Ring Formation and Hydration Effects in Electron Attachment to Misonidazole.
Ontology highlight
ABSTRACT:
SUBMITTER: Oncak M
PROVIDER: S-EPMC6770096 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:Methyl 2-azido-2-deoxy-?-d-lyxofuranoside (1a) and methyl 2-azido-2-deoxy-?-d-ribofuranoside (2) were prepared from d-xylose or d-arabinose, respectively. Employing ESR and DFT/B3LYP/6-31G* calculations, we investigated (i) aminyl radical (RNH·) formation and (ii) reaction pathways of RNH·. Prehydrated electron attachment to 1a and 2 at 77 K produced transient azide anion radical (RN3·-) which reacts via rapid N2 loss at 77 K, forming nitrene anion radical (RN·-). Rapid protonation of RN·- at 77 K formed RNH· and -OH. 15N-labeled-1a confirmed this mechanism. Investigations employing in-house synthesized site-specifically deuterated derivatives of 1a (e.g., CH3 (1b), C4 (1c), and C5 (1d)) established that (a) a facile intramolecular H atom transfer from C5 to RNH· generated C5· and RNH2. C5· formation had a small deuterium kinetic isotope effect suggesting that this reaction does not occur via direct H atom abstraction. (b) Subsequently, C5· underwent a facile unimolecular conversion to ring-opened C4·. Identification of ring-opened C4· intermediate confirms the mechanism of C5'· mediated unaltered base release associated with DNA-strand break. However, for 2, ESR studies established thermally activated intermolecular H atom abstraction by RNH· from the methyl group at C1. Thus, sugar ring configuration strongly influences the site and pathway of RNH· mediated reactions in pentofuranoses.
| S-EPMC5488683 | biostudies-literature
Project description:We investigate dissociative electron attachment to tirapazamine through a crossed electron-molecule beam experiment and quantum chemical calculations. After the electron is attached and the resulting anion reaches the first excited state, D1, we suggest a fast transition into the ground electronic state through a conical intersection with a distorted triazine ring that almost coincides with the minimum in the D1 state. Through analysis of all observed dissociative pathways producing heavier ions (90-161 u), we consider the predissociation of an OH radical with possible roaming mechanism to be the common first step. This destabilizes the triazine ring and leads to dissociation of highly stable nitrogen-containing species. The benzene ring is not altered during the process. Dissociation of small anionic fragments (NO2-, CN2-, CN-, NH2-, O-) cannot be conclusively linked to the OH predissociation mechanism; however, they again do not require dissociation of the benzene ring.
| S-EPMC8003736 | biostudies-literature
Project description:We discuss the quantum dot-ring nanostructure (DRN) as canonical example of a nanosystem, for which the interelectronic interactions can be evaluated exactly. The system has been selected due to its tunability, i.e., its electron wave functions can be modified much easier than in, e.g., quantum dots. We determine many-particle states for Ne?=?2 and 3 electrons and calculate the 3- and 4-state interaction parameters, and discuss their importance. For that purpose, we combine the first- and second-quantization schemes and hence are able to single out the component single-particle contributions to the resultant many-particle state. The method provides both the ground- and the first-excited-state energies, as the exact diagonalization of the many-particle Hamiltonian is carried out. DRN provides one of the few examples for which one can determine theoretically all interaction microscopic parameters to a high accuracy. Thus the evolution of the single-particle vs. many-particle contributions to each state and its energy can be determined and tested with the increasing system size. In this manner, we contribute to the wave-function engineering with the interactions included for those few-electron systems.
| S-EPMC4949483 | biostudies-literature
Project description:Employing electron spin resonance (ESR) spectroscopy, we have characterized the radicals formed in 3'-azido-3'-deoxythymidine (3'-AZT) and in its 5'-analog 5'-azido-5'-deoxythymidine (5'-AZT) after electron attachment in gamma-irradiated aqueous (H(2)O or D(2)O) glassy (7.5 M LiCl) systems. ESR spectral studies and theoretical calculations show that the predominant site of electron capture in 3'-AZT and in 5'-AZT is at the azide group and not at the thymine moiety. The azide group in AZT is therefore more electron affinic than the most electron affinic DNA base, thymine. Electron attachment to 3'-AZT and 5'-AZT results in an unstable azide anion radical intermediate (RN(3)*(-)) that is too short-lived to be observed in our work even at 77 K. At 77 K, we observe the neutral aminyl radical (RNH*) after loss of N(2) from RN(3)*(-) followed by protonation of nitrene anion radical (RN*(-)) to give RNH*. The expected RN*(-) intermediate is not observed as protonation from water is complete at 77 K even under highly basic conditions. Formation of RND* in D(2)O solutions confirms water as the source of the NH proton in the RNH*. Our assignments to these radicals are aided by DFT calculations for hyperfine coupling constants that closely match the experimental values. On annealing to higher temperatures (ca. 160-170 K), RNH* undergoes bimolecular hydrogen abstraction reactions from the thymine methyl group and the sugar moiety resulting in the formation of the thymine allyl radical (UCH(2)*) and two sugar radicals, C3'* and C5'*. RNH* also results in one-electron oxidation of the guanine base in 3'-AZG. This work provides a potential mechanism for the reported radiosensitization effects of AZT.
| S-EPMC2912441 | biostudies-literature
Project description:UnlabelledMany important cellular processes are regulated by reaction-diffusion (RD) of molecules that takes place both in the cytoplasm and on the membrane. To model and analyze such multicompartmental processes, we developed a lattice-based Monte Carlo method, Spatiocyte that supports RD in volume and surface compartments at single molecule resolution. Stochasticity in RD and the excluded volume effect brought by intracellular molecular crowding, both of which can significantly affect RD and thus, cellular processes, are also supported. We verified the method by comparing simulation results of diffusion, irreversible and reversible reactions with the predicted analytical and best available numerical solutions. Moreover, to directly compare the localization patterns of molecules in fluorescence microscopy images with simulation, we devised a visualization method that mimics the microphotography process by showing the trajectory of simulated molecules averaged according to the camera exposure time. In the rod-shaped bacterium Escherichia coli, the division site is suppressed at the cell poles by periodic pole-to-pole oscillations of the Min proteins (MinC, MinD and MinE) arising from carefully orchestrated RD in both cytoplasm and membrane compartments. Using Spatiocyte we could model and reproduce the in vivo MinDE localization dynamics by accounting for the previously reported properties of MinE. Our results suggest that the MinE ring, which is essential in preventing polar septation, is largely composed of MinE that is transiently attached to the membrane independently after recruited by MinD. Overall, Spatiocyte allows simulation and visualization of complex spatial and reaction-diffusion mediated cellular processes in volumes and surfaces. As we showed, it can potentially provide mechanistic insights otherwise difficult to obtain experimentally.Electronic supplementary materialThe online version of this article (doi:10.1007/s11693-009-9047-2) contains supplementary material, which is available to authorized users.
| S-EPMC2816228 | biostudies-literature
Project description:Biomimetic materials with programmable stimuli responsiveness constitute a highly attractive material class for building bioactuators, sensors and active control elements in future biomedical applications. With this background, we demonstrate how energetic electron beams can be utilized to construct tailored stimuli responsive actuators for biomedical applications. Composed of collagen-derived gelatin, they reveal a mechanical response to hydration and changes in pH-value and ion concentration, while maintaining their excellent biocompatibility and biodegradability. While this is explicitly demonstrated by systematic characterizing an electron-beam synthesized gelatin-based actuator of cantilever geometry, the underlying materials processes are also discussed, based on the fundamental physical and chemical principles. When applied within classical electron beam lithography systems, these findings pave the way for a novel class of highly versatile integrated bioactuators from micro- to macroscales.
| S-EPMC5727221 | biostudies-literature
Project description:We report the results of an experimental study of electron ionization of large helium nanodroplets doped with formic acid (FA). Several homologous series of cluster anions are observed, including [FAn-H]-, undissociated FAn-, and these ions complexed with one or more H2O. Some major features resemble those observed upon sputtering of frozen FA films but they differ significantly from results obtained by electron attachment to bare FA clusters in the gas phase. The FAn- and (H2O)[FAn-H]- series show abrupt onsets above n = 2 and 5, respectively. A prominent resonance in the anion yield occurs at 22.5 eV due to the formation of an intermediate He-*. Also observed are homologous series of [FA-H]- or [FA2-H]- complexed with helium. The cation chemistry is dominated by the production of protonated formic acid clusters, [FAnH]+, but various other homologous cluster ion series are observed as well. Graphical Abstract.
| S-EPMC6502787 | biostudies-literature
Project description:Nitrofurans belong to the class of drugs typically used as antibiotics or antimicrobials. The defining structural component is a furan ring with a nitro group attached. In the present investigation, electron attachment to 2-nitrofuran (C4H3NO3), which is considered as a potential radiosensitizer candidate for application in radiotherapy, has been studied in a crossed electron-molecular beams experiment. The present results indicate that low-energy electrons with kinetic energies of about 0-12 eV effectively decompose the molecule. In total, twelve fragment anions were detected within the detection limit of the apparatus, as well as the parent anion of 2-nitrofuran. One major resonance region of ?0-5 eV is observed in which the most abundant anions NO2-, C4H3O-, and C4H3NO3- are detected. The experimental results are supported by ab initio calculations of electronic states in the resulting anion, thermochemical thresholds, connectivity between electronic states of the anion, and reactivity analysis in the hot ground state.
| S-EPMC7727711 | biostudies-literature
Project description:Cyanogen NCCN and cyanoacetylene HCCCN are isoelectronic molecules, and as such, they have many similar properties. We focus on the bond cleavage in these induced by the dissociative electron attachment. In both molecules, resonant electron attachment produces CN- with very similar energy dependence. We investigate the very different dissociation dynamics, in each of the two molecules, revealed by velocity map imaging of this common fragment. Different dynamics are manifested both in the excess energy partitioning and in the angular distributions of fragments. Based on the comparison with electron energy loss spectra, which provide information about possible parent states of the resonances (both optically allowed and forbidden excited states of the neutral target), we ascribe the observed effect to the distortion of the nuclear frame during the formation of core-excited resonance in cyanoacetylene. The proposed mechanism also explains a puzzling difference in the magnitude of the CN- cross section in the two molecules which has been so far unexplained.
| S-EPMC10839900 | biostudies-literature
Project description:In this study, the reactions of electrons with N-acetylproline are investigated by electron spin resonance (ESR) spectroscopy and density functional theory. Electrons are produced by ? irradiation or by photoionization of K(4)Fe(CN)(6) in neutral 7.5 M LiCl-D(2)O aqueous glasses at low temperatures with identical results. Electrons are found to add to both the peptide bond and the carboxyl group of the acetyl-proline moiety at 77 K. On annealing, both the electron adducts undergo fragmentation of the peptide bond between the nitrogen and the ? carbon of the peptide structure. However, the peptide bond electron adduct radical reacts much more rapidly than the carboxyl group electron adduct radical. The DFT calculations predict that the carboxyl adduct is substantially more stable than the peptide bond adduct, with the activation barrier to N-C? cleavage 3.7 kcal/mol for the amide electron adducts and 23 kcal/mol for the carboxyl electron adducts in inagreement with the relative reactivity found by experiment.
| S-EPMC3237938 | biostudies-literature