An ab initio and AIM investigation into the hydration of 2-thioxanthine

<p>Abstract</p> <p>Background</p> <p>Hydration is a universal phenomenon in nature. The interactions between biomolecules and water of hydration play a pivotal role in molecular biology. 2-Thioxanthine (2TX), a thio-modified nucleic acid base, is of significant interest as a DNA inhibitor yet its interactions with hydration water have not been investigated either computationally or experimentally. Here in, we reported an <it>ab initio </it>study of the hydration of 2TX, revealing water can form seven hydrated complexes.</p> <p>Results</p> <p>Hydrogen-bond (H-bond) interactions in 1:1 complexes of 2TX with water are studied at the MP2/6-311G(d, p) and B3LYP/6-311G(d, p) levels. Seven 2TX^...H₂O hydrogen bonded complexes have been theoretically identified and reported for the first time. The proton affinities (PAs) of the O, S, and N atoms and deprotonantion enthalpies (DPEs) of different N-H bonds in 2TX are calculated, factors surrounding why the seven complexes have different hydrogen bond energies are discussed. The theoretical infrared and NMR spectra of hydrated 2TX complexes are reported to probe the characteristics of the proposed H-bonds. An improper blue-shifting H-bond with a shortened C-H bond was found in one case. NBO and AIM analysis were carried out to explain the formation of improper blue-shifting H-bonds, and the H-bonding characteristics are discussed.</p> <p>Conclusion</p> <p>2TX can interact with water by five different H-bonding regimes, N-H^...O, O-H^...N, O-H^...O, O-H^...S and C-H^...O, all of which are medium strength hydrogen bonds. The most stable H-bond complex has a closed structure with two hydrogen bonds (N(7)-H^...O and O-H^...O), whereas the least stable one has an open structure with one H-bond. The interaction energies of the studied complexes are correlated to the PA and DPE involved in H-bond formation. After formation of H-bonds, the calculated IR and NMR spectra of the 2TX-water complexes change greatly, which serves to identify the hydration of 2TX.</p

Impact des ions de faible énergie sur les composants de l'ADN

L'émergence récente de la hadronthérapie (thérapie avec des particules lourdes) constitue à l'heure actuelle une technique de radiothérapie prometteuse pour le traitement de tumeurs solides ancrées en profondeur. L'émission d'un rayonnement primaire composé de particules lourdes traversant les cellules a pour conséquence la génération d'espèces secondaires neutres et chargées. En particulier, la production importante d'ions secondaires d'énergie entre 10 à 300 eV, sur le trajet du faisceau ionisant, engendre l'ionisation et la fragmentation des constituants de la molécule d'ADN, processus-clé des dommages radiobiologiques au niveau moléculaire et finalement cellulaire. L'utilisation d'un système générateur de faisceaux d'ions sous ultravide a permis l'étude des mécanismes d'ionisation et de fragmentation des bases de l' ADN par irradiation ionique en phase condensée et par impact électronique en phase gazeuse. L'appareillage est constitué d'une source d'ions de faible énergie, d'un système de focalisation, d'une chambre de préparation des films moléculaire et d'une chambre de réactions couplée à un spectromètre de masse de haute résolution, permettant le monitoring des rendements des produits de l'irradiation générés. La condensation des bases de l'ADN en forme de films a été préparée in vacuo par évaporation d'un four, ce film étant ensuite irradié aux ions argon Ar+ possédant une énergie entre 1 et 100 eV. Sous l'effet du bombardement, les fragments positifs et négatifs désorbés ont été collectés par un spectromètre de masse quadrupole. L'ionisation et la fragmentation des bases adénine (A), guanine (G), cytosine (C) et 5- aminouracile (5-NH2-uracile) ont été étudiées par observation de l'émission des ions positifs et négatifs pendant l'irradiation avec Ar+ de faible énergie (10 à lOOeV) dans la phase condensée et d'électrons (70 eV) dans la phase gazeuse. Ces observations impliquent des mécanismes de fragmentation engendrés par des réactions de dissociation concertée telles que la désamination des bases A, G et C tant dans la phase condensée que dans la phase gazeuse, ainsi que l'amination de l'adénine dans la phase condensée. Les caractéristiques significatives relevées dans les spectres de masses des quatre bases sont la production d'ions NH/ (18 amu) et CH/ (15 amu) pour la cytosine et le 5-aminouracile, avec des intensités relatives élevées, par comparaison avec le pic le plus haut de chaque spectre (HCNH+, 28 amu). L'utilisation d'isotopes marqués d'A, G et C a révélé les mécanismes initiateurs de clivage des liaisons chimiques, communs à toutes les bases puriques et pyrimidiques constituant l' ADN. Des expériences conduites avec du 5- aminouracile ont confirmé l'hypothèse de désamination des bases A, G et C, par l'impact des ions Ar+ de faible énergie dans la phase condensée et d'électrons dans la phase gazeuse.Abstract: Ion beams have recently emerged as a promising radiotherapy technique for treatment of large, solid, deep seated tumours. As the primary beam of heavy particles traverses through the cell, secondary charged and neutral species are generated. In particular secondary ions with energies up to 100 eV are produced in large numbers along the ionization track. Ionization and fragmentation of DNA components is a key step in radiobiological damage to the cell. An ultrahigh vacuum (UHV) ion beam system has been used to study the ionization and fragmentation pathways of DNA bases by ion irradiation in the condensed phase and electron impact in the gas phase. The apparatus consists of a low energy ion source, beam line, biomolecular film preparation system and a reaction chamber with high-resolution mass spectrometer to monitor desorbing ion yields. Solid condensed films of DNA bases were prepared in vacuo by sample evaporation from an oven and were subsequently irradiated with (1-100 eV) Ar+ ions. Upon bombardment, desorbing positive and negative fragments were collected using a Quadrupole Mass Spectrometer (QMS). Ionization and fragmentation of Adenine (A), Guanine (G), Cytosine (C) and 5-aminouracil bases has been observed by low energy (10-100 eV) Ar + ions in the condensed phase and 70 eV electrons in the gas phase. These observations demonstrate fragmentation mechanisms involve site specific concerted dissociation reactions, deamination of Ade, Gua, Cyt in the condensed phase and the gas phase as well as amination of Adenine in the condensed phase. Of significant features of the mass spectra of all four bases are the production of NH 4+ (18 amu) and CH3+ (15 amu) fragments with high intensities relative to the most intense peak in each spectrum (HCNH+ , 28 amu). Utilizing isotopically labelled Ade, Gua and Cyt common purine and pyrimidine bond cleavage pathways and fragment origin sites were identified. Experiments performed with 5-aminouracil confirmed the deamination hypothesis of A, G and C bases by low energy Ar + ion impact in the condensed phase as well as the low energy electron impact in the gas phase

Molecular basis of the primary and secondary radiation damage to DNA/RNA nucleobases

La interacción radiación-materia ha sido una de las grandes preocupaciones científicas de los últimos tiempos, y es que es clave para entender la vida en la Tierra tal y como la conocemos. En este contexto, son de especial relevancia los procesos inducidos en sistemas celulares por radicación externa, en particular, aquellos localizados en los ácidos nucleicos, ya que éstos son los portadores de la información genética de todos los seres vivos. Sólo la comprensión de la competitividad entre procesos inocuos y lesivos inducidos por radiación llevará al entendimiento del sutil equilibrio entre integridad y cambio, salud y enfermedad, y en términos más globales, inmovilidad y evolución. La Tesis Doctoral que nos ocupa se ha centrado en estudiar los mecanismos de daño a las bases nitrogenadas del ADN/ARN inducidos por radiación UV y/o ionizante a partir de sus principios fundamentales, mediante el uso de modernas metodologías químico-cuánticas. Los avances en el entendimiento del daño primario causado por radiación UV se han centrado, en primer lugar, en el estudio del decaimiento del estado excitado de tipo pi,pi* de la timina mediante los métodos multiconfiguracionales CASSCF y CASPT2, y en segundo lugar, en el estudio de la competición entre los procesos de formación de excímeros entre moléculas de citosina y la transferencia de hidrógeno entre guanina y citosina, usando como modelo el trímero guanina-citosina/citosina. Por otro lado, los procesos de daño secundario abordados son de dos tipos: oxidativos (causados por radiación UV e ionizante) y reductivos (causados por radiación ionizante). Los procesos oxidantes están mediados en su mayoría por el radical OH, que es capaz de adicionarse a los dobles enlaces de las nucleobases. Estas adiciones térmicas se han estudiado haciendo uso de metodologías basadas en el funcional de la densidad, en la teoría de los clústeres acoplados y de tipo multiconfiguracional, mientras que la espectroscopia y la fotoquímica de los correspondientes aductos se ha caracterizado con precisión mediante el protocolo CASPT2//CASSCF. Por otro lado, los procesos reductivos por adición de átomos de hidrógeno al enlace C5=C6 de las pirimidinas se han abordado mediante la fotogeneración del correspondiente aducto en posición C6 y posterior caracterización experimental y teórica, haciendo también uso del protocolo CASPT2//CASSCF, de sus propiedades ópticas en el rango UV-Vis. Por último, los procesos reductivos mediados por adición de electrones de baja energía, que dan lugar a fragmentaciones de las bases de ADN/ARN, se han estudiado en base a la determinación teórica de las afinidades electrónicas, los umbrales de energía de las reacciones de deshidrogenación, los valores mínimos de energía del estado electrónico pi2- y del mapeo de las superficies de energía potencial de los estados electrónicos relevantes a lo largo de las coordenadas de reacción N-H

Hydrated Clusters of Nucleic Acid Bases in Supersonic Beams Probed by Multiphoton Ionization (MPI) Mass Spectrometry

In the present thesis clusters of nucleic acid bases and water are used as model systems of cellular DNA to investigate UV induced radiation damage in the gas phase. A new experimental system has been designed and commissioned to perform multiphoton ionization experiments on hydrogen bonded clusters of the nucleic acid bases: adenine, thymine and uracil, as well as on the related chromophores: 5-fluorouracil and hypoxanthine. As the result of pulsed nanosecond laser irradiation in the wavelength range of 220-230 nm, cluster, monomer and fragment ions were detected using a time-of-flight mass spectrometer. Possible multiphoton ionization pathways of clustered and isolated molecules including the role played by short (singlet) and long-lived (triplet) excited states as well as excited state tautomeric transitions are discussed. Signal intensities as a function of laser pulse fluence were measured. The slope of a logarithmic plot of the signal intensity versus fluence yields the so-called ‘photon order’ and provides information on the number of photons leading to the production of cluster, monomer and fragment ions. The results indicate two-photon ionization for uracil and thymine in dry molecular beams (i.e. photon orders equal to 1.9±0.2 and 1.4±0.1, respectively). An interesting result in the form of photon order equal to 3.0±0.5 has been measured for adenine in a dry molecular beam irradiated with an unfocused laser beam. This suggests a three photon ionization process, however further experimental work is required in order to exclude factors related to stability of the laser beam spatial profile. Hydrated cluster ions with up to 7 water molecules attached to a single uracil and 4 water molecules attached to adenine were unambiguously identified after adding water vapour to the molecular beam source. A maximum of 7 water molecules attached to adenine-uracil base pairs were detected. Possible ionization pathways of such hydrated clusters mediated by excited states tautomeric transitions are discussed. On the basis of photon orders measured under hydrated conditions, it is proposed that sequential MPI processes with 2, 3, and 4 photon absorption lead to production of cluster ions, cluster fragment ions (including protonated monomers), and molecular fragment ions, respectively

Excited state studies of pyramidine bases and radiosensitizing drugs by laser flash photolysis

The mechanism whereby radiosensitizing drugs act in the radio- therapeutic treatment of cancer is yet to be fully elucidated. The prevailing current view (the so-called charge sequestration model) is that cancer cell death is initiated by charge separation induced by the ionising radiation, yielding radical anions (of thymine) and cations (of guanine) in the DNA polymer chain. The radiosensitizer, by virtue of its electron-affinic properties, removes the electron from the (thymine) radical anion, thereby preventing charge recombination and allowing the radical cation to 'fix' the damage via Secondary reactions. To date, most efforts to verify this model have involved the observation of various DNA radical ions by electron spin resonance and pulse radiolysis techniques. However, excited states of DNA or the drug, as well as radical ions, may be involved in the sensitizing action, and there have been a variety of laser flash photolysis studies of reaction between the excited radiosensitizer and ground state nucleic acid bases. The main body of this thesis (Chapter 3) has been to determine, using 249 nm laser flash photolysis, whether reaction in solution occurs between triplet excited nucleic acid bases (in particular thymine and uracil) and (ground state) radiosensitizing drugs. (Such a study has only recently been made feasible by the development of powerful ultraviolet pulsed lasers which are able to produce measurable concentrations of these triplet states in solution; even so, monitoring systems are extended to their limits of detection.) The triplet states of thymine and uracil (in acetonitrile) were quenched by a variety of electron acceptor molecules, including radiosensitizing drugs. The quenching kinetics correlated with the electron affinities of the electron acceptors according to the Weller equation for excited state electron transfer. This constitutes positive evidence that triplet DNA bases can produce the radical cations which are presumed to lead to cell death. Further, in certain cases, the radical anions of the acceptors were observed optically and their yields measured. In Chapter 4 are presented studies of the triplet states of two radiosensitizing drugs, metronidazole and misonidazole (principally by laser flash photolysis), including measurements of their triplet energies. The reduction potentials of these drugs (in acetonitrile) were determined by three methods, which gave comparable results. Attempts were made to develop a fluorescent probe which could be used to measure intracellular concentrations of radiosensitizing drugs. In Chapter 5, the efficient quenching of both excited uranyl ion and triplet benzophenone by nucleic acid bases is detailed. From the results it is concluded that for uranyl ion, the mode of quenching is by an exciplex or reversible charge transfer mechanism, while for triplet benzophenone, chemical quenching occurs. The appendices are mainly concerned with various computer-based techniques developed for this study. An original method is described for analysing oscilloscope transient decays by photographing the oscilloscope screen using a video camera and transferring and digitising the resulting image into a micracomputer screen ram area, where it is manipulated to yield the transient decay constant. Also given is a computer program developed to enable optimum fitting of quenching data to the Weller equation, when the donor oxidation potential is unknown. Finally, evidence for the triplet state of 5-nitroindole is reported. A part of this work has been published, viz. "Electron-transfer Quenching of Triplet State Thymine and Uracil", T.J. Kemp, A.W. Parker, and P. Hardman, J. Chem. Soc, Chem. Commun., 1985, 1377

X-Irradiation of DNA Components in the Solid State: Experimental and Computational Studies of Stabilized Radicals in Guanine Derivatives

Single crystals of sodium salt of guanosine dihydrate and 9 Ethyl Guanine were X-irradiated with the objective of identifying the radical products. Study with K-band EPR, ENDOR, and ENDOR-Induced EPR techniques indicated at least four radical species to appear in both crystals in the temperature range of 6K to room temperature. Three of these radicals (Radicals R1, R2, and R3) were present immediately after irradiation at 6K. Computational chemistry and EPR spectrum simulation methods were also used to assist in radical identifications. Radical R1, the product of net hydrogen addition to N7, and Radical R2, the product of electron loss from the parent molecule, were observed in both systems. Radical R3, in Na+.Guanosine-.2H2O, is the product of net hydrogen abstraction from C1\u27 of ribose group and radical R3 in 9EtG was left unassigned due to insufficient experimental data. Radical R4, the C8-H addition radical, was also detected in both systems. For Na+.Guanosine-.2H2O, R4 was observed after warming the irradiated crystals to the room temperature. But for the 9EtG crystals the corresponding radical form was detected after irradiation at room temperature. Density functional theory (DFT) based computational studies was conducted to investigate the radical formation mechanisms and their stability. Here possibilities of proton transfers from the neighboring molecules were considered. The first approach was to consider the proton affinities of the acceptor sites and deprotonation enthalpies of the donor sites. This approach supported the formation of radicals observed in both systems. The second approach, applied only to the 9EtG system, was based on proton transfers between 9EtG base-pair anion and cation radicals. Even though the charge and spins were localized as expected, the computed thermodynamic data predicted that the proton transfer processes are unfavorable for both anionic and cationic base-pairs. This indicates the need for additional work to draw final conclusions. In addition, DFT methods were used to compute the geometries and hyperfine coupling constants of 9EtG derived radicals in both single molecule and cluster models. The calculated results agreed well with the experimental results

Singlet Oxygen Oxidation of Guanine, 9-Methylguanine and Guanine-Cytosine Base Pair: Dynamics and Kinetics Revealed by Parallel Gas- and Solution-Phase Experiments and Computations

Singlet oxygen (1O2) oxidatively generated damage of DNA gives rise to mutagenesis, carcinogenesis, and cellular death. Guanine is the most susceptible DNA target of 1O2. The related process has been studied over three decades but the mechanism has remained elusive. My thesis research has focused on reaction mechanism, dynamics and kinetics of 1O2 oxidation of guanine, 9-methylguanine and guanine-cytosine base pair, from the gas-phase bare ions, through hydrated clusters, to aqueous solution. Various techniques have been adapted in the work, including 1O2 generation and detection, guided-ion beam tandem mass spectrometry, gas-phase ion-molecule scattering, and on-line spectroscopy and mass spectrometry measurement of solution kinetics. Experimental measurements, corroborated by electronic structure calculations, Rice-Ramsperger-Kassel-Marcus (RRKM) theory and direct dynamics trajectory simulations, have provided insights into the 1O2 oxidation chemistry of guanine. Four projects have been completed, and each of which is described below. In the first project, ion-molecule scattering mass spectrometry was utilized to capture unstable endoperoxides in the collisions of hydrated guanine ions (protonated or deprotonated) with 1O2 at ambient temperature. Theoretical calculations have strongly supported an intermediate structure of 5,8-endoperoxide rather than 4,8-endoperoxide was proposed in literature. Protonation and deprotonation of reactants in the gas phase, vis-à-vis acidic and basic media in solution reactions, lead to different oxidation chemistries starting from initial stage. This project has pieced together reaction mechanisms and dynamics data concerning the early stage of 1O2 induced guanine oxidation, which is missing from conventional condensed-phase studies. In the second experiment of this thesis, gas-phase dry and monohydrated 9-methylguanine (9MG) was utilized as a model compound to examine the early stage oxidation mechanism and dynamics of the guanine nucleoside. Different levels of theory, including Multi-referential CASSCF and CASMP2, were applied for a reliable description of the early-stage reaction potential surface (PES). The oxidation of protonated 9MG is initiated by the formation of a 5,8-endoperoxide via a concerted cycloaddition as protonated guanine. In contrast, the initial stage of deprotonated 9MG oxidation switches to an addition of O2 to the C8 position only. The comparison between the 1O2 oxidation of ionized guanine and 9-methylguanine indicates that the N9-substitution not only affects the reaction mechanism but inhibits the reactivity of guanine toward 1O2. In the third project, a solution-phase kinetic and mechanistic study of 1O2 oxidation of guanine and 9MG was examined at pH 3.0, 7.0 and 10.0, respectively. Oxidation products and the branching ratio were determined, with each structure inferred from collision-induced dissociation (CID) mass spectra. In basic and neutral solutions, the oxidation products of guanine and 9MG are dominated by spiroiminodihydantoin (Sp), whereas in acidic solution guanidinohydantoin (Gh) is the favored product, showing strong pH dependence of oxidation. gem-diol intermediate, which serves as the precursor for the formation of Gh, was detected. On the basis of solution compositions at each pH, first-order rate constants for individual oxidizable species were extracted. That is 3.2 - 3.6 ´ 106 M-1∙s-1 for deprotonated guanine, 1.1 ´ 106 and 4.6 - 4.9 ´ 107 M-1∙s-1 for neutral and deprotonated 9MG, respectively. Guided by density functional theory-calculated reaction potential energy surfaces, transition state theory (TST) was applied to evaluate the kinetics of the 1O2 addition to guanine and 9MG. The comparison of TST predictions with experiment assures that initial 1O2 addition is the rate-limiting for oxidation, and all of the end products evolve from ensuring endoperoxides and/or peroxides which form at an efficiency of £ 2.5% based on previous measurements of the same systems in the gas phase. In the last project, an experimental and trajectory study was reported, focusing on the 1O2 oxidation of gas-phase deprotonated guanine-cytosine base pair [G·C – H]– that is composed of 9HG·[C – H]– and 7HG·[C – H]– (pairing 9H- or 7H-guanine with N1-deprotonated cytosine), and 9HG·[C – H]–_PT and 7HG·[C – H]–_PT (formed by intra-base-pair proton transfer from guanine N1 to the N3 of [C – H]–). Guided-ion-beam mass spectrometry was used to measure the conformer-averaged product and cross section for [G·C – H]– + 1O2. 1O2 collision dynamics with each of the four conformers was simulated at B3LYP/6-31G(d), to explicate conformation-specific reactivities and changes upon and after oxidation. Trajectories showed that 9HG-containing base pairs favor stepwise formation of 4,8-endoperoxide of guanine, whereas 7HG-containing base pairs prefer concerted formation of guanine 5,8-endoperoxide. Oxidation entangles with intra-base-pair proton transfer, and prefers to occur during the time when the base pair adopts a proton-transferred structure. Guided by trajectories, reaction PESs were established using spin-projected density functional theory. PESs indicate that proton-transferred base-pair conformers have lower barriers for oxidation than non-proton-transferred counterparts

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

Computational studies of damaged DNA : an investigation of DNA O-linked adducts formed due to exposure to phenolic carcinogens

This thesis systematically develops a computational model to identify the conformational and base-pairing preferences of PhOdG, 4-Cl-PhOdG, DCP-OdG, TCP-OdG, and PCP-OdG by gradually increasing the size of the system also structural properties of unsubstituted O-linked. All adducts at nucleoside level adopted syn conformation. Moreover, effect of protonation at N3 and N7 site on the structural properties and deglycosilation barrier of adducted guanosine was probed. It was highly desirable to include O-linked phenolic as well as C8-dG adducts into a DNA strand in order to understand the detrimental effect of them and the conformational distortion of double helix duplex the desired modified base into NarI DNA duplex through the employment of molecular dynamic simulation (MD) was assessed. The anti-conformation against cytosine is preferred with this model for all adducts and syn conformer for all unsubstituted O-linked and ortho and para Clinked structures against guanine mismatch is the lowest energy structure.University of Lethbridg

Quantum Chemical Calculation of Electron Ionization Mass Spectra

This thesis reports the computation of electron ionization (EI) mass spectra using a method that combines statistical theory and molecular dynamics. Due to the complexity of the unimolecular reaction space, not all competing fragmentation pathways can be fully treated in an ab initio way using a purely statistical framework. The main idea behind the present simulation protocol is to use approximate quantum chemical potential energy surfaces and simple internal energy distributions to discover the reaction pathways and barriers, and thus the relative rate constants automatically. This idea was proposed, implemented and published in late 2013 by my thesis supervisor Stefan Grimme, and termed QCEIMS. The first part of this thesis gives a brief overview over the physical chemistry of EI mass spectrometry and the most important theoretical methods that I have used. These involve finitetemperature density functional theory and the semi-empirical Geometries, Frequencies and Noncovalent Interaction eXtended Tight Binding Hamiltonian (GFN-xTB). The energies and forces computed at these levels of theory are the input for the subsequent Born-Oppenheimer molecular dynamics simulations. The second part deals with the application of finite-temperature density functional theory. The results show that the fractional occupation number weighted density ρ FOD can be used as a measure for static electron correlation in biradicals and related systems, and that the fractional occupation numbers can be useful for the first guess at a multiconfigurational wave function. Furthermore, potential energy surfaces along model reaction coordinates are explored and the transferability of the ρFOD concept to semi-empirical quantum chemistry is shown. The third part shows the main results of this work related to EI mass spectrometry. In Chapter 4, the literature is reviewed and the “Quantum Chemistry Electron Ionization Mass Spectra” (QCEIMS) method is presented. It is then evaluated concerning the assignment of the charge to a fragment using a series of ethanol homologues. A small mass spectrometric benchmark study is also included, showing that isomers can be distinguished by QCEIMS predicted EI mass spectra, provided their fragmentation pathways differ substantially. In Chapters 5, 6, and 7 QCEIMS applications to large drug molecules, the nucleobase adenine and other nucleobases, are presented. For each case, the fragmentation pathways are analyzed, thereby elucidating the structures of the fragment ions. Finally, in Chapter 8, predicted EI mass spectra for 23 compounds across the whole periodic table are shown. This has been made possible by V. Ásgeirsson’s implementation of GFNxTB into QCEIMS. This robust and efficient method performs remarkably well for organic molecules as well as organometallic compounds and main group inorganic systems while reducing the computational cost by a factor of 1,000 when compared to hybrid density functional calculations