Theoretical kinetics study of thymine tautomerism and interaction of Na+ with its tautomers

The current work is a theoretical study of the tautomerism of thymine in the gas phase. Eighteen structures were found in the isomerisation reaction of thymine, some of which are reported for the first time. Thirty hydrogen transfer reactions were carried out. In 24 of the reactions, the hydrogen abstractions N―H→O, N―H→C and C―H→O were considered. The potential energy surface for all trajectories was determined for 18 tautomers and 40 transition states. The RRKM-TST model was used to calculate the rate constants of the reactions to examine their kinetics. Nonlinear least-squares fitting was used to calculate the rate constants expressions. The interaction of sodium ion and tautomers in the gas phase was also investigated. Three types of interaction of metal cations with thymine were found. In the first, metal cations interact with a lone pair of nitrogen or oxygen tautomers. The second type is the interaction of metal cations with two nitrogen and oxygen of tautomers. The last type is the interaction of metal cations and the electron density of the π-system of thymine in which the metal ion is perpendicular to the ring of tautomers. The stability ranking of the thymine tautomers and their complexes was also determined.     

The thymine radicals and their respective anions: molecular structures and electron affinities

The adiabatic electron affinities (AEA), vertical electron affinities (VEA) and vertical detachment energies (VDE) are predicted for six different radicals derived from thymine by the removal of one hydrogen atom. Geometry optimizations were carried out utilizing the DFT functionals B3LYP, BLYP and BP86 with double-c quality basis sets plus polarization and diffuse functions (DZP++). These methods have been carefully calibrated for the prediction of electron affinities [RIENSTRA-KIRACOFE, J. C., TSCHUMPER, G. S., SCHAEFER, H. F., NANDI, S., and ELLISON, G. B., 2002, Chem. Rev., 102, 231]. All optimized structures were confirmed to be minima via vibrational frequency analyses. Both the neutrals and the anion radicals were observed to possess C_s, symmetry, conserving the parent molecule's qualitative conformation. The electron affinities ranged between 1.04 and 3.74eV for the different radicals, contrasting to the small electron affinities associated with the closed-shell thymine species. The radicals with a hydrogen atom removed from one of the nitrogens present the largest electron affinities of all six radicals investigated (3.22eV for NI and 3.74eV for N3).     

6-硫代鸟嘌呤磺化异构体热力学稳定性的计算研究

采用量子化学密度泛函理论B3LYP方法在6-311++G(d,p)基组水平上,对6-硫代鸟嘌呤硫醇式与硫酮式两类共14种磺化异构体的热力学稳定性进行了计算研究,全自由度优化了各物种构型,进行了振动分析,获得了各磺化异构体的零点能、焓、热力学能以及吉布斯自由能等热力学数据.分析了各异构体磺化前后稳定性的变化情况,探讨了磺化异构体的稳定性问题.结果表明,不论是硫酮式还是硫醇式磺化异构体,当H原子连接到N7上时磺化异构体稳定性均比连接到N9上时较高一些.在6-硫代鸟嘌呤磺化异构体中,STG(3,7,10,10)是最稳定的异构体,STG(1,7,10,10)、STG(1,9,10,10)和STG(1,3,7,10)等异构体也可共存,其他异构体存在的可能性均较小.     

Comparison of the stability of thymine tautomers and the interaction of its tautomers with Na+, K+, Mg2+ and Ca2+ in gas and solvent phases

The present study compared the interactions among Na ⁺, K ⁺, Mg²⁺ and Ca²⁺, thymine and its tautomers in the gas and solvent phase, an interaction dependent upon the electronic construction of the tautomers. Three types of cation interaction with thymine and its tautomers were observed. In the first one, the metal cations interacted with a lone pair of nitrogen or oxygen of the tautomers. In the second type, there was an interaction among the cations, nitrogen and oxygen at the same time; the last one was that of cations with the electron density of thymine π-system, where the cations were perpendicular to the ring of thymine. The interaction of metals cation with tautomers was studied in the gas and solvent phases; a comparison was then made between interactions in two phases. The interaction energy for all complexes indicated the stability of complexes, an energy which was higher in Ca²⁺ and Mg²⁺ compared with Na⁺ and K⁺. Concerning K⁺ and Na⁺, the stability of all complexes of tautomers was greater than that of thymine complexes; however, the stability of certain Ca²⁺ and Mg²⁺ complexes was lower than the complexes of thymine.     

The stability and reactivity of activated acryloylcarbamates as reagents for the synthesis of N‐1 substituted thymine and uracil – an NMR and DFT study

The mechanism of the decomposition of acryloylcarbamates 7a–b yielding highly reactive isocyanates 3a–b was proposed based on NMR measurements and quantum chemical calculations. A good agreement between the experimental kinetic data and DFT calculations allowed us to demonstrate that the stability of 7a–d depends on the presence of methyl in the acryloyl moiety and the position of the nitro group in the nitrophenolic part of the molecule. Furthermore, the reactivity of 7a–d with weakly nucleophilic and sterically hindered 2,4,6‐tri‐tert‐butylaniline was explored by ¹H NMR demonstrating the usefulness of reagents 7a–d offering access to a variety of 1‐N‐substituted uracils and thymines with potentially interesting biological properties. Copyright © 2010 John Wiley & Sons, Ltd.     

Electron resonance spectra of some radicals derived from acetylenes and nitriles

The electron resonance spectra of a series of radicals derived by hydrogen abstraction from substrates containing carbon-carbon or carbon-nitrogen triple bonds have been studied in fluid solutions. The radicals ·CH₂CN, ·CH₂C ≡ CH and ·CH₂C ≡ C·CH₃ which have a linear heavy-atom framework show interesting temperature dependent line-width variations. These are attributed to spin-rotational interactions arising from anisotropic molecular reorientation. It is suggested that the motion about the long axis of these radicals is inertial in character.

The equilibrium geometries and hyperfine coupling constants of the propargyl and cyanomethyl radicals have been estimated from INDO-LCAO-SCF calculations.     

Electron spin resonance spectra of radicals derived from secondary aromatic amines

The electron spin resonance spectra of diphenyl nitric oxide and the diphenylamino radical are described. Hyperfine structure in both spectra is accounted for in terms of the various interacting magnetic nuclei; the improved resolution obtained allows the coupling parameters to be given with greater precision than previous values. A mechanism is suggested for the formation of these radicals in the systems being investigated and a qualitative explanation is put forward to account for the observed variation in line width across the spectra.     

Electron spin resonance study of neutral radicals derived from cyclic and acyclic carbonate esters

An electron-spin resonance study of radicals formed from cyclic and acyclic carbonate esters by loss of a hydrogen atom is reported. The radicals were generated photolytically near room temperature in solutions containing 1 % H₂O₂. Spectra were analyzed and couplings are discussed for two radicals formed from diethyl carbonate, two from propylene carbonate (4-methyl-1,3-dioxolan-2-one), and one each from dimethyl carbonate and ethylene carbonate (1,3-dioxolan-2-one).     

Electron affinities,molecular structures,and thermochemistry of the fluorine,chlorine and bromine substituted methyl radicals

Four independent density functional theory (DFT) methods have been employed to study the structures and electron affinities of the methyl and F-, CI- and Br-substituted methyl radicals and their anions. The methods used have been carefully calibrated against a comprehensive tabulation of experimental electron affinities (Chemical Reviews, 2002, 102, 231). The first dissociation energies together with the vibrational frequencies of these species are also reported. The basis sets used in this work are of double-ζ plus polarization quality with additional s- and p-type diffuse functions, labelled as DZP++. Previously observed trends in the prediction of bond lengths by the DFT methods are also demonstrated for the F-, Cl- and Br-substituted methyl radicals and their anions. Generally, the Hartree-Fock/DFT hybrid methods predict shorter and more reliable bond lengths than the pure DFT methods. Neutral-anion energy differences reported in this work are the adiabatic electron affinity (EA_ad), the vertical electron affinity (EA_vert), and the vertical detachment energy (VDE). Compared with the available experimental electron affinities, the BHLYP method predicts much lower values, while the other methods predict values (EA_ad, EA_vert, VDE) close to each other and almost within the experimental range. For those systems without reliable experimental measurements, our best adiabatic EAs predicted by BLYP are 0.78 (CHF₂), 1.23 (CHFCl), 1.44 (CHFBr), 1.61 (CHClBr), 2.24 (CF₂Cl), 2.42 (CF₂Br), 2.56 (CFBr₂), 2.36 (CCl₂Br), 2.46 (CClBr₂), and 2.44 eV (CFClBr). The most striking feature of these predictions is that they display an inverse relationship between halogen electronegativity and EA. The DZP++B3LYP method determines the vibrational frequencies in best agreement with available experimental results for this series, with an average relative error of ～2%. The value of using a variety of DFT methods is observed in that BHLYP does best for geometries, BLYP for electron affinities, and B3LYP for vibrational frequencies. These theoretical results serve to resolve several disagreements between competing experiments. Several other experiments appear to have drawn incorrect conclusions. For example, CHCl₂ is significantly pyramidal, unlike the experimental inferences, and clearly the experimental CCl₂—Cl dissociation energy is too large.     

EPR study of radicals derived from olefinic alcohols

We have successfully characterized by EPR at approximately 25°C the radicals formed using the TiCl₃H₂O₂ radical-generating method and the olefinic alcohol substrates 2-methyl-3-buten-2-ol, 3-methyl-3-buten-1-ol, and cis-2-butene-1,4-diol. Our EPR results are in agreement with known preferred radical conformations for structurally analogous radicals and further verify that substituent electronic and steric effects influence the apparent reactivity characteristics in aliphatic alcohol substrates as observed in the TiCl₃H₂O₂ radical-generating system.     

Theoretical study of optical and electronic properties of the bis‐dipolar diphenylamino‐endcapped oligoarylfluorenes as promising light emitting materials

We present a detailed study of the structural, electronic, and optical properties of the bis‐dipolar emissive oligoarylfluorenes, OF(2)Ar‐NPhs. The aim of our quantum‐chemical calculations is to investigate the role of the transition and the influence of the optical properties of the various central aryl cores in the oligoarylfluorenes. Geometry optimizations were performed for the ground‐state and for the first electronically excited‐state. The absorption and emission spectra were calculated using time‐dependent density functional theory (TD‐DFT). The results show that the HOMO, LUMO, energy gap, ionization potentials (IP), electron affinities (EA) and reorganization energy (λ) of the oligoarylfluorenes are significantly affected by the electronic withdrawing property and the conjugated length of the central aryl core. Consistently, the stronger the electron withdrawing strength, the lower the LUMO energy is. This thus improves the electron‐accepting and transporting properties by the low LUMO energy levels. The absorption and emission spectra of this series of bis‐dipolar molecules exhibit red shifts to some extent by the electronic nature of the electron affinitive central core in the oligoarylfluorenes. All the calculated results show that the oligoarylfluorenes are promising as useful light emitting materials for OLEDs. Copyright © 2007 John Wiley & Sons, Ltd.     

EPR study of radicals derived from unsaturated cyclic ethers

As an extension of earlier EPR studies of the radicals formed from acyclic olefinic substrates with the use of the TiC1₃H₂O₂ radical-generating method, results are presented of an analogous TiC1₃H₂O₂-based investigation carried out over the temperature range 10–40°C with the use of cyclic unsaturated substrates in acidified aqueous solution, namely, Δ²-dihydrofuran, Δ²-dihydropyran, 2-methylfuran, 2-acetylfuran, and furfurylamine. The EPR spectra of six radicals produced from these cyclic substrates are reported.     

新型鸟嘌呤类似物y-鸟嘌呤及其异构体电子光谱性质的理论研究

荧光核酸碱基类似物的设计合成是众多研究领域的热点课题. 本文利用密度泛函理论(DFT)和含时密度泛函理论(TDDFT)考察了新型鸟嘌呤类似物y-鸟嘌呤(yG-t1) 及其五个异构体(yG-t2到yG-t6)的结构性质、电子性质和光谱性质, 同时考察了甲醇溶剂和碱基配对对其光谱性质的影响. 研究表明, 气相中y-鸟嘌呤的标准结构并不是最稳定的结构, 其具有三个能量相近的异构体, y-鸟嘌呤最有可能以这三种形式存在. 光谱性质研究表明y-鸟嘌呤的最大吸收波长比天然鸟嘌呤大得多, 人们可以对其进行选择性激发. y- 鸟嘌呤的标准结构与其异构体显示出不同的光谱特性, 因此可以利用其电子光谱指纹对它们进行区分. 研究发现甲醇溶剂将使y-鸟嘌呤标准结构的最大吸收波长和荧光发生蓝移, 而使其他异构体相应值发生红移; 与胞嘧啶配对将使yG-t1, yG-t2, yG-t5 和yG-t6的最大吸收波长和荧光波长发生蓝移, 表明y-鸟嘌呤的电子光谱性质受环境影响较大.     

Theoretical study on the static and dynamic first-order hyperpolarisabilities of adenine tautomers

Static and dynamic electronic and vibrational first-order hyperpolarisabilities (β) of the lowest energy neutral adenine tautomers (amine forms A7 and A9) were obtained in gaseous and aqueous phases by using Hartree–Fock, Møller–Plesset second-order and fourth-order perturbation theory (MP2 and MP4-SDQ) and conventional and long-range corrected density functional theory methods with the Dunning's correlation-consistent cc-pVDZ, aug-cc-pVDZ, aug-cc-pVTZ and d-aug-cc-pVDZ basis sets. Frequency-dependent properties were calculated at the characteristic wavelength of the Nd:YAG laser (1064 nm) for the second harmonic generation and electro-optical Pockels effect nonlinear optical processes. Solvent effects were introduced under the polarised continuum model approximation. The electronic β^e values of the investigated isomers are noticeably affected by the theoretical level, basis set and solvation. In vacuum, the static and dynamic β^e values of A9 are greater than the corresponding data of A7, whereas the contribution of the solvent significantly enhances the hyperpolarisabilities of the A7 tautomer, resulting in β^e(A9)/β^e(A7) ratios between 0.5 and 0.6. The vibrational hyperpolarisabilities of the adenine tautomers are quite close to each other.     

钛团簇的结构及电子亲和势的理论研究

基于密度泛函理论详细地研究了金属钛的小尺寸团簇的稳定结构及电子性质。具体采用的计算方法是B3LYP/CEP-121G。在这项工作中,我们发现计算的电子亲和势的值与实验值符合的很好,但与原先的理论研究有些不同。     

Ring inversion kinetics of radicals derived from Mu addition to cycloheptatriene

Upon injection of spin-polarized positive muons into cycloheptatriene three radicals have been observed by transverse field μSR. The temperature dependence of the relaxation rates have been interpreted in terms of a rapid inversion process. The Arrhenius parameters have been determined and an isotope effect with respect to the barrier height of the inversion has been found.     

Electron impact ionization of thymine clusters embedded in superfluid helium droplets

Embedding molecules in helium clusters has become a powerful technique for the preparation of cold targets for spectroscopy experiments, as well as for the assembly of complex, fragile molecular species. We have recently developed a helium cluster source and a pick-up cell to produce neutral beams of doped helium droplets, to be used as targets in studies on electron collisions with molecules of biological relevance. In the present work we present the results of a series of experiments on electron-impact ionization of helium clusters doped with thymine and 1-methylthymine, where several interesting phenomena were observed, i.e., (i) electron impact ionization of molecular clusters inside the helium droplets leads predominantly to protonated clusters; (ii) the appearance energies are close to the ionization threshold of the helium atom but ionization efficiency curves in addition extend down by several eV; (iii) ionized molecular clusters can undergo metastable decay via the loss of one neutral monomer.     

Structural,energetic and spectroscopic characterisation of 5-fluorouracil anticarcinogenic drug isomers,tautomers and ions

ABSTRACT

In many cases, 5-fluorouracil (5-FU) is the first-line drug used in combined chemotherapy and radiotherapy treatments due to its radio-sensitization properties. It could participate in a tautomerization process similar to that of uracil, where 5-FU may couple to adenine in DNA. At present, we performed structural and spectroscopic studies using quantum chemical methods of neutral and cationic isolated 5-FU anticarcinogenic drug tautomers, either interacting with a water molecule or embedded into an implicit water solvent. Also, we determined the stationary points (both stable structures and transition states) on their ground potential energy surfaces playing a role during the tautomerization processes. For neutral and ionic species in the gas phase and in solvent, the ordering of the tautomers is found to be the same, where the di-keto form of 5-FU is the most stable structure, followed by the keto–enol and di-enol structural forms. The energy barriers for tautomerization are strongly reduced in solvent (< 0.5?eV) compared to isolated species (～2?eV). The patterns of their lowest electronic states are also computed. Our data may help for the identification of these species in vivo and in the laboratory.     

Electron affinities of the bromine oxides BrOn,n = 1-4

Bromine oxides are of significant interest due to their importance in atmospheric chemistry. Density functional theory (DFT) methods have been used in conjunction with a DZP++ (double-ζ plus polarization with diffuse functions) basis set to study the molecular geometries and total energies of BrOn and BrO^- _n (n = 1-4). The adiabatic electron affinity (EA_ad), the vertical electron affinity (EA_vert) of the bromine oxide and the vertical detachment energy (VDE) of each anion are reported. Harmonic vibrational frequencies and zero point energies are also reported. Five different DFT methods were employed for comparison. Among these, the BHLYP method predicts the geometries and the vibrational frequencies in best agreement with available experimental data, while the the other methods do better in predicting the limited number of energetic quantities determined observationally. The predicted adiabatic electron affinities are 2.38 eV (BrO, experiment 2.35 eV), 2.36 eV (BrO₂), 3.35 eV (BrOO), 4.32 eV (BrO₃), 2.91 eV (BrOOO) and 5.28 eV (BrO₄). The electronic ground state of BrOO^- is a triplet (³A^") state. Predicted Br–;O bond distances range from 1.61 (BrO₃) to more than 2 Å for Br...O₂ for the neutral molecules; and from 1.61 Å for BrO^- to 1.82 Å for BrO^- to more than 2 Å for Br^-...O₃ among the anions. The BrOO isomer (C_s symmetry) is predicted to lie 17–18 kcal mol^-1 below the C_2v symmetry OBrO structure. The asymmetric ³A^" anion BrOO^- analogously lies below OBrO^-, in this case by 40–41 kcalmol_-1. BrOOO (C_s symmetry) is predicted to lie 42-45 kcalmol-1 below the symmetric C_3v BrO structure. Finally the asymmetric BrOOO- anion (C₁ symmetry) is predicted to lie 10-13kcal mol-1 below symmetric C_3v BrO^- ₃.