iv Abstract Subject: Determination of structure and dynamics of biomolecules by theoretical calcu- lations of NMR spectroscopic parameters Author: Ladislav Benda, ladislav.benda@gmail.com Department/Institute: Institute of Organic Chemistry and Biochemistry, AS CR Supervisor: Dr. Vladim'ır Sychrovsk'y, Institute of Organic Chemistry and Biochemistry, AS CR, vladimir.sychrovsky@uochb.cas.cz Abstract: This doctoral work was focused on theoretical modeling of nuclear magnetic resonance (NMR) parameters in peptides and nucleic acids. Dependences of NMR para- meters on molecular structure and solvation were primarily modeled. Great emphasis was put on the comparison of the calculated data with the NMR experiment. The molecular models studied included the l-alanyl-l-alanine di-peptide (AA) and the phosphate group of nucleic acid backbone. Conformations of all three charged forms of AA in solution were determined and the respective pH-induced changes of experimental NMR chemical shifts and nuclear spin-spin coupling constants were explained. Dependences of NMR cross-correlated relaxation rates on the AA backbone geometry were calibrated. The 31 P NMR parameters in nucleic acid phosphate were systematically calculated in dependence on the backbone conformation and the phosphate solvation pattern. Qualitative rules...

Since the development of the ruthenium containing precatalysts Grubbs 1 (1) and Grubbs 2 (2), there was an increase in the development of new precatalysts. The NMR characterization could not cope with this. The NMR characterization mainly consists of 1H, 31P, COSY and rarely 13C. Due to the high natural abundance of 1H and 31P (99.98% and 100%), these experiments could be carried out quickly and easily. The only change that had to be made was to the spectral width, to accommodate the carbene signal (Ru=CH) between δ 20.02 and δ 17.32 ppm. The lack of 13C characterization is attributed to the low natural abundance of these nuclei that is only 1.10% and the lack of published parameters. Furthermore, the broad spectral width of 300 ppm increases the difficulty because the number of scans has to be increased to increase the sensitivity of the spectra and obtain useful data. In this study the precatalyst 1 was used to learn the NMR technique as well as to acquire the NMR parameters. 2 and two other commercial Grubbs-type precatalysts 3 and 4 underwent NMR characterization so that acquired values could be compared with the literature. Six other non-commercial Grubbs-type precatalysts 5-10 were synthesized and characterized. Due to the instability of the precatalysts and taking into account the duration of these experiments, the characterization was done over three steps. The first step was to do the following experiments: 1H, COSY, HSQC and HMBC, which took four hours. The next step was the DEPT135 experiment of three hours, and finally the 13C experiment of seven hours. The maximum amount of information could be obtained in this way. The combined NMR parameters for this study was obtained and used to characterize the Grubbs-type precatalysts 5-10 partially. Due to the large amount of overlapping peaks in the aromatic and alkane areas the resolution was not sufficient for full characterization. / MSc (Chemistry), North-West University, Potchefstroom Campus, 2014

Since the development of the ruthenium containing precatalysts Grubbs 1 (1) and Grubbs 2 (2), there was an increase in the development of new precatalysts. The NMR characterization could not cope with this. The NMR characterization mainly consists of 1H, 31P, COSY and rarely 13C. Due to the high natural abundance of 1H and 31P (99.98% and 100%), these experiments could be carried out quickly and easily. The only change that had to be made was to the spectral width, to accommodate the carbene signal (Ru=CH) between δ 20.02 and δ 17.32 ppm. The lack of 13C characterization is attributed to the low natural abundance of these nuclei that is only 1.10% and the lack of published parameters. Furthermore, the broad spectral width of 300 ppm increases the difficulty because the number of scans has to be increased to increase the sensitivity of the spectra and obtain useful data. In this study the precatalyst 1 was used to learn the NMR technique as well as to acquire the NMR parameters. 2 and two other commercial Grubbs-type precatalysts 3 and 4 underwent NMR characterization so that acquired values could be compared with the literature. Six other non-commercial Grubbs-type precatalysts 5-10 were synthesized and characterized. Due to the instability of the precatalysts and taking into account the duration of these experiments, the characterization was done over three steps. The first step was to do the following experiments: 1H, COSY, HSQC and HMBC, which took four hours. The next step was the DEPT135 experiment of three hours, and finally the 13C experiment of seven hours. The maximum amount of information could be obtained in this way. The combined NMR parameters for this study was obtained and used to characterize the Grubbs-type precatalysts 5-10 partially. Due to the large amount of overlapping peaks in the aromatic and alkane areas the resolution was not sufficient for full characterization. / MSc (Chemistry), North-West University, Potchefstroom Campus, 2014