PHOTO-OXIDATION OF THYMINE SENSITIZED BY 2-METHYL-1,4-NAPHTHOQUINONE: ANALYSIS OF PRODUCTS INCLUDING THREE NOVEL PHOTO-DIMERS

Abstract —The near-UV photosensitization of thymine by 2-methyl-1,4-naphthoquinone in oxygenated aqueous solution leads to the formation of nine major thymine-derived products. Six of the photoproducts, representing 70% of the initial thymine loss, are also known to be formed by γ-ray or X-ray irradiation of oxygenated water solutions of thymine. They include the cis and trans isomers of 5-hydroperoxy-6-hydroxy-5,6-dihydrothymine, the cis and trans thymine glycols, 5-hydroxy-5-methylhydantoin, and N-formyl-N'-pyruvylurea. The three remaining major products, accounting for a further 25% of the initial thymine loss, are thymine di-adducts of a type not previously reported. Preliminary characterization of these novel photoproducts, based on their UV absorption, mass spectra, and proton and carbon-13 nuclear magnetic resonance spectra, suggests that in each of the three, the thymine moieties are linked by an N(1)-C(5) or N(1)-C(6) bond. A thymine cation radical is implicated as the common precursor of all 9 products. Accordingly. pyrimidine photosensitization by 2-methyl-1,4-naphthoquinone serves as a model system for studying the chemical consequences of radiation-induced ionization of the DNA bases.     

TiO2光催化降解胸腺嘧啶的动力学和机理

考察了用于降解来自嘧啶家族的一种核酸—胸腺嘧啶(C5H6N2O2)的高级氧化过程。结果发现,在光催化剂TiO2作用下,胸腺嘧啶的光降解进行得很快,且在紫外光照射和水溶液中时更为明显。研究了胸腺嘧啶在TiO2催化剂上的吸附、降解动力学、以及pH值对光催化降解胸腺嘧啶性能的影响。另外,考察了胸腺嘧啶降解产物的矿化;比较和讨论了在光催化过程中胸腺嘧啶的消失和矿化速率。同时还研究了氮的矿化,确立了中间产物的识别方法。最后,采用电子密度计算提出了在紫外光照射下TiO2催化剂上胸腺嘧啶降解的可能化学途径。     

The excited states of adenine and thymine nucleoside and nucleotide in aqueous solution: a comparative study by time-dependent DFT calculations

The effect substitutions at nitrogen atom 1 of thymine and nitrogen atom 9 of adenine have on lowest energy excited electronic states has been studied by means of time-dependent PBE0 calculations in aqueous solution. In agreement with the experimental indications, the vertical excitation energy of the bright state of 1,methyl-thymine, thymine nucleoside and thymine nucleotide is red-shifted with respect to that of thymine. Deoxyribose and deoxyribose-phosphate substituents affect mainly the lowest energy dark state of adenine and thymine, slightly increasing their oscillator strength. The excited states of 9, methyl-adenine and 1, methyl-thymine have also been studied by using the recently developed M052X, CAM-B3LYP and LC-ωPBE density functionals. The computed VEE are in good agreement with those obtained by using PBE0, which, however, provides values closer to the experimental band maximum.     

Hydration effects on the reaction with an open-shell transition state: QM/MM-ER study for the dehydration reaction of alcohol in hot water

The reaction mechanism for the dehydration of 1,4-butanediol in hot water has been investigated by means of the hybrid quantum mechanical/molecular mechanical approach combined with the theory of energy representation (QM/MM-ER). We have assumed that the proton transfers along the hydrogen bonds of the water molecules catalyze the reaction, where the transition state (TS) forms a singlet biradical electronic structure. It has been revealed by the simulation that the biradical electronic state at the TS changes to zwitterionic structure in solution due to the hydration of the polar solvent. Such the electronic structure change gives rise to the substantial stabilization of the TS in hot water. As a result, the water-catalytic path becomes more favorable in aqueous solution than another possible path that proceeds without proton transfers as opposed to the reaction mechanism in the gas phase. Furthermore, the activation free energy computed by the present method is in excellent agreement with the experimental result.     

TYROSINE-SENSITIZED PHOTODIMERIZATION OF THYMINE IN AQUEOUS SOLUTION

Abstract. Photodimerization of thymine in aqueous solution in the presence of tyrosine was studied with monochromatic UV irradiation. The total dimer formation was sensitized in the presence of tyrosine. The action spectrum of sensitized total dimer formation has a peak near 280 nm corresponding to the absorption maximum of tyrosine. Triplet quenchers reduced the sensitization substantially. It seems probable that tyrosine-sensitized photodimerization of thymine occurred via triplet-triplet energy transfer from tyrosine to thymine.     

An interaction energy driven biased sampling technique: A faster route to ionization spectra in condensed phase

We introduce a computationally efficient approach for calculating spectroscopic properties, such as ionization energies (IEs) in the condensed phase. Discrete quantum mechanical/molecular mechanical (QM/MM) approaches for spectroscopic properties in a dynamic system, such as aqueous solution, need a large sample space to obtain converged estimates, especially for the cases where particle (electron) number is not conserved, such as IEs or electron affinities (EAs). We devise a biased sampling technique based on an approximate estimate of interaction energy between the solute and solvent, that accelerates the convergence and therefore, reduces the computational cost significantly. The approximate interaction energy also provides a good measure of the spectral width of the chromophores in the condensed phase. This technique has been tested and benchmarked for (i) phenol, (ii) HBDI anion (hydroxybenzylidene dimethyl imidazolinone), and (iii) thymine in water. © 2017 Wiley Periodicals, Inc.     

Microsolvation effects on the electron capturing ability of thymine: thymine-water clusters

The effects of solvation on the stability of thymine and its negative ion have been investigated by explicitly considering the structures of complexes of thymine with up to five water molecules and the respective anions at the B3LYP/DZP++ level of theory. The vertical detachment energy of thymine was predicted to increase gradually with the hydration number, consistent with experimental observations from a photodetachment-photoelectron spectroscopy study J. Schiedt et al., [Chem. Phys. 239, 511 (1998)]. The adiabatic electron affinity of thymine was also found to increase with the hydration number, which implies that while the conventional valence anion of thymine is only marginally bound in the gas phase, it may form a stable anion in aqueous solution.     

新型侧链偶氮聚电解质的合成及性能研究

通过自由基聚合合成了一种侧链型偶氮聚电解质 ,聚丙烯酸 2 [4 (4′ 羧基苯基偶氮 )苯基 ]乙酯(PCAPEA) .详细研究了PCAPEA水溶液的pH值对其紫外 可见光谱和光响应性的影响 .研究发现 ,PCAPEA水溶液的紫外吸收光谱对pH值具有高度敏感性 ,并且在不同pH值条件下其光响应性有很大差别 .这种差别反映了PCAPEA分子中的偶氮苯基团在水溶液中聚集状态的变化 .本论文还研究了PCAPEA与聚二烯丙基二甲基氯化铵 (PDAC)在不同溶剂中的静电逐层自组装 .研究发现 ,PCAPEA的水和有机溶剂的混合溶液也可用来进行自组装 ,这一新方法可用于水溶性差的聚电解质的自组装     

A quantum mechanical/molecular dynamics/mean field study of acrolein in aqueous solution: analysis of H bonding and bulk effects on spectroscopic properties

A novel molecular dynamics methodology recently proposed by our group [Rega et al., Chem. Phys. Lett. 422, 367 (2006)], which is based on an integrated hybrid potential rooted in high level quantum mechanical methods using localized basis functions and nonperiodic boundary conditions, has been applied to study acrolein in aqueous solution. The solute structural rearrangement and its hydrogen-bonding pattern due to the interactions with water have been analyzed in some detail. Moreover, the solvent effects on the UV n-->pi* vertical transition and on the NMR 13C and 17O shielding constants of acrolein have been investigated theoretically by performing a posteriori quantum mechanical calculations on a statistically significant number of snapshots extracted from both gas-phase and aqueous solution simulations. Results show that such effective computational strategy can be successfully used to improve our understanding, at atomic level, of important spectroscopic observables.     

紫外线光照产物——胸腺嘧啶二聚体物理化学性质的研究

本文分离和鉴定了紫外线光照胸腺嘧啶冰冻水溶液时迅速形成的低吸收的胸腺嘧啶二聚体,研究了和光化学与光生物学有关的胸腺嘧啶二聚体的一些性质。除了它的酸和热稳定性之外,实验表明,胸腺嘧啶二聚体的化学稳定性受加入的金属离子Ag⁺、Fe⁺⁺、Cu⁺⁺和EB染料的影响;而且胸腺嘧啶二聚体和胸腺嘧啶之间的相互转换依赖于金属离子的种类和浓度。     

Understanding electron attachment to the DNA double helix: the thymidine monophosphate-adenine pair in the gas phase and aqueous solution

Electron attachment to the 2'-deoxythymidine-5'-monophosphate-adenine pairs (5'-dTMPH-A and 5'-dTMP(-)-A) has been investigated at a carefully calibrated level of theory (B3LYP/DZP++) to investigate the electron-accepting properties of thymine (T) in the DNA double helix under physiological conditions. All molecular structures have been fully optimized in vacuo and in solution. The adiabatic electron affinity of 5'-dTMPH-A in the gas phase has been predicted to be 0.67 eV. Solvent effects greatly increase the electron capture ability of 5'-dTMPH-A. In fact, the adiabatic electron affinity increases to 2.04 eV with solvation. The influence of the solvent environment on the electron-attracting properties of 5'-dTMPH-A arises not only from the stabilization of the corresponding radical anion through charge-dipole interactions, but also by changing the distribution of the unpaired electron in the molecular system. The unpaired electron is covalently bound even during vertical attachment, due to the solvent effects. Solvent effects also weaken the pairing interaction in the thymidine monophosphate-adenine complexes. The phosphate deprotonation is found to have a relatively minor influence on the capture of electrons by the 5'-dTMPH-A species in aqueous solution. The electron distributions, natural population analysis, and geometrical features of the models examined illustrate that the influence of the phosphate deprotonation is limited to the phosphate moiety in aqueous solution. Therefore, it is reasonable to expect that electron attachment to nucleotides will be independent of monovalent counterions in the vicinity of the phosphate group in aqueous solution.     

On the performance of quantum chemical methods to predict solvatochromic effects: the case of acrolein in aqueous solution

The performance of the Hartree-Fock method and the three density functionals B3LYP, PBE0, and CAM-B3LYP is compared to results based on the coupled cluster singles and doubles model in predictions of the solvatochromic effects on the vertical n-->pi* and pi-->pi* electronic excitation energies of acrolein. All electronic structure methods employed the same solvent model, which is based on the combined quantum mechanics/molecular mechanics approach together with a dynamical averaging scheme. In addition to the predicted solvatochromic effects, we have also performed spectroscopic UV measurements of acrolein in vapor phase and aqueous solution. The gas-to-aqueous solution shift of the n-->pi* excitation energy is well reproduced by using all density functional methods considered. However, the B3LYP and PBE0 functionals completely fail to describe the pi-->pi* electronic transition in solution, whereas the recent CAM-B3LYP functional performs well also in this case. The pi-->pi* excitation energy of acrolein in water solution is found to be very dependent on intermolecular induction and nonelectrostatic interactions. The computed excitation energies of acrolein in vacuum and solution compare well to experimental data.     

Thermal and solvent effects on the NMR and UV parameters of some bioreductive drugs

15N NMR chemical shifts and n-->pi* electronic transition energy for metronidazole (1) has been calculated and compared with experimental data. A detailed computational study of 1 is presented, with special attention to the performance of various theoretical methods for reproducing spectroscopic parameters in solution. The most sophisticated approach involves density functional based on the Car-Parrinello molecular dynamics simulations of 1 in aqueous solution (BP86 level) and averaging chemical shifts and deltaE(n-->pi*) over snapshots from the trajectory. In the NMR and UV calculations for these snapshots (performed at the B3LYP level), a small number of discrete water molecules are retained, and the remaining bulk solution effects are included via a polarizable continuum model (PCM). A good agreement with experiment is also obtained using static geometry optimization and NMR computation of pristine 1 employing a PCM approach. Further theoretical predictions are also reported for 17O NMR and deltaE(n-->pi*) of three hydroxycinnamic acid derivatives, which suggest that it is essential to incorporate the dynamics and solvent effects for NMR and UV calculations in the condensed phase.     

Laser spray: electric field-assisted matrix-assisted laser desorption/ionization

A new liquid chromatography/mass spectrometry interface, the laser spray, has been developed. Explosive vaporization and mist formation occur when an aqueous solution effusing out from the tip of the stainless-steel capillary is irradiated from the opposite side of the capillary by a 10.6 microm infrared laser. Weak ion signals could be detected when the plume was sampled through the ion sampling orifice. When a high voltage (3-4 kV) was applied to the stainless-steel capillary, strong ion signals appeared. The ion abundances were found to be orders of magnitude greater than those obtained by conventional electrospray ionization in the case of aqueous solutions. The present method is regarded as an electric-field assisted form of matrix-assisted laser desorption/ionization in which the liquid chromatographic solvent (water, etc.) acts as a liquid matrix. Laser spray ionization is expected to become a versatile method for biological mass spectrometry because this method is compatible with the natural solvent, water.     

Density functional study toward understanding dehydrogenation of the adenine-thymine base pair and its anion

The dehydrogenated radicals and anions of Watson-Crick adenine-thymine (A-T) base pair have been investigated by the B3LYP/DZP++ approach. Calculations show that the dehydrogenated radicals and anions have relatively high stabilities compared with the single base adenine and thymine. The electron attachment to the A-T base pair and its derivatives significantly modifies the hydrogen bond interactions and results in remarkable structural changes. As for the dehydrogenated A-T radicals, they have relatively high electron affinities and different dehydrogenation properties with respect to their constituent elements. The relatively low-cost hydrogen eliminations correspond to the (N9)-H (adenine) and (N1)-H (thymine) bonds cleavage. Both dehydrogenation processes have Gibbs free energies of reaction DeltaG degrees of 13.4 and 17.2 kcal mol-1, respectively. The solvent water exhibits significant effect on electron attachment and dehydrogenation properties of the A-T base pair and its derivatives. In the dehydrogenating process, the anionic A-T fragment gradually changes its electronic configuration from pi* to sigma* state, like the single bases adenine and thymine.     

Absorption profiles of flames used in atomic-absorption spectroscopy

A study has been made of the distributions of metallic atoms in their ground electronic state when an aqueous or an organic solvent containing the metal present in the solution in various combined forms is sprayed into various flames used in atomic-absorption spectroscopy. It has been found that with almost all elements studied, rich flames give greater peak absorbances than lean flames, and the flame stoichiometry determines the number of free atoms in a flame. It has also been observed that the spatial distribution of free atoms in a flame depends not only on the flame stoichiometry but also on the species which the desired metal forms in the solution and the flame, on the other anions, complexing agents, and cations present in the solution, on chemical and physical properties of the solvent, on the type of atomizer-burner and on the flame temperature.     

Theoretical study on ionization process in aqueous solution

Ionization potential (ionization energy) is a fundamental quantity characterizing electronic structure of a molecule. It is known that the energy in solution phase is significantly different from that in the gas phase. In this report, vertical and adiabatic ionization processes in aqueous solution are studied based on a hybrid method of quantum chemistry and statistical mechanics called reference interaction site model-SCF-spacial electron density distribution method. A role of solvation effect is elucidated through molecular level information, i.e., solvent distribution function around solute molecule. By utilizing the linear response regime, a simple expression to evaluate the spectral width from the distribution function is proposed and compared with experimental data.     

Density-functional theory study of Iron(III) hydrolysis in aqueous solution

Fe(III) hydrolysis in aqueous solution has been investigated using density-functional methods (DFT). All possible structures arising from different tautomers and multiplicities have been calculated. The solvation energy has been estimated using the UAHF-PCM method. The hydrolysis free energies have been estimated and compared with the available experimental data. The different hydrolysis species have distinct geometries and electronic structures. We have shown that improvement of theory level in calculating the electronic energy does not necessarily improve the estimated free energies in aqueous solution since the UAHF-PCM is a simple method that neglects specific interactions with the solvent. Therefore, it is important to have the correct balance between theory level used in the electronic calculation and the UAHF-PCM. The PBE/TZVP/UAHF-PCM method has been found to describe correctly the hydrolysis energies of Fe(III), deviating about 3.0 kcal mol(-1) from experimental values.     

PROPERTIES OF AN UNUSUAL PHOTOPRODUCT OF U.V. IRRADIATED THYMIDYLYL-THYMIDINE

Abstract— One of the four major photoproducts formed by UV irradiation of TpT in aqueous solution has a number of unusual properties. This compound, which we arbitrarily call TpT⁴, is produced irreversibly from TpT with single-hit kinetics and seems to represent a novel pathway for TpT photolysis different from the conventional cyclobutane ring dimer formation. This communication describes the preparative isolation of TpT⁴ by ion-exchange chromatography on DEAE-cellulose and its UV, fluorescence and IR spectra. TpT⁴ has an absorption maximum at 325 mμ, fluoresces at 405 mμ when excited at 325 mμ, and has an IR spectrum consistent with the assumption that one of the thymine rings has been converted to a pyrimidin-2-one structure. In addition, TpT⁴ appears to have both pyrimidine rings linked together and does not contain a peroxide group as previously supposed. Spectrophotometric titration shows that TpT⁴ has a pKâ of 10.75 and is unstable to prolonged treatment at extreme pH. A model structure consistent with the present data is given. This model contains the glycosidic and phosphodiester bonds intact with a 5-methylpyrimidine-2-one ring and a thymine ring joined in ether linkage at the C₄ positions, with an OH at the C₄ position in the thymine ring.     

Ultrafast nonradiative decay by hypoxanthine and several methylxanthines in aqueous and acetonitrile solution

Excited state lifetimes of hypoxanthine and four methylxanthine compounds (paraxanthine, theophylline, theobromine, and caffeine) were studied by femtosecond transient absorption spectroscopy in aqueous and acetonitrile solution. Transient absorption signals recorded at visible and UV probe wavelengths reveal that internal conversion from the photoexcited state to the electronic ground state takes place in water on the hundreds of femtoseconds time scale. Excited-state relaxation occurs approximately threefold more slowly in acetonitrile solution than in water. Structural considerations suggest that the deactivating conical intersection for the methylxanthines differs from that responsible for nonradiative decay by hypoxanthine, adenine, and guanine. All compounds studied have ultrashort excited state lifetimes similar to those of adenine and guanine, suggesting that these xanthine derivatives could have been photostable building blocks in prebiotic environments exposed to intense UV radiation.