UV-induced generation of rare tautomers of 2-thiouracils: a matrix isolation study

Unimolecular photoisomerization reactions were studied for 2-thiouracil, 6-aza-2-thiothymine, 1-methyl-2-thiouracil, and 3-methyl-2-thiouracil isolated in low-temperature Ar matrixes. The IR spectra have revealed that before UV irradiation all the matrix-isolated compounds adopted exclusively the oxo-thione tautomeric form. Upon UV (lambda > 320 nm) irradiation of the matrixes, two oxo-thiol photoproducts were generated for monomeric 2-thiouracil as well as for monomeric 6-aza-2-thiothymine. Generation of these products corresponds to transfer of a proton from either the N(1)-H or N(3)-H group to the sulfur atom of the C(2)=S thiocarbonyl moiety. The first of the above reactions was photoreversible. As a consequence, after prolonged UV irradiation most of the material was transformed into the oxo-thiol-N(1)H form. The hydroxy-thiol tautomers of 2-thiouracil and 6-aza-2-thiothymine were also photogenerated as minor products. For 1-methyl-2-thiouracil and 3-methyl-2-thiouracil, thione --> thiol phototautomeric reactions yielded the oxo-thiol isomers of the compounds. Since these reactions were photoreversible, the final stages of the photoinduced processes corresponded, for both methylated 2-thiouracils, to photostationary states. All the products of the investigated photoreactions were identified by comparison of their IR spectra with the spectra calculated at the DFT(B3LYP)/6-311++G(2d,p) level.     

Tautomerism in 4-hydroxypyrimidine, S-methyl-2-thiouracil, and 2-thiouracil

The keto-enol tautomerism of 4-hydroxypyrimidine and of the related molecules S-methyl-2-thiouracil and 2-thiouracil has been investigated using synchrotron-based techniques. The populations of the constituent tautomers and thermodynamic parameters have been obtained by analysis of core-level photoemission spectra. The effect of substituents on the stability of tautomers has been revealed. Attaching additional OH (or SH) groups to the aromatic ring stabilizes the dioxo (or oxo-thione) forms. However, substitution of hydrogen in position 2 by an S-CH(3) group (that is, in going from 4-hydroxypyrimidine to S-methyl-2-thiouracil) does not significantly affect the tautomeric equilibrium.     

Theoretical Studies on the Binding of Cd~（2＋） to Uracil and Its Thio-derivatives

The interaction of Cd2+ with uracil,2-thiouracil,4-thiouracil and 2,4-dithiouracil have been investigated by the density functional theory(DFT) calculations.For uracil and 2,4-dithiouracil,where the two basic sites are the same,Cd2+ attachment to the heteroatom at position 4 is preferred.However,for the systems where both types of basic centers,a carbonyl and a thiocarbonyl groups,are present,Cd2+ association with sulfur is favorable.The enhanced stability of these enolic and thiol forms comes from Cd2+ interaction with two basic sites simultaneously,which thereby triggers a significant aromatization of the ring.More significantly,the Cd2+ binding energy with uracil and its thio-derivatives is larger than the tautomerization barriers connecting the diketo-like forms with the corresponding enolic-like tautomers.Consequently,when associated with Cd2+,all tautomers are energetically accessible and should be observed in the gas phase.     

Ab initio study on tautomerism of 2-thiouracil in the gas phase and in solution

Ab initio geometry optimizations were carried out at the HF/3-21G and HF/6-31+G^** levels for the six tautomeric forms of 2-thiouracil (2TU, 2TU1, 2TU2, 2TU3, 2TU4, 2TU5) in the gas phase and in solution. To obtain a more definitive estimate of the relative stabilities for 2-thiouracil tautomers in the gas phase, single-point MP2/6-31+G^** calculations were performed on the HF/6-31+G^** optimized geometries. The tautomeric equilibria in 1,4-dioxane (=2.21), acetonitrile (=38), and in water (=78.54) were studied using the self-consistent reaction field (SCRF) theory. The calculated relative free energies indicated that 2TU is the energetically preferred tautomer in the gas phase and in solution. The stability order of 2-thiouracil tautomers depends on the level of theory and the dielectric constant of the solvent. The obtained results are compared with the available experimental data.     

Interaction of Ca2+ with uracil and its thio derivatives in the gas phase

The structures and relative stabilities of the complexes formed by uracil and its sulfur derivatives, namely, 2-thio-, 4-thio, and 2,4-dithio-uracil when interacting with Ca(2+) in the gas phase have been analyzed by means of density functional theory (DFT) calculations carried out at the B3LYP/6-311++G(3df,2p)//B3LYP/6-31+G(d,p) level. For uracil and 2,4-dithiouracil, where the two basic sites are the same, Ca(2+) attachment to the heteroatom at position 4 is preferred. However, for the systems where both types of basic centers, a carbonyl or a thiocarbonyl group, are present, Ca(2+)-oxygen association is favored. The most stable complexes correspond to structures with Ca(2+) bridging between the heteroatom at position 2 of the 4-enol (or the 4-enethiol) tautomer and the dehydrogenated ring nitrogen, N3. The enhanced stability of these enolic forms is two-fold, on the one hand Ca(2+) interacts with two basic sites and on the other triggers a significant aromatization of the ring. Besides, Ca(2+) association has a clear catalytic effect on the tautomerization processes which connect the oxo-thione forms with the enol-enethiol tautomers. Hence, although the enol-enethiol tautomers of uracil and its thio derivatives should not be observed in the gas phase, the corresponding Ca(2+) complexes are the most stable species and should be accessible, because the tautomerization barriers are smaller than the Ca(2+) binding energies.     

Infrared spectra and tautomerism of isocytosine; an ab initio and matrix isolation study

Prototropic tautomerism of isocytosine has been investigated using both theoretical ab initio and experimental matrix isolation IR methods. The coexistence of the amino-hydroxy and amino-oxo N(3)H forms, with a clear predominance of the hydroxy form, was observed. The tautomerization constant [oxo]/[hydroxy] obtained from experimental and calculated IR intensities was 0.11 at the micro-oven temperature of 400 K. The ab initio prediction of the relative energies of the tautomers is in reasonable agreement with the experimental estimation. The change of the tautomeric form oxo→hydroxy upon UV irradiation was used to separate the IR spectra of both tautomers. A theoretically assisted interpretation of the IR spectra of both observed tautomers is proposed.     

Heteroannulation of 6-polyfluoroalkyl-2-thiouracils

A multi-component double Mannich cyclocondensation of 6-polyfluoroalkyl-2-thiouracils with formalin and heterocyclic amines (2-aminopyridine, 2-aminopyrimidine, 4-aminoantipyrine) proceeded regiospecifically at the C=S and NH centers giving rise to 3-hetaryl-8-polyfluoroalkylpyrimido[2,1-b][1,3,5]thiadiazines. The regioisomeric structure of the products was established by X-ray crystallography, IR and NMR spectroscopy, GLC-MS spectrometry. 6-Trifluoromethyl-2-thiouracil and 8-polyfluoroalkylpyrimido[2,1-b]thiadiazines exhibited weak tuberculostatic activity.     

Novel uracil derivatives: newly synthesized centrally acting agents.

A series of 1-amino-5-substituted uracils and their 4-thio or 2,4-dithio substituted analogues were synthesized and assayed for anti-conflict activity in rats and anesthetic activity in mice. 1-Amino-5-halogenouracils 3b-e, 1-amino-4-thiouracil (9a), and 1-amino-5-halogeno-4-thiouracils 9c, d showed both anti-conflict and anesthetic activities. The most active compound was 1-amino-5-chloro-4-thiouracil (9d) which showed anxiolytic activity at 2 mg/kg of oral administration (p.o.) on a modified Geller-Seifter conflict schedule. Its minimum effective dose (MED) was lower than that of diazepam. The 50 percent effective dose (ED50) for anesthetic activity in mice of the compound (9d) was 32.9 mg/kg, p.o.     

Permanganate ion oxidations X. Kinetics and mechanisms of the initial stage in the oxidation of 4-hydroxy-2-pyrimidinethiols

Permanganate ion rapidly oxidizes the thiol group in 2-thiouracils (2,3-dihydro-2-thioxo-4(1H)-pyrimidinones, 4-hydroxy-2-pyrimidinethiols) to the corresponding uracil-2-sulfonates in phosphate-buffered solutions. The oxidations, which are first order in oxidant and first order in reductants, are characterized by relatively small energies of activation (E_a ? 4.3–6.7kcal/mol) and relatively large negative entropies of activation (ΔS? = ?24.9–?34.4 eu). The relative rates of oxidation of 2-thiouracil (2), 6-methyl- (4), 6-n-propyl- (6), 1,6-dimethyl-(8), and 3,6-dimethyl-2-thiouracil (9) are 1.00:1.23:0.98:7.32:2.54. The rate of oxidation of 1,3,6-trimethyl-2-thiouracil (12) is several orders of magnitude slower than that of the other thiouracils. Although the thiol group or thiolate anion is probably involved in the rate-determining step, several other possible mechanisms are also considered.     

Tautomerism and infrared spectra of 2-thiopurine: an experimental matrix isolation and theoretical ab initio and density functional theory study

Infrared spectra of 2-thiopurine (2-mercaptopurine, 2-purinethiol ) isolated in low-temperature Ar and N2 matrixes are reported. These spectra indicate that the compound adopts exclusively the thiol N9H tautomeric form. The theoretical calculations of relative energies of 2-thiopurine tautomers have been carried out at the MP4(SDTQ)//HF level using the 6-31G(d,p) basis set. The thiol N9H tautomer was predicted to be the most stable of all isomers of 2-thiopurine. The infrared spectra of the tautomers of 2-thiopurine have been calculated at the DFT(B3LYP)/6-31G(d,p) level. Good agreement between the experimental spectra and the spectra calculated for thiol N9H tautomer supported the identification of the dominant tautomer. It has also allowed for the reliable assignment of the bands observed in the experimental IR spectrum.     

Systematic effect of benzo-annelation on oxo-hydroxy tautomerism of heterocyclic compounds. Experimental matrix-isolation and theoretical study

Oxo-hydroxy tautomerism and phototautomerism of 2-quinolinone, 1-isoquinolinone, 3-hydroxyisoquinoline, 2-quinoxalinone, and 4-quinazolinone were studied using the matrix-isolation technique. These compounds contain a benzene ring fused with a heterocyclic ring of 2-pyridinone, 2-pyrazinone, or 4-pyrimidinone. It turned out that direct attachment of a benzene ring to a heterocycle leads to a very pronounced increase of the relative stability of oxo tautomers (in comparison with the tautomerism of the parent compounds 2-pyridinone, 2-pyrazinone, and 4-pyrimidinone). The only exception concerns 3-hydroxyisoquinoline, where fusion with a benzene ring enforces rearrangement of the double- and single-bond system in the oxo tautomer. This destabilizes substantially the oxo form with respect to the hydroxy tautomer. The ratios of population of the oxo and hydroxy tautomers observed in Ar matrixes correspond to the tautomeric equilibria of the compounds in the gas phase. These equilibria were well reproduced by theoretical calculations carried out at the QCISD and QCISD(T) levels. The combined experimental and theoretical results reveal links between aromaticity and tautomerism. Moreover, a UV-induced phototautomeric reaction transforming the oxo forms into the hydroxy tautomers was observed for all (except 3-hydroxyisoquinoline) studied compounds. This photoeffect allowed separation of the IR spectra of the tautomers in question.     

Synthesis and anti-HIV-1 activity of a series of 1-(alkoxymethyl)-5-alkyl-6-(arylselenenyl)uracils and -2-thiouracils

A series of 1-(alkoxymethyl)-5-alkyl-6-(phenylselenenyl)uracils and -2-thiouracils modified at the 3- and/or 5-position of the C-6 phenylselenenyl ring with methyl or fluoro substituent has been synthesized and tested for their ability to inhibit HIV-1 replication. Lithiation of the acyclic uracil and 2-thiouracil derivatives 11-14 and 27-32 with lithium diisopropylamide or lithium bis(trimethylsilyl)amide followed by reaction with an appropriate diaryl diselenide afforded 6-arylselenenyl compounds 18-26 after removal of the tert-butyldimethylsilyl protecting group and 35-47 . Compounds 48-54 were prepared from compounds 38-44 by oxidative hydrolysis of the thione function. Of these compounds, 50 inhibited HIV -1 replication in human T₄ lymphoblastoid cells at a 50% effective concentration (EC₅₀) of 0.0047 μM with a selectivity index of >42600.     

Raman spectroscopic study of the tautomeric composition of adenine in water

An experimental and theoretical study of the tautomeric composition of adenine (Ade) in water using Raman spectroscopy is reported. Experimental resonance Raman spectra of adenine at excitation wavelengths of 200, 218, and 266 nm were compared with quantum-mechanical calculations of N(9)H- and N(7)H-adenine tautomers and their cations. Both theoretical and experimental studies of nonresonance Raman spectra (457 nm excitation) of adenine were also performed for comparison. A satisfactory agreement of the calculated results with the experimental data was obtained. The Raman spectra are interpreted, and the basic regularities of the Raman intensity distribution are explained. On the basis of the analysis performed, the tautomeric composition of adenine in water is revealed. It is shown that the Ade-N(9),N(1)H(+) cation is the predominant form and that some neutral forms of Ade-N(9)H and Ade-N(7)H tautomers exist in water at pH 3.     

Density functional theory study on molecular structure and vibrational IR spectra of isocytosine

Density functional theory with the combined Becke3-LYP exchange-correlation energy functional [DFT(B3-LYP) method] using the 6-31G(d, p) basis set is applied to predict molecular parameters (geometries, rotational constants, dipole moments) and vibrational IR spectra (harmonic wavenumbers, absolute intensities) of six tautomers of the isocytosine molecule. The results are compared with the corresponding data calculated at the conventional ab initio Hartree-Fock (HF) level using the same basis set and with available experimental data. Calculations show that (a) three amino tautomers are slightly nonplanar species with, evidently, a distorted amino group, (b) the DFT (B3-LYP)/6-31G(d, p) method predicts better molecular parameters, than do the HF calculations, and (c) the DFT(B3-LYP)-calculated vibrational IR spectra of isocytosine agree well with the available recorded IR spectra, and they show marked improvement over the IR spectra predicted at the HF/6-31G(d, p) level. Tautomeric stabilities of isocytosine are discussed on the basis of computed electronic energies by the DFT(B3-LYP) and ab initio approaches [including the MP2 and MP4(SDQ) calculations of electronic energies] and predicted zero-point vibrational energies by DFT(B3-LYP) and HF methods. This relative energies at 0 K of the tautomeric forms of isocytosine predicted by both conventional ab initio and DFT(B3-LYP) methods correlate well with the experimental data, showing the predominance of the aminohydroxy tautomer of isocytosine for an isolated molecule. © 1997 John Wiley & Sons, Inc.     

Diketoacid HIV-1 integrase inhibitors: An ab initio study

The stable tautomeric forms of two representative arene-substituted diketoacid HIV-1 integrase inhibitors, 5-ClTEP and L-731,988, were investigated by B3LYP with 6-31G*, 6-31G(d,p), and 6-31+G(d,p) basis sets. Optimization with MP2/6-31G* was also performed for 5-ClTEP. The solvation effect was considered using a conductor-like screening model. With the density functional theory method, the trans diketo conformations are more stable than the cis conformers. The difference is 14 kJ mol(-1) for 5-ClTEP and 33 kJ mol(-1) for L-731,988. Two trans diketo structures were obtained. The difference between these two trans diketo structures is less than 4 kJ mol(-1) calculated at the B3LYP/6-311+G(3df,2p) level. Two enol forms prevail over the diketo tautomers and are calculated to have the same free energy. Because there is no barrier observed between these two enol forms, they can interchange easily such that a delocalized transition state is suggested to be the observed form. Contradictory to the results of the MP2 method that predicts a preference for the trans diketo forms, the B3LYP method predicts a preference for the enol tautomers, which is in agreement with the experimental results.     

Structure of neutral molecules and monoanions of selected oxopurines in aqueous solutions as studied by NMR spectroscopy and theoretical calculations

A methodology enabling investigation of a multicomponent tautomeric and acid-base equilibria by (13)C NMR spectroscopy supported by theoretical calculations has been proposed. The effectiveness of this method has been illustrated in a study of 2-oxopurine, 6-oxopurine (hypoxanthine), 8-oxopurine, and 2,6-dioxopurine (xanthine) in neutral and alkaline aqueous solutions. For each compound a series of (13)C NMR spectra were recorded at pH ranges in which neutral molecules, monoanions and/or dianions occurred in dynamic equilibrium. The carbon chemical shifts for these three forms of the investigated compounds were retrieved from the analysis of pH-dependence of the measured, dynamically averaged values of these parameters. The structures of several stable tautomers of the neutral and monoanionic oxopurine forms were predicted from theoretical calculations and nuclear magnetic shielding constants for (13)C nuclei in these tautomers were calculated. At both calculation steps (molecular geometry optimization and calculation of NMR parameters) the PBE1PBE/6-311++G(2d,p) level of theory was used. The populations of the most stable tautomers were determined from the experimental data analysis exploiting the fact that they were population-weighted averages of the chemical shifts of particular tautomers. It has been shown that only the oxo forms of the investigated oxopurines are present in aqueous solutions and that the determined populations in most cases remain in a qualitative agreement with the calculated free energies of the appropriate tautomers. The obtained results are in general agreement with other literature reports on oxopurine tautomerism and confirm importance of the hydration phenomena for the investigated systems. The data analysis has shown that the best compliance between theory and experiment is obtained when the hydration phenomenon is modeled by discrete hydration augmented by PCM (polarizable continuum solvation model).     

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.     

Electron propagator and coupled-cluster calculations on the photoelectron spectra of thiouracil and dithiouracil anions

Electron affinities, vertical electron detachment energies, and isomerization energies of 4-thiouracil, 2-thiouracil, and 2,4-dithiouracil and their valence anions have been calculated with ab initio electron propagator and other many-body methods. Anions in which protons have been transferred to the C5 from the N1 or N3 ring positions have been considered, but the canonical forms are most stable for the 4-thiouracil and 2,4-dithiouracil anions. Electron affinities of 0.61, 0.26, and 0.87 eV have been determined for 4-thiouracil, 2-thiouracil, and 2,4-dithiouracil, respectively. Electron propagator calculations on the canonical anions yield vertical electron detachment energies that are in close agreement with experimental peaks at 1.05, 3.21, and 3.32 eV for 4-thiouracil and at 1.4 eV for 2,4-dithiouracil.     

A new theoretical prediction of the infrared spectra of cytosine tautomers

The infrared spectra of the cytosine amino-oxo and amino-hydroxy tautomers predicted theoretically at the ab initio Hartree—Fock level with a 6-31G** basis set are reported. These are compared with the experimental spectra obtained in an argon low-temperature matrix. The IR spectra computed at this level reproduce the experimental spectra closer than the previous predictions.     

Adenine tautomers: relative stabilities, ionization energies, and mismatch with cytosine

In this study, we have investigated 12 tautomers of the DNA base adenine at the BP86/TZ2P and BP86/QZ4P levels of density functional theory. The vertical and adiabatic ionization energies of all tautomers were determined as the difference in energy between the radical cation and the corresponding neutral system. Furthermore, an evaluation is made for the eigenvalue spectra calculated with the SAOP functional, which is shown to lead to substantial improvements for orbital energies compared to BP86. We have also explored the correlations between the Kohn-Sham orbitals of the different tautomers at the BP86/QZ4P and SAOP/QZ4P levels. Finally, we discuss implications of the existence of the tautomeric forms of adenine for the DNA replication.