Stable Tautomeric Forms Research Articles

Prototropic μ-H8,9 and μ-H9,10 Tautomers Derived from the [nido-5,6-C2B8H11]− Anion

Reported is an unusual tautomeric behavior within the [nido-5,6-C2B8H11]- (1a-) cage that has no precedence in the whole area of carborane chemistry. Isolated were two skeletal tautomers, anions [6-Ph-nido-5,6-C2B8H10-μ8,9]- (2d-) and [5,6-Me2-nido-5,6-C2B8H9-μ9,10]- (3b-), which differ in the positioning of the open-face hydrogen bridge. Their structures have been determined by X-ray diffraction analyses. The 3b-structure is stabilized by intermolecular interaction involving Et3NH+ and B8-B9 and H8 atoms in the solid phase; however, its dissolution in CD3CN causes instant conversion to the more stable [5,6-Me2-nido-5,6-C2B8H9-μ8,9]- (2b-) tautomer. The dynamic electron-correlation-based MP2/6-31G* computations suggest that the parent [nido-5,6-C2B8H11-μ8,9]- (2a-) tautomer is 3.9 kcal·mol-1 more stable than the [nido-5,6-C2B8H11-μ9,10]- (3a-) counterpart and the μ8,9 structure 2- is therefore the most stable tautomeric form in the solution, as was also demonstrated by multinuclear (1H, 11B, and 13C) NMR measurements on the whole series of C-substituted compounds.

Solvent-dependent tautomerism of the inverted isomer of meso-tetraphenylporphine: Effect of the polarity of the medium

It is found that aza-imino tautomerism (a ⇆ b) of the inverted porphyrinoids and its mechanism are, along with the stability of tautomeric forms in the Solv–B system, determined by the nature of a base B and the polarity of a solvent Solv. It is shown that the transition from the C6H6–B system to MeCN–B is characterized by an approximate doubling of stability constants KT of the imine form (b), and by a change of the number of molecules B involved in the process (from two to one). According to quantum-chemical data (DFT, B3LYP, CC-pVDZ) and the results from spectral measurements (electronic absorption spectra, EAS), the stability of tautomer b (imino form) falls in the series of solvents DMF > Py ~ Et2NH > MeCN > Me2CO, and tautomer a is to a lesser extent stabilized in the given media by electron donors through the formation of hydrogen bonds (except for Me2CO: DMF > Py ≫ Me2CO ≫ MeCN, Et2NH).

The effects of tautomerization and protonation on the adenine–cytosine mismatches: a density functional theory study

In the present work, we demonstrate the results of a theoretical study concerned with the question how tautomerization and protonation of adenine affect the various properties of adenine–cytosine mismatches. The calculations, in gas phase and in water, are performed at B3LYP/6-311++G(d,p) level. In gas phase, it is observed that any tautomeric form of investigated mismatches is more stabilized when adenine is protonated. As for the neutral mismatches, the mismatches containing amino form of cytosine and imino form of protonated adenine are more stable. The role of aromaticity on the stability of tautomeric forms of mismatches is investigated by NICS(1)ZZ index. The stability of mispairs decreases by going from gas phase to water. It can be explained using dipole moment parameter. The influence of hydrogen bonds on the stability of mismatches is examined by atoms in molecules and natural bond orbital analyses. In addition to geometrical parameters and binding energies, the study of the topological properties of electron charge density aids in better understanding of these mispairs.

Anab initioand density functional theory study on neutral pterin radicals

AbstractThe electronic structures of the five radicals resulting from homolytic elimination of one of the hydrogen atoms from the most stable tautomeric form of neutral pterin were investigated in gas phase as well as in aqueous solution. Molecular wave functions obtained by density functional theory were analysed by quantum theory of atoms in molecules and electron localisation functions (ELF). Spin densities of the radicals as well as electrostatic potential functions were analysed. Radicals resulting from elimination of N-bonded hydrogen atoms are more stable in comparison with radicals obtained after abstraction of C-bonded hydrogen atoms. N-centred radicals show strong delocalisation of spin density over both heteroaromatic rings; in C-centred radicals delocalisation does not occur. ELF analyses showed that in N-derived radicals particularly the lone electron pair at N2′ is strongly involved into the bicyclic heteroaromatic π-electron system. Thereby, bonding geometry at N2′ in these radicals changes from pyramidal to planar. Transition from gas phase to solution phase (water) generally leads to increased polarity of the structures. Pterin-derived free radicals have been implicated in several biologically important reactions; so this investigation provides first insights into the detailed electronic structures of such molecular systems.

Physico-chemical study of the complex formation between 2-(tosylamino)benzaldehyde bishydrazones and transition metal ions

New 2-(tosylamino)benzaldehyde bishydrazones and their complexes with copper(II) and zinc(II) have been synthesized. Structure and properties of the prepared compounds have been studied by means of IR and 1H NMR spectroscopy as well as magnetochemistry. Quantum-chemical simulation of the relative stability of tautomeric forms of the bishydrazones has been performed.

A ratiometric fluorescence chemosensor based on a coumarin–pyrazolone hybrid: the synthesis and an investigation of the photophysical, tautomeric and anion binding properties by spectroscopic techniques and DFT calculations

A fluorescent chemosensor (C-2) having a coumarin ring as a signalling unit and a pyrazolone ring as an H-donor receptor was synthesized for the purpose of recognition of anions in DMSO. The most stable tautomeric form of C-2 was determined using spectroscopic techniques and DFT calculations. The absorption and emission behaviours of C-2 were investigated in solvents of different polarities to confirm the expected tautomeric forms. The absorption and emission bands were blue shifted with increasing solvent polarity because of negative solvatochromism. The selectivity of C-2 for F−, Cl−, Br−, I− and AcO− anions was determined in DMSO and it was found to be suitable for the detection of F− in the presence of Cl−, Br−, I− and AcO− as competing anions at the stoichiometric ratio of 1:1.

Structure, stability, energy barrier and ionization energies of chemically modified DNA-bases: Quantum chemical calculations on 37 favored and rare tautomeric forms of tetraphosphoadenine

Density Functional Theory (BMK and B3LYP) and ab initio complete basis set (CBS-QB3) methods are used to study the stability order and tautomerization processes of all possible 37 tetraphosphoadenine tautomers in the gas phase for the first time. Adiabatic ionization energy (IE) and electron affinity (EA) of all tetraphosphoadenine tautomers were computed at B3LYP/6–311+G(d,p) level of theory at 0K. Positive calculated EA values suggest that the tetraphosphoadenine molecule is an attractive candidate for electron capture. It has been found that all tautomers of tetraphosphoadenine exists within the energy range of 0–150kJmol−1. Similar to adenine, canonical tautomers PA7 and PA9 of tetraphosphoadenine are shown to be the most stable tautomeric forms as predicted by all of the above computational methods. The transition states for the tetraphosphadenine tautomerization processes were investigated for selected systems at B3LYP/6–311+G(d,p) level of theory in the gas phase. Energy barrier for the proton transfer processes of tetraphosphadenine, is up to 97kJmol−1. Dipole moment, full atomic natural charges and bond orders have been computed and discussed.

A theoretical study on tautomeric structures of 4′-nitroazobenzene-2,4-diol and 4-methyl-4′-nitroazobenzene-2,6-diol compounds

The goal of this study is to determine the most stable tautomeric forms, and their ground state conformers of 4′-nitroazobenzene-2,4-diol and 4-methyl-4′-nitroazobenzene-2,6-diol compounds. The calculations have shown that the most stable tautomeric forms of the compounds are hydrazo form for 4′-nitroazobenzene-2,4-diol and azo form for 4-methyl-4′-nitroazobenzene-2,6-diol. Besides, the vibrational frequencies, 1H and 13C NMR shifts, frontier molecular orbital’s energies for the tautomeric forms of the compounds calculated by using density functional theory-B3LYP method with 6-311G(d) basis set were interpreted. All the assignments of the theoretical frequencies were identified by potential energy distribution (PED) analysis. Generally, theoretical spectral results were seen to be in a good agreement with the corresponding experimental data.

Theoretical study of molecular structures, vibrational and NMR spectra on azobenzene derivatives

In this study, we have calculated the most stable tautomeric forms and their ground state conformers of 2,4-dihydroxyazobenzene and 2,4-dihydroxy-6-methyl-4′-nitroazobenzene molecules. Calculations show that the most preferential tautomeric forms of these molecules are azo form for 2,4-dihydroxyazobenzene and hydrazo form for 2,4-dihydroxy-6-methyl-4′-nitroazobenzene. Vibrational frequencies, 1H and 13C NMR shifts of ground state conformers of stable tautomeric forms of the molecules have been calculated by using density functional theory-B3LYP method with 6-311G(d,p) basis set. All assignments of theoretical frequencies have been performed by potential energy distribution analysis. Calculated spectral results are in a good agreement with the corresponding experimental data.

Investigation of the azo-hydrazone tautomeric equilibrium in an azo dye involving the naphthalene moiety by UV–vis spectroscopy and quantum chemistry

Photophysical properties of the azo-hydrazone tautomerism of Eriochrome Blue Black B (1-(1-hydroxy-2-naphthylazo)-2-naphthol-4-sulphonic acid) in DMF, MeCN and water were investigated using UV–visible spectroscopy and quantum chemical calculations. The optimized molecular structure parameters, relative energies, mole fractions, electronic absorption spectra and HOMO–LUMO energies for possible stable tautomeric forms of EBB were theoretically calculated by using hybrid density functional theory, (B3LYP) methods with 6-31G(d) basis set level and polarizable continuum model (PCM) for solvation effect. The effects of varying pH-, dye concentration-, solvent-, temperature-, and time-dependences on the UV–vis spectra of Eriochrome Blue Black B were also investigated experimentally. The calculations showed that the dye exhibited acid–base, azo-hydrazone and aggregate equilibria in DMF solution, while the most probably preferred form in MeCN solution was azo form. Thermodynamic parameters of dimerization reaction in DMF solution proved that entropy was the driving force of this reaction.

FT-IR, dispersive Raman, NMR, DFT and antimicrobial activity studies on 2-(Thiophen-2-yl)-1H-benzo[d]imidazole

2-(Thiophen-2-yl)-1H-benzo[d]imidazole (TBI) was synthesized under microwave conditions and was characterized by FT-IR, dispersive Raman, 1H-, 13C-, DEPT-, HETCOR-NMR spectroscopies and density functional theory (DFT) computations. The FT-IR and dispersive Raman spectra of TBI were recorded in the regions 4000–400cm−1 and 4000–100cm−1. The experimental vibrational spectra were interpreted with the help of normal coordinate analysis based on DFT/B3LYP/6-311++G(d,p) theory level for the more stable tautomeric form (Tautomer 1). The complete vibrational assignments were performed on the basis of the potential energy distribution (PED) of the vibrational modes, calculated with scaled quantum mechanical (SQM) method. A satisfactory consistency between the experimental and theoretical findings was obtained. The frontier molecular orbitals (FMOs), atomic charges and NMR shifts of the two stable tautomeric forms were also obtained at the same theory level without any symmetry restrictions. In addition, the title compound was screened for its antimicrobial activity and was found to be exhibit antifungal and antibacterial effects.

Embedding monomers and dimers of sulfonamide antibiotics into high silica zeolite Y: an experimental and computational study of the tautomeric forms involved

This work is a second step towards the systematic study of the embedding of sulfonamide antibiotics into a synthetic high silica zeolite Y (HSZ-Y) with hydrophobic properties. In the previous paper [Braschi et al., Langmuir 2010, 31, 9524], the irreversible adsorption from water into HSZ-Y of three sulfonamides was studied by enlightening the host–guest interactions and, in the case of the smallest sized sulfadiazine, the guest–guest interactions of dimeric species inside the zeolite cage. Here the HSZ-Y was loaded with six sulfonamides, namely: sulfanilamide, sulfapyridine, sulfathiazole, sulfadimethoxine, sulfadoxine and sulfamerazine. With the exception of sulfanilamide, which showed scarce affinity for HSZ-Y (maximum loading 3% zeolite dry weight), the other sulfa drugs adsorbed at ca. 28% zeolite dry weight on average, and this is relevant for both water depollution and drug delivery issues. The low affinity of sulfanilamide for HSZ-Y was ascribed to its high hydrophilicity (water solubility 15–40 times higher than other drugs). The most stable tautomeric (amide or imide) form of each antibiotic adsorbed in zeolite Y was proposed by means of IR and solid state NMR spectroscopy augmented by computational modelling. The small dimensions and favourable stabilization energy allow the embedding of imidic and amidic dimers of sulfathiazole and sulfapyridine, respectively, inside the zeolite cage whereas the remaining sulfa drugs adsorbed in monomeric amidic forms.

Linear and nonlinear optical properties of nucleic acid bases

Electronic and vibrational (hyper)polarizabilities of neutral nucleic acid bases (uracil, thymine, cytosine, adenine, hypoxanthine and guanine) were determined using Hartree–Fock, correlated MPn (n=2, 4), CCSD and DFT (B3LYP, B97-1, CAM-B3LYP) methods. The computations were performed in gaseous and aqueous phases for the most stable tautomeric forms. Frequency-dependent second-order hyperpolarizabilities were calculated for the OKE, IDRI, EFISHG and THG nonlinear optical processes at the wavelength of 1064nm. The results show that the average electronic polarizabilities increase in the order uracil<cytosine<thymine<hypoxanthine<adenine<guanine. This order is also maintained for the electronic hyperpolarizabilities, with the inversion between cytosine and thymine. The response electric properties for the tautomers are almost similar to each other, whereas group substitution and solvation effects are much more significant. Among the DFT methods, the long-range corrected CAM-B3LYP functional gives the better performances, reproducing satisfactorily the correlated ab initio (hyper)polarizability data.

Density functional theory study of interaction, bonding and affinity of group IIb transition metal cations with nucleic acid bases

The structure, bonding, and energetics of the complexes obtained from the interaction between the most stable tautomeric forms of free DNA and RNA bases and Zn2+, Cd2+ and Hg2+ cations have been studied using density functional B3LYP method. The 6-311+G (2df, 2p) basis set along with LANL2DZ pseudopotentials for the cations are used in the calculations. The tautomerization paths of the nucleobases are investigated and transition states between the tautomeric forms of the free bases are located. The relative stability of the complexes and the tautomers of the free nucleobases are discussed referring to MIA and relative energy values. For uracil, thymine and adenine, interaction of the metal cations with the most stable tautomers form the least stable molecular complexes. For cytosine and guanine, the stability of the metalated complexes differs significantly. The enthalpy (ΔH), entropy (TΔS) and free energy (ΔG) of the complexes at 298K have also been calculated.

Investigating the prototropic tautomerism in (E)-2-[(4-fluorophenyl)iminomethyl]-5-methoxyphenol compound for solid state and solvent media by experimental and quantum computational tools

Abstract The tautomerism in o-Hydroxy Schiff bases appears as a result of intramolecular proton transfer between the phenolic oxygen atom and nitrogen atom. This process results in two tautomeric forms (phenol-imine and keto-amine). The preference of a particular form by the compound changes in solid and solvent media. In the current study, the proton tautomerism in (E)-2-[(4-fluorophenyl)iminomethyl]-5-methoxyphenol (an o-Hydroxy Schiff basis) was investigated for solid and solvent media by experimental (IR and UV–vis) and computational methods (DFT and TD-DFT). Density functional theory (DFT) at B3LYP/6-31G(d) level was used for gas phase geometry optimization. For geometry optimizations in solvent media the polarizable continuum model (PCM) was used. The excitation energies of the title compound were calculated for gas and solution phase with time-depended density functional theory (TD-DFT) approach. Experimental FT-IR studies for the solid phase of the title compound show the preference of enol form, as supported by X-ray analysis results. Experimental and computational UV–vis studies of proton transfer process were carried out for various organic solvents of different polarities (EtOH, DMSO, Benzene and CHCl3). It was found that the stability of the molecule increases with the increase of solvent polarity. In addition, the existence of a new absorption band only in EtOH was attributed to keto form by considering TD-DFT calculations and previous studies. The proton transfer process was further investigated by considering a TS structure in DFT (B3LYP) calculations for gas phase and solvent media. The results for gas phase revealed that the enol form is more stable than keto form. The activation energy for proton transfer reaction was calculated as 6.1 kcal/mol for gas phase. For the proton transfer process in solvent media, it is found that the enol form in Benzene is more stable tautomeric form while the keto form is more stable one in CHCl3, EtOH and DMSO. In addition, the energy gap between enol and keto forms was found to decrease from gas phase to solution phase, proposing that the tautomerization in a polar solvent occurs easier than an apolar solvent.

What roles do boron substitutions play in structural, tautomeric, base pairing and electronic properties of uracil? NBO &amp; AIM analysis

The synthesis of modified versions of deoxyribonucleic acid is an area that is receiving much attention. The replacement of the nitrogen atom on the nucleobases with boron atom has provided insight into deoxyribonucleic acid and ribonucleic acid stability, recognition, and replication at the atomic level. In the present research, we investigated a detailed density functional theory study of the structural, tautomeric, base-pairing ability, bond dissociation energy, and electronic properties of two boron analogues (i.e., boron substitutions at 4-position and 5-position of uracil) of uracil nucleobase. The effects of these modifications on theirs acid–base properties have been considered. Our goal is to gather data to help elucidate the structure and electronic properties of boron analogues of uracil. Density functional theory calculations were performed using a nonlocal hybrid B3LYP and 6-311++G (d,p) atomic basis set. The result of calculation revealed that the canonical ‘keto’ form is the most stable tautomeric form of uracil nucleobase and its boronated analogues in the gas phase at density functional theory and second-order Moller–Plesset levels. Hyperconjugation stabilization factors that affect the stability of generated radicals and anions in these molecules were investigated by natural bond orbital analysis. Furthermore, quantum theory of atoms in molecules analysis was performed to extract the bond critical point properties of various base pairs. The electron density can be considered as a good description of the strength of the different types of hydrogen bonding. Copyright © 2012 John Wiley & Sons, Ltd.

Production of uremic toxin methylguanidine from creatinine via creatol on activated carbon

The mixture of creatinine, activated charcoal and water was stirred. As a result the conversion of creatinine into two products was observed. 1H, 13C NMR and HMBC spectra were recorded and the chemical shifts assigned. Two uremic toxins: creatol and N-methylguanidine were identified. To interpret the NMR data obtained, the optimum structure of creatol, which can exist in the forms of seven tautomers, has been calculated using the DFT B3LYP/6-311G(2d,p) method. The influence of the solvent was described by the polarizable continuum model (PCM). The calculated energy of the most energetically stable tautomeric form A is lower by 12.2, 16.9, 33.8, 81.5, 106.3, 130.4 kJ/mol in water than that of the tautomers B– G, respectively, which suggests that the A form of creatol should prevail in solution. In DMSO, the calculated energy of the most energetically stable tautomeric form A is lower than that of both D and B and the remaining tautomeric forms ( C, E– G) are less energetically stable. Subsequently, we sought the correlations between the experimental and the calculated chemical shifts of protons and carbons-13 for the forms – A, B (in water) and A, B, D (in DMSO) – of creatol. The population of the A tautomer is predominant in both H 2O and DMSO. We have also recorded the spectra of creatol and N-methylguanidine at different pH. Our data are complete enough to be used in the analysis of body fluids.

UV-Induced Oxo → Hydroxy Unimolecular Proton-Transfer Reactions in Hypoxanthine

Monomers of hypoxanthine isolated in low-temperature Ar matrixes were studied using Fourier transform infrared spectroscopy. Two most stable tautomeric forms of hypoxanthine: oxo-N(9)-H and oxo-N(7)-H as well as a very small amount of the minor hydroxy-N(9)-H tautomer were observed in Ar matrixes directly after their deposition. UV irradiation of the matrixes induced conversion of the oxo-N(9)-H and oxo-N(7)-H tautomers of the compound into the hydroxy-N(9)-H and hydroxy-N(7)-H forms, respectively. Upon exposure of the matrixes to the UV (lambda > 270 nm) light, the oxo-N(9)-H --> hydroxy-N(9)-H phototautomeric reaction dominated strongly over the oxo-N(7)-H --> hydroxy-N(7)-H phototransformation. The latter phototautomeric reaction occurred effectively when matrix-isolated hypoxanthine was irradiated with shorter-wavelength (lambda > 230 nm) UV light. Thanks to this wavelength dependency, it was possible to clearly distinguish the oxo --> hydroxy photoreaction within the N(9)-H tautomers from the analogous phototautomeric process within the N(7)-H tautomers. All of the observed isomers of hypoxanthine (substrates and products of the photoreactions) were identified by comparison of their IR spectra with the spectra calculated at the DFT(B3LYP)/6-31++G(d,p) level of theory.

Quantum-chemical study of the structure and reactivity of 4,5-dihydropyrazol-5-ones and their thio and seleno analogs: VIII. Solvation effects and tautomerism of 4,5-dihydropyrazol-5-ones and their thio and seleno analogs

The effect of hydration on the stability of tautomeric forms of 1-methyl-4,5-dihydro-1H-pyrazol-5-one, 1-methyl-4,5-dihydro-1H-pyrazole-5-thione, and 1-methyl-4,5-dihydro-1H-pyrazole-5-selone was analyzed by nonempirical quantum-chemical methods at different theory levels. The results of calculations by all these methods, including density functional theory, with two types of models (continuum and discrete) showed stronger stabilization of the NH tautomers of all the examined heteropyrazolones in water, as compared to their CH and XH tautomers. The strongest stabilization effect is reached in the calculation of discrete complexes in terms of the self-consistent reaction field model. The degree of differentiation of the stability of tautomeric forms considerably decreases when electronic correlation is taken into account, whereas the use of polarization functions on hydrogen atoms in addition to polarization functions on heavy atoms almost does not affect the position of the tautomeric equilibrium.

Porphyrins Bearing Stable meso-Alkylidenyl Double Bonds. A New Family of Nonplanar Porphyrinoids

[Structure: see text] Unique core-modified porphyrinoids, such as oxabenziporphyrins, oxapyriporphyrins, and thiapyriporphyrins, bearing exocyclic C-C double bonds at meso-positions, have been synthesized and characterized. The synthesis was accomplished by utilizing typical "3+1"-type condensation. Two different stable tautomeric forms were isolated, and the two tautomeric forms can be interconvertible upon treatment with base. In contrast, only the structure bearing an exocyclic double bond was isolated in the case of oxapyriporphyrin and oxabenziporphyrin.