Molecular dynamics simulations of aragonite

Mirzaei, Parisa (2024) Molecular dynamics simulations of aragonite. Masters thesis, Memorial University of Newfoundland.

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Abstract

This work presents a molecular dynamics simulation study of aragonite. Aragonite is a naturally occurring crystal form of calcium carbonate found in shells of marine organisms and sedimentary rocks. The vibration of atoms inside the crystal is fundamental to mineral science and solid-state physics studies. Raman and infrared spectroscopy are the two primary techniques for vibrational spectroscopy. These methods provide unique molecular fingerprints for a sample that identifies crystal structures. The vibrational density of states (VDOS) is a key parameter accessible through simulations. A VDOS is a histogram counting the number of the vibrational modes of a given energy and depends on how interactions between atoms are modelled. A force field represents these interactions. There are two recently developed force fields for aragonite. One includes explicit bonding terms between carbon and oxygen atoms within carbonate units (Bond), and the other does not include the bond (No-Bond). These aragonite force fields were developed to work with the OPLS-AA force field, which is commonly used for aqueous and biological systems. In this thesis, our first goal is to reproduce reported results in the literature for the No-Bond model, primarily unit cell parameters, and to test the effect of including the C-O bond on these parameters and on VDOS. As part of this goal, we study the impact of simulation details on the results, including those related to the control of pressure and temperature. Having determined a simulation protocol, we calculate VDOS for the two force field models. The generated VDOS plot for the No-Bond model shows the qualitative agreement with experimental data. Incorporating the spring bond between the carbon and oxygen atoms significantly and detrimentally changes the overall VDOS structure and mode energies.

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