Imino Tautomer Research Articles

Exploring and Re-Assessing Reverse Anomeric Effect in 2-Iminoaldoses Derived from Mono- and Polynuclear Aromatic Aldehydes.

A curious and noticeable structural feature in Schiff bases from 2-aminoaldoses is the fact that imino tautomers arranged equatorially in the most stable ring conformation exhibit a counterintuitive reverse anomeric effect (RAE) in the mutarotational equilibrium, i.e., the most stable and abundant anomer is the equatorial one (β). As shown by our very recent research, this effect arises from the total or partial inhibition of the exo-anomeric effect due to the presence of an intramolecular hydrogen bond between the anomeric hydroxyl and the iminic nitrogen in the axial anomer (α). When the Schiff base adopts either an enamine structure or the imino group is protonated, the exo-anomeric effect is restored, and the axial α-anomer becomes the most stable species. Although the intramolecular H-bonding should appropriately be interpreted as a genuine stereoelectronic effect, the magnitude of the RAE could be affected by other structural parameters. Herein and through a comprehensive analysis of benzylidene, cinnamylidene, naphthalene, phenanthrene, and anthracene aldehydes, we show the robustness of the RAE effect, which is similar in extent to simple aldehydes screened so far, irrespective of the size and/or hydrophobicity of the substituent at the nitrogen atom.

Theoretical Insights into N-Glycoside Bond Cleavage of 5-Carboxycytosine by Thymine DNA Glycosylase: A QM/MM Study.

Thymine DNA glycosylase (TDG)-mediated excision of 5-formylcytosine and 5-carboxylcytosine (5-caC) is a critical step in active DNA demethylation. Herein, we employed a combined quantum mechanics/molecular mechanics approach to investigate the reaction mechanism of TDG-catalyzed N-glycosidic bond cleavage of 5-caC. The calculated results show that TDG-catalyzed 5-caC excision follows a concerted (SN2) mechanism in which glycosidic bond dissociation is coupled with nucleophile attack. Protonation of the 5-caC anion contributes to the cleavage of the N-glycoside bond, in which the N3-protonated zwitterion and imino tautomers are more favorable than carboxyl-protonated amino tautomers. This is consistent with the experimental data. Furthermore, our results reveal that the configuration rearrangement process of the protonated 5-caC would lower the stability of the N-glycoside bond and substantially reduce the barrier height for the subsequent C1'-N1 bond cleavage. This should be attributed to the smaller electrostatic repulsion between the leaving base and the negative phosphate group as a result of the structural rearrangement.

Protein-activated and FRET enhanced excited-state intermolecular proton transfer fluorescent probes for high-resolution imaging of cilia and tunneling nanotubes in live cells

Excited-state intermolecular proton transfer (inter-ESPT) fluorescent probes responsive to specific bioactive molecules should be greatly promising for protein sensing, DNA mutation simulating and cellular process regulating. However, the inter-ESPT molecules are recessive ESPT fluorophores, which need the assistance of other molecules with both hydrogen-bond accepting and donating abilities to turn on the tautomeric fluorescence. Valid design strategies to create powerful inter-ESPT fluorescent probes are poorly developed, particularly for proteins as targets. We recently reported a unique supramolecular strategy to trigger the inter-ESPT process based on the probe-protein recognition by H-bonding and to image protein-based subcellular structures in live cells. Herein, we found that our inter-ESPT probes (inter-ESPT-01) bearing a 2-amino-3-cyanopyridine scaffold can anchor proteins and light up the “invisible” ESPT state, so as to image the proteins or the protein-based subcellular organelles. More importantly, the inter-ESPT emission of inter-ESPT-01 can be significantly enhanced by the FRET process between amino and imino tautomers, endowing the inter-ESPT-01 probes with super-bright tautomeric fluorescence. The expressed proteins Ecallantide and MarTX were selected as the models to light up the inter-ESPT fluorescence of the probes and revealed that the inter-ESPT process can be triggered by the specific probe-protein recognition events. In the use of the super-bright inter-ESPT fluorescence, not only the proteins, but also the protein-based cilia and tunneling nanotubes (TNTs) can be specifically visualized in living cancer cells. Furthermore, such recognition-driven strategy allows us to construct a unique inter-ESPT probe to track and image specific endogenous proteins in live cells, highlighting the potential of inter-ESPT fluorogens as novel intelligent biomaterials.

Determination of the tautomerism of albendazole desmotropes using solution and solid state NMR together with DFT theoretical calculations, both energies and chemical shifts

This paper reports a structural study of albendazole concerning the desmotropy of its amino and imino tautomers, ABZ-I and ABZ-II, mistakenly called polymorphs. Experimental NMR determination in solution, DMSO‑d6, HMPA-d18 and CF3CO2H, and in the solid state, CPMAS, together with DFT calculations, energies and NMR chemical shifts, has allowed to understand the complex problem of prototropy combined with rotation about the benzimidazole C2-N exocyclic group that explain the disorder problem of the S-propyl group. The structure of protonated albendazole, ABZH+, has also been studied. The role of the hybrid HF/DFT B3LYP computational method at the B3LYP/6–311++G(d,p) level has been determinant to solve the problems related to the structure of albendazole in the solid state and in solution and the barrier in solution of a phenomenon resulting either from annular tautomerism or from the rotation about the exocyclic CN bond.

Amino–Imino Tautomerism in the Salt Formation of Albendazole: Hydrobromide and Nitrate Salts

Albendazole (ABZ) is a poorly soluble anthelmintic drug that can exist in amine and imine desmotropic forms. These facts can affect the solubility and bioavailability of the drug product. Here, we ...

Role of different tautomers in the base-pairing abilities of some of the vital antiviral drugs used against COVID-19.

Repurposed drugs are now considered as attractive therapeutics against COVID-19. It is shown that Remdesivir, a nucleoside drug that was originally invented for the Ebola virus, is effective in suppressing the replication of SARS-CoV-2 that causes COVID-19. Similarly, Galidesivir, Favipiravir, Ribavirin, N4-hydroxycytidine (EIDD-1931), and EIDD-2801 (a prodrug of EIDD-1931) were also found to be effective against COVID-19. However, the mechanisms of action of these drugs are not yet fully understood. For example, in some experimental studies, these drugs were proposed to act as a RNA-chain terminator, while in other studies, these were proposed to induce base-pair mutations above the error catastrophe limit to stall the replication of the viral RNA. To understand the mutagenic effects of these drugs, the role of different tautomers in their base-pairing abilities is studied here in detail by employing a reliable dispersion-corrected density functional theoretic method. It is found that Remdesivir and Galidesivir can adopt both amino and imino tautomeric conformations to base-pair with RNA bases. While the insertions of G and U are preferred against the amino tautomers of these drugs, the insertion of C is mainly possible against the imino tautomers. However, although Favipiravir and Ribavirin can make stable base pair interactions by using their keto and enol tautomers, the formation of the latter pairs would be less probable due to the endothermic nature of the products. Interestingly, the insertions of all of the RNA bases are found to be possible against the keto tautomer of Favipiravir, while the keto tautomer of Ribavirin has a clear preference for G. Remarkably, due to the negligible difference in the stability of EIDD-2801 and EIDD-1931, these tautomers would coexist in the biological environment. The insertion of G is found to be preferred against EIDD-1931 and the incorporations of U, A, and G are preferred opposite EIDD-2801. These findings suggest that base-pair mutations are the main causes of the antiviral properties of these drugs.

Photo-induced Dissociation of the N1–H Bond in the Imino Tautomers of Isocytosine in Water Medium

Photo-induced Dissociation of the N1–H Bond in the Imino Tautomers of Isocytosine in Water Medium

On the impact of a phosphoryl group in the recognition capabilities of 2-aminopyridines toward carboxylic acids

Inspired by natural molecular recognition processes, many research efforts have been routed in recent years toward the design of new host–guest molecular systems based on non-covalent interactions. Within this field, 2-aminopyridines (2APs) have been widely studied due to their tunable spectroscopic response in the presence of carboxylic acids. Herein, we present and analyze a novel family of 2AP core compounds based on 2-phosphorylamidopyridine (2PAP). Linear response time-dependent density functional theory (TD-DFT) has been used to characterize and model several spectroscopic properties of 2PAP. Our results, validated through experiments, show that TD-DFT can provide a reliable description of the electronic excited states of these aromatic systems. In addition, we have also studied the amino–imino tautomerization of 2AP and 2PAP in light of TD-DFT tools. We show that the presence of a carboxylic acid has a catalytic effect on the tautomerization reaction, which otherwise does not occur spontaneously at room temperature. These results suggest that this low-cost computational approach can be applied to more complex organic systems derived from 2-aminopyridine, paving the way for the development of potentially useful sensing materials and organic species for molecular recognition.

DFT study of adenine–cytosine mismatch in quaternary systems involving DNA bases

In the present work, the adenine–cytosine mismatch is theoretically investigated in quaternary systems involving DNA bases. The calculations, in gas phase, are performed at M06-2X/6-311++G(d,p) level. The results indicate that the quaternary systems involving G–C base pair are more stable than those containing A–T. Moreover, in the presence of A–T or G–C base pairs, the absolute values of formation energy in quaternary systems involving imino tautomer of adenine (A*) are higher than those including imino form of cytosine (C*). A comparison between systems having A* indicates that the absolute value of formation energy in quaternary systems increases when A* stacks with pyrimidine bases (C or T). In the case of systems containing C*, this behavior is observed when C* stacks with purine bases (G or A). Similar to binary systems, the quaternary systems involving A*–C thermodynamically prefer to transform their geometries into systems containing A–C*. The base pairs are stabilized by hydrogen bonds. The strength of hydrogen bonds in binary and quaternary systems is also examined using atoms in molecules (AIM) and natural bond orbital (NBO) analyses.

Spectroscopic characterization, crystallographic elucidation and DFT investigation of 5-fluoro-6-(4-methylpiperazin-1-yl)benzo[d]thiazol-2-amine

The spectroscopic features and molecular structure of 5-fluoro-6-(4-methylpiperazin-1-yl)benzo[d]thiazol-2-amine (2-ABT) have been determined. Single-crystal X-ray analysis and vibrational spectroscopy have revealed the existence of 2-ABT in the amino tautomeric form in the solid state. Properties of 2-ABT in solution have been investigated using 1H and 13C NMR spectroscopy along with electronic absorption spectroscopy. The experimental data are complemented by DFT and TD-DFT calculations at the B3LYP/6–311 + g(2d,p) level. TD-DTF-predicted spectroscopic and structural properties for both amino and imino tautomers of 2-ABT are compared with the measured data; no strong evidence for the presence of the imino tautomer is found within the experimental data. Calculated energy differences between the tautomers strongly favour the amino tautomer over the other. Indeed, X-ray crystallography has unequivocally shown the amino tautomer which co-crystallized with one water molecule in the orthorhombic space group Pnna. Analysis of the crystal packing reveals an interesting structural motif which comprises an assemblage of the 2-ABT molecules through π···π stacking interactions. Furthermore, there exist hydrogen-bonding interactions involving the lattice solvent and the amino group along with the benzothiazole nitrogen atom.

Anti-Mycobacterial Evaluation of 7-Chloro-4-Aminoquinolines and Hologram Quantitative Structure-Activity Relationship (HQSAR) Modeling of Amino-Imino Tautomers.

In an ongoing research program for the development of new anti-tuberculosis drugs, we synthesized three series (A, B, and C) of 7-chloro-4-aminoquinolines, which were evaluated in vitro against Mycobacterium tuberculosis (MTB). Now, we report the anti-MTB and cytotoxicity evaluations of a new series, D (D01–D21). Considering the active compounds of series A (A01–A13), B (B01–B13), C (C01–C07), and D (D01–D09), we compose a data set of 42 compounds and carried out hologram quantitative structure–activity relationship (HQSAR) analysis. The amino–imino tautomerism of the 4-aminoquinoline moiety was considered using both amino (I) and imino (II) forms as independent datasets. The best HQSAR model from each dataset was internally validated and both models showed significant statistical indexes. Tautomer I model: leave-one-out (LOO) cross-validated correlation coefficient (q2) = 0.80, squared correlation coefficient (r2) = 0.97, standard error (SE) = 0.12, cross-validated standard error (SEcv) = 0.32. Tautomer II model: q2 = 0.77, r2 = 0.98, SE = 0.10, SEcv = 0.35. Both models were externally validated by predicting the activity values of the corresponding test set, and the tautomer II model, which showed the best external prediction performance, was used to predict the biological activity responses of the compounds that were not evaluated in the anti-MTB trials due to poor solubility, pointing out D21 for further solubility studies to attempt to determine its actual biological activity.

Facile one-pot synthesis of 5-aryl/heterylidene-2-(2-hydroxyethyl- and 3-hydroxypropylamino)-thiazol-4-ones via catalytic aminolysis

ABSTRACTA multicomponent synthetic approach for 5-aryl/heterylidene-2-(2-hydroxyethylamino)- and 2-(3-hydroxypropylamino)-thiazol-4-ones starting from 2-thioxothiazolidin-4-one or 2-methylsulfanylthiazol-4-one was developed. The proposed method involves simultaneous aminolysis of 2-thioxo- or 2-methylsulfanyl groups and Knoevenagel condensation with (hetero)aromatic aldehydes using 2-aminoethanol or 3-aminopropan-1-ol as catalysts. Side-chain prototropic amino–imino tautomerism was observed for target 5-ylidene-2-alkylaminothiazol-4-ones.

Supramolecular solid-state structure, potential energy surfaces and evaluation of antiproliferative effect of 2-benzothiazolylhydrazone derivatives in vitro

The in situ condensation reaction of 2-hydrazinobenzothiazole with salicylaldehyde, 3,4-dihydroxybenzaldehyde, 2,4-dihydroxybenzaldehyde, 2,5-dihydroxybenzaldehyde, 2,3-dihydroxybenzaldehyde, 2-hydroxy-1-naphthaldehyde, 2-methoxy-1-naphthaldehyde, 4-methoxy-1-naphthaldehyde and 6-methoxy-2-naphthaldehyde produced 9 hydrazone Schiff bases (L1–L9, respectively) which were identified and characterized by elemental analysis, IR and NMR spectroscopy. The crystal and molecular structures of four Schiff bases (L1, L7–L9) have been determined by the single-crystal X-ray diffraction method confirming the imino form of L1 and the amino tautomeric form of L7–L9 compounds. Molecular structure analysis also confirmed that reported compounds are E-isomers relative to exo C = N imino bond. The Nhydrazino–H group of amino tautomers forms Nhydrazino–H···Nthiazolyl intermolecular hydrogen bonds shaping molecules into R22(8) rings, while imino tautomer of L1 forms C(4) infinite helical chains via Nthiazolyl–H···Nhydrazino type of intermolecular hydrogen bond. The methoxy group (L7–L9) further shaped these primary supramolecular synthons into different supramolecular arrangements via C–H···O, C–H···N and C–H···S intermolecular hydrogen bonds. The role of aryl substituents in the shaping and stabilization of supramolecular architectures of L1, L7–L9 is supported by quantum chemical calculations. Strong antiproliferative effects on tumor cells and cytotoxic effects on fibroblasts are shown for all ligands L1–L9 with exception of L6 and L7 that had no effect on fibroblast cells.

Abiotic amidine and guanidine hydrolysis of lamotrigine-N2-glucuronide and related compounds in wastewater: The role of pH and N2-substitution on reaction kinetics

The stability of lamotrigine (LMG) and its principal human metabolite, lamotrigine N2-glucuronide (LMG-N2-G), was studied as a function of pH (4–9). While LMG was stable across the entire pH range, under neutral-basic conditions, LMG-N2-G was converted to three transformation products (TPs) which were identified using high resolution mass spectrometry (HRMS). The MS fragmentation studies indicated that two TPs were the result of the hydrolysis of the amidine and guanidine moieties. The third TP detected was an intermediate in the guanidine hydrolysis reaction. In order to evaluate the transformation kinetics of the LMG-N2-G degradation, another set of pH-dependent experiments was carried out in hospital effluent, wastewater influent and effluent spiked at 20 and 200 nM after pH adjustment (pH 6.5, 7, 8, 8.5 and 9), demonstrating that, at higher pH, LMG-N2-G is degraded at higher rate. Later, the pH-dependent stability of related compounds with different nitrogen N2-substituents (N2-R) on the 1,2,4-triazine ring was studied. This revealed that because of different imino tautomer equilibrium LMG (N2-H) and LMG-N2-oxide (+N2-O−) were stable at all pHs but N2-methyl-LMG (N2-CH3) as well as LMG-N2-G were susceptible to amidine and guanidine hydrolysis at basic pH. Finally, hospital effluent samples collected over the course of one week were monitored for their presence. LMG, LMG-N2-G and two of its TPs were detected with concentrations ranging between 0.01 and 1 μgL−1.

Static and Dynamic Properties of Fluorinated 4-Aryl-1,5-Benzodiazepinones

Six 4-aryl-6,7,8,9-tetrafluoro-1,5-benzodiazepine-2-ones have been synthesized and fully characterized by 1H, 13C, 15N and 19F NMR in solution and in the solid state. In addition, the structures of three of them have been determined by X-ray crystallography. The imine/enamine tautomerism has been experimentally studied by NMR in solution (in the solid state, only the imino tautomer is present). Three barriers corresponding to the inversion of the seven-membered ring have been determined (N1-unsubstituted derivatives). Both for the tautomerism and for the conformational aspects, theoretical calculations at the B3LYP/6-311++G(d,p) level including GIAO calculations of the NMR chemical shifts have been carried out with satisfying results. Different energy profiles have been considered and several transition states located.

Whether the amino–imino tautomerism of 2-aminopurine is involved into its mutagenicity? Results of a thorough QM investigation

2AP* mutagenic tautomer is able to induce only one incorporation error – transversion – by pairing through the H-bonds into the G·2AP* mispair.

Two Divalent Metal Ions and Conformational Changes Play Roles in the Hammerhead Ribozyme Cleavage Reaction.

The hammerhead ribozyme is a self-cleaving RNA broadly dispersed across all kingdoms of life. Although it was the first of the small, nucleolytic ribozymes discovered, the mechanism by which it catalyzes its reaction remains elusive. The nucleobase of G12 is well positioned to be a general base, but it is unclear if or how this guanine base becomes activated for proton transfer. Metal ions have been implicated in the chemical mechanism, but no interactions between divalent metal ions and the cleavage site have been observed crystallographically. To better understand how this ribozyme functions, we have solved crystal structures of wild-type and G12A mutant ribozymes. We observe a pH-dependent conformational change centered around G12, consistent with this nucleotide becoming deprotonated. Crystallographic and kinetic analysis of the G12A mutant reveals a Zn(2+) specificity switch suggesting a direct interaction between a divalent metal ion and the purine at position 12. The metal ion specificity switch and the pH-rate profile of the G12A mutant suggest that the minor imino tautomer of A12 serves as the general base in the mutant ribozyme. We propose a model in which the hammerhead ribozyme rearranges prior to the cleavage reaction, positioning two divalent metal ions in the process. The first metal ion, positioned near G12, becomes directly coordinated to the O6 keto oxygen, to lower the pKa of the general base and organize the active site. The second metal ion, positioned near G10.1, bridges the N7 of G10.1 and the scissile phosphate and may participate directly in the cleavage reaction.

1-(7-chloro-1,4-dihydroquinolin-4-ylidene)thiosemicarbazide and its hydrochloride: evidence for the existence of a stable imine tautomer in the solid state of 4-aminoquinoline free bases, an anomalous case in nitrogen heterocycles.

In the solid state, crystals of both 1-(7-chloro-1,4-dihydroquinolin-4-ylidene)thiosemicarbazide-methanol-water (2/1/1), 2C10H9ClN4S·CH3OH·H2O, (I), and its hydrochloride salt {systematic name: [(7-chloro-1,4-dihydroquinolin-4-ylidene)azaniumyl]thiourea chloride}, C10H10ClN4S(+)·Cl(-), (II), assume the imine tautomeric form, contrary to other 4-amino-7-chloroquinolines. Of particular interest are the N-C bond lengths, which have appreciable double-bond character, and the C-N-C aromatic ring bond angle. Both of these parameters have been studied extensively in 4-amino-substituted quinolines. The crystal structures of (I) and (II) in this study provide interesting examples of the amino-imino tautomerism which exists in this class of compound and is, to the best of our knowledge, hitherto unreported.

Effect of mono- and di-hydration on the stability and tautomerisms of different tautomers of creatinine: A thermodynamic and mechanistic study

Relative stabilities of nine tautomers of creatinine in gas and aqueous phases and hydrated forms were studied by M062X, MP2 and B3LYP computational methods. It was found that two tautomers (an amino and an imino) have significant stability and relative abundances among all. The imino tautomer is more stable in gas phase while the amino form is more stable in aqueous phase and in di-hydrated form. The stability and relative abundances of the both amino and imino tautomers in mono-hydrated form were approximately the same. Activation energies and Gibbs free energies of isomerizations in creatinine, including intramolecular proton transfers and internal OH rotations, were calculated. The energy barriers of rotations of hydrogen atom of OH group around C–O bond were smaller than 40kJ/mol. Two types of proton transfer reactions including imine↔amine and keto↔enol tautomerisms were considered. The activation energies of keto–enol tautomerisms, in which the proton is transferred between oxygen and carbon atoms, were in the range 270–300kJ/mol. Catalysis effect of one and two water molecules on the intramolecular proton transfers was studied. It was found that the activation energies are decreased by about 130 and 150kJ/mol in the presence of one and two water molecules, respectively.

Role of topological charge stabilization in protomeric tautomerism.

Protomeric tautomerism is analyzed in view of the topological charge stabilization rules. Based on Hückel molecular orbital considerations and modern DFT calculations, it was found that the branching of amino or hydroxyl groups significantly contributes to the stability of major species through the first- and second-order perturbations with respect to the isoelectronic hydrocarbon. While amino-imino tautomerism is almost completely dominated by topological charge stabilization, hydroxyl-oxo tautomerism is affected by changes in the resonance integral of C-O/C═O bonds. Nevertheless, apart from side effects such as hydrogen bonds or solvent effects, a quantitative preference rule for the prediction of the tautomeric stability can be developed using topological π-electron energetics. As well as the analyses of simple bases, applications to complex or extended systems are exemplified analyzing purine bases, polyguanide, and polyuret. The present approach can be useful in conjunction with chemical intuition that comes from conventional valence bond theory.