Stable Tautomeric Forms Research Articles

Quantum simulation of preferred tautomeric state prediction

Prediction of tautomers plays an essential role in computer-aided drug discovery. However, it remains a challenging task nowadays to accurately predict the canonical tautomeric form of a given drug-like molecule. Lack of extensive tautomer databases, most likely due to the difficulty in experimental studies, hampers the development of effective empirical methods for tautomer predictions. A more accurate estimation of the stable tautomeric form can be achieved by quantum chemistry calculations. Yet, the computational cost required prevents quantum chemistry calculation as a standard tool for tautomer prediction in computer-aided drug discovery. In this paper we propose a hybrid quantum chemistry-quantum computation workflow to efficiently predict the dominant tautomeric form. Specifically, we select active-space molecular orbitals based on quantum chemistry methods. Then we utilize efficient encoding methods to map the Hamiltonian onto quantum devices to reduce the qubit resources and circuit depth. Finally, variational quantum eigensolver (VQE) algorithms are employed for ground state estimation where hardware-efficient ansatz circuits are used. To demonstrate the applicability of our methodology, we perform experiments on two tautomeric systems: acetone and Edaravone, each having 52 and 150 spin-orbitals in the Slater Type Orbital - 3 Gaussian (STO-3G) basis set, respectively. Our numerical results show that their tautomeric state prediction agrees with the Coupled Cluster Singles and Doubles (CCSD) benchmarks. Moreover, the required quantum resources are efficient: in the example of Edaravone, we could achieve chemical accuracy with only eight qubits and 80 two-qubit gates.

The synthesis, photophysical properties, DFT study and textile applications of fluorescent azo dyes bearing coumarin-thiazole

In this study, four novel coumarin-thiazole-based azo dyes were prepared by coupling N-methyl-N-phenylaniline and 3-methyl-1-phenyl-2-pyrazoline-5-one with coumarin-2-aminothiazole hybrid and they were characterized by 1H/13C NMR and mass spectroscopic techniques. The photophysical properties of the synthesized dyes were studied, and the absorption spectra in different solvent polarities were observed in the range of 408–513 nm. The effect of acidity on the photophysical properties was also studied. When the solvent-dependent spectral properties of the compounds were studied, they showed a positive solvatochromic shift. Despite the presence of the azo group, the azo dyes were found to be fluorescent with low emission intensity. The coumarin-thiazole-pyrazolone azo dyes exhibited prototropic tautomerism and the determination of most stable tautomeric form of dyes was used 1H NMR spectroscopy method. The stability of the compound was also studied using density functional theory calculations (DFT) by comparing the total energy of the possible tautomeric forms. The thermal study showed that these azo dyes can be used in any dyeing process where the temperature is below 269 °C without decomposition. The textile applications showed that the thiazole and coumarin structures in the molecule provided excellent color fastness properties and color variations on the fabrics.

N,N'-Diphenyldithiomalonodiamide: Structural Features, Acidic Properties, and In Silico Estimation of Biological Activity.

The spectral characteristics of dithiomalondianilide (N,N′-diphenyldithiomalonodiamide) were studied, and the dissociation constant was determined by potentiometric titration. Quantum-chemical methods at the B3LYP-D3BJ/6-311+G (2d,p) level were used to calculate the molecular geometry and vibrational spectra of the most stable tautomeric forms of dithiomalondianilide. The bioavailability parameters were calculated, and possible protein targets were predicted by the protein ligand docking method.

Synthesis, spectroscopic and computational investigation of N1,N4-bis(3-oxobutanoyl)benzene-1,4-dicarbohydrazide as a coupling component for azo dyes from waste poly(ethyleneterephthalate) bottle

In order to contribute to the recycling of waste poly (ethylene terephthalate) (PET) in the industry; N1,N4-bis(3-oxobutanoyl)benzene-1,4-dicarbohydrazide (compound 1), a coupling component, was intended to be obtained from the condensation reaction between benzene-1,4-dicarbohydrazide (TPDH) and excess ethyl acetoacetate (EAA), and compound 1 were synthesized in good yield. Compound 1 was characterized by spectroscopic techniques (FTIR and NMR) and micro elemental analysis. Structural parameters, IR and NMR spectral data of compound 1 were obtained by DFT/B3LYP/6–311++G(d,p) method, considering two possible stable tautomeric forms as tetraketo and diketo-dienol. For detailed evaluation, theoretical IR and NMR data of compound 1 were compared with experimental ones. Results show that compound 1 predominantly exists in tetraketo form in solid state and DMSO. In this study, for the first time, a coupling component that can be used in the synthesis of azo dyes is obtained from TPDH, a degradation product of PET. This idea can lead to a significant contribution to saving raw materials in the industry and preventing environmental pollution caused by waste PET.

Theoretical investigation of the structural and electronic features of SLC-0111, a novel inhibitor of human carbonic anhydrase IX, and its anion

The various tautomers and conformers of SLC-0111, a well-known biologically potent compound, have been investigated using density functional theory (DFT) calculations in the gas phase and aqueous solution. The amide form is found to be the only stable tautomeric form in both the phases, with the trans-cis conformer as the most stable structure in the gas phase and the trans-trans conformer in aqueous solution. The deprotonation of the sulfonamide nitrogen leading to the formation of the SLC-0111 anion occurs at pH > 10. The various intramolecular interactions and reactivity of the molecule have been characterized using natural bond orbital (NBO) analysis and calculation of global reactivity parameters. The effect of the solvent polarity on the energies and nature of the frontier molecular orbitals has been investigated for both the neutral and anionic forms. Further, the electronic spectra and vibrational spectra of both the states have also been computed and the effect of changing solvents on the electronic spectra has been investigated. The calculated nonlinear optical (NLO) properties of the molecule show that the molecule has potential to be featured as an NLO material.

DFT investigation on the linear and nonlinear optical properties of the tautomers and derivatives of 2-aminobenzothiazole (ABT) in the gas phase and different solvents

This effort was performed to investigate the nonlinear optical (NLO) properties of 2-aminobenzothiazole (ABT) molecule at a sophisticated level of theory (DFT/CAM-B3LYP/6-311++G(d,p)). The study included the investigation of NLO properties of the three tautomeric forms of ABT in the gas and solvents of different polarities. The study extended to study the NLO properties of the most stable tautomeric form of ABT (T1ABT) substituted at position C3 with electron-donor/electron-acceptor groups. Additionally, the quantum chemical parameters of the three tautomeric forms in the gas and six solvents were calculated and analyzed.

Experimental and theoretical studies on monoazo dye including diphenylamine and N-methyldiphenylamine derivatives

In this manuscript, two series of azo dyes preparing by coupling diphenylamine and N-methyl diphenylamine and diazotized substituted anilines bearing various substituents were designed and synthesized. These azo dyes were characterized by spectroscopic techniques such as 1H/13C NMR and HRMS or LCMS. Photophysical, NLO and protonation properties were investigated by experimentally and theoretically. The absorption maxima were observed in long wavelength in DMSO. The most stable tautomeric form of dyes which have tautomeric forms, were determined using model compounds. The results showed that the azo dyes are stable in azo form in all solvents used. For the usability as optic dye of the synthesized dyes, thermal property of all dyes was also determined. The all compounds are thermally stable and Td values are bigger than 220 °C.

Benzothiazole-pyridone and benzothiazole-pyrazole clubbed emissive azo dyes and dyeing application on polyester fabric: UPF, biological, photophysical and fastness properties with correlative computational assessments.

Positional isomers of benzothiazole-pyridone and benzothiazole-pyrazole containing disperse azo dyes are reported. These heterocyclic azo dyes are decorated with 'separate ESIPT core' and show emission in seven solvents of different polarity. After application on polyester fabric, "very good to excellent" light and washing fastness properties were observed. Thermal stability of 'dyed fabric' was analysed by sublimation fastness test- and found 'very good to excellent' ratings at 210°C. Ultraviolet Protection Factor (UPF) analysis of four 'dyed fabric' indicates the blocking 96-97% of UV radiation. Dyes were found effective on gram positive and negative bacteria by agar diffusion method and all the 'dyed fabrics' also showed more than 92% or 94% reduction of S. aureus or K. pneumoniae respectively by 'AATCC 100' method. Structures of the dyes were optimized using Density Functional Theory (DFT) to deduce stable tautomeric form. Calculated HOMO-LUMO gap is then compared with antibacterial activities. Electrophilicity index and lightfastness property were also compared and found to have very good correlation.

Elucidating the Catalytic Reaction Mechanism of Orotate Phosphoribosyltransferase by Means of X-ray Crystallography and Computational Simulations

Orotate phosphoribosyltransferase (OPRTase) catalyzes the reaction between the ribose donor α-d-5-phosphoribosyl-1-pyrophosphate (PRPP) and orotate (OA) in the presence of Mg2+ ion to obtain pyrophosphate and pyrimidine nucleotide orotidine 5′-monophosphate (OMP), a key precursor in de novo biosynthesis of pyrimidine nucleotides. In this work, several structures of the dimeric Escherichia coli OPRTase (EcOPRTase) have been determined at high resolution, and kinetic measurements have been carried out to obtain the catalytic rate and Michaelis constants. Molecular dynamics (MD) simulations have been carried out, and structural analysis from the X-ray and MD simulation structures reveals conformational changes related to the flexible catalytic loop that establishes hydrogen bond interactions with the pyrophosphoryl group of PRPP. It is proposed that the OA substrate can be in equilibrium in its tautomeric forms. Starting from the most stable tautomeric form, all the plausible mechanisms have been explored by...

Using Chou’s 5-Step Rule to Evaluate the Stability of Tautomers: Susceptibility of 2-[(Phenylimino)-methyl]-cyclohexane-1,3-diones to Tautomerization Based on the Calculated Gibbs Free Energies

Gibbs free energies, based on DFT (Density Functional Theory) calculations, prove that enaminone (2-(anilinemethylidene)cyclohexane-1,3-dione) and ketamine (2-[(phenylimino)-methyl]cyclohexane-1,3-dione) are the most and least stable tautomeric forms of the studied systems, respectively. 1H and 13C NMR spectra prove that 2-(anilinemethylidene)cyclohexane-1,3-diones are the only tautomeric species present in dimethylsulfoxide solution (a very weak signal can be seen only for the p-methoxy derivatives). The zwitterionic character of these enaminones is strengthened by naphthoannulation and by the insertion of the electron-withdrawing substituent into the benzene ring (the latter weakens the intramolecular hydrogen bond in the compound). Substituent and naphtoannulation have no effect on the stability of the studied tautomers. Slight twisting of the benzene ring, with respect to the CArNC plane (seen in the crystalline state), was proven to also take place in vacuum and in solution.

Спектральное и квантово-химическое изучение таутомерных и ионных превращений 2-(2-(2-гидрокси-5-сульфанилфенил) гидразон)-3-оксо-N-фенилбутанамида

In this paper, using the method DFT/B3LYP of quantum chemical modeling, the stability of tautomeric, conformer, and anionic forms of 2-(2-(2-hydroxy-5-sulfamoylphenyl)hydrazone-3-oxo-N-phenylbutanamide (H2L) was studied and the geometric, electronic structure and bond lengths of molecules in various tautomeric forms were determined. It was shown that the stability of tautomeric molecules H2L as anionic forms was determined by the number of existing intermolecular hydrogen bonds (closing six-membered and five-membered cycles). The most stable tautomeric and conformal forms of an organic molecule and its dianion are proposed. The interatomic distances, angles, charges on atoms, IR and electronic absorption spectra of tautomeric forms of the molecule and dianion (H2L and L2-) were calculated. In this work, we studied the electronic absorption spectra in an aqueous-alcoholic solution and found that in an alkaline medium the molecule transforms into the ionic form with a bathochromic shift of 47 nm, corresponding to the results of the shift of the long-wavelength band electronic absorption spectra upon transition from the hydrazotautomer (form a) to the dianion form (form b’’) at 92 nm obtained by TD-DFT. The calculated results for the distance and angles between atoms are in good agreement with the experimental data of the molecule by X-ray diffraction analysis. It was shown that the IR spectrum of the stable form appears two absorption bands in the region of 1690 and 1655 cm–1, which are attributed to stretching vibrations of carbonyl groups (C=O), bound by a strong intramolecular hydrogen bond and the presence of the NH-hydrazone fragment of the 1H NMR spectrum confirmed the most stable for a neutral molecule is the hydrazone form.

One-Pot Synthesis, Pharmacological Evaluation, Docking Study, and DFT Calculations for Selected Imidazolidine-2,4-Diones

The title compounds with different 5-substituted imidazolidine-2,4-dione were synthesized through a solvent-free reaction. Imidazolidine-2,4-dione derivatives are found to be an active pharmacophore for design and development of various bioactive lead compounds. Positive values of energy obtained for compound 1and 3, while a negative value for compound 2 was calculated by DFT in Gaussian. keto-enol tautomerism was supported by energy values and indicated the most stable tautomeric form. The biological evaluation has been supported by docking studies using molecular operating environment program to show binding with androgen receptor. 
 Supplementary Materials: https://sjuoz.uoz.edu.krd/suppma

Reaction between Indazole and Pd-Bound Isocyanides-A Theoretical Mechanistic Study.

The mechanism of the addition of indazole (Ind)—a bifunctional aromatic N,NH-nucleophile—to cyclohexyl isocyanide coordinated to the palladium(II) center in the model complex cis-[PdCl2(CNMe)(CNCy)] (1) to give the corresponding aminocarbene ligand was investigated in detail by theoretical (DFT) methods. The most plausible mechanism of this reaction is that of the associative type involving nucleophilic attack of Ind by its unprotonated N atom at the isocyanide carbon atom followed by the stepwise proton transfer from the nucleophile molecule to the isocyanide N atom via deprotonation/protonation steps. Two reaction channels based on two tautomeric forms of indazole were found. The channel leading to the experimentally isolated aminocarbene product is based on the less stable tautomeric form. Another channel based on the more stable tautomer of Ind is slightly kinetically more favorable but it is endergonic. Thus, the regioselectivity of this reaction is thermodynamically rather than kinetically driven. The bonding situation in key species was analyzed.

Aminonitrone–iminohydroxamic acid tautomerism: Theoretical and spectroscopic study

The comprehensive theoretical study of the tautomerism of aminonitrone species employing the С-methylaminonitrone MeC(NH2) = N+(Me)O− and the С-phenylaminonitrone PhC(NH2) = N+(Me)O− species as models and direct experimental observation of the tautomeric forms in a chloroform solution by infrared spectroscopy have been reported. All possible tautomeric forms including different (E)/(Z)-configurations of each species and the nature of solvent on their relative energies have been considered at the M06-2X/6-311 + G(d,p) level of theory. Results of theoretical calculations reveal that the most stable tautomeric form in chloroform, dimethyl sulfoxide, and methanol solutions is the (Z)-aminonitrone. The protic solvent (MeOH) significantly stabilizes both zwitter-ionic (E)- and (Z)-aminonitrone forms, whereas all tautomers related to the iminohydroxamic acid remain almost unaffected upon variation of the solvent nature. The phenomenon of intramolecular NH⋯O and OH⋯N hydrogen bonding in (Z)-aminonitrone and (E,Z)-iminohydroxamic acid tautomeric forms was studied by the topological analysis of the electron density distribution (QTAIM method), and estimated energies of these non-covalent interactions vary from 6 to 10 kcal/mol.

Two Macrocycles in One Shot: Synthesis, Spectroscopy, Photophysics, and Tautomerism of 23-Oxahemiporphycene and 21-Oxacorrole-5-carbaldehyde.

The synthesis of 23-oxahemiporphycene, the first monooxa analogue of hemiporphycene, a structural isomer of porphyrin, is reported. Its generation under McMurry reaction conditions is surprisingly accompanied by the appearance of a formyl derivative of oxacorrole, 21-oxacorrole-5-carbaldehyde. A mechanism for the formation of the latter is proposed, relying on pinacol rearrangement of titanium pinacolate. The structures of the most stable tautomeric forms are established for both compounds based on IR and NMR spectra combined with DFT calculations. Spectral and photophysical characteristics are compared with those of structurally similar macrocycles. Replacement of one nitrogen by oxygen in hemiporphycene has only a minor impact. In contrast, for corrole it leads to the enhancement of stability and to strongly reduced rates of nonradiative deactivation of the lowest excited singlet state. This is explained by the planarity of oxacorroles, achieved by removing one of the inner hydrogen atoms from the inner cavity. Unusual crystal packing is observed for the protonated form of 23-oxahemiporphycene, which exhibits a π-π stacked columnar alignment of positively charged macrocycle units.

Structural and energetic properties of tautomeric forms of phosphonyl thioamides

Stable tautomeric forms in a series of phosphonyl thioamides have been studied using DFT methods. The molecules studied in this contribution present a phosphonyl group in β-position of the C–S bond connected to the amine group. The three most stable tautomeric forms with double bonds on either C=N, C=S, or adjacent C=C have been described, and their relative energies together with the transition barriers have been evaluated. In such molecules a six-member ring can be formed by a hydrogen bond between the oxygen of the phosphonyl group and the H–N bond of the thioamide. The tautomeric form involving a C=N double bond is found less stable than the two other forms by more than 10 kcal/mol. The transition barriers between the various tautomers are calculated to be as large as 40 kcal/mol for the isolated molecules, but less than 30 kcal/mol in the presence of one water molecule. Similar results are obtained with various substituents on the phosphorus or on the nitrogen atom. Electronic vertical spectra have been calculated using the TD-DFT approach for the three stable tautomeric forms in a series of six substituted phosphonyl thioamides, and it is found that the signature of each tautomer is sufficiently specific to allow for their clear identification in a mixture using UV–Vis spectroscopy.

A coumarin-pyrazolone based fluorescent probe for selective colorimetric and fluorimetric fluoride detection: Synthesis, spectroscopic properties and DFT calculations

A novel coumarin based fluorescence anion chemosensor (P-1) bearing pyrazolone as a receptoric part was synthesized and characterized by using FT-IR, 1H/13C NMR and HRMS for the purpose of recognition of anions in DMSO. P-1 has four tautomeric structures and the most stable tautomeric form of P-1 was determined experimentally and theoretically. The chemosensor P-1 consists two receptoric parts as free amide NH and enamine NH which is stabilized intramolecular H-bonding with coumarin carbonyl oxygen. P-1 interacts selectively with fluoride anion via amide NH. The selectivity and sensitivity of probe to various anions were determined with spectrophotometric and 1H NMR titration techniques as experimentally and all results were also explained by theoretical calculations.

Computational investigation of the structure and antioxidant activity of some pyrazole and pyrazolone derivatives

Pyrazoles and pyrazolones constitute a group of organic compounds that have various medical applications such as antimicrobial, antipyretic, anti-inflammatory, antitumor and antioxidants. Pyrazolones can exist in different isomeric forms (CH, NH, OH) due to keto-enol, lactam-lactim and imine-enamine tautomerism. Determination of the most stable tautomeric form is thus important for understanding their biological roles at the molecular level. We performed a theoretical investigation of the structural and antioxidant properties of three synthetic pyrazolones (1–3), one synthetic pyrazole (4), one natural pyrazole (5) and two engineered hydroxyl derivatives of 1 (7, 8) and of 5 (9, 10) using the density functional theory at the B3LYP/6-311++G(d,p) level of theory in gas phase and in methanol (using the polarizable continuum model). It is found that substituents and solvents may influence the relative stability of pyrazolone isomers and that the CH tautomer is typically the least stable. Vertical ionization potentials, vertical electron affinities and X–H bond dissociation energies (X = C, N, O, S) are calculated for the global minimum structures and compared with those of the standard antioxidant flavonoid quercetin (6). Calculations predict that compounds 1 and 5 have antioxidant activity similar to 6 and that their mono and dihydroxyl derivatives (7–10) are more efficient antioxidants. Results also indicate that compounds 1–10 preferably interact with free radicals adopting the H atom transfer rather than the sequential electron transfer proton transfer mechanism. The study gives insight into the structural requirements for the design of highly efficient antioxidants.

Theoretical Study on the Stability, Acidity Constants and Molecular Electronic Properties of Certain o-Hydroxy Schiff Bases and their Tautomers

In the present work, certain novel o-hydroxy Schiff bases and possible tautomer forms, which were previously synthesized by our group and their structures elucidated, have been calculated by DFT/6-311g(2d,2p) in both vacuum and polar solvents and the most stable tautomeric forms have been determined. The acidity constants of the Schiff bases have been calculated with the PM6 method by MOPAC2016. HOMO-LUMO values of the studied Schiff bases were calculated with DFT/6-311g(2d,2p) and their possible molecular electronic properties were searched. The results were compared with those experimental values.

A novel coumarin-pyrazole-triazine based fluorescence chemosensor for fluoride detection via deprotonation process: Experimental and theoretical studies

A novel fluorescence coumarin-pyrazole-triazine based chemosensor (CPT) bearing 5-hydroxypyrazole as a receptoric part was synthesized and characterized by using IR, 1H/13C NMR and HRMS for the purpose of recognition of anions in DMSO. The most stable tautomeric form of CPT was determined by experimental techniques and theoretical calculations. The selectivity and sensitivity of CPT towards anions (CN−, F−, Cl−, Br−, I−, AcO−, HSO4−, H2PO4− and ClO4−) were determined using spectrophotometric and 1H NMR titration techniques as the experimental approach, and the results were explained by employing theoretical calculations. It was found to be suitable for the selective detection of F− in the presence of CN− and AcO− as competing anions. In addition, CPT exhibits significant “light-up” effect after interaction with TFA in CH2Cl2.