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.     

Photoelectron spectroscopic study of the negative ions of 4-thiouracil and 2,4-dithiouracil

We report the photoelectron spectra of the negative ions of 4-thiouracil (4-TU)(-) and 2,4-dithiouracil (2,4-DTU)(-). Both of these spectra are indicative of valence anions, and they are each dominated by a single broad band with vertical detachment energies of 1.05 and 1.4 eV, respectively. Complementary calculations by Dolgounitcheva, Zakrzewski, and Ortiz (see companion paper) are in accord with our experimental results and conclude that the (4-TU)(-) and (2,4-DTU)(-) anions, reported herein, are valence anions of canonical 4-thiouracil and canonical dithiouracil. Comparisons among the anions and corresponding neutrals of 4-thiouracil, 2,4-dithiouracil, 5-chlorouracil, 5-fluorouracil, and uracil itself show that both sulfur and halogen modifications of uracil give rise to significant changes in the electronic structure. The electron affinities of the first four are all substantially larger than that of the canonical uracil.     

Interpreting the vibrational spectra of uracil molecules and their deuterated isotopomers using a scaled quantum-chemical quadratic force field

The quadratic force field of the uracil molecule is obtained by MP2(full) calculations using the cc-pVTZ and cc-pVQZ basis sets. Under the assumption that the most stable diketone form of the uracil molecule has a flat configuration with C _s symmetry, the available vibrational gas-phase spectra of uracil and the matrix isolation spectra of its seven N-, C-, and mixed N,C-deuterated derivatives are analyzed jointly for the first time by using Pulay??s force field scaling. Band assignments suggested earlier are corrected. It is shown that sets of 14 scaling factors allow us to reproduce the adjusted interpretation of the spectra and to obtain the most reliable quadratic force constant matrix for uracil among those available, based on joint consideration of the experimental and quantum-chemical calculation results.     

Gas-phase deprotonation of uracil-Cu2+ and thiouracil-Cu2+ complexes

The deprotonation of Cu2+ complexes with uracil, 2-thiouracil, 4-thiouracil, and 2,4-dithiouracil has been investigated by means of B3LYP/ 6-311+G(2df,2p)//6-31G(d) calculations. The most stable [(uracil-H)Cu]+ and [(thiouracil-H)Cu]+ complexes correspond to bidentate structures in which Cu interacts with the deprotonated ring-nitrogen atom and with the oxygen or the sulfur atom of the adjacent carbonyl or thiocarbonyl group. For 2- and 4-thiouracil derivatives, the structures in which the metal cation interacts with the thiocarbonyl group are clearly favored with respect to those in which Cu interacts with the carbonyl group. This is at variance with what was found to be the most stable structure of the corresponding Cu2+ complexes, where association to the carbonyl oxygen was always preferred over the association to the thiocarbonyl group. The [(uracil-H)Cu]+ and [(thiouracil-H)Cu]+ complexes can be viewed as the result of Cu+ attachment to the uracil-H and thiouracil-H radicals formed by the deprotonation of the corresponding uracil+* and thiouracil+* radical cations. As a matter of fact their relative stability is dictated by the intrinsic stability of the corresponding uracil-H and thiouracil-H radical and by the fact that, in general, the N3-deprotonated site is a better electron donor than the N1. In all complexes, the bonding of Cu both to nitrogen and sulfur and to nitrogen and oxygen has a significantly large covalent character.     

FT-IR, FT-Raman spectra, density functional computations of the vibrational spectra and molecular geometry of biomolecule 5-aminouracil

FT-IR and FT-Raman spectra of the biomolecule 5-aminouracil were recorded in the regions 400–4000 cm⁻¹ and 10–3500 cm⁻¹, respectively. The observed vibrational wavenumbers were analyzed and assigned to different normal modes of vibration of the molecule. Density functional calculations were performed to support wavenumber assignments of the observed bands. A comparison with the molecule of uracil was made, and specific scale factors were employed in the predicted wavenumbers of 5-aminouracil. With the purpose of study the important molecule 5-aminouracil, its equilibrium geometry and harmonic wavenumbers were calculated for the first time by the B3LYP DFT method. The vibrational wavenumbers were compared with IR and Raman experimental data. Also good reproduction of the experimental wavenumbers is obtained and the % error is very small. All the tautomeric forms of 5-aminouracil were determined and optimized. The dimer forms were also simulated. The energy, atomic charges and dipole moments were discussed and several general conclusions were underlined.     

DFT study of molecular geometries and vibrational characteristics of uracil and its thio-derivatives and their radical cations

DFT calculations at the B3LYP/6-311++G** level have been carried out to study the vibrational characteristics of the neutral molecules, anionic and cationic radicals of uracil, 2-thiouracil and 4-thiouracil. In the U molecule, CC bond loses its double bond character and magnitude of the CC stretching frequency decreases significantly as a result of radicalization. Frequency for the in-plane deformation mode of CO increases when a sulfur atom is substituted for the oxygen atom at the site C₂ in the uracil molecule but decreases when a sulfur atom is substituted for the oxygen atom at the site C₄. The magnitude of both the N–H stretching frequencies decreases in all the radical cations as compared to their neutral molecules. Radicalization leads to significant changes in the magnitudes and intensities corresponding to some of the normal modes for all the three cases. Removal of an electron leads to decrease in the electronic charge mainly from the sulfur atom in the case of 2-TU and 4-TU, whereas it is distributed over the sites N₁, C₅, O₈ and O₁₀ in case of the U molecule.     

Anti-HIV Active Naphthyl Analogues of HEPT and DABO

 5-Isopropyl-6-naphthyl uracil and 5-isopropyl-6-naphthyl-2-thiouracil were alkylated to give N-1-(ethoxymethyl and methylthiomethyl) uracil and S²-cyclohexyl-thiouracil, respectively. 5-Ethyl-6-naphthyl uracil and 5-ethyl-6-naphthyl-2-thiouracil afforded N-1-(ethoxymethyl, methoxy-methyl, methylthiomethyl, acetoxyethoxy methyl and hydroxyethoxy methyl) uracil and S²-((2,2- diethoxyethyl), methoxycarbonylmethyl, ethoxycarbonylpropyl, methylthiomethyl, ethoxymethyl, methyl and cyclohexyl)-thiouracil upon alkylation.     

Surface-enhanced Raman scattering and density functional theory calculation of uracil on gold and silver nanoparticle surfaces

The adsorption structure of uracil on gold and silver nanoparticle surfaces has been comparatively studied by means of surface-enhanced Raman scattering (SERS). Uracil appeared to assume a perpendicular orientation with respect to the surfaces. The presence of the nu(CH) band in the SERS spectra indicated a vertical orientation of the aromatic ring of uracil on Au and Ag. The density functional theory (DFT) calculation was performed at the levels of B3LYP and MP2 to estimate the energetic stability of the N3- and N1-deprotonated tautomers and their vibrational frequencies on the surfaces. Almost all the vibrational bands in the SERS spectra at high concentrations could be ascribed to the N3-deprotonated uracil. The N3-deprotonated tautomer was predicted to be more favorable on Au than on Ag from the DFT calculation. The metal-N bond distance was assumed to be shorter for Au than for Ag upon adsorption of uracil.     

Anti-HIV Active Naphthyl Analogues of HEPT and DABO

Summary.  5-Isopropyl-6-naphthyl uracil and 5-isopropyl-6-naphthyl-2-thiouracil were alkylated to give N-1-(ethoxymethyl and methylthiomethyl) uracil and S²-cyclohexyl-thiouracil, respectively. 5-Ethyl-6-naphthyl uracil and 5-ethyl-6-naphthyl-2-thiouracil afforded N-1-(ethoxymethyl, methoxy-methyl, methylthiomethyl, acetoxyethoxy methyl and hydroxyethoxy methyl) uracil and S²-((2,2- diethoxyethyl), methoxycarbonylmethyl, ethoxycarbonylpropyl, methylthiomethyl, ethoxymethyl, methyl and cyclohexyl)-thiouracil upon alkylation. Received September 25, 2001. Accepted (revised) December 3, 2001     

Synthesis and characterization of mixed ligand complexes of copper(II), nickel(II), cobalt(II) and zinc(II) with glycine and uracil or 2-thiouracil

Mixed ligand complexes of Cu(II), Ni(II), Co(II) and Zn(II) formed with glycine and uracil or 2-thiouracil have been synthesized and characterized by elemental analysis, conductance, spectral (IR and electronic spectra) and magnetochemical measurements. Results show that glycine is bidentate in all cases; uracil behaves as a bidentate ligand in Cu(II) complex, coordinating through its one carbonyl oxygen and nitrogen, whereas in other cases it is only monodentate, coordinating only through nitrogen. With thiouracil, coordination occurs from carbonyl oxygen and one nitrogen in Cu(II) and Ni(II) complexes, but in the Co(II) complex coordination occurs from thionyl sulphur and nitrogen. In the Zn(II) complex it shows tridentate behaviour, coordinating through oxygen, sulphur and one nitrogen. Mixed Cu(II), Co(II) and Zn(II) complexes of uracil and of Ni(II) and Zn(II) with thiouracil are octahedral, whereas the mixed Ni(II) complex with uracil shows distorted tetrahedral geometry, and the mixed Co(II)-thiouracil complex is square planar. The mixed Cu(II)-thiouracil complex has a binuclear structure, with square planar arrangement around each copper atom.     

The IINS, IR and DFT studies of hydrogen bonds in 6-Furfuryl and 6-Benzylaminopurines

FTIR and IINS spectra of 6-Furfurylaminopurine (6-FAP) and 6-Benzylaminopurine (6-BAP) taken at different temperatures have been analysed and compared with the spectra calculated by the ab initio DFT/B3LYP method and the semiempirical PM3 method in the isolated molecule approximation, for the tautomers N3-H, N7-H and N9-H, and dimers with hydrogen bonds. For 6-FAP the best agreement between the calculated and experimental (at 20 K) spectra has been found for the N9-H tautomer, whose structure was established by X-ray diffraction. For 6-BAP the analogous agreement for the N9-H tautomer structure has been poor and much better for the N7-H tautomer. The vibrational spectra calculated for dimers of the molecules studied involved in hydrogen bonds, permitted also an interpretation of the bands whose positions and FWHM in the FTIR spectra changed with temperature.     

Vibrational studies of biomolecules. I. 2-Thiouracil

IR, far-IR and Raman spectra of 2-thiouracil are reported and interpreted. All the thirty normal modes could be assigned. The Raman spectrum and the vibrational assignments for all the thirty modes are reported for the first time. The ring breathing and Kekule stretching modes for 2-thiouracil are observed to have lower magnitudes when compared to those for uracil which could be due to the mass effect of the sulphur atom in place of the oxygen atom.     

Spontaneous self-association of adenine and uracil in polycrystals from low temperature FTIR spectra in the range below 1000 cm(-1)

FTIR spectra of solid samples of co-crystallized adenine and uracil were measured at 10K in the range below 1000cm(-1). New bands ascribable to the N3H (uracil) and NH(2) (adenine) out of plane vibrations, which disappear upon D-exchange, were revealed in comparison with the spectra of pure polycrystalline adenine and uracil obtained in the same conditions. The observed changes relate to the same groups that establish the H-bonds in base pairs of naturally occurring nucleic acids, despite the presence of an extra proton donor NH-group in both molecules. The well-established empirical correlation between the out of plane NH vibrational frequencies and H-bond energies was successfully applied for estimation of the latter in the mixed crystal.     

The acidity of uracil and uracil analogs in the gas phase: four surprisingly acidic sites and biological implications

The gas phase acidities of a series of uracil derivatives (1-methyluracil, 3-methyluracil, 6-methyluracil, 5,6-dimethyluracil, and 1,3-dimethyluracil) have been bracketed to provide an understanding of the intrinsic reactivity of uracil. The experiments indicate that in the gas phase, uracil has four sites more acidic than water. Among the uracil analogs, the N1-H sites have deltaH(acid) values of 331-333 kcal mol(-1); the acidity of the N3 sites fall between 347-352 kcal mol(-1). The vinylic C6 in 1-methyluracil and 3-methyluracil brackets to 363 kcal mol(-1), and 369 kcal mol(-1) in 1,3-dimethyluracil; the C5 of 1,3-dimethyluracil brackets to 384 kcal mol(-1). Calculations conducted at B3LYP/6-31+G* are in agreement with the experimental values. The bracketing of several of these sites involved utilization of an FTMS protocol to measure the less acidic site in a molecule that has more than one acidic site, establishing the generality of this method. In molecules with multiple acidic sites, only the two most acidic sites were bracketable, which is attributable to a kinetic effect. The measured acidities are in direct contrast to in solution, where the two most acidic sites of uracil (N1 and N3) are indifferentiable. The vinylic C6 site is also particularly acidic, compared to acrolein and pyridine. The biological implications of these results, particularly with respect to enzymes for which uracil is a substrate, are discussed.     

Effects of microsolvation on the adenine-uracil base pair and its radical anion: adenine-uracil mono- and dihydrates

Microhydration effects upon the adenine-uracil (AU) base pair and its radical anion have been investigated by explicitly considering various structures of their mono- and dihydrates at the B3LYP/DZP++ level of theory. For the neutral AU base pair, 5 structures were found for the monohydrate and 14 structures for the dihydrate. In the lowest-energy structures of the neutral mono- and dihydrates, one and two water molecules bind to the AU base pair through a cyclic hydrogen bond via the N(9)-H and N(3) atoms of the adenine moiety, while the lowest-lying anionic mono- and dihydrates have a water molecule which is involved in noncyclic hydrogen bonding via the O4 atom of the uracil unit. Both the vertical detachment energy (VDE) and adiabatic electron affinity (AEA) of the AU base pair are predicted to increase upon hydration. While the VDE and AEA of the unhydrated AU pair are 0.96 and 0.40 eV, respectively, the corresponding predictions for the lowest-lying anionic dihydrates are 1.36 and 0.75 eV, respectively. Because uracil has a greater electron affinity than adenine, an excess electron attached to the AU base pair occupies the pi* orbital of the uracil moiety. When the uracil moiety participates in hydrogen bonding as a hydrogen bond acceptor (e.g., the N(6)-H(6a)...O(4) hydrogen bond between the adenine and uracil bases and the O(w)-H(w)...N and O(w)-H(w)...O hydrogen bonds between the AU pair and the water molecules), the transfer of the negative charge density from the uracil moiety to either the adenine or water molecules efficiently stabilizes the system. In addition, anionic structures which have C-H...O(w) contacts are energetically more favorable than those with N-H...O(w) hydrogen bonds, because the C-H...O(w) contacts do not allow the unfavorable electron density donation from the water to the uracil moiety. This delocalization effect makes the energetic ordering for the anionic hydrates very different from that for the corresponding neutrals.     

Probing the Watson-Crick, wobble, and sugar-edge hydrogen bond sites of uracil and thymine

The nucleobases uracil (U) and thymine (T) offer three hydrogen-bonding sites for double H-bond formation via neighboring N-H and C=O groups, giving rise to the Watson-Crick, wobble and sugar-edge hydrogen bond isomers. We probe the hydrogen bond properties of all three sites by forming hydrogen bonded dimers of U, 1-methyluracil (1MU), 3-methyluracil (3MU), and T with 2-pyridone (2PY). The mass- and isomer-specific S1 <-- S0 vibronic spectra of 2PY.U, 2PY.3MU, 2PY.1MU, and 2PY.T were measured using UV laser resonant two-photon ionization (R2PI). The spectra of the Watson-Crick and wobble isomers of 2PY.1MU were separated using UV-UV spectral hole-burning. We identify the different isomers by combining three different diagnostic tools: (1) Selective methylation of the uracil N3-H group, which allows formation of the sugar-edge isomer only, and methylation of the N1-H group, which leads to formation of the Watson-Crick and wobble isomers. (2) The experimental S1 <-- S0 origins exhibit large spectral blue shifts relative to the 2PY monomer. Ab initio CIS calculations of the spectral shifts of the different hydrogen-bonded dimers show a linear correlation with experiment. This correlation allows us to identify the R2PI spectra of the weakly populated Watson-Crick and wobble isomers of both 2PY.U and 2PY.T. (3) PW91 density functional calculation of the ground-state binding and dissociation energies De and D0 are in agreement with the assignment of the dominant hydrogen bond isomers of 2PY.U, 2PY.3MU and 2PY.T as the sugar-edge form. For 2PY.U, 2PY.T and 2PY.1MU the measured wobble:Watson-Crick:sugar-edge isomer ratios are in good agreement with the calculated ratios, based on the ab initio dissociation energies and gas-phase statistical mechanics. The Watson-Crick and wobble isomers are thereby determined to be several kcal/mol less strongly bound than the sugar-edge isomers. The 36 observed intermolecular frequencies of the nine different H-bonded isomers give detailed insight into the intermolecular force field.     

Infrared spectra and intensities of the H2O and N2 complexes in the range of the nu1- and nu3-bands of water

The IR spectra of complexes of water with nitrogen molecules in the range of the symmetric (nu(1)) and antisymmetric (nu(3)) bands of H(2)O have been studied in helium droplets. The infrared intensities of the nu(3) and nu(1) modes of H(2)O were found to be larger by factors of 1.3 and 2, respectively, in the N(2)-H(2)O complexes. These factors are smaller than those obtained in recent theoretical calculations. The conformation of the N(2)-H(2)O complex was estimated. Spectra and IR intensities of the (N(2))(2)-H(2)O and N(2)-(H(2)O)(2) complexes were also obtained and their structures are discussed.     

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.     

Theoretical studies on the properties of uracil and its dimer upon thioketo substitution

The influences of thioketo substitution on the properties of uracil monomer and dimer and their interactions with Zn²⁺ have been systematically investigated at the B3LYP/6-311+G^*level of theory. Those properties include the structural characteristics, acidities, ionization potentials, and singlet–triplet energy gaps of SU monomers and their dimers, where SU=2-thiouracil, 4-thiouracil, and 2,4-dithiouracil, respectively. Computational results suggest that thioketo substitution leads to an increase in the acidities of the N-H groups for both uracil and its dimer, where the N₁–H group is still the most acidic site relative to that of N₃–H group. However, the opposite behaviors are true for the ionization potentials and the singlet–triplet energy gaps of uracil monomer and its dimer, suggesting that thiouracils are more susceptible to radiation damage relative to the unsubstituted uracil. For uracil and 2-thiouracil, the corresponding triplet excited-state geometries are predicted to be highly nonplanar compared with the planar geometries of the ground state as well as 4-thiouracil and 2,4-dithiouracil upon triplet excitation. As a rule, the intermolecular H-bonds involving the sulfur atom directly have been influenced more significant than those the oxygen atom directly involved for U::U and SU::SU base pairs upon ionization and excitation. Additionally, Zn²⁺ binding is expected to lead to an increase in the stability of U::U and SU::SU base pairs.     

Hydrogen bonding and molecular vibrations of 2,5-dihydroxy-1,4-benzoquinone

Intramolecular hydrogen bonding in 2,5-dihydroxy-1,4-benzoquinone has been investigated by means of quantumchemical calculations and vibrational spectroscopy. Both computations at the MP2/6-31+G** level as well as FT-IR and FT-Raman spectra are in agreement with the predominance of the C_2h conformer with two intramolecular hydrogen bonding interactions. The spectra were interpreted with the aid of normal coordinate analysis based on a scaled Becke3–Lee–Yang–Parr/6-31G* density functional force field. The general scale factors introduced recently by Rauhut and Pulay for this theoretical level allowed a reliable assignment of most of the fundamentals. The scale factors for vibrations affected strongly by the intramolecular hydrogen bonding interaction needed some adjustment and hence were re-optimized in the present study. The final scaled force field reproduced the experimental frequencies of the molecule by a weighted mean deviation of 8.8 cm⁻¹. Based on the calculated results, 32 from a total of 36 fundamentals were assigned in the vibrational spectra of 2,5-dihydroxy-1,4-benzoquinone revising and extending the assignments of earlier less sophisticated investigations.