Benchmarking the Electron Affinity of Uracil

The valence electron affinity of uracil determined by anion cluster photoelectron spectroscopy

The unoccupied π* orbitals of the nucleobases are considered to play important roles in low-energy electron attachment to DNA, inducing damage. While the lowest anionic valence state is vertically unbound in all neutral nucleobases, it remains unclear even for the simplest nucleobase, uracil (U), whether its valence anion (U-) is adiabatically bound, which has important implications on the efficacy of damage processes. Using anion photoelectron spectroscopy, we demonstrate that the valence electron affinity (EAV) of U can be accurately measured within weakly solvating clusters, U-(Ar)n and U-(N2)n. Through extrapolation to the isolated U limit, we show that EAV = -2 ± 18 meV. We discuss these findings in the context of electron attachment to U and its reorganization energy, and more generally establish guidance for the determination of molecular electron affinities from the photoelectron spectroscopy of anion clusters.

Micro-physical parameter dynamic evolution behaviour of a natural ester molecular chain under a changing electric field and its correlation mechanism with lightning impulse discharge: theoretical analysis

The lightning impulse breakdown properties of natural esters are very important for their further applications. This paper focuses on the discharge mechanism investigation of a natural ester insulating liquid under a lightning impulse electric field. Based on density functional theory (DFT), the configuration, electron structure, ionization and electron affinity process, excitation process and molecular orbital of natural ester molecules were calculated under different electric field strengths. A correlation mechanism between the micro-physical parameters of ester insulating liquid molecules and discharge was proposed. The molecular electrostatic potential was used to predict the active point of discharge. The results show that the molecular structure of triglycerides shows yield behaviour under electric field action. The electrons are redistributed in the direction of the source of the electric field. Among the four triglycerides, the ionization and electron affinity process, excitation process and molecular orbital of glycerol tripalmitate were least affected by the electric field. The microscopic properties of other triglycerides were significantly affected by the electric field. According to the electrostatic potential (ESP) result of natural ester molecules, it can be predicted in the experiment that the surface of H atoms of the triglyceride ester group easily forms electron traps to bind electrons, while the surface of an O atom at the ester of a triglyceride undergoes electron collisions resulting in an electrical discharge. The proportion of palmitic acid in natural esters could be increased or pure glycerol tripalmitate could be used as an insulating oil to solve the problem of the low lightning impulse breakdown voltage of natural esters.

Notable effect of water on excess electron attachment to aqueous DNA deoxyribonucleosides

As excess electrons are vertically attached to aqueous deoxyribonucleosides, ∼50% of excess electrons would be delocalized over the water molecules.

Light-Induced Conformational Change of Uracil-Anchored Polythiophene-Regulating Thermo-Responsiveness

Tuning the electronic structure of a π-conjugated polymer from the responsive side chains is generally done to get desired optoelectronic properties, and it would be very fruitful when light is used as an exciting tool that can also affect the backbone chain conformation. For this purpose, polythiophene- g-poly-[ N-(6-methyluracilyl)- N, N-dimethylamino chloride]ethyl methacrylate (PTDU) is synthesized. On exposure to diffuse sunlight, the uracil moieties of the grafted chains cause the absorption maximum of PTDU solution to show gradual blue shift of 87 nm and a gradual blue shift of 46 nm in the emission maximum, quenching its fluorescence with time. These effects occur specifically at the absorption range of polythiophene (PT) chromophore on direct exposure of light of different wavelengths, and the optimum wavelength is found to be 420 nm. Impedance study suggests a decrease in charge transfer resistance upon exposure because of conformational change of PTDU. Theoretical study indicates that on exposure to visible light, uracil moieties move toward the backbone to facilitate photoinduced electron transfer between the PT and the uracil, attributing to the variation in optoelectronic properties. Morphological and light-scattering studies exhibit a decrease in particle size because of coiling of the PT backbone and squeezing of the grafted chain on light exposure. The transparent orange-colored PTDU solution becomes hazy with a hike in emission intensity on addition of sodium halides and becomes reversibly transparent or hazy on heating or cooling. The screening of cationic centers of PTDU by varying halide anion concentration tunes the phase transition temperature. Thus, the light-induced variation in the backbone conformation is responsible for tuning the optoelectronic properties and regulates the thermos-responsiveness of the PTDU solution in the presence of halide ions.

Effects of Positive and Negative Ionization on Prototropy in Pyrimidine Bases: An Unusual Case of Isocytosine

Intramolecular proton-transfers (prototropic conversions) have been studied for the guanine building block isocytosine (iC), and effects of positive ionization, called one-electron oxidation (iC - e → iC^+•), and negative ionization, called one-electron reduction (iC + e → iC^-•), on tautomeric conversions when proceeding from neutral to ionized isocytosine have been discussed. Although radical cations and radical anions are very short-lived species, the ionization effects could be investigated by quantum-chemical methods. Such kind of studies gives some information about the labile protons and the most basic positions in the neutral and radical forms of the tautomeric system. For investigations, the complete isomeric mixture of isocytosine has been considered and calculations performed in two extreme environments, apolar {DFT(B3LYP)/6-311+G(d,p)} and polar {PCM(water)//DFT(B3LYP)/6-311+G(d,p)}. For selected isomers, the G4 theory has also been applied. There are no good relations for energetic parameters of neutral and ionized forms. Ionization energies depend on localization of labile protons. Tautomeric equilibria for neutral and ionized isocytosine, favored sites of protonation and deprotonation, and favored structures of protonated and deprotonated forms strongly depend on environment. Acidity of iC^+• is close to that of the iC conjugate acid, and basicity of iC^-• is close to that of the iC conjugate base. This increase of acid-base properties of charged radicals explains the proton-transfer in ionized pairs of nucleobases. When compared to other pyrimidine bases such as uracil (U) and cytosine (C), which exhibit analogous tautomeric equilibria between nine prototropic tautomers as isocytosine, the tautomeric preferences for iC, iC^+•, iC^-•, U, U^+•, U^-•, C, C^+•, and C^-• are completely different. The differences suggest that acid-base properties of functional groups, their stabilities, and ionization energies play a principal role in proton-transfers for pyrimidine bases and influence compositions of tautomeric mixtures.

Controlled stabilization of anionic forms of the uracil derivatives: A DFT study

Relative stabilities of the N1/N3/О5/О6 anions of 42 substituted uracils in gas phase and aqueous solutions have been theoretically studied using approximation IEFPCM (SMD) - TPSS/aug-cc-pVTZ. The specific solvation of uracil and its anions has been simulated with the first hydrate shell made up with 5 water molecules. The nonspecific solvation has been accounted in terms of the SMD model. We have found a series of relative stability under conditions of both specific and nonspecific hydration. The series is ranked according to the increase of the relative stability of the N3 anion. In gas phase, the N1 anion is significantly more stable than its N3 counterpart: the ΔG_gas values vary in the range from 19.54 (5OH6СН₃U) to 83.14 (5NO₂6NH₂U) kJ/mol that is caused by a more effective delocalization of the excess charge through the uracil framework in the N1 anion. The hydration pronouncedly diminishes ΔG to the range from -0.02 (5OH6СН₃U) to 38.16 (5Br6NO₂U) kJ/mol due to the fact that the polar solvent is prone to stabilize more polar anionic states of uracils. Therefore, less polar uracil anions are more stable. We have defined the main factor influencing the N1/N3/О5/О6 distribution of anions, viz. the presence of the substituents in 5 and 6 positions of the pyrimidine ring. Herewith, the most favorable mechanism of the influence of 5-substituents has been previously defined as resonant whereas, as we found in this work, the inductive mechanism is more pronounced in the case of 6-substituents.

Effects of ionization on stability of 1-methylcytosine - DFT and PCM studies

Consequences of ionization were studied by quantum-chemical methods (DFT and PCM) for 1-methylcytosine (MC)—a model of the nucleobase cytosine (C) connected with sugar in DNA. For calculations, three prototropic tautomers (one amino and two imino forms) and two imino zwitterions were considered, including conformational or configurational isomerism of exo heterogroups. Ionization and interactions between neighboring groups affect intramolecular proton-transfers, geometric and thermodynamic parameters, and electron delocalization for individual isomers. We discovered that an imino isomer is present in the isomeric mixture in the highest amount for positively ionized MC. Its contribution in neutral and negatively ionized MC is considerably smaller. Acid-base parameters for selected radical ions were estimated in the gas phase and compared to those of neutral MC. Gas-phase acidity of radical cations is close to that of the conjugate acid of MC, and gas-phase basicity of radical anions is close to that of the conjugate base of MC. Various routes of amino-imino conversion between neutral and ionized isomers were considered. Energetic-barrier for intramolecular proton-transfer in MC is close to that in the parent system—formamidine.

Electrophilic 5-Substituted Uracils as Potential Radiosensitizers: A Density Functional Theory Study

Although 5-bromo-2'-deoxyuridine (5BrdU) possesses significant radiosensitizing power in vitro, clinical studies do not confirm any advantages of radiotherapy employing 5BrdU. This situation calls for a continuous search for efficient radiosensitizers. Using the proposed mechanism of radiosensitization by 5BrdU, we propose a series of 5-substituted uracils, XYU, that should undergo efficient dissociative electron attachment. The DFT-calculated thermodynamic and kinetic data concerning the XYU degradations induced by electron addition suggests that some of the scrutinized derivatives have much better characteristics than 5BrdU itself. Synthesis of these promising candidates for radiosensitizers, followed by studies of their radiosensitizing properties in DNA context, and ultimately in cancer cells, are further steps to confirm their potential applicability in anticancer treatment.

Mechanisms of Damage to DNA Labeled with Electrophilic Nucleobases Induced by Ionizing or UV Radiation

Hypoxia--a hallmark of solid tumors--makes hypoxic cells radioresistant. On the other hand, DNA, the main target of anticancer therapy, is not sensitive to the near UV photons and hydrated electrons, one of the major products of water radiolysis under hypoxic conditions. A possible way to overcome these obstacles to the efficient radio- and photodynamic therapy of cancer is to sensitize the cellular DNA to electrons and/or ultraviolet radiation. While incorporated into genomic DNA, modified nucleosides, 5-bromo-2'-deoxyuridine in particular, sensitize cells to both near-ultraviolet photons and γ rays. It is believed that, in both sensitization modes, the reactive nucleobase radical is formed as a primary product which swiftly stabilizes, leading to serious DNA damage, like strand breaks or cross-links. However, despite the apparent similarity, such radio- and photosensitization of DNA seems to be ruled by fundamentally different mechanisms. In this review, we demonstrate that the most important factors deciding on radiodamage to the labeled DNA are (i) the electron affinity (EA) of modified nucleoside (mNZ), (ii) the local surroundings of the label that significantly influences the EA of mNZ, and (iii) the strength of the chemical bond holding together the substituent and a nucleobase. On the other hand, we show that the UV damage to sensitized DNA is governed by long-range photoinduced electron transfer, the efficiency of which is controlled by local DNA sequences. A critical review of the literature mechanisms concerning both types of damage to the labeled biopolymer is presented. Ultimately, the perspectives of studies on DNA sensitization in the context of cancer therapy are discussed.

Valence-bound and diffuse-bound anions of 5-azauracil

Structures, isomerization energies, and electron binding energies of 5-azauracil and its anions have been calculated ab initio with perturbative, coupled-cluster, and electron-propagator methods. Tautomeric structures, including those produced by proton transfer to a CH group, have been considered. Dyson orbitals and pole strengths from electron-propagator calculations validated a simple, molecular-orbital picture of anion formation. In one case, an electron may enter a delocalized π orbital, yielding a valence-bound (VB) anion with a puckered ring structure. The corresponding electron affinity is 0.27 eV; the vertical electron detachment energy (VEDE) of this anion 1.05 eV. An electron also may enter a molecular orbital that lies outside the nuclear framework, resulting in a diffuse-bound (DB) anion. In the latter case, the electron affinity is 0.06 eV and the VEDE of the DB anion is 0.09 eV. Another VB isomer that is only 0.02 eV more stable than the neutral molecule has a VEDE of 2.0 eV.