Resonant Formation of Strand Breaks in Sensitized Oligonucleotides Induced by Low‐Energy Electrons (0.5–9 eV)

Halogenated nucleobases are used as radiosensitizers in cancer radiation therapy, enhancing the reactivity of DNA to secondary low‐energy electrons (LEEs). LEEs induce DNA strand breaks at specific energies (resonances) by dissociative electron attachment (DEA). Although halogenated nucleobases show intense DEA resonances at various electron energies in the gas phase, it is inherently difficult to investigate the influence of halogenated nucleobases on the actual DNA strand breakage over the broad range of electron energies at which DEA can take place (<12 eV). By using DNA origami nanostructures, we determined the energy dependence of the strand break cross‐section for oligonucleotides modified with 8‐bromoadenine (^8BrA). These results were evaluated against DEA measurements with isolated ^8BrA in the gas phase. Contrary to expectations, the major contribution to strand breaks is from resonances at around 7 eV while resonances at very low energy (<2 eV) have little influence on strand breaks.     

Sensitizing DNA Towards Low‐Energy Electrons with 2‐Fluoroadenine

2‐Fluoroadenine (^2FA) is a therapeutic agent, which is suggested for application in cancer radiotherapy. The molecular mechanism of DNA radiation damage can be ascribed to a significant extent to the action of low‐energy (<20 eV) electrons (LEEs), which damage DNA by dissociative electron attachment. LEE induced reactions in ^2FA are characterized both isolated in the gas phase and in the condensed phase when it is incorporated into DNA. Information about negative ion resonances and anion‐mediated fragmentation reactions is combined with an absolute quantification of DNA strand breaks in ^2FA‐containing oligonucleotides upon irradiation with LEEs. The incorporation of ^2FA into DNA results in an enhanced strand breakage. The strand‐break cross sections are clearly energy dependent, whereas the strand‐break enhancements by ^2FA at 5.5, 10, and 15 eV are very similar. Thus, ^2FA can be considered an effective radiosensitizer operative at a wide range of electron energies.     

Vacuum-UV and Low-Energy Electron-Induced DNA Strand Breaks – Influence of the DNA Sequence and Substrate

DNA is effectively damaged by radiation, which can on the one hand lead to cancer and is on the other hand directly exploited in the treatment of tumor tissue. DNA strand breaks are already induced by photons having an energy below the ionization energy of DNA. At high photon energies, most of the DNA strand breaks are induced by low-energy secondary electrons. In the present study we quantified photon and electron induced DNA strand breaks in four different 12mer oligonucleotides. They are irradiated directly with 8.44 eV vacuum ultraviolet (VUV) photons and 8.8 eV low energy electrons (LEE). By using Si instead of VUV transparent CaF₂ as a substrate the VUV exposure leads to an additional release of LEEs, which have a maximum energy of 3.6 eV and can significantly enhance strand break cross sections. Atomic force microscopy is used to visualize strand breaks on DNA origami platforms and to determine absolute values for the strand break cross sections. Upon irradiation with 8.44 eV photons all the investigated sequences show very similar strand break cross sections in the range of 1.7–2.3×10⁻¹⁶ cm². The strand break cross sections for LEE irradiation at 8.8 eV are one to two orders of magnitude larger than the ones for VUV photons, and a slight sequence dependence is observed. The sequence dependence is even more pronounced for LEEs with energies <3.6 eV. The present results help to assess DNA damage by photons and electrons close to the ionization threshold.     

Intramolecular electronic communication in a dimethylaminoazobenzene–fullerene C60 dyad: An experimental and TD‐DFT study

An electronically push–pull type dimethylaminoazobenzene–fullerene C₆₀ hybrid was designed and synthesized by tailoring N,N‐dimethylaniline as an electron donating auxochrome that intensified charge density on the β‐azonitrogen, and on N‐methylfulleropyrrolidine (NMFP) as an electron acceptor at the 4 and 4′ positions of the azobenzene moiety, respectively. The absorption and charge transfer behavior of the hybrid donor‐bridge‐acceptor dyad were studied experimentally and by performing TD‐DFT calculations. The TD‐DFT predicted charge transfer interactions of the dyad ranging from 747 to 601 nm were experimentally observed in the UV‐vis spectra at 721 nm in toluene and dichloromethane. A 149 mV anodic shift in the first reduction potential of the N?N group of the dyad in comparison with the model aminoazobenzene derivative further supported the phenomenon. Analysis of the charge transfer band through the orbital picture revealed charge displacement from the n_(N?N) (nonbonding) and π _(N?N) type orbitals centered on the donor part to the purely fullerene centered LUMOs and LUMO+n orbitals, delocalized over the entire molecule. The imposed electronic perturbations on the aminoazobenzene moiety upon coupling it with C₆₀ were analyzed by comparing the TD‐DFT predicted and experimentally observed electronic transition energies of the dyad with the model compounds, NMFP and (E)‐N,N‐dimethyl‐4‐(p‐tolyldiazenyl)aniline (AZNME). The n_(N?N) → π*_(N?N) and π_(N?N) → π*_(N?N) transitions of the dyad were bathochromically shifted with a significant charge transfer character. The shifting of π_(N?N) → π*_(N?N) excitation energy closer to the n → π*_(N?N) in comparison with the model aminoazobenzene emphasized the predominant existence of charge separated quinonoid‐like ground state electronic structure. Increasing solvent polarity introduced hyperchromic effect in the π_(N?N) → π*_(N?N) electronic transition at the expense of transitions involved with benzenic states, and the extent of intensity borrowing was quantified adopting the Gaussian deconvolution method. On a comparative scale, the predicted excitation energies were in reasonable agreement with the observed values, demonstrating the efficiency of TD‐DFT in predicting the localized and the charge transfer nature of transitions involved with large electronically asymmetric molecules with HOMO and LUMO centered on different parts of the molecular framework. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010     

Partial cross sections and density-of-states effects in the valence-band photoemission from solid nitrogen

Photoelectron energy distribution curves from solid nitrogen were measured for excitation energies to 40 cV using synchrotron radiation. Partial cross sections for emission from 3σ_g, 1π_u and 2σ_u derived valence bands show pronounced mauna 3, 4, 2.9 and 3.0 eV above the vacuum levels, interpreted as due to high density of conduction-band final states. These states are related to π*_g negative-ion shape resonances.     

Tayloring standard TDDFT approaches for computing UV/Vis transitions in thiocarbonyl chromophores

We report the development of an accurate computational procedure for the calculation of the n → π* (λ_max?1) and π → π* (λ_max?2) transitions of a set of thiocarbonyl derivatives. To ensure converged results, all calculations are carried out using the 6‐311+G(2df,p) basis set for time‐dependent calculations, and the 6‐311G(2df,p) for the ground‐state geometrical optimization. Starting with two hybrids, PBE0 and B3LYP, the Hartree–Fock exchange percentage (α) used is optimized in order to reach excitation energies that fit experimental data. It turns out that BLYP(α) is the more adequate functional for calibration. For the n → π* excitation, the optimal α value lies in the 0.10–0.20 interval, whereas for the π → π* process setting α equal to 0.10 provides the most accurate results. The corresponding mean absolute errors (MAE) are limited to 17 nm for λ_max?1, and to 10 nm for λ_max?2, allowing a consistent and accurate prediction of both transitions. We also assess the merits of the ZINDO//AM1 scheme and it turns out that the semi‐empirical method only provides a poor prediction of the λ_max of thiocarbonyl derivatives, especially for the n → π* transition. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

Vibrational and electronic excitation in p-benzoquinone by electron impact

Vibrational and electronic excitation by electron impact in p-benzoquinone was studied using a trochoidal electron spectrometer. Two distinct patterns of vibrational excitation were observed. First, low quanta of a few selected vibrations are specifically excited at incident electron energies corresponding to shape resonances. Some resonances excite mainly the CO stretch, others the CH stretch vibration, and this selectivity is used in the discussion of the assignment of the resonances. A second pattern is an unspecific excitation of a quasi-continuum where no structure due to individual vibrational levels can be discerned. This feature peaks at threshold, large amounts of vibrational energy can be deposited in the molecule, and the excitation also proceeds via shape resonances. Electronic excitation spectra in the valence and Rydberg regions are also presented and discussed. A band observed at 4.37 eV with low residual energies has been tentatively assigned to the second π — π* triplet state ³B_3g.     

Sulfur as hydrogen‐bond acceptor in cocrystals of 2‐thio‐modified thymine

Doubly and triply hydrogen‐bonded supramolecular synthons are of particular interest for the rational design of crystal and cocrystal structures in crystal engineering since they show a high robustness due to their high stability and good reliability. The compound 5‐methyl‐2‐thiouracil (2‐thiothymine) contains an ADA hydrogen‐bonding site (A = acceptor and D = donor) if the S atom is considered as an acceptor. We report herein the results of cocrystallization experiments with the coformers 2,4‐diaminopyrimidine, 2,4‐diamino‐6‐phenyl‐1,3,5‐triazine, 6‐amino‐3H‐isocytosine and melamine, which contain complementary DAD hydrogen‐bonding sites and, therefore, should be capable of forming a mixed ADA–DAD N—H…S/N—H…N/N—H…O synthon (denoted synthon 3s_{N·S;N·N;N·O}), consisting of three different hydrogen bonds with 5‐methyl‐2‐thiouracil. The experiments yielded one cocrystal and five solvated cocrystals, namely 5‐methyl‐2‐thiouracil–2,4‐diaminopyrimidine (1/2), C₅H₆N₂OS·2C₄H₆N₄, (I), 5‐methyl‐2‐thiouracil–2,4‐diaminopyrimidine–N,N‐dimethylformamide (2/2/1), 2C₅H₆N₂OS·2C₄H₆N₄·C₃H₇NO, (II), 5‐methyl‐2‐thiouracil–2,4‐diamino‐6‐phenyl‐1,3,5‐triazine–N,N‐dimethylformamide (2/2/1), 2C₅H₆N₂OS·2C₉H₉N₅·C₃H₇NO, (III), 5‐methyl‐2‐thiouracil–6‐amino‐3H‐isocytosine–N,N‐dimethylformamide (2/2/1), (IV), 2C₅H₆N₂OS·2C₄H₆N₄O·C₃H₇NO, (IV), 5‐methyl‐2‐thiouracil–6‐amino‐3H‐isocytosine–N,N‐dimethylacetamide (2/2/1), 2C₅H₆N₂OS·2C₄H₆N₄O·C₄H₉NO, (V), and 5‐methyl‐2‐thiouracil–melamine (3/2), 3C₅H₆N₂OS·2C₃H₆N₆, (VI). Synthon 3s_{N·S;N·N;N·O} was formed in three structures in which two‐dimensional hydrogen‐bonded networks are observed, while doubly hydrogen‐bonded interactions were formed instead in the remaining three cocrystals whereby three‐dimensional networks are preferred. As desired, the S atoms are involved in hydrogen‐bonding interactions in all six structures, thus illustrating the ability of sulfur to act as a hydrogen‐bond acceptor and, therefore, its value for application in crystal engineering.     

N?H···S and S?H···N intramolecular hydrogen bond in β‐thioaminoacrolein: A quantum chemical study

The conformational study of β‐thioaminoacrolein was performed at various theoretical levels, HF, B3LYP, and MP2 with 6‐311++G(d,p) basis set, and the equilibrium conformations were determined. To have more reliable energies, the total energies of all conformers were recomputed at high‐level ab initio methods, G2MP2, G3, and CBS‐QB3. According to these calculations, the intramolecular hydrogen bond is accepted as the origin of conformational preference in thialamine (TAA) and thiolimine groups. The hydrogen bond strength in various resonance‐assisted hydrogen bond systems was evaluated by HB energy, geometrical parameters, topological parameters, and charge transfers corresponding to orbital interactions. Furthermore, our results reveal that the TAA tautomer has extra stability with respect to the other tautomers. The population analyses of the possible conformations by NBO predict that the origin of this preference is mainly due to the π‐electron delocalization in framework of TAA forms, especially usual π_C?C → π*_C?S and Lp (N) → π*_C?C charge transfers. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Single,double, and multiple double strand breaks induced in DNA by 3-100 eV electrons

Nonthermal secondary electrons with initial kinetic energies below 100 eV are an abundant transient species created in irradiated cells and thermalize within picoseconds through successive multiple energy loss events. Here we show that below 15 eV such low-energy electrons induce single (SSB) and double (DSB) strand breaks in plasmid DNA exclusively via formation and decay of molecular resonances involving DNA components (base, sugar, hydration water, etc.). Furthermore, the strand break quantum yields (per incident electron) due to resonances occur with intensities similar to those that appear between 25 and 100 eV electron energy, where nonresonant mechanisms related to excitation/ionizations/dissociations are shown to dominate the yields, although with some contribution from multiple scattering electron energy loss events. We also present the first measurements of the electron energy dependence of multiple double strand breaks (MDSB) induced in DNA by electrons with energies below 100 eV. Unlike the SSB and DSB yields, which remain relatively constant above 25 eV, the MDSB yields show a strong monotonic increase above 30 eV, however with intensities at least 1 order of magnitude smaller than the combined SSB and DSB yields. The observation of MDSB above 30 eV is attributed to strand break clusters (nano-tracks) involving multiple successive interactions of one single electron at sites that are distant in primary sequence along the DNA double strand, but are in close contact; such regions exist in supercoiled DNA (as well as cellular DNA) where the double helix crosses itself or is in close proximity to another part of the same DNA molecule.     

Electronic structure of the azide ion using the SCF Xα SW method

The electronic structure of the azide ion is investigated using the SCF Xα scattered wave method. Calculated ionization energies are compared with values determined by electron spectroscopy. Transition state calculations for π_g → π*_u, σ_u → π*_u and σ_g → π*_u single electron transitions yield excitation energies near 5.7, 11.0, and 12.0 eV respectively.     

Chromium‐metformin ternary complexes: Thermal,DNA interaction and Docking studies

Three chromium ternary complexes with metformin (met) as a primary ligand and bipyridine (bipy) or ortho‐phenylenediamine (opda) or ortho‐phenanthroline (phen) as secondary ligand were synthesized. These complexes [Cr (Cl)₂(Hmet)(bipy)]‐( 1 ), [Cr (Cl)₂(Hmet)(opda)]‐( 2 ) and [Cr (Cl)₂(Hmet)(phen)]‐( 3 ) were characterized by LC–MS, elemental analysis, molar conductance, thermal analysis, infrared spectroscopy, electronic spectroscopy. The geometrical structures have been found to be octahedral. Degradation pattern of the compounds is shown by thermal studies. The Kinetic parameters‐ energy of activation (E_a), enthalpy (ΔH), entropy (ΔS) and free energy changes (ΔG) have been determined by thermogravimetric data. Coats‐Redfern integration method with thirteen kinetic models was used to calculate the kinetic and thermodynamic parameters for the degradation of all the complexes. The stabilities of the complexes were obtained from their molecular orbital structures from which the quantum chemical parameters were calculated using the HOMO‐LUMO energies. UV–Visible absorption, fluorescence, and viscosity measurements have been conducted to assess the interaction of the complexes with CT DNA. The complexes showed absorption hyperchromism in its UV–Vis spectrum with DNA. The binding constants K_b from UV–Vis absorption studies were 3.1x10⁴, 4.4x10⁴, 5x10⁴ M^?1 for 1, 2, 3 respectively and Stern–Volmer quenching constants (K_sq) from fluorescence studies were 0.137, 0.532, 0.631 for 1, 2, 3 respectively. Finally, viscosity measurements revealed that the binding of the complexes with CT‐DNA could be surface binding, mainly due to groove binding. The activity of complexes towards DNA cleavage decrease in the order of 3 > 2 > 1.The light switching properties of the complexes were also evaluated. The complexes were docked in to B‐DNA sequence, 5′(D*AP*CP*CP*GP*AP*CP*GP*TP*CP*GP*GP*T)‐3′ retrieved from protein data bank (PDB ID: 423D), using Discovery Studio 2.1 software.     

Electronic spectra of nitroethylene

A systematic study of the electronic excited states of nitroethylene (C₂H₃NO₂) was carried out using the approximate coupled‐cluster singles‐and‐doubles approach with the resolution of the identity (RI‐CC2), the time dependent density functional theory with the CAMB3LYP functional (TDDFT/CAMB3LYP) and the DFT multireference configuration interaction (DFT/MRCI) method. Vertical transition energies and optical oscillator strengths were computed for a maximum of 20 singlet transitions. Semiclassical simulations of the ultraviolet (UV) spectra were performed at the RI‐CC2 and DFT/MRCI levels. The main features in the UV spectrum were assigned to a weak n‐π* transition, and two higher energy π_CC+O‐π* bands. These characteristics are common to molecules containing NO₂ groups. Simulated spectra are in good agreement with the experimental spectrum. The energy of the bands in the DFT/MRCI simulation agrees quite well with the experiment, although it overestimates the band intensities. RI‐CC2 produced intensities comparable to the experiment, but the bands were blue shifted. A strong π_CC+O‐π* band, not previously measured, was found in the 8–9 eV range. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012     

Capillary electrophoresis coupled with electrochemiluminescence detection for the separation and determination of thyreostatic drugs in animal feed

A rapid, simple, and practical method for the determination of four of the most used thyreostatic drugs (methimazole, 2‐thiouracil, 6‐methyl‐2‐thiouracil, and 6‐propyl‐2‐thiouracil) using CE coupled to electrochemiluminescence detection has been established, based on the electrochemiluminescence enhancement of tris(2,2‐bipyridyl)ruthenium(II) with these analytes. Parameters that affect separation and detection were optimized. Under the optimum experimental conditions, the four analytes could be well separated within 11 min at the separation voltage of 16 kV in a running solution containing 20 mM phosphate buffer (pH 9.0) and 1.0 × 10^?4 M Ru(bpy)₃²⁺, with a solution of 20 mM phosphate buffer (pH 12.0) containing 1.0 × 10^?4 M Ru(bpy)₃²⁺ in the electrochemiluminescence detection cell. The detection limits for methimazole, 6‐methyl‐2‐thiouracil, 6‐propyl‐2‐thiouracil, and 2‐thiouracil were 0.1, 0.05, 0.05, and 0.01 μM, respectively. The proposed method was applied to analyze these drugs in spiked animal feed samples. The recoveries were 88.2～99.0 and 86.4～98.7% for the intraday and interday analyses, respectively. The RSDs were 2.7～4.8 and 1.8～5.0% for the intraday and interday analyses, respectively. The results demonstrate that the proposed method has promising applications in the detection of thyreostatic drugs in animal feeds.     

An AB initio SCF MO CI study of the n → π* transition of methylenimine

The electron correlation energies of both the ground and n → π* excited states of methylenimine (CH₂NH) are investigated by means of ab initio SCF MO CI calculations. Then n → π* singlet and triplet state energies of methylenimine are obtained through 3461-dimensional CI including the singly, doubly and triply excited configurations. the excitation energy from the ground state to the ¹(n → π*) state nearly coincides with that obtained in the framework of the singly excited configuration interaction (SECI) procedure. This result suggests that there is good cancellation of the correlation energy between the ground and the excited singlet sates, proving the usefulness of the SECI method for the excitation energies.     

Photoionization mass spectrometry of molecular clusters using synchrotron radiation

The photoionization and dissociative ionization of molecular aggregates using synchrotron radiation is reported. The main objective of the review is to consider the intracluster relaxation processes after ionization. For hydrogen-bonded systems proton transfer is dominant. For small clusters (n<4) appearance potentials, ionization potentials, absolute proton affinities, proton solvation energies and intermolecular bond energies in the ionic clusters are deduced. For van der Waals aggregates proton transfer can also be used to characterize the intermolecular bond in the ionic cluster. Aggregates of CH₄, SiH₄, CH₃F show proton transfer in contrast to simple aromatic compounds, which reveal no proton transfer. From the fragmentation pattern and appearance potentials relaxation by intracluster ion molecule reactions is discussed. In heterogeneous clusters intracluster Penning ionization is observed. The shift of the charge transfer resonances depends on the π-electron density in the aromatic system. The width and spectral position of these resonances are influenced by the cluster size.     

SINGLE-STRAND BREAKS INDUCED IN DNA BY VACUUM-ULTRAVIOLET RADIATION

Abstract— The efficiency of vacuum u.v. for producing single-strand breaks in DNA was determined for wavelengths between 58 and 254 nm (corresponding to photon energies of 21·2 and 4·9 eV, respectively) by using the supertwisted RF-DNA of bacteriophage φX174. The cross-section for production of single-strand breaks increases continuously by about 5 orders of magnitude between 5 and 10 eV photon energy, whereas from 11 to 21 eV the number of strand breaks produced per unit of incident radiation energy is approximately constant. Thus, absorption of a 10-eV photon causes DNA strand breaks with maximum efficiency. In addition, the number of electrons liberated from DNA by photons below 10 eV is one or two orders of magnitude higher than the frequency of strand breaks, demonstrating that in this energy range only a small fraction of the ionizations leads to strand breakage in DNA.     

Cocrystals of 6‐propyl‐2‐thiouracil: N—H...O versus N—H...S hydrogen bonds

In order to investigate the relative stability of N—H...O and N—H...S hydrogen bonds, we cocrystallized the antithyroid drug 6‐propyl‐2‐thiouracil with two complementary heterocycles. In the cocrystal pyrimidin‐2‐amine–6‐propyl‐2‐thiouracil (1/2), C₄H₅N₃·2C₇H₁₀N₂OS, (I), the `base pair' is connected by one N—H...S and one N—H...N hydrogen bond. Homodimers of 6‐propyl‐2‐thiouracil linked by two N—H...S hydrogen bonds are observed in the cocrystal N‐(6‐acetamidopyridin‐2‐yl)acetamide–6‐propyl‐2‐thiouracil (1/2), C₉H₁₁N₃O₂·2C₇H₁₀N₂OS, (II). The crystal structure of 6‐propyl‐2‐thiouracil itself, C₇H₁₀N₂OS, (III), is stabilized by pairwise N—H...O and N—H...S hydrogen bonds. In all three structures, N—H...S hydrogen bonds occur only within R₂²(8) patterns, whereas N—H...O hydrogen bonds tend to connect the homo‐ and heterodimers into extended networks. In agreement with related structures, the hydrogen‐bonding capability of C=O and C=S groups seems to be comparable.     

Subvalenz bei elektropositiven s‐Block‐Metallen. Unmögliches möglich gemacht

The preparation of subvalent electropositive metal compounds succeeds in general by means of three different concepts: i) Stabilization can be achieved by delocalization of electrons in metallic matrices. A formal subvalence results from the total formula, whereas on closer examination of the bonding situation an expected “normal” valence of the metal atoms according to the octet rule can be concluded. ii) According the rules of determination of the oxidation state a formal subvalence arises from the formation of homonuclear element‐element bonds or metal clusters. However, in the case of M₂²⁺ units a normal valence is realized (which is well‐known in the chemistry of mercury as Hg₂²⁺, e.g. calomel Hg₂Cl₂). iii) The stabilization of subvalent metals with the aid of expanded π*‐systems of aren ligands succeeds when the energy lies between the two first ionization energies of the alkaline earth metal.     

Oligonucleotide Analogues with a Nucleobase‐Including Backbone,Part 7, Molecular Dynamics Simulation of a DNA Duplex Containing a 2′‐Deoxyadenosine 8‐(Hydroxymethyl)‐Derived Nucleotide

The structure and stability of a 14‐mer DNA duplex containing a nucleotide analog with a hydroxymethyl substituent at the C(8) of 2′‐deoxyadenosine has been investigated by molecular‐dynamics simulation. The DNA duplex studied has the sequence 5′‐d(CGTAAGCTCGATAG)‐3′⋅5′‐d(CTATCGA*GCTTACG)‐3′, where the O(3′) of the dG₆ nucleotide in the second strand is linked through a phosphinato group with the O(10) of the dA 2′‐deoxyadenosine‐derived nucleotide. Previous experimental results showed that the stability of this duplex in aqueous solution of 0.1M NaCl at pH 7 and room temperature is significantly lower than that of the corresponding unmodified DNA duplex. Comparison of molecular‐dynamics trajectories of the unmodified and modified B‐DNA duplexes in aqueous solution, at similar conditions than the experiment, shows that the substitution of the dA nucleotide by the dA* nucleotide in the second strand induces stretching of the double helix, which results in opening of the grooves and consequent exposure of the double‐helix core to the solvent.