Ishara Peiris

Motivated Ph.D holder ready to utilize skills and expertise in research. Adept at prepping resources, equipment and materials for research. Extensive background in theoretical research in biomolecules.

Ph.D, (major in computational Chemistry), 01/2019-05/2023, School of Molecular Sciences, La Trobe University, Australia

Gas phase conformational and thermochemical studies of small biomolecules such as amino acids (AA) are important to the understanding fundamental biological properties. The gas phase structure of a molecule in particular represents the intrinsic characteristic of the molecule. Alanine is an excellent test case that has been explored in detail, as it is the simplest chiral amino acid which exhibits fundamental interactions that can be observed in all AAs in general. A series of computational methods and basis sets were tested in a systematic conformer search of alanine to determine the efficiency of each combination of method and basis set to reliably locate all minima of alanine. As part of this work, we identified two new conformers in addition to the 13 previously reported. Several combinations of methods and basis sets were able to locate all 15 minima of alanine. The stability of individual conformations was analysed from intramolecular hydrogen-bonding interactions. Benchmark CCSD(T)-F12 calculated relative energies confirmed that conformer I is the lowest energy conformer, and enabled assessment of HF, DFT, and MP methods in both locating all minima but also providing reliable relative energies. The calculation of barriers to rotation (transition states) between these minima enables a rationalization of the experimental observation of only a small subset of minima. The CCSD(T)-F12 results provide highly accurate and reliable benchmark data for alanine. From a systematic conformer search of glycine, alanine, serine, and cysteine, a streamlined approach to conformer searching was developed. This approach was used for all 20 natural AAs, including their protonated and N-methylated forms, to identify the lowest energy conformers, including both syn-COOH and anti-COOH configurations. The lowest-energy structures of amino acids have been used in the calculation of gas-phase proton affinities for all natural and N-methylated AAs using Gaussian-n thermochemical methods. Vertical ionization energies and electron affinities have also been investigated for all 20 natural AAs, as well as their N-methyl analogues. The effect of N-methylation has been examined and compared through conformer preferences and thermochemical properties. Group II metals play a key role in biological systems and its processes. Here a thorough conformational analysis of the coordination of groups II metals (neutral and divalent) with 20 natural AAs has been carried out in both gas and aqueous phases. A comparison to the metals, their valancies and the effect of solvent phase in terms of their structural and thermochemical properties (complex stabilities, interaction strengths) has been provided to characterize the complexes.

• Routine laboratory tests and experimental techniques
• Chromatography techniques (column, TLC, etc)
• Synthetic techniques
• Crystallization and recrystallization techniques
• Chemical extraction techniques from plants and liquid-liquid extraction techniques such as steam distillation
• Melting and boiling point determination
• Metal ion identification and detection
• Metal ion extraction through precipitation
• Acid base titration techniques
• PH determination
• Standardizing solutions and equipment
• Determination of reaction rates, stoichiometry
• Usage of instruments such as UV-Vis spectrometer, pH meter, etc
• Laboratory safety and chemical waste disposal procedures
• Sample preparation and testing
• Laboratory data collection and management
• Laboratory equipment use and calibration
• Interpreting laboratory results

5 publications are in progress