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DISSERTATION O Attribution COPYRIGHT AND CITATION CONSIDERATIONS FOR THIS THESIS/ DISSERTATION o Attribution — You must give appropriate credit, provide a link to the license, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use. o NonCommercial — You may not use the material for commercial purposes. o ShareAlike — If you remix, transform, or build upon the material, you must distribute your contributions under the same license as the original. How to cite this thesis Surname, Initial(s). (2012) Title of the thesis or dissertation. PhD. (Chemistry)/ M.Sc. (Physics)/ M.A. (Philosophy)/M.Com. (Finance) etc. [Unpublished]: University of Johannesburg. Retrieved from: https://ujcontent.uj.ac.za/vital/access/manager/Index?site_name=Research%20Output (Accessed: Date). FORMATION OF GLYCINE IN THE INTERSTELLAR MEDIUM: COMPUTATIONAL STUDIES ON VARIOUS POSSIBLE REACTION PATHS by ZANELE PRECIOUS NHLABATSI Student Number: 200826464 Thesis Submitted in fulfilment of the requirement for the degree PHILOSOPHIAE DOCTOR in CHEMISTRY in the FACULTY OF SCIENCE of the UNIVERSITY OF JOHANNESBURG Supervisor: Dr. SANYASI SITHA DECLARATION I hereby declare that this thesis, which I herewith submit for the research qualification DOCTORAL DEGREE IN CHEMISTRY to the University of Johannesburg, Department of Chemistry, is apart from the recognised assistance of my supervisors, my own work and has not previously been submitted by me to another institution to obtain a research diploma or degree. _______________________________ on this ____ day of _______________ (Candidate) _______________________________ on this ____ day of _______________ (Supervisor) i DEDICATION I dedicate this work, firstly to GOD ALMIGHTY who made all this possible, my dad Samson Masayidi Nhlabatsi, my mother Zodwa Norah Bhembe, my late sister, Winile Lungile Nhlabatsi (rest in peace Mantini waLanga),and my loving fiancé, and soon to be Husband, Derrick Themba Khumalo. I truly thank you all for your love and support. Last but not least, to the Holy Spirit, who is my counselor, helper and my comforter. Ephesians 3:20 ………………….Now to Him Who is able to do immeasurably more than ALL we ask or imagine, according to His POWER that is at work in us. ii ACKNOWLEDGMENTS Special thanks to God Almighty for HIS loving support and guidance. I wish to greatly acknowledge the following people for their contributions towards the success of this project: Dr. Sanyasi Sitha for his great supervision, advice and mentorship and guidance throughout this work. Prof. I. D. Isabirye (North-West Universty). Prof. R. W. M. Krause (Rhodes University) and Prof. L. M. Cele (Tshwana University of Technology). Apostle Bheki and Pastor Zandile Thwala for their vital spiritual guidance together with Pastor Andrew Mwaikambo and Pastor Themba Manana (LGTG). Computational Chemistry Group Priya Bhasi and Vijay Miriyala for their assistance in many ways. Mr Ali Ilunga Kabeya. Thanks for your all your assistance. Mr Martin Magu and Ephraim Marondedze for your assistance. Everyone who is part of the Department of Chemistry. My siblings, both brothers and sisters, Mduduzi and Thuli Dlamini, and all my family members. iii My dad, Nhlanhla Nhlabatsi and all the Nhlabatsi members, my friends, Refiloe Mota, Noluthando Dlamini, Samkelisiwe Motsa, Dumsile Nyembe, and Xolile Mkoko (for being good friends). National Research Foundation (NRF) for financial support, and the University of Johannesburg for support. iv The work presented in this thesis has been published in peer reviewed journals and presented in national and international conferences for poster presentations. 1. PUBLICATIONS 1. Zanele P. Nhlabatsi, Priya Bhasi and Sanyasi Sitha, “Possible interstellar formation of glycine from the reaction of CH2=NH, CO and H2O: catalysis by extra water molecules through the hydrogen relay transport” Physical Chemistry Chemical Physics 18 (2016) 375-381. 2. Zanele P. Nhlabatsi, Priya Bhasi and Sanyasi Sitha, “Possible interstellar formation of glycine through a concerted mechanism: a computational study on the reaction of CH2=NH, CO2 and H2” Physical Chemistry Chemical Physics, 18 (2016) 20109-20117. 2. OTHER PUBLICATIONS 1. Lungile P. Lukhele, Rui W.M. Krause, Zanele P. Nhlabatsi, Bhekie B. Mamba, Z Maggy NB Momba “Copper and Silver Impregnated Carbon Nanotubes incorporated into Cyclodextrin Polyurethanes for the Removal of Bacterial and Organic Pollutants in Water” Desalination and Water Treatment27 (2011) 299-307. 2. Sanyasi Sitha, Linda L. Jewell, Priya Bhasi, Zanele P. Nhlabatsi, Vijay M. Miriyala “Potential energy surface of the cation-neutral hydroamination reaction: a computational study on the role of an ion-molecule complex in the reaction pathway” Tetrahedron70 (2014) 7906-7911. 3. Priya Bhasi, Zanele P. Nhlabatsi, Sanyasi Sitha, “Reaction between HN and SN: a possible channel for the interstellar formation of N2 and SH in v the cold interstellar clouds”Physical Chemistry Chemical Physics17 (2015) 32455-32463. 4. Priya Bhasi, Zanele P. Nhlabatsi and Sanyasi Sitha, Possible interstellar formation of phosphorus analogue of hydrazoic acid: A computational study on the reaction between HN and PN” Computational and Theoretical Chemistry1078 (2016) 129–137. 5. Priya Bhasi, Zanele P. Nhlabatsi and Sanyasi Sitha, “ Expanding the applicability of electrostatic potentials to the realm of transition states” Physical Chemistry Chemical Physics, 18 (2016) 13002-13009. 3. CONFERENCES 1. Z. P. Nhlabatsi, P. Bhasi, S. Sitha, Pontential energy surface of OH + NO2 HOONO reaction: A computational study, 41st National Convention of the South African Chemical Institute, Poster Presentation, 1-6 December 2013, WSU (Water Sisulu University), South Africa. 2. Z. P. Nhlabatsi, P. Bhasi, S. Sitha, A Computational study on dipole moment and hyperpolarizability of pyridine-borobenzine adduct, 10th Theoretical Chemistry Conference in Africa, Poster Presentation, 6–11 April 2014, University of Venda, Thohoyandou, South Africa. 3. Z. P. Nhlabatsi, P. Bhasi, S. Sitha, Computational study on the Formation of Glycine in the Interstellar Medium (ISM), 10TH Congress of the World Association of Theoretical and Computational Chemists WATOC 2014, Poster Presentation, 5-10 October 2014, Santiago,Chile. vi 4. Z. P. Nhlabatsi, P. Bhasi, S. Sitha, Computational study on the Formation of Glycine, CHPC (Centre for High Performance Computing) National Meeting 2015, 30TH November – 4TH December 2015, Poster Presentation, CSIR (Council of Scientific and Industrial Research) International Convention Centre, South Africa. 4. WORKSHOPS ATTENDED 1. Workshop hosted by Centre for High Performance Computing (CHPC) and Nelson Mandela Metropolitan University (NMMU), 26TH June – 2ND July 2016.Course covered the concepts and theory of parallel computers, and programming for parallel systems with MPI and OpenMP, and possibly CUDA or other co-processors, using the C, Fortran or python programming languages. vii ABSTRACT “How the most essential life elements, i.e., amino-acids, were formed in the interstellar medium (ISM)?” and “What are their roles in the evolution of life in our solar system?” are the two most intriguing questions, which are not yet answered exclusively as indicated in the works of many researchers. Among all the natural amino-acids, glycine (H2N-CH2-COOH) is not only an important biologically active molecule but also is the simplest as well as smallest amino-acid that can be found in all the biological entities found in the earth. The era of the astronomical search for glycine began as soon as the laboratory spectra for it were made available in 1978. Since then astrophysicists have been searching for this glycine in the ISM and many decades have been passed but still without any success. This is in spite of the fact that many amino-acid including the glycine have been found on meteorites, and moreover the distinct isotopic signature of those amino-acids are indicative of their extraterrestrial origin.However, detection of glycine in the interstellar medium is still ambiguous and the major problem arising in the analysis of a large cluster of weak lines collected through various high resolution telescopes. In this present work, using computational calculations many possible as well as favourable reaction paths, which can lead to the formation of Glycine in the interstellar conditions, have been investigated. Detailed mechanisms of those possible reaction paths have been investigated and also aptness of their feasibilities in the ISM has been discussed in the light of the prevailing interstellar conditions. From the mechanistic analysis of these possible reaction paths, it was observed that two of them show concerted type of mechanism, whereas others proceed through multi-stepped paths. One such concerted reaction discussed in this thesis encompasses the reaction of CH2=NH, CO and H2O leading to the formation of glycine. It was observed that this reaction viii proceeds through a large barrier and thus indicating it’s feasible only in the hot-cores of interstellar medium. When the same reaction was investigated in the excess of water molecules where discrete water molecules were treated explicitly as part of reactants, it was surprising to find that with the presence of three or more water molecules, the barrier height reduced so drastically that the reaction behaves like a barrierless type of reaction. Mechanistic study indicates that the extra water molecules exhibit catalytic role through
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