsaturated fragments in the former compounds is reduced. This is the result of the mutual influence of the donor p-π and π-π conjugation having opposite directions. According to the NMR data combined with the density functional theory calculations, the Z isomer of 1-styrylpyrrole has essentially a nonplanar structure because of the steric hindrance. However, the E isomer of 1-styrylpyrrole is also an out-of-plane structure despite the absence of a sterical barrier for the planar one. Deviation of the E isomer from the planar structure seems to be caused by an electronic hindrance produced by a mutual influence of the p-π and π-π conjugation. The structure of the E isomer of the 2-substituted 1-styrylpyrroles is similar to that of the 2-substituted 1-vinylpyrroles. The steric effects in the Z isomer of the 2-substituted 1-styrylpyrroles result in the large increase of the dihedral angle between planes of the pyrrole ring and double bond.

Stereospecificity of (1) H, (13) C and (15) N shielding constants in the isomers of methylglyoxal bisdimethylhydrazone: problem with configurational assignment based on (1) H chemical shifts

In the (13) C NMR spectra of methylglyoxal bisdimethylhydrazone, the (13) C-5 signal is shifted to higher frequencies, while the (13) C-6 signal is shifted to lower frequencies on going from the EE to ZE isomer following the trend found previously. Surprisingly, the (1) H-6 chemical shift and (1) J(C-6,H-6) coupling constant are noticeably larger in the ZE isomer than in the EE isomer, although the configuration around the -CH═N- bond does not change. This paradox can be rationalized by the C-H⋯N intramolecular hydrogen bond in the ZE isomer, which is found from the quantum-chemical calculations including Bader's quantum theory of atoms in molecules analysis. This hydrogen bond results in the increase of δ((1) H-6) and (1) J(C-6,H-6) parameters. The effect of the C-H⋯N hydrogen bond on the (1) H shielding and one-bond (13) C-(1) H coupling complicates the configurational assignment of the considered compound because of these spectral parameters. The (1) H, (13) C and (15) N chemical shifts of the 2- and 8-(CH(3) )(2) N groups attached to the -C(CH(3) )═N- and -CH═N- moieties, respectively, reveal pronounced difference. The ab initio calculations show that the 8-(CH(3) )(2) N group conjugate effectively with the π-framework, and the 2-(CH(3) )(2) N group twisted out from the plane of the backbone and loses conjugation. As a result, the degree of charge transfer from the N-2- and N-8- nitrogen lone pairs to the π-framework varies, which affects the (1) H, (13) C and (15) N shieldings.

Study of stereospecificity of 1H, 13C, 15N and 77Se shielding constants in the configurational isomers of the selenophene-2-carbaldehyde azine by NMR spectroscopy and MP2-GIAO calculations

In the (1)H and (13)C NMR spectra of selenophene-2-carbaldehyde azine, the (1)H-5, (13)C-3 and (13)C-5 signals of the selenophene ring are shifted to higher frequencies, whereas those of the (1)H-1, (13)C-1, (13)C-2 and (13)C-4 are shifted to lower frequencies on going from the EE to ZZ isomer or from the E moiety to the Z moiety of EZ isomer. The (15)N chemical shift is significantly larger in the EE isomer relative to the ZZ isomer and in the E moiety relative to the Z moiety of EZ isomer. A very pronounced difference (60-65 mg/g) between the (77)Se resonance positions is revealed in the studied azine isomers, the (77)Se peak being shifted to higher frequencies in the ZZ isomer and in the Z moiety of EZ isomer. The trends in the changes of the measured chemical shifts are reasonably reproduced by the GIAO calculations at the MP2 level of the (1)H, (13)C, (15)N and (77)Se shielding constants in the energy-favorable conformation with the syn orientation of both selenophene rings relative to the C = N groups. The NBO analysis suggests that such an arrangement of the selenophene rings may take place because of a higher energy of some intramolecular interactions.

Direct evidence for methyl group coordination by carbon-oxygen hydrogen bonds in the lysine methyltransferase SET7/9

SET domain lysine methyltransferases (KMTs) are S-adenosylmethionine (AdoMet)-dependent enzymes that catalyze the site-specific methylation of lysyl residues in histone and non-histone proteins. Based on crystallographic and cofactor binding studies, carbon-oxygen (CH · · · O) hydrogen bonds have been proposed to coordinate the methyl groups of AdoMet and methyllysine within the SET domain active site. However, the presence of these hydrogen bonds has only been inferred due to the uncertainty of hydrogen atom positions in x-ray crystal structures. To experimentally resolve the positions of the methyl hydrogen atoms, we used NMR (1)H chemical shift coupled with quantum mechanics calculations to examine the interactions of the AdoMet methyl group in the active site of the human KMT SET7/9. Our results indicated that at least two of the three hydrogens in the AdoMet methyl group engage in CH · · · O hydrogen bonding. These findings represent direct, quantitative evidence of CH · · · O hydrogen bond formation in the SET domain active site and suggest a role for these interactions in catalysis. Furthermore, thermodynamic analysis of AdoMet binding indicated that these interactions are important for cofactor binding across SET domain enzymes.

Conformational and configurational analysis of an N,N carbonyl dipyrrinone-derived oximate and nitrone by NMR and quantum chemical calculations

The geometries and relative energies of new N,N carbonyl dipyrrinone-derived oxime molecules (E/Z-s-cis 4a and E/Z-s-cis 4b) have been investigated. The calculated energies, molecular geometries, and (1) H/(13) C NMR chemical shifts agree with experimental data, and the results are presented herein. The E-s-cis conformations of 4a and 4b and the Z-s-cis conformation of 5b were found to be the thermodynamically most stable isomers with the oxime hydrogen atom or the methyl functional group adopting an anti-orientation with respect to the dipyrrinone group. This conformation was unambiguously supported by a number of 2D NMR experiments.

15N chemical shifts of a series of isatin oxime ethers and their corresponding nitrone isomers

In this article, we describe the characteristic (15)N chemical shifts of isatin oxime ethers and their isomer nitrone. These oxime ethers and nitrones are the alkylation reaction products of isatin oximes. In our study, the (15)N chemical shifts observed in these oxime ethers were in the 402-408 (or 22-28) ppm range, although those for their corresponding nitrone series were in the 280-320 (or -100 to -60) ppm range. This remarkable difference in (15)N NMR chemical shift values could potentially be used to determine the O- versus N-alkylation of oximes, even when only one isomer is available. In this paper, the differences in (15)N NMR chemical shifts serve as the basis for a discussion about how to distinguish both regioisomers derived from the oximes alkylation.

Study of conformations and hydrogen bonds in the configurational isomers of pyrrole-2-carbaldehyde oxime by 1H, 13C and 15N NMR spectroscopy combined with MP2 and DFT calculations and NBO analysis

The (1)H, (13)C and (15)N NMR studies have shown that the E and Z isomers of pyrrole-2-carbaldehyde oxime adopt preferable conformation with the syn orientation of the oxime group with respect to the pyrrole ring. The syn conformation of E and Z isomers of pyrrole-2-carbaldehyde oxime is stabilized by the N-H...N and N-H...O intramolecular hydrogen bonds, respectively. The N-H...N hydrogen bond in the E isomer causes the high-frequency shift of the bridge proton signal by about 1 ppm and increase the (1)J(N, H) coupling by approximately 3 Hz. The bridge proton shows further deshielding and higher increase of the (1)J(N, H) coupling constant due to the strengthening of the N-H...O hydrogen bond in the Z isomer. The MP2 calculations indicate that the syn conformation of E and Z isomers is by approximately 3.5 kcal/mol energetically less favorable than the anti conformation. The calculations of (1)H shielding and (1)J(N, H) coupling in the syn and anti conformations allow the contribution to these constants from the N-H...N and N-H...O hydrogen bondings to be estimated. The NBO analysis suggests that the N-H...N hydrogen bond in the E isomer is a pure electrostatic interaction while the charge transfer from the oxygen lone pair to the antibonding orbital of the N-H bond through the N-H...O hydrogen bond occurs in the Z isomer.

Pronounced stereospecificity of (1)H, (13)C, (15)N and (77)Se shielding constants in the selenophenyl oximes as shown by NMR spectroscopy and GIAO calculations

In the (1)H and (13)C NMR spectra of 1-(2-selenophenyl)-1-alkanone oximes, the (1)H, the (13)C-3 and (13)C-5 signals of the selenophene ring are shifted by 0.1-0.4, 2.5-3.0 and 5.5-6.0 ppm, respectively, to higher frequencies, whereas those of the (13)C-1, (13)C-2 and (13)C-4 carbons are shifted by 4-5, approximately 11 and approximately 1.7 ppm to lower frequencies on going from the E to Z isomer. The (15)N chemical shift of the oximic nitrogen is larger by 13-16 ppm in the E isomer relative to the Z isomer. An extraordinarily large difference (above 90 ppm) between the (77)Se resonance positions is revealed in the studied oxime isomers, the (77)Se peak being shifted to higher frequencies in the Z isomer. The trends in the changes of the measured chemical shifts are well reproduced by the GIAO calculations of the (1)H, (13)C, (15)N and (77)Se shielding constants in the energy-favorable conformation with the syn orientation of the-C=N-O-H group relative to the selenophene ring.

Comparative analysis of 13C shielding constants stereospecificity in the silicon and germanium derivatives of acetylenic aldehyde and ketone oximes based on the 13C NMR spectroscopy and GIAO calculations

In the acetylenic aldehyde oximes with substituents containing silicon and germanium, the (13)C NMR signal of the C-2 carbon of triple bond is shifted by 3.5 ppm to lower frequency and that of the C-3 carbon is moved by 7 ppm to higher frequency on going from E to Z isomer. A greater low-frequency effect of 5.5 ppm on the C-2 carbon signal and a greater high-frequency effect of 11 ppm on the C-3 carbon signal are observed in the analogous acetylenic ketone oximes. The carbon chemical shift of the C=N bond is larger by 4 ppm in E isomer relative to Z isomer for the aldehyde and ketone oximes. The (29)Si chemical shifts in the silicon containing acetylenic aldehyde and ketone oximes are almost the same for the diverse isomers. The trends in changes of the measured chemical shifts are well reproduced by the gauge-including atomic orbital (GIAO) calculations of the (13)C and (29)Si shielding constants.