Piotr Storoniak

Electron-induced elimination of the bromide anion from brominated nucleobases : a computational study

The enhancement of radiodamage to DNA labeled with halonucleobases is attributed to the reactive radical produced from a halonucleobase by the attachment of an electron. We examined at the B3LYP/6-31++G** level electron capture by four brominated nucleobases (BrNBs): 8-bromo-9-methyladenine, 8-bromo-9-methylguanine, 5-bromo-1-methylcytosine, and 5-bromo-1-methyluracil followed by the release of the bromide anion and a nucleobase radical. We demonstrate that neutral BrNBs in both gas and aqueous phases are better electron acceptors than unsubstituted NBs and that resulting anion radicals, BrNBs(•-), can easily transform into the product complex of the bromide anion and the nucleobase radical ([Br(-)···NB(•)]). The overall thermodynamic stimulus for the process starting with the neutral BrNB and ending with the isolated bromide anion and the NB(•) radical is similar in the case of all four BrNBs studied, which suggests their comparable radiosensitizing capabilities.

Thermodynamics and Kinetics of the Thermal Decomposition of N,N,N-trimethylmethanaminium and 1-methylpyridinium Halides

The decomposition of the quaternary salts mentioned in the title was examined at the quantum mechanical Hartree-Fock level of theory employing pseudopotentials combined with a SBKJ** basis set. This enabled identification of intermediate and transition state species on the reaction pathway and prediction of the thermodynamic and kinetic barriers to the dissociation of the compounds in the gaseous phase. Application of classical methods permitted the lattice energies of salts, whose crystal structures had been established earlier, to be predicted. Combination of these latter characteristics with the heats of formation of gaseous halide ions (available from the literature) and the relevant cations (obtained at the density functional (B 3LYP)/6-31G**level of theory) provided heats of formation of the salts. On the basis of these values, the thermodynamic and kinetic barriers to the dissociation of the compounds were predicted. The characteristics thus obtained compare quite well with those available in the literature or determined in this work on the basis of TG or DSC measurements. These investigations have shed more light on the mechanism of the thermal dissociation of quaternary salts, and more generally on thermal processes involving solids.

STABLE VALENCE ANIONS OF NUCLEIC ACID BASES AND DNA STRAND BREAKS INDUCED BY LOW ENERGY ELECTRONS

The last decade has witnessed immense advances in our understanding of the effects of ionizing radiation on biological systems. As the genetic information carrier in biological systems, DNA is the most important species which is prone to damage by high energy photons. Ionizing radiations destroy DNA indirectly by forming low energy electrons (LEEs) as secondary products of the interaction between ionizing radiation and water. An understanding of the mechanism that leads to the formation of single and double strand breaks may be important in guiding the further development of anticancer radiation therapy. In this article we demonstrate the likely involvement of stable nucleobases anions in the formation of DNA strand breaks – a concept which the radiation research community has not focused on so far. In Section refch21:sec21.1 we discuss the current status of studies related to the interaction between DNA and LEEs. The next section is devoted to the description of proton transfer induced by electron attachment to the complexes between nucleobases and various proton donors – a process leading to the strong stabilization of nucleobases anions. Then, we review our results concerning the anionic binary complexes of nucleobases with particular emphasize on the GC and AT systems. Next, the possible consequences of interactions between DNA and proteins in the context of electron attachment are briefly discussed. Further, we focus on existing proposal of single strand break formation in DNA. Ultimately, open questions as well perspectives of studies on electron induced DNA damage are discussed

Crystal Structure and Lattice Energetics of 10-Methylacridinium Halides

The crystal structures of 10-methylacridinium chloride monohydrate, bromide monohydrate and iodide were determined by X-ray analysis. The compounds crystallize in the triclinic space group, P¯1, with 2 molecules in the unit cell. The molecular arrangement in the crystals revealed that hydrogen bonds (in hydrates) and van der Waals contacts play a significant part in intermolecular interactions. To discover their nature, contributions to the crystal lattice energy arising from electrostatic (the most important since the compounds form ionic crystals), dispersive and repulsive interactions were calculated. Enthalpies of formation of the salts, their stability and susceptibility to decomposition could be predicted from a combination of crystal lattice energies with values of other thermochemical characteristics obtained theoretically or taken from the literature. The role of water in the stabilization of the crystal lattice of the hydrates is also explained. The information gathered has given an insight into the features and behaviour of compounds which can be regarded as models of a large group of aromatic quaternary nitrogen salts.

The Anionic (9-Methyladenine)−(1-Methylthymine) Base Pair Solvated by Formic Acid. A Computational and Photoelectron Spectroscopy Study

The photoelectron spectrum for (1-methylthymine)-(9-methyladenine)...(formic acid) (1MT-9MA...FA) anions with the maximum at ca. 1.87 eV was recorded with 2.54 eV photons and interpreted through the quantum-chemical modeling carried out at the B3LYP/6-31+G(d,p) level. The relative free energies of the anions and their calculated vertical detachment energies suggest that only seven anionic structures contribute to the observed PES signal. We demonstrate that electron binding to the (1MT-9MA...FA) complex can trigger intermolecular proton transfer from formic acid, leading to the strong stabilization of the resulting radical anion. The SOMO distribution indicates that an excess electron may localize not only on the pyrimidine but also on the purine moiety. The biological context of DNA-environment interactions concerning the formation of single-strand breaks induced by excess electrons has been briefly discussed.

Enthalpies of Sublimation and Crystal Lattice Energies of 9-Acridinamine and its Derivatives

Enthalpies of sublimation of acridine, 9-acridinamine, N-methyl-9-acridinamine, 10-methyl-9-acridinimine, N,N-dimethyl-9-acridinamine and N-methyl-10-methyl-9-acridinimine were determined by fitting to thermogravimetric curves with the Clausius-Clapeyron relationship. These values compare well with crystal lattice energies predicted theoretically as the sum of electrostatic, dispersive and repulsive interactions. Partial charges for these calculations were obtained on an ab initio level, while atomic parameters were taken from literature.

Photoelectron spectroscopy and density functional theory studies on the uridine homodimer radical anions.

We report the photoelectron spectrum (PES) of the homogeneous dimer anion radical of uridine, (rU)(2)(●-). It features a broad band consisting of an onset of ∼1.2 eV and a maximum at the electron binding energy (EBE) ranging from 2.0 to 2.5 eV. Calculations performed at the B3LYP∕6-31++G∗∗ level of theory suggest that the PES is dominated by dimeric radical anions in which one uridine nucleoside, hosting the excess charge on the base moiety, forms hydrogen bonds via its O8 atom with hydroxyl of the other neutral nucleosides ribose. The calculated adiabatic electron affinities (AEAGs) and vertical detachment energies (VDEs) of the most stable homodimers show an excellent agreement with the experimental values. The anionic complexes consisting of two intermolecular uracil-uracil hydrogen bonds appeared to be substantially less stable than the uracil-ribose dimers. Despite the fact that uracil-uracil anionic homodimers are additionally stabilized by barrier-free electron-induced proton transfer, their relative thermodynamic stabilities and the calculated VDEs suggest that they do not contribute to the experimental PES spectrum of (rU)(2)(●-).

Barrier-free proton transfer induced by electron attachment to the complexes between 1‐methylcytosine and formic acid

We report the photoelectron spectra of anionic complexes between 1-methylcytosine (mC) and formic acid (FA) in 1 : 1 and 1:2 stoichiometries that have been measured with 2.54 eV photons. Each spectrum consists of a broad peak with maxima at 1.85 and 2.1 eV, respectively, confirming the generation of stable valence anions in the gas phase. The neutral and anionic complexes of mC(FA) and mC(FA)2 were also studied computationally at the B3LYP, second-order Møller–Plesset, and coupled-cluster levels of theory with the 6–31++G** and aug-cc-pVDZ basis sets. Based on the calculations, we conclude that the photoelectron spectra of mC(FA)− and are due to anions that originate from a barrier-free proton transfer (BFPT) triggered by excess electron attachment. They can be viewed as neutral radicals of hydrogenated 1-methylcytosine solvated by a deprotonated formic acid.

Photoelectron spectroscopy and computational modeling of thymidine homodimer anions

The intact thymidine homodimer anion (dT(2)(-)) was generated in the gas phase using an infrared desorption/photoemission source and recorded by a pulsed photoelectron spectrometer. The photoelectron spectrum (PES) revealed a broad signal with the maximum at electron binding energy ∼2.0 eV and the threshold value at 1.1 eV. The relative energies and vertical detachment energies of the possible anion structures were calculated at the B3LYP/6-31++G(d,p) level. Here we report that the most stable anion radical homodimer geometries observed in the PES are the anionic nucleoside coordinated by the O8 atom of thymine to the deoxyribose of the second neutral nucleoside. Unlike previous experimental-computational studies on anionic complexes involving nucleobases with proton donors, the electron-induced proton-transferred structures are not responsible for the shape of the PES of dT(2)(-).

Structure, formation, thermodynamics and interactions in 9-carboxy-10-methylacridinium-based molecular systems

9-Carboxy-10-methylacridinium chloride and trifluoromethanesulfonate, the parent compounds for a wide range of chemiluminogenic salts of practical importance, were synthesized and thoroughly investigated to address problems concerning structural and thermodynamical issues of these cognitively interesting molecular systems. Under various conditions of crystallization, the title salts disclosed three types of crystals: one built from the monomeric form of cations and two containing homoconjugated cations. The title compounds made the first described derivatives of acridine, expressing homoconjugated cationic forms, both in crystalline solid and gaseous phases. The monocrystals were characterized, employing X-ray crystallography and spectroscopic methods such as MALDI-TOF MS, ESI-QTOF MS, NMR and UV-Vis. X-ray crystallography studies revealed the occurrence of the three different molecular architectures, in which not only the counter ions and stoichiometry are different, but also the space group and number of molecules in the unit cell. The energetics and intermolecular interactions occurring within the crystals were explored, applying crystal lattice energy calculations and Hirshfeld surface analysis. In order to elucidate the thermodynamics and origin of the experimentally revealed forms, computations based on the density functional theory were performed, assuming vapour and liquid phases.