First-principles GW calculations for DNA and RNA nucleobases

On the basis of first-principles GW calculations, we study the quasiparticle properties of the guanine, adenine, cytosine, thymine, and uracil DNA and RNA nucleobases. Beyond standard G0W0 calculations, starting from Kohn-Sham eigenstates obtained with (semi)local functionals, a simple self-consistency on the eigenvalues allows to obtain vertical ionization energies and electron affinities within an average 0.11 eV and 0.18 eV error respectively as compared to state-of-the-art coupled-cluster and multi-configurational perturbative quantum chemistry approaches. Further, GW calculations predict the correct \pi -character of the highest occupied state, thanks to several level crossings between density functional and GW calculations. Our study is based on a recent gaussian-basis implementation of GW with explicit treatment of dynamical screening through contour deformation techniques.Comment: 5 pages, 3 figure

A TD-DFT Study on the Photo-Physicochemical Properties of Chrysophanol from Rheum

As a naturally occurring anthraquinone pigment, chrysophanol (MHAQ) has attracted considerable attention in recent years owing to its efficient photosensitivity under the solar spectrum. Considering the successful use of time-dependent density functional theory (TD-DFT) in investigating the photo-physicochemical behaviors of dyes and pigments, we performed a study by means of TD-DFT calculations, which provided us with various excited state properties of chrysophanol, including absorption spectrum, lowest triplet excited-state energy, vertical electron affinity and vertical ionization potential. On the basis of the calculated results, the photosensitive mechanisms of chrysophanol were discussed and some deeper insights were gained. First, we indicated that the experimentally observed chrysophanol’s photo-damage to DNA in oxygen-free media is more likely to arise from MHAQ•+ rather than from T1 state chrysophanol. Second, we revealed that it is the MHAQ•− that is responsible for the O2•− generation in solvents. Based on the photosensitive activities, chrysophanol may be potentially used as the photodynamic medicine for clinical therapy of the diseases occurring on the shallow surface and vascular capillary diseases

LOW-ENERGY ELECTRON DAMAGE IN DNA

In this thesis, Photo-Electron Spectroscopy (PES) and Photo-Electron Imaging (PEI) have been exploited to study low-energy electron and photon-driven damage in DNA derivatives. After an introduction on photoelectron spectroscopy and DNA, an instrumental overview, together with a brief explanation of the theoretical methods used, is given. The results section is divided according to the different chemical systems that have been considered. First, the viability of a dipole-bound state, which are electronic non-valence states that play an important role in electron transfer in DNA, has been studied in a model molecule: despite the presence of an alkyl chain directly poking into it, the dipole-bound state is retained in all cases. Secondly, the possibility of achieving intra-molecular charge transfer as probe for low-energy electron damage has been explored in a carboxylated adenosine analogue. Although no conclusive evidence of charge-transfer from the carboxylic acid to the nucleobase has been observed, this approach has then been applied to different DNA derivatives. The object of the third section of the results chapter is, in fact, the photophysics of the doubly-deprotonated dianion of adenosine-5’-triphosphate, which exhibits electron tunneling through the Repulsive Coulomb Barrier (RCB) upon irradiation at 266 nm; excited states calculation and RCB simulations have been performed to support these findings. Lastly, the photophysics of other doubly-deprotonated di- and tri-phosphorylated purine dianions have been explored in the last section: only one of them, adenosine diphosphate ([ADP–H2]2–), shows evidence of intra-molecular charge transfer, however further research is needed to corroborate this hypothesis

Structural Characterization of Ribonucleic Acids and Their Complexes by Negative-ion Mode Mass Spectrometry

Ribonucleic acids (RNAs) form complexes with deoxyribonucleic acids, proteins, other RNAs, and smaller ligands. Detailed knowledge of RNA interaction sites provides a basis for understanding functions. With limited analytical techniques available to obtain deeper understanding of RNA structure, negative ion mode mass spectrometry (MS) has the potential to significantly expand RNA primary, secondary, tertiary, and quarternary structure information. This dissertation presents novel MS methods for characterizing RNAs and their complexes. Negative-ion electron capture dissociation (niECD) involves ~3.5-6.5 eV electron irradiation to yield charge-increased intermediates that further undergo radical-driven fragmentation. The proposed niECD mechanism involves gas-phase zwitterionic structures in which nucleobases are protonated and the phosphate backbone is deprotonated. We found that electron-capture efficiency is higher for purine nucleobases compared with pyrimidines and that purine radicals are more stable, presumably because purines have higher proton affinities and can form intramolecular hydrogen bonds. niECD efficiency decreases with increased charge state due to Coulomb repulsion. We show that gas-phase proton-transfer reactions can be combined with niECD for improved performance. Electrospray ionization (ESI) of a model RNA hairpin from native-like (10 mM ammonium acetate) and methanol-containing (up to 50%) solvents resulted in identical charge state distributions, suggesting a minor methanol effect on overall conformation. Experimentally determined collision cross sections (CCSs) for the 5- and 6- charge states of this RNA are smaller (789 Å2 and 830Å2, respectively) than those predicted from the NMR structure. Replica-exchange molecular dynamics showed that these charge states adopt globular collapsed structures due to self-solvation whereas the 7- charge state showed hairpin retention. Higher charge states showed extended structures (higher CCSs). Ligand (e.g., paromomycin) binding assays at varied methanol content resulted in strongest binding at 0% methanol (64+6 nM KD). However the KD remained within one standard deviation up to 50% methanol, suggesting that the binding site is mainly unperturbed in methanol. Assays at varied pHs showed strongest binding at neutral pH. Overall, these data suggest that moderate methanol concentrations, which facilitate ESI, can be tolerated in native RNA MS. Crosslinking techniques coupled with MS provide an alternative tool for identifying RNA interaction sites. We show that collisional activation can provide full sequence coverage of the RNA moiety within non-covalent RNA-peptide complexes; however complexes are disrupted, resulting in loss of site-specific information. By contrast, niECD, in combination with infrared multiphoton dissociation provided sufficient sequence coverage while retaining non-covalent interactions. We also show that IR irradiation at 10.6 µm selectively dissociates RNA-peptide crosslinked species within a peptide mixture due to resonance absorption by phosphate groups, thus allowing identification of such species. Microfluidics is a highly efficient technology for biological analysis. Microfluidic-type approaches, including nano-ESI and nano-LC, coupled with MS provide several advantages, e.g., limited sample consumption and enhanced sensitivity. In order to disseminate microfluidic principles, we developed a 2-week (8 hour) laboratory experiment for an undergraduate analytical chemistry course. Students are introduced to soft lithography concepts by designing/characterizing their own agar-based microfluidic chips. They learn about fluid dynamics by approaching the challenge of mixing in microfluidic channels. By varying solvent viscosity and channel geometries, terms that govern the Reynolds number, students achieve mixing. The optimal chip geometry/solvent condition is used to quantify salicylic acid-/iron (III) complex by colorimetric analysis. Overall, this dissertation describes the utility of MS (and its associated tools) for the study of RNA, RNA-small molecule, and RNA-protein complexes.PHDChemistryUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttps://deepblue.lib.umich.edu/bitstream/2027.42/143953/1/ikevin_1.pd

Probing Radiosensitisers in Electron Transfer Experiments

The impact of ionising radiation in the living systems is being investigated for decades, because its capability to induce damage in tissues and cells, compromising the DNA molecule integrity, resulting in mutations and eventually cells death. Considering this, ionising radiation can be very useful in different fields, especially in radiation therapy. However, it is necessary to guarantee that the effects of radiation in normal tissues during a radiation treatment are minimised. Many efforts have been made to improve the radiotherapy protocols, namely by the application of radiosensitisers which enhance the effect of radiation. Recent research investigations have demonstrated the role of secondary low-energy electrons as the main damaging agents in DNA. These secondary electrons can interact directly or indirectly with molecules, producing highly reactive species (ions and radicals). Moreover, it is also known that electrons do not exist freely in the physiological medium, but rather in solvated and/or in pre-solvated states. Therefore, studies on electron transfer between atoms/ions and biomolecules seems crucial to better understand the molecular mechanism of radiation interaction. The work presented in this thesis consists on the study of electron transfer collisions of atoms/ions in molecules of biological relevance. Initially, neutral potassium collisions in imidazole, nitroimidazoles (4-nitroimidazole and 2-nitroimidazole) and methylated compounds (1-methyl-4-nitroimidazole and 1-methyl-5-nitroimidazole) were investigated by time-of-flight (TOF) mass spectrometry in a crossed beam experiment comprising a neutral potassium beam and a molecular effusive beam. In these experiments the anionic fragmentation patterns and yields were obtained. These results present some differences from the dissociative electron attachment (free electrons) results, highlighting the importance of charge transfer studies in understanding the molecular reactions upon radiation. The second part of the work was performed in a novel crossed beam setup where collisions between oxygen anions and molecules as nitrogen, water and pyridine were investigated by measuring positive and negative fragmentation patterns through TOF mass spectrometry. From these studies we obtained for the first time experimental electron detachment cross-section of O2− in water and pyridine

Influence of the π–π interaction on the hydrogen bonding capacity of stacked DNA/RNA bases

The interplay between aromatic stacking and hydrogen bonding in nucleobases has been investigated via high-level quantum chemical calculations. The experimentally observed stacking arrangement between consecutive bases in DNA and RNA/DNA double helices is shown to enhance their hydrogen bonding ability as opposed to gas phase optimized complexes. This phenomenon results from more repulsive electrostatic interactions as is demonstrated in a model system of cytosine stacked offset-parallel with substituted benzenes. Therefore, the H-bonding capacity of the N3 and O2 atoms of cytosine increases linearly with the electrostatic repulsion between the stacked rings. The local hardness, a density functional theory-based reactivity descriptor, appears to be a key index associated with the molecular electrostatic potential (MEP) minima around H-bond accepting atoms, and is inversely proportional to the electrostatic interaction between stacked molecules. Finally, the MEP minima on surfaces around the bases in experimental structures of DNA and RNA–DNA double helices show that their hydrogen bonding capacity increases when taking more neighboring (intra-strand) stacking partners into account

Spectroscopic identification of fragment ions of DNA/RNA building blocks: the case of pyrimidine

Pyrimidine (Pym, 1,3-diazine, 1,3-diazabenzene) is an important N-heterocyclic building block of nucleobases. Understanding the structures of its fragment and precursor ions provides insight into its prebiotic and abiotic synthetic route. The long-standing controversial debate about the structures of the primary fragment ions of the Pym+ cation (C4H4N2+, m/z 80) resulting from loss of HCN, C3H3N+ (m/z 53), is closed herein with the aid of a combined approach utilizing infrared photodissociation (IRPD) spectroscopy in the CH and NH stretch ranges (νCH/NH) and density functional theory (DFT) calculations. IRPD spectra of cold Ar/N2-tagged fragment ions reveal that the C3H3N+ population is dominated by cis-/trans-HCCHNCH+ ions (∼90%) along with a minor contribution of the most stable H2CCCNH+ and cis-/trans-HCCHCNH+ isomers (∼10%). We also spectroscopically confirm that the secondary fragment resulting from further loss of HCN, C2H2+ (m/z 26), is the acetylene cation (HCCH+). The spectroscopic characterization of the identified C3H3N+ isomers and their hydrogen-bonded dimers with Ar and N2 provides insight into the acidity of their CH and NH groups. Finally, the vibrational properties of Pym+ in the 3 μm range are probed by IRPD of Pym+-(N2)1–2 clusters, which shows a high π-binding affinity of Pym+ toward a nonpolar hydrophobic ligand. Its νCH spectrum confirms the different acidity of the three nonequivalent CH groups.TU Berlin, Open-Access-Mittel - 202