Understanding the structure-property relationships of amino acids-the molecular building blocks of life Aravindhan Ganesan Dissertation submitted in fulfillment of requirements for the degree of Doctor of Philosophy Environmental and Biotechnology Centre Faculty of Life & Social Sciences Swinburne University of Technology Victoria, Australia 2013 ©2013 Aravindhan Ganesan Abstract Amino acids are significant molecular building blocks of proteins. Only 20 natural amino acids, whose structures differ in their side chain ‘R-’ groups, control the structures, functions and selectivity of almost all the proteins in biology. The structure-properties of the amino acids must be revealed, in order to understand the methodical behind the nature’s choices in using them as ‘building blocks’. There are several molecular level details of the amino acids, which are still unknown or limitedly known. In this project, the electronic structures, properties and dynamics of the aliphatic and the aromatic amino acids under isolated and defined environmental conditions are studied quantum mechanically. A rich tool chest of ab initio and density functional theory (DFT) methods has been employed. The impacts of alkyl side chain groups on the structure-properties of the aliphatic amino acids are revealed in the gas phase. A number of properties including geometries, molecular dipole moments, ionization energies and spectra, charge re-distributions, vibrational spectra (IR and Raman), vibrational optical activity spectra (VOA), molecular orbitals and momentum spectra are investigated. Dual space analyses (DSA) has been employed as an efficient analytical tool to understand the electronic structures of the amino acids in both the coordinate space and momentum space. Our quantum chemical calculations are validated against the synchrotron-sourced and other experiments, whenever possible. It is revealed that there is no single universal model that is the best for the calculations of all the properties of the amino acids. Different models are able to produce optimal results for different properties and calculations. Electron structure and properties of L-phenylalanine is revealed by studying the interactions of its functional groups (COOH, NH2 and phenyl) and its fragment schemes (alanine/benzene and glycine/toluene) in the gas phase. In order to understand the interactions of the functional groups, the structures of L-Phe and its derivatives, 3-phenylpropionic acid (PPA) and 2- phenethylamine (PEA) are comparatively studied. The ‘fragments-in-molecule’ approach, along with DSA, is employed to study the interactions between the different fragment schemes of phenylalanine, such as alanine/benzene and glycine/toluene. The results indicate that the inner shell of phenylalanine is dominated by the functional group interactions, while the fragment interactions are vital in the valence space of phenylalanine. Further, the phenyl i ring in the phenylalanine serves as a buffer to resist the changes, which is useful for stabilizing the amino acid in the gas phase. The spectroscopy and orbital properties of L-phenylalanine (R=phenyl ring) are combined together with those of L-tyrosine (R=phenol group), in order to understand the structure- properties of L-dopa (R=catechol group), an important neurotransmitter drug, in the gas phase. The impacts of hydroxyl group attachments on the electronic properties of these aromatic molecules are studied in detail. Our quantum mechanical calculations clearly identify the electronic and molecular properties that differentiate the drug molecule (i.e. L- dopa) from its amino acid precursors, L-phenylalanine and L-tyrosine. Next, the dynamics and inter-molecular interactions of the phenylalanine-copper (II) complexes and micro-solvation processes (H2O, n=0-4) are studied using the DFT calculations and Car-Parrinello molecular dynamics (CPMD) simulation. The structures of the Phe-Cu2+ complexes with up to four water molecules are studied. The results indicate that the phenylalanine moiety appears to be in the neutral form in the isolated and mono-hydrated complexes, but in the zwitterionic form in the other hydrated systems. The present CPMD simulations reveal that the maximum coordination number of Cu2+ in the presence of phenylalanine under micro-solvation does not exceed four: the oxygen atoms from up to three water molecules and one carboxyl oxygen atom of phenylalanine. Any excess water molecules will migrate to the second solvation shell. Moreover a unique structural motif, 2+ (N)H···O(3)···H2O– Cu is present in the micro-solvated complexes with more than two water molecules, which is recognized to be significant in stabilizing the structures of the complexes. Extensively rich information of the structures, energetics, hydrogen bonds and dynamics of the lowest energy complexes are discussed. The results presented in this thesis, therefore, help to elucidate the impacts of inter- and intra- molecular interactions on the structure-properties of the amino acids, as well as showcase a successful synergy of our theoretical calculations with the experiments. ii Specially devoted to ‘my beloved’ iii Acknowledgments I am delighted to express my deep sense of gratitude to my principal supervisor, Professor Feng Wang, for kindly accepting to supervise my PhD project and also offering me a postgraduate scholarship from her Vice Chancellors research award at Swinburne. Her kind support, encouragement and suggestions throughout my candidature cannot be simply expressed in words. She offered me numerous opportunities to learn and develop my skills to become a responsible and independent researcher in future. All the achievements that I have seen during my PhD candidature could not have been possible without her. ‘Professor Wang, Thank you very much is all I can say.’ I would also like to sincerely thank my other supervisor, Professor Michael J Brunger in Flinders University, who has also been very supportive and encouraging during the course of my project. I humbly acknowledge the top-up grant offered by him from the ARC Centre of Excellence for Antimatter-Matter studies, Flinders University node. I would also like to extend my sincere thanks to Professor Paolo Carloni, who is also my external supervisor, for his kind support and hospitality during my six months visit to his laboratory in German Research School of Simulation Sciences. All the members in Professor Carloni’s group, especially Dr. Emiliano Ippoliti and Dr. Jens Dreyer, are thanked for providing me a friendly environment during my stay at GRS. Dr. Ippoliti has been very kind and patient in helping me learn the CPMD package to carry out my simulations. His directions and suggestions have been very useful for me to master the skills. And Dr. Dreyer has also been equally supportive and collaborative. Another person, who really spent more time in helping with CPMD, is Dr. Julen Larrucea. I enjoyed all our fascinating discussions about molecular dynamics in Skype. I would also like to thank Professor Kevin C Prince in Elettra Synchrotrone, Trieste, for providing his XPS measurements of the amino acids, which have been useful to validate the calculations in this thesis. I also acknowledge the support and encouragements of Professor Richard Sadus and Professor Billy Todd in Swinburne University. iv DAAD Germany research grant and Tuition fee scholarships from Swinburne University are kindly acknowledged. The computing time required to perform the simulations presented in this thesis has been generously supported by the National Computational Infrastructure (NCI), VPAC, VLSCI and Swinburne’s Green machine. My special thanks go to VLSCI that offered me travel grants to support my attendance in prestigious conferences including SC10 and MM2012. I wish to also thank all my friends in Swinburne University and outside. I greatly appreciate the people in my group, Dr. Ma, Dr. Lalitha, Dr. Fangfang, Anoja, Marawan and Narges, for offering me an excellent friendly environment, which I will always cherish. I am really very proud to have a beautifully gifted family, my mother, father, father-in-law, mother-in-law, sister and brother-in-law, GP and my sweet little Netra darling. Their affection remains true strength in every step of my career. My dear wife, Mrs. Subha Aravindhan is the one person, whose presence makes me complete. Thank you very much dear, for your extra-ordinary patience, dedication, love and understanding. Last but not the least, my thanks to ‘SAI’, you have always been there for me. v Declaration I hereby declare that the thesis entitled “Understanding the structure-property relationships of amino acids-the molecular building blocks of life”, which is submitted in fulfillment of the requirements for the degree of Doctor of Philosophy in the Swinburne University of Technology, is my own work. To the best of my knowledge and belief, it contains no material previously published or written by another person, except where due references are made in the text of the thesis. Any contribution made to the research by colleagues, with whom I have worked at Swinburne or elsewhere, during my candidature, is fully acknowledged. I affirm that this thesis contains no material, which has been accepted for the award to the candidate of any other degree or diploma. Aravindhan Ganesan April 2013 vi Publications 1. Aravindhan Ganesan and Feng Wang, ‘Intramolecular interactions of L-phenylalanine revealed by inner shell chemical shift of model molecules’, J. Chem. Phys., 131, 044321 (2009). 2.