Investigation of the tautomeric equilibrium of nucleic acid bases in aqueous solution

Relative constants of acidity and basicity of nucleic acid bases (NABs) and their tautomeric forms are calculated. The general characteristic of the effect of an aqueous solvent on the tautomeric equilibrium of NABs is formulated. It is shown that during the tautomeric transformation of NABs their acid-base properties change to the opposite ones. One of possible causes of the formation of complementary pairs with rare tautomeric forms of NABs is considered.     

1H and 13C NMR study of the enol–enolic tautomerism of some cyclic β-ketoaldehydes

Aldehyde (δCH) and enolic (δOH) proton chemical shifts, the corresponding spin–spin coupling constants (JCH,OH) and the ¹³C chemical shifts (δC) have been measured for three cyclic β-ketoaldehydes as a function of temperature. A tautomeric equilibrium has been shown to exist between the aldo–enol ( A ) and hydroxymethylene ketone ( B ) forms. The chemical shifts δCH δOH and δC for the two pure tautomeric forms A and B have been calculated. The enthalpy changes ΔH in the tautomeric process A ? B and the percentages of the tautomeric forms have been determined.     

Tautomeric equilibria and pi electron delocalization for some monohydroxyarenes--quantum chemical studies

Keto-enol tautomeric interconversions and variations of the pi-electron distribution were studied for 11 isolated monohydroxyarenes at the DFT(B3LYP)/6-311++G(2df,2p) level. For two monohydroxyarenes (phenol and 9-anthrol), the PCM model of solvation (water) was also applied to the DFT geometries. The geometry-based HOMA index was applied to estimate pi-electron delocalization in the keto and enol tautomeric forms. Thermodynamic parameters of tautomeric interconversions (DeltaET, DeltaGT, TDeltaST, pKT) were calculated to estimate relative stabilities of individual tautomers and their percentage contents in the tautomeric mixtures. In almost all cases, the aromatic enol forms are strongly favored. An exception is 9-anthrol, which prefers its keto form. The resonance stabilization of this form comes from the central ring. Generally, aromaticity is the main factor that influences tautomeric equilibria in monohydroxyarenes. Hydration effect is considerably smaller and it does not change the tautomeric preference.     

苯基及取代苯基四唑异构反应的量子化学研究

与四唑相同，对位取代苯基四唑有两种异构体（见图1）.几十年来，实验工作者对这类化合物在医药和农业等方面的应用研究表现出浓厚兴趣［‘-‘1.最近，我们用从头计算和PM3等方法研究了四唑两种异构体间异构化反应的机理问.为了探明这类反应的取代基效应，本文报导用PM3方法[6]     

CP/MAS spectroscopy in the determination of the tautomeric forms of gossypol, its Schiff bases and hydrazones in the solid state

New Schiff bases and new hydrazones were synthesized and studied by (13)C and (15)N CP/MAS spectroscopy and by (1)H--(1)H COSY, (1)H--(13)C HMBC, (1)H--(13)C HSQC, (1)H--(15)N HMQC and (1)H--(15)N HSQC correlations. The CP/MAS investigation of gossypol has demonstrated that in the solid state it exists exclusively in the aldehyde-aldehyde tautomeric form. In contrast, CP/MAS studies of hydrazones and Schiff bases reveal that these compounds occur in the solid state in the N-imine-N-imine and enamine-enamine tautomeric forms, respectively. It is shown that the (13)C resonances of C-6, C-7 and C-11 carbon atoms are suitable for distinguishing between the tautomeric forms of aza-derivatives of gossypol in the solid state. Furthermore, we have proved that the (15)N CP/MAS spectra can be used to identify these tautomeric forms.     

Study of the tautomeric forms of 3,4-dihydroxyphenylacetic acid by carbon-13 nuclear magnetic resonance spectroscopy

The pH-dependent (13)C chemical shifts indicate an approximately 1:1 ratio of the 3-OH:4-OH tautomeric forms of singly dissociated 3,4-dihydroxyphenylacetic acid. It is found that the (13)C chemical-shift method is an effective technique for determining tautomeric forms from pK values.     

Gas-phase study of molecular switches based on tautomeric proton transfer

The keto-enol tautomeric equilibrium in two newly developed molecular switches was studied by using various mass spectral techniques. In these two compounds, namely 4-(phenyldiazenyl)-2-(piperidin-1- ylmethyl)naphthalen-1-ol and 2-[(1,4,7,10-tetraoxa-13-azacyclopentadecan-13-yl)methyl]-4- (phenyldiazenyl)naphthalen-1-ol, the switching on/off states are achieved by a controlled shift of the tautomeric equilibrium. In the first compound, electron impact-mass spectrometry confirms that the unprotonated dye exists as an enol tautomer, while the electrospray ionization tandem mass spectrometry (ESI-MS/MS) experiment proves the clear shift to the keto tautomeric form under switching with acid addition. In the second compound, the addition of the alkali metal ions causes transition of the tautomeric equilibrium from the pure enol to the pure keto form. The ESI-MS study demonstrated better sensitivity towards lithium ions.     

Chemistry of naphthazarin derivatives. 9. Direct observation of prototropic tautomerism of (poly)hydroxynaphthazarins by IR spectroscopy

A series of substituted (poly)hydroxylated naphthazarins (5,8-dihydroxy-1,4-naphthoquinones) were synthesized. In general, (poly)hydroxynaphthazarins exist in organic aprotic solvents as mixtures of tautomeric 1,4-naphthoquinonoid forms (IR data). The ratio of tautomers was determined for the first time. The effects of the nature of substituents and the solvent polarity on the tautomeric equilibrium were qualitatively estimated.     

Chemistry of naphthazarin derivatives. 12. Synthesis and investigation of prototropic tautomerism of 3-(alk-1-enyl)-2-hydroxynaphthazarins

Substituted 3-(alk-1-enyl)-2-hydroxynaphthazarins were synthesized. According to data from IR spectroscopy, these compounds exist in organic aprotic solvents as mixtures of tautomeric 1,4-naphthoquinonoid forms. The compositions of tautomeric mixtures were quantitatively determined. The effects of the structure of the alkenyl substituent and the polarity of the solvent on the tautomeric equilibrium were qualitatively estimated.__________Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 11, pp. 2519–2525, November, 2004.     

MINDO/3研究胞嘧啶异构体间异构化反应——Ⅰ. N1-氢-4-氨基-2-羰基胞嘧啶与4-亚氨基-2-羰基胞嘧啶异构反应

本文报导用半经验方法研究N_1-氢-4-氨基-2-羰基胞嘧啶与4-亚氨基-2-羰基胞嘧啶异构化反应。用MINDO/3能量梯度法优化了孤立体系的全部自由度, 计算结果表明氨型比亚氨型稳定, △E=33.85 kJ mol~(-1); 限定分子体系在同一平面, 用Powell法优化过渡态几何构型, 计算所得正反应活化势垒为168.87 kJ mol~(-1), 逆反应活化势垒为135.02 kJ mol~(-1)。从IRC途径分析了该异构化反应的物理实质。     

Tautomerism of pyrimidyl-2-methane derivatives: medium effects,thermodynamics, kinetics and mechanism

The Investigation of tautomeric equilibria among pyrimidyl-2-methanes has been undertaken. Pyrimidyl-pyrimidyledene equilibrium has been found in the case of 5-substituted 2-pyrimidyl-cyanoacetic esters. Unsymmetrically substituted pyrimidyl-2-methanes form two types (1-NH and 3-NH) of ylidene tautomers, which differ in ring proton spin coupling constants. The effect of substituents in the pyrimidine ring and of the solvent on tautomeric equilibrium are discussed. A drastic effect is produced by acids (CF₃ COOH) which shift the equilibrium toward the ylidene tautomer of higher basicity. The thermodynamic and kinetic characteristics and the mechanism of the tautomeric equilibrium were examined.     

Calculated tautomeric equilibria and X-ray structures of 2-substituted N-methoxy-9-methyl-9H-purin-6-amines

Density Functional Theory calculations of nine 2-substituted N-methoxy-9-methyl-9H-purin-6-amines in the amino and imino tautomeric forms, as well as the complexes of the same with dimethyl sulfoxide (DMSO), were performed using two functionals (BP86 and B3LYP) and two basis sets (SV(P) and def2-TZVP). Solid-state structures of two of the compounds were obtained from single-crystal X-ray diffraction techniques. It was found that the inclusion of both an explicit hydrogen-bonding partner (DMSO) as well as continuum solvation effects, and vibrational corrections to energy, were necessary for qualitative and reasonable quantitative agreement with observed tautomeric ratios. The solution-optimized geometries and X-ray structures were found to be in good agreement. NMR spectroscopy confirmed the dependence of the tautomeric ratios on hydrogen-bonding abilities, in addition to the dipole moment of the solvent in question. Natural Bond Orbital charges on the N-7 nitrogen, as well as the tautomeric ratios were used to explain the observed reactivities of the compounds toward N-7 alkylation.     

Unique tautomeric properties of isoguanine

The tautomeric properties of isoguanine (also named 2-oxoadenine or 2-hydroxyadenine) have been studied in the gas phase, in different pure solvents, and in the DNA environment using state of the art theoretical methods. Our results show that isoguanine constitutes an unique example of how tautomerism can be modulated by the environment. Compared to the tautomeric preference in the gas phase, both polar solvents and the DNA microenvironment dramatically change the intrinsic tautomeric properties of isoguanine. Tautomers which are important in physiological conditions are less than 1/10(5) of the total population of isoguanine in the gas phase. The impact of the present findings in the understanding of spontaneous mutations and in the design of new nucleobases with multiple recognition properties is discussed.     

Tautomerism in drugs with benzimidazole carbamate moiety: an electronic structure analysis

Several medicinally important compounds carry benzimidazole carbamate moiety. In the scientific literature, these molecules are represented in different tautomeric forms. In this report, conformational and tautomeric preferences were analyzed on the model benzimidazole carbamate (carbendazim), so as to understand the potential energy surface of the title compounds. Quantum chemical calculations have been performed using HF, B3LYP, and MP2 methods in gas phase and solvent phase on model benzimidazole carbamate to understand the conformational and tautomeric preferences. (1) PE surface of amide–imide tautomers, (2) electron distribution, (3) AIM analysis, (4) NBO charges, (5) 1,3-H shift, etc., have been investigated for carbendazim and its conformers. The molecular electrostatic potential (MESP) surfaces of carbendazim have been studied. Further to understand the polymorphism in benzimidazole carbamate, analysis of dimers of carbendazim has been carried out. The results indicate that a neglected tautomer is important and the tautomeric equilibrium is quite subtle in these systems and it should be extensively considered in all studies related to these drugs.     

Tautomeric equilibria of pyridoxal-5'-phosphate (vitamin B6) and 3-hydroxypyridine derivatives: a theoretical study of solvation effects

The tautomeric equilibria of a series of 3-hydroxypyridine derivatives including pyridoxal-5'-phosphate (PLP), the active form of vitamin B(6), have been studied using density functional calculations (B3LYP/6-311+G//B3LYP/6-31G) in the gas phase and in different solvents. Three different approaches, namely continuum, discrete, and hybrid (combined discrete/SCRF), were employed to investigate the effects of solvation on the tautomeric equilibria. In all cases, the neutral hydroxy form is significantly more stable than the zwitterionic oxo form (by 43-56 kJ mol(-)(1)) in the gas phase. The tautomeric energies reduce substantially in the presence of a polarizable dielectric medium. However, the neutral form is calculated to be the dominant form in nonpolar and aprotic polar solvents. On the other hand, a reversal of tautomeric equilibrium, in favor of the zwitterionic form, is predicted in an aqueous medium. This study highlights the role of both water molecules and bulk solvent effect in influencing the tautomeric equilibria of the PLP related compounds. A combination of explicit microsolvation and continuum reaction field is required to account fully for the energetic effect of aqueous solvation. The tautomeric free energy differences (deltaG(298)) of PLP in the gas phase and in aprotic polar (epsilon = 40) and aqueous media are predicted to be 47, 22, and -29 kJ mol(-)(1), respectively.     

Intra and intermolecular hydrogen bonding in formohydroxamic acid

The presence of hydrogen bonding interactions in several tautomeric forms of formohydroxamic acid (FHA) and 1:1 association among the tautomeric forms and water‐coordinated tautomeric forms of FHA is explored theoretically. Out of the seven equilibrium structures, four tautomeric forms have been selected for aggregation with single water molecule and dimer formation. Fifteen aggregates of FHA with H₂O have been optimized at MP2/AUG‐cc‐PVDZ level and analyzed for intramolecular and intermolecular H‐bond interactions. Twenty‐seven dimers of the four tautomeric forms have been obtained at MP2/6‐31+G* level. The stabilization energies associated with dimerization and adduct formation with water are the result of H‐bond interactions and range from very weak to medium. The atomic charges and NBO analysis indicate that the electrostatic and the charge transfer are the important components favoring H‐bond formation. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

Theoretical Investigation of the Prototropic Diad Rearrangement of Salicylphosphorous and Phthalimidophosphorous Acids

The structures and energies of the tautomeric forms of salicylphosphorous and phthalimidophosphorous acids have been calculated by the DFT method. The tautomeric forms are found to be in equilibrium. Both tautomeric forms of phthalimidophosphorous acid may have an intramolecular hydrogen bond.     

Tautocrowns: a concept for a sensing molecule with an active side-arm

A new sensing molecule containing aza-15-crown-5 as a receptor and 4-(phenyldiazenyl)naphthalen-1-ol as a signal converter has been synthesized. In the free ligand, the hydrogen bonding between the tautomeric OH group and the nitrogen atom from the macrocycle fully shifts the tautomeric equilibrium towards the enol form. The complexation reverses the equilibrium as a result of the strong interaction between the metal ion captured in the macrocyclic moiety and the tautomeric carbonyl group. The complex formation is accompanied by strong bathochromic (between 60 and 100 nm) and hyperchromic effects on the absorption spectra. Obviously, the tautomeric OH/CO groups play the role of an active side-arm in the complexation, supporting it via formation of a 3D cavity and giving possibility for ejection of the guest compound under stimuli to shift the tautomeric process back.     

Fast excited-state intramolecular proton transfer and subnanosecond dynamic stokes shift of time-resolved fluorescence spectra of the 5-methoxysalicylic acid/diethyl ether complex

Excited-state intramolecular proton transfer (ESIPT) occurring in the salicylic acid (SA) derivative 5-methoxysalicylic acid (5-MeOSA) in an apolar solvent (cyclohexane) and in the presence of the hydrogen bond accepting agent diethyl ether (DEE) is investigated. Analysis of the directly measured subnanosecond time-resolved emission spectra (TRES) together with conventional steady-state fluorescence and time-correlated single-photon-counting (TCSPC) decays indicates that ESIPT in this system occurs much faster than fluorescence, and that the equilibrium between normal and tautomeric excited states is established before the emission from both states takes place. However, changes in time- and frequency-resolved fluorescence of the 5-MeOSA/DEE complex are observed due to structural relaxation within the complex, which is reflected in the dynamic Stokes shift of the tautomeric fluorescence band. The normal fluorescence band of 5-MeOSA/DEE does not exhibit marked changes within the investigated time range. A single-exponential relaxation time of 460 ps was determined for the dynamic Stokes shift of the tautomeric band, and it is attributed to a geometric change within the 5-MeOSA/DEE complex upon excitation. Since both tautomeric and normal emission bands are well resolved and exhibit different time-dependent behaviors, a double-well potential appears to be adequate to describe the excited state of the system studied.     

Tautomeric equilibria of 5-fluorouracil anionic species in water

It has long been postulated that rare tautomeric or ionized forms of nucleic acid bases may play a role in mispair formation. Therefore, ab initio quantum chemical investigations on the tautomeric equilibrium in 5-fluorouracil (5FU) and its anions (deprotonated from N1, AN1, and from N3, AN3) and their tautomeric forms in water were performed. The effect of the water as solvent was introduced using solute-solvent clusters (four water molecules). The influence of the water molecules on the tautomeric reactions between different forms was considered by multiple proton transfer mechanisms. We show that when a water dimer is located in the reaction site between the two pairs of N-H and C═O groups, the assistive effect of the water molecules is strengthened. All calculations of the solute-water complexes were carried out at an MP2 level of theory and supplemented with correction for higher order correlation terms at CCSD(T) level, using the 6-31+G(d,p) basis set. The ab initio calculated frequencies and Raman intensities of 5FU and its anions AN1, AN3, and dianion are in good agreement with the experimental Raman frequencies in aqueous solution at different pH. In order to establish the pH-induced structural transformation in the molecule of 5FU, further (1)H, (19)F, and (13)C NMR spectra in water solution for pH = 6.9-13.8 were acquired and the chemical shift alterations were determined as a function of pH. On the basis of NMR spectroscopic data obtained for 5FU in aqueous solution at alkaline pH, we suggest the existence of a mixture of the anionic tautomeric forms predicted by our theoretical calculations.