Title: Study of C-C coupling of dienes catalyzed by ruthenium (II) complexes. Author: Bc. Eva Hanikýřová Department: Department of Organic Chemistry Supervisor: Mgr. Jana Roithová, Ph.D. Abstract Transition metal catalyzed cycloadditions have contributed extensively to organic synthesis. The use of ruthenium complexes in those reactions gain importance due to their demonstrated ability in the catalytic carbon-carbon bond formations via ruthenacycle intermediates. In our studies, we have concentrated on the interaction between ruthenium (II) and alkenes using mass spectrometry with electrospray ionization. This technique allows to investigate ruthenium complexes in the ionized states, and allows to investigate these structures by using MS/MS analyse. Our experimental research was complemented by quantum chemical calculations using Density functional theory. The research leads to a more detailed understanding to Ruthenium complexes with unsaturated hydrocarbons reaction mechanism. Key words Gas-phase chemistry, Reaction mechanisms, Electrospray Ionization, Catalyst, [CpRu(CH3CN)3]PF6, Mass Spectrometry

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We report infrared photodissociation (IRPD) spectra for the D2-tagged titanium oxide cluster anions (TiO2)−n with n = 3–8 in the spectral region from 450 to 1200 cm−1. The IRPD spectra are interpreted with the aid of harmonic spectra from BP86/6-311+G* density functional theory calculations of energetically low-lying isomers. We conclusively assign the IRPD spectra of the n = 3 and n = 6 clusters to global minimum energy structures with Cs and C2 symmetry, respectively. The vibrational spectra of the n = 4 and n = 7 clusters can be attributed to contributions of at most two low-lying structures. While our calculations indicate that the n = 5 and n = 8 clusters have many more low-lying isomers than the other clusters, the dominant contributions to their spectra can be assigned to the lowest energy structures. Through comparison between the calculated and experimental spectra, we can draw conclusions about the size-dependent evolution of the properties of (TiO2)−n clusters, and on their potential utility as model systems for catalysis on a bulk TiO2 surface.

We use cryogenic ion trap vibrational spectroscopy in combination with quantum chemical calculations to study the structure of mono- and dialuminum oxide anions. The infrared photodissociation spectra of D2-tagged AlO1-4 − and Al2O3-6 − are measured in the region from 400 to 1200 cm−1. Structures are assigned based on a comparison to simulated harmonic and anharmonic IR spectra derived from electronic structure calculations. The monoaluminum anions contain an even number of electrons and exhibit an electronic closed-shell ground state. The Al2O3-6 − anions are oxygen-centered radicals. As a result of a delicate balance between localization and delocalization of the unpaired electron, only the BHLYP functional is able to qualitatively describe the observed IR spectra of all species with the exception of AlO3 −. Terminal Al–O stretching modes are found between 1140 and 960 cm−1. Superoxo and peroxo stretching modes are found at higher (1120-1010 cm−1) and lower energies (850-570 cm−1), respectively. Four modes in-between 910 and 530 cm−1 represent the IR fingerprint of the common structural motif of dialuminum oxide anions, an asymmetric four-member Al–(O)2–Al ring.

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Presently, much research has been completed focusing on metal coordination complexes in the liquid phase but very little in terms of the gas phase. The purpose of this research is to further investigate these conditions and learn more about the reactions that can occur using Electrospray Ionization Quadrupole Time-of-Flight Mass Spectrometry (ESI QToF MS). This research focuses on Nickel (II) and Iron (III) Nitrate solutions in combination with five ligands: 2,2’-Bipyridine, 4,4’-Bipyridine, 2,2’-Bipyridine-4,4’-Dicarboxylic Acid, 1,10-Phenanthroline and the Baker Group’s SNS Ligand. Observations of these complexes were restricted to the monocations. Those combinations that successfully coordinated in the gas phase were subjected to further analysis to determine their fragmentation pathways under specific conditions. To investigate their interactions, studies were conducted using three different mixing techniques. These techniques included a pre-mixed single-spray solution, a dual-spray injection method, and the TRESI (time-resolved electrospray ionization) method. By using all three methods, the compounds’ ability to react in solution over time can be compared to real-time mixing in both the gas and liquid phases, via dual-spray and TRESI techniques respectively. Further experimentation took place on target complexes, created by each of the ten combinations of starting compounds, to further investigate the gas phase properties and fragmentation patterns that exist. It was observed that most experiments with the Nickel (II) Nitrate solution were successful with all three methods, while the Iron (III) Nitrate however created some problems. In general, single-spray analysis gave the best results compared to dual-spray, which was ineffective for some combinations, particularly the 2,2’-Bipyridine-4,4’-Dicarboxylic Acid and SNS ligands. It was found that both the 2,2’-Bipyridine and 4,4’-Bipyrdine combinations produced very similar results despite their respective bidentate and bridging coordination tendencies. The TRESI method provided limited information due to the delayed reaction times with some combinations. Overall, this work proved useful in its ability to compare metal coordination complex formation in solution and gas phases.

Mass spectrometry (MS) is emerging as an important tool for studying protein and protein complexes. When applying this tool, it is important to understand and investigate whether some of the intramolecular and intermolecular interactions of proteins in solution and are maintained in the gas phase. To investigate if some of these interactions are maintained in the gas phase, we develop and use a method in which the electron-transfer dissociation (ETD) spectra of native proteins are compared with spectra from ETD followed by low amplitude collisional induced dissociation (CID). From these experiments, we find that some intramolecular interactions from solution are maintained in the gas phase for ubiquitin and beta-2-microglobulin (β2m). However, using these approaches, cytochrome c’s structure in the gas phase appears to be quite different than its structure in solution. We also investigated if ETD spectra of intact protein complexes reflect contact site information in these complexes

Our group has been studying chiral recognition in gas phase using mass spectrometry for more than 10 years. We are interested in gas phase studies of fundamental interactions because the gas phase avoids complications and masking effects that may arise upon solvation. Therefore, the results of gas phase experiments can be directly compared with those of high-level computational studies. In chapter 2, I studied the roles of hydrogen bonding and pi stacking in gas phase chiral recognition between aromatic crown molecules and aromatic amines. High affinity between host and guest doesn't necessarily result in better recognition. If the affinity is too high, both host enantiomers will bind to the chiral guest very tightly so little discrimination is observed. In order to build an efficient chiral recognition system, we need to select a host and guest that have intermediate binding affinity. Hydrogen bonding is another significant factor that controls the host-guest affinity. In the case of host 1, more hydrogen bonds results in better recognition. We also find that the degree of chiral recognition is greater in the gas phase than in solution. Modeling at the B3LYP/6-31G* level is qualitatively correct, but quantitative agreement with experiment is poor. Inspired by Rekharsky's work which shows successful induced chiral recognition with an achiral host (cucurbituril) in solution, we tested the possibility of applying cucurbiturils as gas phase chiral recognition containers in chapter 5. Conferring chirality on cucurbiturils makes the chiral recognition happen in a restricted space, which might strengthen or hinder the discrimination. By comparing our results with Rekharsky's, we showed the role of solvent in this chiral recognition process. In the gas phase, the enantiodiscrimination does not happen between the "leaving MP" and the "approaching" stronger chiral binder. Because hydrophobic effects are absent in the gas phase, it is possible that the hydrophobic methyl substituent of 2-methylpiperazine and the stronger chiral binder might not be simultaneously included inside the cavity. Therefore, we do not observe enantiodiscrimination in gas phase. The dissociation experiment for the CB[7] ternary complex shows that sec-butylamine binds externally to the CB[7] host. Further, the heterochiral diastereomer is more stable than the homochiral diastereomer. This conclusion is consistent with Rekharsky's result in solution. For more than 15 years, the most common ionization method in our lab has been electrospray ionization. However, ESI is subject to problems with ion suppression, especially when the sample is a mixture or it has a high concentration of salt. The easily ionized molecules tend to scavenge the available charges in the spray solution and dominate the resulting ion population even though other compounds may be present in high abundance. Nanoelectrospray usually yields cold ionization, and analyte suppression can be greatly reduced at nanospray flow rates. Therefore, we constructed a porous polymer monolith (PPM) nanospray emitter similar to that described by Oleschuk et al. and characterized the properties of the PPM emitter. This work is described in chapter 3. Our tests show that this PPM nanospray emitter possesses some special analytical properties: decreased ion suppression, quite stable spray, strong signal intensity and good reproducibility in emitter performance. Chapter 4 deals with the application of the new CRAFTI method to negative ions. CRAFTI stands for cross-sectional areas by Fourier transform ICR. The CRAFTI technique measures collision cross sections, providing a probe of the gas phase conformations of supramolecular complexes. Our preliminary work has shown that CRAFTI is applicable to positive ions, so we further demonstrate the application of the newly-developed method to negative ions in this work. Based on the fact that the experimental cross sections correlate linearly with the theoretical values, we have obtained evidence that CRAFTI is a valid method for negative ions. However, some problems remain. First, we are still working to understand the physical meaning of the CRAFTI cross sections. The absolute values we obtain are generally greater than those obtained from momentum transfer cross section calculations modeled in helium. Second, the precision of the measurements (currently about 2-3%) is still larger than we desire. We need to carefully tune the excitation and isolation amplitudes to make the signal strong and monoisotopic for weak ions. CRAFTI is a very promising and attractive method because FT-ICR provides accurate mass-to-charge measurement along with the cross section measurement. In other words, one technique is sufficient to obtain the shape, size and mass of a molecule simultaneously.

A molecular beam apparatus has been designed and constructed for the purpose of studying gas phase interactions between ions and molecules. A neutralization-reionization technique has been developed which permits the lifetimes of some short lived molecules to be estimated. In this way the existence of He₂, HeH and HeD molecules has been demonstrated but similar experiments have produced no evidence for the existence of H₃, D₃ or D₂H molecules with the same order of lifetimes. A collisional dissociation technique has been devised which permits analysis of molecular ions in beams and demonstrated the existence of He₃⁺ ions in low temperature helium discharges. / Thesis / Doctor of Philosophy (PhD)

<p> Small nitrogen or silicon containing molecules and their ionized counterparts have attracted a great deal of attention from both experimentalists and theoreticians. This is because such species may play an important role in interstellar chemistry. Small nitrogen containing heterocyclic molecules and ions are of biological importance and are of increasing interest to chemists and biochemists. Therefore, studying the chemistry of such species in the gas phase as solitary ions and neutrals is of considerable importance.</p> <p> The ions studied in this thesis were generated in the rarefied gas phase of the mass spectrometer by (dissociative) electron ionization of selected precursor molecules. The characterization of their structure and reactivity was realized using a variety of tandem mass spectrometry based techniques. These include metastable ion spectra to probe the dissociation chemistry of the low energy ions and (multiple) collision experiments to establish the structure (atom connectivity) of the stable ions. The technique of neutralization-reionization mass spectrometry (NRMS) was used to probe the structure and stability of the neutral counterparts of the ions. The results of theoretical calculations involving the CBS-QB3 model chemistry formed an essential component in the interpretation of the experimental findings.</p> <p> The above approach was used to study various isomers of the CH2N2•+ family of ions, in particular the elusive carbodiimide ion HN=C=NH•+. Unlike other isomers including ionized cyanamide H2N-C≡N•+ and nitrilimine HC=N=NH•+, the carbodiimide ion could only be identified by a strategy that involved the use of the technique of collision-induced dissociative ionization (CIDI) mass spectrometry. Guided by the results of the theoretical calculations, the carbodiimide ion, the global minimum on the CH2N2•+ potential energy surface, could also be generated by the molecule-assisted isomerization of its 1,3-H shift isomer H2N-C≡N•+. This occurs through an ion-molecule interaction with a single molecule of H2O under conditions of chemical ionization : a process termed proton-transport catalysis.</p> <p> The amino-substituted carbodiimide ion, H2N-N=C=NH•+, and nine more isomers have all been calculated to be minima on the potential energy surface of the CH3N3•+ family of ions. Four of these, viz. the aminocarbodiimide ion, the aminonitrilimine ion, H2N-C=N=NH•+, the cyclic C-aminoisodiazirine ion, and the ionized biradical, H2N-N=C(H)=N•+, were generated and characterized by tandem mass spectrometry as stable species in the gas phase. Neutralization-reionization experiments show, in agreement with the CBS-QB3 computational results, that aminocarbodiimide and aminonitrilimine are stable species in the gas phase.</p> <p> Next, the α-distonic ions of a number of heterocyclic nitrogen-containing compounds including pyrazole, pyridazine and aminopyrazine, were characterized and differentiated by tandem mass spectrometry. The stabilities of the neutral counterparts of the ylid ions and their conventional isomers were probed by neutralization-reionization experiments. From these experiments, it follows that the ylid ions have stable neutral counterparts, as predicted by the theoretical calculations.</p> <p> The final component of this work deals with the chemistry of a silicon containing species of potential interest in interstellar chemistry. The reactions of protonated silicic acid, Si(OH)3+, and the mechanisms of these reactions were studied using tandem mass spectrometric experiments and CBS-QB3 model chemistry. The low energy (metastable) ions of Si(OH)3+ dissociate by loss of H2O and SiO2 to form O=SiOH+ and H3O+ ions. Neutralization-reionization experiments show that Si(OH)3• is a stable species in the rarefied gas phase.</p> / Thesis / Master of Science (MSc)